Accuracy Of Gem Predictions For Industrial Ferment

DOI: https://doi.org/10.17485/ijst/2015/v8i1/56501

Paper Machine learning methods for predicting essential metabolic genes from Plasmodium falciparum genome-scale metabolic network

Isewon, Itunuoluwa; Binaansim, Stephen; Adegoke, Faith et al. · 2024 · PLoS ONE · DOI

Full title: Machine learning methods for predicting essential metabolic genes from Plasmodium falciparum genome-scale metabolic network

Authors: Isewon, Itunuoluwa; Binaansim, Stephen; Adegoke, Faith; Emmanuel, Jerry; Oyelade, Jelili

Year: 2024

Venue: PLoS ONE

DOI: https://doi.org/10.1371/journal.pone.0315530

Paper Comparison of Optimization-Modelling Methods for Metabolites Production in Escherichia coli

Lee, Mee K.; Mohamad, Mohd Saberi; Choon, Yee Wen et al. · 2020 · Berichte aus der medizinischen Informatik und Bioinformatik/Journal of integrative bioinformatics · DOI

Full title: Comparison of Optimization-Modelling Methods for Metabolites Production in Escherichia coli

Authors: Lee, Mee K.; Mohamad, Mohd Saberi; Choon, Yee Wen; Daud, Kauthar Mohd; Nasarudin, Nurul Athirah; Ismail, Mohd Arfian; Ibrahim, Zuwairie; Napis, Suhaimi; Sinnott, Richard

Year: 2020

Venue: Berichte aus der medizinischen Informatik und Bioinformatik/Journal of integrative bioinformatics

DOI: https://doi.org/10.1515/jib-2019-0073

Paper Model‐guided development of an evolutionarily stable yeast chassis

Pereira, Filipa; Lopes, Hélder; Maia, Paulo et al. · 2021 · Molecular Systems Biology · DOI

Full title: Model‐guided development of an evolutionarily stable yeast chassis

Authors: Pereira, Filipa; Lopes, Hélder; Maia, Paulo; Meyer, Britta; Nocon, Justyna; Jouhten, Paula; Konstantinidis, Dimitrios; Kafkia, Eleni; Rocha, Miguel; Kötter, Peter; Rocha, Isabel; Patil, Kiran Raosaheb

Year: 2021

Venue: Molecular Systems Biology

DOI: https://doi.org/10.15252/msb.202110253

Paper Parallel Exploitation of Diverse Host Nutrients Enhances Salmonella Virulence

Steeb, Benjamin; Claudi, Beatrice; Burton, Neil A. et al. · 2013 · PLoS Pathogens · DOI

Full title: Parallel Exploitation of Diverse Host Nutrients Enhances Salmonella Virulence

Authors: Steeb, Benjamin; Claudi, Beatrice; Burton, Neil A.; Tienz, Petra; Schmidt, Alexander; Farhan, Hesso; Mazé, Alain; Bumann, Dirk

Year: 2013

Venue: PLoS Pathogens

DOI: https://doi.org/10.1371/journal.ppat.1003301

Paper Genome‐scale metabolic modeling reveals key features of a minimal gene set

Lachance, Jean‐Christophe; Matteau, Dominick; Brodeur, Joëlle et al. · 2021 · Molecular Systems Biology · DOI

Full title: Genome‐scale metabolic modeling reveals key features of a minimal gene set

Authors: Lachance, Jean‐Christophe; Matteau, Dominick; Brodeur, Joëlle; Lloyd, Colton J.; Mih, Nathan; King, Zachary A.; Knight, Thomas F.; Feist, Adam M.; Monk, Jonathan M.; Palsson, Bernhard Ø.; Jacques, Pierre‐Étienne; Rodrigue, Sébastien

Year: 2021

Venue: Molecular Systems Biology

DOI: https://doi.org/10.15252/msb.202010099

Paper In silico Evaluation of the Effect of Pfl Gene Knockout on the Production of D-lactate by Escherichia coli Genome Scale Model Using the Optflux Software Platform

Mienda, Bashir Sajo; Shamsir, Mohd Shahir; Salleh, Faezah Mohd · 2015 · Indian Journal of Science and Technology · DOI

Full title: In silico Evaluation of the Effect of Pfl Gene Knockout on the Production of D-lactate by Escherichia coli Genome Scale Model Using the Optflux Software Platform

Authors: Mienda, Bashir Sajo; Shamsir, Mohd Shahir; Salleh, Faezah Mohd

Year: 2015

Venue: Indian Journal of Science and Technology

Paper Evaluating E. coli genome‐scale metabolic model accuracy with high‐throughput mutant fitness data

Bernstein, David B.; Akkas, Batu; Price, Morgan N. et al. · 2023 · Molecular Systems Biology · DOI

Full title: Evaluating E. coli genome‐scale metabolic model accuracy with high‐throughput mutant fitness data

Authors: Bernstein, David B.; Akkas, Batu; Price, Morgan N.; Arkin, Adam P.

Year: 2023

Venue: Molecular Systems Biology

DOI: https://doi.org/10.15252/msb.202311566

Paper Vibrio natriegens genome‐scale modeling reveals insights into halophilic adaptations and resource allocation

L. Coppens; Tanya Tschirhart; Dagmar H. Leary et al. · 2023 · Molecular Systems Biology · DOI

Full title: Vibrio natriegens genome‐scale modeling reveals insights into halophilic adaptations and resource allocation

Authors: L. Coppens; Tanya Tschirhart; Dagmar H. Leary; S. Colston; J. Compton; W. J. Hervey; K. Dana; G. Vora; S. Bordel; R. Ledesma‐Amaro

Year: 2023

Venue: Molecular Systems Biology

DOI: https://doi.org/10.15252/msb.202110523

Paper Development of a Stoichiometric Model for Estimation of Metabolic Fluxes in Saccharomyces cerevisiae during Tequila Production

Rosa, José Daniel Padilla-de la; Gschaedler, Anne; Gómez-Guzmán, Abril et al. · 2018 · Preprints.org · DOI

Full title: Development of a Stoichiometric Model for Estimation of Metabolic Fluxes in Saccharomyces cerevisiae during Tequila Production

Authors: Rosa, José Daniel Padilla-de la; Gschaedler, Anne; Gómez-Guzmán, Abril; González‐Reynoso, Orfil

Year: 2018

Venue: Preprints.org

DOI: https://doi.org/10.20944/preprints201811.0385.v1

Paper Genetic Optimization Algorithm for Metabolic Engineering Revisited

Alter, Tobias B.; Blank, Lars M.; Ebert, Birgitta E. · 2018 · Metabolites · DOI

Full title: Genetic Optimization Algorithm for Metabolic Engineering Revisited

Authors: Alter, Tobias B.; Blank, Lars M.; Ebert, Birgitta E.

Year: 2018

Venue: Metabolites

Paper Bridging the gap between mechanistic biological models and machine learning surrogates

Gherman, Ioana M.; Abdallah, Zahraa S.; Pang, Wei et al. · 2023 · PLoS Computational Biology · DOI

Full title: Bridging the gap between mechanistic biological models and machine learning surrogates

Authors: Gherman, Ioana M.; Abdallah, Zahraa S.; Pang, Wei; Gorochowski, Thomas E.; Grierson, Claire; Marucci, Lucia

Year: 2023

Venue: PLoS Computational Biology

DOI: https://doi.org/10.20944/preprints202209.0019.v1

Paper Construction and Analysis of an Enzyme‐constrained Metabolic Model of Corynebacterium glutamicum

Niu, Jinhui; Mao, Zhitao; Mao, Yufeng et al. · 2022 · Preprints.org · DOI

Full title: Construction and Analysis of an Enzyme‐constrained Metabolic Model of Corynebacterium glutamicum

Authors: Niu, Jinhui; Mao, Zhitao; Mao, Yufeng; Wu, Ke; Shi, Zhenkun; Yuan, Qianqian; Cai, Jingyi; Ma, Hongwu

Year: 2022

Venue: Preprints.org

Paper ecBSU1: A Genome-scale Enzyme-constrained Model of Bacillus subtilis based on the ECMpy Workflow

Wu, Ke; Mao, Zhitao; Mao, Yufeng et al. · 2022 · Preprints.org · DOI

Full title: ecBSU1: A Genome-scale Enzyme-constrained Model of Bacillus subtilis based on the ECMpy Workflow

Authors: Wu, Ke; Mao, Zhitao; Mao, Yufeng; Niu, Jinhui; Cai, Jingyi; Yuan, Qianqian; Yun, Lili; Liao, Xiaoping; Wang, Zhiwen; Ma, Hongwu

Year: 2022

Venue: Preprints.org

DOI: https://doi.org/10.20944/preprints202211.0351.v1

Paper ECMpy, a Simplified Workflow for Constructing Enzymatic Constrained Metabolic Network Model

Zhitao Mao; Xin Zhao; Xue Yang et al. · 2022 · Biomolecules · DOI

Full title: ECMpy, a Simplified Workflow for Constructing Enzymatic Constrained Metabolic Network Model

Authors: Zhitao Mao; Xin Zhao; Xue Yang; Peiji Zhang; Jiawei Du; Qianqian Yuan; Hongwu Ma

Year: 2022

Venue: Biomolecules

DOI: https://doi.org/10.20944/preprints202302.0037.v1

Paper From Observational to Actionable: Rethinking Omics in Biologics Production

Masson, Helen O.; Karottki, Karen Julie la Cour; Tat, Jasmine et al. · 2023 · Preprints.org · DOI

Full title: From Observational to Actionable: Rethinking Omics in Biologics Production

Authors: Masson, Helen O.; Karottki, Karen Julie la Cour; Tat, Jasmine; Hefzi, Hooman; Lewis, Nathan E.

Year: 2023

Venue: Preprints.org

Paper A Guide for the Bioinformatic Analysis of Metabolomics Data

Santamaria, Guillem; Pinto, Francisco · 2024 · Preprints.org · DOI

Full title: A Guide for the Bioinformatic Analysis of Metabolomics Data

Authors: Santamaria, Guillem; Pinto, Francisco

Year: 2024

Venue: Preprints.org

DOI: https://doi.org/10.20944/preprints202402.0461.v1

Paper From Shallow to Deep Bioprocess Hybrid Modeling: Advances and Future Perspectives

Agharafeie, Roshanak; Ramos, João R. C.; Mendes, Jorge M. et al. · 2023 · Fermentation · DOI

Full title: From Shallow to Deep Bioprocess Hybrid Modeling: Advances and Future Perspectives

Authors: Agharafeie, Roshanak; Ramos, João R. C.; Mendes, Jorge M.; Oliveira, Rui

Year: 2023

Venue: Fermentation

DOI: https://doi.org/10.2225/vol16-issue3-fulltext-14

Paper Designing metabolic engineering strategies with genome-scale metabolic flux modeling

Senger, Ryan S.; Yen, Jiun Y.; Tanniche, Imen et al. · 2015 · Advances in Genomics and Genetics · DOI

Full title: Designing metabolic engineering strategies with genome-scale metabolic flux modeling

Authors: Senger, Ryan S.; Yen, Jiun Y.; Tanniche, Imen; Fisher, Amanda; Gillaspy, Glenda E.; Bevan, David R.

Year: 2015

Venue: Advances in Genomics and Genetics

DOI: https://doi.org/10.2147/agg.s58494

Paper Genome-Scale Metabolic Network Models of Bacillus Species Suggest that Model Improvement is Necessary for Biotechnological Applications

Ghasemi-Kahrizsangi, Tahereh; Marashi, Sayed‐Amir; Hosseini, Zhaleh · 2018 · Iranian Journal of Biotechnology · DOI

Full title: Genome-Scale Metabolic Network Models of Bacillus Species Suggest that Model Improvement is Necessary for Biotechnological Applications

Authors: Ghasemi-Kahrizsangi, Tahereh; Marashi, Sayed‐Amir; Hosseini, Zhaleh

Year: 2018

Venue: Iranian Journal of Biotechnology

DOI: https://doi.org/10.21859/ijb.1684

Paper Metabolic engineering: Use of system-level approaches and application to fuel production in Escherichia coli

González, Ramón · 2013 · Electronic Journal of Biotechnology · DOI

Full title: Metabolic engineering: Use of system-level approaches and application to fuel production in Escherichia coli

Authors: González, Ramón

Year: 2013

Venue: Electronic Journal of Biotechnology

Paper Metabolic pathway reconstruction strategies for central metabolism and natural product biosynthesis

Kotera, Masaaki; Goto, Susumu · 2016 · Biophysics and Physicobiology · DOI

Full title: Metabolic pathway reconstruction strategies for central metabolism and natural product biosynthesis

Authors: Kotera, Masaaki; Goto, Susumu

Year: 2016

Venue: Biophysics and Physicobiology

DOI: https://doi.org/10.2142/biophysico.13.0_195

Paper NCMW: A Python Package to Analyze Metabolic Interactions in the Nasal Microbiome

Glöckler, Manuel; Dräger, Andreas; Mostolizadeh, Reihaneh · 2022 · Frontiers in Bioinformatics · DOI

Full title: NCMW: A Python Package to Analyze Metabolic Interactions in the Nasal Microbiome

Authors: Glöckler, Manuel; Dräger, Andreas; Mostolizadeh, Reihaneh

Year: 2022

Venue: Frontiers in Bioinformatics

DOI: https://doi.org/10.3389/fbinf.2022.827024

Paper Estimation of biomass composition from genomic and transcriptomic information

Santos, Sophia; Rocha, Isabel · 2016 · PubMed · DOI

Full title: Estimation of biomass composition from genomic and transcriptomic information

Authors: Santos, Sophia; Rocha, Isabel

Year: 2016

Venue: PubMed

DOI: https://doi.org/10.2390/biecoll-jib-2016-285

Paper Metabolic Network Discovery by Top-Down and Bottom-Up Approaches and Paths for Reconciliation

Ã‡akÄ±r, Tunahan; Khatibipour, Mohammad Jafar · 2014 · Frontiers in Bioengineering and Biotechnology · DOI

Full title: Metabolic Network Discovery by Top-Down and Bottom-Up Approaches and Paths for Reconciliation

Authors: Ã‡akÄ±r, Tunahan; Khatibipour, Mohammad Jafar

Year: 2014

Venue: Frontiers in Bioengineering and Biotechnology

DOI: https://doi.org/10.3389/fbioe.2014.00062

Paper Editorial: Current Challenges in Modeling Cellular Metabolism

Machado, Daniel; Zhuang, Kai; Sonnenschein, Nikolaus et al. · 2015 · Frontiers in Bioengineering and Biotechnology · DOI

Full title: Editorial: Current Challenges in Modeling Cellular Metabolism

Authors: Machado, Daniel; Zhuang, Kai; Sonnenschein, Nikolaus; Herrgård, Markus J.

Year: 2015

Venue: Frontiers in Bioengineering and Biotechnology

DOI: https://doi.org/10.3389/fbioe.2015.00193

Paper Conceptos básicos de análisis de fluxes metabólicos

Henao, Claudia Patricia Sánchez; Ramírez-Malule, Howard; López-Agudelo, Víctor A. · 2020 · Ingeniería y Competitividad · DOI

Full title: Conceptos básicos de análisis de fluxes metabólicos

Authors: Henao, Claudia Patricia Sánchez; Ramírez-Malule, Howard; López-Agudelo, Víctor A.

Year: 2020

Venue: Ingeniería y Competitividad

DOI: https://doi.org/10.25100/iyc.v23i1.9509

Paper Analysis of genetic variation and potential applications in genome-scale metabolic modeling

Cardoso, João · 2015 · Frontiers in Bioengineering and Biotechnology · DOI

Full title: Analysis of genetic variation and potential applications in genome-scale metabolic modeling

Authors: Cardoso, João

Year: 2015

Venue: Frontiers in Bioengineering and Biotechnology

DOI: https://doi.org/10.3389/fbioe.2015.00013

Paper Computer-Aided Whole-Cell Design: Taking a Holistic Approach by Integrating Synthetic With Systems Biology

Marucci, Lucia; Barberis, Matteo; Karr, Jonathan R. et al. · 2020 · Frontiers in Bioengineering and Biotechnology · DOI

Full title: Computer-Aided Whole-Cell Design: Taking a Holistic Approach by Integrating Synthetic With Systems Biology

Authors: Marucci, Lucia; Barberis, Matteo; Karr, Jonathan R.; Ray, Oliver; Race, Paul R.; Andrade, Miguel de Souza; Grierson, Claire; Hoffmann, Stefan A.; Landon, Sophie; Rech, Elíbio; Rees-Garbutt, Joshua; Seabrook, Richard; Shaw, W. M.; Woods, Christopher

Year: 2020

Venue: Frontiers in Bioengineering and Biotechnology

DOI: https://doi.org/10.3389/fbioe.2020.00942

Paper A Computational Framework to Identify Metabolic Engineering Strategies for the Co-Production of Metabolites

Raajaraam, Lavanya; Raman, Karthik · 2022 · Frontiers in Bioengineering and Biotechnology · DOI

Full title: A Computational Framework to Identify Metabolic Engineering Strategies for the Co-Production of Metabolites

Authors: Raajaraam, Lavanya; Raman, Karthik

Year: 2022

Venue: Frontiers in Bioengineering and Biotechnology

DOI: https://doi.org/10.3389/fbioe.2021.779405

Paper LGEM+: A First-Order Logic Framework for Automated Improvement of Metabolic Network Models Through Abduction

Gower, Alexander H.; Korovin, Konstantin; Brunnsåker, Daniel et al. · 2023 · Lecture notes in computer science · DOI

Full title: LGEM+: A First-Order Logic Framework for Automated Improvement of Metabolic Network Models Through Abduction

Authors: Gower, Alexander H.; Korovin, Konstantin; Brunnsåker, Daniel; Tiukova, Ievgeniia; King, Ross D.

Year: 2023

Venue: Lecture notes in computer science

DOI: https://doi.org/10.1007/978-3-031-45275-8_42

Paper Derivation of a Biomass Proxy for Dynamic Analysis of Whole Genome Metabolic Models

Self, Timothy H.; Gilbert, David; Heiner, Monika · 2018 · Lecture notes in computer science · DOI

Full title: Derivation of a Biomass Proxy for Dynamic Analysis of Whole Genome Metabolic Models

Authors: Self, Timothy H.; Gilbert, David; Heiner, Monika

Year: 2018

Venue: Lecture notes in computer science

DOI: https://doi.org/10.1007/978-3-319-99429-1_3

Paper Characterization of effects of genetic variants via genome-scale metabolic modelling

Tong, Hao; Küken, Anika; Razaghi‐Moghadam, Zahra et al. · 2021 · Cellular and Molecular Life Sciences · DOI

Full title: Characterization of effects of genetic variants via genome-scale metabolic modelling

Authors: Tong, Hao; Küken, Anika; Razaghi‐Moghadam, Zahra; Nikoloski, Zoran

Year: 2021

Venue: Cellular and Molecular Life Sciences

DOI: https://doi.org/10.1007/s00018-021-03844-4

Paper Highlighting Metabolic Strategies Using Network Analysis over Strain Optimization Results

Pinto, José P.; Rocha, Isabel; Rocha, Miguel · 2011 · Lecture notes in computer science · DOI

Full title: Highlighting Metabolic Strategies Using Network Analysis over Strain Optimization Results

Authors: Pinto, José P.; Rocha, Isabel; Rocha, Miguel

Year: 2011

Venue: Lecture notes in computer science

DOI: https://doi.org/10.1007/978-3-642-24855-9_10

Paper Modeling population heterogeneity from microbial communities to immune response in cells

Pecht, Tal; Aschenbrenner, Anna C.; Ulas, Thomas et al. · 2019 · Cellular and Molecular Life Sciences · DOI

Full title: Modeling population heterogeneity from microbial communities to immune response in cells

Authors: Pecht, Tal; Aschenbrenner, Anna C.; Ulas, Thomas; Succurro, A.

Year: 2019

Venue: Cellular and Molecular Life Sciences

DOI: https://doi.org/10.1007/s00018-019-03378-w

Paper Metabolic control analysis enabled the improvement of the L-cysteine production process with Escherichia coli

Cerbon, Daniel Alejandro Caballero; Widmann, J J; Weuster‐Botz, Dirk · 2024 · Applied Microbiology and Biotechnology · DOI

Full title: Metabolic control analysis enabled the improvement of the L-cysteine production process with Escherichia coli

Authors: Cerbon, Daniel Alejandro Caballero; Widmann, J J; Weuster‐Botz, Dirk

Year: 2024

Venue: Applied Microbiology and Biotechnology

DOI: https://doi.org/10.1007/s00253-023-12928-z

Paper Industrial biotechnology of Pseudomonas putida: advances and prospects

Weimer, Anna; Kohlstedt, Michael; Volke, Daniel C. et al. · 2020 · Applied Microbiology and Biotechnology · DOI

Full title: Industrial biotechnology of Pseudomonas putida: advances and prospects

Authors: Weimer, Anna; Kohlstedt, Michael; Volke, Daniel C.; Nikel, Pablo I.; Wittmann, Christoph

Year: 2020

Venue: Applied Microbiology and Biotechnology

DOI: https://doi.org/10.1007/s00253-020-10811-9

Paper Metabolic modeling of Halomonas campaniensis improves polyhydroxybutyrate production under nitrogen limitation

Deantas-Jahn, Carolina; Mendoza, Sebastián N.; Licona‐Cassani, Cuauhtémoc et al. · 2024 · Applied Microbiology and Biotechnology · DOI

Full title: Metabolic modeling of Halomonas campaniensis improves polyhydroxybutyrate production under nitrogen limitation

Authors: Deantas-Jahn, Carolina; Mendoza, Sebastián N.; Licona‐Cassani, Cuauhtémoc; Orellana, Camila A.; Saa, Pedro A.

Year: 2024

Venue: Applied Microbiology and Biotechnology

DOI: https://doi.org/10.1007/s00253-024-13111-8

Paper Genome-scale modeling of Chinese hamster ovary cells by hybrid semi-parametric flux balance analysis

Ramos, João R. C.; Poiares‐Oliveira, Gil; Dumas, Patrick et al. · 2022 · Bioprocess and Biosystems Engineering · DOI

Full title: Genome-scale modeling of Chinese hamster ovary cells by hybrid semi-parametric flux balance analysis

Authors: Ramos, João R. C.; Poiares‐Oliveira, Gil; Dumas, Patrick; Oliveira, Rui

Year: 2022

Venue: Bioprocess and Biosystems Engineering

DOI: https://doi.org/10.1007/s00449-022-02795-9

Paper Current state of genome-scale modeling in filamentous fungi

Brandl, Julian; Andersen, Mikael Rørdam · 2015 · Biotechnology Letters · DOI

Full title: Current state of genome-scale modeling in filamentous fungi

Authors: Brandl, Julian; Andersen, Mikael Rørdam

Year: 2015

Venue: Biotechnology Letters

DOI: https://doi.org/10.1007/s10529-015-1782-8

Paper C/N ratio and carbon source-dependent lipid production profiling in Rhodotorula toruloides

Lopes, Helberth Júnnior Santos; Bonturi, Nemailla; Kerkhoven, Eduard J. et al. · 2020 · Applied Microbiology and Biotechnology · DOI

Full title: C/N ratio and carbon source-dependent lipid production profiling in Rhodotorula toruloides

Authors: Lopes, Helberth Júnnior Santos; Bonturi, Nemailla; Kerkhoven, Eduard J.; Miranda, Everson Alves; Lahtvee, Petri‐Jaan

Year: 2020

Venue: Applied Microbiology and Biotechnology

DOI: https://doi.org/10.1007/s00253-020-10386-5

Paper Insights from 20 years of bacterial genome sequencing

Land, Miriam; Hauser, Loren; Jun, Se‐Ran et al. · 2015 · Functional & Integrative Genomics · DOI

Full title: Insights from 20 years of bacterial genome sequencing

Authors: Land, Miriam; Hauser, Loren; Jun, Se‐Ran; Nookaew, Intawat; Leuze, Michael R.; Ahn, Tae-Hyuk; Karpinets, Tatiana V.; Lund, Ole; Kora, Guruprased; Wassenaar, Trudy M.; Poudel, Suresh; Ussery, David W.

Year: 2015

Venue: Functional & Integrative Genomics

DOI: https://doi.org/10.1007/s10142-015-0433-4

Paper Metabolic shifts: a fitness perspective for microbial cell factories

Goel, Anisha; Wortel, Meike T.; Molenaar, Douwe et al. · 2012 · Biotechnology Letters · DOI

Full title: Metabolic shifts: a fitness perspective for microbial cell factories

Authors: Goel, Anisha; Wortel, Meike T.; Molenaar, Douwe; Teusink, Bas

Year: 2012

Venue: Biotechnology Letters

DOI: https://doi.org/10.1007/s10529-012-1038-9

Paper An analysis of a ‘community-driven’ reconstruction of the human metabolic network

Swainston, Neil; Mendes, Pedro; Kell, Douglas B. · 2013 · Metabolomics · DOI

Full title: An analysis of a ‘community-driven’ reconstruction of the human metabolic network

Authors: Swainston, Neil; Mendes, Pedro; Kell, Douglas B.

Year: 2013

Venue: Metabolomics

DOI: https://doi.org/10.1007/s11306-013-0564-3

Paper Strategies to increase the robustness of microbial cell factories

Xu, Pei; Lin, Nuo-Qiao; Zhang, Zhiqian et al. · 2024 · Advanced Biotechnology · DOI

Full title: Strategies to increase the robustness of microbial cell factories

Authors: Xu, Pei; Lin, Nuo-Qiao; Zhang, Zhiqian; Liu, Jian-Zhong

Year: 2024

Venue: Advanced Biotechnology

DOI: https://doi.org/10.1007/s44307-024-00018-8

Paper Conservation of high-flux backbone in alternate optimal and near-optimal flux distributions of metabolic networks

Samal, Areejit · 2008 · Systems and Synthetic Biology · DOI

Full title: Conservation of high-flux backbone in alternate optimal and near-optimal flux distributions of metabolic networks

Authors: Samal, Areejit

Year: 2008

Venue: Systems and Synthetic Biology

DOI: https://doi.org/10.1007/s11693-009-9025-8

Paper Systems biology and metabolic engineering of Rhodococcus for bioconversion and biosynthesis processes

Donini, Eva; Firrincieli, Andrea; Cappelletti, Martina · 2021 · Folia Microbiologica · DOI

Full title: Systems biology and metabolic engineering of Rhodococcus for bioconversion and biosynthesis processes

Authors: Donini, Eva; Firrincieli, Andrea; Cappelletti, Martina

Year: 2021

Venue: Folia Microbiologica

DOI: https://doi.org/10.1007/s12223-021-00892-y

Paper A genome-scale metabolic reconstruction provides insight into the metabolism of the thermophilic bacterium Rhodothermus marinus

Kristjansdottir, Thordis; Hreggviðsson, Guðmundur Ó.; Stefánsson, Sigmar K. et al. · 2021 · DOI

Full title: A genome-scale metabolic reconstruction provides insight into the metabolism of the thermophilic bacterium Rhodothermus marinus

Authors: Kristjansdottir, Thordis; Hreggviðsson, Guðmundur Ó.; Stefánsson, Sigmar K.; Guðmundsdóttir, Elísabet Eik; Björnsdóttir, Snædís H.; Friðjónsson, Ólafur H.; Karlsson, Eva Nordberg; Vanhalst, Justine; Reynisson, Birkir; Guðmundsson, Steinn

Year: 2021

DOI: https://doi.org/10.1101/2021.05.17.444423

Paper Whole-cell modeling in yeast predicts compartment-specific proteome constraints that drive metabolic strategies

Elsemman, Ibrahim E.; Prado, Angelica Rodriguez; Grigaitis, Pranas et al. · 2022 · Nature Communications · DOI

Full title: Whole-cell modeling in yeast predicts compartment-specific proteome constraints that drive metabolic strategies

Authors: Elsemman, Ibrahim E.; Prado, Angelica Rodriguez; Grigaitis, Pranas; Garcia‐Albornoz, Manuel; Harman, Victoria M.; Holman, Stephen W.; Heerden, Johan H. van; Bruggeman, Frank J.; Bisschops, Mark M. M.; Sonnenschein, Nikolaus; Hubbard, Simon J.; Beynon, Robert J.; Daran‐Lapujade, Pascale; Nielsen, Jens; Teusink, Bas

Year: 2022

Venue: Nature Communications

Paper TRIMER: Transcription Regulation Integrated with MEtabolic Regulation

Niu, Puhua; Soto, Maria J.; Yoon, Byung-Jun et al. · 2021 · DOI

Full title: TRIMER: Transcription Regulation Integrated with MEtabolic Regulation

Authors: Niu, Puhua; Soto, Maria J.; Yoon, Byung-Jun; Dougherty, Edward R.; Alexander, Francis J.; Blaby, Ian K.; Qian, Xiaoning

Year: 2021

DOI: https://doi.org/10.1101/2021.04.09.439167

Paper Investigating the chemolithoautotrophic and formate metabolism of Nitrospira moscoviensis by constraint-based metabolic modeling and 13 C-tracer analysis

Lawson, Christopher E.; Mundinger, Aniela B.; Koch, Hanna et al. · 2021 · DOI

Full title: Investigating the chemolithoautotrophic and formate metabolism of Nitrospira moscoviensis by constraint-based metabolic modeling and 13 C-tracer analysis

Authors: Lawson, Christopher E.; Mundinger, Aniela B.; Koch, Hanna; Jacobson, Tyler B.; Weathersby, Coty A.; Jetten, Mike S. M.; Pabst, Martin; Amador‐Noguez, Daniel; Noguera, Daniel R.; McMahon, Katherine D.; Lücker, Sebastian

Year: 2021

DOI: https://doi.org/10.1101/2021.02.18.431926

Paper Enzyme-constrained models predict the dynamics of Saccharomyces cerevisiae growth in continuous, batch and fed-batch bioreactors

Moreno‐Paz, Sara; Schmitz, Joep; Santos, Vítor A. P. Martins dos et al. · 2022 · Microbial Biotechnology · DOI

Full title: Enzyme-constrained models predict the dynamics of Saccharomyces cerevisiae growth in continuous, batch and fed-batch bioreactors

Authors: Moreno‐Paz, Sara; Schmitz, Joep; Santos, Vítor A. P. Martins dos; Suárez‐Diez, María

Year: 2022

Venue: Microbial Biotechnology

DOI: https://doi.org/10.1111/1751-7915.13995

Paper Genome-scale modeling of Pseudomonas aeruginosa PA14 unveils its broad metabolic capabilities and role of metabolism in drug potentiation

Dahal, Sanjeev; Renz, Alina; Dräger, Andreas et al. · 2021 · DOI

Full title: Genome-scale modeling of Pseudomonas aeruginosa PA14 unveils its broad metabolic capabilities and role of metabolism in drug potentiation

Authors: Dahal, Sanjeev; Renz, Alina; Dräger, Andreas; Yang, Laurence

Year: 2021

DOI: https://doi.org/10.1101/2021.04.15.439930

Paper Genome-Scale Metabolic Model Accurately Predicts Fermentation of Glucose by Chromochloris zofingiensis

Meagher, Michelle; Metcalf, Alex; Ramsey, Stephen A. et al. · 2021 · DOI

Full title: Genome-Scale Metabolic Model Accurately Predicts Fermentation of Glucose by Chromochloris zofingiensis

Authors: Meagher, Michelle; Metcalf, Alex; Ramsey, Stephen A.; Prentice, W. C. H.; Boyle, Nanette

Year: 2021

DOI: https://doi.org/10.1101/2021.06.22.449518

Paper Real-time HRMAS 13 C NMR of obligately anaerobic cells identifies new metabolic targets in the pathogen Clostridioides difficile

Pavao, Aidan; Girinathan, Brintha; Peltier, Johann et al. · 2021 · DOI

Full title: Real-time HRMAS 13 C NMR of obligately anaerobic cells identifies new metabolic targets in the pathogen Clostridioides difficile

Authors: Pavao, Aidan; Girinathan, Brintha; Peltier, Johann; Silva, Pamela Altamirano; Dupuy, Bruno; Cheng, Leo L.; Bry, Lynn

Year: 2021

DOI: https://doi.org/10.1101/2021.05.04.442336

Paper A curated collection of Klebsiella metabolic models reveals variable substrate usage and gene essentiality

Hawkey, Jane; Vezina, Ben; Monk, Jonathan M. et al. · 2022 · Genome Research · DOI

Full title: A curated collection of Klebsiella metabolic models reveals variable substrate usage and gene essentiality

Authors: Hawkey, Jane; Vezina, Ben; Monk, Jonathan M.; Judd, Louise M.; Harshegyi, Taylor; López-Fernández, Sebastián; Rodrigues, Carla; Brisse, Sylvain; Holt, Kathryn E.; Wyres, Kelly L.

Year: 2022

Venue: Genome Research

Paper Optimality of extracellular enzyme production and activity in dynamic flux balance modeling

Quintin, Michael; Dukovski, Ilija; Bhatnagar, Jennifer et al. · 2021 · DOI

Full title: Optimality of extracellular enzyme production and activity in dynamic flux balance modeling

Authors: Quintin, Michael; Dukovski, Ilija; Bhatnagar, Jennifer; Segrè, Daniel

Year: 2021

DOI: https://doi.org/10.1101/2021.11.01.466736

Paper Deep learning based k cat prediction enables improved enzyme constrained model reconstruction

Li, Feiran; Yuan, Le; Lu, Hongzhong et al. · 2021 · DOI

Full title: Deep learning based k cat prediction enables improved enzyme constrained model reconstruction

Authors: Li, Feiran; Yuan, Le; Lu, Hongzhong; Li, Gang; Chen, Yu; Engqvist, Martin K. M.; Kerkhoven, Eduard J.; Nielsen, Jens

Year: 2021

DOI: https://doi.org/10.1101/2021.08.06.455417

Paper Rhythm of The Night (and Day): Predictive metabolic modeling of circadian growth in Chlamydomonas

Metcalf, Alexander J.; Boyle, Nanette · 2022 · DOI

Full title: Rhythm of The Night (and Day): Predictive metabolic modeling of circadian growth in Chlamydomonas

Authors: Metcalf, Alexander J.; Boyle, Nanette

Year: 2022

DOI: https://doi.org/10.1101/2022.01.24.477634

Paper A neural-mechanistic hybrid approach improving the predictive power of genome-scale metabolic models

Faure, Léon; Mollet, Bastien; Liebermeister, Wolfram et al. · 2023 · Nature Communications · DOI

Full title: A neural-mechanistic hybrid approach improving the predictive power of genome-scale metabolic models

Authors: Faure, Léon; Mollet, Bastien; Liebermeister, Wolfram; Faulon, Jean‐Loup

Year: 2023

Venue: Nature Communications

Paper NICEgame: A workflow for annotating the knowledge gaps in metabolic reconstructions, using known and hypothetical reactions

Vayena, Evangelia; Chiappino-Pepe, Anush; MohammadiPeyhani, Homa et al. · 2022 · DOI

Full title: NICEgame: A workflow for annotating the knowledge gaps in metabolic reconstructions, using known and hypothetical reactions

Authors: Vayena, Evangelia; Chiappino-Pepe, Anush; MohammadiPeyhani, Homa; Francioli, Yannick; Hadadi, Noushin; Ataman, Meriç; Hafner, Jasmin; Pavlou, Stavros; Hatzimanikatis, Vassily

Year: 2022

DOI: https://doi.org/10.1101/2022.02.10.479881

Paper Data integration across conditions improves turnover number estimates and metabolic predictions

Wendering, Philipp; Arend, Marius; Razaghi‐Moghadam, Zahra et al. · 2023 · Nature Communications · DOI

Full title: Data integration across conditions improves turnover number estimates and metabolic predictions

Authors: Wendering, Philipp; Arend, Marius; Razaghi‐Moghadam, Zahra; Nikoloski, Zoran

Year: 2023

Venue: Nature Communications

Paper Genome-scale metabolic modelling enables deciphering ethanol metabolism via the acrylate pathway in the propionate-producer Anaerotignum neopropionicum

Benito-Vaquerizo, Sara; Olm, Ivette Parera; Vroet, Thijs de et al. · 2022 · DOI

Full title: Genome-scale metabolic modelling enables deciphering ethanol metabolism via the acrylate pathway in the propionate-producer Anaerotignum neopropionicum

Authors: Benito-Vaquerizo, Sara; Olm, Ivette Parera; Vroet, Thijs de; Schaap, Peter J.; Sousa, Diana Z.; Santos, Vítor A. P. Martins dos; Suárez‐Diez, María

Year: 2022

DOI: https://doi.org/10.1101/2022.04.11.487872

Paper A computational toolbox to investigate the metabolic potential and resource allocation in fission yeast

Grigaitis, Pranas; Grundel, Douwe A. J.; Pelt‐KleinJan, Eunice van et al. · 2022 · DOI

Full title: A computational toolbox to investigate the metabolic potential and resource allocation in fission yeast

Authors: Grigaitis, Pranas; Grundel, Douwe A. J.; Pelt‐KleinJan, Eunice van; Isaku, Mirushe; Xie, Guixiang; Mendoza, Sebastián N.; Teusink, Bas; Heerden, Johan H. van

Year: 2022

DOI: https://doi.org/10.1101/2022.05.04.490403

Paper Strain design optimization using reinforcement learning

Sabzevari, Maryam; Szedmák, Sándor; Penttilä, Merja et al. · 2022 · PLoS Computational Biology · DOI

Full title: Strain design optimization using reinforcement learning

Authors: Sabzevari, Maryam; Szedmák, Sándor; Penttilä, Merja; Jouhten, Paula; Rousu, Juho

Year: 2022

Venue: PLoS Computational Biology

Paper Characterizing the interplay of rubisco and nitrogenase enzymes in anaerobic-photoheterotrophically grown Rhodopseudomonas palustris CGA009 through a genome-scale metabolic and expression model

Chowdhury, Niaz Bahar; Alsiyabi, Adil; Saha, Rajib · 2022 · DOI

Full title: Characterizing the interplay of rubisco and nitrogenase enzymes in anaerobic-photoheterotrophically grown Rhodopseudomonas palustris CGA009 through a genome-scale metabolic and expression model

Authors: Chowdhury, Niaz Bahar; Alsiyabi, Adil; Saha, Rajib

Year: 2022

DOI: https://doi.org/10.1101/2022.03.03.482919

Paper A Genome-Scale Metabolic Model of Marine Heterotroph Vibrio splendidus sp. 1A01

Iffland-Stettner, Arion; Okano, Hiroyuki; Gralka, Matti et al. · 2022 · DOI

Full title: A Genome-Scale Metabolic Model of Marine Heterotroph Vibrio splendidus sp. 1A01

Authors: Iffland-Stettner, Arion; Okano, Hiroyuki; Gralka, Matti; Guessous, Ghita; Amarnath, Kapil; Cordero, Otto X.; Hwa, Terence; Bonhoeffer, Sebastian

Year: 2022

DOI: https://doi.org/10.1101/2022.04.15.488298

Paper Interrogating the effect of enzyme kinetics on metabolism using differentiable constraint-based models

Wilken, St. Elmo; Besançon, Mathieu; Kratochvíl, Miroslav et al. · 2022 · DOI

Full title: Interrogating the effect of enzyme kinetics on metabolism using differentiable constraint-based models

Authors: Wilken, St. Elmo; Besançon, Mathieu; Kratochvíl, Miroslav; Kuate, Chilperic Armel Foko; Trefois, Christophe; Gu, Wei; Ebenhöh, Oliver

Year: 2022

DOI: https://doi.org/10.1101/2022.07.11.499575

Paper Evaluating proteome allocation of Saccharomyces cerevisiae phenotypes with resource balance analysis

Dinh, Hoang V.; Maranas, Costas D. · 2022 · DOI

Full title: Evaluating proteome allocation of Saccharomyces cerevisiae phenotypes with resource balance analysis

Authors: Dinh, Hoang V.; Maranas, Costas D.

Year: 2022

DOI: https://doi.org/10.1101/2022.09.20.508694

Paper Glycolysis revisited: from steady state growth to glucose pulses

Lao‐Martil, David; Schmitz, Joep; Teusink, Bas et al. · 2022 · DOI

Full title: Glycolysis revisited: from steady state growth to glucose pulses

Authors: Lao‐Martil, David; Schmitz, Joep; Teusink, Bas; Riel, N.A.W. van

Year: 2022

DOI: https://doi.org/10.1101/2022.06.22.497165

Paper Metabolic modeling of Hermetia illucens larvae resource allocation for high-value fatty acid production

Grausa, Kristina; Siddiqui, Shahida Anusha; Lameyer, Norbert et al. · 2022 · DOI

Full title: Metabolic modeling of Hermetia illucens larvae resource allocation for high-value fatty acid production

Authors: Grausa, Kristina; Siddiqui, Shahida Anusha; Lameyer, Norbert; Wiesotzki, Karin; Smetana, Sergiy; Pentjuss, Agris

Year: 2022

DOI: https://doi.org/10.1101/2022.10.25.513765

Paper Teasing out Missing Reactions in Genome-scale Metabolic Networks through Graph Convolutional Networks

Chen, Can; Liao, Chen; Liu, Yang‐Yu · 2022 · DOI

Full title: Teasing out Missing Reactions in Genome-scale Metabolic Networks through Graph Convolutional Networks

Authors: Chen, Can; Liao, Chen; Liu, Yang‐Yu

Year: 2022

DOI: https://doi.org/10.1101/2022.06.27.497720

Paper Turnover number predictions for kinetically uncharacterized enzymes using machine and deep learning

Kroll, Alexander; Rousset, Yvan; Hu, Xiao-Pan et al. · 2023 · Nature Communications · DOI

Full title: Turnover number predictions for kinetically uncharacterized enzymes using machine and deep learning

Authors: Kroll, Alexander; Rousset, Yvan; Hu, Xiao-Pan; Liebrand, Nina A.; Lercher, Martin J.

Year: 2023

Venue: Nature Communications

Paper Functional Decomposition of Metabolism allows a system-level quantification of fluxes and protein allocation towards specific metabolic functions

Mori, Matteo; Cheng, Chuankai; Taylor, Brian et al. · 2022 · DOI

Full title: Functional Decomposition of Metabolism allows a system-level quantification of fluxes and protein allocation towards specific metabolic functions

Authors: Mori, Matteo; Cheng, Chuankai; Taylor, Brian; Okano, Hiroyuki; Hwa, Terence

Year: 2022

DOI: https://doi.org/10.1101/2022.10.22.513080

Paper Dynamic genome-based metabolic modeling of the predominant cellulolytic rumen bacterium Fibrobacter succinogenes S85

Fakih, Ibrahim; Got, Jeanne; Robles-Rodríguez, Carlos Eduardo et al. · 2022 · DOI

Full title: Dynamic genome-based metabolic modeling of the predominant cellulolytic rumen bacterium Fibrobacter succinogenes S85

Authors: Fakih, Ibrahim; Got, Jeanne; Robles-Rodríguez, Carlos Eduardo; Siegel, Anne; Forano, Évelyne; Muñoz‐Tamayo, Rafael

Year: 2022

DOI: https://doi.org/10.1101/2022.10.18.512662

Paper Generative machine learning produces kinetic models that accurately characterize intracellular metabolic states

Choudhury, Subham; Narayanan, Bharath; Moret, Michaël et al. · 2024 · Nature Catalysis · DOI

Full title: Generative machine learning produces kinetic models that accurately characterize intracellular metabolic states

Authors: Choudhury, Subham; Narayanan, Bharath; Moret, Michaël; Hatzimanikatis, Vassily; Mišković, Ljubiša

Year: 2024

Venue: Nature Catalysis

DOI: https://doi.org/10.1038/s41929-024-01220-6

Paper Transcriptome guided metabolic network analysis reveals rearrangements of carbon flux distribution in Neisseria gonorrhoeae during neutrophil co-culture

Potter, Aimee D.; Baiocco, Christopher M.; Papin, Jason A. et al. · 2022 · DOI

Full title: Transcriptome guided metabolic network analysis reveals rearrangements of carbon flux distribution in Neisseria gonorrhoeae during neutrophil co-culture

Authors: Potter, Aimee D.; Baiocco, Christopher M.; Papin, Jason A.; Criss, Alison K.

Year: 2022

DOI: https://doi.org/10.1101/2022.12.19.521143

Paper The necessity of considering enzymes as compartments in constraint-based genome-scale metabolic models

Yang, Xue; Mao, Zhitao; Huang, Jianfeng et al. · 2022 · DOI

Full title: The necessity of considering enzymes as compartments in constraint-based genome-scale metabolic models

Authors: Yang, Xue; Mao, Zhitao; Huang, Jianfeng; Wang, Ruoyu; Dong, Huaming; Zhang, Yanfei; Ma, Hongwu

Year: 2022

DOI: https://doi.org/10.1101/2022.12.14.520512

Paper Guidelines for extracting biologically relevant context-specific metabolic models using gene expression data

Gopalakrishnan, Saratram; Joshi, Chintan; Gomez, Miguel Valderrama et al. · 2022 · DOI

Full title: Guidelines for extracting biologically relevant context-specific metabolic models using gene expression data

Authors: Gopalakrishnan, Saratram; Joshi, Chintan; Gomez, Miguel Valderrama; Içten, Elçin; Rolandi, Pablo; Johnson, William; Kontoravdi, Cleo; Lewis, Nathan E.

Year: 2022

DOI: https://doi.org/10.1101/2022.12.04.519052

Paper Elevated energy costs of biomass production in mitochondrial-respiration deficient Saccharomyces cerevisiae

Grigaitis, Pranas; Bogaard, Samira L. van den; Teusink, Bas · 2023 · FEMS Yeast Research · DOI

Full title: Elevated energy costs of biomass production in mitochondrial-respiration deficient Saccharomyces cerevisiae

Authors: Grigaitis, Pranas; Bogaard, Samira L. van den; Teusink, Bas

Year: 2023

Venue: FEMS Yeast Research

DOI: https://doi.org/10.1093/femsyr/foad008

Paper Analysis of the genome-scale metabolic model of Bacillus subtilis to design novel in-silico strategies for native and recombinant L-asparaginase overproduction

Barge, Nisha Sanjay; Sahoo, Ansuman; Dasu, Veeranki Venkata · 2023 · DOI

Full title: Analysis of the genome-scale metabolic model of Bacillus subtilis to design novel in-silico strategies for native and recombinant L-asparaginase overproduction

Authors: Barge, Nisha Sanjay; Sahoo, Ansuman; Dasu, Veeranki Venkata

Year: 2023

DOI: https://doi.org/10.1101/2022.12.29.522229

Paper Critical assessment of E. coli genome-scale metabolic model with high-throughput mutant fitness data

Bernstein, David B.; Akkas, Batu; Price, Morgan N. et al. · 2023 · DOI

Full title: Critical assessment of E. coli genome-scale metabolic model with high-throughput mutant fitness data

Authors: Bernstein, David B.; Akkas, Batu; Price, Morgan N.; Arkin, Adam P.

Year: 2023

DOI: https://doi.org/10.1101/2023.01.05.522875

Paper Accurate flux predictions using tissue-specific gene expression in plant metabolic modeling

Kaste, Joshua A. M.; Shachar‐Hill, Yair · 2022 · DOI

Full title: Accurate flux predictions using tissue-specific gene expression in plant metabolic modeling

Authors: Kaste, Joshua A. M.; Shachar‐Hill, Yair

Year: 2022

DOI: https://doi.org/10.1101/2022.09.05.506655

Paper Coupling Flux Balance Analysis with Reactive Transport Modeling through Machine Learning for Rapid and Stable Simulation of Microbial Metabolic Switching

Song, Hyun‐Seob; Ahamed, Firnaaz; Lee, Joon‐Yong et al. · 2023 · DOI

Full title: Coupling Flux Balance Analysis with Reactive Transport Modeling through Machine Learning for Rapid and Stable Simulation of Microbial Metabolic Switching

Authors: Song, Hyun‐Seob; Ahamed, Firnaaz; Lee, Joon‐Yong; Henry, Christopher C.; Edirisinghe, Janaka N.; Nelson, William; Chen, Xingyuan; Moulton, D.; Scheibe, Tim

Year: 2023

DOI: https://doi.org/10.1101/2023.02.06.527371

Paper A structured evaluation of genome-scale constraint-based modeling tools for microbial consortia

W. T. Scott; Sara Benito-Vaquerizo; Johannes Zimmerman et al. · 2023 · bioRxiv · DOI

Full title: A structured evaluation of genome-scale constraint-based modeling tools for microbial consortia

Authors: W. T. Scott; Sara Benito-Vaquerizo; Johannes Zimmerman; Djordje Bajić; A. Heinken; M. Suárez-Diez; P. Schaap

Year: 2023

Venue: bioRxiv

DOI: https://doi.org/10.1101/2023.02.08.527721

Paper Microbial community-scale metabolic modeling predicts personalized short chain fatty acid production profiles in the human gut

Quinn-Bohmann, Nick; Wilmanski, Tomasz; Sarmiento, Katherine Ramos et al. · 2023 · DOI

Full title: Microbial community-scale metabolic modeling predicts personalized short chain fatty acid production profiles in the human gut

Authors: Quinn-Bohmann, Nick; Wilmanski, Tomasz; Sarmiento, Katherine Ramos; Levy, Lisa; Lampe, Johanna W.; Gurry, Thomas; Rappaport, Noa; Ostrem, Erin M.; Venturelli, Ophelia S.; Diener, Christian; Gibbons, Sean M.

Year: 2023

DOI: https://doi.org/10.1101/2023.02.28.530516

Paper Overall biomass yield on multiple nutrient sources

Golan, Ohad; Gampp, Olivia; Eckert, Lina et al. · 2023 · DOI

Full title: Overall biomass yield on multiple nutrient sources

Authors: Golan, Ohad; Gampp, Olivia; Eckert, Lina; Sauer, Uwe

Year: 2023

DOI: https://doi.org/10.1101/2023.02.16.528813

Paper Accurate prediction of in vivo protein abundances by coupling constraint-based modelling and machine learning

Ferreira, Maurício Alexander de Moura; Wendering, Philipp; Arend, Marius et al. · 2023 · DOI

Full title: Accurate prediction of in vivo protein abundances by coupling constraint-based modelling and machine learning

Authors: Ferreira, Maurício Alexander de Moura; Wendering, Philipp; Arend, Marius; Silveira, Wendel Batista da; Nikoloski, Zoran

Year: 2023

DOI: https://doi.org/10.1101/2023.04.11.536445

Paper BayFlux: A Bay esian method to quantify metabolic Flux es and their uncertainty at the genome scale

Backman, Tyler W. H.; Schenk, Christina; Radivojević, Tijana et al. · 2023 · DOI

Full title: BayFlux: A Bay esian method to quantify metabolic Flux es and their uncertainty at the genome scale

Authors: Backman, Tyler W. H.; Schenk, Christina; Radivojević, Tijana; Ando, David; Singh, Janavi; Czajka, Jeffrey J.; Costello, Zak; Keasling, Jay D.; Tang, Yinjie; Akhmatskaya, Elena; Martín, Héctor García

Year: 2023

DOI: https://doi.org/10.1101/2023.04.19.537435

Paper Computational biology predicts metabolic engineering targets for increased production of 102 valuable chemicals in yeast

Domenzain, Iván; Lü, Yao; Shi, Junling et al. · 2023 · DOI

Full title: Computational biology predicts metabolic engineering targets for increased production of 102 valuable chemicals in yeast

Authors: Domenzain, Iván; Lü, Yao; Shi, Junling; Lu, Hongzhong; Nielsen, Jens

Year: 2023

DOI: https://doi.org/10.1101/2023.01.31.526512

Paper Microbial Interactions from a New Perspective: Reinforcement Learning Reveals New Insights into Microbiome Evolution

Ghadermazi, Parsa; Chan, Siu Hung Joshua · 2023 · DOI

Full title: Microbial Interactions from a New Perspective: Reinforcement Learning Reveals New Insights into Microbiome Evolution

Authors: Ghadermazi, Parsa; Chan, Siu Hung Joshua

Year: 2023

DOI: https://doi.org/10.1101/2023.05.07.539711

Paper Genome-scale and pathway engineering for the sustainable aviation fuel precursor isoprenol production in Pseudomonas putida

Banerjee, Deepanwita; Yunus, Ian Sofian; Wang, Xi et al. · 2023 · DOI

Full title: Genome-scale and pathway engineering for the sustainable aviation fuel precursor isoprenol production in Pseudomonas putida

Authors: Banerjee, Deepanwita; Yunus, Ian Sofian; Wang, Xi; Kim, Jinho; Srinivasan, Aparajitha; Menchavez, Russel; Chen, Yan; Gin, Jennifer; Petzold, Christopher J.; Martín, Héctor García; Adams, Paul D.; Mukhopadhyay, Aindrila; Kim, Joonhoon; Lee, Taek Soon; Kim, Joonhoon; Lee, Taek Soon

Year: 2023

DOI: https://doi.org/10.1101/2023.04.29.538800

Paper Pichia pastoris growth - coupled heme biosynthesis analysis using metabolic modelling

Pentjuss, Agris; Bolmanis, Emīls; Šuleiko, Anastasija et al. · 2023 · DOI

Full title: Pichia pastoris growth - coupled heme biosynthesis analysis using metabolic modelling

Authors: Pentjuss, Agris; Bolmanis, Emīls; Šuleiko, Anastasija; Didrihsone, Elina; Šuleiko, Artūrs; Dubencovs, Konstantīns; Liepiņš, Jānis; Kazāks, Andris; Vanags, Juris

Year: 2023

DOI: https://doi.org/10.1101/2023.05.13.540629

Paper METABOLIC MODELLING AS A POWERFUL TOOL TO IDENTIFY CRITICAL COMPONENTS OF PNEUMOCYSTIS GROWTH MEDIUM

Nev, Olga A.; Zamaraeva, Elena; Oliveira, Romain De et al. · 2023 · DOI

Full title: METABOLIC MODELLING AS A POWERFUL TOOL TO IDENTIFY CRITICAL COMPONENTS OF PNEUMOCYSTIS GROWTH MEDIUM

Authors: Nev, Olga A.; Zamaraeva, Elena; Oliveira, Romain De; Duvenage, Lucian; Abou-Jaoudé, Wassim; Ouattara, Djomangan Adama; Hoving, J. Claire; Gudelj, Ivana; Brown, Alistair J. P.

Year: 2023

DOI: https://doi.org/10.1101/2023.06.07.544035

Paper Genome-scale metabolic models reveal determinants of phenotypic differences in non-Saccharomyces yeasts

Pettersen, Jakob Peder; Castillo, Sandra; Jouhten, Paula et al. · 2023 · BMC Bioinformatics · DOI

Full title: Genome-scale metabolic models reveal determinants of phenotypic differences in non-Saccharomyces yeasts

Authors: Pettersen, Jakob Peder; Castillo, Sandra; Jouhten, Paula; Almaas, Eivind

Year: 2023

Venue: BMC Bioinformatics

Paper Minimization of proteome reallocation explains metabolic transition in hierarchical utilization of carbon sources

Liu, Zhihao; Chen, Minghao; Hu, Jingmin et al. · 2024 · DOI

Full title: Minimization of proteome reallocation explains metabolic transition in hierarchical utilization of carbon sources

Authors: Liu, Zhihao; Chen, Minghao; Hu, Jingmin; Wang, Yonghong; Chen, Yu

Year: 2024

DOI: https://doi.org/10.1101/2024.01.23.576957

Paper DLTKcat: deep learning-based prediction of temperature-dependent enzyme turnover rates

Qiu, Sizhe; Zhao, Simiao; Yang, Aidong · 2023 · Briefings in Bioinformatics · DOI

Full title: DLTKcat: deep learning-based prediction of temperature-dependent enzyme turnover rates

Authors: Qiu, Sizhe; Zhao, Simiao; Yang, Aidong

Year: 2023

Venue: Briefings in Bioinformatics

DOI: https://doi.org/10.1093/bib/bbad506

Paper Exploring the metabolic profiling of A. baumannii for antimicrobial development using genome-scale modelling

Leonidou, Nantia; Xia, Yufan; Friedrich, Lea et al. · 2023 · DOI

Full title: Exploring the metabolic profiling of A. baumannii for antimicrobial development using genome-scale modelling

Authors: Leonidou, Nantia; Xia, Yufan; Friedrich, Lea; Schütz, Monika; Dräger, Andreas

Year: 2023

DOI: https://doi.org/10.1101/2023.09.13.557502

Paper Machine learning predicts system-wide metabolic flux control in cyanobacteria

Kugler, Amit; Stensjö, Karin · 2023 · DOI

Full title: Machine learning predicts system-wide metabolic flux control in cyanobacteria

Authors: Kugler, Amit; Stensjö, Karin

Year: 2023

DOI: https://doi.org/10.1101/2023.10.18.562898

Paper Genome-Scale Modeling of Rothia mucilaginosa Reveals Insights into Metabolic Capabilities and Therapeutic Strategies for Cystic Fibrosis

Leonidou, Nantia; Ostyn, Lisa; Coenye, Tom et al. · 2023 · DOI

Full title: Genome-Scale Modeling of Rothia mucilaginosa Reveals Insights into Metabolic Capabilities and Therapeutic Strategies for Cystic Fibrosis

Authors: Leonidou, Nantia; Ostyn, Lisa; Coenye, Tom; Crabbé, Aurélie; Dräger, Andreas

Year: 2023

DOI: https://doi.org/10.1101/2023.11.20.567620

Paper Improved Production of Taxol® Precursors in S. cerevisiae using Combinatorial in silico Design and Metabolic Engineering

Malcı, Koray; Santibáñez, Rodrigo; Jonguitud‐Borrego, Nestor et al. · 2023 · DOI

Full title: Improved Production of Taxol® Precursors in S. cerevisiae using Combinatorial in silico Design and Metabolic Engineering

Authors: Malcı, Koray; Santibáñez, Rodrigo; Jonguitud‐Borrego, Nestor; Santoyo‐Garcia, Jorge H.; Kherkoven, Eduard J.; Rios‐Solis, Leonardo

Year: 2023

DOI: https://doi.org/10.1101/2023.06.11.544475

Paper Inferring Metabolic States from Single Cell Transcriptomic Data via Geometric Deep Learning

Steach, Holly R.; Viswanath, Siddharth; He, Yixuan et al. · 2023 · DOI

Full title: Inferring Metabolic States from Single Cell Transcriptomic Data via Geometric Deep Learning

Authors: Steach, Holly R.; Viswanath, Siddharth; He, Yixuan; Zhang, Xitong; Ivanova, Natalia; Hirn, Matthew; Perlmutter, Michael; Krishnaswamy, Smita

Year: 2023

DOI: https://doi.org/10.1101/2023.12.05.570153

Paper Dynamic Flux Balance Analysis Models in SBML

König, Matthias; Watanabe, Leandro; Grzegorzewski, Jan et al. · 2018 · DOI

Full title: Dynamic Flux Balance Analysis Models in SBML

Authors: König, Matthias; Watanabe, Leandro; Grzegorzewski, Jan; Myers, Chris J.

Year: 2018

DOI: https://doi.org/10.1101/245076

Paper Flux modelling analysis reveals the metabolic impact of cryptic plasmids and environmental conditions in probiotic Escherichia coli Nissle 1917

Paola Corbín-Agustí; Alba Arévalo-Lalanne; Patricia Álvarez et al. · 2025 · bioRxiv · DOI

Full title: Flux modelling analysis reveals the metabolic impact of cryptic plasmids and environmental conditions in probiotic Escherichia coli Nissle 1917

Authors: Paola Corbín-Agustí; Alba Arévalo-Lalanne; Patricia Álvarez; María Enrique; Daniel Ramón; J. Peretó; Marta Tortajada

Year: 2025

Venue: bioRxiv

DOI: https://doi.org/10.1101/2025.11.17.688048

Paper Modelling dynamic host-pathway interactions at the genome scale with machine learning

Merzbacher, Charlotte; Aodha, Oisin Mac; Oyarzún, Diego A. · 2024 · DOI

Full title: Modelling dynamic host-pathway interactions at the genome scale with machine learning

Authors: Merzbacher, Charlotte; Aodha, Oisin Mac; Oyarzún, Diego A.

Year: 2024

DOI: https://doi.org/10.1101/2024.04.09.588720

Paper MINN: A METABOLIC-INFORMED NEURAL NETWORK FOR INTEGRATING OMICS DATA INTO GENOME-SCALE METABOLIC MODELING

Tazza, Gabriele; Moro, Francesco; Ruggeri, Dario et al. · 2025 · DOI

Full title: MINN: A METABOLIC-INFORMED NEURAL NETWORK FOR INTEGRATING OMICS DATA INTO GENOME-SCALE METABOLIC MODELING

Authors: Tazza, Gabriele; Moro, Francesco; Ruggeri, Dario; Teusink, Bas; Vidács, László

Year: 2025

DOI: https://doi.org/10.1101/2025.05.14.653943

Paper Yeast9: A Consensus Yeast Metabolic Model Enables Quantitative Analysis of Cellular Metabolism By Incorporating Big Data

Zhang, Chengyu; Sanchez, Benjamin; Li, Feiran et al. · 2023 · DOI

Full title: Yeast9: A Consensus Yeast Metabolic Model Enables Quantitative Analysis of Cellular Metabolism By Incorporating Big Data

Authors: Zhang, Chengyu; Sanchez, Benjamin; Li, Feiran; Eiden, Cheng Wei Quan; Scott, William T.; Liebal, Ulf W.; Blank, Lars M.; Mengers, Hendrik G.; Anton, Mihail; Rangel, Albert Tafur; Mendoza, Sebastián N.; Zhang, Lixin; Nielsen, Jens; Lu, Hongzhong; Kerkhoven, Eduard J.

Year: 2023

DOI: https://doi.org/10.1101/2023.12.03.569754

Paper Robustness encoded across essential and accessory replicons in an ecologically versatile bacterium

diCenzo, George C.; Benedict, Alex B.; Fondi, Marco et al. · 2017 · DOI

Full title: Robustness encoded across essential and accessory replicons in an ecologically versatile bacterium

Authors: diCenzo, George C.; Benedict, Alex B.; Fondi, Marco; Walker, Graham C.; Finan, Turlough M.; Mengoni, Alessio; Griffitts, Joel S.

Year: 2017

DOI: https://doi.org/10.1101/209916

Paper Machine Learning and Metabolic Model Guided CRISPRi Reveals a Central Role for Phosphoglycerate Mutase in Chlamydia trachomatis Persistence

Chowdhury, Niaz Bahar; Pokorzynski, Nick D.; Rucks, Elizabeth A. et al. · 2023 · DOI

Full title: Machine Learning and Metabolic Model Guided CRISPRi Reveals a Central Role for Phosphoglycerate Mutase in Chlamydia trachomatis Persistence

Authors: Chowdhury, Niaz Bahar; Pokorzynski, Nick D.; Rucks, Elizabeth A.; Ouellette, Scot P.; Carabeo, Rey A.; Saha, Rajib

Year: 2023

DOI: https://doi.org/10.1101/2023.12.18.572198

Paper Genome-scale metabolic modelling of trimethoprim’s mode of action reveals free ATP salvaged to restore purine pool

Carter, Cailean; Singh, Dipali; Wain, John et al. · 2025 · DOI

Full title: Genome-scale metabolic modelling of trimethoprim’s mode of action reveals free ATP salvaged to restore purine pool

Authors: Carter, Cailean; Singh, Dipali; Wain, John; Langridge, Gemma C.

Year: 2025

DOI: https://doi.org/10.1101/2025.07.25.666800

Paper BOFdat: generating biomass objective function stoichiometric coefficients from experimental data

Lachance, Jean‐Christophe; Monk, Jonathan M.; Lloyd, Colton J. et al. · 2018 · DOI

Full title: BOFdat: generating biomass objective function stoichiometric coefficients from experimental data

Authors: Lachance, Jean‐Christophe; Monk, Jonathan M.; Lloyd, Colton J.; Seif, Yara; Palsson, Bernhard Ø.; Rodrigue, Sébastien; Feist, Adam M.; King, Zachary A.; Jacques, Pierre‐Étienne

Year: 2018

DOI: https://doi.org/10.1101/243881

Paper Tn-Core: context-specific reconstruction of core metabolic models using Tn-seq data

diCenzo, George C.; Mengoni, Alessio; Fondi, Marco · 2017 · DOI

Full title: Tn-Core: context-specific reconstruction of core metabolic models using Tn-seq data

Authors: diCenzo, George C.; Mengoni, Alessio; Fondi, Marco

Year: 2017

DOI: https://doi.org/10.1101/221325

Paper Fast automated reconstruction of genome-scale metabolic models for microbial species and communities

Machado, Daniel; Andrejev, Sergej; Tramontano, Melanie et al. · 2018 · DOI

Full title: Fast automated reconstruction of genome-scale metabolic models for microbial species and communities

Authors: Machado, Daniel; Andrejev, Sergej; Tramontano, Melanie; Patil, Kiran Raosaheb

Year: 2018

DOI: https://doi.org/10.1101/223198

Paper MIMEco: Multi-objective metabolic modeling to predict and explain pairwise interactions

Lambert, Anna; Chaffron, Samuel; Eveillard, Damien · 2025 · DOI

Full title: MIMEco: Multi-objective metabolic modeling to predict and explain pairwise interactions

Authors: Lambert, Anna; Chaffron, Samuel; Eveillard, Damien

Year: 2025

DOI: https://doi.org/10.1101/2025.11.25.690486

Paper A genome-scale metabolic model for Methylococcus capsulatus predicts reduced efficiency uphill electron transfer to pMMO

Lieven, Christian; Petersen, Leander A. H.; Jørgensen, Sten Bay et al. · 2018 · DOI

Full title: A genome-scale metabolic model for Methylococcus capsulatus predicts reduced efficiency uphill electron transfer to pMMO

Authors: Lieven, Christian; Petersen, Leander A. H.; Jørgensen, Sten Bay; Gernaey, Krist V.; Herrgård, Markus J.; Sonnenschein, Nikolaus

Year: 2018

DOI: https://doi.org/10.1101/329714

Paper Metabolic modeling of Pectobacterium parmentieri SCC3193 provides insights into metabolic pathways of plant pathogenic bacteria

Żołędowska, Sabina; Presta, Luana; Fondi, Marco et al. · 2018 · DOI

Full title: Metabolic modeling of Pectobacterium parmentieri SCC3193 provides insights into metabolic pathways of plant pathogenic bacteria

Authors: Żołędowska, Sabina; Presta, Luana; Fondi, Marco; Decorosi, Francesca; Giovannetti, Luciana; Mengoni, Alessio; Łojkowska, Ewa

Year: 2018

DOI: https://doi.org/10.1101/284968

Paper Metabolic modeling of Streptococcus mutans reveals complex nutrient requirements of an oral pathogen

Jijakli, Kenan; Jensen, Paul A. · 2018 · DOI

Full title: Metabolic modeling of Streptococcus mutans reveals complex nutrient requirements of an oral pathogen

Authors: Jijakli, Kenan; Jensen, Paul A.

Year: 2018

DOI: https://doi.org/10.1101/419507

Paper Modeling genome-wide evolution of catalytic turnover rates: Strong epistasis shaped modern enzyme kinetics

Heckmann, David; Zielinski, Daniel C.; Palsson, Bernhard Ø. · 2018 · DOI

Full title: Modeling genome-wide evolution of catalytic turnover rates: Strong epistasis shaped modern enzyme kinetics

Authors: Heckmann, David; Zielinski, Daniel C.; Palsson, Bernhard Ø.

Year: 2018

DOI: https://doi.org/10.1101/318972

Paper System-level analysis of metabolic trade-offs during anaerobic photoheterotrophic growth in Rhodopseudomonas palustris

Navid, Ali; Jiao, Yongqin; Wong, Sergio et al. · 2019 · BMC Bioinformatics · DOI

Full title: System-level analysis of metabolic trade-offs during anaerobic photoheterotrophic growth in Rhodopseudomonas palustris

Authors: Navid, Ali; Jiao, Yongqin; Wong, Sergio; Pett‐Ridge, Jennifer

Year: 2019

Venue: BMC Bioinformatics

Paper SLIMEr: probing flexibility of lipid metabolism in yeast with an improved constraint-based modeling framework

Sánchez, Benjamín J.; Li, Feiran; Kerkhoven, Eduard J. et al. · 2019 · BMC Systems Biology · DOI

Full title: SLIMEr: probing flexibility of lipid metabolism in yeast with an improved constraint-based modeling framework

Authors: Sánchez, Benjamín J.; Li, Feiran; Kerkhoven, Eduard J.; Nielsen, Jens

Year: 2019

Venue: BMC Systems Biology

Paper Flux balance analysis predicts NADP phosphatase and NADH kinase are critical to balancing redox during xylose fermentation in Scheffersomyces stipitis

Correia, Kevin; Khusnutdinova, Anna N.; Li, Peter Yan et al. · 2018 · DOI

Full title: Flux balance analysis predicts NADP phosphatase and NADH kinase are critical to balancing redox during xylose fermentation in Scheffersomyces stipitis

Authors: Correia, Kevin; Khusnutdinova, Anna N.; Li, Peter Yan; Joo, Jeong Chan; Brown, Greg; Yakunin, Alexander F.; Mahadevan, Radhakrishnan

Year: 2018

DOI: https://doi.org/10.1101/390401

Paper Large-scale kinetic metabolic models of Pseudomonas putida for a consistent design of metabolic engineering strategies

Tokic, Milenko; Mišković, Ljubiša; Hatzimanikatis, Vassily · 2019 · DOI

Full title: Large-scale kinetic metabolic models of Pseudomonas putida for a consistent design of metabolic engineering strategies

Authors: Tokic, Milenko; Mišković, Ljubiša; Hatzimanikatis, Vassily

Year: 2019

DOI: https://doi.org/10.1101/569152

Paper Elementary Growth Modes provide a molecular description of cellular self-fabrication

Groot, Daan H. de; Hulshof, Josephus; Teusink, Bas et al. · 2019 · DOI

Full title: Elementary Growth Modes provide a molecular description of cellular self-fabrication

Authors: Groot, Daan H. de; Hulshof, Josephus; Teusink, Bas; Bruggeman, Frank J.; Planqué, Robert

Year: 2019

DOI: https://doi.org/10.1101/608083

Paper Genome-scale metabolic network reconstruction of the chloroform-respiring Dehalobacter restrictus strain CF

Correia, Kevin; Ho, Han‐Chen; Mahadevan, Radhakrishnan · 2018 · DOI

Full title: Genome-scale metabolic network reconstruction of the chloroform-respiring Dehalobacter restrictus strain CF

Authors: Correia, Kevin; Ho, Han‐Chen; Mahadevan, Radhakrishnan

Year: 2018

DOI: https://doi.org/10.1101/375063

Paper Microbial Pathway Thermodynamics: Stoichiometric Models Unveil Anabolic and Catabolic Processes

Ebenhöh, Oliver; Ebeling, Josha; Meyer, R J et al. · 2024 · Life · DOI

Full title: Microbial Pathway Thermodynamics: Stoichiometric Models Unveil Anabolic and Catabolic Processes

Authors: Ebenhöh, Oliver; Ebeling, Josha; Meyer, R J; Pohlkotte, Fabian; Nies, Tim

Year: 2024

Venue: Life

DOI: https://doi.org/10.3390/life14020247

Paper Metabolic Modelling as a Framework for Metabolomics Data Integration and Analysis

Volkova, Svetlana; Matos, Marta R. A.; Mattanovich, Matthias et al. · 2020 · Metabolites · DOI

Full title: Metabolic Modelling as a Framework for Metabolomics Data Integration and Analysis

Authors: Volkova, Svetlana; Matos, Marta R. A.; Mattanovich, Matthias; Mas, Igor Marín de

Year: 2020

Venue: Metabolites

DOI: https://doi.org/10.3390/metabo10080303

Paper Genome-Scale Metabolic Modeling Enables In-Depth Understanding of Big Data

Passi, Anurag; Tibocha‐Bonilla, Juan D.; Kumar, Manish et al. · 2021 · Metabolites · DOI

Full title: Genome-Scale Metabolic Modeling Enables In-Depth Understanding of Big Data

Authors: Passi, Anurag; Tibocha‐Bonilla, Juan D.; Kumar, Manish; Tec-Campos, Diego; Zengler, Karsten; Zúñiga, Cristal

Year: 2021

Venue: Metabolites

DOI: https://doi.org/10.3390/metabo12010014

Paper Towards Predicting Gut Microbial Metabolism: Integration of Flux Balance Analysis and Untargeted Metabolomics

Kuang, Ellen; Marney, Matthew W.; Cuevas, Daniel et al. · 2020 · Metabolites · DOI

Full title: Towards Predicting Gut Microbial Metabolism: Integration of Flux Balance Analysis and Untargeted Metabolomics

Authors: Kuang, Ellen; Marney, Matthew W.; Cuevas, Daniel; Edwards, Robert A.; Forsberg, Erica M.

Year: 2020

Venue: Metabolites

DOI: https://doi.org/10.3390/metabo10040156

Paper Drought Stress Responses in Context-Specific Genome-Scale Metabolic Models of Arabidopsis thaliana

Siriwach, Ratklao; Matsuda, Fumio; Yano, Kentaro et al. · 2020 · Metabolites · DOI

Full title: Drought Stress Responses in Context-Specific Genome-Scale Metabolic Models of Arabidopsis thaliana

Authors: Siriwach, Ratklao; Matsuda, Fumio; Yano, Kentaro; Hirai, Masami Yokota

Year: 2020

Venue: Metabolites

DOI: https://doi.org/10.3390/metabo10040159

Paper Algal Cell Factories: Approaches, Applications, and Potentials

Fu, Weiqi; Chaiboonchoe, Amphun; Khraiwesh, Basel et al. · 2016 · Marine Drugs · DOI

Full title: Algal Cell Factories: Approaches, Applications, and Potentials

Authors: Fu, Weiqi; Chaiboonchoe, Amphun; Khraiwesh, Basel; Nelson, David R.; Al-Khairy, Dina; Mystikou, Alexandra; Alzahmi, Amnah; Salehi‐Ashtiani, Kourosh

Year: 2016

Venue: Marine Drugs

DOI: https://doi.org/10.3390/md14120225

Paper State-of-the-Art Genetic Modalities to Engineer Cyanobacteria for Sustainable Biosynthesis of Biofuel and Fine-Chemicals to Meet Bio–Economy Challenges

Khan, Aqib Zafar; Bilal, Muhammad; Mehmood, Shahid et al. · 2019 · Life · DOI

Full title: State-of-the-Art Genetic Modalities to Engineer Cyanobacteria for Sustainable Biosynthesis of Biofuel and Fine-Chemicals to Meet Bio–Economy Challenges

Authors: Khan, Aqib Zafar; Bilal, Muhammad; Mehmood, Shahid; Sharma, Ashutosh; Iqbal, Hafiz M.N.

Year: 2019

Venue: Life

DOI: https://doi.org/10.3390/life9030054

Paper Development of Synechocystis sp. PCC 6803 as a Phototrophic Cell Factory

Yu, Yi; You, Le; Liu, Dianyi et al. · 2013 · Marine Drugs · DOI

Full title: Development of Synechocystis sp. PCC 6803 as a Phototrophic Cell Factory

Authors: Yu, Yi; You, Le; Liu, Dianyi; Hollinshead, Whitney D.; Tang, Yinjie; Zhang, Fuzhong

Year: 2013

Venue: Marine Drugs

DOI: https://doi.org/10.3390/md11082894

Paper Reconstruction of a Genome-Scale Metabolic Model of Streptomyces albus J1074: Improved Engineering Strategies in Natural Product Synthesis

Kittikunapong, Cheewin; Ye, Suhui; Magadán‐Corpas, Patricia et al. · 2021 · Metabolites · DOI

Full title: Reconstruction of a Genome-Scale Metabolic Model of Streptomyces albus J1074: Improved Engineering Strategies in Natural Product Synthesis

Authors: Kittikunapong, Cheewin; Ye, Suhui; Magadán‐Corpas, Patricia; Pérez‐Valero, Álvaro; Villar, Claudio J.; Lombó, Felipe; Kerkhoven, Eduard J.

Year: 2021

Venue: Metabolites

DOI: https://doi.org/10.3390/metabo11050304

Paper Revealing the Metabolic Alterations during Biofilm Development of Burkholderia cenocepacia Based on Genome-Scale Metabolic Modeling

Altay, Özlem; Zhang, Cheng; Türkez, Hasan et al. · 2021 · Metabolites · DOI

Full title: Revealing the Metabolic Alterations during Biofilm Development of Burkholderia cenocepacia Based on Genome-Scale Metabolic Modeling

Authors: Altay, Özlem; Zhang, Cheng; Türkez, Hasan; Nielsen, Jens; Uhlén, Mathias; Mardinoğlu, Adil

Year: 2021

Venue: Metabolites

DOI: https://doi.org/10.3390/metabo11040221

Paper Optimality Principles in the Regulation of Metabolic Networks

Berkhout, Jan; Bruggeman, Frank J.; Teusink, Bas · 2012 · Metabolites · DOI

Full title: Optimality Principles in the Regulation of Metabolic Networks

Authors: Berkhout, Jan; Bruggeman, Frank J.; Teusink, Bas

Year: 2012

Venue: Metabolites

DOI: https://doi.org/10.3390/metabo2030529

Paper Metabolic Modeling of Hermetia illucens Larvae Resource Allocation for High-Value Fatty Acid Production

Grausa, Kristina; Siddiqui, Shahida Anusha; Lameyer, Norbert et al. · 2023 · Metabolites · DOI

Full title: Metabolic Modeling of Hermetia illucens Larvae Resource Allocation for High-Value Fatty Acid Production

Authors: Grausa, Kristina; Siddiqui, Shahida Anusha; Lameyer, Norbert; Wiesotzki, Karin; Smetana, Sergiy; Pentjuss, Agris

Year: 2023

Venue: Metabolites

DOI: https://doi.org/10.3390/metabo13060724

Paper Genome-Scale Metabolic Modelling Approach to Understand the Metabolism of the Opportunistic Human Pathogen Staphylococcus epidermidis RP62A

Calvo, Teresa Díaz; Tejera, Noemı́; McNamara, Iain et al. · 2022 · Metabolites · DOI

Full title: Genome-Scale Metabolic Modelling Approach to Understand the Metabolism of the Opportunistic Human Pathogen Staphylococcus epidermidis RP62A

Authors: Calvo, Teresa Díaz; Tejera, Noemı́; McNamara, Iain; Langridge, Gemma C.; Wain, John; Poolman, Mark G.; Singh, Dipali

Year: 2022

Venue: Metabolites

DOI: https://doi.org/10.3390/metabo12020136

Paper The Metano Modeling Toolbox MMTB: An Intuitive, Web-Based Toolbox Introduced by Two Use Cases

Koblitz, Julia; Will, Sabine; Riemer, S. Alexander et al. · 2021 · Metabolites · DOI

Full title: The Metano Modeling Toolbox MMTB: An Intuitive, Web-Based Toolbox Introduced by Two Use Cases

Authors: Koblitz, Julia; Will, Sabine; Riemer, S. Alexander; Ulas, Thomas; Neumann‐Schaal, Meina; Schomburg, Dietmar

Year: 2021

Venue: Metabolites

DOI: https://doi.org/10.3390/metabo11020113

Paper Nutritional Interactions between Bacterial Species Colonising the Human Nasal Cavity: Current Knowledge and Future Prospects

Adolf, Lea Antje; Heilbronner, Simon · 2022 · Metabolites · DOI

Full title: Nutritional Interactions between Bacterial Species Colonising the Human Nasal Cavity: Current Knowledge and Future Prospects

Authors: Adolf, Lea Antje; Heilbronner, Simon

Year: 2022

Venue: Metabolites

DOI: https://doi.org/10.3390/metabo12060489

Paper Construction of a Genome-Scale Kinetic Model of Mycobacterium Tuberculosis Using Generic Rate Equations

Adiamah, Delali A.; Schwartz, Jean‐Marc · 2012 · Metabolites · DOI

Full title: Construction of a Genome-Scale Kinetic Model of Mycobacterium Tuberculosis Using Generic Rate Equations

Authors: Adiamah, Delali A.; Schwartz, Jean‐Marc

Year: 2012

Venue: Metabolites

DOI: https://doi.org/10.3390/metabo2030382

Paper Achieving Metabolic Flux Analysis for S. cerevisiae at a Genome-Scale: Challenges, Requirements, and Considerations

Gopalakrishnan, Saratram; Maranas, Costas D. · 2015 · Metabolites · DOI

Full title: Achieving Metabolic Flux Analysis for S. cerevisiae at a Genome-Scale: Challenges, Requirements, and Considerations

Authors: Gopalakrishnan, Saratram; Maranas, Costas D.

Year: 2015

Venue: Metabolites

DOI: https://doi.org/10.3390/metabo5030521

Paper Metabolism at Evolutionary Optimal States

Rabbers, Iraes; Heerden, Johan H. van; Nordholt, Niclas et al. · 2015 · Metabolites · DOI

Full title: Metabolism at Evolutionary Optimal States

Authors: Rabbers, Iraes; Heerden, Johan H. van; Nordholt, Niclas; Bachmann, Herwig; Teusink, Bas; Bruggeman, Frank J.

Year: 2015

Venue: Metabolites

DOI: https://doi.org/10.3390/metabo5020311

Paper Isotope-Assisted Metabolic Flux Analysis: A Powerful Technique to Gain New Insights into the Human Metabolome in Health and Disease

Moiz, Bilal; Li, Andrew; Padmanabhan, Surya et al. · 2022 · Metabolites · DOI

Full title: Isotope-Assisted Metabolic Flux Analysis: A Powerful Technique to Gain New Insights into the Human Metabolome in Health and Disease

Authors: Moiz, Bilal; Li, Andrew; Padmanabhan, Surya; Sriram, Ganesh; Clyne, Alisa Morss

Year: 2022

Venue: Metabolites

DOI: https://doi.org/10.3390/metabo12111066

Paper Using Gene Essentiality and Synthetic Lethality Information to Correct Yeast and CHO Cell Genome-Scale Models

Chowdhury, Ratul; Chowdhury, Anupam; Maranas, Costas D. · 2015 · Metabolites · DOI

Full title: Using Gene Essentiality and Synthetic Lethality Information to Correct Yeast and CHO Cell Genome-Scale Models

Authors: Chowdhury, Ratul; Chowdhury, Anupam; Maranas, Costas D.

Year: 2015

Venue: Metabolites

DOI: https://doi.org/10.3390/metabo5040536

Paper Genetic Optimization Algorithm for Metabolic Engineering Revisited

Alter, Tobias B.; Blank, Lars M.; Ebert, Birgitta E. · 2018 · Metabolites · DOI

Full title: Genetic Optimization Algorithm for Metabolic Engineering Revisited

Authors: Alter, Tobias B.; Blank, Lars M.; Ebert, Birgitta E.

Year: 2018

Venue: Metabolites

DOI: https://doi.org/10.3390/microorganisms10020267

Paper Machine Learning Methods for Analysis of Metabolic Data and Metabolic Pathway Modeling

Čuperlović‐Culf, Miroslava · 2018 · Metabolites · DOI

Full title: Machine Learning Methods for Analysis of Metabolic Data and Metabolic Pathway Modeling

Authors: Čuperlović‐Culf, Miroslava

Year: 2018

Venue: Metabolites

DOI: https://doi.org/10.3390/metabo8010004

Paper Extracellular Microbial Metabolomics: The State of the Art

Pinu, Farhana R.; Villas‐Bôas, Silas G. · 2017 · Metabolites · DOI

Full title: Extracellular Microbial Metabolomics: The State of the Art

Authors: Pinu, Farhana R.; Villas‐Bôas, Silas G.

Year: 2017

Venue: Metabolites

DOI: https://doi.org/10.3390/metabo7030043

Paper Quantification of Microbial Phenotypes

Martínez, Verónica S.; Krömer, Jens O. · 2016 · Metabolites · DOI

Full title: Quantification of Microbial Phenotypes

Authors: Martínez, Verónica S.; Krömer, Jens O.

Year: 2016

Venue: Metabolites

DOI: https://doi.org/10.3390/metabo6040045

Paper The Effect of Recombinant Protein Production in Lactococcus lactis Transcriptome and Proteome

Monteiro, Gabriel A.; Duarte, Sofia O. D. · 2022 · Microorganisms · DOI

Full title: The Effect of Recombinant Protein Production in Lactococcus lactis Transcriptome and Proteome

Authors: Monteiro, Gabriel A.; Duarte, Sofia O. D.

Year: 2022

Venue: Microorganisms

Paper An Improved Genome-Scale Metabolic Model of Arthrospira platensis C1 (iAK888) and Its Application in Glycogen Overproduction

Klanchui, Amornpan; Dulsawat, Sudarat; Chaloemngam, Kullapat et al. · 2018 · Metabolites · DOI

Full title: An Improved Genome-Scale Metabolic Model of Arthrospira platensis C1 (iAK888) and Its Application in Glycogen Overproduction

Authors: Klanchui, Amornpan; Dulsawat, Sudarat; Chaloemngam, Kullapat; Cheevadhanarak, Supapon; Prommeenate, Peerada; Meechai, Asawin

Year: 2018

Venue: Metabolites

DOI: https://doi.org/10.3390/metabo8040084

Paper Systematic Applications of Metabolomics in Metabolic Engineering

Dromms, Robert; Styczynski, Mark P. · 2012 · Metabolites · DOI

Full title: Systematic Applications of Metabolomics in Metabolic Engineering

Authors: Dromms, Robert; Styczynski, Mark P.

Year: 2012

Venue: Metabolites

DOI: https://doi.org/10.3390/metabo2041090

Paper A Genome-Scale Metabolic Model of Thalassiosira pseudonana CCMP 1335 for a Systems-Level Understanding of Its Metabolism and Biotechnological Potential

Ahmad, Ahmad; Tiwari, Archana; Srivastava, Shireesh · 2020 · Microorganisms · DOI

Full title: A Genome-Scale Metabolic Model of Thalassiosira pseudonana CCMP 1335 for a Systems-Level Understanding of Its Metabolism and Biotechnological Potential

Authors: Ahmad, Ahmad; Tiwari, Archana; Srivastava, Shireesh

Year: 2020

Venue: Microorganisms

DOI: https://doi.org/10.3390/microorganisms8091396

Paper Substrate Utilisation and Energy Metabolism in Non-Growing Campylobacter jejuni M1cam

Stoakes, Emily; Savva, George M.; Coates, Ruby et al. · 2022 · Microorganisms · DOI

Full title: Substrate Utilisation and Energy Metabolism in Non-Growing Campylobacter jejuni M1cam

Authors: Stoakes, Emily; Savva, George M.; Coates, Ruby; Tejera, Noemı́; Poolman, Mark G.; Grant, Andrew J.; Wain, John; Singh, Dipali

Year: 2022

Venue: Microorganisms

DOI: https://doi.org/10.3390/microorganisms10071355

Paper ecBSU1: A Genome-Scale Enzyme-Constrained Model of Bacillus subtilis Based on the ECMpy Workflow.

Wu, Ke; Mao, Zhitao; Mao, Yufeng et al. · 2023 · Microorganisms · DOI

Full title: ecBSU1: A Genome-Scale Enzyme-Constrained Model of Bacillus subtilis Based on the ECMpy Workflow.

Authors: Wu, Ke; Mao, Zhitao; Mao, Yufeng; Niu, Jinhui; Cai, Jingyi; Yuan, Qianqian; Yun, Lili; Liao, Xiaoping; Wang, Zhiwen; Ma, Hongwu

Year: 2023

Venue: Microorganisms

DOI: https://doi.org/10.3390/microorganisms11010178

Paper The Quantitative Measurement of Peptidoglycan Components Obtained from Acidic Hydrolysis in Gram-Positive and Gram-Negative Bacteria via Hydrophilic Interaction Liquid Chromatography Coupled with Mass Spectrometry

Pismennõi, Dmitri; Kattel, Anna; Belouah, Isma et al. · 2023 · Microorganisms · DOI

Full title: The Quantitative Measurement of Peptidoglycan Components Obtained from Acidic Hydrolysis in Gram-Positive and Gram-Negative Bacteria via Hydrophilic Interaction Liquid Chromatography Coupled with Mass Spectrometry

Authors: Pismennõi, Dmitri; Kattel, Anna; Belouah, Isma; Nahku, Ranno; Vilu, Raivo; Kobrin, Eeva‐Gerda

Year: 2023

Venue: Microorganisms

DOI: https://doi.org/10.3390/microorganisms11092134

Paper The Use of Interdisciplinary Approaches to Understand the Biology of Campylobacter jejuni

Dzianach, Paulina A.; Pérez‐Reche, Francisco J.; Strachan, Norval J. C. et al. · 2022 · Microorganisms · DOI

Full title: The Use of Interdisciplinary Approaches to Understand the Biology of Campylobacter jejuni

Authors: Dzianach, Paulina A.; Pérez‐Reche, Francisco J.; Strachan, Norval J. C.; Forbes, Ken J.; Dykes, Gary A.

Year: 2022

Venue: Microorganisms

DOI: https://doi.org/10.3390/microorganisms10122498

Paper Genome-Scale Metabolic Network Reconstruction and In Silico Analysis of Hexanoic acid Producing Megasphaera elsdenii

Lee, Na-Rae; Lee, Choong Hwan; Lee, Dong‐Yup et al. · 2020 · Microorganisms · DOI

Full title: Genome-Scale Metabolic Network Reconstruction and In Silico Analysis of Hexanoic acid Producing Megasphaera elsdenii

Authors: Lee, Na-Rae; Lee, Choong Hwan; Lee, Dong‐Yup; Park, Jin‐Byung

Year: 2020

Venue: Microorganisms

DOI: https://doi.org/10.3390/microorganisms8040539

Paper The Expanding Computational Toolbox for Engineering Microbial Phenotypes at the Genome Scale

Zielinski, Daniel C.; Patel, Arjun; Palsson, Bernhard Ø. · 2020 · Microorganisms · DOI

Full title: The Expanding Computational Toolbox for Engineering Microbial Phenotypes at the Genome Scale

Authors: Zielinski, Daniel C.; Patel, Arjun; Palsson, Bernhard Ø.

Year: 2020

Venue: Microorganisms

DOI: https://doi.org/10.3390/microorganisms8122050

Paper Systems Biology Approach to Bioremediation of Nitroaromatics: Constraint-Based Analysis of 2,4,6-Trinitrotoluene Biotransformation by Escherichia coli

Iman, Maryam; Sobati, Tabassom; Panahi, Yunes et al. · 2017 · Molecules · DOI

Full title: Systems Biology Approach to Bioremediation of Nitroaromatics: Constraint-Based Analysis of 2,4,6-Trinitrotoluene Biotransformation by Escherichia coli

Authors: Iman, Maryam; Sobati, Tabassom; Panahi, Yunes; Mobasheri, Meysam

Year: 2017

Venue: Molecules

DOI: https://doi.org/10.3390/molecules22081242

Paper Computational Modeling of the Human Microbiome

Chowdhury, Shomeek; Fong, Stephen S. · 2020 · Microorganisms · DOI

Full title: Computational Modeling of the Human Microbiome

Authors: Chowdhury, Shomeek; Fong, Stephen S.

Year: 2020

Venue: Microorganisms

DOI: https://doi.org/10.3390/microorganisms8020197

Paper Understanding Plant Nitrogen Metabolism through Metabolomics and Computational Approaches

Beatty, Perrin H.; Klein, Matthias S.; Fischer, Jeffrey et al. · 2016 · Plants · DOI

Full title: Understanding Plant Nitrogen Metabolism through Metabolomics and Computational Approaches

Authors: Beatty, Perrin H.; Klein, Matthias S.; Fischer, Jeffrey; Lewis, Ian A.; Muench, Douglas G.; Good, Allen G.

Year: 2016

Venue: Plants

DOI: https://doi.org/10.3390/plants5040039

Paper A Genome-Scale Metabolic Model of 2,3-Butanediol Production by Thermophilic Bacteria Geobacillus icigianus

Kulyashov, Mikhail A.; Peltek, S. E.; Akberdin, Ilya R. · 2020 · Microorganisms · DOI

Full title: A Genome-Scale Metabolic Model of 2,3-Butanediol Production by Thermophilic Bacteria Geobacillus icigianus

Authors: Kulyashov, Mikhail A.; Peltek, S. E.; Akberdin, Ilya R.

Year: 2020

Venue: Microorganisms

DOI: https://doi.org/10.3390/microorganisms8071002

Paper Metabolic Modeling of Pectobacterium parmentieri SCC3193 Provides Insights into Metabolic Pathways of Plant Pathogenic Bacteria

Żołędowska, Sabina; Presta, Luana; Fondi, Marco et al. · 2019 · Microorganisms · DOI

Full title: Metabolic Modeling of Pectobacterium parmentieri SCC3193 Provides Insights into Metabolic Pathways of Plant Pathogenic Bacteria

Authors: Żołędowska, Sabina; Presta, Luana; Fondi, Marco; Decorosi, Francesca; Giovannetti, Luciana; Mengoni, Alessio; Łojkowska, Ewa

Year: 2019

Venue: Microorganisms

DOI: https://doi.org/10.3390/microorganisms7040101

Paper Key Challenges in Designing CHO Chassis Platforms

Hamdi, Anis; Széliová, Diana; Ruckerbauer, David E. et al. · 2020 · Processes · DOI

Full title: Key Challenges in Designing CHO Chassis Platforms

Authors: Hamdi, Anis; Széliová, Diana; Ruckerbauer, David E.; Rocha, Isabel; Borth, Nicole; Zanghellini, Jürgen

Year: 2020

Venue: Processes

DOI: https://doi.org/10.3390/pr8060643

Paper Dynamic Metabolic Analysis of Cupriavidus necator DSM545 Producing Poly(3-hydroxybutyric acid) from Glycerol

Sun, Chenhao; Pérez‐Rivero, Cristina; Webb, Colin et al. · 2020 · Processes · DOI

Full title: Dynamic Metabolic Analysis of Cupriavidus necator DSM545 Producing Poly(3-hydroxybutyric acid) from Glycerol

Authors: Sun, Chenhao; Pérez‐Rivero, Cristina; Webb, Colin; Theodoropoulos, Constantinos

Year: 2020

Venue: Processes

DOI: https://doi.org/10.3390/pr8060657

Paper Uncovering Novel Pathways for Enhancing Hyaluronan Synthesis in Recombinant Lactococcus lactis: Genome-Scale Metabolic Modeling and Experimental Validation

Badri, Abinaya; Raman, Karthik; Jayaraman, Guhan · 2019 · Processes · DOI

Full title: Uncovering Novel Pathways for Enhancing Hyaluronan Synthesis in Recombinant Lactococcus lactis: Genome-Scale Metabolic Modeling and Experimental Validation

Authors: Badri, Abinaya; Raman, Karthik; Jayaraman, Guhan

Year: 2019

Venue: Processes

DOI: https://doi.org/10.3390/pr7060343

Paper Effect of Delays on the Response of Microalgae When Exposed to Dynamic Environmental Conditions

Zúñiga, Héctor; Vergara, Christian; Donoso‐Bravo, Andrés et al. · 2020 · Processes · DOI

Full title: Effect of Delays on the Response of Microalgae When Exposed to Dynamic Environmental Conditions

Authors: Zúñiga, Héctor; Vergara, Christian; Donoso‐Bravo, Andrés; Jeison, David

Year: 2020

Venue: Processes

DOI: https://doi.org/10.3390/pr8010087

Paper Arduino Soft Sensor for Monitoring Schizochytrium sp. Fermentation, a Proof of Concept for the Industrial Application of Genome-Scale Metabolic Models in the Context of Pharma 4.0

Alarcón, Claudio; Shene, Carolina · 2022 · Processes · DOI

Full title: Arduino Soft Sensor for Monitoring Schizochytrium sp. Fermentation, a Proof of Concept for the Industrial Application of Genome-Scale Metabolic Models in the Context of Pharma 4.0

Authors: Alarcón, Claudio; Shene, Carolina

Year: 2022

Venue: Processes

DOI: https://doi.org/10.3390/pr10112226

Paper Systems Biology of the Fluxome

Aon, Miguel A.; Cortassa, Sonia · 2015 · Processes · DOI

Full title: Systems Biology of the Fluxome

Authors: Aon, Miguel A.; Cortassa, Sonia

Year: 2015

Venue: Processes

DOI: https://doi.org/10.3390/pr3030607

Paper Biosynthesis of fatty acids and biosurfactants by the yeast Yarrowia lipolytica with emphasis on metabolic networks and bioinformatics

Bauer, Cláudia Marlene; Schmitz, Caroline; Landell, Melissa Fontes et al. · 2022 · Biotechnology Research and Innovation · DOI

Full title: Biosynthesis of fatty acids and biosurfactants by the yeast Yarrowia lipolytica with emphasis on metabolic networks and bioinformatics

Authors: Bauer, Cláudia Marlene; Schmitz, Caroline; Landell, Melissa Fontes; Maraschin, Marcelo

Year: 2022

Venue: Biotechnology Research and Innovation

DOI: https://doi.org/10.4322/biori.202201

Paper Pangenome-Scale Mathematical Modelling of ANAMMOX Bacteria Metabolism

Bielski, Roman G.; Islam, M. Ahsanul · 2024 · SynBio · DOI

Full title: Pangenome-Scale Mathematical Modelling of ANAMMOX Bacteria Metabolism

Authors: Bielski, Roman G.; Islam, M. Ahsanul

Year: 2024

Venue: SynBio

DOI: https://doi.org/10.3390/synbio2010005

Paper Strengths and Weaknesses of Selected Modeling Methods Used in Systems Biology

Kahlem, Pascal; DiCara, Alessandro; Durot, Maxime et al. · 2011 · InTech eBooks · DOI

Full title: Strengths and Weaknesses of Selected Modeling Methods Used in Systems Biology

Authors: Kahlem, Pascal; DiCara, Alessandro; Durot, Maxime; McLaughlin, John; Klipp, Edda; Schächter, Vincent; Segal, Eran; Xénarios, Ioannis; Birney, Ewan; Mendoz, Luis

Year: 2011

Venue: InTech eBooks

DOI: https://doi.org/10.5772/22126

Paper Dynamic in silico assessment of potential gene targets for enhancing clavulanic acid production in Streptomyces clavuligerus submerged cultures

Gómez-Ríos, David; Ramírez-Malule, Howard; López-Agudelo, Victor A. · 2022 · Journal of Applied Pharmaceutical Science · DOI

Full title: Dynamic in silico assessment of potential gene targets for enhancing clavulanic acid production in Streptomyces clavuligerus submerged cultures

Authors: Gómez-Ríos, David; Ramírez-Malule, Howard; López-Agudelo, Victor A.

Year: 2022

Venue: Journal of Applied Pharmaceutical Science

DOI: https://doi.org/10.7324/japs.2023.130207

Paper Multi –omics and metabolic modelling pipelines: challenges and tools for systems microbiology

Fondi, Marco; Lió, Píetro · 2015 · DOI

Full title: Multi –omics and metabolic modelling pipelines: challenges and tools for systems microbiology

Authors: Fondi, Marco; Lió, Píetro

Year: 2015

DOI: https://doi.org/10.1101/013532

Paper Combining inferred regulatory and reconstructed metabolic networks enhances phenotype prediction in yeast

Wang, Zhuo; Danziger, Samuel A.; Heavner, Ben et al. · 2017 · PLoS Computational Biology · DOI

Full title: Combining inferred regulatory and reconstructed metabolic networks enhances phenotype prediction in yeast

Authors: Wang, Zhuo; Danziger, Samuel A.; Heavner, Ben; Ma, Shuyi; Smith, Jennifer J.; Song, Li; Herricks, Thurston; Simeonidis, Evangelos; Baliga, Nitin S.; Aitchison, John D.; Price, Nathan D.

Year: 2017

Venue: PLoS Computational Biology

Paper A systematic simulation of the effect of salicylic acid on sphingolipid metabolism

Shi, Chao; Yin, Jian; Liu, Zhe et al. · 2015 · Frontiers in Plant Science · DOI

Full title: A systematic simulation of the effect of salicylic acid on sphingolipid metabolism

Authors: Shi, Chao; Yin, Jian; Liu, Zhe; Wu, Jianxin; Zhao, Qi; Ren, Jian; Yao, Nan

Year: 2015

Venue: Frontiers in Plant Science

DOI: https://doi.org/10.3389/fpls.2015.00186

Paper A yield-cost tradeoff governs Escherichia coli’s decision between fermentation and respiration in carbon-limited growth

Mori, Matteo; Marinari, Enzo; Martino, Andrea De · 2019 · npj Systems Biology and Applications · DOI

Full title: A yield-cost tradeoff governs Escherichia coli’s decision between fermentation and respiration in carbon-limited growth

Authors: Mori, Matteo; Marinari, Enzo; Martino, Andrea De

Year: 2019

Venue: npj Systems Biology and Applications

Paper DeepMetabolism: A Deep Learning System to Predict Phenotype from Genome Sequencing

Guo, Weihua; Xu, You Lin; Feng, Xueyang · 2017 · DOI

Full title: DeepMetabolism: A Deep Learning System to Predict Phenotype from Genome Sequencing

Authors: Guo, Weihua; Xu, You Lin; Feng, Xueyang

Year: 2017

DOI: https://doi.org/10.1101/135574

Paper Sequence Specific Modeling of E. coli Cell-Free Protein Synthesis

Vilkhovoy, Michael; Horvath, Nicholas; Shih, Che-Hsiao et al. · 2017 · DOI

Full title: Sequence Specific Modeling of E. coli Cell-Free Protein Synthesis

Authors: Vilkhovoy, Michael; Horvath, Nicholas; Shih, Che-Hsiao; Wayman, Joseph A.; Calhoun, Kara; Swartz, James R.; Varner, Jeffrey D.

Year: 2017

DOI: https://doi.org/10.1101/139774

Paper Emergence of microbial diversity due to cross-feeding interactions in a spatial model of gut microbial metabolism

Hoek, Milan J. A.; Merks, Roeland M. H. · 2017 · BMC Systems Biology · DOI

Full title: Emergence of microbial diversity due to cross-feeding interactions in a spatial model of gut microbial metabolism

Authors: Hoek, Milan J. A.; Merks, Roeland M. H.

Year: 2017

Venue: BMC Systems Biology

Paper Gene-centric constraint of metabolic models

Fyson, Nick; Kim, Min Kyung; Lun, Desmond S. et al. · 2017 · DOI

Full title: Gene-centric constraint of metabolic models

Authors: Fyson, Nick; Kim, Min Kyung; Lun, Desmond S.; Colijn, Caroline

Year: 2017

DOI: https://doi.org/10.1101/116558

Paper The DOE Systems Biology Knowledgebase (KBase)

Arkin, Adam P.; Stevens, Rick; Cottingham, Robert W. et al. · 2016 · DOI

Full title: The DOE Systems Biology Knowledgebase (KBase)

Authors: Arkin, Adam P.; Stevens, Rick; Cottingham, Robert W.; Maslov, Sergei; Henry, Christopher S.; Dehal, Paramvir; Ware, Doreen; Pérez, Fernando; Harris, Nomi L.; Canon, Shane; Sneddon, Michael W.; Henderson, Matthew; Riehl, William J.; Gunter, Dan; Murphy-Olson, Dan; Chan, Stephen Y.; Kamimura, Roy T.; Brettin, Thomas; Meyer, Folker; Chivian, Dylan; Weston, David J.; Glass, Elizabeth M.; Davison, Brian H.; Kumari, Sunita; Allen, Benjamin; Baumohl, Jason K.; Best, Aaron A.; Bowen, Ben; Brenner, Steven E.; Bun, Christopher; Chandonia, John‐Marc; Chia, Jer-Ming; Colasanti, Ric; Conrad, Neal; Davis, James J.; DeJongh, Matthew; Devoid, Scott; Dietrich, Emily; Drake, Meghan M.; Dubchak, Inna; Edirisinghe, Janaka N.; Fang, Gang; Faria, José P.; Frybarger, Paul M; Gerlach, Wolfgang; Gerstein, Mark; Gurtowski, James; Haun, Holly L; He, Fei; Jain, Rashmi; Joachimiak, Marcin P.; Keegan, Kevin; Kondo, Shinnosuke; Kumar, Vivek; Land, Miriam; Mills, Marissa; Novichkov, Pavel S.; Oh, Taeyun; Olsen, Gary J.; Olson, Bob; Parrello, Bruce; Pasternak, Shiran; Pearson, Erik; Poon, Sarah S; Price, Gavin A; Ramakrishnan, Srividya; Ranjan, Priya; Ronald, Pamela C.; Schatz, Michael C.; Seaver, Samuel M. D.; Shukla, Maulik; Sutormin, Roman A.; Syed, Mustafa; Thomason, James; Tintle, Nathan; Wang, Daifeng; Xia, Fangfang; Yoo, Hyunseung; Yoo, Shinjae

Year: 2016

DOI: https://doi.org/10.1101/096354

Paper Expanding the computable reactome in Pseudomonas putida reveals metabolic cycles providing robustness

Nogales, Juan; Guðmundsson, Steinn; Duque, Estrella et al. · 2017 · DOI

Full title: Expanding the computable reactome in Pseudomonas putida reveals metabolic cycles providing robustness

Authors: Nogales, Juan; Guðmundsson, Steinn; Duque, Estrella; Ramos, Juan L.; Palsson, Bernhard Ø.

Year: 2017

DOI: https://doi.org/10.1101/139121

Paper Benchmarking kinetic models of Escherichia coli metabolism

Shepelin, Denis; Machado, Daniel; Nielsen, Lars K. et al. · 2020 · DOI

Full title: Benchmarking kinetic models of Escherichia coli metabolism

Authors: Shepelin, Denis; Machado, Daniel; Nielsen, Lars K.; Herrgård, Markus J.

Year: 2020

DOI: https://doi.org/10.1101/2020.01.16.908921

Paper Proteome overabundance enables respiration but limitation onsets carbon overflow

Kumar, Rahul; Lahtvee, Petri‐Jaan · 2020 · DOI

Full title: Proteome overabundance enables respiration but limitation onsets carbon overflow

Authors: Kumar, Rahul; Lahtvee, Petri‐Jaan

Year: 2020

DOI: https://doi.org/10.1101/2020.02.20.957662

Paper Improving Designer Glycan Production in Escherichia coli through Model-Guided Metabolic Engineering

Wayman, Joseph A.; Glasscock, Cameron J.; Mansell, Thomas J. et al. · 2017 · DOI

Full title: Improving Designer Glycan Production in Escherichia coli through Model-Guided Metabolic Engineering

Authors: Wayman, Joseph A.; Glasscock, Cameron J.; Mansell, Thomas J.; DeLisa, Matthew P.; Varner, Jeffrey D.

Year: 2017

DOI: https://doi.org/10.1101/160853

Paper The number of active metabolic pathways is bounded by the number of cellular constraints at maximal metabolic rates

Groot, Daan H. de; Boxtel, Coco van; Planqué, Robert et al. · 2019 · PLoS Computational Biology · DOI

Full title: The number of active metabolic pathways is bounded by the number of cellular constraints at maximal metabolic rates

Authors: Groot, Daan H. de; Boxtel, Coco van; Planqué, Robert; Bruggeman, Frank J.; Teusink, Bas

Year: 2019

Venue: PLoS Computational Biology

Paper Genome-scale metabolic rewiring to achieve predictable titers rates and yield of a non-native product at scale

Banerjee, Deepanwita; Eng, Thomas; Lau, Andrew K. et al. · 2020 · DOI

Full title: Genome-scale metabolic rewiring to achieve predictable titers rates and yield of a non-native product at scale

Authors: Banerjee, Deepanwita; Eng, Thomas; Lau, Andrew K.; Wang, Brenda; Sasaki, Yusuke; Herbert, Robin A.; Chen, Yan; Liu, Yuzhong; Prahl, Jan‐Philip; Singan, Vasanth; Tanjore, Deepti; Petzold, Christopher J.; Keasling, Jay D.; Mukhopadhyay, Aindrila

Year: 2020

DOI: https://doi.org/10.1101/2020.02.21.954792

Paper Development of a genome-scale metabolic model of Clostridium thermocellum and its applications for integration of multi-omics datasets and strain design

Garcia, Sergio; Thompson, R. Adam; Giannone, Richard J. et al. · 2020 · DOI

Full title: Development of a genome-scale metabolic model of Clostridium thermocellum and its applications for integration of multi-omics datasets and strain design

Authors: Garcia, Sergio; Thompson, R. Adam; Giannone, Richard J.; Dash, Satyakam; Maranas, Costas D.; Trinh, Cong T.

Year: 2020

DOI: https://doi.org/10.1101/2020.04.02.022376

Paper Protein allocation and enzymatic constraints explain Escherichia coli wildtype and mutant phenotypes

Alter, Tobias B.; Blank, Lars M.; Ebert, Birgitta E. · 2020 · DOI

Full title: Protein allocation and enzymatic constraints explain Escherichia coli wildtype and mutant phenotypes

Authors: Alter, Tobias B.; Blank, Lars M.; Ebert, Birgitta E.

Year: 2020

DOI: https://doi.org/10.1101/2020.02.10.941294

Paper gapseq: informed prediction of bacterial metabolic pathways and reconstruction of accurate metabolic models

Zimmermann, Johannes; Kaleta, Christoph; Waschina, Silvio · 2021 · Genome biology · DOI

Full title: gapseq: informed prediction of bacterial metabolic pathways and reconstruction of accurate metabolic models

Authors: Zimmermann, Johannes; Kaleta, Christoph; Waschina, Silvio

Year: 2021

Venue: Genome biology

Paper Bayesian genome scale modelling identifies thermal determinants of yeast metabolism

Li, Gang; Hu, Yating; Zrimec, Jan et al. · 2021 · Nature Communications · DOI

Full title: Bayesian genome scale modelling identifies thermal determinants of yeast metabolism

Authors: Li, Gang; Hu, Yating; Zrimec, Jan; Luo, Hao; Wang, Hao; Zelezniak, Aleksej; Ji, Boyang; Nielsen, Jens

Year: 2021

Venue: Nature Communications

Paper Providing new insights on the byphasic lifestyle of the predatory bacterium Bdellovibrio bacteriovorus through genome-scale metabolic modeling

Herencias, Cristina; Prieto, M. Auxiliadora; Nogales, Juan · 2020 · DOI

Full title: Providing new insights on the byphasic lifestyle of the predatory bacterium Bdellovibrio bacteriovorus through genome-scale metabolic modeling

Authors: Herencias, Cristina; Prieto, M. Auxiliadora; Nogales, Juan

Year: 2020

DOI: https://doi.org/10.1101/2020.01.13.904078

Paper A genome-scale study of metabolic complementation in endosymbiotic consortia: the case of the cedar aphid

Ponce-de-León, Miguel; Tamarit, Daniel; Calle-Espinosa, Jorge et al. · 2017 · DOI

Full title: A genome-scale study of metabolic complementation in endosymbiotic consortia: the case of the cedar aphid

Authors: Ponce-de-León, Miguel; Tamarit, Daniel; Calle-Espinosa, Jorge; Mori, Matteo; Latorre, Amparo; Montero, Francisco; Peretό, Juli

Year: 2017

DOI: https://doi.org/10.1101/179127

Paper Error propagation in constraint-based modeling of Chinese hamster ovary cells

Széliová, Diana; Iurashev, Dmytro; Ruckerbauer, David E. et al. · 2020 · DOI

Full title: Error propagation in constraint-based modeling of Chinese hamster ovary cells

Authors: Széliová, Diana; Iurashev, Dmytro; Ruckerbauer, David E.; Koellensperger, Gunda; Borth, Nicole; Melcher, Michael; Zanghellini, Jürgen

Year: 2020

DOI: https://doi.org/10.1101/2020.07.09.195594

Paper A novel yeast hybrid modeling framework integrating Boolean and enzyme-constrained networks enables exploration of the interplay between signaling and metabolism

Österberg, Linnea; Domenzain, Iván; Münch, Julia et al. · 2020 · DOI

Full title: A novel yeast hybrid modeling framework integrating Boolean and enzyme-constrained networks enables exploration of the interplay between signaling and metabolism

Authors: Österberg, Linnea; Domenzain, Iván; Münch, Julia; Nielsen, Jens; Hohmann, Stefan; Cvijović, Marija

Year: 2020

DOI: https://doi.org/10.1101/2020.09.11.290817

Paper Computation of condition-dependent proteome allocation reveals variability in the macro and micro nutrient requirements for growth

Lloyd, Colton J.; Monk, Jonathan M.; Yang, Laurence et al. · 2021 · PLoS Computational Biology · DOI

Full title: Computation of condition-dependent proteome allocation reveals variability in the macro and micro nutrient requirements for growth

Authors: Lloyd, Colton J.; Monk, Jonathan M.; Yang, Laurence; Ebrahim, Ali; Palsson, Bernhard Ø.

Year: 2021

Venue: PLoS Computational Biology

Paper Simulating single-cell metabolism using a stochastic flux-balance analysis algorithm

Tourigny, David S.; Goldberg, Arthur P.; Karr, Jonathan R. · 2020 · DOI

Full title: Simulating single-cell metabolism using a stochastic flux-balance analysis algorithm

Authors: Tourigny, David S.; Goldberg, Arthur P.; Karr, Jonathan R.

Year: 2020

DOI: https://doi.org/10.1101/2020.05.22.110577

Paper Modeling a co-culture of Clostridium autoethanogenum and Clostridium kluyveri to increase syngas conversion to medium-chain fatty-acids

Benito-Vaquerizo, Sara; Diender, Martijn; Olm, Ivette Parera et al. · 2020 · DOI

Full title: Modeling a co-culture of Clostridium autoethanogenum and Clostridium kluyveri to increase syngas conversion to medium-chain fatty-acids

Authors: Benito-Vaquerizo, Sara; Diender, Martijn; Olm, Ivette Parera; Santos, Vítor A. P. Martins dos; Schaap, Peter J.; Sousa, Diana Z.; Suárez‐Diez, María

Year: 2020

DOI: https://doi.org/10.1101/2020.06.23.167189

Paper Scalable metabolic pathway analysis

Øyås, Ove; Stelling, Jörg · 2020 · DOI

Full title: Scalable metabolic pathway analysis

Authors: Øyås, Ove; Stelling, Jörg

Year: 2020

DOI: https://doi.org/10.1101/2020.07.31.230177

Paper Protein Abundance Prediction Through Machine Learning Methods

Ferreira, Maurício Alexander de Moura; Ventorim, Rafaela Zandonade; Almeida, Eduardo Luís Menezes de et al. · 2020 · DOI

Full title: Protein Abundance Prediction Through Machine Learning Methods

Authors: Ferreira, Maurício Alexander de Moura; Ventorim, Rafaela Zandonade; Almeida, Eduardo Luís Menezes de; Silveira, Sabrina de Azevedo; Silveira, Wendel Batista da

Year: 2020

DOI: https://doi.org/10.1101/2020.09.17.302182

Paper A genome-scale metabolic network model and machine learning predict amino acid concentrations in Chinese Hamster Ovary cell cultures

Schinn, Song-Min; Morrison, Carly; Wei, Wei et al. · 2020 · DOI

Full title: A genome-scale metabolic network model and machine learning predict amino acid concentrations in Chinese Hamster Ovary cell cultures

Authors: Schinn, Song-Min; Morrison, Carly; Wei, Wei; Zhang, Lin; Lewis, Nathan E.

Year: 2020

DOI: https://doi.org/10.1101/2020.09.02.279687

Paper ΔFBA: Predicting metabolic flux alterations using genome-scale metabolic models and differential transcriptomic data

Ravi, Sudharshan; Gunawan, Rudiyanto · 2021 · DOI

Full title: ΔFBA: Predicting metabolic flux alterations using genome-scale metabolic models and differential transcriptomic data

Authors: Ravi, Sudharshan; Gunawan, Rudiyanto

Year: 2021

DOI: https://doi.org/10.1101/2021.01.18.427188

Paper Prediction of Michaelis constants from structural features using deep learning

Kroll, Alexander; Heckmann, David; Lercher, Martin J. · 2020 · DOI

Full title: Prediction of Michaelis constants from structural features using deep learning

Authors: Kroll, Alexander; Heckmann, David; Lercher, Martin J.

Year: 2020

DOI: https://doi.org/10.1101/2020.12.01.405928

Paper Inclusion of maintenance energy improves the intracellular flux predictions of CHO

Széliová, Diana; Štor, Jerneja; Thiel, Isabella et al. · 2020 · DOI

Full title: Inclusion of maintenance energy improves the intracellular flux predictions of CHO

Authors: Széliová, Diana; Štor, Jerneja; Thiel, Isabella; Weinguny, Marcus; Hanscho, Michael; Lhota, Gabriele; Borth, Nicole; Zanghellini, Jürgen; Ruckerbauer, David E.; Rocha, Isabel

Year: 2020

DOI: https://doi.org/10.1101/2020.12.21.423738

Paper Active and machine learning-based approaches to rapidly enhance microbial chemical production

Kumar, Prashant; Adamczyk, Paul; Zhang, Xiaolin et al. · 2020 · DOI

Full title: Active and machine learning-based approaches to rapidly enhance microbial chemical production

Authors: Kumar, Prashant; Adamczyk, Paul; Zhang, Xiaolin; Andrade, Ramon Bonela; Romero, Philip A.; Ramanathan, Parameswaran; Reed, Jennifer L.

Year: 2020

DOI: https://doi.org/10.1101/2020.12.01.406439

Paper A genome-scale metabolic model of Saccharomyces cerevisiae that integrates expression constraints and reaction thermodynamics

Oftadeh, Omid; Salvy, Pierre; Masid, María et al. · 2021 · DOI

Full title: A genome-scale metabolic model of Saccharomyces cerevisiae that integrates expression constraints and reaction thermodynamics

Authors: Oftadeh, Omid; Salvy, Pierre; Masid, María; Curvat, Maxime; Mišković, Ljubiša; Hatzimanikatis, Vassily

Year: 2021

DOI: https://doi.org/10.1101/2021.02.17.431671

Paper Nitrogenous Compound Utilization and Production of Volatile Organic Compounds among Commercial Wine Yeasts Highlight Strain-Specific Metabolic Diversity

Scott, William T.; Mastrigt, Oscar van; Block, David E. et al. · 2021 · DOI

Full title: Nitrogenous Compound Utilization and Production of Volatile Organic Compounds among Commercial Wine Yeasts Highlight Strain-Specific Metabolic Diversity

Authors: Scott, William T.; Mastrigt, Oscar van; Block, David E.; Notebaart, Richard A.; Smid, Eddy J.

Year: 2021

DOI: https://doi.org/10.1101/2021.03.29.437628

Paper merlin v4.0: an updated platform for the reconstruction of high-quality genome-scale metabolic models

Capela, João; Lagoa, Davide; Rodrigues, Rúben et al. · 2021 · DOI

Full title: merlin v4.0: an updated platform for the reconstruction of high-quality genome-scale metabolic models

Authors: Capela, João; Lagoa, Davide; Rodrigues, Rúben; Cunha, Emanuel; Cruz, Fernando; Barbosa, Ana; Bastos, José Roberto Henrique; Lima, Diogo; Ferreira, Eugénio C.; Rocha, Miguel; Dias, Óscar

Year: 2021

DOI: https://doi.org/10.1101/2021.02.24.432752

Paper Proteome constraints reveal targets for improving microbial fitness in nutrient‐rich environments

Chen, Yu; Pelt‐KleinJan, Eunice van; Olst, Berdien van et al. · 2021 · Molecular Systems Biology · DOI

Full title: Proteome constraints reveal targets for improving microbial fitness in nutrient‐rich environments

Authors: Chen, Yu; Pelt‐KleinJan, Eunice van; Olst, Berdien van; Douwenga, Sieze; Boeren, Sjef; Bachmann, Herwig; Molenaar, Douwe; Nielsen, Jens; Teusink, Bas

Year: 2021

Venue: Molecular Systems Biology

Paper Genome-scale metabolic modelling of P. thermoglucosidasius NCIMB 11955 reveals metabolic bottlenecks in anaerobic metabolism

Mol, Viviënne; Bennett, Martyn; Sánchez, Benjamín J. et al. · 2021 · DOI

Full title: Genome-scale metabolic modelling of P. thermoglucosidasius NCIMB 11955 reveals metabolic bottlenecks in anaerobic metabolism

Authors: Mol, Viviënne; Bennett, Martyn; Sánchez, Benjamín J.; Lisowska, Beata K.; Herrgård, Markus J.; Nielsen, Alex Toftgaard; Leak, David J.; Sonnenschein, Nikolaus

Year: 2021

DOI: https://doi.org/10.1101/2021.02.01.429138

Paper Genome-scale metabolic modelling when changes in environmental conditions affect biomass composition

Schulz, Christian; Kumelj, Tjaša; Karlsen, Emil et al. · 2020 · DOI

Full title: Genome-scale metabolic modelling when changes in environmental conditions affect biomass composition

Authors: Schulz, Christian; Kumelj, Tjaša; Karlsen, Emil; Almaas, Eivind

Year: 2020

DOI: https://doi.org/10.1101/2020.12.03.409565

Paper Investigating metabolic interactions in a microbial co-culture through integrated modelling and experiments

Ravikrishnan, Aarthi; Blank, Lars M.; Srivastava, Smita et al. · 2020 · Computational and Structural Biotechnology Journal · DOI

Full title: Investigating metabolic interactions in a microbial co-culture through integrated modelling and experiments

Authors: Ravikrishnan, Aarthi; Blank, Lars M.; Srivastava, Smita; Raman, Karthik

Year: 2020

Venue: Computational and Structural Biotechnology Journal

DOI: https://doi.org/10.1016/j.csbj.2020.03.019

Paper Continuous in vivo metabolism by NMR

Judge, Michael T.; Wu, Yue; Tayyari, Fariba et al. · 2018 · DOI

Full title: Continuous in vivo metabolism by NMR

Authors: Judge, Michael T.; Wu, Yue; Tayyari, Fariba; Hattori, Ayuna; Glushka, John; Ito, Takahiro; Arnold, Jonathan; Edison, Arthur S.

Year: 2018

DOI: https://doi.org/10.1101/501577

Paper Functional Anabolic Network Analysis of Human-associated Lactobacillus Strains

Moutinho, Thomas J.; Neubert, Benjamin C.; Jenior, Matthew L. et al. · 2019 · DOI

Full title: Functional Anabolic Network Analysis of Human-associated Lactobacillus Strains

Authors: Moutinho, Thomas J.; Neubert, Benjamin C.; Jenior, Matthew L.; Carey, Maureen A.; Medlock, Gregory L.; Kolling, Glynis L.; Papin, Jason A.

Year: 2019

DOI: https://doi.org/10.1101/746420

Paper Metabolic Modeling Elucidates the Transactions in the Rumen Microbiome and the Shifts Upon Virome Interactions

Islam, Mohammad Mazharul; Fernando, Samodha C.; Saha, Rajib · 2019 · Frontiers in Microbiology · DOI

Full title: Metabolic Modeling Elucidates the Transactions in the Rumen Microbiome and the Shifts Upon Virome Interactions

Authors: Islam, Mohammad Mazharul; Fernando, Samodha C.; Saha, Rajib

Year: 2019

Venue: Frontiers in Microbiology

DOI: https://doi.org/10.3389/fmicb.2019.02412

Paper Transcriptome-guided parsimonious flux analysis improves predictions with metabolic networks in complex environments

Jenior, Matthew L.; Moutinho, Thomas J.; Dougherty, Bonnie V. et al. · 2019 · DOI

Full title: Transcriptome-guided parsimonious flux analysis improves predictions with metabolic networks in complex environments

Authors: Jenior, Matthew L.; Moutinho, Thomas J.; Dougherty, Bonnie V.; Papin, Jason A.

Year: 2019

DOI: https://doi.org/10.1101/637124

Paper A quantitative method for proteome reallocation using minimal regulatory interventions

Lastiri-Pancardo, Gustavo; Mercado-Hernández, Jonathan S.; Kim, Juhyun et al. · 2019 · DOI

Full title: A quantitative method for proteome reallocation using minimal regulatory interventions

Authors: Lastiri-Pancardo, Gustavo; Mercado-Hernández, Jonathan S.; Kim, Juhyun; Jiménez, José I.; Utrilla, José

Year: 2019

DOI: https://doi.org/10.1101/733592

Paper Genome-Scale reconstruction of Paenarthrobacter aurescens TC1 metabolic model towards the study of atrazine bioremediation

Ofaim, Shany; Zarecki, Raphy; Porob, Seema et al. · 2019 · DOI

Full title: Genome-Scale reconstruction of Paenarthrobacter aurescens TC1 metabolic model towards the study of atrazine bioremediation

Authors: Ofaim, Shany; Zarecki, Raphy; Porob, Seema; Gat, Daniella; Lahav, Tamar; Xu, Xihui; Kashi, Yechezkel; Aly, Radi; Jiang, Jiandong; Eizenberg, Hanan; Ronen, Zeev; Freilich, Shiri

Year: 2019

DOI: https://doi.org/10.1101/536011

Paper Mechanistic insights into bacterial metabolic reprogramming from omics-integrated genome-scale models

Hadadi, Noushin; Pandey, Vikash; Chiappino-Pepe, Anush et al. · 2020 · npj Systems Biology and Applications · DOI

Full title: Mechanistic insights into bacterial metabolic reprogramming from omics-integrated genome-scale models

Authors: Hadadi, Noushin; Pandey, Vikash; Chiappino-Pepe, Anush; Morales, Marian; Gallart‐Ayala, Héctor; Mehl, Florence; Ivanišević, Julijana; Sentchilo, Vladimir; Meer, Jan Roelof van der

Year: 2020

Venue: npj Systems Biology and Applications

Paper Predictive engineering and optimization of tryptophan metabolism in yeast through a combination of mechanistic and machine learning models

Zhang, Jie; Petersen, Søren D.; Radivojević, Tijana et al. · 2019 · DOI

Full title: Predictive engineering and optimization of tryptophan metabolism in yeast through a combination of mechanistic and machine learning models

Authors: Zhang, Jie; Petersen, Søren D.; Radivojević, Tijana; Ramirez, Andrés; Perez, Andrés M.; Abeliuk, Eduardo; Sánchez, Benjamín J.; Costello, Zachary; Chen, Yu; Fero, Mike; Martín, Héctor García; Nielsen, Jens; Keasling, Jay D.; Jensen, Michael K.

Year: 2019

DOI: https://doi.org/10.1101/858464

Paper Reconstruction and Validation of Saccharomyces cerevisiae iND750, a Fully Compartmentalized Genome-Scale Metabolic Model

Duarte, Natalie C.; Herrgård, Markus J.; Palsson, Bernhard Ø. · 2004 · Genome Research · DOI

Full title: Reconstruction and Validation of Saccharomyces cerevisiae iND750, a Fully Compartmentalized Genome-Scale Metabolic Model

Authors: Duarte, Natalie C.; Herrgård, Markus J.; Palsson, Bernhard Ø.

Year: 2004

Venue: Genome Research

DOI: https://doi.org/10.1101/gr.2250904

Paper A Virtual Nodule Environment (ViNE) for modelling the inter-kingdom metabolic integration during symbiotic nitrogen fixation

diCenzo, George C.; Tesi, Michelangelo; Pfau, Thomas et al. · 2019 · DOI

Full title: A Virtual Nodule Environment (ViNE) for modelling the inter-kingdom metabolic integration during symbiotic nitrogen fixation

Authors: diCenzo, George C.; Tesi, Michelangelo; Pfau, Thomas; Mengoni, Alessio; Fondi, Marco

Year: 2019

DOI: https://doi.org/10.1101/765271

Paper Deciphering the metabolic capabilities of Bifidobacteria using genome-scale metabolic models

Devika, N. T.; Raman, Karthik · 2019 · Scientific Reports · DOI

Full title: Deciphering the metabolic capabilities of Bifidobacteria using genome-scale metabolic models

Authors: Devika, N. T.; Raman, Karthik

Year: 2019

Venue: Scientific Reports

Paper Modeling the Interplay between Photosynthesis, CO 2 Fixation, and the Quinone Pool in a Purple Non-Sulfur Bacterium

Alsiyabi, Adil; Immethun, Cheryl M.; Saha, Rajib · 2019 · DOI

Full title: Modeling the Interplay between Photosynthesis, CO 2 Fixation, and the Quinone Pool in a Purple Non-Sulfur Bacterium

Authors: Alsiyabi, Adil; Immethun, Cheryl M.; Saha, Rajib

Year: 2019

DOI: https://doi.org/10.1101/704130

Paper Systematic condition-dependent annotation of metabolic genes

Shlomi, Tomer; Herrgård, Markus J.; Portnoy, Vasiliy A. et al. · 2007 · Genome Research · DOI

Full title: Systematic condition-dependent annotation of metabolic genes

Authors: Shlomi, Tomer; Herrgård, Markus J.; Portnoy, Vasiliy A.; Naim, Efrat; Palsson, Bernhard Ø.; Sharan, Roded; Ruppin, Eytan

Year: 2007

Venue: Genome Research

DOI: https://doi.org/10.1101/gr.6678707

Paper A curated collection of Klebsiella metabolic models reveals variable substrate usage and gene essentiality

Hawkey, Jane; Vezina, Ben; Monk, Jonathan M. et al. · 2022 · Genome Research · DOI

Full title: A curated collection of Klebsiella metabolic models reveals variable substrate usage and gene essentiality

Authors: Hawkey, Jane; Vezina, Ben; Monk, Jonathan M.; Judd, Louise M.; Harshegyi, Taylor; López-Fernández, Sebastián; Rodrigues, Carla; Brisse, Sylvain; Holt, Kathryn E.; Wyres, Kelly L.

Year: 2022

Venue: Genome Research

Paper Integrated analysis of regulatory and metabolic networks reveals novel regulatory mechanisms in Saccharomyces cerevisiae

Herrgård, Markus J.; Lee, Baek-Seok; Portnoy, Vasiliy A. et al. · 2006 · Genome Research · DOI

Full title: Integrated analysis of regulatory and metabolic networks reveals novel regulatory mechanisms in Saccharomyces cerevisiae

Authors: Herrgård, Markus J.; Lee, Baek-Seok; Portnoy, Vasiliy A.; Palsson, Bernhard Ø.

Year: 2006

Venue: Genome Research

DOI: https://doi.org/10.1101/gr.4083206

Paper Kinetic profiling of metabolic specialists demonstrates stability and consistency of in vivo enzyme turnover numbers

Heckmann, David; Campeau, Anaamika; Lloyd, Colton J. et al. · 2020 · Proceedings of the National Academy of Sciences · DOI

Full title: Kinetic profiling of metabolic specialists demonstrates stability and consistency of in vivo enzyme turnover numbers

Authors: Heckmann, David; Campeau, Anaamika; Lloyd, Colton J.; Phaneuf, Patrick V.; Hefner, Ying; Carrillo-Terrazas, Marvic; Feist, Adam M.; Gonzalez, David J.; Palsson, Bernhard Ø.

Year: 2020

Venue: Proceedings of the National Academy of Sciences

DOI: https://doi.org/10.1073/pnas.2001562117

Paper Metabolic functions of duplicate genes in Saccharomyces cerevisiae

Kuepfer, Lars; Sauer, Uwe; Blank, Lars M. · 2005 · Genome Research · DOI

Full title: Metabolic functions of duplicate genes in Saccharomyces cerevisiae

Authors: Kuepfer, Lars; Sauer, Uwe; Blank, Lars M.

Year: 2005

Venue: Genome Research

DOI: https://doi.org/10.1101/gr.3992505

Paper Genome-scale analysis of Streptomyces coelicolor A3(2) metabolism

Borodina, Irina; Krabben, Preben; Nielsen, Jens · 2005 · Genome Research · DOI

Full title: Genome-scale analysis of Streptomyces coelicolor A3(2) metabolism

Authors: Borodina, Irina; Krabben, Preben; Nielsen, Jens

Year: 2005

Venue: Genome Research

DOI: https://doi.org/10.1101/gr.3364705

Paper A New Approach to an Old Problem: Synthetic Biology Tools for Human Disease and Metabolism

Burrill, Devin R.; Boyle, P. M.; Silver, Pamela A. · 2011 · Cold Spring Harbor Symposia on Quantitative Biology · DOI

Full title: A New Approach to an Old Problem: Synthetic Biology Tools for Human Disease and Metabolism

Authors: Burrill, Devin R.; Boyle, P. M.; Silver, Pamela A.

Year: 2011

Venue: Cold Spring Harbor Symposia on Quantitative Biology

DOI: https://doi.org/10.1101/sqb.2011.76.010686

Paper Evaluation of predicted network modules in yeast metabolism using NMR-based metabolite profiling.

Bundy, Jacob G; Papp, Balázs; Harmston, Rebecca et al. · 2007 · Genome research · DOI

Full title: Evaluation of predicted network modules in yeast metabolism using NMR-based metabolite profiling.

Authors: Bundy, Jacob G; Papp, Balázs; Harmston, Rebecca; Browne, Roy A; Clayson, Edward M; Burton, Nicola; Reece, Richard J; Oliver, Stephen G; Brindle, Kevin M

Year: 2007

Venue: Genome research

DOI: https://doi.org/10.1101/gr.5662207

Paper A metabolic reconstruction of Lactobacillus reuteri JCM 1112 and analysis of its potential as a cell factory

Kristjansdottir, Thordis; Bosma, Elleke F.; Santos, Filipe Branco dos et al. · 2019 · DOI

Full title: A metabolic reconstruction of Lactobacillus reuteri JCM 1112 and analysis of its potential as a cell factory

Authors: Kristjansdottir, Thordis; Bosma, Elleke F.; Santos, Filipe Branco dos; Özdemir, Emre; Herrgård, Markus J.; França, Lucas; Ferreira, Bruno Sommer; Nielsen, Alex Toftgaard; Guðmundsson, Steinn

Year: 2019

DOI: https://doi.org/10.1101/708875

Paper ChiMera: an easy to use pipeline for bacterial genome based metabolic network reconstruction, evaluation and visualization

Tamasco, Gustavo; Kumar, Manish; Zengler, Karsten et al. · 2022 · BMC Bioinformatics · DOI

Full title: ChiMera: an easy to use pipeline for bacterial genome based metabolic network reconstruction, evaluation and visualization

Authors: Tamasco, Gustavo; Kumar, Manish; Zengler, Karsten; Silva‐Rocha, Rafael; Silva, Ricardo

Year: 2022

Venue: BMC Bioinformatics

Paper Genome-scale analysis to the impact of gene deletion on the metabolism of E. coli: constraint-based simulation approach

Xu, Zixiang; Sun, Xiao; Yu, Shihai · 2009 · BMC Bioinformatics · DOI

Full title: Genome-scale analysis to the impact of gene deletion on the metabolism of E. coli: constraint-based simulation approach

Authors: Xu, Zixiang; Sun, Xiao; Yu, Shihai

Year: 2009

Venue: BMC Bioinformatics

DOI: https://doi.org/10.1186/1471-2105-10-s1-s62

Paper Acorn: A grid computing system for constraint based modeling and visualization of the genome scale metabolic reaction networks via a web interface

Sroka, Jacek; Bieniasz-Krzywiec, Łukasz; Gwóźdź, Szymon et al. · 2011 · BMC Bioinformatics · DOI

Full title: Acorn: A grid computing system for constraint based modeling and visualization of the genome scale metabolic reaction networks via a web interface

Authors: Sroka, Jacek; Bieniasz-Krzywiec, Łukasz; Gwóźdź, Szymon; Leniowski, Dariusz; Łącki, Jakub; Markowski, Mateusz; Avignone–Rossa, Claudio; Bushell, Michael E.; McFadden, Johnjoe; Kierzek, Andrzej

Year: 2011

Venue: BMC Bioinformatics

DOI: https://doi.org/10.1186/1471-2105-12-196

Paper Low degree metabolites explain essential reactions and enhance modularity in biological networks

Samal, Areejit; Singh, Shalini; Giri, Varun et al. · 2006 · BMC Bioinformatics · DOI

Full title: Low degree metabolites explain essential reactions and enhance modularity in biological networks

Authors: Samal, Areejit; Singh, Shalini; Giri, Varun; Krishna, Sandeep; Raghuram, Nandula; Jain, Sanjay

Year: 2006

Venue: BMC Bioinformatics

DOI: https://doi.org/10.1186/1471-2105-7-118

Paper SNA – a toolbox for the stoichiometric analysis of metabolic networks

Urbanczik, Robert · 2006 · BMC Bioinformatics · DOI

Full title: SNA – a toolbox for the stoichiometric analysis of metabolic networks

Authors: Urbanczik, Robert

Year: 2006

Venue: BMC Bioinformatics

DOI: https://doi.org/10.1186/1471-2105-7-129

Paper Computing minimal nutrient sets from metabolic networks via linear constraint solving

Eker, Steven; Krummenacker, Markus; Shearer, Alexander G. et al. · 2013 · BMC Bioinformatics · DOI

Full title: Computing minimal nutrient sets from metabolic networks via linear constraint solving

Authors: Eker, Steven; Krummenacker, Markus; Shearer, Alexander G.; Tiwari, Ashish; Keseler, Ingrid M.; Talcott, Carolyn; Karp, Peter D.

Year: 2013

Venue: BMC Bioinformatics

DOI: https://doi.org/10.1186/1471-2105-14-114

Paper Accelerating the reconstruction of genome-scale metabolic networks

Notebaart, Richard A.; Enckevort, Frank HJ van; Francke, Christof et al. · 2006 · BMC Bioinformatics · DOI

Full title: Accelerating the reconstruction of genome-scale metabolic networks

Authors: Notebaart, Richard A.; Enckevort, Frank HJ van; Francke, Christof; Siezen, Roland J.; Teusink, Bas

Year: 2006

Venue: BMC Bioinformatics

DOI: https://doi.org/10.1186/1471-2105-7-296

Paper Metabolic modeling and analysis of the metabolic switch in Streptomyces coelicolor

Alam, Mohammad Tauqeer; Merlo, Maria Elena; Hodgson, David A. et al. · 2010 · BMC Genomics · DOI

Full title: Metabolic modeling and analysis of the metabolic switch in Streptomyces coelicolor

Authors: Alam, Mohammad Tauqeer; Merlo, Maria Elena; Hodgson, David A.; Wellington, Elizabeth M. H.; Takano, Eriko; Breitling, Rainer

Year: 2010

Venue: BMC Genomics

DOI: https://doi.org/10.1186/1471-2164-11-202

Paper Systems biology analysis of the Clostridioides difficile core-genome contextualizes microenvironmental evolutionary pressures leading to genotypic and phenotypic divergence

Norsigian, Charles J.; Danhof, Heather A.; Brand, Colleen K. et al. · 2020 · npj Systems Biology and Applications · DOI

Full title: Systems biology analysis of the Clostridioides difficile core-genome contextualizes microenvironmental evolutionary pressures leading to genotypic and phenotypic divergence

Authors: Norsigian, Charles J.; Danhof, Heather A.; Brand, Colleen K.; Oezguen, Numan; Midani, Firas S.; Palsson, Bernhard Ø.; Savidge, Tor; Britton, Robert A.; Spinler, Jennifer K.; Monk, Jonathan M.

Year: 2020

Venue: npj Systems Biology and Applications

DOI: https://doi.org/10.1038/s41540-020-00151-9

Paper An unconventional uptake rate objective function approach enhances applicability of genome-scale models for mammalian cells

Chen, Yiqun; McConnell, Brian O.; Dhara, Venkata Gayatri et al. · 2019 · npj Systems Biology and Applications · DOI

Full title: An unconventional uptake rate objective function approach enhances applicability of genome-scale models for mammalian cells

Authors: Chen, Yiqun; McConnell, Brian O.; Dhara, Venkata Gayatri; Naik, Harnish Mukesh; Li, Chien‐Ting; Antoniewicz, Maciek R.; Betenbaugh, Michael J.

Year: 2019

Venue: npj Systems Biology and Applications

DOI: https://doi.org/10.1038/s41540-019-0103-6

Paper A yield-cost tradeoff governs Escherichia coli’s decision between fermentation and respiration in carbon-limited growth

Mori, Matteo; Marinari, Enzo; Martino, Andrea De · 2019 · npj Systems Biology and Applications · DOI

Full title: A yield-cost tradeoff governs Escherichia coli’s decision between fermentation and respiration in carbon-limited growth

Authors: Mori, Matteo; Marinari, Enzo; Martino, Andrea De

Year: 2019

Venue: npj Systems Biology and Applications

Paper Identifying the essential nutritional requirements of the probiotic bacteria Bifidobacterium animalis and Bifidobacterium longum through genome-scale modeling

Schöpping, Marie; Gaspar, Paula; Neves, Ana Rute et al. · 2021 · npj Systems Biology and Applications · DOI

Full title: Identifying the essential nutritional requirements of the probiotic bacteria Bifidobacterium animalis and Bifidobacterium longum through genome-scale modeling

Authors: Schöpping, Marie; Gaspar, Paula; Neves, Ana Rute; Franzén, Carl Johan; Zeidan, Ahmad A.

Year: 2021

Venue: npj Systems Biology and Applications

DOI: https://doi.org/10.1038/s41540-021-00207-4

Paper Optimization of nutrient utilization efficiency and productivity for algal cultures under light and dark cycles using genome-scale model process control

Li, Chien‐Ting; Eng, Richard; Zúñiga, Cristal et al. · 2023 · npj Systems Biology and Applications · DOI

Full title: Optimization of nutrient utilization efficiency and productivity for algal cultures under light and dark cycles using genome-scale model process control

Authors: Li, Chien‐Ting; Eng, Richard; Zúñiga, Cristal; Huang, Kai-Wen; Chen, Yiqun; Zengler, Karsten; Betenbaugh, Michael J.

Year: 2023

Venue: npj Systems Biology and Applications

DOI: https://doi.org/10.1038/s41540-022-00260-7

Paper Data-driven synthetic microbes for sustainable future

Mariam, Iqra; Rova, Ulrika; Christakopoulos, Paul et al. · 2025 · npj Systems Biology and Applications · DOI

Full title: Data-driven synthetic microbes for sustainable future

Authors: Mariam, Iqra; Rova, Ulrika; Christakopoulos, Paul; Μάτσακας, Λεωνίδας; Patel, Alok

Year: 2025

Venue: npj Systems Biology and Applications

DOI: https://doi.org/10.1038/s41540-025-00556-4

Paper Addressing genome scale design tradeoffs in Pseudomonas putida for bioconversion of an aromatic carbon source

Banerjee, Deepanwita; Menasalvas, Javier; Chen, Yan et al. · 2025 · npj Systems Biology and Applications · DOI

Full title: Addressing genome scale design tradeoffs in Pseudomonas putida for bioconversion of an aromatic carbon source

Authors: Banerjee, Deepanwita; Menasalvas, Javier; Chen, Yan; Gin, Jennifer; Baidoo, Edward E. K.; Petzold, Christopher J.; Eng, Thomas; Mukhopadhyay, Aindrila

Year: 2025

Venue: npj Systems Biology and Applications

DOI: https://doi.org/10.1038/s41540-024-00480-z

Paper Dynamic resource allocation drives growth under nitrogen starvation in eukaryotes

Tibocha‐Bonilla, Juan D.; Kumar, Manish; Richelle, Anne et al. · 2020 · npj Systems Biology and Applications · DOI

Full title: Dynamic resource allocation drives growth under nitrogen starvation in eukaryotes

Authors: Tibocha‐Bonilla, Juan D.; Kumar, Manish; Richelle, Anne; Godoy‐Silva, Rubén Darío; Zengler, Karsten; Zúñiga, Cristal

Year: 2020

Venue: npj Systems Biology and Applications

DOI: https://doi.org/10.1038/s41540-020-0135-y

Paper Metabolic function-based normalization improves transcriptome data-driven reduction of genome-scale metabolic models.

Jalili, Mahdi; Scharm, Martin; Wolkenhauer, Olaf et al. · 2023 · NPJ systems biology and applications · DOI

Full title: Metabolic function-based normalization improves transcriptome data-driven reduction of genome-scale metabolic models.

Authors: Jalili, Mahdi; Scharm, Martin; Wolkenhauer, Olaf; Salehzadeh-Yazdi, Ali

Year: 2023

Venue: NPJ systems biology and applications

DOI: https://doi.org/10.1038/s41540-023-00281-w

Paper Genome-scale modeling and transcriptome analysis of Leuconostoc mesenteroides unravel the redox governed metabolic states in obligate heterofermentative lactic acid bacteria

Koduru, Lokanand; Kim, Yu‐Jin; Bang, Jeongsu et al. · 2017 · Scientific Reports · DOI

Full title: Genome-scale modeling and transcriptome analysis of Leuconostoc mesenteroides unravel the redox governed metabolic states in obligate heterofermentative lactic acid bacteria

Authors: Koduru, Lokanand; Kim, Yu‐Jin; Bang, Jeongsu; Lakshmanan, Meiyappan; Han, Nam Soo; Lee, Dong‐Yup

Year: 2017

Venue: Scientific Reports

DOI: https://doi.org/10.1038/s41598-017-16026-9

Paper Constraint-based modeling identifies new putative targets to fight colistin-resistant A. baumannii infections

Presta, Luana; Bosi, Emanuele; Mansouri, Leila et al. · 2017 · Scientific Reports · DOI

Full title: Constraint-based modeling identifies new putative targets to fight colistin-resistant A. baumannii infections

Authors: Presta, Luana; Bosi, Emanuele; Mansouri, Leila; Dijkshoorn, Lenie; Fani, Renato; Fondi, Marco

Year: 2017

Venue: Scientific Reports

DOI: https://doi.org/10.1038/s41598-017-03416-2

Paper Predicting the murine enterocyte metabolic response to diets that differ in lipid and carbohydrate composition

Sinha, Neeraj; Suárez‐Diez, María; Schothorst, Evert M. van et al. · 2017 · Scientific Reports · DOI

Full title: Predicting the murine enterocyte metabolic response to diets that differ in lipid and carbohydrate composition

Authors: Sinha, Neeraj; Suárez‐Diez, María; Schothorst, Evert M. van; Keijer, Jaap; Santos, Vítor A. P. Martins dos; Hooiveld, Guido

Year: 2017

Venue: Scientific Reports

DOI: https://doi.org/10.1038/s41598-017-07350-1

Paper Resolving the central metabolism of Arabidopsis guard cells

Robaina‐Estévez, Semidán; Daloso, Danilo M.; Zhang, Youjun et al. · 2017 · Scientific Reports · DOI

Full title: Resolving the central metabolism of Arabidopsis guard cells

Authors: Robaina‐Estévez, Semidán; Daloso, Danilo M.; Zhang, Youjun; Fernie, Alisdair R.; Nikoloski, Zoran

Year: 2017

Venue: Scientific Reports

DOI: https://doi.org/10.1038/s41598-017-07132-9

Paper Methane utilization in Methylomicrobium alcaliphilum 20ZR: a systems approach

Akberdin, Ilya R.; Thompson, Merlin; Hamilton, Richard et al. · 2018 · Scientific Reports · DOI

Full title: Methane utilization in Methylomicrobium alcaliphilum 20ZR: a systems approach

Authors: Akberdin, Ilya R.; Thompson, Merlin; Hamilton, Richard; Desai, Nalini; Alexander, Danny; Henard, Calvin A.; Guarnieri, Michael T.; Kalyuzhnaya, Marina

Year: 2018

Venue: Scientific Reports

DOI: https://doi.org/10.1038/s41598-018-20574-z

Paper Reconstruction and analysis of carbon metabolic pathway of Ketogulonicigenium vulgare SPU B805 by genome and transcriptome

Wang, Caiyun; Li, Ye; Gao, Ziwei et al. · 2018 · Scientific Reports · DOI

Full title: Reconstruction and analysis of carbon metabolic pathway of Ketogulonicigenium vulgare SPU B805 by genome and transcriptome

Authors: Wang, Caiyun; Li, Ye; Gao, Ziwei; Liu, Licheng; Wu, Ying-Cai; Zhang, Mengyue; Zhang, Tianyuan; Zhang, Yi-Xuan

Year: 2018

Venue: Scientific Reports

DOI: https://doi.org/10.1038/s41598-018-36038-3

Paper Reconstruction of a Genome-scale Metabolic Network of Komagataeibacter nataicola RZS01 for Cellulose Production

Zhang, Heng; Ye, Chao; Xu, Nan et al. · 2017 · Scientific Reports · DOI

Full title: Reconstruction of a Genome-scale Metabolic Network of Komagataeibacter nataicola RZS01 for Cellulose Production

Authors: Zhang, Heng; Ye, Chao; Xu, Nan; Chen, Chuntao; Chen, Xiao Dong; Yuan, Fanshu; Xu, Yunhua; Yang, Jiazhi; Sun, Dongping

Year: 2017

Venue: Scientific Reports

DOI: https://doi.org/10.1038/s41598-017-06918-1

Paper Modeling the Interplay between Photosynthesis, CO2 Fixation, and the Quinone Pool in a Purple Non-Sulfur Bacterium

Alsiyabi, Adil; Immethun, Cheryl M.; Saha, Rajib · 2019 · Scientific Reports · DOI

Full title: Modeling the Interplay between Photosynthesis, CO2 Fixation, and the Quinone Pool in a Purple Non-Sulfur Bacterium

Authors: Alsiyabi, Adil; Immethun, Cheryl M.; Saha, Rajib

Year: 2019

Venue: Scientific Reports

DOI: https://doi.org/10.1038/s41598-019-49079-z

Paper Comparative genomics study reveals Red Sea Bacillus with characteristics associated with potential microbial cell factories (MCFs)

Othoum, Ghofran; Prigent, Claude; Derouiche, Abderahmane et al. · 2019 · Scientific Reports · DOI

Full title: Comparative genomics study reveals Red Sea Bacillus with characteristics associated with potential microbial cell factories (MCFs)

Authors: Othoum, Ghofran; Prigent, Claude; Derouiche, Abderahmane; Shi, Lei; Bokhari, Awais; Alamoudi, Soha A.; Bougouffa, Salim; Gao, Xin; Hoehndorf, Robert; Arold, Stefan T.; Gojobori, Takashi; Hirt, Heribert; Lafi, Feras F.; Nielsen, Jens; Bajić, Vladimir B.; Mijakovic̀, Ivan; Essack, Magbubah

Year: 2019

Venue: Scientific Reports

DOI: https://doi.org/10.1038/s41598-019-55726-2

Paper The landscape of tiered regulation of breast cancer cell metabolism

Katzir, Rotem; Polat, Ibrahim H.; Harel, Michal et al. · 2019 · Scientific Reports · DOI

Full title: The landscape of tiered regulation of breast cancer cell metabolism

Authors: Katzir, Rotem; Polat, Ibrahim H.; Harel, Michal; Katz, Shir; Foguet, Carles; Selivanov, Vitaly A.; Sabatier, Philippe; Cascante, Marta; Geiger, Tamar; Ruppin, Eytan

Year: 2019

Venue: Scientific Reports

DOI: https://doi.org/10.1038/s41598-019-54221-y

Paper Bridging substrate intake kinetics and bacterial growth phenotypes with flux balance analysis incorporating proteome allocation

Zeng, Hong; Yang, Aidong · 2020 · Scientific Reports · DOI

Full title: Bridging substrate intake kinetics and bacterial growth phenotypes with flux balance analysis incorporating proteome allocation

Authors: Zeng, Hong; Yang, Aidong

Year: 2020

Venue: Scientific Reports

DOI: https://doi.org/10.1038/s41598-020-61174-0

Paper Find_tfSBP: find thermodynamics-feasible and smallest balanced pathways with high yield from large-scale metabolic networks

Xu, Zixiang; Sun, Jibin; Wu, Qiaqing et al. · 2017 · Scientific Reports · DOI

Full title: Find_tfSBP: find thermodynamics-feasible and smallest balanced pathways with high yield from large-scale metabolic networks

Authors: Xu, Zixiang; Sun, Jibin; Wu, Qiaqing; Zhu, Dunming

Year: 2017

Venue: Scientific Reports

DOI: https://doi.org/10.1038/s41598-017-17552-2

Paper Multiscale Multiobjective Systems Analysis (MiMoSA): an advanced metabolic modeling framework for complex systems

Gardner, Joseph; Hodge, Bri‐Mathias; Boyle, Nanette · 2019 · Scientific Reports · DOI

Full title: Multiscale Multiobjective Systems Analysis (MiMoSA): an advanced metabolic modeling framework for complex systems

Authors: Gardner, Joseph; Hodge, Bri‐Mathias; Boyle, Nanette

Year: 2019

Venue: Scientific Reports

DOI: https://doi.org/10.1038/s41598-019-53188-0

Paper Reconstruction and analysis of genome-scale metabolic model of weak Crabtree positive yeast Lachancea kluyveri

Nanda, Piyush; Patra, Pradipta; Das, Manali et al. · 2020 · Scientific Reports · DOI

Full title: Reconstruction and analysis of genome-scale metabolic model of weak Crabtree positive yeast Lachancea kluyveri

Authors: Nanda, Piyush; Patra, Pradipta; Das, Manali; Ghosh, Amit

Year: 2020

Venue: Scientific Reports

DOI: https://doi.org/10.1038/s41598-020-73253-3

Paper Manually curated genome-scale reconstruction of the metabolic network of Bacillus megaterium DSM319

Javad Aminian-Dehkordi; S. Mousavi; A. Jafari et al. · 2019 · Scientific Reports · DOI

Full title: Manually curated genome-scale reconstruction of the metabolic network of Bacillus megaterium DSM319

Authors: Javad Aminian-Dehkordi; S. Mousavi; A. Jafari; I. Mijakovic; S. Marashi

Year: 2019

Venue: Scientific Reports

DOI: https://doi.org/10.1038/s41598-019-55041-w

Paper Improved production of the non-native cofactor F420 in Escherichia coli

Shah, Mihir V.; Nazem‐Bokaee, Hadi; Antoney, James et al. · 2021 · Scientific Reports · DOI

Full title: Improved production of the non-native cofactor F420 in Escherichia coli

Authors: Shah, Mihir V.; Nazem‐Bokaee, Hadi; Antoney, James; Kang, Suk Woo; Jackson, Colin J.; Scott, Colin

Year: 2021

Venue: Scientific Reports

DOI: https://doi.org/10.1038/s41598-021-01224-3

Paper Deciphering the metabolic capabilities of Bifidobacteria using genome-scale metabolic models

Devika, N. T.; Raman, Karthik · 2019 · Scientific Reports · DOI

Full title: Deciphering the metabolic capabilities of Bifidobacteria using genome-scale metabolic models

Authors: Devika, N. T.; Raman, Karthik

Year: 2019

Venue: Scientific Reports

Paper Characterization and engineering of Streptomyces griseofuscus DSM 40191 as a potential host for heterologous expression of biosynthetic gene clusters

Gren, Tetiana; Whitford, Christopher M.; Mohite, Omkar S. et al. · 2021 · Scientific Reports · DOI

Full title: Characterization and engineering of Streptomyces griseofuscus DSM 40191 as a potential host for heterologous expression of biosynthetic gene clusters

Authors: Gren, Tetiana; Whitford, Christopher M.; Mohite, Omkar S.; Jørgensen, Tue Sparholt; Kontou, Eftychia Eva; Nielsen, Julie B.; Lee, Sang Yup; Weber, Tilmann

Year: 2021

Venue: Scientific Reports

DOI: https://doi.org/10.1038/s41598-021-97571-2

Paper Integrating glycolysis, citric acid cycle, pentose phosphate pathway, and fatty acid beta-oxidation into a single computational model

Kloska, Sylwester M.; Pałczyński, Krzysztof; Marciniak, Tomasz et al. · 2023 · Scientific Reports · DOI

Full title: Integrating glycolysis, citric acid cycle, pentose phosphate pathway, and fatty acid beta-oxidation into a single computational model

Authors: Kloska, Sylwester M.; Pałczyński, Krzysztof; Marciniak, Tomasz; Talaśka, Tomasz; Wysocki, Beata J.; Davis, Paul H.; Wysocki, Tadeusz A.

Year: 2023

Venue: Scientific Reports

DOI: https://doi.org/10.1038/s41598-023-41765-3

Paper Deep learning-based kcat prediction enables improved enzyme-constrained model reconstruction

Li, Feiran; Yuan, Le; Lu, Hongzhong et al. · 2022 · Nature Catalysis · DOI

Full title: Deep learning-based kcat prediction enables improved enzyme-constrained model reconstruction

Authors: Li, Feiran; Yuan, Le; Lu, Hongzhong; Li, Gang; Chen, Yu; Engqvist, Martin K. M.; Kerkhoven, Eduard J.; Nielsen, Jens

Year: 2022

Venue: Nature Catalysis

DOI: https://doi.org/10.1038/s41929-022-00798-z

Paper Genome-scale reconstruction of Paenarthrobacter aurescens TC1 metabolic model towards the study of atrazine bioremediation

Ofaim, Shany; Zarecki, Raphy; Porob, Seema et al. · 2020 · Scientific Reports · DOI

Full title: Genome-scale reconstruction of Paenarthrobacter aurescens TC1 metabolic model towards the study of atrazine bioremediation

Authors: Ofaim, Shany; Zarecki, Raphy; Porob, Seema; Gat, Daniella; Lahav, Tamar; Kashi, Yechezkel; Aly, Radi; Eizenberg, Hanan; Ronen, Zeev; Freilich, Shiri

Year: 2020

Venue: Scientific Reports

DOI: https://doi.org/10.1038/s41598-020-69509-7

Paper Unveiling metabolic pathways involved in the extreme desiccation tolerance of an Atacama cyanobacterium

Moore, Rachel A.; Azúa-Bustos, Armando; González‐Silva, Carlos et al. · 2023 · Scientific Reports · DOI

Full title: Unveiling metabolic pathways involved in the extreme desiccation tolerance of an Atacama cyanobacterium

Authors: Moore, Rachel A.; Azúa-Bustos, Armando; González‐Silva, Carlos; Carr, Christopher E.

Year: 2023

Venue: Scientific Reports

DOI: https://doi.org/10.1038/s41598-023-41879-8

Paper Adaptive laboratory evolution enhances methanol tolerance and conversion in engineered Corynebacterium glutamicum

Wang, Yu; Fan, Liwen; Tuyishime, Philibert et al. · 2020 · Communications Biology · DOI

Full title: Adaptive laboratory evolution enhances methanol tolerance and conversion in engineered Corynebacterium glutamicum

Authors: Wang, Yu; Fan, Liwen; Tuyishime, Philibert; Liu, Jiao; Zhang, Kun; Gao, Ning; Zhang, Zhihui; Ni, Xiaomeng; Feng, Jinhui; Yuan, Qianqian; Ma, Hongwu; Zheng, Ping; Sun, Jibin; Ma, Yanhe

Year: 2020

Venue: Communications Biology

DOI: https://doi.org/10.1038/s42003-020-0954-9

Paper Flux balance analysis predicts essential genes in clear cell renal cell carcinoma metabolism

Gatto, Francesco; Miess, Heike; Schulze, Almut et al. · 2015 · Scientific Reports · DOI

Full title: Flux balance analysis predicts essential genes in clear cell renal cell carcinoma metabolism

Authors: Gatto, Francesco; Miess, Heike; Schulze, Almut; Nielsen, Jens

Year: 2015

Venue: Scientific Reports

DOI: https://doi.org/10.1038/srep10738

Paper Pichia pastoris growth—coupled heme biosynthesis analysis using metabolic modelling

Pentjuss, Agris; Bolmanis, Emīls; Šuleiko, Anastasija et al. · 2023 · Scientific Reports · DOI

Full title: Pichia pastoris growth—coupled heme biosynthesis analysis using metabolic modelling

Authors: Pentjuss, Agris; Bolmanis, Emīls; Šuleiko, Anastasija; Didrihsone, Elina; Šuleiko, Artūrs; Dubencovs, Konstantīns; Liepiņš, Jānis; Kazāks, Andris; Vanags, Juris

Year: 2023

Venue: Scientific Reports

DOI: https://doi.org/10.1038/s41598-023-42865-w

Paper Understanding the interactions between bacteria in the human gut through metabolic modeling

Shoaie, Saeed; Karlsson, Fredrik; Mardinoğlu, Adil et al. · 2013 · Scientific Reports · DOI

Full title: Understanding the interactions between bacteria in the human gut through metabolic modeling

Authors: Shoaie, Saeed; Karlsson, Fredrik; Mardinoğlu, Adil; Nookaew, Intawat; Bordel, Sergio; Nielsen, Jens

Year: 2013

Venue: Scientific Reports

DOI: https://doi.org/10.1038/srep02532

Paper Genome-scale model of Pseudomonas aeruginosa metabolism unveils virulence and drug potentiation

Dahal, Sanjeev; Renz, Alina; Dräger, Andreas et al. · 2023 · Communications Biology · DOI

Full title: Genome-scale model of Pseudomonas aeruginosa metabolism unveils virulence and drug potentiation

Authors: Dahal, Sanjeev; Renz, Alina; Dräger, Andreas; Yang, Laurence

Year: 2023

Venue: Communications Biology

DOI: https://doi.org/10.1038/s42003-023-04540-8

Paper A simple strategy guides the complex metabolic regulation in Escherichia coli

Facchetti, Giuseppe · 2016 · Scientific Reports · DOI

Full title: A simple strategy guides the complex metabolic regulation in Escherichia coli

Authors: Facchetti, Giuseppe

Year: 2016

Venue: Scientific Reports

DOI: https://doi.org/10.1038/srep27660

Paper Personalized modeling of gut microbiome metabolism throughout the first year of life

Shaaban, Rola; Busi, Susheel Bhanu; Wilmes, Paul et al. · 2024 · Communications Medicine · DOI

Full title: Personalized modeling of gut microbiome metabolism throughout the first year of life

Authors: Shaaban, Rola; Busi, Susheel Bhanu; Wilmes, Paul; Guéant, Jean‐Louis; Heinken, Almut

Year: 2024

Venue: Communications Medicine

DOI: https://doi.org/10.1038/s43856-024-00715-4

Paper Thermochemical hydrolysis of macroalgae Ulva for biorefinery: Taguchi robust design method

Jiang, Rui; Linzon, Yoav; Vitkin, Edward et al. · 2016 · Scientific Reports · DOI

Full title: Thermochemical hydrolysis of macroalgae Ulva for biorefinery: Taguchi robust design method

Authors: Jiang, Rui; Linzon, Yoav; Vitkin, Edward; Yakhini, Zohar; Chudnovsky, Alexandra; Golberg, Alexander

Year: 2016

Venue: Scientific Reports

DOI: https://doi.org/10.1038/srep27761

Paper Systems biology-guided identification of synthetic lethal gene pairs and its potential use to discover antibiotic combinations

Aziz, Ramy K.; Monk, Jonathan M.; Lewis, Robert M. et al. · 2015 · Scientific Reports · DOI

Full title: Systems biology-guided identification of synthetic lethal gene pairs and its potential use to discover antibiotic combinations

Authors: Aziz, Ramy K.; Monk, Jonathan M.; Lewis, Robert M.; Loh, Suh In; Mishra, Arti; Nagle, Amrita Abhay; Satyanarayana, Chitkala; Dhakshinamoorthy, Saravanakumar; Luche, Michele; Kitchen, Douglas B.; Andrews, Kathleen A.; Fong, Nicole L.; Li, Howard J.; Palsson, Bernhard Ø.; Charusanti, Pep

Year: 2015

Venue: Scientific Reports

DOI: https://doi.org/10.1038/srep16025

Paper Principles of proteome allocation are revealed using proteomic data and genome-scale models

Yang, Laurence; Yurkovich, James T.; Lloyd, Colton J. et al. · 2016 · Scientific Reports · DOI

Full title: Principles of proteome allocation are revealed using proteomic data and genome-scale models

Authors: Yang, Laurence; Yurkovich, James T.; Lloyd, Colton J.; Ebrahim, Ali; Saunders, Michael A.; Palsson, Bernhard Ø.

Year: 2016

Venue: Scientific Reports

DOI: https://doi.org/10.1038/srep36734

Paper Quantitative constraint-based computational model of tumor-to-stroma coupling via lactate shuttle

Capuani, Fabrizio; Martino, Daniele De; Marinari, Enzo et al. · 2015 · Scientific Reports · DOI

Full title: Quantitative constraint-based computational model of tumor-to-stroma coupling via lactate shuttle

Authors: Capuani, Fabrizio; Martino, Daniele De; Marinari, Enzo; Martino, Andrea De

Year: 2015

Venue: Scientific Reports

DOI: https://doi.org/10.1038/srep11880

Paper Optimization of chondroitin production in E. coli using genome scale models

Couto, Márcia R.; Rodrigues, Joana L.; Braga, Adelaide et al. · 2024 · Molecular Systems Design & Engineering · DOI

Full title: Optimization of chondroitin production in E. coli using genome scale models

Authors: Couto, Márcia R.; Rodrigues, Joana L.; Braga, Adelaide; Dias, Óscar; Rodrigues, L. R.

Year: 2024

Venue: Molecular Systems Design & Engineering

DOI: https://doi.org/10.1039/d3me00199g

Paper Revisiting the chlorophyll biosynthesis pathway using genome scale metabolic model of Oryza sativa japonica

Chatterjee, A.; Kundu, Sudip · 2015 · Scientific Reports · DOI

Full title: Revisiting the chlorophyll biosynthesis pathway using genome scale metabolic model of Oryza sativa japonica

Authors: Chatterjee, A.; Kundu, Sudip

Year: 2015

Venue: Scientific Reports

DOI: https://doi.org/10.1038/srep14975

Paper Predictive analytics of environmental adaptability in multi-omic network models

Angione, Claudio; Lió, Píetro · 2015 · Scientific Reports · DOI

Full title: Predictive analytics of environmental adaptability in multi-omic network models

Authors: Angione, Claudio; Lió, Píetro

Year: 2015

Venue: Scientific Reports

DOI: https://doi.org/10.1038/srep15147

Paper EColiCore2: a reference network model of the central metabolism of Escherichia coli and relationships to its genome-scale parent model

Hädicke, Oliver; Klamt, Steffen · 2017 · Scientific Reports · DOI

Full title: EColiCore2: a reference network model of the central metabolism of Escherichia coli and relationships to its genome-scale parent model

Authors: Hädicke, Oliver; Klamt, Steffen

Year: 2017

Venue: Scientific Reports

DOI: https://doi.org/10.1038/srep39647

Paper Yeast metabolic chassis designs for diverse biotechnological products

Jouhten, Paula; Boruta, Tomasz; Andrejev, Sergej et al. · 2016 · Scientific Reports · DOI

Full title: Yeast metabolic chassis designs for diverse biotechnological products

Authors: Jouhten, Paula; Boruta, Tomasz; Andrejev, Sergej; Pereira, Filipa; Rocha, Isabel; Patil, Kiran Raosaheb

Year: 2016

Venue: Scientific Reports

DOI: https://doi.org/10.1038/srep29694

Paper Discovering missing reactions of metabolic networks by using gene co-expression data

Hosseini, Zhaleh; Marashi, Sayed‐Amir · 2017 · Scientific Reports · DOI

Full title: Discovering missing reactions of metabolic networks by using gene co-expression data

Authors: Hosseini, Zhaleh; Marashi, Sayed‐Amir

Year: 2017

Venue: Scientific Reports

DOI: https://doi.org/10.1038/srep41774

Paper Systems approach to characterize the metabolism of liver cancer stem cells expressing CD133

Hur, Wonhee; Ryu, Jae Yong; Kim, Hyun Uk et al. · 2017 · Scientific Reports · DOI

Full title: Systems approach to characterize the metabolism of liver cancer stem cells expressing CD133

Authors: Hur, Wonhee; Ryu, Jae Yong; Kim, Hyun Uk; Hong, Sung Woo; Lee, Eun Byul; Lee, Sang Yup; Yoon, Seung Kew

Year: 2017

Venue: Scientific Reports

DOI: https://doi.org/10.1038/srep45557

Paper A multiscale spatiotemporal model including a switch from aerobic to anaerobic metabolism reproduces succession in the early infant gut microbiota

Versluis, David M.; Schoemaker, Ruud; Looijesteijn, Ellen et al. · 2021 · DOI

Full title: A multiscale spatiotemporal model including a switch from aerobic to anaerobic metabolism reproduces succession in the early infant gut microbiota

Authors: Versluis, David M.; Schoemaker, Ruud; Looijesteijn, Ellen; Muysken, Daniël; Jeurink, Prescilla V.; Paques, Marcel; Geurts, Jan M.W.; Merks, Roeland M. H.

Year: 2021

DOI: https://doi.org/10.1101/2021.08.22.457032

Paper An Automated Scientist to Design and Optimize Microbial Strains for the Industrial Production of Small Molecules

Singh, Amoolya H.; Kaufmann-Malaga, Benjamin; Lerman, Joshua A. et al. · 2023 · DOI

Full title: An Automated Scientist to Design and Optimize Microbial Strains for the Industrial Production of Small Molecules

Authors: Singh, Amoolya H.; Kaufmann-Malaga, Benjamin; Lerman, Joshua A.; Dougherty, Daniel P.; Zhang, Yang; Kilbo, Alexander L.; Wilson, Erin; Ng, Chiam Yu; Erbilgin, Onur; Curran, Kate A.; Reeves, Christopher D.; Hung, John E.; Mantovani, Simone; King, Zachary A.; Ayson, Marites J.; Denery, Judith R.; Lu, Chia‐Wei; Norton, Phillip; Tran, Carol; Platt, Darren; Cherry, Joel R.; Chandran, Sunil S.; Meadows, Adam L.

Year: 2023

DOI: https://doi.org/10.1101/2023.01.03.521657

Paper A digital twin of bacterial metabolism during cheese production

Lecomte, Maxime; Cao, Wenfan; Aubert, Julie et al. · 2023 · DOI

Full title: A digital twin of bacterial metabolism during cheese production

Authors: Lecomte, Maxime; Cao, Wenfan; Aubert, Julie; Sherman, David James; Falentin, Hélène; Frioux, Clémence; Labarthe, Simon

Year: 2023

DOI: https://doi.org/10.1101/2023.05.05.539417

Paper Statistical prediction of microbial metabolic traits from genomes

Li, Zeqian; Selim, Ahmed; Kuehn, Seppe · 2023 · PLoS Computational Biology · DOI

Full title: Statistical prediction of microbial metabolic traits from genomes

Authors: Li, Zeqian; Selim, Ahmed; Kuehn, Seppe

Year: 2023

Venue: PLoS Computational Biology

Paper A genome-scale metabolic flux model of Escherichia coli K–12 derived from the EcoCyc database

Weaver, Daniel; Keseler, Ingrid M.; Mackie, Amanda et al. · 2014 · BMC Systems Biology · DOI

Full title: A genome-scale metabolic flux model of Escherichia coli K–12 derived from the EcoCyc database

Authors: Weaver, Daniel; Keseler, Ingrid M.; Mackie, Amanda; Paulsen, Ian T.; Karp, Peter D.

Year: 2014

Venue: BMC Systems Biology

DOI: https://doi.org/10.1186/1752-0509-8-79

Paper gapseq: informed prediction of bacterial metabolic pathways and reconstruction of accurate metabolic models

Zimmermann, Johannes; Kaleta, Christoph; Waschina, Silvio · 2021 · Genome biology · DOI

Full title: gapseq: informed prediction of bacterial metabolic pathways and reconstruction of accurate metabolic models

Authors: Zimmermann, Johannes; Kaleta, Christoph; Waschina, Silvio

Year: 2021

Venue: Genome biology

Paper Systems biology elucidates the distinctive metabolic niche filled by the human gut microbe Eggerthella lenta

Noecker, Cecilia; Sánchez, Juan M.; Bisanz, Jordan E. et al. · 2023 · PLoS Biology · DOI

Full title: Systems biology elucidates the distinctive metabolic niche filled by the human gut microbe Eggerthella lenta

Authors: Noecker, Cecilia; Sánchez, Juan M.; Bisanz, Jordan E.; Escalante, Veronica; Alexander, Margaret; Trepka, Kai; Heinken, Almut; Liu, Yuanyuan; Dodd, Dylan; Thiele, Ines; DeFelice, Brian C.; Turnbaugh, Peter J.

Year: 2023

Venue: PLoS Biology

DOI: https://doi.org/10.1371/journal.pbio.3002125

Paper Statistical prediction of microbial metabolic traits from genomes

Li, Zeqian; Selim, Ahmed; Kuehn, Seppe · 2023 · PLoS Computational Biology · DOI

Full title: Statistical prediction of microbial metabolic traits from genomes

Authors: Li, Zeqian; Selim, Ahmed; Kuehn, Seppe

Year: 2023

Venue: PLoS Computational Biology

DOI: https://doi.org/10.3390/microorganisms11051252

Paper Integrating Kinetic Model of E. coli with Genome Scale Metabolic Fluxes Overcomes Its Open System Problem and Reveals Bistability in Central Metabolism

Mannan, Ahmad A.; Toya, Yoshihiro; Shimizu, Kazuyuki et al. · 2015 · PLoS ONE · DOI

Full title: Integrating Kinetic Model of E. coli with Genome Scale Metabolic Fluxes Overcomes Its Open System Problem and Reveals Bistability in Central Metabolism

Authors: Mannan, Ahmad A.; Toya, Yoshihiro; Shimizu, Kazuyuki; McFadden, Johnjoe; Kierzek, Andrzej; Rocco, Andrea

Year: 2015

Venue: PLoS ONE

DOI: https://doi.org/10.1371/journal.pone.0139507

Paper Metabolic characterization and viable delivery of Akkermansia muciniphila for its future application

Ark, Kees van der · 2018 · DOI

Full title: Metabolic characterization and viable delivery of Akkermansia muciniphila for its future application

Authors: Ark, Kees van der

Year: 2018

DOI: https://doi.org/10.18174/427507

Paper New concepts and tools in constraint-based analysis of metabolic networks

Larhlimi, Abdelhalim · 2009 · DOI

Full title: New concepts and tools in constraint-based analysis of metabolic networks

Authors: Larhlimi, Abdelhalim

Year: 2009

DOI: https://doi.org/10.17169/refubium-11716

Paper Systems analysis of Mycoplasma hyopneumoniae to improve vaccine production

Kamminga, Tjerko · 2017 · DOI

Full title: Systems analysis of Mycoplasma hyopneumoniae to improve vaccine production

Authors: Kamminga, Tjerko

Year: 2017

DOI: https://doi.org/10.18174/420702

Paper Improved functional annotations are key to realize the potential of algal biotechnology

M. Reijnders · 2018 · DOI

Full title: Improved functional annotations are key to realize the potential of algal biotechnology

Authors: M. Reijnders

Year: 2018

DOI: https://doi.org/10.18174/462782

Paper Continuous Cultivation as a Tool Toward the Rational Bioprocess Development With Pichia Pastoris Cell Factory

Nieto‐Taype, Miguel Angel; Garcia‐Ortega, Xavier; Albiol, Joan et al. · 2020 · Frontiers in Bioengineering and Biotechnology · DOI

Full title: Continuous Cultivation as a Tool Toward the Rational Bioprocess Development With Pichia Pastoris Cell Factory

Authors: Nieto‐Taype, Miguel Angel; Garcia‐Ortega, Xavier; Albiol, Joan; Montesinos, José Luis González; Valero, Francisco

Year: 2020

Venue: Frontiers in Bioengineering and Biotechnology

DOI: https://doi.org/10.3389/fbioe.2020.00632

Paper Production of Vitamin B2 (Riboflavin) by Microorganisms: An Overview

Averianova, Liudmila; Balabanova, Larissa; Son, Oksana et al. · 2020 · Frontiers in Bioengineering and Biotechnology · DOI

Full title: Production of Vitamin B2 (Riboflavin) by Microorganisms: An Overview

Authors: Averianova, Liudmila; Balabanova, Larissa; Son, Oksana; Podvolotskaya, Anna; Tekutyeva, Liudmila

Year: 2020

Venue: Frontiers in Bioengineering and Biotechnology

DOI: https://doi.org/10.3389/fbioe.2020.570828

Paper New Applications of Synthetic Biology Tools for Cyanobacterial Metabolic Engineering

Santos‐Merino, María; Singh, Amit Kumar; Ducat, Daniel C. · 2019 · Frontiers in Bioengineering and Biotechnology · DOI

Full title: New Applications of Synthetic Biology Tools for Cyanobacterial Metabolic Engineering

Authors: Santos‐Merino, María; Singh, Amit Kumar; Ducat, Daniel C.

Year: 2019

Venue: Frontiers in Bioengineering and Biotechnology

DOI: https://doi.org/10.3389/fbioe.2019.00033

Paper Metabolic Network Modeling of Microbial Interactions in Natural and Engineered Environmental Systems

Perez‐Garcia, Octavio; Lear, Gavin; Singhal, Naresh · 2016 · Frontiers in Microbiology · DOI

Full title: Metabolic Network Modeling of Microbial Interactions in Natural and Engineered Environmental Systems

Authors: Perez‐Garcia, Octavio; Lear, Gavin; Singhal, Naresh

Year: 2016

Venue: Frontiers in Microbiology

DOI: https://doi.org/10.3389/fmicb.2016.00673

Paper A Review of Dynamic Modeling Approaches and Their Application in Computational Strain Optimization for Metabolic Engineering

Kim, Osvaldo D.; Rocha, Miguel; Maia, Paulo · 2018 · Frontiers in Microbiology · DOI

Full title: A Review of Dynamic Modeling Approaches and Their Application in Computational Strain Optimization for Metabolic Engineering

Authors: Kim, Osvaldo D.; Rocha, Miguel; Maia, Paulo

Year: 2018

Venue: Frontiers in Microbiology

DOI: https://doi.org/10.3389/fmicb.2018.01690

Paper Fungal Alcohol Dehydrogenases: Physiological Function, Molecular Properties, Regulation of Their Production, and Biotechnological Potential

Gutiérrez-Corona, J. Félix; Hernández, Gloria Angélica González; Padilla-Guerrero, Israel Enrique et al. · 2023 · Cells · DOI

Full title: Fungal Alcohol Dehydrogenases: Physiological Function, Molecular Properties, Regulation of Their Production, and Biotechnological Potential

Authors: Gutiérrez-Corona, J. Félix; Hernández, Gloria Angélica González; Padilla-Guerrero, Israel Enrique; Olmedo‐Monfil, Vianey; Martínez-Rocha, Ana Lilia; Patiño-Medina, J. Alberto; Meza‐Carmen, Víctor; Guzmán, Juan Carlos Torres

Year: 2023

Venue: Cells

DOI: https://doi.org/10.3390/cells12182239

Paper Computational Strategies for a System-Level Understanding of Metabolism

Cazzaniga, Paolo; Damiani, Chiara; Besozzi, Daniela et al. · 2014 · Metabolites · DOI

Full title: Computational Strategies for a System-Level Understanding of Metabolism

Authors: Cazzaniga, Paolo; Damiani, Chiara; Besozzi, Daniela; Colombo, Riccardo; Nobile, Marco S.; Gaglio, Daniela; Pescini, Dario; Molinari, Sara; Mauri, Giancarlo; Alberghina, Lilia; Vanoni, Marco

Year: 2014

Venue: Metabolites

DOI: https://doi.org/10.3390/metabo4041034

Paper Metabolic Engineering of Model Microorganisms for the Production of Xanthophyll

Wang, Nan; Peng, Huakang; Yang, Caifeng et al. · 2023 · Microorganisms · DOI

Full title: Metabolic Engineering of Model Microorganisms for the Production of Xanthophyll

Authors: Wang, Nan; Peng, Huakang; Yang, Caifeng; Guo, Wenfang; Wang, Mengqi; Li, Gangqiang; Liu, Dehu

Year: 2023

Venue: Microorganisms

Paper Inferring Metabolic States in Uncharacterized Environments Using Gene-Expression Measurements

Rossell, Sergio; Huynen, Martijn A.; Notebaart, Richard A. · 2013 · PLoS Computational Biology · DOI

Full title: Inferring Metabolic States in Uncharacterized Environments Using Gene-Expression Measurements

Authors: Rossell, Sergio; Huynen, Martijn A.; Notebaart, Richard A.

Year: 2013

Venue: PLoS Computational Biology

DOI: https://doi.org/10.1371/journal.pcbi.1002988

Paper Temporal Expression-based Analysis of Metabolism

Collins, Sara B.; Reznik, Ed; Segrè, Daniel · 2012 · PLoS Computational Biology · DOI

Full title: Temporal Expression-based Analysis of Metabolism

Authors: Collins, Sara B.; Reznik, Ed; Segrè, Daniel

Year: 2012

Venue: PLoS Computational Biology

DOI: https://doi.org/10.1371/journal.pcbi.1002781

Paper A Peptide-Based Method for 13C Metabolic Flux Analysis in Microbial Communities

Ghosh, Amit; Nilmeier, Jerome P.; Weaver, Daniel et al. · 2014 · PLoS Computational Biology · DOI

Full title: A Peptide-Based Method for 13C Metabolic Flux Analysis in Microbial Communities

Authors: Ghosh, Amit; Nilmeier, Jerome P.; Weaver, Daniel; Adams, Paul D.; Keasling, Jay D.; Mukhopadhyay, Aindrila; Petzold, Christopher J.; Martín, Héctor García

Year: 2014

Venue: PLoS Computational Biology

DOI: https://doi.org/10.1371/journal.pcbi.1003827

Paper k-OptForce: Integrating Kinetics with Flux Balance Analysis for Strain Design

Chowdhury, Anupam; Zomorrodi, Ali R.; Maranas, Costas D. · 2014 · PLoS Computational Biology · DOI

Full title: k-OptForce: Integrating Kinetics with Flux Balance Analysis for Strain Design

Authors: Chowdhury, Anupam; Zomorrodi, Ali R.; Maranas, Costas D.

Year: 2014

Venue: PLoS Computational Biology

DOI: https://doi.org/10.1371/journal.pcbi.1003487

Paper Flux Balance Analysis of Cyanobacterial Metabolism: The Metabolic Network of Synechocystis sp. PCC 6803

Knoop, Henning; Gründel, Marianne; Zilliges, Yvonne et al. · 2013 · PLoS Computational Biology · DOI

Full title: Flux Balance Analysis of Cyanobacterial Metabolism: The Metabolic Network of Synechocystis sp. PCC 6803

Authors: Knoop, Henning; Gründel, Marianne; Zilliges, Yvonne; Lehmann, Robert; Hoffmann, Sabrina; Lockau, Wolfgang; Steuer, Ralf

Year: 2013

Venue: PLoS Computational Biology

DOI: https://doi.org/10.1371/journal.pcbi.1003081

Paper Metabolic Constraint-Based Refinement of Transcriptional Regulatory Networks

Chandrasekaran, Sriram; Price, Nathan D. · 2013 · PLoS Computational Biology · DOI

Full title: Metabolic Constraint-Based Refinement of Transcriptional Regulatory Networks

Authors: Chandrasekaran, Sriram; Price, Nathan D.

Year: 2013

Venue: PLoS Computational Biology

DOI: https://doi.org/10.1371/journal.pcbi.1003370

Paper Swimming in Light: A Large-Scale Computational Analysis of the Metabolism of Dinoroseobacter shibae

Rex, René; Bill, Nelli; Schmidt‐Hohagen, Kerstin et al. · 2013 · PLoS Computational Biology · DOI

Full title: Swimming in Light: A Large-Scale Computational Analysis of the Metabolism of Dinoroseobacter shibae

Authors: Rex, René; Bill, Nelli; Schmidt‐Hohagen, Kerstin; Schomburg, Dietmar

Year: 2013

Venue: PLoS Computational Biology

DOI: https://doi.org/10.1371/journal.pcbi.1003224

Paper Semi-automated Curation of Metabolic Models via Flux Balance Analysis: A Case Study with Mycoplasma gallisepticum

Bautista, Eddy J.; Zinski, Joseph; Szczepanek, Steven M. et al. · 2013 · PLoS Computational Biology · DOI

Full title: Semi-automated Curation of Metabolic Models via Flux Balance Analysis: A Case Study with Mycoplasma gallisepticum

Authors: Bautista, Eddy J.; Zinski, Joseph; Szczepanek, Steven M.; Johnson, E. L.; Tulman, E. R.; Ching, Wei‐Mei; Geary, Steven J.; Srivastava, Ranjan

Year: 2013

Venue: PLoS Computational Biology

DOI: https://doi.org/10.1371/journal.pcbi.1003208

Paper Reconstruction and Validation of a Genome-Scale Metabolic Model for the Filamentous Fungus Neurospora crassa Using FARM

Dreyfuss, Jonathan M.; Zucker, Jeremy; Hood, Heather M. et al. · 2013 · PLoS Computational Biology · DOI

Full title: Reconstruction and Validation of a Genome-Scale Metabolic Model for the Filamentous Fungus Neurospora crassa Using FARM

Authors: Dreyfuss, Jonathan M.; Zucker, Jeremy; Hood, Heather M.; Ocasio, Linda R.; Sachs, Matthew S.; Galagan, James E.

Year: 2013

Venue: PLoS Computational Biology

DOI: https://doi.org/10.1371/journal.pcbi.1003126

Paper Comparative Analysis of Yeast Metabolic Network Models Highlights Progress, Opportunities for Metabolic Reconstruction

Heavner, Ben; Price, Nathan D. · 2015 · PLoS Computational Biology · DOI

Full title: Comparative Analysis of Yeast Metabolic Network Models Highlights Progress, Opportunities for Metabolic Reconstruction

Authors: Heavner, Ben; Price, Nathan D.

Year: 2015

Venue: PLoS Computational Biology

DOI: https://doi.org/10.1371/journal.pcbi.1004530

Paper A Method to Constrain Genome-Scale Models with 13C Labeling Data

Martín, Héctor García; Kumar, Vinay; Weaver, Daniel et al. · 2015 · PLoS Computational Biology · DOI

Full title: A Method to Constrain Genome-Scale Models with 13C Labeling Data

Authors: Martín, Héctor García; Kumar, Vinay; Weaver, Daniel; Ghosh, Amit; Chubukov, Victor; Mukhopadhyay, Aindrila; Arkin, Adam P.; Keasling, Jay D.

Year: 2015

Venue: PLoS Computational Biology

DOI: https://doi.org/10.1371/journal.pcbi.1004363

Paper Systematic Evaluation of Methods for Integration of Transcriptomic Data into Constraint-Based Models of Metabolism

Machado, Daniel; Herrgård, Markus J. · 2014 · PLoS Computational Biology · DOI

Full title: Systematic Evaluation of Methods for Integration of Transcriptomic Data into Constraint-Based Models of Metabolism

Authors: Machado, Daniel; Herrgård, Markus J.

Year: 2014

Venue: PLoS Computational Biology

DOI: https://doi.org/10.1371/journal.pcbi.1003580

Paper A Novel Nutritional Predictor Links Microbial Fastidiousness with Lowered Ubiquity, Growth Rate, and Cooperativeness

Zarecki, Raphy; Oberhardt, Matthew; Reshef, Leah et al. · 2014 · PLoS Computational Biology · DOI

Full title: A Novel Nutritional Predictor Links Microbial Fastidiousness with Lowered Ubiquity, Growth Rate, and Cooperativeness

Authors: Zarecki, Raphy; Oberhardt, Matthew; Reshef, Leah; Gophna, Uri; Ruppin, Eytan

Year: 2014

Venue: PLoS Computational Biology

DOI: https://doi.org/10.1371/journal.pcbi.1003726

Paper Metabolic fluxes-oriented control of bioreactors: a novel approach to tune micro-aeration and substrate feeding in fermentations

Mesquita, Thiago José Barbosa; Sargo, Cíntia Regina; Fuzer, José Roberto et al. · 2019 · Microbial Cell Factories · DOI

Full title: Metabolic fluxes-oriented control of bioreactors: a novel approach to tune micro-aeration and substrate feeding in fermentations

Authors: Mesquita, Thiago José Barbosa; Sargo, Cíntia Regina; Fuzer, José Roberto; Paredes, Sheyla Alexandra Hidalgo; Giordano, Roberto C.; Horta, Antônio Carlos Luperni; Zangirolami, Teresa Cristina

Year: 2019

Venue: Microbial Cell Factories

DOI: https://doi.org/10.1186/s12934-019-1198-6

Paper Visualization of Metabolic Interaction Networks in Microbial Communities Using VisANT 5.0

Granger, Brian R.; Chang, Yi-Chien; Wang, Yan et al. · 2016 · PLoS Computational Biology · DOI

Full title: Visualization of Metabolic Interaction Networks in Microbial Communities Using VisANT 5.0

Authors: Granger, Brian R.; Chang, Yi-Chien; Wang, Yan; DeLisi, Charles; Segrè, Daniel; Hu, Zhenjun

Year: 2016

Venue: PLoS Computational Biology

DOI: https://doi.org/10.1371/journal.pcbi.1004875

Paper Genome-Scale Metabolic Network Validation of Shewanella oneidensis Using Transposon Insertion Frequency Analysis

Yang, Hong; Krumholz, Elias W.; Brutinel, Evan D. et al. · 2014 · PLoS Computational Biology · DOI

Full title: Genome-Scale Metabolic Network Validation of Shewanella oneidensis Using Transposon Insertion Frequency Analysis

Authors: Yang, Hong; Krumholz, Elias W.; Brutinel, Evan D.; Palani, Nagendra P.; Sadowsky, Michael J.; Odlyzko, Andrew; Gralnick, Jeffrey A.; Libourel, Igor G. L.

Year: 2014

Venue: PLoS Computational Biology

DOI: https://doi.org/10.1371/journal.pcbi.1003848

Paper Emergent Biosynthetic Capacity in Simple Microbial Communities

Chiu, Hsuan; Levy, Roie; Borenstein, Elhanan · 2014 · PLoS Computational Biology · DOI

Full title: Emergent Biosynthetic Capacity in Simple Microbial Communities

Authors: Chiu, Hsuan; Levy, Roie; Borenstein, Elhanan

Year: 2014

Venue: PLoS Computational Biology

DOI: https://doi.org/10.1371/journal.pcbi.1003695

Paper Stoichiometric Representation of Gene–Protein–Reaction Associations Leverages Constraint-Based Analysis from Reaction to Gene-Level Phenotype Prediction

Machado, Daniel; Herrgård, Markus J.; Rocha, Isabel · 2016 · PLoS Computational Biology · DOI

Full title: Stoichiometric Representation of Gene–Protein–Reaction Associations Leverages Constraint-Based Analysis from Reaction to Gene-Level Phenotype Prediction

Authors: Machado, Daniel; Herrgård, Markus J.; Rocha, Isabel

Year: 2016

Venue: PLoS Computational Biology

DOI: https://doi.org/10.1371/journal.pcbi.1005140

Paper lumpGEM: Systematic generation of subnetworks and elementally balanced lumped reactions for the biosynthesis of target metabolites

Ataman, Meriç; Hatzimanikatis, Vassily · 2017 · PLoS Computational Biology · DOI

Full title: lumpGEM: Systematic generation of subnetworks and elementally balanced lumped reactions for the biosynthesis of target metabolites

Authors: Ataman, Meriç; Hatzimanikatis, Vassily

Year: 2017

Venue: PLoS Computational Biology

DOI: https://doi.org/10.1371/journal.pcbi.1005513

Paper Metabolic regulation is sufficient for global and robust coordination of glucose uptake, catabolism, energy production and growth in Escherichia coli

Millard, Pierre; Smallbone, Kieran; Mendes, Pedro · 2017 · PLoS Computational Biology · DOI

Full title: Metabolic regulation is sufficient for global and robust coordination of glucose uptake, catabolism, energy production and growth in Escherichia coli

Authors: Millard, Pierre; Smallbone, Kieran; Mendes, Pedro

Year: 2017

Venue: PLoS Computational Biology

DOI: https://doi.org/10.1371/journal.pcbi.1005396

Paper Combining inferred regulatory and reconstructed metabolic networks enhances phenotype prediction in yeast

Wang, Zhuo; Danziger, Samuel A.; Heavner, Ben et al. · 2017 · PLoS Computational Biology · DOI

Full title: Combining inferred regulatory and reconstructed metabolic networks enhances phenotype prediction in yeast

Authors: Wang, Zhuo; Danziger, Samuel A.; Heavner, Ben; Ma, Shuyi; Smith, Jennifer J.; Song, Li; Herricks, Thurston; Simeonidis, Evangelos; Baliga, Nitin S.; Aitchison, John D.; Price, Nathan D.

Year: 2017

Venue: PLoS Computational Biology

Paper Bioenergetics-based modeling of Plasmodium falciparum metabolism reveals its essential genes, nutritional requirements, and thermodynamic bottlenecks

Chiappino-Pepe, Anush; Tymoshenko, Stepan; Ataman, Meriç et al. · 2017 · PLoS Computational Biology · DOI

Full title: Bioenergetics-based modeling of Plasmodium falciparum metabolism reveals its essential genes, nutritional requirements, and thermodynamic bottlenecks

Authors: Chiappino-Pepe, Anush; Tymoshenko, Stepan; Ataman, Meriç; Soldati‐Favre, Dominique; Hatzimanikatis, Vassily

Year: 2017

Venue: PLoS Computational Biology

DOI: https://doi.org/10.1371/journal.pcbi.1005397

Paper Metabolic dynamics restricted by conserved carriers: Jamming and feedback

Hatakeyama, Tetsuhiro; Furusawa, Chikara · 2017 · PLoS Computational Biology · DOI

Full title: Metabolic dynamics restricted by conserved carriers: Jamming and feedback

Authors: Hatakeyama, Tetsuhiro; Furusawa, Chikara

Year: 2017

Venue: PLoS Computational Biology

DOI: https://doi.org/10.1371/journal.pcbi.1005847

Paper Managing uncertainty in metabolic network structure and improving predictions using EnsembleFBA

Biggs, Matthew B.; Papin, Jason A. · 2017 · PLoS Computational Biology · DOI

Full title: Managing uncertainty in metabolic network structure and improving predictions using EnsembleFBA

Authors: Biggs, Matthew B.; Papin, Jason A.

Year: 2017

Venue: PLoS Computational Biology

DOI: https://doi.org/10.1371/journal.pcbi.1005413

Paper Population FBA predicts metabolic phenotypes in yeast

Labhsetwar, Piyush; Melo, Marcelo C. R.; Cole, John A. et al. · 2017 · PLoS Computational Biology · DOI

Full title: Population FBA predicts metabolic phenotypes in yeast

Authors: Labhsetwar, Piyush; Melo, Marcelo C. R.; Cole, John A.; Luthey‐Schulten, Zaida

Year: 2017

Venue: PLoS Computational Biology

DOI: https://doi.org/10.1371/journal.pcbi.1005728

Paper OptRAM: In-silico strain design via integrative regulatory-metabolic network modeling.

Shen, Fangzhou; Sun, Renliang; Yao, Jie et al. · 2019 · PLoS computational biology · DOI

Full title: OptRAM: In-silico strain design via integrative regulatory-metabolic network modeling.

Authors: Shen, Fangzhou; Sun, Renliang; Yao, Jie; Li, Jian; Liu, Qian; Price, Nathan D; Liu, Chenguang; Wang, Zhuo

Year: 2019

Venue: PLoS computational biology

DOI: https://doi.org/10.1371/journal.pcbi.1006835

Paper BacArena: Individual-based metabolic modeling of heterogeneous microbes in complex communities

Bauer, Eugen; Zimmermann, Johannes; Baldini, Federico et al. · 2017 · PLoS Computational Biology · DOI

Full title: BacArena: Individual-based metabolic modeling of heterogeneous microbes in complex communities

Authors: Bauer, Eugen; Zimmermann, Johannes; Baldini, Federico; Thiele, Ines; Kaleta, Christoph

Year: 2017

Venue: PLoS Computational Biology

DOI: https://doi.org/10.1371/journal.pcbi.1005544

Paper redGEM: Systematic reduction and analysis of genome-scale metabolic reconstructions for development of consistent core metabolic models

Ataman, Meriç; Gardiol, Daniel F. Hernandez; Fengos, Georgios et al. · 2017 · PLoS Computational Biology · DOI

Full title: redGEM: Systematic reduction and analysis of genome-scale metabolic reconstructions for development of consistent core metabolic models

Authors: Ataman, Meriç; Gardiol, Daniel F. Hernandez; Fengos, Georgios; Hatzimanikatis, Vassily

Year: 2017

Venue: PLoS Computational Biology

DOI: https://doi.org/10.1371/journal.pcbi.1005444

Paper Characterizing steady states of genome-scale metabolic networks in continuous cell cultures

Fernández-de-Cossio-Díaz, Jorge; León, Kalet; Mulet, Roberto · 2017 · PLoS Computational Biology · DOI

Full title: Characterizing steady states of genome-scale metabolic networks in continuous cell cultures

Authors: Fernández-de-Cossio-Díaz, Jorge; León, Kalet; Mulet, Roberto

Year: 2017

Venue: PLoS Computational Biology

DOI: https://doi.org/10.1371/journal.pcbi.1005835

Paper BOFdat: Generating biomass objective functions for genome-scale metabolic models from experimental data

Lachance, Jean‐Christophe; Lloyd, Colton J.; Monk, Jonathan M. et al. · 2019 · PLoS Computational Biology · DOI

Full title: BOFdat: Generating biomass objective functions for genome-scale metabolic models from experimental data

Authors: Lachance, Jean‐Christophe; Lloyd, Colton J.; Monk, Jonathan M.; Yang, Laurence; Sastry, Anand V.; Seif, Yara; Palsson, Bernhard Ø.; Rodrigue, Sébastien; Feist, Adam M.; King, Zachary A.; Jacques, Pierre‐Étienne

Year: 2019

Venue: PLoS Computational Biology

DOI: https://doi.org/10.1371/journal.pcbi.1006971

Paper Quantification and Classification of E. coli Proteome Utilization and Unused Protein Costs across Environments

O’Brien, Edward J.; Utrilla, José; Palsson, Bernhard Ø. · 2016 · PLoS Computational Biology · DOI

Full title: Quantification and Classification of E. coli Proteome Utilization and Unused Protein Costs across Environments

Authors: O’Brien, Edward J.; Utrilla, José; Palsson, Bernhard Ø.

Year: 2016

Venue: PLoS Computational Biology

DOI: https://doi.org/10.1371/journal.pcbi.1004998

Paper The number of active metabolic pathways is bounded by the number of cellular constraints at maximal metabolic rates

Groot, Daan H. de; Boxtel, Coco van; Planqué, Robert et al. · 2019 · PLoS Computational Biology · DOI

Full title: The number of active metabolic pathways is bounded by the number of cellular constraints at maximal metabolic rates

Authors: Groot, Daan H. de; Boxtel, Coco van; Planqué, Robert; Bruggeman, Frank J.; Teusink, Bas

Year: 2019

Venue: PLoS Computational Biology

Paper Machine and deep learning meet genome-scale metabolic modeling

Zampieri, Guido; Vijayakumar, Supreeta; Yaneske, Elisabeth et al. · 2019 · PLoS Computational Biology · DOI

Full title: Machine and deep learning meet genome-scale metabolic modeling

Authors: Zampieri, Guido; Vijayakumar, Supreeta; Yaneske, Elisabeth; Angione, Claudio

Year: 2019

Venue: PLoS Computational Biology

DOI: https://doi.org/10.1371/journal.pcbi.1007084

Paper From Escherichia coli mutant 13C labeling data to a core kinetic model: A kinetic model parameterization pipeline

Foster, Charles; Gopalakrishnan, Saratram; Antoniewicz, Maciek R. et al. · 2019 · PLoS Computational Biology · DOI

Full title: From Escherichia coli mutant 13C labeling data to a core kinetic model: A kinetic model parameterization pipeline

Authors: Foster, Charles; Gopalakrishnan, Saratram; Antoniewicz, Maciek R.; Maranas, Costas D.

Year: 2019

Venue: PLoS Computational Biology

DOI: https://doi.org/10.1371/journal.pcbi.1007319

Paper Enhanced flux prediction by integrating relative expression and relative metabolite abundance into thermodynamically consistent metabolic models

Pandey, Vikash; Hadadi, Noushin; Hatzimanikatis, Vassily · 2019 · PLoS Computational Biology · DOI

Full title: Enhanced flux prediction by integrating relative expression and relative metabolite abundance into thermodynamically consistent metabolic models

Authors: Pandey, Vikash; Hadadi, Noushin; Hatzimanikatis, Vassily

Year: 2019

Venue: PLoS Computational Biology

DOI: https://doi.org/10.1371/journal.pcbi.1007036

Paper A steady-state model of microbial acclimation to substrate limitation

Casey, John R.; Follows, Michael J. · 2020 · PLoS Computational Biology · DOI

Full title: A steady-state model of microbial acclimation to substrate limitation

Authors: Casey, John R.; Follows, Michael J.

Year: 2020

Venue: PLoS Computational Biology

DOI: https://doi.org/10.1371/journal.pcbi.1008140

Paper Statistical inference in ensemble modeling of cellular metabolism

Tuure, Hameri; Boldi, Marc‐Olivier; Hatzimanikatis, Vassily · 2019 · PLoS Computational Biology · DOI

Full title: Statistical inference in ensemble modeling of cellular metabolism

Authors: Tuure, Hameri; Boldi, Marc‐Olivier; Hatzimanikatis, Vassily

Year: 2019

Venue: PLoS Computational Biology

DOI: https://doi.org/10.1371/journal.pcbi.1007536

Paper Bayesian inference of metabolic kinetics from genome-scale multiomics data

John, Peter C. St.; Strutz, Jonathan; Broadbelt, Linda J. et al. · 2019 · PLoS Computational Biology · DOI

Full title: Bayesian inference of metabolic kinetics from genome-scale multiomics data

Authors: John, Peter C. St.; Strutz, Jonathan; Broadbelt, Linda J.; Tyo, Keith E. J.; Bomble, Yannick J.

Year: 2019

Venue: PLoS Computational Biology

DOI: https://doi.org/10.1371/journal.pcbi.1007424

Paper Dissecting the regulatory roles of ORM proteins in the sphingolipid pathway of plants

Alsiyabi, Adil; González‐Solís, Ariadna; Cahoon, Edgar B. et al. · 2021 · PLoS Computational Biology · DOI

Full title: Dissecting the regulatory roles of ORM proteins in the sphingolipid pathway of plants

Authors: Alsiyabi, Adil; González‐Solís, Ariadna; Cahoon, Edgar B.; Saha, Rajib

Year: 2021

Venue: PLoS Computational Biology

DOI: https://doi.org/10.1371/journal.pcbi.1008284

Paper BayFlux: A Bayesian method to quantify metabolic Fluxes and their uncertainty at the genome scale

Backman, Tyler W. H.; Schenk, Christina; Radivojević, Tijana et al. · 2023 · PLoS Computational Biology · DOI

Full title: BayFlux: A Bayesian method to quantify metabolic Fluxes and their uncertainty at the genome scale

Authors: Backman, Tyler W. H.; Schenk, Christina; Radivojević, Tijana; Ando, David; Singh, Jahnavi; Czajka, Jeffrey J.; Costello, Zak; Keasling, Jay D.; Tang, Yinjie; Akhmatskaya, Elena; Martín, Héctor García

Year: 2023

Venue: PLoS Computational Biology

DOI: https://doi.org/10.1371/journal.pcbi.1011111

Paper Physicochemical and metabolic constraints for thermodynamics-based stoichiometric modelling under mesophilic growth conditions

Tomi-Andrino, Claudio; Norman, Rupert; Millat, Thomas et al. · 2021 · PLoS Computational Biology · DOI

Full title: Physicochemical and metabolic constraints for thermodynamics-based stoichiometric modelling under mesophilic growth conditions

Authors: Tomi-Andrino, Claudio; Norman, Rupert; Millat, Thomas; Soucaille, Philippe; Winzer, Klaus; Barrett, David A.; King, John R.; Kim, Dong‐Hyun

Year: 2021

Venue: PLoS Computational Biology

DOI: https://doi.org/10.1371/journal.pcbi.1007694

Paper Genetic buffering and potentiation in metabolism

Poyatos, Juan F. · 2020 · PLoS Computational Biology · DOI

Full title: Genetic buffering and potentiation in metabolism

Authors: Poyatos, Juan F.

Year: 2020

Venue: PLoS Computational Biology

DOI: https://doi.org/10.1371/journal.pcbi.1008185

Paper MASSpy: Building, simulating, and visualizing dynamic biological models in Python using mass action kinetics

Haiman, Zachary B.; Zielinski, Daniel C.; Koike, Yuko et al. · 2021 · PLoS Computational Biology · DOI

Full title: MASSpy: Building, simulating, and visualizing dynamic biological models in Python using mass action kinetics

Authors: Haiman, Zachary B.; Zielinski, Daniel C.; Koike, Yuko; Yurkovich, James T.; Palsson, Bernhard Ø.

Year: 2021

Venue: PLoS Computational Biology

DOI: https://doi.org/10.1371/journal.pcbi.1008208

Paper Computation of condition-dependent proteome allocation reveals variability in the macro and micro nutrient requirements for growth

Lloyd, Colton J.; Monk, Jonathan M.; Yang, Laurence et al. · 2021 · PLoS Computational Biology · DOI

Full title: Computation of condition-dependent proteome allocation reveals variability in the macro and micro nutrient requirements for growth

Authors: Lloyd, Colton J.; Monk, Jonathan M.; Yang, Laurence; Ebrahim, Ali; Palsson, Bernhard Ø.

Year: 2021

Venue: PLoS Computational Biology

Paper Model-driven analysis of mutant fitness experiments improves genome-scale metabolic models of Zymomonas mobilis ZM4

Ong, Wai Kit; Courtney, Dylan K.; Pan, Shu et al. · 2020 · PLoS Computational Biology · DOI

Full title: Model-driven analysis of mutant fitness experiments improves genome-scale metabolic models of Zymomonas mobilis ZM4

Authors: Ong, Wai Kit; Courtney, Dylan K.; Pan, Shu; Andrade, Ramon Bonela; Kiley, Patricia J.; Pfleger, Brian F.; Reed, Jennifer L.

Year: 2020

Venue: PLoS Computational Biology

DOI: https://doi.org/10.1371/journal.pcbi.1008137

Paper Strain design optimization using reinforcement learning

Sabzevari, Maryam; Szedmák, Sándor; Penttilä, Merja et al. · 2022 · PLoS Computational Biology · DOI

Full title: Strain design optimization using reinforcement learning

Authors: Sabzevari, Maryam; Szedmák, Sándor; Penttilä, Merja; Jouhten, Paula; Rousu, Juho

Year: 2022

Venue: PLoS Computational Biology

Paper Bacterial fitness landscapes stratify based on proteome allocation associated with discrete aero-types

Chen, Ke; Anand, Amitesh; Olson, Connor A. et al. · 2021 · PLoS Computational Biology · DOI

Full title: Bacterial fitness landscapes stratify based on proteome allocation associated with discrete aero-types

Authors: Chen, Ke; Anand, Amitesh; Olson, Connor A.; Sandberg, Troy E.; Gao, Ye; Mih, Nathan; Palsson, Bernhard Ø.

Year: 2021

Venue: PLoS Computational Biology

DOI: https://doi.org/10.1371/journal.pcbi.1008596

Paper Bridging the gap between mechanistic biological models and machine learning surrogates

Gherman, Ioana M.; Abdallah, Zahraa S.; Pang, Wei et al. · 2023 · PLoS Computational Biology · DOI

Full title: Bridging the gap between mechanistic biological models and machine learning surrogates

Authors: Gherman, Ioana M.; Abdallah, Zahraa S.; Pang, Wei; Gorochowski, Thomas E.; Grierson, Claire; Marucci, Lucia

Year: 2023

Venue: PLoS Computational Biology

Paper Flux balance analysis of the ammonia-oxidizing bacterium Nitrosomonas europaea ATCC19718 unravels specific metabolic activities while degrading toxic compounds

Gabriela Canto-Encalada; Diego Tec-Campos; Juan D. Tibocha-Bonilla et al. · 2022 · PLoS Comput. Biol. · DOI

Full title: Flux balance analysis of the ammonia-oxidizing bacterium Nitrosomonas europaea ATCC19718 unravels specific metabolic activities while degrading toxic compounds

Authors: Gabriela Canto-Encalada; Diego Tec-Campos; Juan D. Tibocha-Bonilla; K. Zengler; A. Zepeda; C. Zúñiga

Year: 2022

Venue: PLoS Comput. Biol.

DOI: https://doi.org/10.1371/journal.pcbi.1009828

Paper Genome-scale metabolic modeling of the human gut bacterium Bacteroides fragilis strain 638R

Neal, M J; Thiruppathy, Deepan; Zengler, Karsten · 2023 · PLoS Computational Biology · DOI

Full title: Genome-scale metabolic modeling of the human gut bacterium Bacteroides fragilis strain 638R

Authors: Neal, M J; Thiruppathy, Deepan; Zengler, Karsten

Year: 2023

Venue: PLoS Computational Biology

DOI: https://doi.org/10.1371/journal.pcbi.1011594

Paper Harnessing the optimization of enzyme catalytic rates in engineering of metabolic phenotypes

Zahra Razaghi-Moghadam; Fayaz Soleymani Babadi; Z. Nikoloski · 2024 · PLoS Comput. Biol. · DOI

Full title: Harnessing the optimization of enzyme catalytic rates in engineering of metabolic phenotypes

Authors: Zahra Razaghi-Moghadam; Fayaz Soleymani Babadi; Z. Nikoloski

Year: 2024

Venue: PLoS Comput. Biol.

DOI: https://doi.org/10.1371/journal.pcbi.1012576

Paper Epistatic Interaction Maps Relative to Multiple Metabolic Phenotypes

Snitkin, Evan S.; Segrè, Daniel · 2011 · PLoS Genetics · DOI

Full title: Epistatic Interaction Maps Relative to Multiple Metabolic Phenotypes

Authors: Snitkin, Evan S.; Segrè, Daniel

Year: 2011

Venue: PLoS Genetics

DOI: https://doi.org/10.1371/journal.pgen.1001294

Paper Flux balance analysis-based metabolic modeling of microbial secondary metabolism: Current status and outlook

Sizhe Qiu; Ai-ying Yang; H. Zeng · 2023 · PLoS Comput. Biol. · DOI

Full title: Flux balance analysis-based metabolic modeling of microbial secondary metabolism: Current status and outlook

Authors: Sizhe Qiu; Ai-ying Yang; H. Zeng

Year: 2023

Venue: PLoS Comput. Biol.

DOI: https://doi.org/10.1371/journal.pcbi.1011391

Paper The genome-scale metabolic model for the purple non-sulfur bacterium Rhodopseudomonas palustris Bis A53 accurately predicts phenotypes under chemoheterotrophic, chemoautotrophic, photoheterotrophic, and photoautotrophic growth conditions

Tec-Campos, Diego; Posadas, Camila; Tibocha‐Bonilla, Juan D. et al. · 2023 · PLoS Computational Biology · DOI

Full title: The genome-scale metabolic model for the purple non-sulfur bacterium Rhodopseudomonas palustris Bis A53 accurately predicts phenotypes under chemoheterotrophic, chemoautotrophic, photoheterotrophic, and photoautotrophic growth conditions

Authors: Tec-Campos, Diego; Posadas, Camila; Tibocha‐Bonilla, Juan D.; Thiruppathy, Deepan; Glonek, Nathan; Zúñiga, Cristal; Zepeda, Alejandro; Zengler, Karsten

Year: 2023

Venue: PLoS Computational Biology

DOI: https://doi.org/10.1371/journal.pcbi.1011371

Paper Inferring Carbon Sources from Gene Expression Profiles Using Metabolic Flux Models

Brandes, Aaron; Lun, Desmond S.; Ip, Kuhn et al. · 2012 · PLoS ONE · DOI

Full title: Inferring Carbon Sources from Gene Expression Profiles Using Metabolic Flux Models

Authors: Brandes, Aaron; Lun, Desmond S.; Ip, Kuhn; Zucker, Jeremy; Colijn, Caroline; Weiner, Brian; Galagan, James E.

Year: 2012

Venue: PLoS ONE

DOI: https://doi.org/10.1371/journal.pone.0036947

Paper Zea mays iRS1563: A Comprehensive Genome-Scale Metabolic Reconstruction of Maize Metabolism

Saha, Rajib; Suthers, Patrick F.; Maranas, Costas D. · 2011 · PLoS ONE · DOI

Full title: Zea mays iRS1563: A Comprehensive Genome-Scale Metabolic Reconstruction of Maize Metabolism

Authors: Saha, Rajib; Suthers, Patrick F.; Maranas, Costas D.

Year: 2011

Venue: PLoS ONE

DOI: https://doi.org/10.1371/journal.pone.0021784

Paper Exploring Metabolic Pathway Reconstruction and Genome-Wide Expression Profiling in Lactobacillus reuteri to Define Functional Probiotic Features

Saulnier, Delphine; Santos, Filipe Duarte; Roos, Stefan et al. · 2011 · PLoS ONE · DOI

Full title: Exploring Metabolic Pathway Reconstruction and Genome-Wide Expression Profiling in Lactobacillus reuteri to Define Functional Probiotic Features

Authors: Saulnier, Delphine; Santos, Filipe Duarte; Roos, Stefan; Mistretta, Toni-Ann; Spinler, Jennifer K.; Molenaar, Douwe; Teusink, Bas; Versalovic, James

Year: 2011

Venue: PLoS ONE

DOI: https://doi.org/10.1371/journal.pone.0018783

Paper Evolutionary Systems Biology of Amino Acid Biosynthetic Cost in Yeast

Barton, Michael D.; Delneri, Daniela; Oliver, Stephen G. et al. · 2010 · PLoS ONE · DOI

Full title: Evolutionary Systems Biology of Amino Acid Biosynthetic Cost in Yeast

Authors: Barton, Michael D.; Delneri, Daniela; Oliver, Stephen G.; Rattray, Magnus; Bergman, Casey

Year: 2010

Venue: PLoS ONE

DOI: https://doi.org/10.1371/journal.pone.0011935

Paper A genome-scale metabolic model for the denitrifying bacterium Thauera sp. MZ1T accurately predicts degradation of pollutants and production of polymers

Tec-Campos, Diego; Tibocha‐Bonilla, Juan D.; Jiang, Chunguo et al. · 2025 · PLoS Computational Biology · DOI

Full title: A genome-scale metabolic model for the denitrifying bacterium Thauera sp. MZ1T accurately predicts degradation of pollutants and production of polymers

Authors: Tec-Campos, Diego; Tibocha‐Bonilla, Juan D.; Jiang, Chunguo; Passi, Anurag; Thiruppathy, Deepan; Zúñiga, Cristal; Posadas, Camila; Zepeda, Alejandro; Zengler, Karsten

Year: 2025

Venue: PLoS Computational Biology

DOI: https://doi.org/10.1371/journal.pcbi.1012736

Paper Genome-Scale Consequences of Cofactor Balancing in Engineered Pentose Utilization Pathways in Saccharomyces cerevisiae

Ghosh, Amit; Zhao, Huimin; Price, Nathan D. · 2011 · PLoS ONE · DOI

Full title: Genome-Scale Consequences of Cofactor Balancing in Engineered Pentose Utilization Pathways in Saccharomyces cerevisiae

Authors: Ghosh, Amit; Zhao, Huimin; Price, Nathan D.

Year: 2011

Venue: PLoS ONE

DOI: https://doi.org/10.1371/journal.pone.0027316

Paper Characterization of the Metabolic Requirements in Yeast Meiosis

Ray, Debjit; Ye, Ping · 2013 · PLoS ONE · DOI

Full title: Characterization of the Metabolic Requirements in Yeast Meiosis

Authors: Ray, Debjit; Ye, Ping

Year: 2013

Venue: PLoS ONE

DOI: https://doi.org/10.1371/journal.pone.0063707

Paper Genome-Scale Reconstruction and Analysis of the Metabolic Network in the Hyperthermophilic Archaeon Sulfolobus Solfataricus

Ulas, Thomas; Riemer, S. Alexander; Zaparty, Melanie et al. · 2012 · PLoS ONE · DOI

Full title: Genome-Scale Reconstruction and Analysis of the Metabolic Network in the Hyperthermophilic Archaeon Sulfolobus Solfataricus

Authors: Ulas, Thomas; Riemer, S. Alexander; Zaparty, Melanie; Siebers, Bettina; Schomburg, Dietmar

Year: 2012

Venue: PLoS ONE

DOI: https://doi.org/10.1371/journal.pone.0043401

Paper Reconstruction and In Silico Analysis of Metabolic Network for an Oleaginous Yeast, Yarrowia lipolytica

Pan, Pengcheng; Hua, Qiang · 2012 · PLoS ONE · DOI

Full title: Reconstruction and In Silico Analysis of Metabolic Network for an Oleaginous Yeast, Yarrowia lipolytica

Authors: Pan, Pengcheng; Hua, Qiang

Year: 2012

Venue: PLoS ONE

DOI: https://doi.org/10.1371/journal.pone.0051535

Paper Identification of Metabolic Engineering Targets through Analysis of Optimal and Sub-Optimal Routes

Soons, Zita; Ferreira, Eugénio C.; Patil, Kiran Raosaheb et al. · 2013 · PLoS ONE · DOI

Full title: Identification of Metabolic Engineering Targets through Analysis of Optimal and Sub-Optimal Routes

Authors: Soons, Zita; Ferreira, Eugénio C.; Patil, Kiran Raosaheb; Rocha, Isabel

Year: 2013

Venue: PLoS ONE

DOI: https://doi.org/10.1371/journal.pone.0061648

Paper Fumaric Acid Production in Saccharomyces cerevisiae by In Silico Aided Metabolic Engineering

Xu, Guoqiang; Zou, Wei; Chen, Xiulai et al. · 2012 · PLoS ONE · DOI

Full title: Fumaric Acid Production in Saccharomyces cerevisiae by In Silico Aided Metabolic Engineering

Authors: Xu, Guoqiang; Zou, Wei; Chen, Xiulai; Xu, Nan; Liu, Li; Chen, Jian

Year: 2012

Venue: PLoS ONE

DOI: https://doi.org/10.1371/journal.pone.0052086

Paper ReacKnock: Identifying Reaction Deletion Strategies for Microbial Strain Optimization Based on Genome-Scale Metabolic Network

Xu, Zixiang; Zheng, Ping; Sun, Jibin et al. · 2013 · PLoS ONE · DOI

Full title: ReacKnock: Identifying Reaction Deletion Strategies for Microbial Strain Optimization Based on Genome-Scale Metabolic Network

Authors: Xu, Zixiang; Zheng, Ping; Sun, Jibin; Ma, Yanhe

Year: 2013

Venue: PLoS ONE

DOI: https://doi.org/10.1371/journal.pone.0072150

Paper Multiscale Modeling of Metabolism and Macromolecular Synthesis in E. coli and Its Application to the Evolution of Codon Usage

Thiele, Ines; Fleming, Ronan M. T.; Que, Richard et al. · 2012 · PLoS ONE · DOI

Full title: Multiscale Modeling of Metabolism and Macromolecular Synthesis in E. coli and Its Application to the Evolution of Codon Usage

Authors: Thiele, Ines; Fleming, Ronan M. T.; Que, Richard; Bordbar, Aarash; Diep, Dinh; Palsson, Bernhard Ø.

Year: 2012

Venue: PLoS ONE

DOI: https://doi.org/10.1371/journal.pone.0045635

Paper Construction and Analysis of the Model of Energy Metabolism in E. coli

Xu, Zixiang; Sun, Xiao; Sun, Jibin · 2013 · PLoS ONE · DOI

Full title: Construction and Analysis of the Model of Energy Metabolism in E. coli

Authors: Xu, Zixiang; Sun, Xiao; Sun, Jibin

Year: 2013

Venue: PLoS ONE

DOI: https://doi.org/10.1371/journal.pone.0055137

Paper Maximal Sum of Metabolic Exchange Fluxes Outperforms Biomass Yield as a Predictor of Growth Rate of Microorganisms

Zarecki, Raphy; Oberhardt, Matthew; Yizhak, Keren et al. · 2014 · PLoS ONE · DOI

Full title: Maximal Sum of Metabolic Exchange Fluxes Outperforms Biomass Yield as a Predictor of Growth Rate of Microorganisms

Authors: Zarecki, Raphy; Oberhardt, Matthew; Yizhak, Keren; Wagner, Allon; Segal, E.; Freilich, Shiri; Henry, Christopher S.; Gophna, Uri; Ruppin, Eytan

Year: 2014

Venue: PLoS ONE

DOI: https://doi.org/10.1371/journal.pone.0098372

Paper Genome-Scale NAD(H/+) Availability Patterns as a Differentiating Feature between Saccharomyces cerevisiae and Scheffersomyces stipitis in Relation to Fermentative Metabolism

Acevedo, Alejandro; Aroca, Germán; Conejeros, Raúl · 2014 · PLoS ONE · DOI

Full title: Genome-Scale NAD(H/+) Availability Patterns as a Differentiating Feature between Saccharomyces cerevisiae and Scheffersomyces stipitis in Relation to Fermentative Metabolism

Authors: Acevedo, Alejandro; Aroca, Germán; Conejeros, Raúl

Year: 2014

Venue: PLoS ONE

DOI: https://doi.org/10.1371/journal.pone.0087494

Paper Rapid Countermeasure Discovery against Francisella tularensis Based on a Metabolic Network Reconstruction

Chaudhury, Sidhartha; AbdulHameed, Mohamed Diwan M.; Singh, Narender et al. · 2013 · PLoS ONE · DOI

Full title: Rapid Countermeasure Discovery against Francisella tularensis Based on a Metabolic Network Reconstruction

Authors: Chaudhury, Sidhartha; AbdulHameed, Mohamed Diwan M.; Singh, Narender; Tawa, Gregory J.; D’haeseleer, Patrik; Zemła, Adam; Navid, Ali; Zhou, Carol E.; Franklin, Matthew C.; Cheung, Jonah; Rudolph, M.; Love, J.; Graf, John; Rozak, David A.; Dankmeyer, Jennifer L.; Amemiya, Kei; Daefler, Simon; Wallqvist, Anders

Year: 2013

Venue: PLoS ONE

DOI: https://doi.org/10.1371/journal.pone.0063369

Paper Combining Chemoinformatics with Bioinformatics: In Silico Prediction of Bacterial Flavor-Forming Pathways by a Chemical Systems Biology Approach “Reverse Pathway Engineering”

Liu, Mengjin; Bienfait, Bruno; Sacher, Oliver et al. · 2014 · PLoS ONE · DOI

Full title: Combining Chemoinformatics with Bioinformatics: In Silico Prediction of Bacterial Flavor-Forming Pathways by a Chemical Systems Biology Approach “Reverse Pathway Engineering”

Authors: Liu, Mengjin; Bienfait, Bruno; Sacher, Oliver; Gasteiger, Johann; Siezen, Roland J.; Nauta, Arjen; Geurts, Jan M.W.

Year: 2014

Venue: PLoS ONE

DOI: https://doi.org/10.1371/journal.pone.0084769

Paper Industrial Systems Biology of Saccharomyces cerevisiae Enables Novel Succinic Acid Cell Factory

Otero, José M.; Cimini, Donatella; Patil, Kiran Raosaheb et al. · 2013 · PLoS ONE · DOI

Full title: Industrial Systems Biology of Saccharomyces cerevisiae Enables Novel Succinic Acid Cell Factory

Authors: Otero, José M.; Cimini, Donatella; Patil, Kiran Raosaheb; Poulsen, Simon G.; Olsson, Lisbeth; Nielsen, Jens

Year: 2013

Venue: PLoS ONE

DOI: https://doi.org/10.1371/journal.pone.0054144

Paper Reconstruction and Comparison of the Metabolic Potential of Cyanobacteria Cyanothece sp. ATCC 51142 and Synechocystis sp. PCC 6803

Saha, Rajib; Verseput, Alex T.; Berla, Bertram M. et al. · 2012 · PLoS ONE · DOI

Full title: Reconstruction and Comparison of the Metabolic Potential of Cyanobacteria Cyanothece sp. ATCC 51142 and Synechocystis sp. PCC 6803

Authors: Saha, Rajib; Verseput, Alex T.; Berla, Bertram M.; Mueller, Thomas J. J.; Pakrasi, Himadri B.; Maranas, Costas D.

Year: 2012

Venue: PLoS ONE

DOI: https://doi.org/10.1371/journal.pone.0048285

Paper Integration of enzymatic data in Bacillus subtilis genome-scale metabolic model improves phenotype predictions and enables in silico design of poly-γ-glutamic acid production strains.

Massaiu, Ilaria; Pasotti, Lorenzo; Sonnenschein, Nikolaus et al. · 2019 · Microbial cell factories · DOI

Full title: Integration of enzymatic data in Bacillus subtilis genome-scale metabolic model improves phenotype predictions and enables in silico design of poly-γ-glutamic acid production strains.

Authors: Massaiu, Ilaria; Pasotti, Lorenzo; Sonnenschein, Nikolaus; Rama, Erlinda; Cavaletti, Matteo; Magni, Paolo; Calvio, Cinzia; Herrgård, Markus J

Year: 2019

Venue: Microbial cell factories

DOI: https://doi.org/10.1186/s12934-018-1052-2

Paper Engineering microbial consortia by division of labor

Roell, Garrett W.; Zha, Jian; Carr, Rhiannon et al. · 2019 · Microbial Cell Factories · DOI

Full title: Engineering microbial consortia by division of labor

Authors: Roell, Garrett W.; Zha, Jian; Carr, Rhiannon; Koffas, Mattheos; Fong, Stephen S.; Tang, Yinjie

Year: 2019

Venue: Microbial Cell Factories

DOI: https://doi.org/10.1186/s12934-019-1083-3

Paper Metabolic role of pyrophosphate-linked phosphofructokinase pfk for C1 assimilation in Methylotuvimicrobium alcaliphilum 20Z

Nguyen, Anh Duc; Nam, Gayoung; Kim, Donghyuk et al. · 2020 · Microbial Cell Factories · DOI

Full title: Metabolic role of pyrophosphate-linked phosphofructokinase pfk for C1 assimilation in Methylotuvimicrobium alcaliphilum 20Z

Authors: Nguyen, Anh Duc; Nam, Gayoung; Kim, Donghyuk; Lee, Eun Yeol

Year: 2020

Venue: Microbial Cell Factories

DOI: https://doi.org/10.1186/s12934-020-01382-5

Paper Strain engineering and metabolic flux analysis of a probiotic yeast Saccharomyces boulardii for metabolizing l-fucose, a mammalian mucin component

Kim, Jungyeon; Cheong, Yu Eun; Yu, Sora et al. · 2022 · Microbial Cell Factories · DOI

Full title: Strain engineering and metabolic flux analysis of a probiotic yeast Saccharomyces boulardii for metabolizing l-fucose, a mammalian mucin component

Authors: Kim, Jungyeon; Cheong, Yu Eun; Yu, Sora; Jin, Yong-Su; Kim, Kyoung Heon

Year: 2022

Venue: Microbial Cell Factories

DOI: https://doi.org/10.1186/s12934-022-01926-x

Paper Improved production of Taxol® precursors in S. cerevisiae using combinatorial in silico design and metabolic engineering

Malcı, Koray; Santibáñez, Rodrigo; Jonguitud‐Borrego, Nestor et al. · 2023 · Microbial Cell Factories · DOI

Full title: Improved production of Taxol® precursors in S. cerevisiae using combinatorial in silico design and metabolic engineering

Authors: Malcı, Koray; Santibáñez, Rodrigo; Jonguitud‐Borrego, Nestor; Santoyo‐Garcia, Jorge H.; Kerkhoven, Eduard J.; Rios‐Solis, Leonardo

Year: 2023

Venue: Microbial Cell Factories

DOI: https://doi.org/10.1186/s12934-023-02251-7

Paper Metabolic engineering design to enhance (R,R)-2,3-butanediol production from glycerol in Bacillus subtilis based on flux balance analysis

Vikromvarasiri, Nunthaphan; Shirai, Tomokazu; Kondo, Akihiko · 2021 · Microbial Cell Factories · DOI

Full title: Metabolic engineering design to enhance (R,R)-2,3-butanediol production from glycerol in Bacillus subtilis based on flux balance analysis

Authors: Vikromvarasiri, Nunthaphan; Shirai, Tomokazu; Kondo, Akihiko

Year: 2021

Venue: Microbial Cell Factories

DOI: https://doi.org/10.1186/s12934-021-01688-y

Paper Resource-aware whole-cell model of division of labour in a microbial consortium for complex-substrate degradation

Atkinson, Eliza; Tuza, Zoltán A.; Perrino, Giansimone et al. · 2022 · Microbial Cell Factories · DOI

Full title: Resource-aware whole-cell model of division of labour in a microbial consortium for complex-substrate degradation

Authors: Atkinson, Eliza; Tuza, Zoltán A.; Perrino, Giansimone; Stan, Guy‐Bart; Ledesma‐Amaro, Rodrigo

Year: 2022

Venue: Microbial Cell Factories

DOI: https://doi.org/10.1186/s12934-022-01842-0

Paper Automation assisted anaerobic phenotyping for metabolic engineering

Raj, Kaushik; Venayak, Naveen; Diep, Patrick et al. · 2021 · Microbial Cell Factories · DOI

Full title: Automation assisted anaerobic phenotyping for metabolic engineering

Authors: Raj, Kaushik; Venayak, Naveen; Diep, Patrick; Golla, Sai Akhil; Yakunin, Alexander F.; Mahadevan, Radhakrishnan

Year: 2021

Venue: Microbial Cell Factories

DOI: https://doi.org/10.1186/s12934-021-01675-3

Paper Adaptation of central metabolite pools to variations in growth rate and cultivation conditions in Saccharomyces cerevisiae

Kumar, Kanhaiya; Venkatraman, Vishwesh; Bruheim, Per · 2021 · Microbial Cell Factories · DOI

Full title: Adaptation of central metabolite pools to variations in growth rate and cultivation conditions in Saccharomyces cerevisiae

Authors: Kumar, Kanhaiya; Venkatraman, Vishwesh; Bruheim, Per

Year: 2021

Venue: Microbial Cell Factories

DOI: https://doi.org/10.1186/s12934-021-01557-8

Paper High throughput 13C-metabolic flux analysis of 3-hydroxypropionic acid producing Pichia pastoris reveals limited availability of acetyl-CoA and ATP due to tight control of the glycolytic flux

Fina, Albert; Millard, Pierre; Albiol, Joan et al. · 2023 · Microbial Cell Factories · DOI

Full title: High throughput 13C-metabolic flux analysis of 3-hydroxypropionic acid producing Pichia pastoris reveals limited availability of acetyl-CoA and ATP due to tight control of the glycolytic flux

Authors: Fina, Albert; Millard, Pierre; Albiol, Joan; Ferrer, Pau; Heux, Stéphanie

Year: 2023

Venue: Microbial Cell Factories

DOI: https://doi.org/10.1186/s12934-023-02123-0

Paper FastKnock: an efficient next-generation approach to identify all knockout strategies for strain optimization

Hassani, Leila; Moosavi, Mohammad R.; Setoodeh, Payam et al. · 2024 · Microbial Cell Factories · DOI

Full title: FastKnock: an efficient next-generation approach to identify all knockout strategies for strain optimization

Authors: Hassani, Leila; Moosavi, Mohammad R.; Setoodeh, Payam; Zare, Habil

Year: 2024

Venue: Microbial Cell Factories

DOI: https://doi.org/10.1186/s12934-023-02277-x

Paper A novel engineered strain of Methylorubrum extorquens for methylotrophic production of glycolic acid

Dietz, K.-J.; Sagstetter, Carina; Speck, Melanie et al. · 2024 · Microbial Cell Factories · DOI

Full title: A novel engineered strain of Methylorubrum extorquens for methylotrophic production of glycolic acid

Authors: Dietz, K.-J.; Sagstetter, Carina; Speck, Melanie; Roth, Arne; Klamt, Steffen; Fabarius, Jonathan Thomas

Year: 2024

Venue: Microbial Cell Factories

DOI: https://doi.org/10.1186/s12934-024-02583-y

Paper Designing minimal microbial strains of desired functionality using a genetic algorithm

Nair, Govind; Jungreuthmayer, Christian; Hanscho, Michael et al. · 2015 · Algorithms for Molecular Biology · DOI

Full title: Designing minimal microbial strains of desired functionality using a genetic algorithm

Authors: Nair, Govind; Jungreuthmayer, Christian; Hanscho, Michael; Zanghellini, Jürgen

Year: 2015

Venue: Algorithms for Molecular Biology

DOI: https://doi.org/10.1186/s13015-015-0060-6

Paper Sulfate limitation increases specific plasmid DNA yield and productivity in E. coli fed-batch processes

Gotsmy, Mathias; Strobl, Florian; Weiß, Florian et al. · 2023 · Microbial Cell Factories · DOI

Full title: Sulfate limitation increases specific plasmid DNA yield and productivity in E. coli fed-batch processes

Authors: Gotsmy, Mathias; Strobl, Florian; Weiß, Florian; Gruber, Petra; Kraus, Barbara; Mairhofer, Juergen; Zanghellini, Jürgen

Year: 2023

Venue: Microbial Cell Factories

DOI: https://doi.org/10.1186/s12934-023-02248-2

Paper Engineering the synthetic β-alanine pathway in Komagataella phaffii for conversion of methanol into 3-hydroxypropionic acid

Àvila-Cabré, Sílvia; Pérez‐Trujillo, Míriam; Albiol, Joan et al. · 2023 · Microbial Cell Factories · DOI

Full title: Engineering the synthetic β-alanine pathway in Komagataella phaffii for conversion of methanol into 3-hydroxypropionic acid

Authors: Àvila-Cabré, Sílvia; Pérez‐Trujillo, Míriam; Albiol, Joan; Ferrer, Pau

Year: 2023

Venue: Microbial Cell Factories

DOI: https://doi.org/10.1186/s12934-023-02241-9

Paper Construction of an enzyme-constrained metabolic network model for Myceliophthora thermophila using machine learning-based kcat data.

Wang, Yutao; Mao, Zhitao; Dong, Jiacheng et al. · 2024 · Microbial cell factories · DOI

Full title: Construction of an enzyme-constrained metabolic network model for Myceliophthora thermophila using machine learning-based kcat data.

Authors: Wang, Yutao; Mao, Zhitao; Dong, Jiacheng; Zhang, Peiji; Gao, Qiang; Liu, Defei; Tian, Chaoguang; Ma, Hongwu

Year: 2024

Venue: Microbial cell factories

DOI: https://doi.org/10.1186/s12934-024-02415-z

Paper Mapping the landscape of metabolic goals of a cell

Zhao, Qi; Stettner, Arion; Reznik, Ed et al. · 2016 · Genome biology · DOI

Full title: Mapping the landscape of metabolic goals of a cell

Authors: Zhao, Qi; Stettner, Arion; Reznik, Ed; Paschalidis, Ioannis Ch.; Segrè, Daniel

Year: 2016

Venue: Genome biology

DOI: https://doi.org/10.1186/s13059-016-0968-2

Paper A systematic assessment of current genome-scale metabolic reconstruction tools

Mendoza, Sebastián N.; Olivier, Brett G.; Molenaar, Douwe et al. · 2019 · Genome biology · DOI

Full title: A systematic assessment of current genome-scale metabolic reconstruction tools

Authors: Mendoza, Sebastián N.; Olivier, Brett G.; Molenaar, Douwe; Teusink, Bas

Year: 2019

Venue: Genome biology

DOI: https://doi.org/10.1186/s13059-019-1769-1

Paper Addressing uncertainty in genome-scale metabolic model reconstruction and analysis

Bernstein, David B.; Sulheim, Snorre; Almaas, Eivind et al. · 2021 · Genome biology · DOI

Full title: Addressing uncertainty in genome-scale metabolic model reconstruction and analysis

Authors: Bernstein, David B.; Sulheim, Snorre; Almaas, Eivind; Segrè, Daniel

Year: 2021

Venue: Genome biology

DOI: https://doi.org/10.1186/s13059-021-02289-z

Paper Model-driven intracellular redox status modulation for increasing isobutanol production in Escherichia coli

Liu, Jiao; Qi, Haishan; Wang, Cheng et al. · 2015 · Biotechnology for Biofuels · DOI

Full title: Model-driven intracellular redox status modulation for increasing isobutanol production in Escherichia coli

Authors: Liu, Jiao; Qi, Haishan; Wang, Cheng; Wen, Jianping

Year: 2015

Venue: Biotechnology for Biofuels

DOI: https://doi.org/10.1186/s13068-015-0291-2

Paper Current status and applications of genome-scale metabolic models

Gu, Changdai; Kim, Gi Bae; Kim, Won Jun et al. · 2019 · Genome biology · DOI

Full title: Current status and applications of genome-scale metabolic models

Authors: Gu, Changdai; Kim, Gi Bae; Kim, Won Jun; Kim, Hyun Uk; Lee, Sang Yup

Year: 2019

Venue: Genome biology

DOI: https://doi.org/10.1186/s13059-019-1730-3

Paper Enumeration of minimal stoichiometric precursor sets in metabolic networks

Andrade, Ricardo; Wannagat, Martin; Klein, Cecília C. et al. · 2016 · Algorithms for Molecular Biology · DOI

Full title: Enumeration of minimal stoichiometric precursor sets in metabolic networks

Authors: Andrade, Ricardo; Wannagat, Martin; Klein, Cecília C.; Acuña, Vicente; Marchetti-Spaccamela, Alberto; Milreu, Paulo V.; Stougie, Leen; Sagot, Marie-France

Year: 2016

Venue: Algorithms for Molecular Biology

DOI: https://doi.org/10.1186/s13015-016-0087-3

Paper Capturing the response of Clostridium acetobutylicumto chemical stressors using a regulated genome-scale metabolic model

Dash, Satyakam; Mueller, Thomas J. J.; Venkataramanan, Keerthi P. et al. · 2014 · Biotechnology for Biofuels · DOI

Full title: Capturing the response of Clostridium acetobutylicumto chemical stressors using a regulated genome-scale metabolic model

Authors: Dash, Satyakam; Mueller, Thomas J. J.; Venkataramanan, Keerthi P.; Papoutsakis, Eleftherios T.; Maranas, Costas D.

Year: 2014

Venue: Biotechnology for Biofuels

DOI: https://doi.org/10.1186/s13068-014-0144-4

Paper Enhancement of photosynthetic isobutanol production in engineered cells of Synechocystis PCC 6803

Miao, Rui; Xie, Hao; Lindblad, Peter · 2018 · Biotechnology for Biofuels · DOI

Full title: Enhancement of photosynthetic isobutanol production in engineered cells of Synechocystis PCC 6803

Authors: Miao, Rui; Xie, Hao; Lindblad, Peter

Year: 2018

Venue: Biotechnology for Biofuels

DOI: https://doi.org/10.1186/s13068-018-1268-8

Paper Insight into metabolic pathways of the potential biofuel producer, Paenibacillus polymyxa ICGEB2008

Adlakha, Nidhi; Pfau, Thomas; Ebenhöh, Oliver et al. · 2015 · Biotechnology for Biofuels · DOI

Full title: Insight into metabolic pathways of the potential biofuel producer, Paenibacillus polymyxa ICGEB2008

Authors: Adlakha, Nidhi; Pfau, Thomas; Ebenhöh, Oliver; Yazdani, Syed Shams

Year: 2015

Venue: Biotechnology for Biofuels

DOI: https://doi.org/10.1186/s13068-015-0338-4

Paper Engineering Yarrowia lipolytica to produce biodiesel from raw starch

Ledesma‐Amaro, Rodrigo; Dulermo, Thierry; Nicaud, Jean‐Marc · 2015 · Biotechnology for Biofuels · DOI

Full title: Engineering Yarrowia lipolytica to produce biodiesel from raw starch

Authors: Ledesma‐Amaro, Rodrigo; Dulermo, Thierry; Nicaud, Jean‐Marc

Year: 2015

Venue: Biotechnology for Biofuels

DOI: https://doi.org/10.1186/s13068-015-0335-7

Paper Exploring complex cellular phenotypes and model-guided strain design with a novel genome-scale metabolic model of Clostridium thermocellum DSM 1313 implementing an adjustable cellulosome

Thompson, R. Adam; Dahal, Sanjeev; Garcia, Sergio et al. · 2016 · Biotechnology for Biofuels · DOI

Full title: Exploring complex cellular phenotypes and model-guided strain design with a novel genome-scale metabolic model of Clostridium thermocellum DSM 1313 implementing an adjustable cellulosome

Authors: Thompson, R. Adam; Dahal, Sanjeev; Garcia, Sergio; Nookaew, Intawat; Trinh, Cong T.

Year: 2016

Venue: Biotechnology for Biofuels

DOI: https://doi.org/10.1186/s13068-016-0607-x

Paper A new genome-scale metabolic model of Corynebacterium glutamicum and its application

Zhang, Yu; Cai, Jingyi; Shang, Xiuling et al. · 2017 · Biotechnology for Biofuels · DOI

Full title: A new genome-scale metabolic model of Corynebacterium glutamicum and its application

Authors: Zhang, Yu; Cai, Jingyi; Shang, Xiuling; Wang, Bo; Liu, Shuwen; Chai, Xin; Tan, Tianwei; Zhang, Yun; Wen, Tingyi

Year: 2017

Venue: Biotechnology for Biofuels

DOI: https://doi.org/10.1186/s13068-017-0856-3

Paper Transcriptional program for nitrogen starvation-induced lipid accumulation in Chlamydomonas reinhardtii

Lomana, Adrián López García de; Schäuble, Sascha; Valenzuela, Jacob J. et al. · 2015 · Biotechnology for Biofuels · DOI

Full title: Transcriptional program for nitrogen starvation-induced lipid accumulation in Chlamydomonas reinhardtii

Authors: Lomana, Adrián López García de; Schäuble, Sascha; Valenzuela, Jacob J.; Imam, Saheed; Carter, Warren; Bilgin, Damla D.; Yohn, Christopher B.; Turkarslan, Serdar; Reiss, David J.; Orellana, Mónica V.; Price, Nathan D.; Baliga, Nitin S.

Year: 2015

Venue: Biotechnology for Biofuels

DOI: https://doi.org/10.1186/s13068-015-0391-z

Paper Model-based driving mechanism analysis for butyric acid production in Clostridium tyrobutyricum

Feng, Jun; Guo, Xiaolong; Cai, Feifei et al. · 2022 · Biotechnology for Biofuels and Bioproducts · DOI

Full title: Model-based driving mechanism analysis for butyric acid production in Clostridium tyrobutyricum

Authors: Feng, Jun; Guo, Xiaolong; Cai, Feifei; Fu, Hongxin; Wang, Jufang

Year: 2022

Venue: Biotechnology for Biofuels and Bioproducts

DOI: https://doi.org/10.1186/s13068-022-02169-z

Paper A design–build–test cycle using modeling and experiments reveals interdependencies between upper glycolysis and xylose uptake in recombinant S. cerevisiae and improves predictive capabilities of large-scale kinetic models

Mišković, Ljubiša; Alff-Tuomala, Susanne; Soh, Keng Cher et al. · 2017 · Biotechnology for Biofuels · DOI

Full title: A design–build–test cycle using modeling and experiments reveals interdependencies between upper glycolysis and xylose uptake in recombinant S. cerevisiae and improves predictive capabilities of large-scale kinetic models

Authors: Mišković, Ljubiša; Alff-Tuomala, Susanne; Soh, Keng Cher; Barth, Dorothee; Salusjärvi, Laura; Pitkänen, Juha‐Pekka; Ruohonen, Laura; Penttilä, Merja; Hatzimanikatis, Vassily

Year: 2017

Venue: Biotechnology for Biofuels

DOI: https://doi.org/10.1186/s13068-017-0838-5

Paper Whole-genome metabolic model of Trichoderma reesei built by comparative reconstruction

Castillo, Sandra; Barth, Dorothee; Arvas, Mikko et al. · 2016 · Biotechnology for Biofuels · DOI

Full title: Whole-genome metabolic model of Trichoderma reesei built by comparative reconstruction

Authors: Castillo, Sandra; Barth, Dorothee; Arvas, Mikko; Pakula, Tiina; Pitkänen, Esa; Blomberg, Peter; Seppänen‐Laakso, Tuulikki; Nygrén, Heli; Sivasiddarthan, Dhinakaran; Penttilä, Merja; Oja, Merja

Year: 2016

Venue: Biotechnology for Biofuels

DOI: https://doi.org/10.1186/s13068-016-0665-0

Paper An accurate description of Aspergillus niger organic acid batch fermentation through dynamic metabolic modelling

Upton, Daniel J.; McQueen‐Mason, Simon J.; Wood, A. Jamie · 2017 · Biotechnology for Biofuels · DOI

Full title: An accurate description of Aspergillus niger organic acid batch fermentation through dynamic metabolic modelling

Authors: Upton, Daniel J.; McQueen‐Mason, Simon J.; Wood, A. Jamie

Year: 2017

Venue: Biotechnology for Biofuels

DOI: https://doi.org/10.1186/s13068-017-0950-6

Paper Alignment of microbial fitness with engineered product formation: obligatory coupling between acetate production and photoautotrophic growth

Du, W.; Jongbloets, Joeri A.; Boxtel, Coco van et al. · 2018 · Biotechnology for Biofuels · DOI

Full title: Alignment of microbial fitness with engineered product formation: obligatory coupling between acetate production and photoautotrophic growth

Authors: Du, W.; Jongbloets, Joeri A.; Boxtel, Coco van; Hernández, Hugo Pineda; Lips, David; Oliver, Brett G.; Hellingwerf, Klaas J.; Santos, Filipe Branco dos

Year: 2018

Venue: Biotechnology for Biofuels

DOI: https://doi.org/10.1186/s13068-018-1037-8

Paper In silico-guided metabolic engineering of Bacillus subtilis for efficient biosynthesis of purine nucleosides by blocking the key backflow nodes

Deng, Aihua; Qiu, Qidi; Sun, Qinyun et al. · 2022 · Biotechnology for Biofuels and Bioproducts · DOI

Full title: In silico-guided metabolic engineering of Bacillus subtilis for efficient biosynthesis of purine nucleosides by blocking the key backflow nodes

Authors: Deng, Aihua; Qiu, Qidi; Sun, Qinyun; Chen, Zhenxiang; Wang, Junyue; Zhang, Yu; Liu, Shuwen; Wen, Tingyi

Year: 2022

Venue: Biotechnology for Biofuels and Bioproducts

DOI: https://doi.org/10.1186/s13068-022-02179-x

Paper Single mutation at a highly conserved region of chloramphenicol acetyltransferase enables isobutyl acetate production directly from cellulose by Clostridium thermocellum at elevated temperatures

Seo, Hyeongmin; Lee, Jong‐Won; Garcia, Sergio et al. · 2019 · Biotechnology for Biofuels · DOI

Full title: Single mutation at a highly conserved region of chloramphenicol acetyltransferase enables isobutyl acetate production directly from cellulose by Clostridium thermocellum at elevated temperatures

Authors: Seo, Hyeongmin; Lee, Jong‐Won; Garcia, Sergio; Trinh, Cong T.

Year: 2019

Venue: Biotechnology for Biofuels

DOI: https://doi.org/10.1186/s13068-019-1583-8

Paper A metabolic model of Lipomyces starkeyi for predicting lipogenesis potential from diverse low-cost substrates

Zhou, Wei; Wang, Yanan; Zhang, Junlu et al. · 2021 · Biotechnology for Biofuels · DOI

Full title: A metabolic model of Lipomyces starkeyi for predicting lipogenesis potential from diverse low-cost substrates

Authors: Zhou, Wei; Wang, Yanan; Zhang, Junlu; Zhao, Man; Tang, Mou; Zhou, Wenting; Gong, Zhiwei

Year: 2021

Venue: Biotechnology for Biofuels

DOI: https://doi.org/10.1186/s13068-021-01997-9

Paper Deciphering cell wall sensors enabling the construction of robust P. pastoris for single-cell protein production

Gao, Le; Meng, Jiao; Dai, Wuling et al. · 2023 · Biotechnology for Biofuels and Bioproducts · DOI

Full title: Deciphering cell wall sensors enabling the construction of robust P. pastoris for single-cell protein production

Authors: Gao, Le; Meng, Jiao; Dai, Wuling; Zhang, Zhaokun; Dong, Haofan; Yuan, Qianqian; Zhang, Wuyuan; Liu, Shuguang; Wu, Xin

Year: 2023

Venue: Biotechnology for Biofuels and Bioproducts

DOI: https://doi.org/10.1186/s13068-023-02428-7

Paper Genome-scale metabolic modeling underscores the potential of Cutaneotrichosporon oleaginosus ATCC 20509 as a cell factory for biofuel production

Pham, Nhung; Reijnders, Maarten; Suárez‐Diez, María et al. · 2021 · Biotechnology for Biofuels · DOI

Full title: Genome-scale metabolic modeling underscores the potential of Cutaneotrichosporon oleaginosus ATCC 20509 as a cell factory for biofuel production

Authors: Pham, Nhung; Reijnders, Maarten; Suárez‐Diez, María; Nijsse, Bart; Springer, Jan; Eggink, Gerrit; Schaap, Peter J.

Year: 2021

Venue: Biotechnology for Biofuels

DOI: https://doi.org/10.1186/s13068-020-01838-1

Paper Discovery and implementation of a novel pathway for n-butanol production via 2-oxoglutarate

Ferreira, Sofia; Pereira, Rui; Liu, Filipe et al. · 2019 · Biotechnology for Biofuels · DOI

Full title: Discovery and implementation of a novel pathway for n-butanol production via 2-oxoglutarate

Authors: Ferreira, Sofia; Pereira, Rui; Liu, Filipe; Vilaça, Paulo; Rocha, Isabel

Year: 2019

Venue: Biotechnology for Biofuels

DOI: https://doi.org/10.1186/s13068-019-1565-x

Paper Dynamic flux balance modeling to increase the production of high-value compounds in green microalgae

Flassig, Robert; Fachet, Melanie; Höffner, Kai et al. · 2016 · Biotechnology for Biofuels · DOI

Full title: Dynamic flux balance modeling to increase the production of high-value compounds in green microalgae

Authors: Flassig, Robert; Fachet, Melanie; Höffner, Kai; Barton, Paul I.; Sundmacher, Kai

Year: 2016

Venue: Biotechnology for Biofuels

DOI: https://doi.org/10.1186/s13068-016-0556-4

Paper In silico identification of metabolic engineering strategies for improved lipid production in Yarrowia lipolytica by genome-scale metabolic modeling

Kim, Minsuk; Park, Beom Gi; Kim, Eun-Jung et al. · 2019 · Biotechnology for Biofuels · DOI

Full title: In silico identification of metabolic engineering strategies for improved lipid production in Yarrowia lipolytica by genome-scale metabolic modeling

Authors: Kim, Minsuk; Park, Beom Gi; Kim, Eun-Jung; Kim, Joonwon; Kim, Byung‐Gee

Year: 2019

Venue: Biotechnology for Biofuels

DOI: https://doi.org/10.1186/s13068-019-1518-4

Paper Mathematical models of cancer metabolism

Markert, Elke; Vázquez, Alexei · 2015 · Cancer & Metabolism · DOI

Full title: Mathematical models of cancer metabolism

Authors: Markert, Elke; Vázquez, Alexei

Year: 2015

Venue: Cancer & Metabolism

DOI: https://doi.org/10.1186/s40170-015-0140-6

Paper In silico profiling of cell growth and succinate production in Escherichia coli NZN111

Jian, Xingxing; Li, Ningchuan; Zhang, Cheng et al. · 2016 · Bioresources and Bioprocessing · DOI

Full title: In silico profiling of cell growth and succinate production in Escherichia coli NZN111

Authors: Jian, Xingxing; Li, Ningchuan; Zhang, Cheng; Hua, Qiang

Year: 2016

Venue: Bioresources and Bioprocessing

DOI: https://doi.org/10.1186/s40643-016-0125-5

Paper Understanding the host-microbe interactions using metabolic modeling

Jansma, Jack; Aidy, Sahar El · 2021 · Microbiome · DOI

Full title: Understanding the host-microbe interactions using metabolic modeling

Authors: Jansma, Jack; Aidy, Sahar El

Year: 2021

Venue: Microbiome

DOI: https://doi.org/10.1186/s40168-020-00955-1

Paper Pyrophosphate-free glycolysis in Clostridium thermocellum increases both thermodynamic driving force and ethanol titers

Sharma, Bishal Dev; Hon, Shuen; Thusoo, Eashant et al. · 2024 · Biotechnology for Biofuels and Bioproducts · DOI

Full title: Pyrophosphate-free glycolysis in Clostridium thermocellum increases both thermodynamic driving force and ethanol titers

Authors: Sharma, Bishal Dev; Hon, Shuen; Thusoo, Eashant; Stevenson, David; Amador‐Noguez, Daniel; Guss, Adam M.; Lynd, Lee R.; Olson, Daniel G.

Year: 2024

Venue: Biotechnology for Biofuels and Bioproducts

DOI: https://doi.org/10.1186/s13068-024-02591-5

Paper More than just a gut feeling: constraint-based genome-scale metabolic models for predicting functions of human intestinal microbes

Ark, Kees C. H. van der; Heck, Ruben; Santos, Vítor A. P. Martins dos et al. · 2017 · Microbiome · DOI

Full title: More than just a gut feeling: constraint-based genome-scale metabolic models for predicting functions of human intestinal microbes

Authors: Ark, Kees C. H. van der; Heck, Ruben; Santos, Vítor A. P. Martins dos; Belzer, Clara; Vos, Willem M. de

Year: 2017

Venue: Microbiome

DOI: https://doi.org/10.1186/s40168-017-0299-x

Paper Comprehensive reconstruction and evaluation of Pichia pastoris genome-scale metabolic model that accounts for 1243 ORFs

Ye, Rui; Huang, Mingzhi; Lu, Hongzhong et al. · 2017 · Bioresources and Bioprocessing · DOI

Full title: Comprehensive reconstruction and evaluation of Pichia pastoris genome-scale metabolic model that accounts for 1243 ORFs

Authors: Ye, Rui; Huang, Mingzhi; Lu, Hongzhong; Qian, Jiangchao; Lin, Weilu; Chu, Ju; Zhuang, Yingping; Zhang, Siliang

Year: 2017

Venue: Bioresources and Bioprocessing

DOI: https://doi.org/10.1186/s40643-017-0152-x

Paper Current status and future perspectives of kinetic modeling for the cell metabolism with incorporation of the metabolic regulation mechanism

Matsuoka, Yu; Shimizu, Kazuyuki · 2015 · Bioresources and Bioprocessing · DOI

Full title: Current status and future perspectives of kinetic modeling for the cell metabolism with incorporation of the metabolic regulation mechanism

Authors: Matsuoka, Yu; Shimizu, Kazuyuki

Year: 2015

Venue: Bioresources and Bioprocessing

DOI: https://doi.org/10.1186/s40643-014-0031-7

Paper Evaluation of synthetic formaldehyde and methanol assimilation pathways in Yarrowia lipolytica

Vartiainen, Eija; Blomberg, Peter; Ilmén, Marja et al. · 2019 · Fungal Biology and Biotechnology · DOI

Full title: Evaluation of synthetic formaldehyde and methanol assimilation pathways in Yarrowia lipolytica

Authors: Vartiainen, Eija; Blomberg, Peter; Ilmén, Marja; Andberg, Martina; Toivari, Mervi; Penttilä, Merja

Year: 2019

Venue: Fungal Biology and Biotechnology

DOI: https://doi.org/10.1186/s40694-019-0090-9

Paper In silico reconstruction and experimental validation of Saccharopolyspora erythraea genome-scale metabolic model iZZ1342 that accounts for 1685 ORFs

Zhendong Zhuang; Mingzhi Huang; J. Chu · 2018 · Bioresources and Bioprocessing · DOI

Full title: In silico reconstruction and experimental validation of Saccharopolyspora erythraea genome-scale metabolic model iZZ1342 that accounts for 1685 ORFs

Authors: Zhendong Zhuang; Mingzhi Huang; J. Chu

Year: 2018

Venue: Bioresources and Bioprocessing

DOI: https://doi.org/10.1186/s40643-018-0212-x

Paper Reconstruction of genome-scale metabolic model of Yarrowia lipolytica and its application in overproduction of triacylglycerol

Wei, Songsong; Jian, Xingxing; Chen, Jun et al. · 2017 · Bioresources and Bioprocessing · DOI

Full title: Reconstruction of genome-scale metabolic model of Yarrowia lipolytica and its application in overproduction of triacylglycerol

Authors: Wei, Songsong; Jian, Xingxing; Chen, Jun; Zhang, Cheng; Hua, Qiang

Year: 2017

Venue: Bioresources and Bioprocessing

DOI: https://doi.org/10.1186/s40643-017-0180-6

Paper Engineering microbial chemical factories using metabolic models

Sarkar, Debolina; Maranas, Costas D. · 2019 · BMC Chemical Engineering · DOI

Full title: Engineering microbial chemical factories using metabolic models

Authors: Sarkar, Debolina; Maranas, Costas D.

Year: 2019

Venue: BMC Chemical Engineering

DOI: https://doi.org/10.1186/s42480-019-0021-9

Paper Elucidating genomic gaps using phenotypic profiles

Cuevas, Daniel; Garza, Daniel; Sanchez, Savannah E. et al. · 2016 · F1000Research · DOI

Full title: Elucidating genomic gaps using phenotypic profiles

Authors: Cuevas, Daniel; Garza, Daniel; Sanchez, Savannah E.; Rostron, Jason; Henry, Chris; Vonstein, Veronika; Overbeek, Ross; Segall, Anca M.; Rohwer, Forest; Dinsdale, Elizabeth A.; Edwards, Robert A.

Year: 2016

Venue: F1000Research

Paper Identification of Genome-Scale Metabolic Network Models Using Experimentally Measured Flux Profiles

Herrgård, Markus J.; Fong, Stephen S.; Palsson, Bernhard Ø. · 2006 · PLoS Computational Biology · DOI

Full title: Identification of Genome-Scale Metabolic Network Models Using Experimentally Measured Flux Profiles

Authors: Herrgård, Markus J.; Fong, Stephen S.; Palsson, Bernhard Ø.

Year: 2006

Venue: PLoS Computational Biology

DOI: https://doi.org/10.1371/journal.pcbi.0020072

Paper Elucidating genomic gaps using phenotypic profiles

Cuevas, Daniel; Garza, Daniel; Sanchez, Savannah E. et al. · 2016 · F1000Research · DOI

Full title: Elucidating genomic gaps using phenotypic profiles

Year: 2016

Venue: F1000Research

DOI: https://doi.org/10.1371/journal.pcbi.0010046.eor

Paper Metabolic Reconstruction and Modeling of Nitrogen Fixation in Rhizobium etli

Reséndis-Antonio, Osbaldo; Reed, Jennifer L.; Encarnación‐Guevara, Sergio et al. · 2007 · PLoS Computational Biology · DOI

Full title: Metabolic Reconstruction and Modeling of Nitrogen Fixation in Rhizobium etli

Authors: Reséndis-Antonio, Osbaldo; Reed, Jennifer L.; Encarnación‐Guevara, Sergio; Collado‐Vides, Julio; Palsson, Bernhard Ø.

Year: 2007

Venue: PLoS Computational Biology

DOI: https://doi.org/10.1371/journal.pcbi.0030192

Paper Deep learning allows genome-scale prediction of Michaelis constants from structural features

Kroll, Alexander; Engqvist, Martin K. M.; Heckmann, David et al. · 2021 · PLoS Biology · DOI

Full title: Deep learning allows genome-scale prediction of Michaelis constants from structural features

Authors: Kroll, Alexander; Engqvist, Martin K. M.; Heckmann, David; Lercher, Martin J.

Year: 2021

Venue: PLoS Biology

DOI: https://doi.org/10.1371/journal.pbio.3001402

Paper The Activity Reaction Core and Plasticity of Metabolic Networks

Almaas, Eivind; Oltvai, Zoltán N.; Barabási, Albert-Ĺaszló · 2005 · PLoS Computational Biology · DOI

Full title: The Activity Reaction Core and Plasticity of Metabolic Networks

Authors: Almaas, Eivind; Oltvai, Zoltán N.; Barabási, Albert-Ĺaszló

Year: 2005

Venue: PLoS Computational Biology

DOI: https://doi.org/10.1371/journal.pcbi.0010068

Paper Flux Balance Analysis of Mycolic Acid Pathway: Targets for Anti-tubercular Drugs

Raman, Karthik V.; Rajagopalan, P. T. Ravi; Chandra, Nagasuma · 2005 · PLoS Computational Biology · DOI

Full title: Flux Balance Analysis of Mycolic Acid Pathway: Targets for Anti-tubercular Drugs

Authors: Raman, Karthik V.; Rajagopalan, P. T. Ravi; Chandra, Nagasuma

Year: 2005

Venue: PLoS Computational Biology

Paper Context-Specific Metabolic Networks Are Consistent with Experiments

Becker, Scott A.; Palsson, Bernhard Ø. · 2008 · PLoS Computational Biology · DOI

Full title: Context-Specific Metabolic Networks Are Consistent with Experiments

Authors: Becker, Scott A.; Palsson, Bernhard Ø.

Year: 2008

Venue: PLoS Computational Biology

DOI: https://doi.org/10.1371/journal.pcbi.1000082

Paper Spontaneous Reaction Silencing in Metabolic Optimization

Nishikawa, Takashi; Gulbahce, Natali; Motter, Adilson E. · 2008 · PLoS Computational Biology · DOI

Full title: Spontaneous Reaction Silencing in Metabolic Optimization

Authors: Nishikawa, Takashi; Gulbahce, Natali; Motter, Adilson E.

Year: 2008

Venue: PLoS Computational Biology

DOI: https://doi.org/10.1371/journal.pcbi.1000236

Paper Conservation of Expression and Sequence of Metabolic Genes Is Reflected by Activity Across Metabolic States

Bilu, Yonatan; Shlomi, Tomer; Barkai, Naama et al. · 2006 · PLoS Computational Biology · DOI

Full title: Conservation of Expression and Sequence of Metabolic Genes Is Reflected by Activity Across Metabolic States

Authors: Bilu, Yonatan; Shlomi, Tomer; Barkai, Naama; Ruppin, Eytan

Year: 2006

Venue: PLoS Computational Biology

DOI: https://doi.org/10.1371/journal.pcbi.0020106

Paper Prediction of Microbial Growth Rate versus Biomass Yield by a Metabolic Network with Kinetic Parameters

Adadi, Roi; Volkmer, Benjamin; Milo, Ron et al. · 2012 · PLoS Computational Biology · DOI

Full title: Prediction of Microbial Growth Rate versus Biomass Yield by a Metabolic Network with Kinetic Parameters

Authors: Adadi, Roi; Volkmer, Benjamin; Milo, Ron; Heinemann, Matthias; Shlomi, Tomer

Year: 2012

Venue: PLoS Computational Biology

DOI: https://doi.org/10.1371/journal.pcbi.1002575

Paper GrowMatch: An Automated Method for Reconciling In Silico/In Vivo Growth Predictions

Kumar, Vinay; Maranas, Costas D. · 2009 · PLoS Computational Biology · DOI

Full title: GrowMatch: An Automated Method for Reconciling In Silico/In Vivo Growth Predictions

Authors: Kumar, Vinay; Maranas, Costas D.

Year: 2009

Venue: PLoS Computational Biology

DOI: https://doi.org/10.1371/journal.pcbi.1000308

Paper Dynamic Analysis of Integrated Signaling, Metabolic, and Regulatory Networks

Lee, Jong Min; Gianchandani, Erwin P.; Eddy, James A. et al. · 2008 · PLoS Computational Biology · DOI

Full title: Dynamic Analysis of Integrated Signaling, Metabolic, and Regulatory Networks

Authors: Lee, Jong Min; Gianchandani, Erwin P.; Eddy, James A.; Papin, Jason A.

Year: 2008

Venue: PLoS Computational Biology

DOI: https://doi.org/10.1371/journal.pcbi.1000086

Paper System-Level Insights into Yeast Metabolism by Thermodynamic Analysis of Elementary Flux Modes

Jol, Stefan J.; Kümmel, Anne; Terzer, Marco et al. · 2012 · PLoS Computational Biology · DOI

Full title: System-Level Insights into Yeast Metabolism by Thermodynamic Analysis of Elementary Flux Modes

Authors: Jol, Stefan J.; Kümmel, Anne; Terzer, Marco; Stelling, Jörg; Heinemann, Matthias

Year: 2012

Venue: PLoS Computational Biology

DOI: https://doi.org/10.1371/journal.pcbi.1002415

Paper A Genome-Scale Metabolic Reconstruction of Mycoplasma genitalium, iPS189

Suthers, Patrick F.; Dasika, Madhukar S.; Kumar, Vinay et al. · 2009 · PLoS Computational Biology · DOI

Full title: A Genome-Scale Metabolic Reconstruction of Mycoplasma genitalium, iPS189

Authors: Suthers, Patrick F.; Dasika, Madhukar S.; Kumar, Vinay; Denisov, Gennady; Glass, John I.; Maranas, Costas D.

Year: 2009

Venue: PLoS Computational Biology

DOI: https://doi.org/10.1371/journal.pcbi.1000285

Paper An Automated Phenotype-Driven Approach (GeneForce) for Refining Metabolic and Regulatory Models

Barua, Dipak; Kim, Joonhoon; Reed, Jennifer L. · 2010 · PLoS Computational Biology · DOI

Full title: An Automated Phenotype-Driven Approach (GeneForce) for Refining Metabolic and Regulatory Models

Authors: Barua, Dipak; Kim, Joonhoon; Reed, Jennifer L.

Year: 2010

Venue: PLoS Computational Biology

DOI: https://doi.org/10.1371/journal.pcbi.1000970

Paper OptForce: An Optimization Procedure for Identifying All Genetic Manipulations Leading to Targeted Overproductions

Ranganathan, Sridhar; Suthers, Patrick F.; Maranas, Costas D. · 2010 · PLoS Computational Biology · DOI

Full title: OptForce: An Optimization Procedure for Identifying All Genetic Manipulations Leading to Targeted Overproductions

Authors: Ranganathan, Sridhar; Suthers, Patrick F.; Maranas, Costas D.

Year: 2010

Venue: PLoS Computational Biology

DOI: https://doi.org/10.1371/journal.pcbi.1000744

Paper Genome-Scale Metabolic Modeling Elucidates the Role of Proliferative Adaptation in Causing the Warburg Effect

Shlomi, Tomer; Benyamini, Tomer; Gottlieb, Eyal et al. · 2011 · PLoS Computational Biology · DOI

Full title: Genome-Scale Metabolic Modeling Elucidates the Role of Proliferative Adaptation in Causing the Warburg Effect

Authors: Shlomi, Tomer; Benyamini, Tomer; Gottlieb, Eyal; Sharan, Roded; Ruppin, Eytan

Year: 2011

Venue: PLoS Computational Biology

DOI: https://doi.org/10.1371/journal.pcbi.1002018

Paper Characterizing the Metabolism of Dehalococcoides with a Constraint-Based Model

Islam, M. Ahsanul; Edwards, Elizabeth A.; Mahadevan, Radhakrishnan · 2010 · PLoS Computational Biology · DOI

Full title: Characterizing the Metabolism of Dehalococcoides with a Constraint-Based Model

Authors: Islam, M. Ahsanul; Edwards, Elizabeth A.; Mahadevan, Radhakrishnan

Year: 2010

Venue: PLoS Computational Biology

DOI: https://doi.org/10.1371/journal.pcbi.1000887

Paper Environments that Induce Synthetic Microbial Ecosystems

Klitgord, Niels; Segrè, Daniel · 2010 · PLoS Computational Biology · DOI

Full title: Environments that Induce Synthetic Microbial Ecosystems

Authors: Klitgord, Niels; Segrè, Daniel

Year: 2010

Venue: PLoS Computational Biology

DOI: https://doi.org/10.1371/journal.pcbi.1001002

Paper Modeling Phenotypic Metabolic Adaptations of Mycobacterium tuberculosis H37Rv under Hypoxia

Fang, Xin; Wallqvist, Anders; Reifman, Jaques · 2012 · PLoS Computational Biology · DOI

Full title: Modeling Phenotypic Metabolic Adaptations of Mycobacterium tuberculosis H37Rv under Hypoxia

Authors: Fang, Xin; Wallqvist, Anders; Reifman, Jaques

Year: 2012

Venue: PLoS Computational Biology

DOI: https://doi.org/10.1371/journal.pcbi.1002688

Paper Impact of Stoichiometry Representation on Simulation of Genotype-Phenotype Relationships in Metabolic Networks

Brochado, Ana Rita; Andrejev, Sergej; Maranas, Costas D. et al. · 2012 · PLoS Computational Biology · DOI

Full title: Impact of Stoichiometry Representation on Simulation of Genotype-Phenotype Relationships in Metabolic Networks

Authors: Brochado, Ana Rita; Andrejev, Sergej; Maranas, Costas D.; Patil, Kiran Raosaheb

Year: 2012

Venue: PLoS Computational Biology

DOI: https://doi.org/10.1371/journal.pcbi.1002758

Paper The RAVEN Toolbox and Its Use for Generating a Genome-scale Metabolic Model for Penicillium chrysogenum

Ågren, Rasmus; Liu, Li; Shoaie, Saeed et al. · 2013 · PLoS Computational Biology · DOI

Full title: The RAVEN Toolbox and Its Use for Generating a Genome-scale Metabolic Model for Penicillium chrysogenum

Authors: Ågren, Rasmus; Liu, Li; Shoaie, Saeed; Vongsangnak, Wanwipa; Nookaew, Intawat; Nielsen, Jens

Year: 2013

Venue: PLoS Computational Biology

DOI: https://doi.org/10.1371/journal.pcbi.1002980

Paper Phenomenological Model for Predicting the Catabolic Potential of an Arbitrary Nutrient

Seaver, Samuel M. D.; Sales‐Pardo, Marta; Guimerà, Roger et al. · 2012 · PLoS Computational Biology · DOI

Full title: Phenomenological Model for Predicting the Catabolic Potential of an Arbitrary Nutrient

Authors: Seaver, Samuel M. D.; Sales‐Pardo, Marta; Guimerà, Roger; Amaral, Luı́s A. Nunes

Year: 2012

Venue: PLoS Computational Biology

DOI: https://doi.org/10.1371/journal.pcbi.1002762

Paper Exploring metabolism flexibility in complex organisms through quantitative study of precursor sets for system outputs

Abdou-Arbi, Oumarou; Lemosquet, Sophie; Milgen, Jaap J. van et al. · 2014 · BMC Systems Biology · DOI

Full title: Exploring metabolism flexibility in complex organisms through quantitative study of precursor sets for system outputs

Authors: Abdou-Arbi, Oumarou; Lemosquet, Sophie; Milgen, Jaap J. van; Siegel, Anne; Bourdon, Jérémie

Year: 2014

Venue: BMC Systems Biology

DOI: https://doi.org/10.1186/1752-0509-8-8

Paper Bridging the gap between gene expression and metabolic phenotype via kinetic models

Vital-Lopez, Francisco G; Wallqvist, Anders; Reifman, Jaques · 2013 · BMC Systems Biology · DOI

Full title: Bridging the gap between gene expression and metabolic phenotype via kinetic models

Authors: Vital-Lopez, Francisco G; Wallqvist, Anders; Reifman, Jaques

Year: 2013

Venue: BMC Systems Biology

DOI: https://doi.org/10.1186/1752-0509-7-63

Paper Global insights into energetic and metabolic networks in Rhodobacter sphaeroides

Imam, Saheed; Noguera, Daniel R.; Donohue, Timothy J. · 2013 · BMC Systems Biology · DOI

Full title: Global insights into energetic and metabolic networks in Rhodobacter sphaeroides

Authors: Imam, Saheed; Noguera, Daniel R.; Donohue, Timothy J.

Year: 2013

Venue: BMC Systems Biology

DOI: https://doi.org/10.1186/1752-0509-7-89

Paper Genome-scale metabolic reconstructions of Bifidobacterium adolescentis L2-32 and Faecalibacterium prausnitzii A2-165 and their interaction

Elsemman, Ibrahim E.; Karlsson, Fredrik; Shoaie, Saeed et al. · 2014 · BMC Systems Biology · DOI

Full title: Genome-scale metabolic reconstructions of Bifidobacterium adolescentis L2-32 and Faecalibacterium prausnitzii A2-165 and their interaction

Authors: Elsemman, Ibrahim E.; Karlsson, Fredrik; Shoaie, Saeed; Nookaew, Intawat; Soliman, Taysir Hassan A.; Nielsen, Jens

Year: 2014

Venue: BMC Systems Biology

DOI: https://doi.org/10.1186/1752-0509-8-41

Paper Systematic Comparison of C3 and C4 Plants Based on Metabolic Network Analysis

Wang, Chuanli; Guo, Longyun; Li, Yixue et al. · 2012 · BMC Systems Biology · DOI

Full title: Systematic Comparison of C3 and C4 Plants Based on Metabolic Network Analysis

Authors: Wang, Chuanli; Guo, Longyun; Li, Yixue; Wang, Zhuo

Year: 2012

Venue: BMC Systems Biology

DOI: https://doi.org/10.1186/1752-0509-6-s2-s9

Paper Comparisons of Shewanella strains based on genome annotations, modeling, and experiments

Ong, Wai Kit; Vu, Trang T.; Lovendahl, Klaus N. et al. · 2014 · BMC Systems Biology · DOI

Full title: Comparisons of Shewanella strains based on genome annotations, modeling, and experiments

Authors: Ong, Wai Kit; Vu, Trang T.; Lovendahl, Klaus N.; Llull, Jenna M; Serres, Margrethe H.; Romine, Margaret F.; Reed, Jennifer L.

Year: 2014

Venue: BMC Systems Biology

DOI: https://doi.org/10.1186/1752-0509-8-31

Paper Thermodynamic analysis of regulation in metabolic networks using constraint-based modeling

Garg, Srinath; Yang, Laurence; Mahadevan, Radhakrishnan · 2010 · BMC Research Notes · DOI

Full title: Thermodynamic analysis of regulation in metabolic networks using constraint-based modeling

Authors: Garg, Srinath; Yang, Laurence; Mahadevan, Radhakrishnan

Year: 2010

Venue: BMC Research Notes

DOI: https://doi.org/10.1186/1756-0500-3-125

Paper Dynamic metabolic modeling of a microaerobic yeast co-culture: predicting and optimizing ethanol production from glucose/xylose mixtures

Hanly, Timothy J.; Henson, Michael A. · 2013 · Biotechnology for Biofuels · DOI

Full title: Dynamic metabolic modeling of a microaerobic yeast co-culture: predicting and optimizing ethanol production from glucose/xylose mixtures

Authors: Hanly, Timothy J.; Henson, Michael A.

Year: 2013

Venue: Biotechnology for Biofuels

DOI: https://doi.org/10.1186/1754-6834-6-44

Paper The influence of HMF and furfural on redox-balance and energy-state of xylose-utilizing Saccharomyces cerevisiae

Ask, Magnus; Bettiga, Maurizio; Mapelli, Valeria et al. · 2013 · Biotechnology for Biofuels · DOI

Full title: The influence of HMF and furfural on redox-balance and energy-state of xylose-utilizing Saccharomyces cerevisiae

Authors: Ask, Magnus; Bettiga, Maurizio; Mapelli, Valeria; Olsson, Lisbeth

Year: 2013

Venue: Biotechnology for Biofuels

DOI: https://doi.org/10.1186/1754-6834-6-22

Paper Model-driven elucidation of the inherent capacity of Geobacter sulfurreducens for electricity generation

Mao, Longfei; Verwoerd, W.S. · 2013 · Journal of Biological Engineering · DOI

Full title: Model-driven elucidation of the inherent capacity of Geobacter sulfurreducens for electricity generation

Authors: Mao, Longfei; Verwoerd, W.S.

Year: 2013

Venue: Journal of Biological Engineering

DOI: https://doi.org/10.1186/1754-1611-7-14

Paper Engineering of acetyl-CoA metabolism for the improved production of polyhydroxybutyrate in Saccharomyces cerevisiae

Kocharin, Kanokarn; Chen, Yun; Siewers, Verena et al. · 2012 · AMB Express · DOI

Full title: Engineering of acetyl-CoA metabolism for the improved production of polyhydroxybutyrate in Saccharomyces cerevisiae

Authors: Kocharin, Kanokarn; Chen, Yun; Siewers, Verena; Nielsen, Jens

Year: 2012

Venue: AMB Express

DOI: https://doi.org/10.1186/2191-0855-2-52

Paper Large-scale 13C-flux analysis reveals mechanistic principles of metabolic network robustness to null mutations in yeast

Blank, Lars M.; Kuepfer, Lars; Sauer, Uwe · 2005 · Genome biology · DOI

Full title: Large-scale 13C-flux analysis reveals mechanistic principles of metabolic network robustness to null mutations in yeast

Authors: Blank, Lars M.; Kuepfer, Lars; Sauer, Uwe

Year: 2005

Venue: Genome biology

DOI: https://doi.org/10.1186/gb-2005-6-6-r49

Paper Modeling formalisms in Systems Biology

Machado, Daniel; Costa, Rafael S.; Rocha, Miguel et al. · 2011 · AMB Express · DOI

Full title: Modeling formalisms in Systems Biology

Authors: Machado, Daniel; Costa, Rafael S.; Rocha, Miguel; Ferreira, Eugénio C.; Tidor, Bruce; Rocha, Isabel

Year: 2011

Venue: AMB Express

DOI: https://doi.org/10.1186/2191-0855-1-45

Paper GSMN-TB: a web-based genome-scale network model of Mycobacterium tuberculosismetabolism

Beste, Dany J. V.; Hooper, Tracy.; Stewart, Graham R. et al. · 2007 · Genome biology · DOI

Full title: GSMN-TB: a web-based genome-scale network model of Mycobacterium tuberculosismetabolism

Authors: Beste, Dany J. V.; Hooper, Tracy.; Stewart, Graham R.; Bonde, Bhushan; Avignone–Rossa, Claudio; Bushell, Michael E.; Wheeler, Paul R.; Klamt, Steffen; Kierzek, Andrzej; McFadden, Johnjoe

Year: 2007

Venue: Genome biology

DOI: https://doi.org/10.1186/gb-2007-8-5-r89

Paper A constraint-based model of Scheffersomyces stipitis for improved ethanol production

Liu, Ting; Zou, Wei; Liu, Li et al. · 2012 · Biotechnology for Biofuels · DOI

Full title: A constraint-based model of Scheffersomyces stipitis for improved ethanol production

Authors: Liu, Ting; Zou, Wei; Liu, Li; Chen, Jian

Year: 2012

Venue: Biotechnology for Biofuels

DOI: https://doi.org/10.1186/1754-6834-5-72

Paper Modeling Neisseria meningitidis metabolism: from genome to metabolic fluxes

Baart, Gino; Zomer, Bert; Haan, Alex de et al. · 2007 · Genome biology · DOI

Full title: Modeling Neisseria meningitidis metabolism: from genome to metabolic fluxes

Authors: Baart, Gino; Zomer, Bert; Haan, Alex de; Pol, Leo A. van der; Beuvery, E. C.; Tramper, J.; Martens, Dirk E.

Year: 2007

Venue: Genome biology

DOI: https://doi.org/10.1186/gb-2007-8-7-r136

Paper Model-driven analysis of experimentally determined growth phenotypes for 465 yeast gene deletion mutants under 16 different conditions

Snitkin, Evan S.; Dudley, Aimée M.; Janse, Daniel M. et al. · 2008 · Genome biology · DOI

Full title: Model-driven analysis of experimentally determined growth phenotypes for 465 yeast gene deletion mutants under 16 different conditions

Authors: Snitkin, Evan S.; Dudley, Aimée M.; Janse, Daniel M.; Wong, K.K.; Church, George M.; Segrè, Daniel

Year: 2008

Venue: Genome biology

DOI: https://doi.org/10.1186/gb-2008-9-9-r140

Paper CiliateGEM: an open-project and a tool for predictions of ciliate metabolic variations and experimental condition design

Mancini, Alessio; Eyassu, Filmon; Conway, Maxwell et al. · 2018 · BMC Bioinformatics · DOI

Full title: CiliateGEM: an open-project and a tool for predictions of ciliate metabolic variations and experimental condition design

Authors: Mancini, Alessio; Eyassu, Filmon; Conway, Maxwell; Occhipinti, Annalisa; Lió, Píetro; Angione, Claudio; Pucciarelli, Sandra

Year: 2018

Venue: BMC Bioinformatics

DOI: https://doi.org/10.1186/s12859-018-2422-9

Paper iBsu1103: a new genome-scale metabolic model of Bacillus subtilisbased on SEED annotations

Henry, Christopher S.; Zinner, Jenifer F.; Cohoon, Matthew et al. · 2009 · Genome biology · DOI

Full title: iBsu1103: a new genome-scale metabolic model of Bacillus subtilisbased on SEED annotations

Authors: Henry, Christopher S.; Zinner, Jenifer F.; Cohoon, Matthew; Stevens, Rick

Year: 2009

Venue: Genome biology

DOI: https://doi.org/10.1186/gb-2009-10-6-r69

Paper Comparison of pathway analysis and constraint-based methods for cell factory design

Vieira, Vítor; Maia, Paulo; Rocha, Miguel et al. · 2019 · BMC Bioinformatics · DOI

Full title: Comparison of pathway analysis and constraint-based methods for cell factory design

Authors: Vieira, Vítor; Maia, Paulo; Rocha, Miguel; Rocha, Isabel

Year: 2019

Venue: BMC Bioinformatics

DOI: https://doi.org/10.1186/s12859-019-2934-y

Paper MIRAGE: a functional genomics-based approach for metabolic network model reconstruction and its application to cyanobacteria networks

Vitkin, Edward; Shlomi, Tomer · 2012 · Genome biology · DOI

Full title: MIRAGE: a functional genomics-based approach for metabolic network model reconstruction and its application to cyanobacteria networks

Authors: Vitkin, Edward; Shlomi, Tomer

Year: 2012

Venue: Genome biology

DOI: https://doi.org/10.1186/gb-2012-13-11-r111

Paper Multiplex methods provide effective integration of multi-omic data in genome-scale models

Angione, Claudio; Conway, Max; Lió, Píetro · 2016 · BMC Bioinformatics · DOI

Full title: Multiplex methods provide effective integration of multi-omic data in genome-scale models

Authors: Angione, Claudio; Conway, Max; Lió, Píetro

Year: 2016

Venue: BMC Bioinformatics

DOI: https://doi.org/10.1186/s12859-016-0912-1

Paper Flux balance analysis accounting for metabolite dilution

Benyamini, Tomer; Folger, Ori; Ruppin, Eytan et al. · 2010 · Genome biology · DOI

Full title: Flux balance analysis accounting for metabolite dilution

Authors: Benyamini, Tomer; Folger, Ori; Ruppin, Eytan; Shlomi, Tomer

Year: 2010

Venue: Genome biology

DOI: https://doi.org/10.1186/gb-2010-11-4-r43

Paper Interrogation of global mutagenesis data with a genome scale model of Neisseria meningitidis to assess gene fitness in vitro and in sera

Mendum, Tom A.; Newcombe, Jane; Mannan, Ahmad A. et al. · 2011 · Genome biology · DOI

Full title: Interrogation of global mutagenesis data with a genome scale model of Neisseria meningitidis to assess gene fitness in vitro and in sera

Authors: Mendum, Tom A.; Newcombe, Jane; Mannan, Ahmad A.; Kierzek, Andrzej; McFadden, Johnjoe

Year: 2011

Venue: Genome biology

DOI: https://doi.org/10.1186/gb-2011-12-12-r127

Paper Broad metabolic sensitivity profiling of a prototrophic yeast deletion collection

VanderSluis, Benjamin; Hess, David; Pesyna, Colin et al. · 2014 · Genome biology · DOI

Full title: Broad metabolic sensitivity profiling of a prototrophic yeast deletion collection

Authors: VanderSluis, Benjamin; Hess, David; Pesyna, Colin; Krumholz, Elias W.; Syed, Tahin; Szappanos, Balázs; Nislow, Corey; Papp, Balázs; Troyanskaya, Olga G.; Myers, Chad L.; Caudy, Amy A.

Year: 2014

Venue: Genome biology

DOI: https://doi.org/10.1186/gb-2014-15-4-r64

Paper MOMO - multi-objective metabolic mixed integer optimization: application to yeast strain engineering

Andrade, Ricardo; Doostmohammadi, Mahdi; Santos, João et al. · 2020 · BMC Bioinformatics · DOI

Full title: MOMO - multi-objective metabolic mixed integer optimization: application to yeast strain engineering

Authors: Andrade, Ricardo; Doostmohammadi, Mahdi; Santos, João; Sagot, Marie‐France; Mira, Nuno P.; Vinga, Susana

Year: 2020

Venue: BMC Bioinformatics

DOI: https://doi.org/10.1186/s12859-020-3377-1

Paper Automatic construction of metabolic models with enzyme constraints

Bekiaris, Pavlos Stephanos; Klamt, Steffen · 2020 · BMC Bioinformatics · DOI

Full title: Automatic construction of metabolic models with enzyme constraints

Authors: Bekiaris, Pavlos Stephanos; Klamt, Steffen

Year: 2020

Venue: BMC Bioinformatics

DOI: https://doi.org/10.1186/s12859-019-3329-9

Paper Metabolic characterization of the chitinolytic bacterium Serratia marcescens using a genome-scale metabolic model

Yan, Qiang; Robert, Seth; Brooks, J. Paul et al. · 2019 · BMC Bioinformatics · DOI

Full title: Metabolic characterization of the chitinolytic bacterium Serratia marcescens using a genome-scale metabolic model

Authors: Yan, Qiang; Robert, Seth; Brooks, J. Paul; Fong, Stephen S.

Year: 2019

Venue: BMC Bioinformatics

DOI: https://doi.org/10.1186/s12859-019-2826-1

Paper RetSynth: determining all optimal and sub-optimal synthetic pathways that facilitate synthesis of target compounds in chassis organisms

Whitmore, Leanne S.; Nguyen, Bernard; Pınar, Ali et al. · 2019 · BMC Bioinformatics · DOI

Full title: RetSynth: determining all optimal and sub-optimal synthetic pathways that facilitate synthesis of target compounds in chassis organisms

Authors: Whitmore, Leanne S.; Nguyen, Bernard; Pınar, Ali; George, Anthe; Hudson, Corey

Year: 2019

Venue: BMC Bioinformatics

DOI: https://doi.org/10.1186/s12859-019-3025-9

Paper Understanding and mathematical modelling of cellular resource allocation in microorganisms: a comparative synthesis

Zeng, Hong; Rohani, Reza; Huang, Wei E. et al. · 2021 · BMC Bioinformatics · DOI

Full title: Understanding and mathematical modelling of cellular resource allocation in microorganisms: a comparative synthesis

Authors: Zeng, Hong; Rohani, Reza; Huang, Wei E.; Yang, Aidong

Year: 2021

Venue: BMC Bioinformatics

DOI: https://doi.org/10.1186/s12859-021-04382-3

Paper System-level analysis of metabolic trade-offs during anaerobic photoheterotrophic growth in Rhodopseudomonas palustris

Navid, Ali; Jiao, Yongqin; Wong, Sergio et al. · 2019 · BMC Bioinformatics · DOI

Full title: System-level analysis of metabolic trade-offs during anaerobic photoheterotrophic growth in Rhodopseudomonas palustris

Authors: Navid, Ali; Jiao, Yongqin; Wong, Sergio; Pett‐Ridge, Jennifer

Year: 2019

Venue: BMC Bioinformatics

Paper Reconstruction and analysis of a carbon-core metabolic network for Dunaliella salina

Fachet, Melanie; Witte, Carina; Flassig, Robert et al. · 2020 · BMC Bioinformatics · DOI

Full title: Reconstruction and analysis of a carbon-core metabolic network for Dunaliella salina

Authors: Fachet, Melanie; Witte, Carina; Flassig, Robert; Rihko‐Struckmann, Liisa; McKie‐Krisberg, Zaid; Polle, Jürgen E.W.; Sundmacher, Kai

Year: 2020

Venue: BMC Bioinformatics

DOI: https://doi.org/10.1186/s12859-019-3325-0

Paper High-quality genome-scale metabolic network reconstruction of probiotic bacterium Escherichia coli Nissle 1917

Hof, Max van ‘t; Mohite, Omkar S.; Monk, Jonathan M. et al. · 2022 · BMC Bioinformatics · DOI

Full title: High-quality genome-scale metabolic network reconstruction of probiotic bacterium Escherichia coli Nissle 1917

Authors: Hof, Max van ‘t; Mohite, Omkar S.; Monk, Jonathan M.; Weber, Tilmann; Palsson, Bernhard Ø.; Sommer, Morten Otto Alexander

Year: 2022

Venue: BMC Bioinformatics

DOI: https://doi.org/10.1186/s12859-022-05108-9

Paper Assumptions on decision making and environment can yield multiple steady states in microbial community models

Theorell, Axel; Stelling, Jörg · 2023 · BMC Bioinformatics · DOI

Full title: Assumptions on decision making and environment can yield multiple steady states in microbial community models

Authors: Theorell, Axel; Stelling, Jörg

Year: 2023

Venue: BMC Bioinformatics

DOI: https://doi.org/10.1186/s12859-023-05325-w

Paper Linear programming based gene expression model (LPM-GEM) predicts the carbon source for Bacillus subtilis

Thanamit, Kulwadee; Hoerhold, Franziska; Oswald, Marcus et al. · 2022 · BMC Bioinformatics · DOI

Full title: Linear programming based gene expression model (LPM-GEM) predicts the carbon source for Bacillus subtilis

Authors: Thanamit, Kulwadee; Hoerhold, Franziska; Oswald, Marcus; Koenig, Rainer

Year: 2022

Venue: BMC Bioinformatics

DOI: https://doi.org/10.1186/s12859-022-04742-7

Paper ChiMera: an easy to use pipeline for bacterial genome based metabolic network reconstruction, evaluation and visualization

Tamasco, Gustavo; Kumar, Manish; Zengler, Karsten et al. · 2022 · BMC Bioinformatics · DOI

Full title: ChiMera: an easy to use pipeline for bacterial genome based metabolic network reconstruction, evaluation and visualization

Authors: Tamasco, Gustavo; Kumar, Manish; Zengler, Karsten; Silva‐Rocha, Rafael; Silva, Ricardo

Year: 2022

Venue: BMC Bioinformatics

Paper MLAGO: machine learning-aided global optimization for Michaelis constant estimation of kinetic modeling

Maeda, Kazuhiro; Hatae, Aoi; Sakai, Yukie et al. · 2022 · BMC Bioinformatics · DOI

Full title: MLAGO: machine learning-aided global optimization for Michaelis constant estimation of kinetic modeling

Authors: Maeda, Kazuhiro; Hatae, Aoi; Sakai, Yukie; Boogerd, Fred C.; Kurata, Hiroyuki

Year: 2022

Venue: BMC Bioinformatics

DOI: https://doi.org/10.1186/s12859-022-05009-x

Paper ICON-GEMs: integration of co-expression network in genome-scale metabolic models, shedding light through systems biology

Paklao, Thummarat; Suratanee, Apichat; Plaimas, Kitiporn · 2023 · BMC Bioinformatics · DOI

Full title: ICON-GEMs: integration of co-expression network in genome-scale metabolic models, shedding light through systems biology

Authors: Paklao, Thummarat; Suratanee, Apichat; Plaimas, Kitiporn

Year: 2023

Venue: BMC Bioinformatics

DOI: https://doi.org/10.1186/s12859-023-05599-0

Paper Development and validation of an updated computational model of Streptomyces coelicolor primary and secondary metabolism

Amara, Adam; Takano, Eriko; Breitling, Rainer · 2018 · BMC Genomics · DOI

Full title: Development and validation of an updated computational model of Streptomyces coelicolor primary and secondary metabolism

Authors: Amara, Adam; Takano, Eriko; Breitling, Rainer

Year: 2018

Venue: BMC Genomics

DOI: https://doi.org/10.1186/s12864-018-4905-5

Paper In silico screening for candidate chassis strains of free fatty acid-producing cyanobacteria

Motwalli, Olaa; Essack, Magbubah; Janković, Boris R. et al. · 2017 · BMC Genomics · DOI

Full title: In silico screening for candidate chassis strains of free fatty acid-producing cyanobacteria

Authors: Motwalli, Olaa; Essack, Magbubah; Janković, Boris R.; Ji, Boyang; Liu, Xinyao; Ansari, Hifzur Rahman; Hoehndorf, Robert; Gao, Xin; Arold, Stefan T.; Mineta, Katsuhiko; Archer, John A. C.; Gojobori, Takashi; Mijakovic̀, Ivan; Bajić, Vladimir B.

Year: 2017

Venue: BMC Genomics

DOI: https://doi.org/10.1186/s12864-016-3389-4

Paper Modelling microbial metabolic rewiring during growth in a complex medium

Fondi, Marco; Bosi, Emanuele; Presta, Luana et al. · 2016 · BMC Genomics · DOI

Full title: Modelling microbial metabolic rewiring during growth in a complex medium

Authors: Fondi, Marco; Bosi, Emanuele; Presta, Luana; Natoli, Diletta; Fani, Renato

Year: 2016

Venue: BMC Genomics

DOI: https://doi.org/10.1186/s12864-016-3311-0

Paper Genome-scale metabolic network model and phenome of solvent-tolerant Pseudomonas putida S12

Han, Sol; Kim, Dohyeon; Kim, Young-Shin et al. · 2024 · BMC Genomics · DOI

Full title: Genome-scale metabolic network model and phenome of solvent-tolerant Pseudomonas putida S12

Authors: Han, Sol; Kim, Dohyeon; Kim, Young-Shin; Yoon, Sung Ho

Year: 2024

Venue: BMC Genomics

DOI: https://doi.org/10.1186/s12864-023-09940-y

Paper Predicting microbial interactions with approaches based on flux balance analysis: an evaluation

Joseph, Clémence; Zafeiropoulos, Haris; Bernaerts, Kristel et al. · 2024 · BMC Bioinformatics · DOI

Full title: Predicting microbial interactions with approaches based on flux balance analysis: an evaluation

Authors: Joseph, Clémence; Zafeiropoulos, Haris; Bernaerts, Kristel; Faust, Karoline

Year: 2024

Venue: BMC Bioinformatics

DOI: https://doi.org/10.1186/s12859-024-05651-7

Paper Metabolic flux analysis for metabolome data validation of naturally xylose-fermenting yeasts

Veras, Henrique; Campos, Christiane Gonçalves; Nascimento, Igor Ferreira do et al. · 2019 · BMC Biotechnology · DOI

Full title: Metabolic flux analysis for metabolome data validation of naturally xylose-fermenting yeasts

Authors: Veras, Henrique; Campos, Christiane Gonçalves; Nascimento, Igor Ferreira do; Abdelnur, Patrícia Verardi; Almeida, João Ricardo Moreira de; Parachin, Nádia Skorupa

Year: 2019

Venue: BMC Biotechnology

DOI: https://doi.org/10.1186/s12896-019-0548-0

Paper Predicting internal cell fluxes at sub-optimal growth

Schultz, André; Qutub, Amina A. · 2015 · BMC Systems Biology · DOI

Full title: Predicting internal cell fluxes at sub-optimal growth

Authors: Schultz, André; Qutub, Amina A.

Year: 2015

Venue: BMC Systems Biology

DOI: https://doi.org/10.1186/s12918-015-0153-3

Paper Genome-scale insights into the metabolic versatility of Limosilactobacillus reuteri

Luo, Hao; Li, Peishun; Wang, Hao et al. · 2021 · BMC Biotechnology · DOI

Full title: Genome-scale insights into the metabolic versatility of Limosilactobacillus reuteri

Authors: Luo, Hao; Li, Peishun; Wang, Hao; Roos, Stefan; Ji, Boyang; Nielsen, Jens

Year: 2021

Venue: BMC Biotechnology

DOI: https://doi.org/10.1186/s12896-021-00702-w

Paper Genome-scale resources for Thermoanaerobacterium saccharolyticum

Currie, Devin H.; Raman, Babu; Gowen, Christopher M. et al. · 2015 · BMC Systems Biology · DOI

Full title: Genome-scale resources for Thermoanaerobacterium saccharolyticum

Authors: Currie, Devin H.; Raman, Babu; Gowen, Christopher M.; Tschaplinski, Timothy J.; Land, Miriam; Brown, Steven D.; Covalla, Sean F.; Klingeman, Dawn M.; Yang, Zamin K.; Engle, Nancy L.; Johnson, Courtney M.; Rodríguez, Miguel; Shaw, A. Joe; Kenealy, William R.; Lynd, Lee R.; Fong, Stephen S.; Mielenz, Jonathan R.; Davison, Brian H.; Hogsett, David A.; Herring, Christopher D.

Year: 2015

Venue: BMC Systems Biology

DOI: https://doi.org/10.1186/s12918-015-0159-x

Paper Flux-sum analysis identifies metabolite targets for strain improvement

Lakshmanan, Meiyappan; Kim, Tae Yong; Chung, Bevan Kai Sheng et al. · 2015 · BMC Systems Biology · DOI

Full title: Flux-sum analysis identifies metabolite targets for strain improvement

Authors: Lakshmanan, Meiyappan; Kim, Tae Yong; Chung, Bevan Kai Sheng; Lee, Sang Yup; Lee, Dong‐Yup

Year: 2015

Venue: BMC Systems Biology

DOI: https://doi.org/10.1186/s12918-015-0198-3

Paper MetaNET - a web-accessible interactive platform for biological metabolic network analysis

Narang, Pankaj; Khan, Shawez; Hemrom, Anmol Jaywant et al. · 2014 · BMC Systems Biology · DOI

Full title: MetaNET - a web-accessible interactive platform for biological metabolic network analysis

Authors: Narang, Pankaj; Khan, Shawez; Hemrom, Anmol Jaywant; Lynn, Andrew M.

Year: 2014

Venue: BMC Systems Biology

DOI: https://doi.org/10.1186/s12918-014-0130-2

Paper Dynamic genome-scale metabolic modeling of the yeast Pichia pastoris

Saitua, Francisco; Torres, Paulina; Pérez‐Correa, José Ricardo et al. · 2017 · BMC Systems Biology · DOI

Full title: Dynamic genome-scale metabolic modeling of the yeast Pichia pastoris

Authors: Saitua, Francisco; Torres, Paulina; Pérez‐Correa, José Ricardo; Agosín, Eduardo

Year: 2017

Venue: BMC Systems Biology

DOI: https://doi.org/10.1186/s12918-017-0408-2

Paper A curated C. difficile strain 630 metabolic network: prediction of essential targets and inhibitors

Larocque, Monica; Chénard, Thierry; Najmanovich, Rafaël · 2014 · BMC Systems Biology · DOI

Full title: A curated C. difficile strain 630 metabolic network: prediction of essential targets and inhibitors

Authors: Larocque, Monica; Chénard, Thierry; Najmanovich, Rafaël

Year: 2014

Venue: BMC Systems Biology

DOI: https://doi.org/10.1186/s12918-014-0117-z

Paper Proteomics-based metabolic modeling and characterization of the cellulolytic bacterium Thermobifida fusca

Vanee, Niti; Brooks, J. Paul; Spicer, Victor et al. · 2014 · BMC Systems Biology · DOI

Full title: Proteomics-based metabolic modeling and characterization of the cellulolytic bacterium Thermobifida fusca

Authors: Vanee, Niti; Brooks, J. Paul; Spicer, Victor; Shamshurin, Dmitriy; Krokhin, Oleg V.; Wilkins, John A.; Deng, Yu; Fong, Stephen S.

Year: 2014

Venue: BMC Systems Biology

DOI: https://doi.org/10.1186/s12918-014-0086-2

Paper Emergence of microbial diversity due to cross-feeding interactions in a spatial model of gut microbial metabolism

Hoek, Milan J. A.; Merks, Roeland M. H. · 2017 · BMC Systems Biology · DOI

Full title: Emergence of microbial diversity due to cross-feeding interactions in a spatial model of gut microbial metabolism

Authors: Hoek, Milan J. A.; Merks, Roeland M. H.

Year: 2017

Venue: BMC Systems Biology

Paper Metabolic modeling predicts metabolite changes in Mycobacterium tuberculosis

Garay, Christopher; Dreyfuss, Jonathan M.; Galagan, James E. · 2015 · BMC Systems Biology · DOI

Full title: Metabolic modeling predicts metabolite changes in Mycobacterium tuberculosis

Authors: Garay, Christopher; Dreyfuss, Jonathan M.; Galagan, James E.

Year: 2015

Venue: BMC Systems Biology

DOI: https://doi.org/10.1186/s12918-015-0206-7

Paper Genome-scale model-driven strain design for dicarboxylic acid production in Yarrowia lipolytica

Mishra, Pranjul; Lee, Na‐Rae; Lakshmanan, Meiyappan et al. · 2018 · BMC Systems Biology · DOI

Full title: Genome-scale model-driven strain design for dicarboxylic acid production in Yarrowia lipolytica

Authors: Mishra, Pranjul; Lee, Na‐Rae; Lakshmanan, Meiyappan; Kim, Minsuk; Kim, Byung‐Gee; Lee, Dong‐Yup

Year: 2018

Venue: BMC Systems Biology

DOI: https://doi.org/10.1186/s12918-018-0542-5

Paper The use of genome-scale metabolic network reconstruction to predict fluxes and equilibrium composition of N-fixing versus C-fixing cells in a diazotrophic cyanobacterium, Trichodesmium erythraeum

Gardner, Joseph; Boyle, Nanette · 2017 · BMC Systems Biology · DOI

Full title: The use of genome-scale metabolic network reconstruction to predict fluxes and equilibrium composition of N-fixing versus C-fixing cells in a diazotrophic cyanobacterium, Trichodesmium erythraeum

Authors: Gardner, Joseph; Boyle, Nanette

Year: 2017

Venue: BMC Systems Biology

DOI: https://doi.org/10.1186/s12918-016-0383-z

Paper Genome-scale metabolic model of Rhodococcus jostii RHA1 (iMT1174) to study the accumulation of storage compounds during nitrogen-limited condition

Tajparast, Mohammad; Frigon, Dominic · 2015 · BMC Systems Biology · DOI

Full title: Genome-scale metabolic model of Rhodococcus jostii RHA1 (iMT1174) to study the accumulation of storage compounds during nitrogen-limited condition

Authors: Tajparast, Mohammad; Frigon, Dominic

Year: 2015

Venue: BMC Systems Biology

DOI: https://doi.org/10.1186/s12918-015-0190-y

Paper Optimization of lipid production with a genome-scale model of Yarrowia lipolytica

Kavšček, Martin; Bhutada, Govindprasad; Madl, Tobias et al. · 2015 · BMC Systems Biology · DOI

Full title: Optimization of lipid production with a genome-scale model of Yarrowia lipolytica

Authors: Kavšček, Martin; Bhutada, Govindprasad; Madl, Tobias; Natter, Klaus

Year: 2015

Venue: BMC Systems Biology

DOI: https://doi.org/10.1186/s12918-015-0217-4

Paper SSER: Species specific essential reactions database

Labena, Abraham Alemayehu; Ye, Yuan‐Nong; Dong, Chuan et al. · 2017 · BMC Systems Biology · DOI

Full title: SSER: Species specific essential reactions database

Authors: Labena, Abraham Alemayehu; Ye, Yuan‐Nong; Dong, Chuan; Zhang, Fa-Z; Guo, Feng‐Biao

Year: 2017

Venue: BMC Systems Biology

DOI: https://doi.org/10.1186/s12918-017-0426-0

Paper Use of genome-scale models to get new insights into the marine actinomycete genus Salinispora

Contador, Carolina A.; Rodríguez, Vida; Andrews, Bárbara A. et al. · 2019 · BMC Systems Biology · DOI

Full title: Use of genome-scale models to get new insights into the marine actinomycete genus Salinispora

Authors: Contador, Carolina A.; Rodríguez, Vida; Andrews, Bárbara A.; Asenjo, Juan A.

Year: 2019

Venue: BMC Systems Biology

DOI: https://doi.org/10.1186/s12918-019-0683-1

Paper Global connectivity in genome-scale metabolic networks revealed by comprehensive FBA-based pathway analysis

Gao, Yajie; Yuan, Qianqian; Mao, Zhitao et al. · 2021 · BMC Microbiology · DOI

Full title: Global connectivity in genome-scale metabolic networks revealed by comprehensive FBA-based pathway analysis

Authors: Gao, Yajie; Yuan, Qianqian; Mao, Zhitao; Liu, Hao; Ma, Hongwu

Year: 2021

Venue: BMC Microbiology

DOI: https://doi.org/10.1186/s12866-021-02357-1

Paper PFA toolbox: a MATLAB tool for Metabolic Flux Analysis

Morales, Yeimy; Bosque, Gabriel; Vehı́, Josep et al. · 2016 · BMC Systems Biology · DOI

Full title: PFA toolbox: a MATLAB tool for Metabolic Flux Analysis

Authors: Morales, Yeimy; Bosque, Gabriel; Vehı́, Josep; Picó, Jesús; Llaneras, Francisco

Year: 2016

Venue: BMC Systems Biology

DOI: https://doi.org/10.1186/s12918-016-0284-1

Paper Modelling overflow metabolism in Escherichia coli with flux balance analysis incorporating differential proteomic efficiencies of energy pathways

Zeng, Hong; Yang, Aidong · 2019 · BMC Systems Biology · DOI

Full title: Modelling overflow metabolism in Escherichia coli with flux balance analysis incorporating differential proteomic efficiencies of energy pathways

Authors: Zeng, Hong; Yang, Aidong

Year: 2019

Venue: BMC Systems Biology

DOI: https://doi.org/10.1186/s12918-018-0677-4

Paper DMPy: a Python package for automated mathematical model construction of large-scale metabolic systems

Smith, Robert W.; Rosmalen, Rik P. van; Santos, Vítor A. P. Martins dos et al. · 2018 · BMC Systems Biology · DOI

Full title: DMPy: a Python package for automated mathematical model construction of large-scale metabolic systems

Authors: Smith, Robert W.; Rosmalen, Rik P. van; Santos, Vítor A. P. Martins dos; Fleck, Christian

Year: 2018

Venue: BMC Systems Biology

DOI: https://doi.org/10.1186/s12918-018-0584-8

Paper Reconstruction of a genome-scale metabolic model for Actinobacillus succinogenes 130Z

Pereira, Bruno; Miguel, Joana; Vilaça, Paulo et al. · 2018 · BMC Systems Biology · DOI

Full title: Reconstruction of a genome-scale metabolic model for Actinobacillus succinogenes 130Z

Authors: Pereira, Bruno; Miguel, Joana; Vilaça, Paulo; Soares, Simão; Rocha, Isabel; Carneiro, Sónia

Year: 2018

Venue: BMC Systems Biology

DOI: https://doi.org/10.1186/s12918-018-0585-7

Paper Clostridium butyricum maximizes growth while minimizing enzyme usage and ATP production: metabolic flux distribution of a strain cultured in glycerol

Serrano‐Bermúdez, Luis Miguel; Barrios, Andrés Fernando González; Maranas, Costas D. et al. · 2017 · BMC Systems Biology · DOI

Full title: Clostridium butyricum maximizes growth while minimizing enzyme usage and ATP production: metabolic flux distribution of a strain cultured in glycerol

Authors: Serrano‐Bermúdez, Luis Miguel; Barrios, Andrés Fernando González; Maranas, Costas D.; Castaño, Dolly Montoya

Year: 2017

Venue: BMC Systems Biology

DOI: https://doi.org/10.1186/s12918-017-0434-0

Paper Microbial production of vitamin B12: a review and future perspectives

Fang, Huan; Kang, Jie; Zhang, Dawei · 2017 · Microbial Cell Factories · DOI

Full title: Microbial production of vitamin B12: a review and future perspectives

Authors: Fang, Huan; Kang, Jie; Zhang, Dawei

Year: 2017

Venue: Microbial Cell Factories

DOI: https://doi.org/10.1186/s12934-017-0631-y

Paper SLIMEr: probing flexibility of lipid metabolism in yeast with an improved constraint-based modeling framework

Sánchez, Benjamín J.; Li, Feiran; Kerkhoven, Eduard J. et al. · 2019 · BMC Systems Biology · DOI

Full title: SLIMEr: probing flexibility of lipid metabolism in yeast with an improved constraint-based modeling framework

Authors: Sánchez, Benjamín J.; Li, Feiran; Kerkhoven, Eduard J.; Nielsen, Jens

Year: 2019

Venue: BMC Systems Biology

DOI: https://doi.org/10.3390/bioengineering10060744

Paper Flux measurements and maintenance energy for carbon dioxide utilization by Methanococcus maripaludis

Goyal, Nishu; Padhiary, Mrutyunjay; Karimi, Iftekhar A. et al. · 2015 · Microbial Cell Factories · DOI

Full title: Flux measurements and maintenance energy for carbon dioxide utilization by Methanococcus maripaludis

Authors: Goyal, Nishu; Padhiary, Mrutyunjay; Karimi, Iftekhar A.; Zhou, Zhi

Year: 2015

Venue: Microbial Cell Factories

DOI: https://doi.org/10.1186/s12934-015-0336-z

Paper A scalable metabolite supplementation strategy against antibiotic resistant pathogen Chromobacterium violaceum induced by NAD+/NADH+ imbalance

Banerjee, Deepanwita; Parmar, Dharmeshkumar; Bhattacharya, Nivedita et al. · 2017 · BMC Systems Biology · DOI

Full title: A scalable metabolite supplementation strategy against antibiotic resistant pathogen Chromobacterium violaceum induced by NAD+/NADH+ imbalance

Authors: Banerjee, Deepanwita; Parmar, Dharmeshkumar; Bhattacharya, Nivedita; Ghanate, Avinash; Panchagnula, Venkateswarlu; Raghunathan, Anu

Year: 2017

Venue: BMC Systems Biology

DOI: https://doi.org/10.1186/s12918-017-0427-z

Paper Production of β-ionone by combined expression of carotenogenic and plant CCD1 genes in Saccharomyces cerevisiae

López, Javiera; Essus, Karen; Kim, Il‐Kwon et al. · 2015 · Microbial Cell Factories · DOI

Full title: Production of β-ionone by combined expression of carotenogenic and plant CCD1 genes in Saccharomyces cerevisiae

Authors: López, Javiera; Essus, Karen; Kim, Il‐Kwon; Pereira, Rui; Herzog, Jan; Siewers, Verena; Nielsen, Jens; Agosín, Eduardo

Year: 2015

Venue: Microbial Cell Factories

DOI: https://doi.org/10.1186/s12934-015-0273-x

Paper In silico model-guided identification of transcriptional regulator targets for efficient strain design

Lokanand Koduru; Meiyappan Lakshmanan; Dong-Yup Lee · 2018 · Microbial Cell Factories · DOI

Full title: In silico model-guided identification of transcriptional regulator targets for efficient strain design

Authors: Lokanand Koduru; Meiyappan Lakshmanan; Dong-Yup Lee

Year: 2018

Venue: Microbial Cell Factories

DOI: https://doi.org/10.1186/s12934-018-1015-7

Paper Genomic sequencing, genome-scale metabolic network reconstruction, and in silico flux analysis of the grape endophytic fungus Alternaria sp. MG1

Lü, Yao; Ye, Chao; Che, Jinxin et al. · 2019 · Microbial Cell Factories · DOI

Full title: Genomic sequencing, genome-scale metabolic network reconstruction, and in silico flux analysis of the grape endophytic fungus Alternaria sp. MG1

Authors: Lü, Yao; Ye, Chao; Che, Jinxin; Xu, Xiaoguang; Shao, Dongyan; Jiang, Chunmei; Liu, Yanlin; Shi, Junling

Year: 2019

Venue: Microbial Cell Factories

DOI: https://doi.org/10.1186/s12934-019-1063-7

Paper OptPipe - a pipeline for optimizing metabolic engineering targets

Hartmann, András; Vila-Santa, Ana; Kallscheuer, Nicolai et al. · 2017 · BMC Systems Biology · DOI

Full title: OptPipe - a pipeline for optimizing metabolic engineering targets

Authors: Hartmann, András; Vila-Santa, Ana; Kallscheuer, Nicolai; Vogt, Michael; Julien-Laferrière, Alice; Sagot, Marie-France; Marienhagen, Jan; Vinga, Susana

Year: 2017

Venue: BMC Systems Biology

DOI: https://doi.org/10.1186/s12918-017-0515-0

Paper Metabolic engineering of Synechococcus elongatus PCC 7942 for improvement of 1,3-propanediol and glycerol production based on in silico simulation of metabolic flux distribution

Hirokawa, Yasutaka; Matsuo, Shingo; Hamada, Hiroyuki et al. · 2017 · Microbial Cell Factories · DOI

Full title: Metabolic engineering of Synechococcus elongatus PCC 7942 for improvement of 1,3-propanediol and glycerol production based on in silico simulation of metabolic flux distribution

Authors: Hirokawa, Yasutaka; Matsuo, Shingo; Hamada, Hiroyuki; Matsuda, Fumio; Hanai, Taizo

Year: 2017

Venue: Microbial Cell Factories

DOI: https://doi.org/10.1186/s12934-017-0824-4

Paper Role of phosphate limitation and pyruvate decarboxylase in rewiring of the metabolic network for increasing flux towards isoprenoid pathway in a TATA binding protein mutant of Saccharomyces cerevisiae

Wadhwa, Manisha; Srinivasan, Sumana; Bachhawat, Anand et al. · 2018 · Microbial Cell Factories · DOI

Full title: Role of phosphate limitation and pyruvate decarboxylase in rewiring of the metabolic network for increasing flux towards isoprenoid pathway in a TATA binding protein mutant of Saccharomyces cerevisiae

Authors: Wadhwa, Manisha; Srinivasan, Sumana; Bachhawat, Anand; Venkatesh, K. V.

Year: 2018

Venue: Microbial Cell Factories

DOI: https://doi.org/10.1186/s12934-018-1000-1

Paper Genome-scale metabolic reconstructions and theoretical investigation of methane conversion in Methylomicrobium buryatense strain 5G(B1)

Torre, Andrea De La; Metivier, Aisha; Chu, Frances et al. · 2015 · Microbial Cell Factories · DOI

Full title: Genome-scale metabolic reconstructions and theoretical investigation of methane conversion in Methylomicrobium buryatense strain 5G(B1)

Authors: Torre, Andrea De La; Metivier, Aisha; Chu, Frances; Laurens, Lieve M. L.; Beck, David A. C.; Pienkos, Philip T.; Lidstrom, Mary E.; Kalyuzhnaya, Marina

Year: 2015

Venue: Microbial Cell Factories

DOI: https://doi.org/10.1186/s12934-015-0377-3

Paper Metabolic network model guided engineering ethylmalonyl-CoA pathway to improve ascomycin production in Streptomyces hygroscopicus var. ascomyceticus

Wang, Junhua; Wang, Cheng; Song, Kejing et al. · 2017 · Microbial Cell Factories · DOI

Full title: Metabolic network model guided engineering ethylmalonyl-CoA pathway to improve ascomycin production in Streptomyces hygroscopicus var. ascomyceticus

Authors: Wang, Junhua; Wang, Cheng; Song, Kejing; Wen, Jianping

Year: 2017

Venue: Microbial Cell Factories

DOI: https://doi.org/10.1186/s12934-017-0787-5

Paper Metabolic engineering of Corynebacterium glutamicum for anthocyanin production

Zha, Jian; Zang, Ying; Mattozzi, Matthew D. et al. · 2018 · Microbial Cell Factories · DOI

Full title: Metabolic engineering of Corynebacterium glutamicum for anthocyanin production

Authors: Zha, Jian; Zang, Ying; Mattozzi, Matthew D.; Plassmeier, Jens; Gupta, Mamta; Wu, Xia; Clarkson, Sonya M.; Koffas, Mattheos

Year: 2018

Venue: Microbial Cell Factories

DOI: https://doi.org/10.1186/s12934-018-0990-z

Paper Integration of enzyme constraints in a genome-scale metabolic model of Aspergillus niger improves phenotype predictions

Jingru Zhou; Y. Zhuang; Jianye Xia · 2021 · Microbial Cell Factories · DOI

Full title: Integration of enzyme constraints in a genome-scale metabolic model of Aspergillus niger improves phenotype predictions

Authors: Jingru Zhou; Y. Zhuang; Jianye Xia

Year: 2021

Venue: Microbial Cell Factories

DOI: https://doi.org/10.1186/s12934-021-01614-2

Paper Shikimic Acid Production in Escherichia coli: From Classical Metabolic Engineering Strategies to Omics Applied to Improve Its Production

Martínez, Juan A.; Bolívar, Francisco; Escalante, Adelfo · 2015 · Frontiers in Bioengineering and Biotechnology · DOI

Full title: Shikimic Acid Production in Escherichia coli: From Classical Metabolic Engineering Strategies to Omics Applied to Improve Its Production

Authors: Martínez, Juan A.; Bolívar, Francisco; Escalante, Adelfo

Year: 2015

Venue: Frontiers in Bioengineering and Biotechnology

DOI: https://doi.org/10.3389/fbioe.2015.00145

Paper Systems Biology of Microbial Exopolysaccharides Production

Duru, Özlem Ateş · 2015 · Frontiers in Bioengineering and Biotechnology · DOI

Full title: Systems Biology of Microbial Exopolysaccharides Production

Authors: Duru, Özlem Ateş

Year: 2015

Venue: Frontiers in Bioengineering and Biotechnology

DOI: https://doi.org/10.3389/fbioe.2015.00200

Paper Production of 3-Hydroxypropanoic Acid From Glycerol by Metabolically Engineered Bacteria

Carsten Jers; Aida Kalantari; Abhroop Garg et al. · 2019 · Frontiers in Bioengineering and Biotechnology · DOI

Full title: Production of 3-Hydroxypropanoic Acid From Glycerol by Metabolically Engineered Bacteria

Authors: Carsten Jers; Aida Kalantari; Abhroop Garg; I. Mijakovic

Year: 2019

Venue: Frontiers in Bioengineering and Biotechnology

DOI: https://doi.org/10.3389/fbioe.2019.00124

Paper Combining metabolite doping and metabolic engineering to improve 2-phenylethanol production by engineered cyanobacteria

Usai, Giulia; Cordara, Alessandro; Re, Angela et al. · 2022 · Frontiers in Bioengineering and Biotechnology · DOI

Full title: Combining metabolite doping and metabolic engineering to improve 2-phenylethanol production by engineered cyanobacteria

Authors: Usai, Giulia; Cordara, Alessandro; Re, Angela; Polli, Maria Francesca; Mannino, Giuseppe; Bertea, Cinzia M.; Fino, Debora; Pirri, Candido Fabrizio; Menin, Barbara

Year: 2022

Venue: Frontiers in Bioengineering and Biotechnology

DOI: https://doi.org/10.3389/fbioe.2022.1005960

Paper Engineering Saccharomyces cerevisiae for the Overproduction of β-Ionone and Its Precursor β-Carotene

López, Javiera; Bustos, D.P. Jaramillo; Camilo, Conrado et al. · 2020 · Frontiers in Bioengineering and Biotechnology · DOI

Full title: Engineering Saccharomyces cerevisiae for the Overproduction of β-Ionone and Its Precursor β-Carotene

Authors: López, Javiera; Bustos, D.P. Jaramillo; Camilo, Conrado; Arenas, N; Saa, Pedro A.; Agosín, Eduardo

Year: 2020

Venue: Frontiers in Bioengineering and Biotechnology

DOI: https://doi.org/10.3389/fbioe.2020.578793

Paper Microbial Biosynthesis of L-Malic Acid and Related Metabolic Engineering Strategies: Advances and Prospects

Wei, Zhen; Xu, Yongxue; Xu, Qing et al. · 2021 · Frontiers in Bioengineering and Biotechnology · DOI

Full title: Microbial Biosynthesis of L-Malic Acid and Related Metabolic Engineering Strategies: Advances and Prospects

Authors: Wei, Zhen; Xu, Yongxue; Xu, Qing; Cao, Wei; Huang, He; Liu, Hao

Year: 2021

Venue: Frontiers in Bioengineering and Biotechnology

DOI: https://doi.org/10.3389/fbioe.2021.765685

Paper Construction and application of the genome-scale metabolic model of Streptomyces radiopugnans

Zhidong Zhang; Qi Guo; Jinyi Qian et al. · 2023 · Frontiers in Bioengineering and Biotechnology · DOI

Full title: Construction and application of the genome-scale metabolic model of Streptomyces radiopugnans

Authors: Zhidong Zhang; Qi Guo; Jinyi Qian; Chao Ye; He Huang

Year: 2023

Venue: Frontiers in Bioengineering and Biotechnology

DOI: https://doi.org/10.3389/fbioe.2023.1108412

Paper Opportunities at the Interface of Network Science and Metabolic Modeling

Dusad, Varshit; Thiel, Denise; Barahona, Mauricio et al. · 2021 · Frontiers in Bioengineering and Biotechnology · DOI

Full title: Opportunities at the Interface of Network Science and Metabolic Modeling

Authors: Dusad, Varshit; Thiel, Denise; Barahona, Mauricio; Keun, Hector C.; Oyarzún, Diego A.

Year: 2021

Venue: Frontiers in Bioengineering and Biotechnology

DOI: https://doi.org/10.3389/fbioe.2020.591049

Paper Production of biopolymer precursors beta-alanine and L-lactic acid from CO2 with metabolically versatile Rhodococcus opacus DSM 43205

Salusjärvi, Laura; Ojala, Leo S.; Gopalacharyulu, Peddinti et al. · 2022 · Frontiers in Bioengineering and Biotechnology · DOI

Full title: Production of biopolymer precursors beta-alanine and L-lactic acid from CO2 with metabolically versatile Rhodococcus opacus DSM 43205

Authors: Salusjärvi, Laura; Ojala, Leo S.; Gopalacharyulu, Peddinti; Lienemann, Michael; Jouhten, Paula; Pitkänen, Juha‐Pekka; Toivari, Mervi

Year: 2022

Venue: Frontiers in Bioengineering and Biotechnology

DOI: https://doi.org/10.3389/fbioe.2022.989481

Paper Perspectives and Challenges in Microbial Communities Metabolic Modeling

Bosi, Emanuele; Bacci, Giovanni; Mengoni, Alessio et al. · 2017 · Frontiers in Genetics · DOI

Full title: Perspectives and Challenges in Microbial Communities Metabolic Modeling

Authors: Bosi, Emanuele; Bacci, Giovanni; Mengoni, Alessio; Fondi, Marco

Year: 2017

Venue: Frontiers in Genetics

DOI: https://doi.org/10.3389/fgene.2017.00088

Paper Multi-scale models of whole cells: progress and challenges

Georgouli, Konstantia; Yeom, Jae-Seung; Blake, Robert C. et al. · 2023 · Frontiers in Cell and Developmental Biology · DOI

Full title: Multi-scale models of whole cells: progress and challenges

Authors: Georgouli, Konstantia; Yeom, Jae-Seung; Blake, Robert C.; Navid, Ali

Year: 2023

Venue: Frontiers in Cell and Developmental Biology

DOI: https://doi.org/10.3389/fcell.2023.1260507

Paper Integration of Proteomics and Metabolomics Into the Design, Build, Test, Learn Cycle to Improve 3-Hydroxypropionic Acid Production in Aspergillus pseudoterreus

Pomraning, Kyle; Dai, Ziyu; Munoz, Nathalie Munoz et al. · 2021 · Frontiers in Bioengineering and Biotechnology · DOI

Full title: Integration of Proteomics and Metabolomics Into the Design, Build, Test, Learn Cycle to Improve 3-Hydroxypropionic Acid Production in Aspergillus pseudoterreus

Authors: Pomraning, Kyle; Dai, Ziyu; Munoz, Nathalie Munoz; Kim, Young‐Mo; Gao, Yuqian; Deng, Shuang; Kim, Joonhoon; Hofstad, Beth A.; Swita, Marie; Lemmon, Teresa; Collett, James R.; Panisko, Ellen; Webb‐Robertson, Bobbie‐Jo; Zucker, Jeremy; Nicora, Carrie; Paoli, Henrique De; Baker, Scott; Burnum-Johnson, Kristin; Hillson, Nathan J.; Magnuson, Jon

Year: 2021

Venue: Frontiers in Bioengineering and Biotechnology

DOI: https://doi.org/10.3389/fbioe.2021.603832

Paper Characterization of the enzyme kinetics of EMP and HMP pathway in Corynebacterium glutamicum: reference for modeling metabolic networks

Liu, Yang; Li, Xia; Zhang, Yaping et al. · 2023 · Frontiers in Bioengineering and Biotechnology · DOI

Full title: Characterization of the enzyme kinetics of EMP and HMP pathway in Corynebacterium glutamicum: reference for modeling metabolic networks

Authors: Liu, Yang; Li, Xia; Zhang, Yaping; Chen, Linlin; Ouyang, Zhilin; Liao, Daocheng; Zhao, Fengguang; Han, Shuangyan

Year: 2023

Venue: Frontiers in Bioengineering and Biotechnology

DOI: https://doi.org/10.3389/fbioe.2023.1296880

Paper RobOKoD: microbial strain design for (over)production of target compounds

Stanford, Natalie; Millard, Pierre; Swainston, Neil · 2015 · Frontiers in Cell and Developmental Biology · DOI

Full title: RobOKoD: microbial strain design for (over)production of target compounds

Authors: Stanford, Natalie; Millard, Pierre; Swainston, Neil

Year: 2015

Venue: Frontiers in Cell and Developmental Biology

DOI: https://doi.org/10.3389/fcell.2015.00017

Paper Modeling the Metabolism of Arabidopsis thaliana: Application of Network Decomposition and Network Reduction in the Context of Petri Nets

Koch, Ina; Nöthen, J.; Schleiff, Enrico · 2017 · Frontiers in Genetics · DOI

Full title: Modeling the Metabolism of Arabidopsis thaliana: Application of Network Decomposition and Network Reduction in the Context of Petri Nets

Authors: Koch, Ina; Nöthen, J.; Schleiff, Enrico

Year: 2017

Venue: Frontiers in Genetics

DOI: https://doi.org/10.3389/fgene.2017.00085

Paper Metabolic analyses elucidate non-trivial gene targets for amplifying dihydroartemisinic acid production in yeast

Misra, Ashish; Conway, Matthew F.; Johnnie, Joseph et al. · 2013 · Frontiers in Microbiology · DOI

Full title: Metabolic analyses elucidate non-trivial gene targets for amplifying dihydroartemisinic acid production in yeast

Authors: Misra, Ashish; Conway, Matthew F.; Johnnie, Joseph; Qureshi, Tabish M.; Lige, Bao; Derrick, Anne M.; Agbo, Eddy C.; Sriram, Ganesh

Year: 2013

Venue: Frontiers in Microbiology

DOI: https://doi.org/10.3389/fmicb.2013.00200

Paper Data-driven integration of genome-scale regulatory and metabolic network models

Imam, Saheed; Schäuble, Sascha; Brooks, Aaron N. et al. · 2015 · Frontiers in Microbiology · DOI

Full title: Data-driven integration of genome-scale regulatory and metabolic network models

Authors: Imam, Saheed; Schäuble, Sascha; Brooks, Aaron N.; Baliga, Nitin S.; Price, Nathan D.

Year: 2015

Venue: Frontiers in Microbiology

DOI: https://doi.org/10.3389/fmicb.2015.00409

Paper Synthetic biology of cyanobacteria: unique challenges and opportunities

Berla, Bertram M.; Saha, Rajib; Immethun, Cheryl M. et al. · 2013 · Frontiers in Microbiology · DOI

Full title: Synthetic biology of cyanobacteria: unique challenges and opportunities

Authors: Berla, Bertram M.; Saha, Rajib; Immethun, Cheryl M.; Maranas, Costas D.; Moon, Tae Seok; Pakrasi, Himadri B.

Year: 2013

Venue: Frontiers in Microbiology

DOI: https://doi.org/10.3389/fmicb.2013.00246

Paper Challenges and Advances for Genetic Engineering of Non-model Bacteria and Uses in Consolidated Bioprocessing

Yan, Qiang; Fong, Stephen S. · 2017 · Frontiers in Microbiology · DOI

Full title: Challenges and Advances for Genetic Engineering of Non-model Bacteria and Uses in Consolidated Bioprocessing

Authors: Yan, Qiang; Fong, Stephen S.

Year: 2017

Venue: Frontiers in Microbiology

DOI: https://doi.org/10.3389/fmicb.2017.02060

Paper Modeling of Zymomonas mobilis central metabolism for novel metabolic engineering strategies

Kalnenieks, Uldis; Pentjuss, Agris; Rutkis, Reinis et al. · 2014 · Frontiers in Microbiology · DOI

Full title: Modeling of Zymomonas mobilis central metabolism for novel metabolic engineering strategies

Authors: Kalnenieks, Uldis; Pentjuss, Agris; Rutkis, Reinis; Stalidzāns, Egils; Fell, David A.

Year: 2014

Venue: Frontiers in Microbiology

DOI: https://doi.org/10.3389/fmicb.2014.00042

Paper Reconstruction and in silico analysis of an Actinoplanes sp. SE50/110 genome-scale metabolic model for acarbose production

Wang, Yali; Xu, Nan; Ye, Chao et al. · 2015 · Frontiers in Microbiology · DOI

Full title: Reconstruction and in silico analysis of an Actinoplanes sp. SE50/110 genome-scale metabolic model for acarbose production

Authors: Wang, Yali; Xu, Nan; Ye, Chao; Liu, Li; Shi, Zhongping; Wu, Jing

Year: 2015

Venue: Frontiers in Microbiology

DOI: https://doi.org/10.3389/fmicb.2015.00632

Paper Genome-Scale Reconstruction of the Metabolic Network in Oenococcus oeni to Assess Wine Malolactic Fermentation

Mendoza, Sebastián N.; Cañón, Pablo; Contreras, Ángela et al. · 2017 · Frontiers in Microbiology · DOI

Full title: Genome-Scale Reconstruction of the Metabolic Network in Oenococcus oeni to Assess Wine Malolactic Fermentation

Authors: Mendoza, Sebastián N.; Cañón, Pablo; Contreras, Ángela; Ribbeck, Magdalena; Agosín, Eduardo

Year: 2017

Venue: Frontiers in Microbiology

DOI: https://doi.org/10.3389/fmicb.2017.00534

Paper Metabolic functions of Pseudomonas fluorescens strains from Populus deltoides depend on rhizosphere or endosphere isolation compartment

Timm, Collin M.; Campbell, Alisha G.; Utturkar, Sagar M. et al. · 2015 · Frontiers in Microbiology · DOI

Full title: Metabolic functions of Pseudomonas fluorescens strains from Populus deltoides depend on rhizosphere or endosphere isolation compartment

Authors: Timm, Collin M.; Campbell, Alisha G.; Utturkar, Sagar M.; Jun, Se‐Ran; Parales, Rebecca E.; Tan, Watumesa Agustina; Robeson, Michael S.; Lu, Tse-Yuan S.; Jawdy, Sara; Brown, Steven D.; Ussery, David W.; Schadt, Christopher W.; Tuskan, Gerald A.; Doktycz, Mitchel J.; Weston, David J.; Pelletier, Dale A.

Year: 2015

Venue: Frontiers in Microbiology

DOI: https://doi.org/10.3389/fmicb.2015.01118

Paper A Bayesian Framework for the Classification of Microbial Gene Activity States

Disselkoen, Craig; Greco, Brian; Cook, Kaitlyn et al. · 2016 · Frontiers in Microbiology · DOI

Full title: A Bayesian Framework for the Classification of Microbial Gene Activity States

Authors: Disselkoen, Craig; Greco, Brian; Cook, Kaitlyn; Koch, Kristin A.; Lerebours, Reginald; Viss, Chase; Cape, Joshua; Held, Elizabeth; Ashenafi, Yonatan; Fischer, Karen; Acosta, A.V.Y.B.; Cunningham, Mark; Best, Aaron A.; DeJongh, Matthew; Tintle, Nathan

Year: 2016

Venue: Frontiers in Microbiology

DOI: https://doi.org/10.3389/fmicb.2016.01191

Paper Metabolic Engineering of Oleaginous Yeasts for Production of Fuels and Chemicals

Shi, Shuobo; Zhao, Huimin · 2017 · Frontiers in Microbiology · DOI

Full title: Metabolic Engineering of Oleaginous Yeasts for Production of Fuels and Chemicals

Authors: Shi, Shuobo; Zhao, Huimin

Year: 2017

Venue: Frontiers in Microbiology

DOI: https://doi.org/10.3389/fmicb.2017.02185

Paper Network Analyses in Plant Pathogens

Botero, David; Alvarado, Camilo; Bernal, Adriana et al. · 2018 · Frontiers in Microbiology · DOI

Full title: Network Analyses in Plant Pathogens

Authors: Botero, David; Alvarado, Camilo; Bernal, Adriana; Danies, Giovanna; Restrepo, Silvia

Year: 2018

Venue: Frontiers in Microbiology

DOI: https://doi.org/10.3389/fmicb.2018.00035

Paper Simulation of Escherichia coli Dynamics in Biofilms and Submerged Colonies with an Individual-Based Model Including Metabolic Network Information

Tack, Ignace; Nimmegeers, Philippe; Akkermans, Simen et al. · 2017 · Frontiers in Microbiology · DOI

Full title: Simulation of Escherichia coli Dynamics in Biofilms and Submerged Colonies with an Individual-Based Model Including Metabolic Network Information

Authors: Tack, Ignace; Nimmegeers, Philippe; Akkermans, Simen; Hashem, Ihab; Impe, Jan Van

Year: 2017

Venue: Frontiers in Microbiology

DOI: https://doi.org/10.3389/fmicb.2017.02509

Paper Lipid Metabolic Versatility in Malassezia spp. Yeasts Studied through Metabolic Modeling

Triana, Sergio; Cock, Hans de; Ohm, Robin A. et al. · 2017 · Frontiers in Microbiology · DOI

Full title: Lipid Metabolic Versatility in Malassezia spp. Yeasts Studied through Metabolic Modeling

Authors: Triana, Sergio; Cock, Hans de; Ohm, Robin A.; Danies, Giovanna; Wösten, Han A. B.; Restrepo, Silvia; Barrios, Andrés Fernando González; Ramírez, Adriana Marcela Celis

Year: 2017

Venue: Frontiers in Microbiology

DOI: https://doi.org/10.3389/fmicb.2017.01772

Paper Time-Resolved Transcriptomics and Constraint-Based Modeling Identify System-Level Metabolic Features and Overexpression Targets to Increase Spiramycin Production in Streptomyces ambofaciens

Fondi, Marco; Pinatel, Eva; Talà, Adelfia et al. · 2017 · Frontiers in Microbiology · DOI

Full title: Time-Resolved Transcriptomics and Constraint-Based Modeling Identify System-Level Metabolic Features and Overexpression Targets to Increase Spiramycin Production in Streptomyces ambofaciens

Authors: Fondi, Marco; Pinatel, Eva; Talà, Adelfia; Damiano, Fabrizio; Consolandi, Clarissa; Mattorre, Benedetta; Fico, Daniela; Testini, Mariangela; Benedetto, Giuseppe Egidio De; Siculella, Luisa; Bellis, Gianluca De; Alifano, Pietro; Peano, Clelia

Year: 2017

Venue: Frontiers in Microbiology

DOI: https://doi.org/10.3389/fmicb.2017.00835

Paper Identification of FadAB Complexes Involved in Fatty Acid β-Oxidation in Streptomyces coelicolor and Construction of a Triacylglycerol Overproducing strain

Menéndez-Bravo, Simón; Paganini, Julián; Avignone–Rossa, Claudio et al. · 2017 · Frontiers in Microbiology · DOI

Full title: Identification of FadAB Complexes Involved in Fatty Acid β-Oxidation in Streptomyces coelicolor and Construction of a Triacylglycerol Overproducing strain

Authors: Menéndez-Bravo, Simón; Paganini, Julián; Avignone–Rossa, Claudio; Gramajo, Hugo; Arabolaza, Ana

Year: 2017

Venue: Frontiers in Microbiology

DOI: https://doi.org/10.3389/fmicb.2017.01428

Paper Analysis of Piscirickettsia salmonis Metabolism Using Genome-Scale Reconstruction, Modeling, and Testing

Cortés, María Paz; Mendoza, Sebastián N.; Travisany, Dante et al. · 2017 · Frontiers in Microbiology · DOI

Full title: Analysis of Piscirickettsia salmonis Metabolism Using Genome-Scale Reconstruction, Modeling, and Testing

Authors: Cortés, María Paz; Mendoza, Sebastián N.; Travisany, Dante; Gaete, Alexis; Siegel, Anne; Cambiazo, Verónica; Maass, Alejandro

Year: 2017

Venue: Frontiers in Microbiology

DOI: https://doi.org/10.3389/fmicb.2017.02462

Paper Bioproduction of the Recombinant Sweet Protein Thaumatin: Current State of the Art and Perspectives

Joseph, Jewel Ann; Akkermans, Simen; Nimmegeers, Philippe et al. · 2019 · Frontiers in Microbiology · DOI

Full title: Bioproduction of the Recombinant Sweet Protein Thaumatin: Current State of the Art and Perspectives

Authors: Joseph, Jewel Ann; Akkermans, Simen; Nimmegeers, Philippe; Impe, Jan Van

Year: 2019

Venue: Frontiers in Microbiology

DOI: https://doi.org/10.3389/fmicb.2019.00695

Paper Physiological Response of Corynebacterium glutamicum to Increasingly Nutrient-Rich Growth Conditions

Graf, Michaela; Zieringer, Julia; Haas, Thorsten et al. · 2018 · Frontiers in Microbiology · DOI

Full title: Physiological Response of Corynebacterium glutamicum to Increasingly Nutrient-Rich Growth Conditions

Authors: Graf, Michaela; Zieringer, Julia; Haas, Thorsten; Nieß, Alexander; Blombach, Bastian; Takors, Ralf

Year: 2018

Venue: Frontiers in Microbiology

DOI: https://doi.org/10.3389/fmicb.2018.02058

Paper The Genome-Scale Integrated Networks in Microorganisms

Hao, Tong; Wu, Dan; Zhao, Lingxuan et al. · 2018 · Frontiers in Microbiology · DOI

Full title: The Genome-Scale Integrated Networks in Microorganisms

Authors: Hao, Tong; Wu, Dan; Zhao, Lingxuan; Wang, Qian; Wang, Edwin; Sun, Jinsheng

Year: 2018

Venue: Frontiers in Microbiology

DOI: https://doi.org/10.3389/fmicb.2018.00296

Paper In Silico Analysis of the Small Molecule Content of Outer Membrane Vesicles Produced by Bacteroides thetaiotaomicron Indicates an Extensive Metabolic Link between Microbe and Host

Bryant, William A; Stentz, Régis; Gall, Gwénaëlle Le et al. · 2017 · Frontiers in Microbiology · DOI

Full title: In Silico Analysis of the Small Molecule Content of Outer Membrane Vesicles Produced by Bacteroides thetaiotaomicron Indicates an Extensive Metabolic Link between Microbe and Host

Authors: Bryant, William A; Stentz, Régis; Gall, Gwénaëlle Le; Sternberg, Michael J.E.; Carding, Simon R.; Wilhelm, Thomas

Year: 2017

Venue: Frontiers in Microbiology

DOI: https://doi.org/10.3389/fmicb.2017.02440

Paper Determinism and Contingency Shape Metabolic Complementation in an Endosymbiotic Consortium

Ponce-de-León, Miguel; Tamarit, Daniel; Calle-Espinosa, Jorge et al. · 2017 · Frontiers in Microbiology · DOI

Full title: Determinism and Contingency Shape Metabolic Complementation in an Endosymbiotic Consortium

Authors: Ponce-de-León, Miguel; Tamarit, Daniel; Calle-Espinosa, Jorge; Mori, Matteo; Latorre, Amparo; Montero, Francisco; Peretό, Juli

Year: 2017

Venue: Frontiers in Microbiology

DOI: https://doi.org/10.3389/fmicb.2017.02290

Paper Reconstruction and Analysis of a Genome-Scale Metabolic Model of Ganoderma lucidum for Improved Extracellular Polysaccharide Production

Ma, Zhongbao; Ye, Chao; Deng, Wei‐Wei et al. · 2018 · Frontiers in Microbiology · DOI

Full title: Reconstruction and Analysis of a Genome-Scale Metabolic Model of Ganoderma lucidum for Improved Extracellular Polysaccharide Production

Authors: Ma, Zhongbao; Ye, Chao; Deng, Wei‐Wei; Xu, Mengmeng; Wang, Qiong; Liu, Gao‐Qiang; Wang, Feng; Liu, Li; Xu, Zhenghong; Shi, Guiyang; Ding, Zhongyang

Year: 2018

Venue: Frontiers in Microbiology

DOI: https://doi.org/10.3389/fmicb.2018.03076

Paper Approaches to Computational Strain Design in the Multiomics Era

John, Peter C. St.; Bomble, Yannick J. · 2019 · Frontiers in Microbiology · DOI

Full title: Approaches to Computational Strain Design in the Multiomics Era

Authors: John, Peter C. St.; Bomble, Yannick J.

Year: 2019

Venue: Frontiers in Microbiology

DOI: https://doi.org/10.3389/fmicb.2019.00597

Paper Does It Pay Off to Explicitly Link Functional Gene Expression to Denitrification Rates in Reaction Models?

Störiko, Anna; Pagel, Holger; Mellage, Adrian et al. · 2021 · Frontiers in Microbiology · DOI

Full title: Does It Pay Off to Explicitly Link Functional Gene Expression to Denitrification Rates in Reaction Models?

Authors: Störiko, Anna; Pagel, Holger; Mellage, Adrian; Cirpka, Olaf A.

Year: 2021

Venue: Frontiers in Microbiology

DOI: https://doi.org/10.3389/fmicb.2021.684146

Paper iDS372, a Phenotypically Reconciled Model for the Metabolism of Streptococcus pneumoniae Strain R6

Dias, Óscar; Saraiva, J.; Faria, Cristiana et al. · 2019 · Frontiers in Microbiology · DOI

Full title: iDS372, a Phenotypically Reconciled Model for the Metabolism of Streptococcus pneumoniae Strain R6

Authors: Dias, Óscar; Saraiva, J.; Faria, Cristiana; Ramirez, Mário; Pinto, Francisco; Rocha, Isabel

Year: 2019

Venue: Frontiers in Microbiology

DOI: https://doi.org/10.3389/fmicb.2019.01283

Paper Metagenomics-Based, Strain-Level Analysis of Escherichia coli From a Time-Series of Microbiome Samples From a Crohn's Disease Patient

Fang, Xin; Monk, Jonathan M.; Nurk, Sergey et al. · 2018 · Frontiers in Microbiology · DOI

Full title: Metagenomics-Based, Strain-Level Analysis of Escherichia coli From a Time-Series of Microbiome Samples From a Crohn's Disease Patient

Authors: Fang, Xin; Monk, Jonathan M.; Nurk, Sergey; Akseshina, Margarita; Zhu, Qiyun; Gemmell, Christopher; Gianetto-Hill, Connor; Leung, Nelly; Szubin, Richard; Sanders, Jon G.; Beck, Paul L.; Li, Weizhong; Sandborn, William J.; Gray‐Owen, Scott D.; Knight, Rob; Allen‐Vercoe, Emma; Palsson, Bernhard Ø.; Smarr, Larry

Year: 2018

Venue: Frontiers in Microbiology

DOI: https://doi.org/10.3389/fmicb.2018.02559

Paper Synergies of Systems Biology and Synthetic Biology in Human Microbiome Studies

Ezzamouri, Bouchra; Shoaie, Saeed; Ledesma‐Amaro, Rodrigo · 2021 · Frontiers in Microbiology · DOI

Full title: Synergies of Systems Biology and Synthetic Biology in Human Microbiome Studies

Authors: Ezzamouri, Bouchra; Shoaie, Saeed; Ledesma‐Amaro, Rodrigo

Year: 2021

Venue: Frontiers in Microbiology

DOI: https://doi.org/10.3389/fmicb.2021.681982

Paper Rewiring of Metabolic Network in Mycobacterium tuberculosis During Adaptation to Different Stresses

Rizvi, Arshad; Shankar, Arvind Jaya; Chatterjee, A. et al. · 2019 · Frontiers in Microbiology · DOI

Full title: Rewiring of Metabolic Network in Mycobacterium tuberculosis During Adaptation to Different Stresses

Authors: Rizvi, Arshad; Shankar, Arvind Jaya; Chatterjee, A.; More, Tushar H.; Bose, Tungadri; Dutta, Anirban; Balakrishnan, Kannan; Madugulla, Lavanya; Rapole, Srikanth; Mande, Sharmila S.; Banerjee, Sharmistha; Mande, Shekhar C.

Year: 2019

Venue: Frontiers in Microbiology

DOI: https://doi.org/10.3389/fmicb.2019.02417

Paper Systems Biology – A Guide for Understanding and Developing Improved Strains of Lactic Acid Bacteria

Liu, Jianming; Chan, Siu Hung Joshua; Chen, Jun et al. · 2019 · Frontiers in Microbiology · DOI

Full title: Systems Biology – A Guide for Understanding and Developing Improved Strains of Lactic Acid Bacteria

Authors: Liu, Jianming; Chan, Siu Hung Joshua; Chen, Jun; Solem, Christian; Jensen, Peter Ruhdal

Year: 2019

Venue: Frontiers in Microbiology

DOI: https://doi.org/10.3389/fmicb.2019.00876

Paper Uncovering the Role of Metabolism in Oomycete–Host Interactions Using Genome-Scale Metabolic Models

Rodenburg, Sander Y.A.; Seidl, Michael; Ridder, Dick de et al. · 2021 · Frontiers in Microbiology · DOI

Full title: Uncovering the Role of Metabolism in Oomycete–Host Interactions Using Genome-Scale Metabolic Models

Authors: Rodenburg, Sander Y.A.; Seidl, Michael; Ridder, Dick de; Govers, Francine

Year: 2021

Venue: Frontiers in Microbiology

DOI: https://doi.org/10.3389/fmicb.2021.748178

Paper Reconstructed Metabolic Network Models Predict Flux-Level Metabolic Reprogramming in Glioblastoma

Özcan, Emrah; Çakır, Tunahan · 2016 · Frontiers in Neuroscience · DOI

Full title: Reconstructed Metabolic Network Models Predict Flux-Level Metabolic Reprogramming in Glioblastoma

Authors: Özcan, Emrah; Çakır, Tunahan

Year: 2016

Venue: Frontiers in Neuroscience

DOI: https://doi.org/10.3389/fnins.2016.00156

Paper Combination of Genome-Scale Models and Bioreactor Dynamics to Optimize the Production of Commodity Chemicals

Lázaro, Jorge; Jansen, Giorgio; Yang, Yiheng et al. · 2022 · Frontiers in Molecular Biosciences · DOI

Full title: Combination of Genome-Scale Models and Bioreactor Dynamics to Optimize the Production of Commodity Chemicals

Authors: Lázaro, Jorge; Jansen, Giorgio; Yang, Yiheng; Torres‐Acosta, Mario A.; Lye, Gary J.; Oliver, Stephen G.; Júlvez, Jorge

Year: 2022

Venue: Frontiers in Molecular Biosciences

DOI: https://doi.org/10.3389/fmolb.2022.855735

Paper Metabolic network reconstruction of Euglena gracilis: Current state, challenges, and applications

Inwongwan, Sahutchai; Pekkoh, Jeeraporn; Pumas, Chayakorn et al. · 2023 · Frontiers in Microbiology · DOI

Full title: Metabolic network reconstruction of Euglena gracilis: Current state, challenges, and applications

Authors: Inwongwan, Sahutchai; Pekkoh, Jeeraporn; Pumas, Chayakorn; Sattayawat, Pachara

Year: 2023

Venue: Frontiers in Microbiology

DOI: https://doi.org/10.3389/fmicb.2023.1143770

Paper Combining metabolic flux analysis with proteomics to shed light on the metabolic flexibility: the case of Desulfovibrio vulgaris Hildenborough

Marbehan, Xavier; Roger, Magali; Fournier, Frantz et al. · 2024 · Frontiers in Microbiology · DOI

Full title: Combining metabolic flux analysis with proteomics to shed light on the metabolic flexibility: the case of Desulfovibrio vulgaris Hildenborough

Authors: Marbehan, Xavier; Roger, Magali; Fournier, Frantz; Infossi, Pascale; Guédon, Emmanuel; Delecourt, Louis; Lebrun, Régine; Giudici‐Orticoni, Marie‐Thérèse; Delaunay, Stéphane

Year: 2024

Venue: Frontiers in Microbiology

DOI: https://doi.org/10.3389/fmicb.2024.1336360

Paper Metabolic behavior for a mutant Oenococcus oeni strain with high resistance to ethanol to survive under oenological multi-stress conditions

Contreras, Ángela; Díaz, Gabriela; Mendoza, Sebastián N. et al. · 2023 · Frontiers in Microbiology · DOI

Full title: Metabolic behavior for a mutant Oenococcus oeni strain with high resistance to ethanol to survive under oenological multi-stress conditions

Authors: Contreras, Ángela; Díaz, Gabriela; Mendoza, Sebastián N.; Canto, Mauricio; Agosín, Eduardo

Year: 2023

Venue: Frontiers in Microbiology

DOI: https://doi.org/10.3389/fmicb.2023.1100501

Paper Flux balance analysis reveals acetate metabolism modulates cyclic electron flow and alternative glycolytic pathways in Chlamydomonas reinhardtii

Chapman, Stephen P.; Paget, Caroline M.; Johnson, Giles N. et al. · 2015 · Frontiers in Plant Science · DOI

Full title: Flux balance analysis reveals acetate metabolism modulates cyclic electron flow and alternative glycolytic pathways in Chlamydomonas reinhardtii

Authors: Chapman, Stephen P.; Paget, Caroline M.; Johnson, Giles N.; Schwartz, Jean‐Marc

Year: 2015

Venue: Frontiers in Plant Science

DOI: https://doi.org/10.3389/fpls.2015.00474

Paper Applications of Genome-Scale Metabolic Models in Biotechnology and Systems Medicine

Zhang, Cheng; Hua, Qiang · 2016 · Frontiers in Physiology · DOI

Full title: Applications of Genome-Scale Metabolic Models in Biotechnology and Systems Medicine

Authors: Zhang, Cheng; Hua, Qiang

Year: 2016

Venue: Frontiers in Physiology

DOI: https://doi.org/10.3389/fphys.2015.00413

Paper Predictive sulfur metabolism â€“ a field in flux

Calderwood, Alexander; Morris, Richard J.; Kopřiva, Stanislav · 2014 · Frontiers in Plant Science · DOI

Full title: Predictive sulfur metabolism â€“ a field in flux

Authors: Calderwood, Alexander; Morris, Richard J.; Kopřiva, Stanislav

Year: 2014

Venue: Frontiers in Plant Science

DOI: https://doi.org/10.3389/fpls.2014.00646

Paper Bioinformatic Analysis of Metabolomic Data: From Raw Spectra to Biological Insight

Santamaria, Guillem; Pinto, Francisco · 2024 · BioChem · DOI

Full title: Bioinformatic Analysis of Metabolomic Data: From Raw Spectra to Biological Insight

Authors: Santamaria, Guillem; Pinto, Francisco

Year: 2024

Venue: BioChem

DOI: https://doi.org/10.3390/biochem4020005

Paper Flux Balance Analysis of Plant Metabolism: The Effect of Biomass Composition and Model Structure on Model Predictions

Yuan, Huili; Cheung, C. Y. Maurice; Hilbers, P.A.J. et al. · 2016 · Frontiers in Plant Science · DOI

Full title: Flux Balance Analysis of Plant Metabolism: The Effect of Biomass Composition and Model Structure on Model Predictions

Authors: Yuan, Huili; Cheung, C. Y. Maurice; Hilbers, P.A.J.; Riel, N.A.W. van

Year: 2016

Venue: Frontiers in Plant Science

DOI: https://doi.org/10.3389/fpls.2016.00537

Paper Questions, data and models underpinning metabolic engineering

Rosmalen, Rik P. van; Santos, Vítor A. P. Martins dos; Suárez‐Diez, María · 2022 · Frontiers in Systems Biology · DOI

Full title: Questions, data and models underpinning metabolic engineering

Authors: Rosmalen, Rik P. van; Santos, Vítor A. P. Martins dos; Suárez‐Diez, María

Year: 2022

Venue: Frontiers in Systems Biology

DOI: https://doi.org/10.3389/fsysb.2022.998048

Paper Integration of metabolomics data into metabolic networks

TÃ¶pfer, Nadine; Kleeßen, Sabrina; Nikoloski, Zoran · 2015 · Frontiers in Plant Science · DOI

Full title: Integration of metabolomics data into metabolic networks

Authors: TÃ¶pfer, Nadine; Kleeßen, Sabrina; Nikoloski, Zoran

Year: 2015

Venue: Frontiers in Plant Science

DOI: https://doi.org/10.3389/fpls.2015.00049

Paper From Spatial-Temporal Multiscale Modeling to Application: Bridging the Valley of Death in Industrial Biotechnology

Wang, Xueting; Mohsin, Ali; Sun, Yifei et al. · 2023 · Bioengineering · DOI

Full title: From Spatial-Temporal Multiscale Modeling to Application: Bridging the Valley of Death in Industrial Biotechnology

Authors: Wang, Xueting; Mohsin, Ali; Sun, Yifei; Li, Chao; Zhuang, Yingping; Wang, Guan

Year: 2023

Venue: Bioengineering

Paper Prediction of Metabolic Flux Distribution by Flux Sampling: As a Case Study, Acetate Production from Glucose in Escherichia coli

Kuriya, Yuki; Murata, Masahiro; Yamamoto, Masaki et al. · 2023 · Bioengineering · DOI

Full title: Prediction of Metabolic Flux Distribution by Flux Sampling: As a Case Study, Acetate Production from Glucose in Escherichia coli

Authors: Kuriya, Yuki; Murata, Masahiro; Yamamoto, Masaki; Watanabe, Naoki; Araki, Michihiro

Year: 2023

Venue: Bioengineering

DOI: https://doi.org/10.3390/bioengineering10060636

Paper Genome-Scale Metabolic Reconstruction and in Silico Perturbation Analysis of the Polar Diatom Fragilariopsis cylindrus Predicts High Metabolic Robustness

Lavoie, Michel; Saint‐Béat, Blanche; Strauss, Jan et al. · 2020 · Biology · DOI

Full title: Genome-Scale Metabolic Reconstruction and in Silico Perturbation Analysis of the Polar Diatom Fragilariopsis cylindrus Predicts High Metabolic Robustness

Authors: Lavoie, Michel; Saint‐Béat, Blanche; Strauss, Jan; Guérin, Sébastien; Allard, Antoine; Hardy, Simon; Falciatore, Angela; Lavaud, Johann

Year: 2020

Venue: Biology

DOI: https://doi.org/10.3390/biology9020030

Paper Probing Genome-Scale Model Reveals Metabolic Capability and Essential Nutrients for Growth of Probiotic Limosilactobacillus reuteri KUB-AC5

Namrak, Thanawat; Raethong, Nachon; Jatuponwiphat, Theeraphol et al. · 2022 · Biology · DOI

Full title: Probing Genome-Scale Model Reveals Metabolic Capability and Essential Nutrients for Growth of Probiotic Limosilactobacillus reuteri KUB-AC5

Authors: Namrak, Thanawat; Raethong, Nachon; Jatuponwiphat, Theeraphol; Nitisinprasert, Sunee; Vongsangnak, Wanwipa; Nakphaichit, Massalin

Year: 2022

Venue: Biology

DOI: https://doi.org/10.3390/biology11020294

Paper Simultaneous Integration of Gene Expression and Nutrient Availability for Studying the Metabolism of Hepatocellular Carcinoma Cell Lines

Węglarz‐Tomczak, Ewelina; Mondeel, Thierry D.G.A.; Piebes, Diewertje et al. · 2021 · Biomolecules · DOI

Full title: Simultaneous Integration of Gene Expression and Nutrient Availability for Studying the Metabolism of Hepatocellular Carcinoma Cell Lines

Authors: Węglarz‐Tomczak, Ewelina; Mondeel, Thierry D.G.A.; Piebes, Diewertje; Westerhoff, Hans V.

Year: 2021

Venue: Biomolecules

DOI: https://doi.org/10.3390/biom11040490

Paper Optimization and Scale-Up of Fermentation Processes Driven by Models

Du, Yuan‐Hang; Wang, Min-Yu; Yang, Linhui et al. · 2022 · Bioengineering · DOI

Full title: Optimization and Scale-Up of Fermentation Processes Driven by Models

Authors: Du, Yuan‐Hang; Wang, Min-Yu; Yang, Linhui; Tong, Lingling; Guo, Dong‐Sheng; Ji, Xiao‐Jun

Year: 2022

Venue: Bioengineering

DOI: https://doi.org/10.3390/bioengineering9090473

Paper ECMpy, a Simplified Workflow for Constructing Enzymatic Constrained Metabolic Network Model

Zhitao Mao; Xin Zhao; Xue Yang et al. · 2022 · Biomolecules · DOI

Full title: ECMpy, a Simplified Workflow for Constructing Enzymatic Constrained Metabolic Network Model

Authors: Zhitao Mao; Xin Zhao; Xue Yang; Peiji Zhang; Jiawei Du; Qianqian Yuan; Hongwu Ma

Year: 2022

Venue: Biomolecules

DOI: https://doi.org/10.3390/bioengineering8080103

Paper TCA Cycle and Its Relationship with Clavulanic Acid Production: A Further Interpretation by Using a Reduced Genome-Scale Metabolic Model of Streptomyces clavuligerus

Ramírez-Malule, Howard; López-Agudelo, Víctor A.; Gómez-Ríos, David et al. · 2021 · Bioengineering · DOI

Full title: TCA Cycle and Its Relationship with Clavulanic Acid Production: A Further Interpretation by Using a Reduced Genome-Scale Metabolic Model of Streptomyces clavuligerus

Authors: Ramírez-Malule, Howard; López-Agudelo, Víctor A.; Gómez-Ríos, David; Ochoa, Silvia; Ríos‐Estepa, Rigoberto; Junne, Stefan; Neubauer, Peter

Year: 2021

Venue: Bioengineering

Paper In Silico Design Strategies for the Production of Target Chemical Compounds Using Iterative Single-Level Linear Programming Problems

Shirai, Tomokazu; Kondo, Akihiko · 2022 · Biomolecules · DOI

Full title: In Silico Design Strategies for the Production of Target Chemical Compounds Using Iterative Single-Level Linear Programming Problems

Authors: Shirai, Tomokazu; Kondo, Akihiko

Year: 2022

Venue: Biomolecules

DOI: https://doi.org/10.3390/biom12050620

Paper From Shallow to Deep Bioprocess Hybrid Modeling: Advances and Future Perspectives

Agharafeie, Roshanak; Ramos, João R. C.; Mendes, Jorge M. et al. · 2023 · Fermentation · DOI

Full title: From Shallow to Deep Bioprocess Hybrid Modeling: Advances and Future Perspectives

Authors: Agharafeie, Roshanak; Ramos, João R. C.; Mendes, Jorge M.; Oliveira, Rui

Year: 2023

Venue: Fermentation

Paper Substrate Gas Utilization and C3/C4 Metabolic Analysis of Actinobacillus succinogenes: Integration into a Model for Fermentation Prediction in BES

Tix, Julian; Bode, Joshua; Gotthardt, Leon et al. · 2025 · Fermentation · DOI

Full title: Substrate Gas Utilization and C3/C4 Metabolic Analysis of Actinobacillus succinogenes: Integration into a Model for Fermentation Prediction in BES

Authors: Tix, Julian; Bode, Joshua; Gotthardt, Leon; Tippkötter, N.

Year: 2025

Venue: Fermentation

DOI: https://doi.org/10.3390/fermentation11050263

Paper Insights on the Advancements of In Silico Metabolic Studies of Succinic Acid Producing Microorganisms: A Review with Emphasis on Actinobacillus succinogenes

Dessie, Wubliker; Wang, Zongcheng; Luo, Xiaofang et al. · 2021 · Fermentation · DOI

Full title: Insights on the Advancements of In Silico Metabolic Studies of Succinic Acid Producing Microorganisms: A Review with Emphasis on Actinobacillus succinogenes

Authors: Dessie, Wubliker; Wang, Zongcheng; Luo, Xiaofang; Wang, Meifeng; Qin, Zuodong

Year: 2021

Venue: Fermentation

DOI: https://doi.org/10.3390/fermentation7040220

Paper Construction of Multiscale Genome-Scale Metabolic Models: Frameworks and Challenges

Bi, Xinyu; Liu, Yanfeng; Li, Jianghua et al. · 2022 · Biomolecules · DOI

Full title: Construction of Multiscale Genome-Scale Metabolic Models: Frameworks and Challenges

Authors: Bi, Xinyu; Liu, Yanfeng; Li, Jianghua; Du, Guocheng; Lv, Xueqin; Liu, Long

Year: 2022

Venue: Biomolecules

DOI: https://doi.org/10.3390/biom12050721

Paper Impact of Waste as a Substrate on Biomass Formation, and Optimization of Spent Microbial Biomass Re-Use by Sustainable Metabolic Engineering

Stikane, Anna; Baumanis, Matiss Ricards; Muiznieks, Reinis et al. · 2023 · Fermentation · DOI

Full title: Impact of Waste as a Substrate on Biomass Formation, and Optimization of Spent Microbial Biomass Re-Use by Sustainable Metabolic Engineering

Authors: Stikane, Anna; Baumanis, Matiss Ricards; Muiznieks, Reinis; Stalidzāns, Egils

Year: 2023

Venue: Fermentation

DOI: https://doi.org/10.3390/fermentation9060531

Paper A Genome-Scale Metabolic Model for the Human Pathogen Candida Parapsilosis and Early Identification of Putative Novel Antifungal Drug Targets

Viana, Romeu; Couceiro, Diogo; Carreiro, Tiago et al. · 2022 · Genes · DOI

Full title: A Genome-Scale Metabolic Model for the Human Pathogen Candida Parapsilosis and Early Identification of Putative Novel Antifungal Drug Targets

Authors: Viana, Romeu; Couceiro, Diogo; Carreiro, Tiago; Dias, Óscar; Rocha, Isabel; Teixeira, Miguel C.

Year: 2022

Venue: Genes

DOI: https://doi.org/10.3390/genes13020303

Paper Optimized De Novo Eriodictyol Biosynthesis in Streptomyces albidoflavus Using an Expansion of the Golden Standard Toolkit for Its Use in Actinomycetes

Magadán‐Corpas, Patricia; Ye, Suhui; Pérez‐Valero, Álvaro et al. · 2023 · International Journal of Molecular Sciences · DOI

Full title: Optimized De Novo Eriodictyol Biosynthesis in Streptomyces albidoflavus Using an Expansion of the Golden Standard Toolkit for Its Use in Actinomycetes

Authors: Magadán‐Corpas, Patricia; Ye, Suhui; Pérez‐Valero, Álvaro; McAlpine, Patrick L.; Valdés-Chiara, Paula; Torres‐Bacete, Jesús; Nogales, Juan; Villar, Claudio J.; Lombó, Felipe

Year: 2023

Venue: International Journal of Molecular Sciences

DOI: https://doi.org/10.3390/ijms24108879

Paper Genome-Scale Metabolic Model of Actinosynnema pretiosum ATCC 31280 and Its Application for Ansamitocin P-3 Production Improvement

Li, Jian; Sun, Renliang; Ning, Xinjuan et al. · 2018 · Genes · DOI

Full title: Genome-Scale Metabolic Model of Actinosynnema pretiosum ATCC 31280 and Its Application for Ansamitocin P-3 Production Improvement

Authors: Li, Jian; Sun, Renliang; Ning, Xinjuan; Wang, Xinran; Wang, Zhuo

Year: 2018

Venue: Genes

DOI: https://doi.org/10.3390/genes9070364

Paper Metabolic model integration of the bibliome, genome, metabolome and reactome of Aspergillus niger

Andersen, Mikael Rørdam; Nielsen, Michael Lynge; Nielsen, Jens · 2008 · Molecular Systems Biology · DOI

Full title: Metabolic model integration of the bibliome, genome, metabolome and reactome of Aspergillus niger

Authors: Andersen, Mikael Rørdam; Nielsen, Michael Lynge; Nielsen, Jens

Year: 2008

Venue: Molecular Systems Biology

DOI: https://doi.org/10.1038/msb.2008.12

Paper A genome‐scale computational study of the interplay between transcriptional regulation and metabolism

Shlomi, Tomer; Eisenberg, Yariv; Sharan, Roded et al. · 2007 · Molecular Systems Biology · DOI

Full title: A genome‐scale computational study of the interplay between transcriptional regulation and metabolism

Authors: Shlomi, Tomer; Eisenberg, Yariv; Sharan, Roded; Ruppin, Eytan

Year: 2007

Venue: Molecular Systems Biology

DOI: https://doi.org/10.1038/msb4100141

Paper Integrative genome‐scale metabolic analysis of Vibrio vulnificus for drug targeting and discovery

Kim, Hyun Uk; Kim, Soo Young; Jeong, Haeyoung et al. · 2011 · Molecular Systems Biology · DOI

Full title: Integrative genome‐scale metabolic analysis of Vibrio vulnificus for drug targeting and discovery

Authors: Kim, Hyun Uk; Kim, Soo Young; Jeong, Haeyoung; Kim, Tae Yong; Kim, Jae Jong; Choy, Hyon E.; Yi, Kyu Yang; Rhee, Joon Haeng; Lee, Sang Yup

Year: 2011

Venue: Molecular Systems Biology

DOI: https://doi.org/10.1038/msb.2010.115

Paper Omic data from evolved E. coli are consistent with computed optimal growth from genome‐scale models

Lewis, Nathan E.; Hixson, Kim; Conrad, Tom M et al. · 2010 · Molecular Systems Biology · DOI

Full title: Omic data from evolved E. coli are consistent with computed optimal growth from genome‐scale models

Authors: Lewis, Nathan E.; Hixson, Kim; Conrad, Tom M; Lerman, Joshua A.; Charusanti, Pep; Polpitiya, Ashoka D.; Adkins, Joshua; Schramm, Gunnar; Purvine, Samuel; López‐Ferrer, Daniel; Weitz, Karl; Eils, Roland; König, Rainer; Smith, Richard; Palsson, Bernhard Ø.

Year: 2010

Venue: Molecular Systems Biology

DOI: https://doi.org/10.1038/msb.2010.47

Paper Reconstruction and flux‐balance analysis of the Plasmodium falciparum metabolic network

Plata, Germán; Hsiao, Tzu‐Lin; Olszewski, Kellen et al. · 2010 · Molecular Systems Biology · DOI

Full title: Reconstruction and flux‐balance analysis of the Plasmodium falciparum metabolic network

Authors: Plata, Germán; Hsiao, Tzu‐Lin; Olszewski, Kellen; Llinás, Manuel; Vitkup, Dennis

Year: 2010

Venue: Molecular Systems Biology

DOI: https://doi.org/10.1038/msb.2010.60

Paper Reconciled rat and human metabolic networks for comparative toxicogenomics and biomarker predictions

Blais, Edik M.; Rawls, Kristopher D.; Dougherty, Bonnie V. et al. · 2017 · Nature Communications · DOI

Full title: Reconciled rat and human metabolic networks for comparative toxicogenomics and biomarker predictions

Authors: Blais, Edik M.; Rawls, Kristopher D.; Dougherty, Bonnie V.; Li, Zhuo I.; Kolling, Glynis L.; Ye, Ping; Wallqvist, Anders; Papin, Jason A.

Year: 2017

Venue: Nature Communications

DOI: https://doi.org/10.1038/ncomms14250

Paper A genome-scale Escherichia coli kinetic metabolic model k-ecoli457 satisfying flux data for multiple mutant strains

Khodayari, Ali; Maranas, Costas D. · 2016 · Nature Communications · DOI

Full title: A genome-scale Escherichia coli kinetic metabolic model k-ecoli457 satisfying flux data for multiple mutant strains

Authors: Khodayari, Ali; Maranas, Costas D.

Year: 2016

Venue: Nature Communications

DOI: https://doi.org/10.1038/ncomms13806

Paper Characterization and modelling of interspecies electron transfer mechanisms and microbial community dynamics of a syntrophic association

Nagarajan, Harish; Embree, Mallory; Rotaru, Amelia‐Elena et al. · 2013 · Nature Communications · DOI

Full title: Characterization and modelling of interspecies electron transfer mechanisms and microbial community dynamics of a syntrophic association

Authors: Nagarajan, Harish; Embree, Mallory; Rotaru, Amelia‐Elena; Shrestha, Pravin Malla; Feist, Adam M.; Palsson, Bernhard Ø.; Lovley, Derek R.; Zengler, Karsten

Year: 2013

Venue: Nature Communications

DOI: https://doi.org/10.1038/ncomms3809

Paper Integrating highly quantitative proteomics and genome-scale metabolic modeling to study pH adaptation in the human pathogen Enterococcus faecalis

Großeholz, Ruth; Koh, Ching-Chiek; Veith, Nadine et al. · 2016 · npj Systems Biology and Applications · DOI

Full title: Integrating highly quantitative proteomics and genome-scale metabolic modeling to study pH adaptation in the human pathogen Enterococcus faecalis

Authors: Großeholz, Ruth; Koh, Ching-Chiek; Veith, Nadine; Fiedler, Tomas; Strauß, Madlen; Olivier, Brett G.; Collins, Ben C.; Schubert, Olga T.; Bergmann, Frank; Kreikemeyer, Bernd; Aebersold, Ruedi; Kummer, Ursula

Year: 2016

Venue: npj Systems Biology and Applications

DOI: https://doi.org/10.1038/npjsba.2016.17

Paper Predicting network functions with nested patterns

Ganter, Mathias; Kaltenbach, Hans‐Michael; Stelling, Jörg · 2014 · Nature Communications · DOI

Full title: Predicting network functions with nested patterns

Authors: Ganter, Mathias; Kaltenbach, Hans‐Michael; Stelling, Jörg

Year: 2014

Venue: Nature Communications

DOI: https://doi.org/10.1038/ncomms4006

Paper COBRA Toolbox 2.0

Hyduke, Daniel R.; Hyduke, Daniel R.; Schellenberger, Jan et al. · 2011 · Protocol Exchange · DOI

Full title: COBRA Toolbox 2.0

Authors: Hyduke, Daniel R.; Hyduke, Daniel R.; Schellenberger, Jan; Que, Richard; Fleming, Ronan M. T.; Thiele, Ines; Orth, Jeffery; Feist, Adam M.; Zielinski, Daniel C.; Bordbar, Aarash; Lewis, Nathan E.; Rahmanian, Sorena; Kang, Joseph; Palsson, Bernhard Ø.

Year: 2011

Venue: Protocol Exchange

DOI: https://doi.org/10.1038/protex.2011.234

Paper MUFINS: multi-formalism interaction network simulator

Wu, Huihai; Kamp, Axel von; Leoncikas, Vytautas et al. · 2016 · npj Systems Biology and Applications · DOI

Full title: MUFINS: multi-formalism interaction network simulator

Authors: Wu, Huihai; Kamp, Axel von; Leoncikas, Vytautas; Mori, Wataru; Sahin, Nilgun; Gevorgyan, Albert; Linley, Catherine; Grabowski, M.; Mannan, Ahmad A.; Stoy, Nicholas; Stewart, Graham R.; Ward, Lara; Lewis, David; Sroka, Jacek; Matsuno, Hiroshi; Klamt, Steffen; Westerhoff, Hans V.; McFadden, Johnjoe; Plant, Nick; Kierzek, Andrzej

Year: 2016

Venue: npj Systems Biology and Applications

DOI: https://doi.org/10.1038/npjsba.2016.32

Paper Synthetic and systems biology for microbial production of commodity chemicals

Chubukov, Victor; Mukhopadhyay, Aindrila; Petzold, Christopher J. et al. · 2016 · npj Systems Biology and Applications · DOI

Full title: Synthetic and systems biology for microbial production of commodity chemicals

Authors: Chubukov, Victor; Mukhopadhyay, Aindrila; Petzold, Christopher J.; Keasling, Jay D.; Martín, Héctor García

Year: 2016

Venue: npj Systems Biology and Applications

DOI: https://doi.org/10.1038/npjsba.2016.9

Paper Microbial carbon use efficiency predicted from genome-scale metabolic models

Saifuddin, Mustafa; Bhatnagar, Jennifer; Segrè, Daniel et al. · 2019 · Nature Communications · DOI

Full title: Microbial carbon use efficiency predicted from genome-scale metabolic models

Authors: Saifuddin, Mustafa; Bhatnagar, Jennifer; Segrè, Daniel; Finzi, Adrien C.

Year: 2019

Venue: Nature Communications

DOI: https://doi.org/10.1038/s41467-019-11488-z

Paper Costless metabolic secretions as drivers of interspecies interactions in microbial ecosystems

Pacheco, Alan R.; Moel, Mauricio; Segrè, Daniel · 2019 · Nature Communications · DOI

Full title: Costless metabolic secretions as drivers of interspecies interactions in microbial ecosystems

Authors: Pacheco, Alan R.; Moel, Mauricio; Segrè, Daniel

Year: 2019

Venue: Nature Communications

DOI: https://doi.org/10.1038/s41467-018-07946-9

Paper A consensus S. cerevisiae metabolic model Yeast8 and its ecosystem for comprehensively probing cellular metabolism

Lu, Hongzhong; Li, Feiran; Sánchez, Benjamín J. et al. · 2019 · Nature Communications · DOI

Full title: A consensus S. cerevisiae metabolic model Yeast8 and its ecosystem for comprehensively probing cellular metabolism

Authors: Lu, Hongzhong; Li, Feiran; Sánchez, Benjamín J.; Zhu, Zhengming; Li, Gang; Domenzain, Iván; Marcišauskas, Simonas; Anton, Mihail; Lappa, Dimitra; Lieven, Christian; Beber, Moritz E.; Sonnenschein, Nikolaus; Kerkhoven, Eduard J.; Nielsen, Jens

Year: 2019

Venue: Nature Communications

DOI: https://doi.org/10.1038/s41467-019-11581-3

Paper Machine learning applied to enzyme turnover numbers reveals protein structural correlates and improves metabolic models

Heckmann, David; Lloyd, Colton J.; Mih, Nathan et al. · 2018 · Nature Communications · DOI

Full title: Machine learning applied to enzyme turnover numbers reveals protein structural correlates and improves metabolic models

Authors: Heckmann, David; Lloyd, Colton J.; Mih, Nathan; Ha, Yuanchi; Zielinski, Daniel C.; Haiman, Zachary B.; Desouki, Abdelmoneim Amer; Lercher, Martin J.; Palsson, Bernhard Ø.

Year: 2018

Venue: Nature Communications

DOI: https://doi.org/10.1038/s41467-018-07652-6

Paper Genome-driven evolutionary game theory helps understand the rise of metabolic interdependencies in microbial communities

Zomorrodi, Ali R.; Segrè, Daniel · 2017 · Nature Communications · DOI

Full title: Genome-driven evolutionary game theory helps understand the rise of metabolic interdependencies in microbial communities

Authors: Zomorrodi, Ali R.; Segrè, Daniel

Year: 2017

Venue: Nature Communications

DOI: https://doi.org/10.1038/s41467-017-01407-5

Paper Dissecting the energy metabolism in Mycoplasma pneumoniae through genome‐scale metabolic modeling

Wodke, Judith A. H.; Puchałka, Jacek; Lluch‐Senar, María et al. · 2013 · Molecular Systems Biology · DOI

Full title: Dissecting the energy metabolism in Mycoplasma pneumoniae through genome‐scale metabolic modeling

Authors: Wodke, Judith A. H.; Puchałka, Jacek; Lluch‐Senar, María; Marcos, Josep; Yus, Eva; Godinho, Miguel; Gutiérrez–Gallego, Ricardo; Santos, Vítor A. P. Martins dos; Serrano, Luís; Klipp, Edda; Maier, Tobias

Year: 2013

Venue: Molecular Systems Biology

DOI: https://doi.org/10.1038/msb.2013.6

Paper Enhanced succinic acid production by Mannheimia employing optimal malate dehydrogenase

Ahn, Jung Ho; Seo, Hogyun; Park, Woojin et al. · 2020 · Nature Communications · DOI

Full title: Enhanced succinic acid production by Mannheimia employing optimal malate dehydrogenase

Authors: Ahn, Jung Ho; Seo, Hogyun; Park, Woojin; Seok, Jihye; Lee, Jong An; Kim, Won Jun; Kim, Gi Bae; Kim, Kyung‐Jin; Lee, Sang Yup

Year: 2020

Venue: Nature Communications

DOI: https://doi.org/10.1038/s41467-020-15839-z

Paper Nitrogen limitation reveals large reserves in metabolic and translational capacities of yeast

Yu, Rosemary; Campbell, Kate; Pereira, Rui et al. · 2020 · Nature Communications · DOI

Full title: Nitrogen limitation reveals large reserves in metabolic and translational capacities of yeast

Authors: Yu, Rosemary; Campbell, Kate; Pereira, Rui; Björkeroth, Johan; Qi, Qi; Vorontsov, Egor; Sihlbom, Carina; Nielsen, Jens

Year: 2020

Venue: Nature Communications

DOI: https://doi.org/10.1038/s41467-020-15749-0

Paper Synthetic microbial communities of heterotrophs and phototrophs facilitate sustainable growth

Zúñiga, Cristal; Li, Tingting; Guarnieri, Michael T. et al. · 2020 · Nature Communications · DOI

Full title: Synthetic microbial communities of heterotrophs and phototrophs facilitate sustainable growth

Authors: Zúñiga, Cristal; Li, Tingting; Guarnieri, Michael T.; Jenkins, Jackson; Li, Chien‐Ting; Bingol, Kerem; Kim, Young‐Mo; Betenbaugh, Michael J.; Zengler, Karsten

Year: 2020

Venue: Nature Communications

DOI: https://doi.org/10.1038/s41467-020-17612-8

Paper Rewiring carbon metabolism in yeast for high level production of aromatic chemicals

Liu, Quanli; Yu, Tao; Li, Xiaowei et al. · 2019 · Nature Communications · DOI

Full title: Rewiring carbon metabolism in yeast for high level production of aromatic chemicals

Authors: Liu, Quanli; Yu, Tao; Li, Xiaowei; Chen, Yu; Campbell, Kate; Nielsen, Jens; Chen, Yun

Year: 2019

Venue: Nature Communications

DOI: https://doi.org/10.1038/s41467-019-12961-5

Paper Design of synthetic human gut microbiome assembly and butyrate production

Clark, Ryan L.; Connors, Bryce; Stevenson, David et al. · 2021 · Nature Communications · DOI

Full title: Design of synthetic human gut microbiome assembly and butyrate production

Authors: Clark, Ryan L.; Connors, Bryce; Stevenson, David; Hromada, Susan; Hamilton, Joshua J.; Amador‐Noguez, Daniel; Venturelli, Ophelia S.

Year: 2021

Venue: Nature Communications

DOI: https://doi.org/10.1038/s41467-021-22938-y

Paper Regulatory mechanisms underlying coordination of amino acid and glucose catabolism in Escherichia coli

Zampieri, Mattia; Hörl, Manuel; Hotz, Florian et al. · 2019 · Nature Communications · DOI

Full title: Regulatory mechanisms underlying coordination of amino acid and glucose catabolism in Escherichia coli

Authors: Zampieri, Mattia; Hörl, Manuel; Hotz, Florian; Müller, Nicola F.; Sauer, Uwe

Year: 2019

Venue: Nature Communications

DOI: https://doi.org/10.1038/s41467-019-11331-5

Paper Modeling genome-wide enzyme evolution predicts strong epistasis underlying catalytic turnover rates

Heckmann, David; Zielinski, Daniel C.; Palsson, Bernhard Ø. · 2018 · Nature Communications · DOI

Full title: Modeling genome-wide enzyme evolution predicts strong epistasis underlying catalytic turnover rates

Authors: Heckmann, David; Zielinski, Daniel C.; Palsson, Bernhard Ø.

Year: 2018

Venue: Nature Communications

DOI: https://doi.org/10.1038/s41467-018-07649-1

Paper Genome-scale metabolic rewiring improves titers rates and yields of the non-native product indigoidine at scale

Banerjee, Deepanwita; Eng, Thomas; Lau, Andrew K. et al. · 2020 · Nature Communications · DOI

Full title: Genome-scale metabolic rewiring improves titers rates and yields of the non-native product indigoidine at scale

Authors: Banerjee, Deepanwita; Eng, Thomas; Lau, Andrew K.; Sasaki, Yusuke; Wang, Brenda; Chen, Yan; Prahl, Jan‐Philip; Singan, Vasanth; Herbert, Robin A.; Liu, Yuzhong; Tanjore, Deepti; Petzold, Christopher J.; Keasling, Jay D.; Mukhopadhyay, Aindrila

Year: 2020

Venue: Nature Communications

DOI: https://doi.org/10.1038/s41467-020-19171-4

Paper Whole-cell modeling in yeast predicts compartment-specific proteome constraints that drive metabolic strategies

Elsemman, Ibrahim E.; Prado, Angelica Rodriguez; Grigaitis, Pranas et al. · 2022 · Nature Communications · DOI

Full title: Whole-cell modeling in yeast predicts compartment-specific proteome constraints that drive metabolic strategies

Year: 2022

Venue: Nature Communications

Paper De novo biosynthesis of rubusoside and rebaudiosides in engineered yeasts

Xu, Yameng; Wang, Xinglong; Zhang, Chenyang et al. · 2022 · Nature Communications · DOI

Full title: De novo biosynthesis of rubusoside and rebaudiosides in engineered yeasts

Authors: Xu, Yameng; Wang, Xinglong; Zhang, Chenyang; Zhou, Xuan; Xu, Xianhao; Han, Luyao; Lv, Xueqin; Liu, Yanfeng; Liu, Song; Li, Jianghua; Du, Guocheng; Chen, Jian; Ledesma‐Amaro, Rodrigo; Liu, Long

Year: 2022

Venue: Nature Communications

DOI: https://doi.org/10.1038/s41467-022-30826-2

Paper Bayesian genome scale modelling identifies thermal determinants of yeast metabolism

Li, Gang; Hu, Yating; Zrimec, Jan et al. · 2021 · Nature Communications · DOI

Full title: Bayesian genome scale modelling identifies thermal determinants of yeast metabolism

Authors: Li, Gang; Hu, Yating; Zrimec, Jan; Luo, Hao; Wang, Hao; Zelezniak, Aleksej; Ji, Boyang; Nielsen, Jens

Year: 2021

Venue: Nature Communications

Paper Combining mechanistic and machine learning models for predictive engineering and optimization of tryptophan metabolism

Zhang, Jie; Petersen, Søren D.; Radivojević, Tijana et al. · 2020 · Nature Communications · DOI

Full title: Combining mechanistic and machine learning models for predictive engineering and optimization of tryptophan metabolism

Authors: Zhang, Jie; Petersen, Søren D.; Radivojević, Tijana; Ramirez, Andrés; Pérez-Manríquez, Andrés; Abeliuk, Eduardo; Sánchez, Benjamín J.; Costello, Zak; Chen, Yu; Fero, M.J.; Martín, Héctor García; Nielsen, Jens; Keasling, Jay D.; Jensen, Michael K.

Year: 2020

Venue: Nature Communications

DOI: https://doi.org/10.1038/s41467-020-17910-1

Paper Improving recombinant protein production by yeast through genome-scale modeling using proteome constraints

Li, Feiran; Chen, Yu; Qi, Qi et al. · 2022 · Nature Communications · DOI

Full title: Improving recombinant protein production by yeast through genome-scale modeling using proteome constraints

Authors: Li, Feiran; Chen, Yu; Qi, Qi; Wang, Yanyan; Yuan, Le; Huang, Mingtao; Elsemman, Ibrahim E.; Feizi, Amir; Kerkhoven, Eduard J.; Nielsen, Jens

Year: 2022

Venue: Nature Communications

DOI: https://doi.org/10.1038/s41467-022-30689-7

Paper Teasing out missing reactions in genome-scale metabolic networks through hypergraph learning

Chen, Can; Liao, Chen; Liu, Yang‐Yu · 2023 · Nature Communications · DOI

Full title: Teasing out missing reactions in genome-scale metabolic networks through hypergraph learning

Authors: Chen, Can; Liao, Chen; Liu, Yang‐Yu

Year: 2023

Venue: Nature Communications

DOI: https://doi.org/10.1038/s41467-023-38110-7

Paper Functional comparison of metabolic networks across species

Ramon, Charlotte; Stelling, Jörg · 2023 · Nature Communications · DOI

Full title: Functional comparison of metabolic networks across species

Authors: Ramon, Charlotte; Stelling, Jörg

Year: 2023

Venue: Nature Communications

DOI: https://doi.org/10.1038/s41467-023-37429-5

Paper Genome-scale metabolic modeling of Aspergillus fumigatus strains reveals growth dependencies on the lung microbiome

Mirhakkak, Mohammad H.; Chen, Xiuqiang; Ni, Yueqiong et al. · 2023 · Nature Communications · DOI

Full title: Genome-scale metabolic modeling of Aspergillus fumigatus strains reveals growth dependencies on the lung microbiome

Authors: Mirhakkak, Mohammad H.; Chen, Xiuqiang; Ni, Yueqiong; Heinekamp, Thorsten; Sae-Ong, Tongta; Xu, Lin-Lin; Kurzai, Oliver; Barber, Amelia E.; Brakhage, Axel A.; Boutin, Sébastien; Schäuble, Sascha; Panagiotou, Gianni

Year: 2023

Venue: Nature Communications

DOI: https://doi.org/10.1038/s41467-023-39982-5

Paper Data integration across conditions improves turnover number estimates and metabolic predictions

Wendering, Philipp; Arend, Marius; Razaghi‐Moghadam, Zahra et al. · 2023 · Nature Communications · DOI

Full title: Data integration across conditions improves turnover number estimates and metabolic predictions

Authors: Wendering, Philipp; Arend, Marius; Razaghi‐Moghadam, Zahra; Nikoloski, Zoran

Year: 2023

Venue: Nature Communications

Paper Reconstruction of a catalogue of genome-scale metabolic models with enzymatic constraints using GECKO 2.0

Iván Domenzain; Benjamín J. Sánchez; Mihail Anton et al. · 2021 · Nature Communications · DOI

Full title: Reconstruction of a catalogue of genome-scale metabolic models with enzymatic constraints using GECKO 2.0

Authors: Iván Domenzain; Benjamín J. Sánchez; Mihail Anton; E. Kerkhoven; Aarón Millán-Oropeza; C. Henry; V. Siewers; J. Morrissey; Nikolaus Sonnenschein; J. Nielsen

Year: 2021

Venue: Nature Communications

DOI: https://doi.org/10.1038/s41467-022-31421-1

Paper A neural-mechanistic hybrid approach improving the predictive power of genome-scale metabolic models

Faure, Léon; Mollet, Bastien; Liebermeister, Wolfram et al. · 2023 · Nature Communications · DOI

Full title: A neural-mechanistic hybrid approach improving the predictive power of genome-scale metabolic models

Authors: Faure, Léon; Mollet, Bastien; Liebermeister, Wolfram; Faulon, Jean‐Loup

Year: 2023

Venue: Nature Communications

Paper Local flux coordination and global gene expression regulation in metabolic modeling

Li, Gaoyang; Liu, Li; Du, Wei et al. · 2023 · Nature Communications · DOI

Full title: Local flux coordination and global gene expression regulation in metabolic modeling

Authors: Li, Gaoyang; Liu, Li; Du, Wei; Cao, Huansheng

Year: 2023

Venue: Nature Communications

DOI: https://doi.org/10.1038/s41467-023-41392-6

Paper Modeling bacterial interactions uncovers the importance of outliers in the coastal lignin-degrading consortium

Peng, Qiannan; Zhao, Cheng; Wang, Xiaopeng et al. · 2025 · Nature Communications · DOI

Full title: Modeling bacterial interactions uncovers the importance of outliers in the coastal lignin-degrading consortium

Authors: Peng, Qiannan; Zhao, Cheng; Wang, Xiaopeng; Cheng, Kai; Wang, Congcong; Xu, Xihui; Lin, Lu

Year: 2025

Venue: Nature Communications

DOI: https://doi.org/10.1038/s41467-025-56012-8

Paper A genome-scale metabolic model of parasitic whipworm

Bay, Ömer F.; Hayes, Kelly S.; Schwartz, Jean‐Marc et al. · 2023 · Nature Communications · DOI

Full title: A genome-scale metabolic model of parasitic whipworm

Authors: Bay, Ömer F.; Hayes, Kelly S.; Schwartz, Jean‐Marc; Grencis, Richard K.; Roberts, Ian S.

Year: 2023

Venue: Nature Communications

DOI: https://doi.org/10.1038/s41467-023-42552-4

Paper Engineering a new-to-nature cascade for phosphate-dependent formate to formaldehyde conversion in vitro and in vivo

Nattermann, Maren; Wenk, Sebastian; Pfister, Pascal et al. · 2023 · Nature Communications · DOI

Full title: Engineering a new-to-nature cascade for phosphate-dependent formate to formaldehyde conversion in vitro and in vivo

Authors: Nattermann, Maren; Wenk, Sebastian; Pfister, Pascal; He, Hai; Lee, Seung Hwan; Szymański, Witold; Guntermann, Nils; Zhu, Fayin; Nickel, Lennart; Wallner, Charlotte; Zarzycki, Jan; Paczia, Nicole; Gaißert, Nina; Franciò, Giancarlo; Leitner, Walter; González, Ramón; Erb, Tobias J.

Year: 2023

Venue: Nature Communications

DOI: https://doi.org/10.1038/s41467-023-38072-w

Paper Turnover number predictions for kinetically uncharacterized enzymes using machine and deep learning

Kroll, Alexander; Rousset, Yvan; Hu, Xiao-Pan et al. · 2023 · Nature Communications · DOI

Full title: Turnover number predictions for kinetically uncharacterized enzymes using machine and deep learning

Authors: Kroll, Alexander; Rousset, Yvan; Hu, Xiao-Pan; Liebrand, Nina A.; Lercher, Martin J.

Year: 2023

Venue: Nature Communications

Paper Linking metabolic phenotypes to pathogenic traits among “Candidatus Liberibacter asiaticus” and its hosts

Zúñiga, Cristal; Peacock, Beth B.; Liang, Bo et al. · 2020 · npj Systems Biology and Applications · DOI

Full title: Linking metabolic phenotypes to pathogenic traits among “Candidatus Liberibacter asiaticus” and its hosts

Authors: Zúñiga, Cristal; Peacock, Beth B.; Liang, Bo; McCollum, Greg; Irigoyen, Sonia; Tec-Campos, Diego; Marotz, Clarisse; Weng, Nien-Chen; Zepeda, Alejandro; Vidalakis, Georgios; Mandadi, Kranthi K.; Borneman, James; Zengler, Karsten

Year: 2020

Venue: npj Systems Biology and Applications

DOI: https://doi.org/10.1038/s41540-020-00142-w

Paper Utilizing genome-scale models to optimize nutrient supply for sustained algal growth and lipid productivity

Li, Chien‐Ting; Yelsky, Jacob Stephan; Chen, Yiqun et al. · 2019 · npj Systems Biology and Applications · DOI

Full title: Utilizing genome-scale models to optimize nutrient supply for sustained algal growth and lipid productivity

Authors: Li, Chien‐Ting; Yelsky, Jacob Stephan; Chen, Yiqun; Zúñiga, Cristal; Eng, Richard; Jiang, Liqun; Shapiro, Alison J.; Huang, Kai-Wen; Zengler, Karsten; Betenbaugh, Michael J.

Year: 2019

Venue: npj Systems Biology and Applications

DOI: https://doi.org/10.1038/s41540-019-0110-7

Paper Engineering a synthetic energy-efficient formaldehyde assimilation cycle in Escherichia coli

Wu, Tong; Gómez-Coronado, Paul A.; Kubis, Armin et al. · 2023 · Nature Communications · DOI

Full title: Engineering a synthetic energy-efficient formaldehyde assimilation cycle in Escherichia coli

Authors: Wu, Tong; Gómez-Coronado, Paul A.; Kubis, Armin; Lindner, Steffen N.; Marlière, Philippe; Erb, Tobias J.; Bar‐Even, Arren; He, Hai

Year: 2023

Venue: Nature Communications

DOI: https://doi.org/10.1038/s41467-023-44247-2

Paper RETRACTED ARTICLE: Systems engineering of Escherichia coli for high-level glutarate production from glucose

Zhang, Zhilan; Chu, Ruyin; Wei, Wanqing et al. · 2024 · Nature Communications · DOI

Full title: RETRACTED ARTICLE: Systems engineering of Escherichia coli for high-level glutarate production from glucose

Authors: Zhang, Zhilan; Chu, Ruyin; Wei, Wanqing; Song, Wei; Ye, Chao; Chen, Xiulai; Wu, Jing; Liu, Li; Gao, Cong

Year: 2024

Venue: Nature Communications

DOI: https://doi.org/10.1038/s41467-024-45448-z

Paper Growth phase estimation for abundant bacterial populations sampled longitudinally from human stool metagenomes

Lim, Joe Jongpyo; Diener, Christian; Wilson, James G. et al. · 2023 · Nature Communications · DOI

Full title: Growth phase estimation for abundant bacterial populations sampled longitudinally from human stool metagenomes

Authors: Lim, Joe Jongpyo; Diener, Christian; Wilson, James G.; Valenzuela, Jacob J.; Baliga, Nitin S.; Gibbons, Sean M.

Year: 2023

Venue: Nature Communications

DOI: https://doi.org/10.1038/s41467-023-41424-1

Paper Mechanistic insights into bacterial metabolic reprogramming from omics-integrated genome-scale models

Hadadi, Noushin; Pandey, Vikash; Chiappino-Pepe, Anush et al. · 2020 · npj Systems Biology and Applications · DOI

Full title: Mechanistic insights into bacterial metabolic reprogramming from omics-integrated genome-scale models

Authors: Hadadi, Noushin; Pandey, Vikash; Chiappino-Pepe, Anush; Morales, Marian; Gallart‐Ayala, Héctor; Mehl, Florence; Ivanišević, Julijana; Sentchilo, Vladimir; Meer, Jan Roelof van der

Year: 2020

Venue: npj Systems Biology and Applications

Paper Protein engineering and iterative multimodule optimization for vitamin B6 production in Escherichia coli

Liu, Linxia; Li, Jinlong; Gai, Yuanming et al. · 2023 · Nature Communications · DOI

Full title: Protein engineering and iterative multimodule optimization for vitamin B6 production in Escherichia coli

Authors: Liu, Linxia; Li, Jinlong; Gai, Yuanming; Tian, Zhizhong; Wang, Yanyan; Wang, Tenghe; Liu, Pi; Yuan, Qianqian; Ma, Hongwu; Lee, Sang Yup; Zhang, Dawei

Year: 2023

Venue: Nature Communications

DOI: https://doi.org/10.1038/s41467-023-40928-0

Paper An integrated computational and experimental study to investigate Staphylococcus aureus metabolism

Islam, Mohammad Mazharul; Thomas, Vinai C.; Beek, Matthew Van et al. · 2020 · npj Systems Biology and Applications · DOI

Full title: An integrated computational and experimental study to investigate Staphylococcus aureus metabolism

Authors: Islam, Mohammad Mazharul; Thomas, Vinai C.; Beek, Matthew Van; Ahn, Jongsam; Alqarzaee, Abdulelah A.; Zhou, Chunyi; Fey, Paul D.; Bayles, Kenneth W.; Saha, Rajib

Year: 2020

Venue: npj Systems Biology and Applications

DOI: https://doi.org/10.1038/s41540-019-0122-3

Paper From metagenomic data to personalized in silico microbiotas: predicting dietary supplements for Crohn’s disease

Bauer, Eugen; Thiele, Ines · 2018 · npj Systems Biology and Applications · DOI

Full title: From metagenomic data to personalized in silico microbiotas: predicting dietary supplements for Crohn’s disease

Authors: Bauer, Eugen; Thiele, Ines

Year: 2018

Venue: npj Systems Biology and Applications

DOI: https://doi.org/10.1038/s41540-018-0063-2

Paper An updated genome-scale metabolic network reconstruction of Pseudomonas aeruginosa PA14 to characterize mucin-driven shifts in bacterial metabolism

Payne, Dawson; Renz, Alina; Dunphy, Laura J. et al. · 2021 · npj Systems Biology and Applications · DOI

Full title: An updated genome-scale metabolic network reconstruction of Pseudomonas aeruginosa PA14 to characterize mucin-driven shifts in bacterial metabolism

Authors: Payne, Dawson; Renz, Alina; Dunphy, Laura J.; Lewis, Taylor; Dräger, Andreas; Papin, Jason A.

Year: 2021

Venue: npj Systems Biology and Applications

DOI: https://doi.org/10.1038/s41540-021-00198-2

Paper Predicting stress response and improved protein overproduction in Bacillus subtilis

Tibocha‐Bonilla, Juan D.; Zúñiga, Cristal; Lekbua, Asama et al. · 2022 · npj Systems Biology and Applications · DOI

Full title: Predicting stress response and improved protein overproduction in Bacillus subtilis

Authors: Tibocha‐Bonilla, Juan D.; Zúñiga, Cristal; Lekbua, Asama; Lloyd, Colton J.; Rychel, Kevin; Short, Katie; Zengler, Karsten

Year: 2022

Venue: npj Systems Biology and Applications

DOI: https://doi.org/10.1038/s41540-022-00259-0

Paper Whole genome sequencing of Saccharomyces cerevisiae: from genotype to phenotype for improved metabolic engineering applications

Otero, José M.; Vongsangnak, Wanwipa; Asadollahi, Mohammad Ali et al. · 2010 · BMC Genomics · DOI

Full title: Whole genome sequencing of Saccharomyces cerevisiae: from genotype to phenotype for improved metabolic engineering applications

Authors: Otero, José M.; Vongsangnak, Wanwipa; Asadollahi, Mohammad Ali; Olivares‐Hernández, Roberto; Maury, Jérôme; Farinelli, Laurent; Barlocher, Loïc; Østerås, Magne; Schalk, Michel; Clark, Anthony; Nielsen, Jens

Year: 2010

Venue: BMC Genomics

DOI: https://doi.org/10.1186/1471-2164-11-723

Paper In vivo and in silico determination of essential genes of Campylobacter jejuni

Métris, Aline; Reuter, Mark; Gaskin, Duncan J. H. et al. · 2011 · BMC Genomics · DOI

Full title: In vivo and in silico determination of essential genes of Campylobacter jejuni

Authors: Métris, Aline; Reuter, Mark; Gaskin, Duncan J. H.; Baranyi, József; Vliet, Arnoud H. M. van

Year: 2011

Venue: BMC Genomics

DOI: https://doi.org/10.1186/1471-2164-12-535

Paper Using a logical model to predict the growth of yeast

Whelan, KE; King, Ross D. · 2008 · BMC Bioinformatics · DOI

Full title: Using a logical model to predict the growth of yeast

Authors: Whelan, KE; King, Ross D.

Year: 2008

Venue: BMC Bioinformatics

DOI: https://doi.org/10.1186/1471-2105-9-97

Paper Natural computation meta-heuristics for the in silico optimization of microbial strains

Rocha, Miguel; Maia, Paulo; Mendes, Rui et al. · 2008 · BMC Bioinformatics · DOI

Full title: Natural computation meta-heuristics for the in silico optimization of microbial strains

Authors: Rocha, Miguel; Maia, Paulo; Mendes, Rui; Pinto, José P.; Ferreira, Eugénio C.; Nielsen, Jens; Patil, Kiran Raosaheb; Rocha, Isabel

Year: 2008

Venue: BMC Bioinformatics

DOI: https://doi.org/10.1186/1471-2105-9-499

Paper Early adaptation to oxygen is key to the industrially important traits of Lactococcus lactis ssp. cremoris during milk fermentation

Cretenet, Marina; Gall, Gwénaëlle Le; Wegmann, Udo et al. · 2014 · BMC Genomics · DOI

Full title: Early adaptation to oxygen is key to the industrially important traits of Lactococcus lactis ssp. cremoris during milk fermentation

Authors: Cretenet, Marina; Gall, Gwénaëlle Le; Wegmann, Udo; Even, Sergine; Shearman, Claire; Stentz, Régis; Jeanson, Sophie

Year: 2014

Venue: BMC Genomics

DOI: https://doi.org/10.1186/1471-2164-15-1054

Paper Characterization of Proton Production and Consumption Associated with Microbial Metabolism

Srinivasan, K.; Mahadevan, Radhakrishnan · 2010 · BMC Biotechnology · DOI

Full title: Characterization of Proton Production and Consumption Associated with Microbial Metabolism

Authors: Srinivasan, K.; Mahadevan, Radhakrishnan

Year: 2010

Venue: BMC Biotechnology

DOI: https://doi.org/10.1186/1472-6750-10-2

Paper Integrated analysis of metabolic phenotypes in Saccharomyces cerevisiae

Duarte, Natalie C.; Palsson, Bernhard Ø.; Fu, Pengcheng · 2004 · BMC Genomics · DOI

Full title: Integrated analysis of metabolic phenotypes in Saccharomyces cerevisiae

Authors: Duarte, Natalie C.; Palsson, Bernhard Ø.; Fu, Pengcheng

Year: 2004

Venue: BMC Genomics

DOI: https://doi.org/10.1186/1471-2164-5-63

Paper Reconciling in vivo and in silico key biological parameters of Pseudomonas putidaKT2440 during growth on glucose under carbon-limited condition

Duuren, Jozef B. J. H. van; Puchałka, Jacek; Mars, Astrid E. et al. · 2013 · BMC Biotechnology · DOI

Full title: Reconciling in vivo and in silico key biological parameters of Pseudomonas putidaKT2440 during growth on glucose under carbon-limited condition

Authors: Duuren, Jozef B. J. H. van; Puchałka, Jacek; Mars, Astrid E.; Bücker, René; Eggink, Gerrit; Wittmann, Christoph; Santos, Vítor A. P. Martins dos

Year: 2013

Venue: BMC Biotechnology

DOI: https://doi.org/10.1186/1472-6750-13-93

Paper Predicting biological system objectives de novo from internal state measurements

Gianchandani, Erwin P.; Oberhardt, Matthew; Burgard, Anthony P. et al. · 2008 · BMC Bioinformatics · DOI

Full title: Predicting biological system objectives de novo from internal state measurements

Authors: Gianchandani, Erwin P.; Oberhardt, Matthew; Burgard, Anthony P.; Maranas, Costas D.; Papin, Jason A.

Year: 2008

Venue: BMC Bioinformatics

DOI: https://doi.org/10.1186/1471-2105-9-43

Paper Genome-scale reconstruction of the metabolic network in Staphylococcus aureus N315: an initial draft to the two-dimensional annotation

Becker, Scott A.; Palsson, Bernhard Ø. · 2005 · BMC Microbiology · DOI

Full title: Genome-scale reconstruction of the metabolic network in Staphylococcus aureus N315: an initial draft to the two-dimensional annotation

Authors: Becker, Scott A.; Palsson, Bernhard Ø.

Year: 2005

Venue: BMC Microbiology

DOI: https://doi.org/10.1186/1471-2180-5-8

Paper Improved annotation through genome-scale metabolic modeling of Aspergillus oryzae

Vongsangnak, Wanwipa; Olsen, Peter; Hansen, Kim et al. · 2008 · BMC Genomics · DOI

Full title: Improved annotation through genome-scale metabolic modeling of Aspergillus oryzae

Authors: Vongsangnak, Wanwipa; Olsen, Peter; Hansen, Kim; Krogsgaard, Steen; Nielsen, Jens

Year: 2008

Venue: BMC Genomics

DOI: https://doi.org/10.1186/1471-2164-9-245

Paper Genome-scale comparison and constraint-based metabolic reconstruction of the facultative anaerobic Fe(III)-reducer Rhodoferax ferrireducens

Risso, Carla; Sun, Jun; Zhuang, Kai et al. · 2009 · BMC Genomics · DOI

Full title: Genome-scale comparison and constraint-based metabolic reconstruction of the facultative anaerobic Fe(III)-reducer Rhodoferax ferrireducens

Authors: Risso, Carla; Sun, Jun; Zhuang, Kai; Mahadevan, Radhakrishnan; DeBoy, Robert T.; Ismail, Wael; Shrivastava, Susmita; Huot, Heather; Kothari, Sagar; Daugherty, Sean C.; Bui, Olivia; Schilling, Christophe H.; Lovley, Derek R.; Methé, Barbara A.

Year: 2009

Venue: BMC Genomics

DOI: https://doi.org/10.1186/1471-2164-10-447

Paper Systems biology of lactic acid bacteria: a critical review

Teusink, Bas; Bachmann, Herwig; Molenaar, Douwe · 2011 · Microbial Cell Factories · DOI

Full title: Systems biology of lactic acid bacteria: a critical review

Authors: Teusink, Bas; Bachmann, Herwig; Molenaar, Douwe

Year: 2011

Venue: Microbial Cell Factories

DOI: https://doi.org/10.1186/1475-2859-10-s1-s11

Paper Design and testing of a synthetic biology framework for genetic engineering of Corynebacterium glutamicum

Ravasi, Pablo; Peirú, Salvador; Gramajo, Hugo et al. · 2012 · Microbial Cell Factories · DOI

Full title: Design and testing of a synthetic biology framework for genetic engineering of Corynebacterium glutamicum

Authors: Ravasi, Pablo; Peirú, Salvador; Gramajo, Hugo; Menzella, Hugo G.

Year: 2012

Venue: Microbial Cell Factories

DOI: https://doi.org/10.1186/1475-2859-11-147

Paper The metabolic costs of improving ethanol yield by reducing glycerol formation capacity under anaerobic conditions in Saccharomyces cerevisiae

Pagliardini, Julien; Hubmann, Georg; Alfenore, Sandrine et al. · 2013 · Microbial Cell Factories · DOI

Full title: The metabolic costs of improving ethanol yield by reducing glycerol formation capacity under anaerobic conditions in Saccharomyces cerevisiae

Authors: Pagliardini, Julien; Hubmann, Georg; Alfenore, Sandrine; Nevoigt, Elke; Bideaux, Carine; Guillouet, Stéphane

Year: 2013

Venue: Microbial Cell Factories

DOI: https://doi.org/10.1186/1475-2859-12-29

Paper Production of 2,3-butanediol in Saccharomyces cerevisiae by in silico aided metabolic engineering

Ng, ChiamYu; Jung, Moo-Young; Lee, Jinwon et al. · 2012 · Microbial Cell Factories · DOI

Full title: Production of 2,3-butanediol in Saccharomyces cerevisiae by in silico aided metabolic engineering

Authors: Ng, ChiamYu; Jung, Moo-Young; Lee, Jinwon; Oh, Min‐Kyu

Year: 2012

Venue: Microbial Cell Factories

DOI: https://doi.org/10.1186/1475-2859-11-68

Paper Genome-scale reconstruction and in silico analysis of Klebsiella oxytoca for 2,3-butanediol production

Park, Jong Myoung; Song, Hyohak; Lee, Hee Jong et al. · 2013 · Microbial Cell Factories · DOI

Full title: Genome-scale reconstruction and in silico analysis of Klebsiella oxytoca for 2,3-butanediol production

Authors: Park, Jong Myoung; Song, Hyohak; Lee, Hee Jong; Seung, Doyoung

Year: 2013

Venue: Microbial Cell Factories

DOI: https://doi.org/10.1186/1475-2859-12-20

Paper Model-based analysis of an adaptive evolution experiment with Escherichia coli in a pyruvate limited continuous culture with glycerol

Feuer, Ronny; Gottlieb, Katrin; Viertel, Gero et al. · 2012 · EURASIP Journal on Bioinformatics and Systems Biology · DOI

Full title: Model-based analysis of an adaptive evolution experiment with Escherichia coli in a pyruvate limited continuous culture with glycerol

Authors: Feuer, Ronny; Gottlieb, Katrin; Viertel, Gero; Klotz, Johannes; Schober, Steffen; Bossert, Martin; Sawodny, Oliver; Sprenger, Georg A.; Ederer, Michael

Year: 2012

Venue: EURASIP Journal on Bioinformatics and Systems Biology

DOI: https://doi.org/10.1186/1687-4153-2012-14

Paper In silico profiling of Escherichia coli and Saccharomyces cerevisiae as terpenoid factories

Gruchattka, Evamaria; Hädicke, Oliver; Klamt, Steffen et al. · 2013 · Microbial Cell Factories · DOI

Full title: In silico profiling of Escherichia coli and Saccharomyces cerevisiae as terpenoid factories

Authors: Gruchattka, Evamaria; Hädicke, Oliver; Klamt, Steffen; Schütz, Verena; Kayser, Oliver

Year: 2013

Venue: Microbial Cell Factories

DOI: https://doi.org/10.1186/1475-2859-12-84

Paper Reconstruction and analysis of a genome-scale metabolic model for Scheffersomyces stipitis

Balagurunathan, Balaji; Jonnalagadda, Sudhakar; Tan, Lily et al. · 2012 · Microbial Cell Factories · DOI

Full title: Reconstruction and analysis of a genome-scale metabolic model for Scheffersomyces stipitis

Authors: Balagurunathan, Balaji; Jonnalagadda, Sudhakar; Tan, Lily; Srinivasan, Rajagopalan

Year: 2012

Venue: Microbial Cell Factories

DOI: https://doi.org/10.1186/1475-2859-11-27

Paper Process inhomogeneity leads to rapid side product turnover in cultivation of Corynebacterium glutamicum

Käß, Friedrich; Junne, Stefan; Neubauer, Peter et al. · 2014 · Microbial Cell Factories · DOI

Full title: Process inhomogeneity leads to rapid side product turnover in cultivation of Corynebacterium glutamicum

Authors: Käß, Friedrich; Junne, Stefan; Neubauer, Peter; Wiechert, Wolfgang; Oldiges, Marco

Year: 2014

Venue: Microbial Cell Factories

DOI: https://doi.org/10.1186/1475-2859-13-6

Paper Genome-scale metabolic network reconstruction and in silico flux analysis of the thermophilic bacterium Thermus thermophilus HB27

Lee, Na‐Rae; Lakshmanan, Meiyappan; Aggarwal, Shilpi et al. · 2014 · Microbial Cell Factories · DOI

Full title: Genome-scale metabolic network reconstruction and in silico flux analysis of the thermophilic bacterium Thermus thermophilus HB27

Authors: Lee, Na‐Rae; Lakshmanan, Meiyappan; Aggarwal, Shilpi; Song, Ji‐Won; Karimi, Iftekhar A.; Lee, Dong‐Yup; Park, Jin‐Byung

Year: 2014

Venue: Microbial Cell Factories

DOI: https://doi.org/10.1186/1475-2859-13-61

Paper Increased 3-hydroxypropionic acid production from glycerol, by modification of central metabolism in Escherichia coli

Kento Tokuyama; S. Ohno; Katsunori Yoshikawa et al. · 2014 · Microbial Cell Factories · DOI

Full title: Increased 3-hydroxypropionic acid production from glycerol, by modification of central metabolism in Escherichia coli

Authors: Kento Tokuyama; S. Ohno; Katsunori Yoshikawa; Takashi Hirasawa; Shotaro Tanaka; C. Furusawa; H. Shimizu

Year: 2014

Venue: Microbial Cell Factories

DOI: https://doi.org/10.1186/1475-2859-13-64

Paper Genome-scale metabolic network reconstruction of Saccharopolyspora spinosa for Spinosad Production improvement

Wang, Xiaoyang; Zhang, Chuanbo; Wang, Meiling et al. · 2014 · Microbial Cell Factories · DOI

Full title: Genome-scale metabolic network reconstruction of Saccharopolyspora spinosa for Spinosad Production improvement

Authors: Wang, Xiaoyang; Zhang, Chuanbo; Wang, Meiling; Lu, Wenyu

Year: 2014

Venue: Microbial Cell Factories

DOI: https://doi.org/10.1186/1475-2859-13-41

Paper Characterizing acetogenic metabolism using a genome-scale metabolic reconstruction of Clostridium ljungdahlii

Nagarajan, Harish; Şahin, Merve; Nogales, Juan et al. · 2013 · Microbial Cell Factories · DOI

Full title: Characterizing acetogenic metabolism using a genome-scale metabolic reconstruction of Clostridium ljungdahlii

Authors: Nagarajan, Harish; Şahin, Merve; Nogales, Juan; Latif, Haythem; Lovley, Derek R.; Ebrahim, Ali; Zengler, Karsten

Year: 2013

Venue: Microbial Cell Factories

DOI: https://doi.org/10.1186/1475-2859-12-118

Paper Genome-scale metabolic network guided engineering of Streptomyces tsukubaensis for FK506 production improvement

Huang, Di; Li, Shanshan; Xia, Menglei et al. · 2013 · Microbial Cell Factories · DOI

Full title: Genome-scale metabolic network guided engineering of Streptomyces tsukubaensis for FK506 production improvement

Authors: Huang, Di; Li, Shanshan; Xia, Menglei; Wen, Jianping; Jia, Xiaoqiang

Year: 2013

Venue: Microbial Cell Factories

DOI: https://doi.org/10.1186/1475-2859-12-52

Paper Physiological responses to folate overproduction in Lactobacillus plantarum WCFS1

Wegkamp, Arno; Mars, Astrid E.; Faijes, Magda et al. · 2010 · Microbial Cell Factories · DOI

Full title: Physiological responses to folate overproduction in Lactobacillus plantarum WCFS1

Authors: Wegkamp, Arno; Mars, Astrid E.; Faijes, Magda; Molenaar, Douwe; Vos, Ric CH de; Klaus, Sebastian; Hanson, Andrew D.; Vos, Willem M. de; Smid, Eddy J.

Year: 2010

Venue: Microbial Cell Factories

DOI: https://doi.org/10.1186/1475-2859-9-100

Paper Challenges in experimental data integration within genome-scale metabolic models

Bourguignon, Pierre-Yves; Samal, Areejit; Képès, François et al. · 2010 · Algorithms for Molecular Biology · DOI

Full title: Challenges in experimental data integration within genome-scale metabolic models

Authors: Bourguignon, Pierre-Yves; Samal, Areejit; Képès, François; Jost, Jürgen; Martin, Olivier

Year: 2010

Venue: Algorithms for Molecular Biology

DOI: https://doi.org/10.1186/1748-7188-5-20

Paper Reconstruction and analysis of the genetic and metabolic regulatory networks of the central metabolism of Bacillus subtilis

Goelzer, Anne; Brikci, Fadia Bekkal; Martin‐Verstraete, Isabelle et al. · 2008 · BMC Systems Biology · DOI

Full title: Reconstruction and analysis of the genetic and metabolic regulatory networks of the central metabolism of Bacillus subtilis

Authors: Goelzer, Anne; Brikci, Fadia Bekkal; Martin‐Verstraete, Isabelle; Noirot, Philippe; Bessières, Philippe; Aymerich, Stéphane; Fromion, Vincent

Year: 2008

Venue: BMC Systems Biology

DOI: https://doi.org/10.1186/1752-0509-2-20

Paper Genome-scale metabolic reconstruction and in silico analysis of methylotrophic yeast Pichia pastoris for strain improvement

Chung, Bevan KS; Selvarasu, Suresh; Camattari, Andrea et al. · 2010 · Microbial Cell Factories · DOI

Full title: Genome-scale metabolic reconstruction and in silico analysis of methylotrophic yeast Pichia pastoris for strain improvement

Authors: Chung, Bevan KS; Selvarasu, Suresh; Camattari, Andrea; Ryu, Ji-Myoung; Lee, Hyeokweon; Ahn, Jungoh; Lee, Hongweon; Lee, Dong‐Yup

Year: 2010

Venue: Microbial Cell Factories

DOI: https://doi.org/10.1186/1475-2859-9-50

Paper Macromolecular and elemental composition analysis and extracellular metabolite balances of Pichia pastoris growing at different oxygen levels

Carnicer, Marc; Baumann, Kristin; Töplitz, Isabelle et al. · 2009 · Microbial Cell Factories · DOI

Full title: Macromolecular and elemental composition analysis and extracellular metabolite balances of Pichia pastoris growing at different oxygen levels

Authors: Carnicer, Marc; Baumann, Kristin; Töplitz, Isabelle; Sánchez-Ferrando, Francesc; Mattanovich, Diethard; Ferrer, Pau; Albiol, Joan

Year: 2009

Venue: Microbial Cell Factories

DOI: https://doi.org/10.1186/1475-2859-8-65

Paper Integration of enzyme activities into metabolic flux distributions by elementary mode analysis

Kurata, Hiroyuki; Zhao, Quanyu; Okuda, Ryuichi et al. · 2007 · BMC Systems Biology · DOI

Full title: Integration of enzyme activities into metabolic flux distributions by elementary mode analysis

Authors: Kurata, Hiroyuki; Zhao, Quanyu; Okuda, Ryuichi; Shimizu, Kazuyuki

Year: 2007

Venue: BMC Systems Biology

DOI: https://doi.org/10.1186/1752-0509-1-31

Paper Flux-sum analysis: a metabolite-centric approach for understanding the metabolic network

Chung, Bevan Kai Sheng; Lee, Dong‐Yup · 2009 · BMC Systems Biology · DOI

Full title: Flux-sum analysis: a metabolite-centric approach for understanding the metabolic network

Authors: Chung, Bevan Kai Sheng; Lee, Dong‐Yup

Year: 2009

Venue: BMC Systems Biology

DOI: https://doi.org/10.1186/1752-0509-3-117

Paper Quantitative evaluation of yeast's requirement for glycerol formation in very high ethanol performance fed-batch process

Pagliardini, Julien; Hubmann, Georg; Bideaux, Carine et al. · 2010 · Microbial Cell Factories · DOI

Full title: Quantitative evaluation of yeast's requirement for glycerol formation in very high ethanol performance fed-batch process

Authors: Pagliardini, Julien; Hubmann, Georg; Bideaux, Carine; Alfenore, Sandrine; Nevoigt, Elke; Guillouet, Stéphane

Year: 2010

Venue: Microbial Cell Factories

DOI: https://doi.org/10.1186/1475-2859-9-36

Paper Constraint-based analysis of metabolic capacity of Salmonella typhimurium during host-pathogen interaction

Raghunathan, Anu; Reed, Jennifer L.; Shin, Sookil et al. · 2009 · BMC Systems Biology · DOI

Full title: Constraint-based analysis of metabolic capacity of Salmonella typhimurium during host-pathogen interaction

Authors: Raghunathan, Anu; Reed, Jennifer L.; Shin, Sookil; Palsson, Bernhard Ø.; Daefler, Simon

Year: 2009

Venue: BMC Systems Biology

DOI: https://doi.org/10.1186/1752-0509-3-38

Paper Iterative reconstruction of a global metabolic model of Acinetobacter baylyi ADP1 using high-throughput growth phenotype and gene essentiality data

Durot, Maxime; Fèvre, François Le; Berardinis, Véronique de et al. · 2008 · BMC Systems Biology · DOI

Full title: Iterative reconstruction of a global metabolic model of Acinetobacter baylyi ADP1 using high-throughput growth phenotype and gene essentiality data

Authors: Durot, Maxime; Fèvre, François Le; Berardinis, Véronique de; Kreimeyer, Annett; Vallenet, David; Combe, Cyril; Smidtas, Serge; Salanoubat, Marcel; Weissenbach, Jean; Schächter, Vincent

Year: 2008

Venue: BMC Systems Biology

DOI: https://doi.org/10.1186/1752-0509-2-85

Paper Oxygen dependence of metabolic fluxes and energy generation of Saccharomyces cerevisiae CEN.PK113-1A

Jouhten, Paula; Rintala, Eija; Huuskonen, Anne et al. · 2008 · BMC Systems Biology · DOI

Full title: Oxygen dependence of metabolic fluxes and energy generation of Saccharomyces cerevisiae CEN.PK113-1A

Authors: Jouhten, Paula; Rintala, Eija; Huuskonen, Anne; Tamminen, Anu; Toivari, Mervi; Wiebe, Marilyn G.; Ruohonen, Laura; Penttilä, Merja; Maaheimo, Hannu

Year: 2008

Venue: BMC Systems Biology

DOI: https://doi.org/10.1186/1752-0509-2-60

Paper The genome-scale metabolic network analysis of Zymomonas mobilis ZM4 explains physiological features and suggests ethanol and succinic acid production strategies

Kyung Yun Lee; J. Park; T. Kim et al. · 2010 · Microbial Cell Factories · DOI

Full title: The genome-scale metabolic network analysis of Zymomonas mobilis ZM4 explains physiological features and suggests ethanol and succinic acid production strategies

Authors: Kyung Yun Lee; J. Park; T. Kim; H. Yun; S. Lee

Year: 2010

Venue: Microbial Cell Factories

DOI: https://doi.org/10.1186/1475-2859-9-94

Paper The genome-scale metabolic model iIN800 of Saccharomyces cerevisiae and its validation: a scaffold to query lipid metabolism

Nookaew, Intawat; Jewett, Michael C.; Meechai, Asawin et al. · 2008 · BMC Systems Biology · DOI

Full title: The genome-scale metabolic model iIN800 of Saccharomyces cerevisiae and its validation: a scaffold to query lipid metabolism

Authors: Nookaew, Intawat; Jewett, Michael C.; Meechai, Asawin; Thammarongtham, Chinae; Laoteng, Kobkul; Cheevadhanarak, Supapon; Nielsen, Jens; Bhumiratana, Sakarindr

Year: 2008

Venue: BMC Systems Biology

DOI: https://doi.org/10.1186/1752-0509-2-71

Paper Development and experimental verification of a genome-scale metabolic model for Corynebacterium glutamicum

Shinfuku, Yohei; Sorpitiporn, Natee; Sono, Masahiro et al. · 2009 · Microbial Cell Factories · DOI

Full title: Development and experimental verification of a genome-scale metabolic model for Corynebacterium glutamicum

Authors: Shinfuku, Yohei; Sorpitiporn, Natee; Sono, Masahiro; Furusawa, Chikara; Hirasawa, Takashi; Shimizu, Hiroshi

Year: 2009

Venue: Microbial Cell Factories

DOI: https://doi.org/10.1186/1475-2859-8-43

Paper Genome-scale constraint-based modeling of Geobacter metallireducens

Sun, Jun; Sayyar, Bahareh; Butler, Jessica et al. · 2009 · BMC Systems Biology · DOI

Full title: Genome-scale constraint-based modeling of Geobacter metallireducens

Authors: Sun, Jun; Sayyar, Bahareh; Butler, Jessica; Pharkya, Priti; Fahland, Tom R; Famili, Iman; Schilling, Christophe H.; Lovley, Derek R.; Mahadevan, Radhakrishnan

Year: 2009

Venue: BMC Systems Biology

DOI: https://doi.org/10.1186/1752-0509-3-15

Paper Genome-scale reconstruction and in silico analysis of the Ralstonia eutropha H16 for polyhydroxyalkanoate synthesis, lithoautotrophic growth, and 2-methyl citric acid production

Park, Jong Myoung; Kim, Tae Yong; Lee, Sang Yup · 2011 · BMC Systems Biology · DOI

Full title: Genome-scale reconstruction and in silico analysis of the Ralstonia eutropha H16 for polyhydroxyalkanoate synthesis, lithoautotrophic growth, and 2-methyl citric acid production

Authors: Park, Jong Myoung; Kim, Tae Yong; Lee, Sang Yup

Year: 2011

Venue: BMC Systems Biology

DOI: https://doi.org/10.1186/1752-0509-5-101

Paper Reconstruction and analysis of genome-scale metabolic model of a photosynthetic bacterium

Montagud, Arnau; Navarro, Emilio; Córdoba, Pedro Fernández de et al. · 2010 · BMC Systems Biology · DOI

Full title: Reconstruction and analysis of genome-scale metabolic model of a photosynthetic bacterium

Authors: Montagud, Arnau; Navarro, Emilio; Córdoba, Pedro Fernández de; Urchueguía, Javier F.; Patil, Kiran Raosaheb

Year: 2010

Venue: BMC Systems Biology

DOI: https://doi.org/10.1186/1752-0509-4-156

Paper Improving the iMM904 S. cerevisiae metabolic model using essentiality and synthetic lethality data

Zomorrodi, Ali R.; Maranas, Costas D. · 2010 · BMC Systems Biology · DOI

Full title: Improving the iMM904 S. cerevisiae metabolic model using essentiality and synthetic lethality data

Authors: Zomorrodi, Ali R.; Maranas, Costas D.

Year: 2010

Venue: BMC Systems Biology

DOI: https://doi.org/10.1186/1752-0509-4-178

Paper Integration of metabolic databases for the reconstruction of genome-scale metabolic networks

Radrich, Karin; Tsuruoka, Yoshimasa; Dobson, Paul D. et al. · 2010 · BMC Systems Biology · DOI

Full title: Integration of metabolic databases for the reconstruction of genome-scale metabolic networks

Authors: Radrich, Karin; Tsuruoka, Yoshimasa; Dobson, Paul D.; Gevorgyan, Albert; Swainston, Neil; Baart, Gino; Schwartz, Jean‐Marc

Year: 2010

Venue: BMC Systems Biology

DOI: https://doi.org/10.1186/1752-0509-4-114

Paper Constraint-based modeling analysis of the metabolism of two Pelobacter species

Sun, Jun; Haveman, Shelley A.; Bui, Olivia et al. · 2010 · BMC Systems Biology · DOI

Full title: Constraint-based modeling analysis of the metabolism of two Pelobacter species

Authors: Sun, Jun; Haveman, Shelley A.; Bui, Olivia; Fahland, Tom R; Lovley, Derek R.

Year: 2010

Venue: BMC Systems Biology

DOI: https://doi.org/10.1186/1752-0509-4-174

Paper Connecting extracellular metabolomic measurements to intracellular flux states in yeast

Mo, Monica L.; Palsson, Bernhard Ø.; Herrgård, Markus J. · 2009 · BMC Systems Biology · DOI

Full title: Connecting extracellular metabolomic measurements to intracellular flux states in yeast

Authors: Mo, Monica L.; Palsson, Bernhard Ø.; Herrgård, Markus J.

Year: 2009

Venue: BMC Systems Biology

DOI: https://doi.org/10.1186/1752-0509-3-37

Paper Machine learning based analyses on metabolic networks supports high-throughput knockout screens

Plaimas, Kitiporn; Mallm, Jan‐Philipp; Oswald, Marcus et al. · 2008 · BMC Systems Biology · DOI

Full title: Machine learning based analyses on metabolic networks supports high-throughput knockout screens

Authors: Plaimas, Kitiporn; Mallm, Jan‐Philipp; Oswald, Marcus; Svara, Fabian; Sourjik, Victor; Eils, Roland; König, Rainer

Year: 2008

Venue: BMC Systems Biology

DOI: https://doi.org/10.1186/1752-0509-2-67

Paper A systems biology framework for modeling metabolic enzyme inhibition of Mycobacterium tuberculosis

Fang, Xin; Wallqvist, Anders; Reifman, Jaques · 2009 · BMC Systems Biology · DOI

Full title: A systems biology framework for modeling metabolic enzyme inhibition of Mycobacterium tuberculosis

Authors: Fang, Xin; Wallqvist, Anders; Reifman, Jaques

Year: 2009

Venue: BMC Systems Biology

DOI: https://doi.org/10.1186/1752-0509-3-92

Paper iRsp1095: A genome-scale reconstruction of the Rhodobacter sphaeroides metabolic network

Imam, Saheed; Yılmaz, Şafak; Sohmen, Ugur et al. · 2011 · BMC Systems Biology · DOI

Full title: iRsp1095: A genome-scale reconstruction of the Rhodobacter sphaeroides metabolic network

Authors: Imam, Saheed; Yılmaz, Şafak; Sohmen, Ugur; Gorzalski, Alexander S.; Reed, Jennifer L.; Noguera, Daniel R.; Donohue, Timothy J.

Year: 2011

Venue: BMC Systems Biology

DOI: https://doi.org/10.1186/1752-0509-5-116

Paper A computational exploration of bacterial metabolic diversity identifying metabolic interactions and growth-efficient strain communities

Tzamali, Eleftheria; Poirazi, Panayiota; Tollis, Ioannis G. et al. · 2011 · BMC Systems Biology · DOI

Full title: A computational exploration of bacterial metabolic diversity identifying metabolic interactions and growth-efficient strain communities

Authors: Tzamali, Eleftheria; Poirazi, Panayiota; Tollis, Ioannis G.; Reczko, Martin

Year: 2011

Venue: BMC Systems Biology

DOI: https://doi.org/10.1186/1752-0509-5-167

Paper OptFlux: an open-source software platform for in silico metabolic engineering

Rocha, Isabel; Maia, Paulo; Evangelista, Pedro et al. · 2010 · BMC Systems Biology · DOI

Full title: OptFlux: an open-source software platform for in silico metabolic engineering

Authors: Rocha, Isabel; Maia, Paulo; Evangelista, Pedro; Vilaça, Paulo; Soares, Simão; Pinto, José P.; Nielsen, Jens; Patil, Kiran Raosaheb; Ferreira, Eugénio C.; Rocha, Miguel

Year: 2010

Venue: BMC Systems Biology

DOI: https://doi.org/10.1186/1752-0509-4-45

Paper Genome-scale reconstruction of metabolic network for a halophilic extremophile, Chromohalobacter salexigens DSM 3043

Duru, Özlem Ateş; Öner, Ebru Toksoy; Arğa, Kazım Yalçın · 2011 · BMC Systems Biology · DOI

Full title: Genome-scale reconstruction of metabolic network for a halophilic extremophile, Chromohalobacter salexigens DSM 3043

Authors: Duru, Özlem Ateş; Öner, Ebru Toksoy; Arğa, Kazım Yalçın

Year: 2011

Venue: BMC Systems Biology

DOI: https://doi.org/10.1186/1752-0509-5-12

Paper Flux balance analysis of primary metabolism in Chlamydomonas reinhardtii

Boyle, Nanette; Morgan, John A. · 2009 · BMC Systems Biology · DOI

Full title: Flux balance analysis of primary metabolism in Chlamydomonas reinhardtii

Authors: Boyle, Nanette; Morgan, John A.

Year: 2009

Venue: BMC Systems Biology

DOI: https://doi.org/10.1186/1752-0509-3-4

Paper A detailed genome-wide reconstruction of mouse metabolism based on human Recon 1

Sigurðsson, Martin I.; Jamshidi, Neema; Steingrı́msson, Eirı́kur et al. · 2010 · BMC Systems Biology · DOI

Full title: A detailed genome-wide reconstruction of mouse metabolism based on human Recon 1

Authors: Sigurðsson, Martin I.; Jamshidi, Neema; Steingrı́msson, Eirı́kur; Thiele, Ines; Palsson, Bernhard Ø.

Year: 2010

Venue: BMC Systems Biology

DOI: https://doi.org/10.1186/1752-0509-4-140

Paper Systems approach to investigating host-pathogen interactions in infections with the biothreat agent Francisella. Constraints-based model of Francisella tularensis

Raghunathan, Anu; Shin, Sookil; Daefler, Simon · 2010 · BMC Systems Biology · DOI

Full title: Systems approach to investigating host-pathogen interactions in infections with the biothreat agent Francisella. Constraints-based model of Francisella tularensis

Authors: Raghunathan, Anu; Shin, Sookil; Daefler, Simon

Year: 2010

Venue: BMC Systems Biology

DOI: https://doi.org/10.1186/1752-0509-4-118

Paper Genome-scale metabolic analysis of Clostridium thermocellum for bioethanol production

Roberts, Seth B.; Gowen, Christopher M.; Brooks, J. Paul et al. · 2010 · BMC Systems Biology · DOI

Full title: Genome-scale metabolic analysis of Clostridium thermocellum for bioethanol production

Authors: Roberts, Seth B.; Gowen, Christopher M.; Brooks, J. Paul; Fong, Stephen S.

Year: 2010

Venue: BMC Systems Biology

DOI: https://doi.org/10.1186/1752-0509-4-31

Paper Proteomic and network analysis characterize stage-specific metabolism in Trypanosoma cruzi

Roberts, Seth B.; Robichaux, Jennifer L; Chavali, Arvind K. et al. · 2009 · BMC Systems Biology · DOI

Full title: Proteomic and network analysis characterize stage-specific metabolism in Trypanosoma cruzi

Authors: Roberts, Seth B.; Robichaux, Jennifer L; Chavali, Arvind K.; Manque, Patrício; Lee, Vladimir; Lara, Ana M.; Papin, Jason A.; Buck, Gregory A.

Year: 2009

Venue: BMC Systems Biology

DOI: https://doi.org/10.1186/1752-0509-3-52

Paper Development and analysis of an in vivo-compatible metabolic network of Mycobacterium tuberculosis

Fang, Xin; Wallqvist, Anders; Reifman, Jaques · 2010 · BMC Systems Biology · DOI

Full title: Development and analysis of an in vivo-compatible metabolic network of Mycobacterium tuberculosis

Authors: Fang, Xin; Wallqvist, Anders; Reifman, Jaques

Year: 2010

Venue: BMC Systems Biology

DOI: https://doi.org/10.1186/1752-0509-4-160

Paper Microarray data can predict diurnal changes of starch content in the picoalga Ostreococcus

Sorokina, Oksana; Corellou, Florence; Dauvillée, David et al. · 2011 · BMC Systems Biology · DOI

Full title: Microarray data can predict diurnal changes of starch content in the picoalga Ostreococcus

Authors: Sorokina, Oksana; Corellou, Florence; Dauvillée, David; Sorokin, Anatoly; Goryanin, Igor; Ball, Steven; Bouget, François‐Yves; Millar, Andrew J.

Year: 2011

Venue: BMC Systems Biology

DOI: https://doi.org/10.1186/1752-0509-5-36

Paper Metabolic network reconstruction and genome-scale model of butanol-producing strain Clostridium beijerinckii NCIMB 8052

Milne, Caroline B.; Eddy, James A.; Raju, Ravali et al. · 2011 · BMC Systems Biology · DOI

Full title: Metabolic network reconstruction and genome-scale model of butanol-producing strain Clostridium beijerinckii NCIMB 8052

Authors: Milne, Caroline B.; Eddy, James A.; Raju, Ravali; Ardekani, Soroush; Kim, Pan‐Jun; Senger, Ryan S.; Jin, Yong‐Su; Blaschek, Hans P.; Price, Nathan D.

Year: 2011

Venue: BMC Systems Biology

DOI: https://doi.org/10.1186/1752-0509-5-130

Paper Expanding a dynamic flux balance model of yeast fermentation to genome-scale

Vargas, Felipe; Pizarro, Francisco; Pérez‐Correa, José Ricardo et al. · 2011 · BMC Systems Biology · DOI

Full title: Expanding a dynamic flux balance model of yeast fermentation to genome-scale

Authors: Vargas, Felipe; Pizarro, Francisco; Pérez‐Correa, José Ricardo; Agosín, Eduardo

Year: 2011

Venue: BMC Systems Biology

DOI: https://doi.org/10.1186/1752-0509-5-75

Paper Systems biology of bacterial nitrogen fixation: High-throughput technology and its integrative description with constraint-based modeling

Reséndis-Antonio, Osbaldo; Hernández, Magdalena; Salazar, Emmanuel et al. · 2011 · BMC Systems Biology · DOI

Full title: Systems biology of bacterial nitrogen fixation: High-throughput technology and its integrative description with constraint-based modeling

Authors: Reséndis-Antonio, Osbaldo; Hernández, Magdalena; Salazar, Emmanuel; Contreras, Sandra; Batallar, G. Martínez; Mora, Yolanda; Encarnación‐Guevara, Sergio

Year: 2011

Venue: BMC Systems Biology

DOI: https://doi.org/10.1186/1752-0509-5-120

Paper Comparative multi-goal tradeoffs in systems engineering of microbial metabolism

Byrne, David; Dumitriu, Alexandra; Segrè, Daniel · 2012 · BMC Systems Biology · DOI

Full title: Comparative multi-goal tradeoffs in systems engineering of microbial metabolism

Authors: Byrne, David; Dumitriu, Alexandra; Segrè, Daniel

Year: 2012

Venue: BMC Systems Biology

DOI: https://doi.org/10.1186/1752-0509-6-127

Paper The evolution of metabolic networks of E. coli

Baumler, David J.; Peplinski, Roman G; Reed, Jennifer L. et al. · 2011 · BMC Systems Biology · DOI

Full title: The evolution of metabolic networks of E. coli

Authors: Baumler, David J.; Peplinski, Roman G; Reed, Jennifer L.; Glasner, Jeremy D.; Perna, Nicole T.

Year: 2011

Venue: BMC Systems Biology

DOI: https://doi.org/10.1186/1752-0509-5-182

Paper A retrosynthetic biology approach to metabolic pathway design for therapeutic production

Carbonell, Pablo; Planson, Anne‐Gaëlle; Fichera, Davide et al. · 2011 · BMC Systems Biology · DOI

Full title: A retrosynthetic biology approach to metabolic pathway design for therapeutic production

Authors: Carbonell, Pablo; Planson, Anne‐Gaëlle; Fichera, Davide; Faulon, Jean‐Loup

Year: 2011

Venue: BMC Systems Biology

DOI: https://doi.org/10.1186/1752-0509-5-122

Paper Exploring the metabolic network of the epidemic pathogen Burkholderia cenocepacia J2315 via genome-scale reconstruction

Fang, Kechi; Zhao, Hansheng; Sun, Changyue et al. · 2011 · BMC Systems Biology · DOI

Full title: Exploring the metabolic network of the epidemic pathogen Burkholderia cenocepacia J2315 via genome-scale reconstruction

Authors: Fang, Kechi; Zhao, Hansheng; Sun, Changyue; Lam, Carolyn MC; Chang, Suhua; Zhang, Kunlin; Panda, Gurudutta; Godinho, Miguel; Santos, Vítor A. P. Martins dos; Wang, Jing

Year: 2011

Venue: BMC Systems Biology

DOI: https://doi.org/10.1186/1752-0509-5-83

Paper Flux variability scanning based on enforced objective flux for identifying gene amplification targets

Park, Jong Myoung; Park, Hye Min; Kim, Won Jun et al. · 2012 · BMC Systems Biology · DOI

Full title: Flux variability scanning based on enforced objective flux for identifying gene amplification targets

Authors: Park, Jong Myoung; Park, Hye Min; Kim, Won Jun; Kim, Hyun Uk; Kim, Tae Yong; Lee, Sang Yup

Year: 2012

Venue: BMC Systems Biology

DOI: https://doi.org/10.1186/1752-0509-6-106

Paper Dynamic regulatory on/off minimization for biological systems under internal temporal perturbations

Kleeßen, Sabrina; Nikoloski, Zoran · 2012 · BMC Systems Biology · DOI

Full title: Dynamic regulatory on/off minimization for biological systems under internal temporal perturbations

Authors: Kleeßen, Sabrina; Nikoloski, Zoran

Year: 2012

Venue: BMC Systems Biology

DOI: https://doi.org/10.1186/1752-0509-6-16

Paper Yeast 5 – an expanded reconstruction of the Saccharomyces cerevisiae metabolic network

Heavner, Ben; Smallbone, Kieran; Barker, Brandon et al. · 2012 · BMC Systems Biology · DOI

Full title: Yeast 5 – an expanded reconstruction of the Saccharomyces cerevisiae metabolic network

Authors: Heavner, Ben; Smallbone, Kieran; Barker, Brandon; Mendes, Pedro; Walker, Larry P.

Year: 2012

Venue: BMC Systems Biology

DOI: https://doi.org/10.1186/1752-0509-6-55

Paper VANTED v2: a framework for systems biology applications

Rohn, Hendrik; Junker, Astrid; Hartmann, Anja et al. · 2012 · BMC Systems Biology · DOI

Full title: VANTED v2: a framework for systems biology applications

Authors: Rohn, Hendrik; Junker, Astrid; Hartmann, Anja; Grafahrend‐Belau, Eva; Treutler, Hendrik; Klapperstück, Matthias; Czauderna, Tobias; Klukas, Christian; Schreiber, Falk

Year: 2012

Venue: BMC Systems Biology

DOI: https://doi.org/10.1186/1752-0509-6-139

Paper Redox balance is key to explaining full vs. partial switching to low-yield metabolism

Hoek, Milan JA van; Merks, Roeland M. H. · 2012 · BMC Systems Biology · DOI

Full title: Redox balance is key to explaining full vs. partial switching to low-yield metabolism

Authors: Hoek, Milan JA van; Merks, Roeland M. H.

Year: 2012

Venue: BMC Systems Biology

DOI: https://doi.org/10.1186/1752-0509-6-22

Paper Integration of time-resolved transcriptomics data with flux-based methods reveals stress-induced metabolic adaptation in Escherichia coli

Töpfer, Nadine; Jozefczuk, Szymon; Nikoloski, Zoran · 2012 · BMC Systems Biology · DOI

Full title: Integration of time-resolved transcriptomics data with flux-based methods reveals stress-induced metabolic adaptation in Escherichia coli

Authors: Töpfer, Nadine; Jozefczuk, Szymon; Nikoloski, Zoran

Year: 2012

Venue: BMC Systems Biology

DOI: https://doi.org/10.1186/1752-0509-6-148

Paper Genome-level transcription data of Yersinia pestis analyzed with a New metabolic constraint-based approach

Navid, Ali; Almaas, Eivind · 2012 · BMC Systems Biology · DOI

Full title: Genome-level transcription data of Yersinia pestis analyzed with a New metabolic constraint-based approach

Authors: Navid, Ali; Almaas, Eivind

Year: 2012

Venue: BMC Systems Biology

DOI: https://doi.org/10.1186/1752-0509-6-150

Paper A genome-scale metabolic model of the lipid-accumulating yeast Yarrowia lipolytica

Loira, Nicolás; Dulermo, Thierry; Nicaud, Jean‐Marc et al. · 2012 · BMC Systems Biology · DOI

Full title: A genome-scale metabolic model of the lipid-accumulating yeast Yarrowia lipolytica

Authors: Loira, Nicolás; Dulermo, Thierry; Nicaud, Jean‐Marc; Sherman, David James

Year: 2012

Venue: BMC Systems Biology

DOI: https://doi.org/10.1186/1752-0509-6-35

Paper Genome-scale modeling using flux ratio constraints to enable metabolic engineering of clostridial metabolism in silico

McAnulty, Michael J.; Yen, Jiun Y.; Freedman, Benjamin G. et al. · 2012 · BMC Systems Biology · DOI

Full title: Genome-scale modeling using flux ratio constraints to enable metabolic engineering of clostridial metabolism in silico

Authors: McAnulty, Michael J.; Yen, Jiun Y.; Freedman, Benjamin G.; Senger, Ryan S.

Year: 2012

Venue: BMC Systems Biology

DOI: https://doi.org/10.1186/1752-0509-6-42

Paper Hybrid metabolic flux analysis: combining stoichiometric and statistical constraints to model the formation of complex recombinant products

Carinhas, Nuno; Bernal, Vicente; Teixeira, Ana P. et al. · 2011 · BMC Systems Biology · DOI

Full title: Hybrid metabolic flux analysis: combining stoichiometric and statistical constraints to model the formation of complex recombinant products

Authors: Carinhas, Nuno; Bernal, Vicente; Teixeira, Ana P.; Carrondo, Manuel J.T.; Alves, Paula M.; Oliveira, Rui

Year: 2011

Venue: BMC Systems Biology

DOI: https://doi.org/10.1186/1752-0509-5-34

Paper FluxMap: A VANTED add-on for the visual exploration of flux distributions in biological networks

Rohn, Hendrik; Hartmann, Anja; Junker, Astrid et al. · 2012 · BMC Systems Biology · DOI

Full title: FluxMap: A VANTED add-on for the visual exploration of flux distributions in biological networks

Authors: Rohn, Hendrik; Hartmann, Anja; Junker, Astrid; Junker, Björn H.; Schreiber, Falk

Year: 2012

Venue: BMC Systems Biology

DOI: https://doi.org/10.1186/1752-0509-6-33

Paper Network-based assessment of the selectivity of metabolic drug targets in Plasmodium falciparum with respect to human liver metabolism

Bazzani, Susanna; Hoppe, Andreas; Holzhütter, Hermann−Georg · 2012 · BMC Systems Biology · DOI

Full title: Network-based assessment of the selectivity of metabolic drug targets in Plasmodium falciparum with respect to human liver metabolism

Authors: Bazzani, Susanna; Hoppe, Andreas; Holzhütter, Hermann−Georg

Year: 2012

Venue: BMC Systems Biology

DOI: https://doi.org/10.1186/1752-0509-6-118

Paper Genome-scale metabolic model of the fission yeast Schizosaccharomyces pombe and the reconciliation of in silico/in vivo mutant growth

Sohn, Seung Bum; Kim, Tae Yong; Lee, Jay H. et al. · 2012 · BMC Systems Biology · DOI

Full title: Genome-scale metabolic model of the fission yeast Schizosaccharomyces pombe and the reconciliation of in silico/in vivo mutant growth

Authors: Sohn, Seung Bum; Kim, Tae Yong; Lee, Jay H.; Lee, Sang Yup

Year: 2012

Venue: BMC Systems Biology

DOI: https://doi.org/10.1186/1752-0509-6-49

Paper A metabolite-centric view on flux distributions in genome-scale metabolic models

Riemer, S. Alexander; Rex, René; Schomburg, Dietmar · 2013 · BMC Systems Biology · DOI

Full title: A metabolite-centric view on flux distributions in genome-scale metabolic models

Authors: Riemer, S. Alexander; Rex, René; Schomburg, Dietmar

Year: 2013

Venue: BMC Systems Biology

DOI: https://doi.org/10.1186/1752-0509-7-33

Paper Improving metabolic flux predictions using absolute gene expression data.

Lee, Dave; Smallbone, Kieran; Dunn, Warwick B et al. · 2012 · BMC systems biology · DOI

Full title: Improving metabolic flux predictions using absolute gene expression data.

Authors: Lee, Dave; Smallbone, Kieran; Dunn, Warwick B; Murabito, Ettore; Winder, Catherine L; Kell, Douglas B; Mendes, Pedro; Swainston, Neil

Year: 2012

Venue: BMC systems biology

DOI: https://doi.org/10.1186/1752-0509-6-73

Paper MC3: a steady-state model and constraint consistency checker for biochemical networks

Yousofshahi, Mona; Ullah, Ehsan; Stern, Russell et al. · 2013 · BMC Systems Biology · DOI

Full title: MC3: a steady-state model and constraint consistency checker for biochemical networks

Authors: Yousofshahi, Mona; Ullah, Ehsan; Stern, Russell; Hassoun, Soha

Year: 2013

Venue: BMC Systems Biology

DOI: https://doi.org/10.1186/1752-0509-7-129

Paper Mapping global effects of the anti-sigma factor MucA in Pseudomonas fluorescens SBW25 through genome-scale metabolic modeling

Borgos, Sven Even; Bordel, Sergio; Sletta, Håvard et al. · 2013 · BMC Systems Biology · DOI

Full title: Mapping global effects of the anti-sigma factor MucA in Pseudomonas fluorescens SBW25 through genome-scale metabolic modeling

Authors: Borgos, Sven Even; Bordel, Sergio; Sletta, Håvard; Ertesvåg, Helga; Jakobsen, Øyvind; Bruheim, Per; Ellingsen, Trond E.; Nielsen, Jens; Valla, Svein

Year: 2013

Venue: BMC Systems Biology

DOI: https://doi.org/10.1186/1752-0509-7-19

Paper Genome-scale metabolic reconstructions of Pichia stipitis and Pichia pastoris and in silico evaluation of their potentials

Caspeta, Luis; Shoaie, Saeed; Ågren, Rasmus et al. · 2012 · BMC Systems Biology · DOI

Full title: Genome-scale metabolic reconstructions of Pichia stipitis and Pichia pastoris and in silico evaluation of their potentials

Authors: Caspeta, Luis; Shoaie, Saeed; Ågren, Rasmus; Nookaew, Intawat; Nielsen, Jens

Year: 2012

Venue: BMC Systems Biology

DOI: https://doi.org/10.1186/1752-0509-6-24

Paper MicrobesFlux: a web platform for drafting metabolic models from the KEGG database

Feng, Xueyang; Xu, You; Chen, Yixin et al. · 2012 · BMC Systems Biology · DOI

Full title: MicrobesFlux: a web platform for drafting metabolic models from the KEGG database

Authors: Feng, Xueyang; Xu, You; Chen, Yixin; Tang, Yinjie

Year: 2012

Venue: BMC Systems Biology

DOI: https://doi.org/10.1186/1752-0509-6-94

Paper Glucose-methanol co-utilization in Pichia pastoris studied by metabolomics and instationary 13C flux analysis

Jordà, Joel; Suarez-Mendez, Camilo; Carnicer, Marc et al. · 2013 · BMC Systems Biology · DOI

Full title: Glucose-methanol co-utilization in Pichia pastoris studied by metabolomics and instationary 13C flux analysis

Authors: Jordà, Joel; Suarez-Mendez, Camilo; Carnicer, Marc; Pierick, Angela ten; Heijnen, Joseph J.; Gulik, Walter van; Ferrer, Pau; Albiol, Joan; Wahl, A.

Year: 2013

Venue: BMC Systems Biology

DOI: https://doi.org/10.1186/1752-0509-7-17

Paper i AK692: A genome-scale metabolic model of Spirulina platensis C1

Klanchui, Amornpan; Khannapho, Chiraphan; Phodee, Atchara et al. · 2012 · BMC Systems Biology · DOI

Full title: i AK692: A genome-scale metabolic model of Spirulina platensis C1

Authors: Klanchui, Amornpan; Khannapho, Chiraphan; Phodee, Atchara; Cheevadhanarak, Supapon; Meechai, Asawin

Year: 2012

Venue: BMC Systems Biology

DOI: https://doi.org/10.1186/1752-0509-6-71

Paper Inferring ancient metabolism using ancestral core metabolic models of enterobacteria

Baumler, David J.; Ma, Bing; Reed, Jennifer L. et al. · 2013 · BMC Systems Biology · DOI

Full title: Inferring ancient metabolism using ancestral core metabolic models of enterobacteria

Authors: Baumler, David J.; Ma, Bing; Reed, Jennifer L.; Perna, Nicole T.

Year: 2013

Venue: BMC Systems Biology

DOI: https://doi.org/10.1186/1752-0509-7-46

Paper Fine-tuning mitochondrial activity in Yarrowia lipolytica for citrate overproduction

Moreira, Jorgelindo da Veiga; Jolicœur, Mario; Schwartz, Laurent et al. · 2021 · Scientific Reports · DOI

Full title: Fine-tuning mitochondrial activity in Yarrowia lipolytica for citrate overproduction

Authors: Moreira, Jorgelindo da Veiga; Jolicœur, Mario; Schwartz, Laurent; Pérès, Sabine

Year: 2021

Venue: Scientific Reports

DOI: https://doi.org/10.1038/s41598-020-79577-4

Paper Understanding the metabolism of the tetralin degrader Sphingopyxis granuli strain TFA through genome-scale metabolic modelling

García‐Romero, Inmaculada; Nogales, Juan; Dı́az, Eduardo et al. · 2020 · Scientific Reports · DOI

Full title: Understanding the metabolism of the tetralin degrader Sphingopyxis granuli strain TFA through genome-scale metabolic modelling

Authors: García‐Romero, Inmaculada; Nogales, Juan; Dı́az, Eduardo; Santero, Eduardo; Floriano, Belén

Year: 2020

Venue: Scientific Reports

DOI: https://doi.org/10.1038/s41598-020-65258-9

Paper Genome scale modeling of the protein secretory pathway reveals novel targets for improved recombinant protein production in yeast

Li, Feiran; Chen, Yu; Qi, Qi et al. · 2021 · DOI

Full title: Genome scale modeling of the protein secretory pathway reveals novel targets for improved recombinant protein production in yeast

Authors: Li, Feiran; Chen, Yu; Qi, Qi; Wang, Yanyan; Yuan, Le; Huang, Mingtao; Elsemman, Ibrahim E.; Feizi, Amir; Kerkhoven, Eduard J.; Nielsen, Jens

Year: 2021

DOI: https://doi.org/10.1101/2021.10.16.464630

Paper Improved vanillin production in baker's yeast through in silico design

Brochado, Ana Rita; Matos, Claudia; Møller, Birger Lindberg et al. · 2010 · Microbial Cell Factories · DOI

Full title: Improved vanillin production in baker's yeast through in silico design

Authors: Brochado, Ana Rita; Matos, Claudia; Møller, Birger Lindberg; Hansen, Josie; Mortensen, Uffe Hasbro; Patil, Kiran Raosaheb

Year: 2010

Venue: Microbial Cell Factories

DOI: https://doi.org/10.1186/1475-2859-9-84

Paper Genome-scale metabolic models reveal determinants of phenotypic differences in non-Saccharomyces yeasts

Pettersen, Jakob Peder; Castillo, Sandra; Jouhten, Paula et al. · 2023 · BMC Bioinformatics · DOI

Full title: Genome-scale metabolic models reveal determinants of phenotypic differences in non-Saccharomyces yeasts

Authors: Pettersen, Jakob Peder; Castillo, Sandra; Jouhten, Paula; Almaas, Eivind

Year: 2023

Venue: BMC Bioinformatics

DOI: https://infoscience.epfl.ch/handle/20.500.14299/166535

Paper A metabolic reconstruction of Lactobacillus reuteri JCM 1112 and analysis of its potential as a cell factory.

Kristjansdottir, Thordis; Bosma, Elleke F; Branco Dos Santos, Filipe et al. · 2019 · Microbial cell factories · DOI

Full title: A metabolic reconstruction of Lactobacillus reuteri JCM 1112 and analysis of its potential as a cell factory.

Authors: Kristjansdottir, Thordis; Bosma, Elleke F; Branco Dos Santos, Filipe; Özdemir, Emre; Herrgård, Markus J; França, Lucas; Ferreira, Bruno; Nielsen, Alex T; Gudmundsson, Steinn

Year: 2019

Venue: Microbial cell factories

DOI: https://doi.org/10.1186/s12934-019-1229-3

Thesis Mapping and Analysis of the Complexity of Lipid Metabolism for Applications in Health and Sustainability

Tsouka, Sofia · 2020 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: Mapping and Analysis of the Complexity of Lipid Metabolism for Applications in Health and Sustainability

Authors: Tsouka, Sofia

Year: 2020

Venue: École polytechnique fédérale de Lausanne (EPFL)

Thesis Optimization methods and objective functions for analysis of metabolic network models

Hosseini, Zhaleh · 2020 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: Optimization methods and objective functions for analysis of metabolic network models

Authors: Hosseini, Zhaleh

Year: 2020

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/173904

Thesis Modelling the Intracellular Environment under Uncertainty, from Post-translational Modification to Metabolic Networks

Denhardt-Eriksson, Robin Alexander · 2021 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: Modelling the Intracellular Environment under Uncertainty, from Post-translational Modification to Metabolic Networks

Authors: Denhardt-Eriksson, Robin Alexander

Year: 2021

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/178699

Thesis Modeling, analysis, and design of complex biological networks

Oftadeh, Mohammad Omid · 2023 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: Modeling, analysis, and design of complex biological networks

Authors: Oftadeh, Mohammad Omid

Year: 2023

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/194929

Thesis Reconstruction and analysis of genome-scale metabolic networks in single organisms and microbial communities

Vagena, Evangelia · 2024 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: Reconstruction and analysis of genome-scale metabolic networks in single organisms and microbial communities

Authors: Vagena, Evangelia

Year: 2024

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/205778

Thesis Navigating and Managing the Complexity of Genome Scale Metabolic Networks for Studies in Cellular Physiology and Industrial Biotechnology

Ataman, Meriç · 2016 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: Navigating and Managing the Complexity of Genome Scale Metabolic Networks for Studies in Cellular Physiology and Industrial Biotechnology

Authors: Ataman, Meriç

Year: 2016

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/130548

Thesis Evolution of Yeast Respiro-Fermentative Lifestyle and the Underlying Mechanisms Behind Aerobic Fermentation

Hagman, Arne · 2013 · Lund University (LUP) · DOI

Full title: Evolution of Yeast Respiro-Fermentative Lifestyle and the Underlying Mechanisms Behind Aerobic Fermentation

Authors: Hagman, Arne

Year: 2013

Venue: Lund University (LUP)

DOI: https://lup.lub.lu.se/record/4065087

Thesis Reconstruction of Genome-Scale Metabolic Models with Concomitant Constraint-Based Modelling for Flux Prediction – a Case Study of Syngas Consuming Hydrogenophaga pseudoflava

Ollagnier Widén, Cristopher · 2020 · Lund University Student Papers · DOI

Full title: Reconstruction of Genome-Scale Metabolic Models with Concomitant Constraint-Based Modelling for Flux Prediction – a Case Study of Syngas Consuming Hydrogenophaga pseudoflava

Authors: Ollagnier Widén, Cristopher

Year: 2020

Venue: Lund University Student Papers

DOI: http://lup.lub.lu.se/student-papers/record/9018713

Thesis Cellular Processes and Mechanisms in Saccharomyces cerevisiae Influencing Anaerobic Xylose Fermentation

Bergdahl, Basti · 2013 · Lund University (LUP) · DOI

Full title: Cellular Processes and Mechanisms in Saccharomyces cerevisiae Influencing Anaerobic Xylose Fermentation

Authors: Bergdahl, Basti

Year: 2013

Venue: Lund University (LUP)

DOI: https://lup.lub.lu.se/record/3633658

Thesis Development of a Theoretical Workflow for Metabolic Engineering and its Application to Terpenoid Production in Escherichia coli

Valderrama Gomez, Miguel Angel · 2018 · Technical University of Munich (TUM) · DOI

Full title: Development of a Theoretical Workflow for Metabolic Engineering and its Application to Terpenoid Production in Escherichia coli

Authors: Valderrama Gomez, Miguel Angel

Year: 2018

Venue: Technical University of Munich (TUM)

DOI: https://mediatum.ub.tum.de/1435464

Thesis Genome-scale metabolic modeling of cyanbacteria: network structure, interactions, reconstruction and dynamics

Joshi, Chintan Jagdishchandra, author; Prasad, Ashok, advisor; Peebles, Christie A. M., committee member et al. · 2017 · Colorado State University · DOI

Full title: Genome-scale metabolic modeling of cyanbacteria: network structure, interactions, reconstruction and dynamics

Authors: Joshi, Chintan Jagdishchandra, author; Prasad, Ashok, advisor; Peebles, Christie A. M., committee member; Reardon, Kenneth, committee member; Peers, Graham, committee member

Year: 2017

Venue: Colorado State University

DOI: http://hdl.handle.net/10217/178913

Thesis Effect of environmental factors on succinate production by metabolically engineered Escherichia coli

Lu, Shiying · 2024 · University of Georgia - UGA Open Scholar · DOI

Full title: Effect of environmental factors on succinate production by metabolically engineered Escherichia coli

Authors: Lu, Shiying

Year: 2024

Venue: University of Georgia - UGA Open Scholar

DOI: https://openscholar.uga.edu/record/18071/files/lu_shiying_200905_phd.pdf

Thesis Total proton flux and balancing in genome-scale models: The case for the updated model of Clostridium acetobutylicum ATCC 824

McAnulty, Michael Justin · 2014 · Virginia Tech - VTechWorks · DOI

Full title: Total proton flux and balancing in genome-scale models: The case for the updated model of Clostridium acetobutylicum ATCC 824

Authors: McAnulty, Michael Justin

Year: 2014

Venue: Virginia Tech - VTechWorks

DOI: http://hdl.handle.net/10919/44199

Thesis Systems metabolic engineering through application of genome-scale metabolic flux modeling

Nazem Bokaee, Hadi · 2015 · Virginia Tech - VTechWorks · DOI

Full title: Systems metabolic engineering through application of genome-scale metabolic flux modeling

Authors: Nazem Bokaee, Hadi

Year: 2015

Venue: Virginia Tech - VTechWorks

DOI: http://hdl.handle.net/10919/56838

Thesis Computational Modeling of Planktonic and Biofilm Metabolism

Guo, Weihua · 2017 · Virginia Tech - VTechWorks · DOI

Full title: Computational Modeling of Planktonic and Biofilm Metabolism

Authors: Guo, Weihua

Year: 2017

Venue: Virginia Tech - VTechWorks

DOI: http://hdl.handle.net/10919/79669

Thesis Systems metabolic engineering of Arabidopsis for increased cellulose production

Yen, Jiun Yang · 2015 · Virginia Tech - VTechWorks · DOI

Full title: Systems metabolic engineering of Arabidopsis for increased cellulose production

Authors: Yen, Jiun Yang

Year: 2015

Venue: Virginia Tech - VTechWorks

DOI: http://hdl.handle.net/10919/54589

Thesis Reconstruction of linlog kinetics combining constraint-based and bayesian methodologies

Gotama, Michael · 2017 · UNSW Sydney · DOI

Full title: Reconstruction of linlog kinetics combining constraint-based and bayesian methodologies

Authors: Gotama, Michael

Year: 2017

Venue: UNSW Sydney

DOI: http://hdl.handle.net/1959.4/59730

Thesis Extension of the yeast metabolic model to include iron metabolism and its use to estimate global levels of iron-recruiting enzyme abundance from cofactor requirements.

Dikicioglu, Duygu; Oliver, Stephen G · 2019 · University of Cambridge · DOI

Full title: Extension of the yeast metabolic model to include iron metabolism and its use to estimate global levels of iron-recruiting enzyme abundance from cofactor requirements.

Authors: Dikicioglu, Duygu; Oliver, Stephen G

Year: 2019

Venue: University of Cambridge

DOI: https://www.repository.cam.ac.uk/handle/1810/287651

Thesis Model-guided Analysis of Plant Metabolism and Design of Metabolic Engineering Strategies

Yen, Jiun Yang · 2018 · Virginia Tech - VTechWorks · DOI

Full title: Model-guided Analysis of Plant Metabolism and Design of Metabolic Engineering Strategies

Authors: Yen, Jiun Yang

Year: 2018

Venue: Virginia Tech - VTechWorks

DOI: http://hdl.handle.net/10919/85179

Thesis Computational methods for multi-omic models of cell metabolism and their importance for theoretical computer science

Angione, Claudio · 2015 · University of Cambridge · DOI

Full title: Computational methods for multi-omic models of cell metabolism and their importance for theoretical computer science

Authors: Angione, Claudio

Year: 2015

Venue: University of Cambridge

DOI: https://www.repository.cam.ac.uk/handle/1810/252943

Thesis Increasing biomass production in bioreactors applying metabolic analysis and engineering tools

Comas Sanchez, Pere · 2021 · Universitat Autònoma de Barcelona (TDX) · DOI

Full title: Increasing biomass production in bioreactors applying metabolic analysis and engineering tools

Authors: Comas Sanchez, Pere

Year: 2021

Venue: Universitat Autònoma de Barcelona (TDX)

DOI: http://hdl.handle.net/10803/671074

Thesis PERISCOPE-Opt: Machine learning-based prediction of optimal fermentation conditions and yields of recombinant periplasmic protein expressed in Escherichia coli

Packiam, KAR; Ooi, CW; Li, F et al. · 2022 · University of Melbourne · DOI

Full title: PERISCOPE-Opt: Machine learning-based prediction of optimal fermentation conditions and yields of recombinant periplasmic protein expressed in Escherichia coli

Authors: Packiam, KAR; Ooi, CW; Li, F; Mei, S; Tey, BT; Ong, HF; Song, J; Ramanan, RN

Year: 2022

Venue: University of Melbourne

DOI: https://hdl.handle.net/11343/316279

Thesis Whole-cell modeling in yeast predicts compartment-specific proteome constraints that drive metabolic strategies.

Elsemman, Ibrahim E; Rodriguez Prado, Angelica; Grigaitis, Pranas et al. · 2022 · University of Liverpool · DOI

Full title: Whole-cell modeling in yeast predicts compartment-specific proteome constraints that drive metabolic strategies.

Authors: Elsemman, Ibrahim E; Rodriguez Prado, Angelica; Grigaitis, Pranas; Garcia Albornoz, Manuel; Harman, Victoria; Holman, Stephen W; van Heerden, Johan; Bruggeman, Frank J; Bisschops, Mark MM; Sonnenschein, Nikolaus; Hubbard, Simon; Beynon, Rob; Daran-Lapujade, Pascale; Nielsen, Jens; Teusink, Bas

Year: 2022

Venue: University of Liverpool

DOI: https://livrepository.liverpool.ac.uk/3149305/1/s41467-022-28467-6.pdf

Thesis Modelling of the metabolism of Escherichia coli for the bio-based production of 1,4-BDO

Velez Jimenez, Guillermo · 2025 · Lund University Student Papers · DOI

Full title: Modelling of the metabolism of Escherichia coli for the bio-based production of 1,4-BDO

Authors: Velez Jimenez, Guillermo

Year: 2025

Venue: Lund University Student Papers

DOI: http://lup.lub.lu.se/student-papers/record/9185902

Thesis Optimization of lipid production with a genome-scale model of Yarrowia lipolytica

Kavšček, Martin; Bhutada, Govindprasad; Madl, Tobias et al. · 2015 · Technical University of Munich (TUM) · DOI

Full title: Optimization of lipid production with a genome-scale model of Yarrowia lipolytica

Authors: Kavšček, Martin;Bhutada, Govindprasad;Madl, Tobias;Natter, Klaus

Year: 2015

Venue: Technical University of Munich (TUM)

DOI: https://mediatum.ub.tum.de/1343213

Thesis FBA-PRCC. Partial Rank Correlation Coefficient (PRCC) Global Sensitivity Analysis (GSA) in Application to Constraint-Based Models

Sorokin, Anatoly; Goryanin, Igor · 2023 · Okinawa Institute of Science and Technology (OIST) · DOI

Full title: FBA-PRCC. Partial Rank Correlation Coefficient (PRCC) Global Sensitivity Analysis (GSA) in Application to Constraint-Based Models

Authors: Sorokin, Anatoly; Goryanin, Igor

Year: 2023

Venue: Okinawa Institute of Science and Technology (OIST)

DOI: https://oist.repo.nii.ac.jp/record/2956/files/Sorokin-2023-FBA-PRCC. Partial Rank Correlatio.pdf

Thesis Flux balance analysis of metabolic models: a review of recent advances and applications

Estep, Forrest Earnest, author; Peebles, Christie, advisor; Shipman, Patrick, committee member et al. · 2016 · Colorado State University · DOI

Full title: Flux balance analysis of metabolic models: a review of recent advances and applications

Authors: Estep, Forrest Earnest, author; Peebles, Christie, advisor; Shipman, Patrick, committee member; Snow, Chris, committee member

Year: 2016

Venue: Colorado State University

DOI: http://hdl.handle.net/10217/173463

Thesis Biosynthetic pathway to produce esters in Escherichia coli

Shipmon, Jacoby Courtland · 2024 · University of Georgia - UGA Open Scholar · DOI

Full title: Biosynthetic pathway to produce esters in Escherichia coli

Authors: Shipmon, Jacoby Courtland

Year: 2024

Venue: University of Georgia - UGA Open Scholar

DOI: https://openscholar.uga.edu/record/3174/files/Ester%20Thesis%2004.19.pdf

Thesis Development of an integrated fermentation pervaporation model for bioethanol production

Hamid, Zentou · 2021 · Universiti Putra Malaysia (PSAS IR) · DOI

Full title: Development of an integrated fermentation pervaporation model for bioethanol production

Authors: Hamid, Zentou

Year: 2021

Venue: Universiti Putra Malaysia (PSAS IR)

DOI: http://psasir.upm.edu.my/id/eprint/98171/1/FK%202021%2087%20-%20IR.pdf

Thesis Large-scale kinetic metabolic models of Pseudomonas putida KT2440 for consistent design of metabolic engineering strategies

Tokic, Milenko; Hatzimanikatis, Vassily; Miskovic, Ljubisa · 2020 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: Large-scale kinetic metabolic models of Pseudomonas putida KT2440 for consistent design of metabolic engineering strategies

Authors: Tokic, Milenko; Hatzimanikatis, Vassily; Miskovic, Ljubisa

Year: 2020

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/166566

Thesis The ETFL formulation allows multi-omics integration in thermodynamics-compliant metabolism and expression models

Salvy, Pierre; Hatzimanikatis, Vassily · 2020 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: The ETFL formulation allows multi-omics integration in thermodynamics-compliant metabolism and expression models

Authors: Salvy, Pierre; Hatzimanikatis, Vassily

Year: 2020

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/164621

Thesis redLips: a comprehensive mechanistic model of the lipid metabolic network of yeast

Tsouka, S.; Hatzimanikatis, V · 2020 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: redLips: a comprehensive mechanistic model of the lipid metabolic network of yeast

Authors: Tsouka, S.; Hatzimanikatis, V

Year: 2020

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/169261

Thesis Rational strain design with minimal phenotype perturbation

Narayanan, Bharath; Weilandt, Daniel R.; Masid, Maria et al. · 2024 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: Rational strain design with minimal phenotype perturbation

Authors: Narayanan, Bharath; Weilandt, Daniel R.; Masid, Maria; Miskovic, Ljubisa; Hatzimanikatis, Vassily

Year: 2024

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/205399

Thesis A genome-scale metabolic model of Saccharomyces cerevisiae that integrates expression constraints and reaction thermodynamics

Oftadeh, Omid; Salvy, Pierre; Masid, Maria et al. · 2021 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: A genome-scale metabolic model of Saccharomyces cerevisiae that integrates expression constraints and reaction thermodynamics

Authors: Oftadeh, Omid; Salvy, Pierre; Masid, Maria; Curvat, Maxime; Miskovic, Ljubisa; Hatzimanikatis, Vassily

Year: 2021

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/180917

Thesis Mechanistic insights into bacterial metabolic reprogramming from omics-integrated genome-scale models

Hadadi, Noushin; Pandey, Vikash; Chiappino-Pepe, Anush et al. · 2020 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: Mechanistic insights into bacterial metabolic reprogramming from omics-integrated genome-scale models

Authors: Hadadi, Noushin; Pandey, Vikash; Chiappino-Pepe, Anush; Morales, Marian; Gallart-Ayala, Hector; Mehl, Florence; Ivanisevic, Julijana; Sentchilo, Vladimir; van der Meer, Jan R.

Year: 2020

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/166672

Thesis Reconstructing Kinetic Models for Dynamical Studies of Metabolism using Generative Adversarial Networks

Choudhury, Subham; Moret, Michael; Salvy, Pierre et al. · 2022 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: Reconstructing Kinetic Models for Dynamical Studies of Metabolism using Generative Adversarial Networks

Authors: Choudhury, Subham; Moret, Michael; Salvy, Pierre; Weilandt, Daniel; Hatzimanikatis, Vassily; Miskovic, Ljubisa

Year: 2022

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/190649

Thesis Emergence of diauxie as an optimal growth strategy under resource allocation constraints in cellular metabolism

Salvy, Pierre; Hatzimanikatis, Vassily · 2021 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: Emergence of diauxie as an optimal growth strategy under resource allocation constraints in cellular metabolism

Authors: Salvy, Pierre; Hatzimanikatis, Vassily

Year: 2021

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/176236

Thesis Constraint-based metabolic control analysis for rational strain engineering

Tsouka, Sofia; Ataman, Meriç; Hameri, Tuure Eelis et al. · 2021 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: Constraint-based metabolic control analysis for rational strain engineering

Authors: Tsouka, Sofia; Ataman, Meriç; Hameri, Tuure Eelis; Miskovic, Ljubisa; Hatzimanikatis, Vassily

Year: 2021

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/178061

Thesis The effects of model complexity and size on metabolic flux distribution and control: case study in Escherichia coli

Hameri, Tuure; Fengos, Georgios; Hatzimanikatis, Vassily · 2021 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: The effects of model complexity and size on metabolic flux distribution and control: case study in Escherichia coli

Authors: Hameri, Tuure; Fengos, Georgios; Hatzimanikatis, Vassily

Year: 2021

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/177097

Thesis Production of biofuels and biochemicals: in need of an ORACLE

Miskovic, Ljubisa; Hatzimanikatis, Vassily · 2010 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: Production of biofuels and biochemicals: in need of an ORACLE

Authors: Miskovic, Ljubisa; Hatzimanikatis, Vassily

Year: 2010

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/48064

Thesis From network models to network responses: integration of thermodynamic and kinetic properties of yeast genome-scale metabolic networks

Soh, Keng Cher; Miskovic, Ljubisa; Hatzimanikatis, Vassily · 2011 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: From network models to network responses: integration of thermodynamic and kinetic properties of yeast genome-scale metabolic networks

Authors: Soh, Keng Cher; Miskovic, Ljubisa; Hatzimanikatis, Vassily

Year: 2011

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/73129

Thesis Identification of Feasible Metabolic Fluxes and Metabolite Concentrations using Large-scale Kinetic Models

Chakrabarti, Anirikh; Miskovic, Ljubisa; Soh, Keng Cher et al. · 2013 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: Identification of Feasible Metabolic Fluxes and Metabolite Concentrations using Large-scale Kinetic Models

Authors: Chakrabarti, Anirikh; Miskovic, Ljubisa; Soh, Keng Cher; Hatzimanikatis, Vassily

Year: 2013

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/93237

Thesis Data, Parameters & Nonlinearities: Development and Applications of Large-scale Dynamic Models of Metabolism

Chakrabarti, Anirikh; Miskovic, Ljubisa; Soh, Keng Cher et al. · 2013 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: Data, Parameters & Nonlinearities: Development and Applications of Large-scale Dynamic Models of Metabolism

Authors: Chakrabarti, Anirikh; Miskovic, Ljubisa; Soh, Keng Cher; Hatzimanikatis, Vassily

Year: 2013

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/93236

Thesis Towards kinetic modeling of genome-scale metabolic networks without sacrificing stoichiometric, thermodynamic and physiology constraints

Chakrabarti, Anirikh; Miskovic, Ljubisa; Soh, Keng Cher et al. · 2013 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: Towards kinetic modeling of genome-scale metabolic networks without sacrificing stoichiometric, thermodynamic and physiology constraints

Authors: Chakrabarti, Anirikh; Miskovic, Ljubisa; Soh, Keng Cher; Hatzimanikatis, Vassily

Year: 2013

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/91902

Thesis Metabolic Needs and Capabilities of Toxoplasma gondii through Combined Computational and Experimental Analysis

Tymoshenko, Stepan; Oppenheim, Rebecca D.; Agren, Rasmus et al. · 2015 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: Metabolic Needs and Capabilities of Toxoplasma gondii through Combined Computational and Experimental Analysis

Authors: Tymoshenko, Stepan; Oppenheim, Rebecca D.; Agren, Rasmus; Nielsen, Jens; Soldati-Favre, Dominique; Hatzimanikatis, Vassily

Year: 2015

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/114047

Thesis Identification of metabolic engineering targets for the enhancement of 1,4-butanediol production in recombinant E. coli using large-scale kinetic models

Andreozzi, Stefano; Charkrabarti, Anirikh; Soh, Keng Cher et al. · 2016 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: Identification of metabolic engineering targets for the enhancement of 1,4-butanediol production in recombinant E. coli using large-scale kinetic models

Authors: Andreozzi, Stefano; Charkrabarti, Anirikh; Soh, Keng Cher; Burgard, Anthony; Yang, Tae-Hoon; Van Dien, Stephen; Miskovic, Ljubisa; Hatzimanikatis, Vassily

Year: 2016

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/123298

Thesis redGEM: Systematic reduction and analysis of genome-scale metabolic reconstructions for development of consistent core metabolic models

Ataman, Meric; Gardiol, Daniel F. Hernandez; Fengos, Georgios et al. · 2017 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: redGEM: Systematic reduction and analysis of genome-scale metabolic reconstructions for development of consistent core metabolic models

Authors: Ataman, Meric; Gardiol, Daniel F. Hernandez; Fengos, Georgios; Hatzimanikatis, Vassily

Year: 2017

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/140242

Thesis A Design-Build-Test cycle using modeling and experiments reveals interdependencies between upper glycolysis and xylose uptake in recombinant S. cerevisiae and improves predictive capabilities of large-scale kinetic models

Miskovic, Ljubisa; Alff-Tuomala, Susanne; Soh, Keng Cher et al. · 2017 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: A Design-Build-Test cycle using modeling and experiments reveals interdependencies between upper glycolysis and xylose uptake in recombinant S. cerevisiae and improves predictive capabilities of large-scale kinetic models

Authors: Miskovic, Ljubisa; Alff-Tuomala, Susanne; Soh, Keng Cher; Barth, Dorothee; Salusjärvi, Laura; Pitkänen, Juha-Pekka; Ruohonen, Laura; Penttilä, Merja; Hatzimanikatis, Vassily

Year: 2017

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/138110

Thesis A curated collection of Klebsiella metabolic models reveals variable substrate usage and gene essentiality

Hawkey, J; Vezina, B; Monk, JM et al. · 2022 · University of Melbourne · DOI

Full title: A curated collection of Klebsiella metabolic models reveals variable substrate usage and gene essentiality

Authors: Hawkey, J; Vezina, B; Monk, JM; Judd, LM; Harshegyi, T; López-Fernández, S; Rodrigues, C; Brisse, S; Holt, KE; Wyres, KL

Year: 2022

Venue: University of Melbourne

DOI: https://hdl.handle.net/11343/307882

Thesis Comparison of Optimization-Modelling Methods for Metabolites Production in Escherichia coli

Lee, MK; Mohamad, MS; Choon, YW et al. · 2020 · University of Melbourne · DOI

Full title: Comparison of Optimization-Modelling Methods for Metabolites Production in Escherichia coli

Authors: Lee, MK; Mohamad, MS; Choon, YW; Daud, KM; Nasarudin, NA; Ismail, MA; Ibrahim, Z; Napis, S; Sinnott, RO

Year: 2020

Venue: University of Melbourne

DOI: https://hdl.handle.net/11343/241429

Thesis Modular dynamic biomolecular modelling with bond graphs: The unification of stoichiometry, thermodynamics, kinetics and data

Gawthrop, PJ; Pan, M; Crampin, EJ · 2021 · University of Melbourne · DOI

Full title: Modular dynamic biomolecular modelling with bond graphs: The unification of stoichiometry, thermodynamics, kinetics and data

Authors: Gawthrop, PJ; Pan, M; Crampin, EJ

Year: 2021

Venue: University of Melbourne

DOI: https://hdl.handle.net/11343/287796

Thesis Metabolic engineering of Saccharomyces cerevisiae for second-generation ethanol production from xylo-oligosaccharides and acetate

Procópio, Dielle Pierotti; Lee, Jae Won; Shin, Jonghyeok et al. · 2025 · Universidade Estadual Paulista (UNESP) · DOI

Full title: Metabolic engineering of Saccharomyces cerevisiae for second-generation ethanol production from xylo-oligosaccharides and acetate

Authors: Procópio, Dielle Pierotti; Lee, Jae Won; Shin, Jonghyeok; Tramontina, Robson; Ávila, Patrícia Felix; Brenelli, Lívia Beatriz; Squina, Fabio Márcio; Damasio, André; Rabelo, Sarita Cândida [UNESP]; Goldbeck, Rosana; Franco, Telma Teixeira; Leak, David; Jin, Yong-Su; Basso, Thiago Olitta

Year: 2025

Venue: Universidade Estadual Paulista (UNESP)

DOI: http://dx.doi.org/10.1038/s41598-023-46293-8

Thesis Quantitative evaluation of anaerobic microbial metabolism via comparative genomics and metabolic modeling

Tang, Wentao · 2022 · Hong Kong University of Science and Technology (HKUST) · DOI

Full title: Quantitative evaluation of anaerobic microbial metabolism via comparative genomics and metabolic modeling

Authors: Tang, Wentao

Year: 2022

Venue: Hong Kong University of Science and Technology (HKUST)

DOI: http://repository.hkust.edu.hk/ir/Record/1783.1-150041

Thesis Enhancement of Lipid Production in Rhodosporidium toruloides: Designing Feeding Strategies Through Dynamic Flux Balance Analysis

Castañeda, María Teresita; Nuñez, Sebastián; Jamilis Ricaldoni, Martín Ignacio et al. · 2025 · National University of La Plata – SeDiCI · DOI

Full title: Enhancement of Lipid Production in Rhodosporidium toruloides: Designing Feeding Strategies Through Dynamic Flux Balance Analysis

Authors: Castañeda, María Teresita; Nuñez, Sebastián; Jamilis Ricaldoni, Martín Ignacio; De Battista, Hernán

Year: 2025

Venue: National University of La Plata – SeDiCI

DOI: http://sedici.unlp.edu.ar/handle/10915/189167

Thesis Opportunities at the interface of network science and metabolic modelling

Dusad, Varshit; Thiel, Denise; Barahona, Mauricio et al. · 2021 · Imperial College London · DOI

Full title: Opportunities at the interface of network science and metabolic modelling

Authors: Dusad, Varshit; Thiel, Denise; Barahona, Mauricio; Keun, Hector; Oyarzun, Diego

Year: 2021

Venue: Imperial College London

DOI: https://www.frontiersin.org/articles/10.3389/fbioe.2020.591049/full

Thesis Multi-Omics and Genome-Scale Modeling Reveal a Metabolic Shift During C. elegans Aging.

Hastings, Janna; Mains, Abraham; Virk, Bhupinder et al. · 2019 · University of Cambridge · DOI

Full title: Multi-Omics and Genome-Scale Modeling Reveal a Metabolic Shift During C. elegans Aging.

Authors: Hastings, Janna; Mains, Abraham; Virk, Bhupinder; Rodriguez, Nicolas; Murdoch, Sharlene; Pearce, Juliette; Bergmann, Sven; Le Novère, Nicolas; Casanueva, Olivia

Year: 2019

Venue: University of Cambridge

DOI: https://www.repository.cam.ac.uk/handle/1810/294238

Thesis Predictive evolution of metabolic phenotypes using model-designed environments.

Jouhten, Paula; Konstantinidis, Dimitrios; Pereira, Filipa et al. · 2022 · University of Cambridge · DOI

Full title: Predictive evolution of metabolic phenotypes using model-designed environments.

Year: 2022

Venue: University of Cambridge

DOI: https://www.repository.cam.ac.uk/handle/1810/341759

Thesis Predictive analytics of environmental adaptability in multi-omic network models.

Angione, Claudio; Lió, Pietro · 2018 · University of Cambridge · DOI

Full title: Predictive analytics of environmental adaptability in multi-omic network models.

Authors: Angione, Claudio; Lió, Pietro

Year: 2018

Venue: University of Cambridge

DOI: https://www.repository.cam.ac.uk/handle/1810/284993

Thesis Biomass composition: the "elephant in the room" of metabolic modelling.

Dikicioglu, Duygu; Kırdar, Betul; Oliver, Stephen G · 2015 · University of Cambridge · DOI

Full title: Biomass composition: the "elephant in the room" of metabolic modelling.

Authors: Dikicioglu, Duygu; Kırdar, Betul; Oliver, Stephen G

Year: 2015

Venue: University of Cambridge

DOI: https://www.repository.cam.ac.uk/handle/1810/248653

Thesis Combination of Genome-Scale Models and Bioreactor Dynamics to Optimize the Production of Commodity Chemicals.

Lázaro, Jorge; Jansen, Giorgio; Yang, Yiheng et al. · 2022 · University of Cambridge · DOI

Full title: Combination of Genome-Scale Models and Bioreactor Dynamics to Optimize the Production of Commodity Chemicals.

Authors: Lázaro, Jorge; Jansen, Giorgio; Yang, Yiheng; Torres-Acosta, Mario A; Lye, Gary; Oliver, Stephen G; Júlvez, Jorge

Year: 2022

Venue: University of Cambridge

DOI: https://www.repository.cam.ac.uk/handle/1810/334789

Thesis Simulation and optimization of dynamic flux balance analysis models using an interior point method reformulation

Scott, Felipe; Wilson, Pamela; Conejeros, Raúl et al. · 2018 · University of Cambridge · DOI

Full title: Simulation and optimization of dynamic flux balance analysis models using an interior point method reformulation

Authors: Scott, Felipe; Wilson, Pamela; Conejeros, Raúl; Vassiliadis, Vassilios S

Year: 2018

Venue: University of Cambridge

DOI: https://www.repository.cam.ac.uk/handle/1810/285147

Thesis Pareto optimal metabolic engineering for the growth-coupled overproduction of sustainable chemicals.

Amaradio, Matteo N; Ojha, Varun; Jansen, Giorgio et al. · 2022 · University of Cambridge · DOI

Full title: Pareto optimal metabolic engineering for the growth-coupled overproduction of sustainable chemicals.

Authors: Amaradio, Matteo N; Ojha, Varun; Jansen, Giorgio; Gulisano, Massimo; Costanza, Jole; Nicosia, Giuseppe

Year: 2022

Venue: University of Cambridge

DOI: https://www.repository.cam.ac.uk/handle/1810/336332

Thesis Adaptive laboratory evolution of microbial co-cultures for improved metabolite secretion.

Konstantinidis, Dimitrios; Pereira, Filipa; Geissen, Eva-Maria et al. · 2021 · University of Cambridge · DOI

Full title: Adaptive laboratory evolution of microbial co-cultures for improved metabolite secretion.

Authors: Konstantinidis, Dimitrios; Pereira, Filipa; Geissen, Eva-Maria; Grkovska, Kristina; Kafkia, Eleni; Jouhten, Paula; Kim, Yongkyu; Devendran, Saravanan; Zimmermann, Michael; Patil, Kiran Raosaheb

Year: 2021

Venue: University of Cambridge

DOI: https://www.repository.cam.ac.uk/handle/1810/328503

Thesis Spatiotemporal modeling of microbial metabolism

Chen, Jin; Phalak, Poonam; Gomez, Jose A. et al. · 2016 · Massachusetts Institute of Technology (MIT) · DOI

Full title: Spatiotemporal modeling of microbial metabolism

Authors: Chen, Jin; Phalak, Poonam; Gomez, Jose A.; Barton, Paul I.; Henson, Michael A.; Hoeffner, Kai

Year: 2016

Venue: Massachusetts Institute of Technology (MIT)

DOI: http://hdl.handle.net/1721.1/101418

Thesis Reversing the directionality of reactions between non-oxidative pentose phosphate pathway and glycolytic pathway boosts mycosporine-like amino acid production in Saccharomyces cerevisiae

Hengardi, Miselle Tiana; Liang, Cui; Madivannan, Keshiniy et al. · 2024 · Nanyang Technological University (NTU) · DOI

Full title: Reversing the directionality of reactions between non-oxidative pentose phosphate pathway and glycolytic pathway boosts mycosporine-like amino acid production in Saccharomyces cerevisiae

Authors: Hengardi, Miselle Tiana; Liang, Cui; Madivannan, Keshiniy; Yang, Kien Yang; Koduru, Lokanand; Kanagasundaram, Yoganathan; Arumugam, Prakash

Year: 2024

Venue: Nanyang Technological University (NTU)

DOI: https://hdl.handle.net/10356/179607

Thesis Deregulation of S-adenosylmethionine biosynthesis and regeneration improves methylation in the E. coli de novo vanillin biosynthesis pathway

Hyun, Jason C.; Kunjapur, Aditya Mohan; Prather, Kristala L. Jones · 2016 · Massachusetts Institute of Technology (MIT) · DOI

Full title: Deregulation of S-adenosylmethionine biosynthesis and regeneration improves methylation in the E. coli de novo vanillin biosynthesis pathway

Authors: Hyun, Jason C.; Kunjapur, Aditya Mohan; Prather, Kristala L. Jones

Year: 2016

Venue: Massachusetts Institute of Technology (MIT)

DOI: http://hdl.handle.net/1721.1/102272

Thesis Towards predicting the environmental metabolome from metagenomics with a mechanistic model

Garza, Daniel R; van Verk, Marcel C; Huynen, Martijn A et al. · 2018 · Utrecht University · DOI

Full title: Towards predicting the environmental metabolome from metagenomics with a mechanistic model

Authors: Garza, Daniel R; van Verk, Marcel C; Huynen, Martijn A; Dutilh, Bas E

Year: 2018

Venue: Utrecht University

DOI: https://dspace.library.uu.nl/handle/1874/369051

Thesis Screening and modular design for metabolic pathway optimization

Boock, Jason; Gupta, Apoorv; Jones, Kristala L. · 2017 · Massachusetts Institute of Technology (MIT) · DOI

Full title: Screening and modular design for metabolic pathway optimization

Authors: Boock, Jason; Gupta, Apoorv; Jones, Kristala L.

Year: 2017

Venue: Massachusetts Institute of Technology (MIT)

DOI: http://hdl.handle.net/1721.1/108027

Thesis Improvement of glucaric acid production in E. coli via dynamic control of metabolic fluxes

Stenger, Andrew R.; Gupta, Apoorv; Connors, Neal C. et al. · 2016 · Massachusetts Institute of Technology (MIT) · DOI

Full title: Improvement of glucaric acid production in E. coli via dynamic control of metabolic fluxes

Authors: Stenger, Andrew R.; Gupta, Apoorv; Connors, Neal C.; Brockman Reizman, Irene M.; Reisch, Christopher R.; Prather, Kristala L. Jones

Year: 2016

Venue: Massachusetts Institute of Technology (MIT)

DOI: http://hdl.handle.net/1721.1/101230

Thesis From sugars to biodiesel using microalgae and yeast

Barton, Paul I.; Gomez, Jose Alberto; Hoeffner, Kai · 2016 · Massachusetts Institute of Technology (MIT) · DOI

Full title: From sugars to biodiesel using microalgae and yeast

Authors: Barton, Paul I.; Gomez, Jose Alberto; Hoeffner, Kai

Year: 2016

Venue: Massachusetts Institute of Technology (MIT)

DOI: http://hdl.handle.net/1721.1/101915

Thesis Genome-scale metabolic reconstruction of 7,302 human microorganisms for personalized medicine

Heinken, Almut; Hertel, Johannes; Acharya, Geeta et al. · 2023 · Utrecht University · DOI

Full title: Genome-scale metabolic reconstruction of 7,302 human microorganisms for personalized medicine

Authors: Heinken, Almut; Hertel, Johannes; Acharya, Geeta; Ravcheev, Dmitry A.; Nyga, Malgorzata; Okpala, Onyedika Emmanuel; Hogan, Marcus; Magnúsdóttir, Stefanía; Martinelli, Filippo; Nap, Bram; Preciat, German; Edirisinghe, Janaka N.; Henry, Christopher S.; Fleming, Ronan M.T.; Thiele, Ines

Year: 2023

Venue: Utrecht University

DOI: https://dspace.library.uu.nl/handle/1874/456011

Thesis Experimental design-aided systematic pathway optimization of glucose uptake and deoxyxylulose phosphate pathway for improved amorphadiene production

Zhang, Congqiang; Zou, Ruiyang; Chen, Xixian et al. · 2016 · Massachusetts Institute of Technology (MIT) · DOI

Full title: Experimental design-aided systematic pathway optimization of glucose uptake and deoxyxylulose phosphate pathway for improved amorphadiene production

Authors: Zhang, Congqiang; Zou, Ruiyang; Chen, Xixian; Stephanopoulos, Gregory; Too, Heng-Phon

Year: 2016

Venue: Massachusetts Institute of Technology (MIT)

DOI: http://hdl.handle.net/1721.1/104360

Thesis Exploring the gap between dynamic and constraint-based models of metabolism

Machado, Daniel; Costa, Rafael S.; Rocha, Isabel et al. · 2016 · Massachusetts Institute of Technology (MIT) · DOI

Full title: Exploring the gap between dynamic and constraint-based models of metabolism

Authors: Machado, Daniel; Costa, Rafael S.; Rocha, Isabel; Tidor, Bruce; Ferreira, Eugenio C.

Year: 2016

Venue: Massachusetts Institute of Technology (MIT)

DOI: http://hdl.handle.net/1721.1/101078

Thesis Origins of Cell-to-Cell Bioprocessing Diversity and Implications of the Extracellular Environment Revealed at the Single-Cell Level

Vasdekis, A. E.; Silverman, Andrew M.; Stephanopoulos, Gregory · 2016 · Massachusetts Institute of Technology (MIT) · DOI

Full title: Origins of Cell-to-Cell Bioprocessing Diversity and Implications of the Extracellular Environment Revealed at the Single-Cell Level

Authors: Vasdekis, A. E.; Silverman, Andrew M.; Stephanopoulos, Gregory

Year: 2016

Venue: Massachusetts Institute of Technology (MIT)

DOI: http://hdl.handle.net/1721.1/100931

Thesis Ensemble Kinetic Modeling of Metabolic Networks from Dynamic Metabolic Profiles

Jia, Gengjie; Stephanopoulos, Gregory; Gunawan, Rudiyanto · 2018 · Massachusetts Institute of Technology (MIT) · DOI

Full title: Ensemble Kinetic Modeling of Metabolic Networks from Dynamic Metabolic Profiles

Authors: Jia, Gengjie; Stephanopoulos, Gregory; Gunawan, Rudiyanto

Year: 2018

Venue: Massachusetts Institute of Technology (MIT)

DOI: http://hdl.handle.net/1721.1/113357

Thesis Distributing a metabolic pathway among a microbial consortium enhances production of natural products

Zhou, Kang; Qiao, Kangjian; Stephanopoulos, Gregory et al. · 2016 · Massachusetts Institute of Technology (MIT) · DOI

Full title: Distributing a metabolic pathway among a microbial consortium enhances production of natural products

Authors: Zhou, Kang; Qiao, Kangjian; Stephanopoulos, Gregory; Edgar, Steven McBride

Year: 2016

Venue: Massachusetts Institute of Technology (MIT)

DOI: http://hdl.handle.net/1721.1/102311

Thesis Metabolomic and [superscript 13]C-metabolic flux analysis of a xylose-consuming Saccharomyces cerevisiae strain expressing xylose isomerase

Wasylenko, Thomas M.; Stephanopoulos, Gregory; Wasylenko, Thomas Michael · 2017 · Massachusetts Institute of Technology (MIT) · DOI

Full title: Metabolomic and [superscript 13]C-metabolic flux analysis of a xylose-consuming Saccharomyces cerevisiae strain expressing xylose isomerase

Authors: Wasylenko, Thomas M.; Stephanopoulos, Gregory; Wasylenko, Thomas Michael

Year: 2017

Venue: Massachusetts Institute of Technology (MIT)

DOI: http://hdl.handle.net/1721.1/109764

Thesis Integrating Genome-Scale and Superstructure Optimization Models in Techno-Economic Studies of Biorefineries

Akbari, Amir; Barton, Paul I · 2021 · Massachusetts Institute of Technology (MIT) · DOI

Full title: Integrating Genome-Scale and Superstructure Optimization Models in Techno-Economic Studies of Biorefineries

Authors: Akbari, Amir; Barton, Paul I

Year: 2021

Venue: Massachusetts Institute of Technology (MIT)

DOI: https://hdl.handle.net/1721.1/134815

Thesis Reply to "Do genome-scale models need exact solvers or clearer standards?"

Chindelevitch, Leonid; Regev, Aviv; Berger Leighton, Bonnie et al. · 2016 · Massachusetts Institute of Technology (MIT) · DOI

Full title: Reply to "Do genome-scale models need exact solvers or clearer standards?"

Authors: Chindelevitch, Leonid; Regev, Aviv; Berger Leighton, Bonnie; Trigg, Jason

Year: 2016

Venue: Massachusetts Institute of Technology (MIT)

DOI: http://hdl.handle.net/1721.1/104072

Thesis Dynamic regulation of metabolic flux in engineered bacteria using a pathway-independent quorum-sensing circuit

Gupta, Apoorv; Brockman Reizman, Irene M.; Reisch, Christopher R. et al. · 2020 · Massachusetts Institute of Technology (MIT) · DOI

Full title: Dynamic regulation of metabolic flux in engineered bacteria using a pathway-independent quorum-sensing circuit

Authors: Gupta, Apoorv; Brockman Reizman, Irene M.; Reisch, Christopher R.; Prather, Kristala L

Year: 2020

Venue: Massachusetts Institute of Technology (MIT)

DOI: https://hdl.handle.net/1721.1/126255

Thesis A systematic approach for finding the objective function and active constraints for dynamic flux balance analysis

Nikdel, Ali; Braatz, Richard D; Budman, Hector M · 2021 · Massachusetts Institute of Technology (MIT) · DOI

Full title: A systematic approach for finding the objective function and active constraints for dynamic flux balance analysis

Authors: Nikdel, Ali; Braatz, Richard D; Budman, Hector M

Year: 2021

Venue: Massachusetts Institute of Technology (MIT)

DOI: https://hdl.handle.net/1721.1/131356

Thesis Layered dynamic regulation for improving metabolic pathway productivity in Escherichia coli

Doong, Stephanie; Gupta, Apoorv; Jones, Kristala L. · 2018 · Massachusetts Institute of Technology (MIT) · DOI

Full title: Layered dynamic regulation for improving metabolic pathway productivity in Escherichia coli

Authors: Doong, Stephanie; Gupta, Apoorv; Jones, Kristala L.

Year: 2018

Venue: Massachusetts Institute of Technology (MIT)

DOI: http://hdl.handle.net/1721.1/119416

Thesis Dynamic flux balance modeling to increase the production of high-value compounds in green microalgae

Fachet, Melanie; Höffner, Kai; Sundmacher, Kai et al. · 2017 · Massachusetts Institute of Technology (MIT) · DOI

Full title: Dynamic flux balance modeling to increase the production of high-value compounds in green microalgae

Authors: Fachet, Melanie; Höffner, Kai; Sundmacher, Kai; Flassig, Robert J.; Barton, Paul I

Year: 2017

Venue: Massachusetts Institute of Technology (MIT)

DOI: http://hdl.handle.net/1721.1/107153

Thesis Large-scale identification of genetic design strategies using local search

Lun, Desmond S.; Rockwell, Graham; Guido, Nicholas J. et al. · 2011 · Massachusetts Institute of Technology (MIT) · DOI

Full title: Large-scale identification of genetic design strategies using local search

Authors: Lun, Desmond S.; Rockwell, Graham; Guido, Nicholas J.; Baym, Michael Hartmann; Kelner, Jonathan Adam; Berger, Bonnie; Galagan, James E.; Church, George M.

Year: 2011

Venue: Massachusetts Institute of Technology (MIT)

DOI: http://hdl.handle.net/1721.1/60870

Thesis Statistics-based model for prediction of chemical biosynthesis yield from Saccharomyces cerevisiae

Xiao, Yi; Leonard, Effendi; Varman, Arul M. et al. · 2011 · Massachusetts Institute of Technology (MIT) · DOI

Full title: Statistics-based model for prediction of chemical biosynthesis yield from Saccharomyces cerevisiae

Authors: Xiao, Yi; Leonard, Effendi; Varman, Arul M.; Tang, Yinjie J.

Year: 2011

Venue: Massachusetts Institute of Technology (MIT)

DOI: http://hdl.handle.net/1721.1/65336

Thesis Engineering alternative butanol production platforms in heterologous bacteria

Nielsen, David R.; Leonard, Effendi; Yoon, Sang-Hwal et al. · 2012 · Massachusetts Institute of Technology (MIT) · DOI

Full title: Engineering alternative butanol production platforms in heterologous bacteria

Authors: Nielsen, David R.; Leonard, Effendi; Yoon, Sang-Hwal; Tseng, Hsien-chung; Yuan, Clara J.; Prather, Kristala L. Jones

Year: 2012

Venue: Massachusetts Institute of Technology (MIT)

DOI: http://hdl.handle.net/1721.1/68704

Thesis Using Topology of the Metabolic Network to Predict Viability of Mutant Strains

Mirny, Leonid A.; Wunderlich, Zeba · 2010 · Massachusetts Institute of Technology (MIT) · DOI

Full title: Using Topology of the Metabolic Network to Predict Viability of Mutant Strains

Authors: Mirny, Leonid A.; Wunderlich, Zeba

Year: 2010

Venue: Massachusetts Institute of Technology (MIT)

DOI: http://hdl.handle.net/1721.1/59195

Thesis Linking high-resolution metabolic flux phenotypes and transcriptional regulation in yeast modulated by the global regulator Gcn4p

Moxley, Joel F.; Jewett, Michael C.; Antoniewicz, Maciek R. et al. · 2009 · Massachusetts Institute of Technology (MIT) · DOI

Full title: Linking high-resolution metabolic flux phenotypes and transcriptional regulation in yeast modulated by the global regulator Gcn4p

Authors: Moxley, Joel F.; Jewett, Michael C.; Antoniewicz, Maciek R.; Villas-Boas, Silas G.; Alper, Hal; Wheeler, Robert T.; Tong, Lily V.; Hinnebusch, Alan G.; Ideker, Trey; Nielsen, Jens Kromann; Stephanopoulos, Gregory

Year: 2009

Venue: Massachusetts Institute of Technology (MIT)

DOI: http://hdl.handle.net/1721.1/50252

Thesis Porting the synthetic D-glucaric acid pathway fromEscherichia colito Saccharomyces cerevisiae

Gupta, Amita; Hicks, Michael A.; Manchester, Shawn et al. · 2019 · Massachusetts Institute of Technology (MIT) · DOI

Full title: Porting the synthetic D-glucaric acid pathway fromEscherichia colito Saccharomyces cerevisiae

Authors: Gupta, Amita; Hicks, Michael A.; Manchester, Shawn; Prather, Kristala L

Year: 2019

Venue: Massachusetts Institute of Technology (MIT)

DOI: https://hdl.handle.net/1721.1/122605

Thesis Inferring Carbon Sources from Gene Expression Profiles Using Metabolic Flux Models

Brandes, Aaron; Lun, Desmond S.; Ip, Kuhn et al. · 2012 · Massachusetts Institute of Technology (MIT) · DOI

Full title: Inferring Carbon Sources from Gene Expression Profiles Using Metabolic Flux Models

Authors: Brandes, Aaron; Lun, Desmond S.; Ip, Kuhn; Zucker, Jeremy; Colijn, Caroline; Weiner, Brian; Galagan, James E.

Year: 2012

Venue: Massachusetts Institute of Technology (MIT)

DOI: http://hdl.handle.net/1721.1/71733

Thesis Assessment of heterologous butyrate and butanol pathway activity by measurement of intracellular pathway intermediates in recombinant Escherichia coli

Fischer, Curt R.; Tseng, Hsien-Chung; Tai, Mitchell et al. · 2013 · Massachusetts Institute of Technology (MIT) · DOI

Full title: Assessment of heterologous butyrate and butanol pathway activity by measurement of intracellular pathway intermediates in recombinant Escherichia coli

Authors: Fischer, Curt R.; Tseng, Hsien-Chung; Tai, Mitchell; Stephanopoulos, Gregory; Prather, Kristala L. Jones

Year: 2013

Venue: Massachusetts Institute of Technology (MIT)

DOI: http://hdl.handle.net/1721.1/82623

Thesis Improving fatty acids production by engineering dynamic pathway regulation and metabolic control

Xu, Peng; Li, Lingyun; Zhang, Fuming et al. · 2015 · Massachusetts Institute of Technology (MIT) · DOI

Full title: Improving fatty acids production by engineering dynamic pathway regulation and metabolic control

Authors: Xu, Peng; Li, Lingyun; Zhang, Fuming; Stephanopoulos, Gregory; Koffas, Mattheos

Year: 2015

Venue: Massachusetts Institute of Technology (MIT)

DOI: http://hdl.handle.net/1721.1/95755

Thesis Metabolic modeling of synthesis gas fermentation in bubble column reactors

Chen, Jin; Henson, Michael A; Gomez, Jose Alberto et al. · 2015 · Massachusetts Institute of Technology (MIT) · DOI

Full title: Metabolic modeling of synthesis gas fermentation in bubble column reactors

Authors: Chen, Jin; Henson, Michael A; Gomez, Jose Alberto; Hoeffner, Kai; Barton, Paul I.

Year: 2015

Venue: Massachusetts Institute of Technology (MIT)

DOI: http://hdl.handle.net/1721.1/97554

Thesis Interpreting expression data with metabolic flux models: predicting Mycobacterium tuberculosis mycolic acid production

Murray, Megan B.; Moody, D. Branch; Cheng, Tan-Yun et al. · 2010 · Massachusetts Institute of Technology (MIT) · DOI

Full title: Interpreting expression data with metabolic flux models: predicting Mycobacterium tuberculosis mycolic acid production

Authors: Murray, Megan B.; Moody, D. Branch; Cheng, Tan-Yun; Farhat, Maha R.; Galagan, James E.; Weiner, Brian; Lun, Desmond S.; Brandes, Aaron; Colijn, Caroline; Zucker, Jeremy

Year: 2010

Venue: Massachusetts Institute of Technology (MIT)

DOI: http://hdl.handle.net/1721.1/52472

Thesis Employing metabolic models of Salmonella Typhimurium to predict synthetically lethal gene pairs to guide antibiotic discovery

Fong, Nicole Liu · 2012 · University of California, San Diego (UCSD) · DOI

Full title: Employing metabolic models of Salmonella Typhimurium to predict synthetically lethal gene pairs to guide antibiotic discovery

Authors: Fong, Nicole Liu

Year: 2012

Venue: University of California, San Diego (UCSD)

DOI: https://escholarship.org/uc/item/2p4591jj

Thesis Identification of growth-coupled and kinetically robust production in strain designs using genome-scale models

Dinh, Hoang Viet · 2017 · University of California, San Diego (UCSD) · DOI

Full title: Identification of growth-coupled and kinetically robust production in strain designs using genome-scale models

Authors: Dinh, Hoang Viet

Year: 2017

Venue: University of California, San Diego (UCSD)

DOI: https://escholarship.org/uc/item/6n17t91b

Thesis Genome-scale models of metabolism and expression predict the metabolic burden of recombinant protein expression

Oftadeh, Omid; Hatzimanikatis, Vassily · 2025 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: Genome-scale models of metabolism and expression predict the metabolic burden of recombinant protein expression

Authors: Oftadeh, Omid; Hatzimanikatis, Vassily

Year: 2025

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/243102

Thesis Designing pathways for bioproducing complex chemicals by combining tools for pathway extraction and ranking

Sveshnikova, Anastasia; Oftadeh, Omid; Hatzimanikatis, Vassily · 2025 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: Designing pathways for bioproducing complex chemicals by combining tools for pathway extraction and ranking

Authors: Sveshnikova, Anastasia; Oftadeh, Omid; Hatzimanikatis, Vassily

Year: 2025

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/250909

Thesis The Dawn of High-throughput and Genome-scale Kinetic Modeling: Recent Advances and Future Directions

Toumpe, Ilias; Choudhury, Subham; Hatzimanikatis, Vassily et al. · 2025 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: The Dawn of High-throughput and Genome-scale Kinetic Modeling: Recent Advances and Future Directions

Authors: Toumpe, Ilias; Choudhury, Subham; Hatzimanikatis, Vassily; Miskovic, Ljubisa

Year: 2025

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/249860

Thesis Enhanced flux prediction by integrating relative expression and relative metabolite abundance into thermodynamically consistent metabolic models

Pandey, Vikash; Hadadi, Noushin; Hatzimanikatis, Vassily · 2019 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: Enhanced flux prediction by integrating relative expression and relative metabolite abundance into thermodynamically consistent metabolic models

Authors: Pandey, Vikash; Hadadi, Noushin; Hatzimanikatis, Vassily

Year: 2019

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/156452

Thesis Strain- and bioprocess-design strategies to increase production of (R)-3-hydroxybutyrate by Escherichia coli

Guevara-Martínez, Mónica · 2019 · KTH Royal Institute of Technology · DOI

Full title: Strain- and bioprocess-design strategies to increase production of (R)-3-hydroxybutyrate by Escherichia coli

Authors: Guevara-Martínez, Mónica

Year: 2019

Venue: KTH Royal Institute of Technology

DOI: http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-251096

Thesis Metabolic engineering and cultivation strategies for recombinant production of (R)-3-hydroxybutyrate

Perez-Zabaleta, Mariel · 2019 · KTH Royal Institute of Technology · DOI

Full title: Metabolic engineering and cultivation strategies for recombinant production of (R)-3-hydroxybutyrate

Authors: Perez-Zabaleta, Mariel

Year: 2019

Venue: KTH Royal Institute of Technology

DOI: http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-251048

Thesis Modeling and analysis of the rapid aerobic metabolism of Geobacillus sp. LC300

Ljungqvist, Emil E. · 2024 · KTH Royal Institute of Technology · DOI

Full title: Modeling and analysis of the rapid aerobic metabolism of Geobacillus sp. LC300

Authors: Ljungqvist, Emil E.

Year: 2024

Venue: KTH Royal Institute of Technology

DOI: http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-352052

Thesis Improving cyanobacteria productivity: From theory to assay

Shabestary, Kiyan · 2020 · KTH Royal Institute of Technology · DOI

Full title: Improving cyanobacteria productivity: From theory to assay

Authors: Shabestary, Kiyan

Year: 2020

Venue: KTH Royal Institute of Technology

DOI: http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-278997

Thesis Carbon Catabolite Repression Relaxation: Approaches for Sugar Co-Utilization in Escherichia coli

Fox, Kevin J. · 2022 · Massachusetts Institute of Technology (MIT) · DOI

Full title: Carbon Catabolite Repression Relaxation: Approaches for Sugar Co-Utilization in Escherichia coli

Authors: Fox, Kevin J.

Year: 2022

Venue: Massachusetts Institute of Technology (MIT)

DOI: https://hdl.handle.net/1721.1/144499

Thesis Flux balance techniques for modelling metabolic networks and comparison with kinetic models

Coleman, Matthew · 2018 · University of Nottingham · DOI

Full title: Flux balance techniques for modelling metabolic networks and comparison with kinetic models

Authors: Coleman, Matthew

Year: 2018

Venue: University of Nottingham

DOI: https://eprints.nottingham.ac.uk/50999/1/M%20Coleman%20revised%20thesis.pdf

Thesis Genome-scale metabolic modelling of Clostridium autoethanogenum

Norman, Rupert O.J. · 2019 · University of Nottingham · DOI

Full title: Genome-scale metabolic modelling of Clostridium autoethanogenum

Authors: Norman, Rupert O.J.

Year: 2019

Venue: University of Nottingham

DOI: https://eprints.nottingham.ac.uk/56439/1/main.pdf

Thesis Genome-scale reconstruction and analysis of eukaryotic metabolic networks

Hurlen, Natalie Christine · 2006 · University of California, San Diego (UCSD) · DOI

Full title: Genome-scale reconstruction and analysis of eukaryotic metabolic networks

Authors: Hurlen, Natalie Christine

Year: 2006

Venue: University of California, San Diego (UCSD)

DOI: https://escholarship.org/uc/item/2mm7814g

Thesis From bacteria to cancer exploiting metabolic networks for industrial and therapeutic purposes

Tomi Andrino, Claudio · 2023 · University of Nottingham · DOI

Full title: From bacteria to cancer exploiting metabolic networks for industrial and therapeutic purposes

Authors: Tomi Andrino, Claudio

Year: 2023

Venue: University of Nottingham

DOI: https://eprints.nottingham.ac.uk/72462/2/From%20bacteria%20to%20cancer%20exploiting%20metabolic%20networks%20for%20industrial%20and%20therapeutic%20purposes.pdf

Thesis A stoichiometric model of Escherichia coli 's macromolecular synthesis machinery and its integration with metabolism

Thiele, Ines · 2009 · University of California, San Diego (UCSD) · DOI

Full title: A stoichiometric model of Escherichia coli 's macromolecular synthesis machinery and its integration with metabolism

Authors: Thiele, Ines

Year: 2009

Venue: University of California, San Diego (UCSD)

DOI: https://escholarship.org/uc/item/1z9752m7

Thesis Development and Dissemination of Computational Methods for Genome-scale Modeling

Ebrahim, Ali · 2016 · University of California, San Diego (UCSD) · DOI

Full title: Development and Dissemination of Computational Methods for Genome-scale Modeling

Authors: Ebrahim, Ali

Year: 2016

Venue: University of California, San Diego (UCSD)

DOI: https://escholarship.org/uc/item/1w98620m

Thesis Model-driven discovery of adaptive mechanisms and underground metabolism in Escherichia coli

Guzman, Gabriela Ines · 2018 · University of California, San Diego (UCSD) · DOI

Full title: Model-driven discovery of adaptive mechanisms and underground metabolism in Escherichia coli

Authors: Guzman, Gabriela Ines

Year: 2018

Venue: University of California, San Diego (UCSD)

DOI: https://escholarship.org/uc/item/0wm8j4xm

Thesis Expanding the Scope of Genome-scale Models of Metabolism and Gene Expression

Lloyd, Colton Joseph · 2019 · University of California, San Diego (UCSD) · DOI

Full title: Expanding the Scope of Genome-scale Models of Metabolism and Gene Expression

Authors: Lloyd, Colton Joseph

Year: 2019

Venue: University of California, San Diego (UCSD)

DOI: https://escholarship.org/uc/item/0544w4s8

Thesis The genetic basis for adaptation of Escherichia coli to growth in minimal media

Conrad, Thomas · 2010 · University of California, San Diego (UCSD) · DOI

Full title: The genetic basis for adaptation of Escherichia coli to growth in minimal media

Authors: Conrad, Thomas

Year: 2010

Venue: University of California, San Diego (UCSD)

DOI: https://escholarship.org/uc/item/2m58s9b0

Thesis Model driven analysis of Escherichia coli metabolism

Reed, Jennifer Leanne · 2005 · University of California, San Diego (UCSD) · DOI

Full title: Model driven analysis of Escherichia coli metabolism

Authors: Reed, Jennifer Leanne

Year: 2005

Venue: University of California, San Diego (UCSD)

DOI: https://escholarship.org/uc/item/4qn471t6

Thesis Characterizing complex phenotypes in metabolism : an "omics"-driven systems approach

Mo, Monica L. · 2009 · University of California, San Diego (UCSD) · DOI

Full title: Characterizing complex phenotypes in metabolism : an "omics"-driven systems approach

Authors: Mo, Monica L.

Year: 2009

Venue: University of California, San Diego (UCSD)

DOI: https://escholarship.org/uc/item/5ds062cp

Thesis Utilizing genome-scale models to enhance high-throughput data analysis : : from pathways to dynamics

Bordbar, Aarash · 2014 · University of California, San Diego (UCSD) · DOI

Full title: Utilizing genome-scale models to enhance high-throughput data analysis : : from pathways to dynamics

Authors: Bordbar, Aarash

Year: 2014

Venue: University of California, San Diego (UCSD)

DOI: https://escholarship.org/uc/item/3h54t9fb

Thesis Employing Systems Biology for Discovery and Engineering in Phototrophic Microorganisms

Broddrick, Jared Thomas · 2018 · University of California, San Diego (UCSD) · DOI

Full title: Employing Systems Biology for Discovery and Engineering in Phototrophic Microorganisms

Authors: Broddrick, Jared Thomas

Year: 2018

Venue: University of California, San Diego (UCSD)

DOI: https://escholarship.org/uc/item/0h0933r1

Thesis Comparative Systems Biology Analysis of Microbial Pathogens

Monk, Jonathan Mayock · 2015 · University of California, San Diego (UCSD) · DOI

Full title: Comparative Systems Biology Analysis of Microbial Pathogens

Authors: Monk, Jonathan Mayock

Year: 2015

Venue: University of California, San Diego (UCSD)

DOI: https://escholarship.org/uc/item/0qn486q4

Thesis Predicting growth optimization strategies with metabolic/expression models

Liu, Joanne · 2017 · University of California, San Diego (UCSD) · DOI

Full title: Predicting growth optimization strategies with metabolic/expression models

Authors: Liu, Joanne

Year: 2017

Venue: University of California, San Diego (UCSD)

DOI: https://escholarship.org/uc/item/6nr2539t

Thesis Model-driven metabolic engineering of Escherichia coli : a systems biology approach

Feist, Adam Michael · 2008 · University of California, San Diego (UCSD) · DOI

Full title: Model-driven metabolic engineering of Escherichia coli : a systems biology approach

Authors: Feist, Adam Michael

Year: 2008

Venue: University of California, San Diego (UCSD)

DOI: https://escholarship.org/uc/item/55w152gs

Thesis Systems biology analysis of Escherichia coli for discovery and metabolic engineering

Orth, Jeffrey David · 2012 · University of California, San Diego (UCSD) · DOI

Full title: Systems biology analysis of Escherichia coli for discovery and metabolic engineering

Authors: Orth, Jeffrey David

Year: 2012

Venue: University of California, San Diego (UCSD)

DOI: https://escholarship.org/uc/item/3h74m1h6

Thesis Multi-scale modeling to elucidate biological network structure and properties

Du, Bin · 2019 · University of California, San Diego (UCSD) · DOI

Full title: Multi-scale modeling to elucidate biological network structure and properties

Authors: Du, Bin

Year: 2019

Venue: University of California, San Diego (UCSD)

DOI: https://escholarship.org/uc/item/75m8m4s5

Thesis Proteome allocation trade-offs in bacterial evolution and regulation

OBrien, Edward · 2015 · University of California, San Diego (UCSD) · DOI

Full title: Proteome allocation trade-offs in bacterial evolution and regulation

Authors: OBrien, Edward

Year: 2015

Venue: University of California, San Diego (UCSD)

DOI: https://escholarship.org/uc/item/54s624tj

Thesis The Impact of Saccharomyces cerevisiae Metabolism on Enological Fermentation Performance: A Systems Biology Approach

Scott, William · 2021 · University of California, Davis · DOI

Full title: The Impact of Saccharomyces cerevisiae Metabolism on Enological Fermentation Performance: A Systems Biology Approach

Authors: Scott, William

Year: 2021

Venue: University of California, Davis

DOI: https://escholarship.org/uc/item/5k153983

Thesis Model-driven development and utilization of an oxygen-independent platform strain

Portnoy, Vasiliy A. · 2010 · University of California, San Diego (UCSD) · DOI

Full title: Model-driven development and utilization of an oxygen-independent platform strain

Authors: Portnoy, Vasiliy A.

Year: 2010

Venue: University of California, San Diego (UCSD)

DOI: https://escholarship.org/uc/item/7n78s64z

Thesis A novel approach to dynamic flux balance analysis that accounts for the dynamic transfer of information by internal metabolites

Iizuka, Kazuki · 2016 · White Rose eTheses (Leeds, Sheffield, York) · DOI

Full title: A novel approach to dynamic flux balance analysis that accounts for the dynamic transfer of information by internal metabolites

Authors: Iizuka, Kazuki

Year: 2016

Venue: White Rose eTheses (Leeds, Sheffield, York)

DOI: https://etheses.whiterose.ac.uk/id/eprint/21661/1/correctedThesisIizuka.pdf

Thesis Genome-scale Models of Metabolism and Gene Expression : : Construction and Use for Growth Phenotype Prediction

Lerman, Joshua Adam · 2014 · University of California, San Diego (UCSD) · DOI

Full title: Genome-scale Models of Metabolism and Gene Expression : : Construction and Use for Growth Phenotype Prediction

Authors: Lerman, Joshua Adam

Year: 2014

Venue: University of California, San Diego (UCSD)

DOI: https://escholarship.org/uc/item/8zq4p227

Thesis In silico guided metabolic engineering of Aspergillus niger for sustainable organic acid production

Upton, Daniel · 2017 · White Rose eTheses (Leeds, Sheffield, York) · DOI

Full title: In silico guided metabolic engineering of Aspergillus niger for sustainable organic acid production

Authors: Upton, Daniel

Year: 2017

Venue: White Rose eTheses (Leeds, Sheffield, York)

DOI: https://etheses.whiterose.ac.uk/id/eprint/21533/1/Daniel_Upton_PhD_Thesis_Corrected.pdf

Thesis Optimization of microbial cell factories with systems biology

King, Zachary Andrew · 2016 · University of California, San Diego (UCSD) · DOI

Full title: Optimization of microbial cell factories with systems biology

Authors: King, Zachary Andrew

Year: 2016

Venue: University of California, San Diego (UCSD)

DOI: https://escholarship.org/uc/item/83d340c7

Thesis Pan-Genome Enriched Analytics: Systems Biology Examination of the Diversity of Microbial Pathogens

Norsigian, Charles Joseph · 2021 · University of California, San Diego (UCSD) · DOI

Full title: Pan-Genome Enriched Analytics: Systems Biology Examination of the Diversity of Microbial Pathogens

Authors: Norsigian, Charles Joseph

Year: 2021

Venue: University of California, San Diego (UCSD)

DOI: https://escholarship.org/uc/item/7qx5d57h

Thesis Development of Machine Learning methods for the kinetic modelling of metabolic networks for biotechnological and biomedical applications

Choudhury, Subham · 2024 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: Development of Machine Learning methods for the kinetic modelling of metabolic networks for biotechnological and biomedical applications

Authors: Choudhury, Subham

Year: 2024

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/241277

Thesis Towards comprehensive and consistent kinetic models of metabolism under uncertainty

Hameri, Tuure Eelis · 2019 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: Towards comprehensive and consistent kinetic models of metabolism under uncertainty

Authors: Hameri, Tuure Eelis

Year: 2019

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/154871

Thesis Computational studies of industrial hosts for improved production of the 2nd generation of biofuels

Tokic, Milenko · 2019 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: Computational studies of industrial hosts for improved production of the 2nd generation of biofuels

Authors: Tokic, Milenko

Year: 2019

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/154212

Thesis New and improved methods for integrated models of metabolism and gene expression

Salvy, Pierre Guy Rémy · 2021 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: New and improved methods for integrated models of metabolism and gene expression

Authors: Salvy, Pierre Guy Rémy

Year: 2021

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/175275

Thesis An Improved Multi-parametric Programming Algorithm for Flux Balance Analysis of Metabolic Networks

Akbari, Amir; Barton, Paul I · 2021 · Massachusetts Institute of Technology (MIT) · DOI

Full title: An Improved Multi-parametric Programming Algorithm for Flux Balance Analysis of Metabolic Networks

Authors: Akbari, Amir; Barton, Paul I

Year: 2021

Venue: Massachusetts Institute of Technology (MIT)

DOI: https://hdl.handle.net/1721.1/135037

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Paper Novel Computational Tools for Linking Genotypes to Microbial Community Phenotypes

Biggs, Matthew · 2016 · Libra · DOI

Full title: Novel Computational Tools for Linking Genotypes to Microbial Community Phenotypes

Authors: Biggs, Matthew

Year: 2016

Venue: Libra

DOI: https://doi.org/10.18130/v34p5b

Paper Mapping Condition-Dependent Regulation of Lipid Metabolism in Saccharomyces cerevisiae

Jewett, Michael C.; Workman, Christopher T.; Nookaew, Intawat et al. · 2013 · G3 Genes Genomes Genetics · DOI

Full title: Mapping Condition-Dependent Regulation of Lipid Metabolism in Saccharomyces cerevisiae

Authors: Jewett, Michael C.; Workman, Christopher T.; Nookaew, Intawat; Pizarro, Francisco A; Agosín, Eduardo; Hellgren, Lars; Nielsen, Jens

Year: 2013

Venue: G3 Genes Genomes Genetics

DOI: https://doi.org/10.1534/g3.113.006601

Paper Towards applications of genome‐scale metabolic model‐based approaches in designing synthetic microbial communities

Du, Huan; Li, Meng; Liu, Yang · 2023 · Quantitative Biology · DOI

Full title: Towards applications of genome‐scale metabolic model‐based approaches in designing synthetic microbial communities

Authors: Du, Huan; Li, Meng; Liu, Yang

Year: 2023

Venue: Quantitative Biology

DOI: https://doi.org/10.15302/j-qb-022-0313

Paper Comparative Systems Analysis of Opportunistic Gram-Negative Pathogens

Bartell, Jennifer · 2015 · Libra · DOI

Full title: Comparative Systems Analysis of Opportunistic Gram-Negative Pathogens

Authors: Bartell, Jennifer

Year: 2015

Venue: Libra

DOI: https://doi.org/10.18130/v3726f

Paper Dynamic simulations of microbial communities under perturbations: opportunities for microbiome engineering

García-Jiménez, Beatriz; Carrasco, Jorge; Medina, Joaquı́n et al. · 2020 · DOI

Full title: Dynamic simulations of microbial communities under perturbations: opportunities for microbiome engineering

Authors: García-Jiménez, Beatriz; Carrasco, Jorge; Medina, Joaquı́n; Wilkinson, Mark D.

Year: 2020

DOI: https://doi.org/10.21203/rs.2.24431/v1

Paper Genome‐scale metabolic models applied for human health and biopharmaceutical engineering

Li, Feiran; Chen, Yu; Gustafsson, Johan et al. · 2023 · Quantitative Biology · DOI

Full title: Genome‐scale metabolic models applied for human health and biopharmaceutical engineering

Authors: Li, Feiran; Chen, Yu; Gustafsson, Johan; Wang, Hao; Wang, Yi; Zhang, Chong; Xing, Xin‐Hui

Year: 2023

Venue: Quantitative Biology

DOI: https://doi.org/10.1002/qub2.21

Paper Reconstruction and analysis of genome-scale metabolic model of weak Crabtree positive yeast Lachancea kluyveri

Nanda, Piyush; Patra, Pradipta; Das, Manali et al. · 2020 · Scientific Reports · DOI

Full title: Reconstruction and analysis of genome-scale metabolic model of weak Crabtree positive yeast Lachancea kluyveri

Authors: Nanda, Piyush; Patra, Pradipta; Das, Manali; Ghosh, Amit

Year: 2020

Venue: Scientific Reports

DOI: https://doi.org/10.1038/s41598-020-73253-3

Paper A Pan-Genome Guided Metabolic Network Reconstruction of Five Propionibacterium Species Reveals Extensive Metabolic Diversity

McCubbin, Tim; González-García, R. Axayácatl; Palfreyman, Robin et al. · 2020 · Genes · DOI

Full title: A Pan-Genome Guided Metabolic Network Reconstruction of Five Propionibacterium Species Reveals Extensive Metabolic Diversity

Authors: McCubbin, Tim; González-García, R. Axayácatl; Palfreyman, Robin; Stowers, Chris C.; Nielsen, Lars K.; Marcellin, Esteban

Year: 2020

Venue: Genes

DOI: https://doi.org/10.3390/genes11101115

Paper Deep learning-driven automatic reconstruction of genome-scale metabolic networks

Liu, Xiaoyi; Yang, Hongpeng; Ai, Chengwei et al. · 2023 · DOI

Full title: Deep learning-driven automatic reconstruction of genome-scale metabolic networks

Authors: Liu, Xiaoyi; Yang, Hongpeng; Ai, Chengwei; Ding, Yijie; Tang, Jijun; Guo, Fei

Year: 2023

DOI: https://doi.org/10.21203/rs.3.rs-2605759/v1

Paper Elucidation of the metabolic mechanism for malate production in Myceliophthora thermophila via 13C metabolic flux analysis

Jiang, Junfeng; Liu, Defei; Tian, Chaoguang et al. · 2022 · Research Square (Research Square) · DOI

Full title: Elucidation of the metabolic mechanism for malate production in Myceliophthora thermophila via 13C metabolic flux analysis

Authors: Jiang, Junfeng; Liu, Defei; Tian, Chaoguang; Xia, Jianye

Year: 2022

Venue: Research Square (Research Square)

DOI: https://doi.org/10.21203/rs.3.rs-2123109/v1

Paper Genome Scale Constraint-Based Metabolic Reconstruction of Propionibacterium Freudenreichii DSM 20271

Borghei, Mahsa Sadat Razavi; Mobasheri, Meysam; Sobati, Tabassom · 2021 · Research Square (Research Square) · DOI

Full title: Genome Scale Constraint-Based Metabolic Reconstruction of Propionibacterium Freudenreichii DSM 20271

Authors: Borghei, Mahsa Sadat Razavi; Mobasheri, Meysam; Sobati, Tabassom

Year: 2021

Venue: Research Square (Research Square)

DOI: https://doi.org/10.21203/rs.3.rs-847511/v1

Paper Genome-scale metabolic modelling underscores the potential of Cutaneotrichosporon oleaginosus ATCC 20509 as a cell factory for biofuel production

Pham, Nhung; Reijnders, Maarten; Suárez‐Diez, María et al. · 2020 · Research Square (Research Square) · DOI

Full title: Genome-scale metabolic modelling underscores the potential of Cutaneotrichosporon oleaginosus ATCC 20509 as a cell factory for biofuel production

Authors: Pham, Nhung; Reijnders, Maarten; Suárez‐Diez, María; Nijsse, Bart; Springer, Jan; Eggink, Gerrit; Schaap, Peter J.

Year: 2020

Venue: Research Square (Research Square)

DOI: https://doi.org/10.21203/rs.3.rs-26414/v2

Paper Integration of enzyme constraints in a genome-scale metabolic model of Aspergillus niger improves phenotype predictions

Jingru Zhou; Y. Zhuang; Jianye Xia · 2021 · Microbial Cell Factories · DOI

Full title: Integration of enzyme constraints in a genome-scale metabolic model of Aspergillus niger improves phenotype predictions

Authors: Jingru Zhou; Y. Zhuang; Jianye Xia

Year: 2021

Venue: Microbial Cell Factories

DOI: https://doi.org/10.1186/s12934-021-01614-2

Paper Genome-Scale Metabolic Model Based Engineering of Escherichia Coli Enhances Recombinant Single Chain Antibody Fragment Production

Behravan, Aidin; Hashemi, Atieh; Marashi, Sayed‐Amir et al. · 2021 · DOI

Full title: Genome-Scale Metabolic Model Based Engineering of Escherichia Coli Enhances Recombinant Single Chain Antibody Fragment Production

Authors: Behravan, Aidin; Hashemi, Atieh; Marashi, Sayed‐Amir; Fouladiha, Hamideh

Year: 2021

DOI: https://doi.org/10.21203/rs.3.rs-412220/v1

Paper Automation and machine learning drive rapid optimization of isoprenol production in Pseudomonas putida

Kinnunen, Patrick C.; Kinnunen, Patrick C.; Li, Ye et al. · 2025 · DOI

Full title: Automation and machine learning drive rapid optimization of isoprenol production in Pseudomonas putida

Authors: Kinnunen, Patrick C.; Kinnunen, Patrick C.; Li, Ye; Chen, Yan; Yunus, Ian Sofian; Yunus, Ian Sofian; Galliard, William; Adams, Paul D.; Adams, Paul D.; Singh, Anup K.; Sustarich, Jess; Mukhopadhyay, Aindrila; Martín, Héctor García; Lee, Taek Soon; Lee, Taek Soon

Year: 2025

DOI: https://doi.org/10.21203/rs.3.rs-6846062/v1

Paper A constraint-based modeling approach to reach an improved chemically defined minimal medium for recombinant antiEpEX-scFv production by Escherichia coli

A. Behravan; Hashemi A; S. Marashi · 2021 · DOI

Full title: A constraint-based modeling approach to reach an improved chemically defined minimal medium for recombinant antiEpEX-scFv production by Escherichia coli

Authors: A. Behravan; Hashemi A; S. Marashi

Year: 2021

DOI: https://doi.org/10.22541/au.161864062.20817783/v1

Paper Comparative analysis of metabolic models of microbial communities reconstructed from automated tools and consensus approaches

Nikoloski, Zoran; Hsieh, Yunli Eric; Tandon, Kshitij et al. · 2024 · DOI

Full title: Comparative analysis of metabolic models of microbial communities reconstructed from automated tools and consensus approaches

Authors: Nikoloski, Zoran; Hsieh, Yunli Eric; Tandon, Kshitij; Verbruggen, Heroen

Year: 2024

DOI: https://doi.org/10.21203/rs.3.rs-3839946/v1

Paper Construction of an enzyme-constrained metabolic network model for Myceliophthora thermophila using machine learning-based kcat data.

Wang, Yutao; Mao, Zhitao; Dong, Jiacheng et al. · 2024 · Microbial cell factories · DOI

Full title: Construction of an enzyme-constrained metabolic network model for Myceliophthora thermophila using machine learning-based kcat data.

Authors: Wang, Yutao; Mao, Zhitao; Dong, Jiacheng; Zhang, Peiji; Gao, Qiang; Liu, Defei; Tian, Chaoguang; Ma, Hongwu

Year: 2024

Venue: Microbial cell factories

DOI: https://doi.org/10.1186/s12934-024-02415-z

Paper PARROT: Prediction of enzyme abundances using protein-constrained metabolic models

Ferreira, Maurício Alexander de Moura; Silveira, Wendel Batista da; Nikoloski, Zoran · 2023 · DOI

Full title: PARROT: Prediction of enzyme abundances using protein-constrained metabolic models

Authors: Ferreira, Maurício Alexander de Moura; Silveira, Wendel Batista da; Nikoloski, Zoran

Year: 2023

DOI: https://doi.org/10.22541/au.166117417.77605988/v2

Paper Systems-level approaches for understanding and engineering of the oleaginous cell factory Yarrowia lipolytica

Poorinmohammad, Naghmeh; Kerkhoven, Eduard J. · 2020 · DOI

Full title: Systems-level approaches for understanding and engineering of the oleaginous cell factory Yarrowia lipolytica

Authors: Poorinmohammad, Naghmeh; Kerkhoven, Eduard J.

Year: 2020

DOI: https://doi.org/10.22541/au.160315273.31313281/v1

Paper Metabolic Engineering of Serratia marcescens

Yan, Qiang · 2018 · VCU Scholars Compass (Virginia Commonwealth University) · DOI

Full title: Metabolic Engineering of Serratia marcescens

Authors: Yan, Qiang

Year: 2018

Venue: VCU Scholars Compass (Virginia Commonwealth University)

DOI: https://doi.org/10.25772/43af-me96

Paper Constraint-based modeling and machine learning applications for analysis and optimization of fermentation parameters

Khaleghi, Mohammad Karim; Savizi, Iman Shahidi Pour; Lewis, Nathan E. et al. · 2021 · DOI

Full title: Constraint-based modeling and machine learning applications for analysis and optimization of fermentation parameters

Authors: Khaleghi, Mohammad Karim; Savizi, Iman Shahidi Pour; Lewis, Nathan E.; Shojaosadati, Seyed Abbas

Year: 2021

DOI: https://doi.org/10.22541/au.162083622.21592768/v1

Paper Modelling Consolidated Bioprocessing of Cellulose via Population Balances Coupled with Cybernetic Models

Ahamed, Firnaaz · 2020 · Figshare · DOI

Full title: Modelling Consolidated Bioprocessing of Cellulose via Population Balances Coupled with Cybernetic Models

Authors: Ahamed, Firnaaz

Year: 2020

Venue: Figshare

DOI: https://doi.org/10.26180/5f6b082bdafb5

Paper Significant Differences in Media Components and Predicted Growth Rates of 58 Escherichia coli Genome-scale Models

Tan, Felicia Leyi; Kuan, Zhi Jue; Amir-Hamzah, Nabil et al. · 2022 · ACTA SCIENTIFIC MICROBIOLOGY · DOI

Full title: Significant Differences in Media Components and Predicted Growth Rates of 58 Escherichia coli Genome-scale Models

Authors: Tan, Felicia Leyi; Kuan, Zhi Jue; Amir-Hamzah, Nabil; Kng, Xander; Wee, Yik Yew; Sor, Si Xian; Ling, Maurice HT

Year: 2022

Venue: ACTA SCIENTIFIC MICROBIOLOGY

DOI: https://doi.org/10.31080/asmi.2022.05.1004

Paper Engineered yeast for efficient de novo synthesis of 7‐dehydrocholesterol

Qu, Lisha; Xiu, Xiang; Sun, Guoyun et al. · 2022 · Biotechnology and Bioengineering · DOI

Full title: Engineered yeast for efficient de novo synthesis of 7‐dehydrocholesterol

Authors: Qu, Lisha; Xiu, Xiang; Sun, Guoyun; Zhang, Chenyang; Yang, Haiquan; Liu, Yanfeng; Li, Jianghua; Du, Guocheng; Lv, Xueqin; Liu, Long

Year: 2022

Venue: Biotechnology and Bioengineering

DOI: https://doi.org/10.1002/bit.28055

Paper Predicting complex phenotype–genotype interactions to enable yeast engineering: Saccharomyces cerevisiae as a model organism and a cell factory

Dikicioǧlu, Duygu; Pir, Pınar; Oliver, Stephen G. · 2013 · Biotechnology Journal · DOI

Full title: Predicting complex phenotype–genotype interactions to enable yeast engineering: Saccharomyces cerevisiae as a model organism and a cell factory

Authors: Dikicioǧlu, Duygu; Pir, Pınar; Oliver, Stephen G.

Year: 2013

Venue: Biotechnology Journal

DOI: https://doi.org/10.1002/biot.201300138

Paper Glucose‐based microbial production of the hormone melatonin in yeast Saccharomyces cerevisiae

Germann, Susanne M.; Jacobsen, Simo Abdessamad Baallal; Schneider, Konstantin et al. · 2015 · Biotechnology Journal · DOI

Full title: Glucose‐based microbial production of the hormone melatonin in yeast Saccharomyces cerevisiae

Authors: Germann, Susanne M.; Jacobsen, Simo Abdessamad Baallal; Schneider, Konstantin; Harrison, Scott J.; Jensen, Niels Bjerg; Chen, Xiao; Stahlhut, Steen G.; Borodina, Irina; Luo, Hao; Zhu, Jiangfeng; Maury, Jérôme; Förster, Jochen

Year: 2015

Venue: Biotechnology Journal

DOI: https://doi.org/10.1002/biot.201500143

Paper Scientific discovery as a combinatorial optimisation problem: How best to navigate the landscape of possible experiments?

Kell, Douglas B. · 2012 · BioEssays · DOI

Full title: Scientific discovery as a combinatorial optimisation problem: How best to navigate the landscape of possible experiments?

Authors: Kell, Douglas B.

Year: 2012

Venue: BioEssays

DOI: https://doi.org/10.1002/bies.201100144

Paper Genome‐scale metabolic model of methylotrophic yeast Pichia pastoris and its use for in silico analysis of heterologous protein production

Sohn, Seung Bum; Graf, Alexandra B.; Kim, Tae Yong et al. · 2010 · Biotechnology Journal · DOI

Full title: Genome‐scale metabolic model of methylotrophic yeast Pichia pastoris and its use for in silico analysis of heterologous protein production

Authors: Sohn, Seung Bum; Graf, Alexandra B.; Kim, Tae Yong; Gasser, Brigitte; Maurer, Michael; Ferrer, Pau; Mattanovich, Diethard; Lee, Sang Yup

Year: 2010

Venue: Biotechnology Journal

DOI: https://doi.org/10.1002/biot.201000078

Paper Systems‐level approaches for understanding and engineering of the oleaginous cell factory Yarrowia lipolytica

Poorinmohammad, Naghmeh; Kerkhoven, Eduard J. · 2021 · Biotechnology and Bioengineering · DOI

Full title: Systems‐level approaches for understanding and engineering of the oleaginous cell factory Yarrowia lipolytica

Authors: Poorinmohammad, Naghmeh; Kerkhoven, Eduard J.

Year: 2021

Venue: Biotechnology and Bioengineering

DOI: https://doi.org/10.1002/bit.27859

Paper Microbial Methylotrophic Metabolism: Recent Metabolic Modeling Efforts and Their Applications In Industrial Biotechnology

Lieven, Christian; Herrgård, Markus J.; Sonnenschein, Nikolaus · 2018 · Biotechnology Journal · DOI

Full title: Microbial Methylotrophic Metabolism: Recent Metabolic Modeling Efforts and Their Applications In Industrial Biotechnology

Authors: Lieven, Christian; Herrgård, Markus J.; Sonnenschein, Nikolaus

Year: 2018

Venue: Biotechnology Journal

DOI: https://doi.org/10.1002/biot.201800011

Paper Protein constraints in genome‐scale metabolic models: Data integration, parameter estimation, and prediction of metabolic phenotypes

Ferreira, Maurício Alexander de Moura; Silveira, Wendel Batista da; Nikoloski, Zoran · 2024 · Biotechnology and Bioengineering · DOI

Full title: Protein constraints in genome‐scale metabolic models: Data integration, parameter estimation, and prediction of metabolic phenotypes

Authors: Ferreira, Maurício Alexander de Moura; Silveira, Wendel Batista da; Nikoloski, Zoran

Year: 2024

Venue: Biotechnology and Bioengineering

DOI: https://doi.org/10.1002/bit.28650

Paper Yeast Systems Biology: Model Organism and Cell Factory

Nielsen, Jens · 2019 · Biotechnology Journal · DOI

Full title: Yeast Systems Biology: Model Organism and Cell Factory

Authors: Nielsen, Jens

Year: 2019

Venue: Biotechnology Journal

DOI: https://doi.org/10.1002/biot.201800421

Paper Fermentative butanol production by clostridia

Lee, Sang Yup; Park, Jin Hwan; Jang, Seh Hee et al. · 2008 · Biotechnology and Bioengineering · DOI

Full title: Fermentative butanol production by clostridia

Authors: Lee, Sang Yup; Park, Jin Hwan; Jang, Seh Hee; Nielsen, Lars K.; Kim, Jae Hyun; Jung, Kwang S.

Year: 2008

Venue: Biotechnology and Bioengineering

DOI: https://doi.org/10.1002/bit.22003

Paper Modeling leucine's metabolic pathway and knockout prediction improving the production of surfactin, a biosurfactant from Bacillus subtilis

Coutte, François; Niehren, Joachim; Dhali, Debarun et al. · 2015 · Biotechnology Journal · DOI

Full title: Modeling leucine's metabolic pathway and knockout prediction improving the production of surfactin, a biosurfactant from Bacillus subtilis

Authors: Coutte, François; Niehren, Joachim; Dhali, Debarun; John, Mathias; Versari, Cristian; Jacques, Philippe

Year: 2015

Venue: Biotechnology Journal

DOI: https://doi.org/10.1002/biot.201400541

Paper How reliable are Chinese hamster ovary (CHO) cell genome‐scale metabolic models?

Strain, Benjamin; Morrissey, James; Antonakoudis, Athanasios et al. · 2023 · Biotechnology and Bioengineering · DOI

Full title: How reliable are Chinese hamster ovary (CHO) cell genome‐scale metabolic models?

Authors: Strain, Benjamin; Morrissey, James; Antonakoudis, Athanasios; Kontoravdi, Cleo

Year: 2023

Venue: Biotechnology and Bioengineering

DOI: https://doi.org/10.1002/bit.28366

Paper Detecting the Significant Flux Backbone of Escherichia coli metabolism

Güell, Oriol; Sagués, Francesc; Serrano, M. Ángeles · 2017 · FEBS Letters · DOI

Full title: Detecting the Significant Flux Backbone of Escherichia coli metabolism

Authors: Güell, Oriol; Sagués, Francesc; Serrano, M. Ángeles

Year: 2017

Venue: FEBS Letters

DOI: https://doi.org/10.1002/1873-3468.12650

Paper Clostridioides difficile 630Δerm in silico and in vivo – quantitative growth and extensive polysaccharide secretion

Dannheim, Henning; Will, Sabine; Schomburg, Dietmar et al. · 2017 · FEBS Open Bio · DOI

Full title: Clostridioides difficile 630Δerm in silico and in vivo – quantitative growth and extensive polysaccharide secretion

Authors: Dannheim, Henning; Will, Sabine; Schomburg, Dietmar; Neumann‐Schaal, Meina

Year: 2017

Venue: FEBS Open Bio

DOI: https://doi.org/10.1002/2211-5463.12208

Paper iOD907, the first genome‐scale metabolic model for the milk yeast Kluyveromyces lactis

Dias, Óscar; Pereira, Rui; Gombert, Andreas et al. · 2014 · Biotechnology Journal · DOI

Full title: iOD907, the first genome‐scale metabolic model for the milk yeast Kluyveromyces lactis

Authors: Dias, Óscar; Pereira, Rui; Gombert, Andreas; Ferreira, Eugénio C.; Rocha, Isabel

Year: 2014

Venue: Biotechnology Journal

DOI: https://doi.org/10.1002/biot.201300242

Paper A model‐driven quantitative metabolomics analysis of aerobic and anaerobic metabolism in E. coli K‐12 MG1655 that is biochemically and thermodynamically consistent

McCloskey, Douglas; Gangoiti, Jon A.; King, Zachary A. et al. · 2013 · Biotechnology and Bioengineering · DOI

Full title: A model‐driven quantitative metabolomics analysis of aerobic and anaerobic metabolism in E. coli K‐12 MG1655 that is biochemically and thermodynamically consistent

Authors: McCloskey, Douglas; Gangoiti, Jon A.; King, Zachary A.; Naviaux, Robert K.; Barshop, Bruce A.; Palsson, Bernhard Ø.; Feist, Adam M.

Year: 2013

Venue: Biotechnology and Bioengineering

DOI: https://doi.org/10.1002/bit.25133

Paper Industrial systems biology

Otero, José M.; Nielsen, Jens · 2009 · Biotechnology and Bioengineering · DOI

Full title: Industrial systems biology

Authors: Otero, José M.; Nielsen, Jens

Year: 2009

Venue: Biotechnology and Bioengineering

DOI: https://doi.org/10.1002/bit.22592

Paper Genome scale metabolic modeling of the riboflavin overproducer Ashbya gossypii

Rodrigo Ledesma‐Amaro; E. Kerkhoven; J. Revuelta et al. · 2014 · Biotechnology and Bioengineering · DOI

Full title: Genome scale metabolic modeling of the riboflavin overproducer Ashbya gossypii

Authors: Rodrigo Ledesma‐Amaro; E. Kerkhoven; J. Revuelta; J. Nielsen

Year: 2014

Venue: Biotechnology and Bioengineering

DOI: https://doi.org/10.1002/bit.25167

Paper Model validation and selection in metabolic flux analysis and flux balance analysis

Kaste, Joshua A. M.; Shachar‐Hill, Yair · 2023 · Biotechnology Progress · DOI

Full title: Model validation and selection in metabolic flux analysis and flux balance analysis

Authors: Kaste, Joshua A. M.; Shachar‐Hill, Yair

Year: 2023

Venue: Biotechnology Progress

DOI: https://doi.org/10.1002/btpr.3413

Paper Comparative genome‐scale analysis of Pichia pastoris variants informs selection of an optimal base strain

Brady, Joseph R.; Whittaker, Charles A.; Tan, Melody C. et al. · 2019 · Biotechnology and Bioengineering · DOI

Full title: Comparative genome‐scale analysis of Pichia pastoris variants informs selection of an optimal base strain

Authors: Brady, Joseph R.; Whittaker, Charles A.; Tan, Melody C.; Kristensen, D. Lee; Ma, Duanduan; Dalvie, Neil C.; Love, Kerry R.; Love, J. Christopher

Year: 2019

Venue: Biotechnology and Bioengineering

DOI: https://doi.org/10.1002/bit.27209

Paper Assessing Escherichia coli metabolism models and simulation approaches in phenotype predictions: Validation against experimental data

Costa, Rafael S.; Vinga, Susana · 2018 · Biotechnology Progress · DOI

Full title: Assessing Escherichia coli metabolism models and simulation approaches in phenotype predictions: Validation against experimental data

Authors: Costa, Rafael S.; Vinga, Susana

Year: 2018

Venue: Biotechnology Progress

DOI: https://doi.org/10.1002/btpr.2700

Paper Corynebacterium glutamicum , a natural overproducer of succinic acid?

Briki, Amani; Kaboré, Karim; Olmos, Éric et al. · 2020 · Engineering in Life Sciences · DOI

Full title: Corynebacterium glutamicum , a natural overproducer of succinic acid?

Authors: Briki, Amani; Kaboré, Karim; Olmos, Éric; Bosselaar, Sabine; Blanchard, Fabrice; Fick, Michel; Guédon, Emmanuel; Fournier, Frantz; Delaunay, Stéphane

Year: 2020

Venue: Engineering in Life Sciences

DOI: https://doi.org/10.1002/elsc.201900141

Paper Systems biology of host–microbe metabolomics

Heinken, Almut; Thiele, Ines · 2015 · WIREs Systems Biology and Medicine · DOI

Full title: Systems biology of host–microbe metabolomics

Authors: Heinken, Almut; Thiele, Ines

Year: 2015

Venue: WIREs Systems Biology and Medicine

DOI: https://doi.org/10.1002/wsbm.1301

Paper Genome-scale metabolic models of Saccharomyces cerevisiae.

Nookaew, Intawat; Olivares-Hernández, Roberto; Bhumiratana, Sakarindr et al. · 2011 · Methods in molecular biology (Clifton, N.J.) · DOI

Full title: Genome-scale metabolic models of Saccharomyces cerevisiae.

Authors: Nookaew, Intawat; Olivares-Hernández, Roberto; Bhumiratana, Sakarindr; Nielsen, Jens

Year: 2011

Venue: Methods in molecular biology (Clifton, N.J.)

DOI: https://doi.org/10.1007/978-1-61779-173-4_25

Paper Network reduction methods for genome-scale metabolic models.

Singh, Dipali; Lercher, Martin J · 2020 · Cellular and molecular life sciences : CMLS · DOI

Full title: Network reduction methods for genome-scale metabolic models.

Authors: Singh, Dipali; Lercher, Martin J

Year: 2020

Venue: Cellular and molecular life sciences : CMLS

DOI: https://doi.org/10.1007/s00018-019-03383-z

Paper Model-based biotechnological potential analysis of Kluyveromyces marxianus central metabolism

Pentjuss, Agris; Stalidzāns, Egils; Liepiņš, Jānis et al. · 2017 · Journal of Industrial Microbiology & Biotechnology · DOI

Full title: Model-based biotechnological potential analysis of Kluyveromyces marxianus central metabolism

Authors: Pentjuss, Agris; Stalidzāns, Egils; Liepiņš, Jānis; Kokina, Agnese; Martynova, Jekaterina; Zikmanis, Pēteris; Mozga, Ivars; Scherbaka, Rita; Hartman, Hassan; Poolman, Mark G.; Fell, David A.; Vīgants, Armands

Year: 2017

Venue: Journal of Industrial Microbiology & Biotechnology

DOI: https://doi.org/10.1007/s10295-017-1946-8

Paper In silico design of anaerobic growth-coupled product formation in Escherichia coli: experimental validation using a simple polyol, glycerol.

Balagurunathan, Balaji; Jain, Vishist Kumar; Tear, Crystal Jing Ying et al. · 2017 · Bioprocess and biosystems engineering · DOI

Full title: In silico design of anaerobic growth-coupled product formation in Escherichia coli: experimental validation using a simple polyol, glycerol.

Authors: Balagurunathan, Balaji; Jain, Vishist Kumar; Tear, Crystal Jing Ying; Lim, Chan Yuen; Zhao, Hua

Year: 2017

Venue: Bioprocess and biosystems engineering

DOI: https://doi.org/10.1007/s00449-016-1703-9

Paper Genome-scale modeling enables metabolic engineering of Saccharomyces cerevisiae for succinic acid production

Rasmus Agren; J. Otero; J. Nielsen · 2013 · Journal of Industrial Microbiology & Biotechnology · DOI

Full title: Genome-scale modeling enables metabolic engineering of Saccharomyces cerevisiae for succinic acid production

Authors: Rasmus Agren; J. Otero; J. Nielsen

Year: 2013

Venue: Journal of Industrial Microbiology & Biotechnology

DOI: https://doi.org/10.1007/s10295-013-1269-3

Paper Applications of genome-scale metabolic network model in metabolic engineering

Kim, Byoung‐Jin; Kim, Won Jun; Kim, Dong In et al. · 2014 · Journal of Industrial Microbiology & Biotechnology · DOI

Full title: Applications of genome-scale metabolic network model in metabolic engineering

Authors: Kim, Byoung‐Jin; Kim, Won Jun; Kim, Dong In; Lee, Sang Yup

Year: 2014

Venue: Journal of Industrial Microbiology & Biotechnology

DOI: https://doi.org/10.1007/s10295-014-1554-9

Paper Probing the bioethanol production potential of Scheffersomyces (Pichia) stipitis using validated genome-scale model

Lisha K. Parambil; D. Sarkar · 2014 · Biotechnology Letters · DOI

Full title: Probing the bioethanol production potential of Scheffersomyces (Pichia) stipitis using validated genome-scale model

Authors: Lisha K. Parambil; D. Sarkar

Year: 2014

Venue: Biotechnology Letters

DOI: https://doi.org/10.1007/s10529-014-1629-8

Paper Genome-scale modeling for metabolic engineering

Simeonidis, Evangelos; Price, Nathan D. · 2015 · Journal of Industrial Microbiology & Biotechnology · DOI

Full title: Genome-scale modeling for metabolic engineering

Authors: Simeonidis, Evangelos; Price, Nathan D.

Year: 2015

Venue: Journal of Industrial Microbiology & Biotechnology

DOI: https://doi.org/10.1007/s10295-014-1576-3

Paper Construction of advanced producers of first- and second-generation ethanol in Saccharomyces cerevisiae and selected species of non-conventional yeasts ( Scheffersomyces stipitis, Ogataea polymorpha )

Ruchała, Justyna; Kurylenko, Olena; Dmytruk, Kostyantyn et al. · 2019 · Journal of Industrial Microbiology & Biotechnology · DOI

Full title: Construction of advanced producers of first- and second-generation ethanol in Saccharomyces cerevisiae and selected species of non-conventional yeasts ( Scheffersomyces stipitis, Ogataea polymorpha )

Authors: Ruchała, Justyna; Kurylenko, Olena; Dmytruk, Kostyantyn; Sibirny, Andriy А.

Year: 2019

Venue: Journal of Industrial Microbiology & Biotechnology

DOI: https://doi.org/10.1007/s10295-019-02242-x

Paper Metabolic pathway databases and model repositories

Labena, Abraham Alemayehu; Gao, Yi‐Zhou; Dong, Chuan et al. · 2017 · Quantitative Biology · DOI

Full title: Metabolic pathway databases and model repositories

Authors: Labena, Abraham Alemayehu; Gao, Yi‐Zhou; Dong, Chuan; Hua, Hong‐Li; Guo, Feng‐Biao

Year: 2017

Venue: Quantitative Biology

DOI: https://doi.org/10.1007/s40484-017-0108-3

Paper Development of a Framework for Metabolic Pathway Analysis-Driven Strain Optimization Methods

Vieira, Vítor; Maia, Paulo; Rocha, Isabel et al. · 2017 · Interdisciplinary Sciences Computational Life Sciences · DOI

Full title: Development of a Framework for Metabolic Pathway Analysis-Driven Strain Optimization Methods

Authors: Vieira, Vítor; Maia, Paulo; Rocha, Isabel; Rocha, Miguel

Year: 2017

Venue: Interdisciplinary Sciences Computational Life Sciences

DOI: https://doi.org/10.1007/s12539-017-0218-7

Paper Network thermodynamic curation of human and yeast genome-scale metabolic models.

Martínez, Verónica S; Quek, Lake-Ee; Nielsen, Lars K · 2014 · Biophysical journal · DOI

Full title: Network thermodynamic curation of human and yeast genome-scale metabolic models.

Authors: Martínez, Verónica S; Quek, Lake-Ee; Nielsen, Lars K

Year: 2014

Venue: Biophysical journal

DOI: https://doi.org/10.1016/j.bpj.2014.05.029

Paper Kinetic ensemble model of gas fermenting Clostridium autoethanogenum for improved ethanol production

Greene, Jennifer L.; Daniell, James; Köpke, Michael et al. · 2019 · Biochemical Engineering Journal · DOI

Full title: Kinetic ensemble model of gas fermenting Clostridium autoethanogenum for improved ethanol production

Authors: Greene, Jennifer L.; Daniell, James; Köpke, Michael; Broadbelt, Linda J.; Tyo, Keith E. J.

Year: 2019

Venue: Biochemical Engineering Journal

DOI: https://doi.org/10.1016/j.bej.2019.04.021

Paper Ashbya gossypii beyond industrial riboflavin production: A historical perspective and emerging biotechnological applications

Aguiar, Tatiana Quinta; Silva, Rui; Domingues, Lucı́lia · 2015 · Biotechnology Advances · DOI

Full title: Ashbya gossypii beyond industrial riboflavin production: A historical perspective and emerging biotechnological applications

Authors: Aguiar, Tatiana Quinta; Silva, Rui; Domingues, Lucı́lia

Year: 2015

Venue: Biotechnology Advances

DOI: https://doi.org/10.1016/j.biotechadv.2015.10.001

Paper Systems biology's role in leveraging microalgal biomass potential: Current status and future perspectives

Cunha, Emanuel; Sousa, Vítor; Geada, Pedro et al. · 2022 · Algal Research · DOI

Full title: Systems biology's role in leveraging microalgal biomass potential: Current status and future perspectives

Authors: Cunha, Emanuel; Sousa, Vítor; Geada, Pedro; Teixeira, J. A.; Vicente, António A.; Dias, Óscar

Year: 2022

Venue: Algal Research

DOI: https://doi.org/10.1016/j.algal.2022.102963

Paper Investigating metabolic interactions in a microbial co-culture through integrated modelling and experiments

Ravikrishnan, Aarthi; Blank, Lars M.; Srivastava, Smita et al. · 2020 · Computational and Structural Biotechnology Journal · DOI

Full title: Investigating metabolic interactions in a microbial co-culture through integrated modelling and experiments

Authors: Ravikrishnan, Aarthi; Blank, Lars M.; Srivastava, Smita; Raman, Karthik

Year: 2020

Venue: Computational and Structural Biotechnology Journal

DOI: https://doi.org/10.1016/j.csbj.2020.03.019

Paper A review of metabolic and enzymatic engineering strategies for designing and optimizing performance of microbial cell factories

Fisher, Amanda K.; Freedman, Benjamin G.; Bevan, David R. et al. · 2014 · Computational and Structural Biotechnology Journal · DOI

Full title: A review of metabolic and enzymatic engineering strategies for designing and optimizing performance of microbial cell factories

Authors: Fisher, Amanda K.; Freedman, Benjamin G.; Bevan, David R.; Senger, Ryan S.

Year: 2014

Venue: Computational and Structural Biotechnology Journal

DOI: https://doi.org/10.1016/j.csbj.2014.08.010

Paper Advances in flux balance analysis by integrating machine learning and mechanism-based models

Sahu, Ankur; Blätke, Mary Ann; Szymański, Jędrzej et al. · 2021 · Computational and Structural Biotechnology Journal · DOI

Full title: Advances in flux balance analysis by integrating machine learning and mechanism-based models

Authors: Sahu, Ankur; Blätke, Mary Ann; Szymański, Jędrzej; Töpfer, Nadine

Year: 2021

Venue: Computational and Structural Biotechnology Journal

DOI: https://doi.org/10.1016/j.csbj.2021.08.004

Paper Enzyme-constrained metabolic model and in silico metabolic engineering of Clostridium ljungdahlii for the development of sustainable production processes

Caivano, Antonio; Winden, Wouter van; Dragone, Giuliano et al. · 2023 · Computational and Structural Biotechnology Journal · DOI

Full title: Enzyme-constrained metabolic model and in silico metabolic engineering of Clostridium ljungdahlii for the development of sustainable production processes

Authors: Caivano, Antonio; Winden, Wouter van; Dragone, Giuliano; Mussatto, Solange I.

Year: 2023

Venue: Computational and Structural Biotechnology Journal

DOI: https://doi.org/10.1016/j.csbj.2023.09.015

Paper Predicting metabolic fluxes from omics data via machine learning: Moving from knowledge-driven towards data-driven approaches

Gonçalves, Daniel; Henriques, Rui; Costa, Rafael S. · 2023 · Computational and Structural Biotechnology Journal · DOI

Full title: Predicting metabolic fluxes from omics data via machine learning: Moving from knowledge-driven towards data-driven approaches

Authors: Gonçalves, Daniel; Henriques, Rui; Costa, Rafael S.

Year: 2023

Venue: Computational and Structural Biotechnology Journal

DOI: https://doi.org/10.1016/j.csbj.2023.10.002

Paper Metabolomics methods for the synthetic biology of secondary metabolism

Nguyen, Quoc‐Thai; Merlo, Maria Elena; Medema, Marnix H. et al. · 2012 · FEBS Letters · DOI

Full title: Metabolomics methods for the synthetic biology of secondary metabolism

Authors: Nguyen, Quoc‐Thai; Merlo, Maria Elena; Medema, Marnix H.; Jankevics, Andris; Breitling, Rainer; Takano, Eriko

Year: 2012

Venue: FEBS Letters

DOI: https://doi.org/10.1016/j.febslet.2012.02.008

Paper Machine learning-assisted medium optimization revealed the discriminated strategies for improved production of the foreign and native metabolites

Aida, Honoka; Uchida, Keisuke; Nagai, Motoki et al. · 2023 · Computational and Structural Biotechnology Journal · DOI

Full title: Machine learning-assisted medium optimization revealed the discriminated strategies for improved production of the foreign and native metabolites

Authors: Aida, Honoka; Uchida, Keisuke; Nagai, Motoki; Hashizume, Takamasa; Masuo, Shunsuke; Takaya, Naoki; Ying, Bei‐Wen

Year: 2023

Venue: Computational and Structural Biotechnology Journal

DOI: https://doi.org/10.1016/j.csbj.2023.04.020

Paper Improving designer glycan production in Escherichia coli through model-guided metabolic engineering

Wayman, Joseph A.; Glasscock, Cameron J.; Mansell, Thomas J. et al. · 2019 · Metabolic Engineering Communications · DOI

Full title: Improving designer glycan production in Escherichia coli through model-guided metabolic engineering

Authors: Wayman, Joseph A.; Glasscock, Cameron J.; Mansell, Thomas J.; DeLisa, Matthew P.; Varner, Jeffrey D.

Year: 2019

Venue: Metabolic Engineering Communications

DOI: https://doi.org/10.1016/j.mec.2019.e00088

Paper CFSA: Comparative flux sampling analysis as a guide for strain design.

van Rosmalen, R P; Moreno-Paz, S; Duman-Özdamar, Z E et al. · 2024 · Metabolic engineering communications · DOI

Full title: CFSA: Comparative flux sampling analysis as a guide for strain design.

Authors: van Rosmalen, R P; Moreno-Paz, S; Duman-Özdamar, Z E; Suarez-Diez, M

Year: 2024

Venue: Metabolic engineering communications

DOI: https://doi.org/10.1016/j.mec.2024.e00244

Paper A Genome Scale Model of Geobacillus thermoglucosidasius (C56-YS93) reveals its biotechnological potential on rice straw hydrolysate

Ahmad, Ahmad; Hartman, Hassan; Krishnakumar, Shyam S. et al. · 2017 · Journal of Biotechnology · DOI

Full title: A Genome Scale Model of Geobacillus thermoglucosidasius (C56-YS93) reveals its biotechnological potential on rice straw hydrolysate

Authors: Ahmad, Ahmad; Hartman, Hassan; Krishnakumar, Shyam S.; Fell, David A.; Poolman, Mark G.; Srivastava, Shireesh

Year: 2017

Venue: Journal of Biotechnology

DOI: https://doi.org/10.1016/j.jbiotec.2017.03.031

Paper Model-driven evaluation of microbial physiology: insights from protein allocation

Ferreira, Maurício Alexander de Moura · 2024 · DOI

Full title: Model-driven evaluation of microbial physiology: insights from protein allocation

Authors: Ferreira, Maurício Alexander de Moura

Year: 2024

DOI: https://doi.org/10.47328/ufvbbt.2024.425

Paper Systems Biotechnology: an Energing Trend in Metabolic Engineering of Industrial Microorganisms

Chellapandi, P. · 2010 · Journal of Computer Science & Systems Biology · DOI

Full title: Systems Biotechnology: an Energing Trend in Metabolic Engineering of Industrial Microorganisms

Authors: Chellapandi, P.

Year: 2010

Venue: Journal of Computer Science & Systems Biology

DOI: https://doi.org/10.4172/jcsb.1000054

Paper Interval and Possibilistic Methods for Constraint-Based Metabolic Models

Estrada, Francisco Llaneras · 2011 · DOI

Full title: Interval and Possibilistic Methods for Constraint-Based Metabolic Models

Authors: Estrada, Francisco Llaneras

Year: 2011

DOI: https://doi.org/10.4995/thesis/10251/10528

Paper Constrain-based analysis of gene deletion on the metabolic flux redistribution of Saccharomyces Cerevisiae

Xu, Zixiang; Sun, Xiao · 2008 · Journal of Biomedical Science and Engineering · DOI

Full title: Constrain-based analysis of gene deletion on the metabolic flux redistribution of Saccharomyces Cerevisiae

Authors: Xu, Zixiang; Sun, Xiao

Year: 2008

Venue: Journal of Biomedical Science and Engineering

DOI: https://doi.org/10.4236/jbise.2008.12020

Paper Exploring Biomass Precursor Synthesis as a Determinant in Microbial Adaptation to Unadapted Carbon Sources with AdaptUC

Cai, Jingyi; Liu, Jiayu; Fan, Wei et al. · 2025 · Research · DOI

Full title: Exploring Biomass Precursor Synthesis as a Determinant in Microbial Adaptation to Unadapted Carbon Sources with AdaptUC

Authors: Cai, Jingyi; Liu, Jiayu; Fan, Wei; Wu, Wenjun; Xu, Wenqi; Wang, Yuhong; Yuan, Qianqian; Ma, Hongwu

Year: 2025

Venue: Research

DOI: https://doi.org/10.34133/research.0881

Paper Constrain and conquer

Grigaitis, Pranas · 2023 · DOI

Full title: Constrain and conquer

Authors: Grigaitis, Pranas

Year: 2023

DOI: https://doi.org/10.5463/thesis.15

Paper Bactabolize: A tool for high-throughput generation of bacterial strain-specific metabolic models

Vezina, Ben; Watts, Stephen C.; Hawkey, Jane et al. · 2023 · DOI

Full title: Bactabolize: A tool for high-throughput generation of bacterial strain-specific metabolic models

Authors: Vezina, Ben; Watts, Stephen C.; Hawkey, Jane; Cooper, Helena B.; Judd, Louise M.; Jenney, Adam; Monk, Jonathan M.; Holt, Kathryn E.; Wyres, Kelly L.

Year: 2023

DOI: https://doi.org/10.7554/elife.87406.2

Paper Development of simple kinetic models and parameter estimation for simulation of recombinant human serum albumin production by Pichia pastoris

Panchiga, Chongchittapiban; Jӧrgen, Borg; Waiprib, Yaowapha et al. · 2016 · AFRICAN JOURNAL OF BIOTECHNOLOGY · DOI

Full title: Development of simple kinetic models and parameter estimation for simulation of recombinant human serum albumin production by Pichia pastoris

Authors: Panchiga, Chongchittapiban; Jӧrgen, Borg; Waiprib, Yaowapha; Jindarat, Pimsamarn; Anan, Tongta

Year: 2016

Venue: AFRICAN JOURNAL OF BIOTECHNOLOGY

DOI: https://doi.org/10.5897/ajb2015.15121

Paper Inference of metabolic flux distributions from transcriptomic data

Kim, Min Kyung · 2017 · DOI

Full title: Inference of metabolic flux distributions from transcriptomic data

Authors: Kim, Min Kyung

Year: 2017

DOI: https://doi.org/10.7282/t39889sq

Paper From In Silico Prediction To In Vivo Validation: Advancing Biohydrogen Production Through Metabolic Engineering Of E. Coli MG1655

Madavi, Tanushree Baldeo; Chauhan, Sushma · 2024 · International Journal of Environmental Sciences · DOI

Full title: From In Silico Prediction To In Vivo Validation: Advancing Biohydrogen Production Through Metabolic Engineering Of E. Coli MG1655

Authors: Madavi, Tanushree Baldeo; Chauhan, Sushma

Year: 2024

Venue: International Journal of Environmental Sciences

DOI: https://doi.org/10.64252/jkge8311

Paper Current Status and Applications of Adaptive Laboratory Evolution in Industrial Microorganisms

Lee, SuRin; Kim, Pil · 2020 · Journal of Microbiology and Biotechnology · DOI

Full title: Current Status and Applications of Adaptive Laboratory Evolution in Industrial Microorganisms

Authors: Lee, SuRin; Kim, Pil

Year: 2020

Venue: Journal of Microbiology and Biotechnology

DOI: https://doi.org/10.4014/jmb.2003.03072

Paper Overflow metabolism originates from growth optimization and cell heterogeneity

Wang, Xin · 2024 · eLife · DOI

Full title: Overflow metabolism originates from growth optimization and cell heterogeneity

Authors: Wang, Xin

Year: 2024

Venue: eLife

DOI: https://doi.org/10.7554/elife.94586

Paper Model driven analysis of Escherichia coli metabolism

Reed, Jennifer L. · 2005 · eScholarship (California Digital Library)

Full title: Model driven analysis of Escherichia coli metabolism

Authors: Reed, Jennifer L.

Year: 2005

Venue: eScholarship (California Digital Library)

Paper Application of machine learning in systems biology

Li, Gang · 2020 · Chalmers Research (Chalmers University of Technology)

Full title: Application of machine learning in systems biology

Authors: Li, Gang

Year: 2020

Venue: Chalmers Research (Chalmers University of Technology)

Paper Evolutionary dynamics of metabolic adaptation

Hoek, Milan J. A. · 2008 · Data Archiving and Networked Services (DANS)

Full title: Evolutionary dynamics of metabolic adaptation

Authors: Hoek, Milan J. A.

Year: 2008

Venue: Data Archiving and Networked Services (DANS)

Paper A method for dynamic flux balance analysis with global constraints

Karlsen, Emil · 2017 · BIBSYS Brage (BIBSYS (Norway))

Full title: A method for dynamic flux balance analysis with global constraints

Authors: Karlsen, Emil

Year: 2017

Venue: BIBSYS Brage (BIBSYS (Norway))

Paper Bactabolize is a tool for high-throughput generation of bacterial strain-specific metabolic models

Vezina, Ben; Watts, Stephen C.; Hawkey, Jane et al. · 2023 · eLife · DOI

Full title: Bactabolize is a tool for high-throughput generation of bacterial strain-specific metabolic models

Authors: Vezina, Ben; Watts, Stephen C.; Hawkey, Jane; Cooper, Helena B.; Judd, Louise M.; Jenney, Adam; Monk, Jonathan M.; Holt, Kathryn E.; Wyres, Kelly L.

Year: 2023

Venue: eLife

DOI: https://doi.org/10.7554/elife.87406.3

Paper Investigating host-microbiota cooperation with gap-filling optimization problems

Frioux, Clémence · 2018 · ORI-OAI warehouse (University of Rennes)

Full title: Investigating host-microbiota cooperation with gap-filling optimization problems

Authors: Frioux, Clémence

Year: 2018

Venue: ORI-OAI warehouse (University of Rennes)

Paper On metabolic networks and multi-omics integration

Ågren, Rasmus · 2013 · Chalmers Publication Library (Chalmers University of Technology)

Full title: On metabolic networks and multi-omics integration

Authors: Ågren, Rasmus

Year: 2013

Venue: Chalmers Publication Library (Chalmers University of Technology)

Paper Industrial Systems Biology and Metabolic Engineering of Saccharomyces cerevisiae

O. Romero; J. Manuel · 2009

Full title: Industrial Systems Biology and Metabolic Engineering of Saccharomyces cerevisiae

Authors: O. Romero; J. Manuel

Year: 2009

Paper Genome-scale constraint-based metabolic modeling and analysis of Nannochloropsis Sp.

Pham, Nhung · 2016 · BIBSYS Brage (BIBSYS (Norway))

Full title: Genome-scale constraint-based metabolic modeling and analysis of Nannochloropsis Sp.

Authors: Pham, Nhung

Year: 2016

Venue: BIBSYS Brage (BIBSYS (Norway))

Paper Developing strategies for systems metabolic engineering of Pichia pastoris

Tomàs‐Gamisans, Màrius · 2017 · LA Referencia (Red Federada de Repositorios Institucionales de Publicaciones Científicas)

Full title: Developing strategies for systems metabolic engineering of Pichia pastoris

Authors: Tomàs‐Gamisans, Màrius

Year: 2017

Venue: LA Referencia (Red Federada de Repositorios Institucionales de Publicaciones Científicas)

Paper Development and application of computer-aided design methods for cell factory optimization

Cardoso, João; Andersen, Mikael Rørdam; Herrgård, Markus J. et al. · 2017

Full title: Development and application of computer-aided design methods for cell factory optimization

Authors: Cardoso, João; Andersen, Mikael Rørdam; Herrgård, Markus J.; Sonnenschein, Nikolaus

Year: 2017

Paper Metabolic Engineering for Substrate Co-utilization

Gawand, Pratish · 2014 · TSpace (University of Toronto)

Full title: Metabolic Engineering for Substrate Co-utilization

Authors: Gawand, Pratish

Year: 2014

Venue: TSpace (University of Toronto)

Paper Proteome allocation trade-offs in bacterial evolution and regulation

O’Brien, Edward J. · 2015 · eScholarship (California Digital Library)

Full title: Proteome allocation trade-offs in bacterial evolution and regulation

Authors: O’Brien, Edward J.

Year: 2015

Venue: eScholarship (California Digital Library)

Paper Optimization of microbial cell factories with systems biology

King, Zachary A. · 2016 · eScholarship (California Digital Library)

Full title: Optimization of microbial cell factories with systems biology

Authors: King, Zachary A.

Year: 2016

Venue: eScholarship (California Digital Library)

Paper METABOLIC MODELING AND OMICS-INTEGRATIVE ANALYSIS OF SINGLE AND MULTI-ORGANISM SYSTEMS: DISCOVERY AND REDESIGN

Islam, Mohammad Mazharul · 2021 · Insecta mundi

Full title: METABOLIC MODELING AND OMICS-INTEGRATIVE ANALYSIS OF SINGLE AND MULTI-ORGANISM SYSTEMS: DISCOVERY AND REDESIGN

Authors: Islam, Mohammad Mazharul

Year: 2021

Venue: Insecta mundi

Paper Quantitative prediction of Basfia succiniciproducens metabolic potential, for succinic acid and 1,4-butanediol production, with constraint-based models

Z. Bodor; Hunor Bartos; K. Bodor et al. · 2018

Full title: Quantitative prediction of Basfia succiniciproducens metabolic potential, for succinic acid and 1,4-butanediol production, with constraint-based models

Authors: Z. Bodor; Hunor Bartos; K. Bodor; Marta Both-Fodor; C. Kalman; S. Lányi; Ildikó Miklóssy

Year: 2018

Paper Ontwikkeling van hybride modellen in (Bio)Chemische Heterogene Populatiesystemen

Michiel, Busschaert, · 2025 · Lirias (KU Leuven)

Full title: Ontwikkeling van hybride modellen in (Bio)Chemische Heterogene Populatiesystemen

Authors: Michiel, Busschaert,

Year: 2025

Venue: Lirias (KU Leuven)

Paper Context-specific metabolic network reconstruction of a naphthalene-degrading bacterial community guided by metaproteomic data

Tobalina, Luis; Bargiela, Rafael; Pey, Jon et al. · 2015 · Bioinformatics · DOI

Full title: Context-specific metabolic network reconstruction of a naphthalene-degrading bacterial community guided by metaproteomic data

Authors: Tobalina, Luis; Bargiela, Rafael; Pey, Jon; Herbst, Florian‐Alexander; Lores, Iván; Rojo, David; Barbas, Coral; Peláez, Ana I.; Sánchez, Jesús; Bergen�, Martin von; Seifert, Jana; Ferrer, Manuel; Planes, Francisco J.

Year: 2015

Venue: Bioinformatics

DOI: https://doi.org/10.1093/bioinformatics/btv036

Paper Computing the shortest elementary flux modes in genome-scale metabolic networks

Figueiredo, Luís F. de; Podhorski, Adam; Rubio, Ángel et al. · 2009 · Bioinformatics · DOI

Full title: Computing the shortest elementary flux modes in genome-scale metabolic networks

Authors: Figueiredo, Luís F. de; Podhorski, Adam; Rubio, Ángel; Kaleta, Christoph; Beasley, J. E.; Schuster, Stefan; Planes, Francisco J.

Year: 2009

Venue: Bioinformatics

DOI: https://doi.org/10.1093/bioinformatics/btp564

Paper Bayesian-based selection of metabolic objective functions

Knorr, Andrea L.; Jain, Rishi K.; Srivastava, Ranjan · 2006 · Bioinformatics · DOI

Full title: Bayesian-based selection of metabolic objective functions

Authors: Knorr, Andrea L.; Jain, Rishi K.; Srivastava, Ranjan

Year: 2006

Venue: Bioinformatics

DOI: https://doi.org/10.1093/bioinformatics/btl619

Paper TRFBA: an algorithm to integrate genome-scale metabolic and transcriptional regulatory networks with incorporation of expression data

Motamedian, Ehsan; Mohammadi, Maryam; Shojaosadati, Seyed Abbas et al. · 2016 · Bioinformatics · DOI

Full title: TRFBA: an algorithm to integrate genome-scale metabolic and transcriptional regulatory networks with incorporation of expression data

Authors: Motamedian, Ehsan; Mohammadi, Maryam; Shojaosadati, Seyed Abbas; Heydari, Mona

Year: 2016

Venue: Bioinformatics

DOI: https://doi.org/10.1093/bioinformatics/btw772

Paper Underground metabolism as a rich reservoir for pathway engineering

Kovács, Szabolcs Cselgő; Szappanos, Balázs; Tengölics, Roland et al. · 2022 · Bioinformatics · DOI

Full title: Underground metabolism as a rich reservoir for pathway engineering

Authors: Kovács, Szabolcs Cselgő; Szappanos, Balázs; Tengölics, Roland; Notebaart, Richard A.; Papp, Balázs

Year: 2022

Venue: Bioinformatics

DOI: https://doi.org/10.1093/bioinformatics/btac282

Paper MEMOSys 2.0: an update of the bioinformatics database for genome-scale models and genomic data

Pabinger, Stephan; Snajder, René; Hardiman, Timo et al. · 2014 · Database · DOI

Full title: MEMOSys 2.0: an update of the bioinformatics database for genome-scale models and genomic data

Authors: Pabinger, Stephan; Snajder, René; Hardiman, Timo; Willi, Michaela; Dander, Andreas; Trajanoski, Zlatko

Year: 2014

Venue: Database

DOI: https://doi.org/10.1093/database/bau004

Paper Integrating proteomic or transcriptomic data into metabolic models using linear bound flux balance analysis

Tian, Mingyuan; Reed, Jennifer L. · 2018 · Bioinformatics · DOI

Full title: Integrating proteomic or transcriptomic data into metabolic models using linear bound flux balance analysis

Authors: Tian, Mingyuan; Reed, Jennifer L.

Year: 2018

Venue: Bioinformatics

DOI: https://doi.org/10.1093/bioinformatics/bty445

Paper Predicting Nash equilibria for microbial metabolic interactions

Cai, Jingyi; Tan, Tianwei; Chan, Siu Hung Joshua · 2020 · Bioinformatics · DOI

Full title: Predicting Nash equilibria for microbial metabolic interactions

Authors: Cai, Jingyi; Tan, Tianwei; Chan, Siu Hung Joshua

Year: 2020

Venue: Bioinformatics

DOI: https://doi.org/10.1093/bioinformatics/btaa1014

Paper Multimodal regularized linear models with flux balance analysis for mechanistic integration of omics data

Magazzù, Giuseppe; Zampieri, Guido; Angione, Claudio · 2021 · Bioinformatics · DOI

Full title: Multimodal regularized linear models with flux balance analysis for mechanistic integration of omics data

Authors: Magazzù, Giuseppe; Zampieri, Guido; Angione, Claudio

Year: 2021

Venue: Bioinformatics

DOI: https://doi.org/10.1093/bioinformatics/btab324

Paper BeReTa: a systematic method for identifying target transcriptional regulators to enhance microbial production of chemicals

Kim, Minsuk; Sun, Gwanggyu; Lee, Dong‐Yup et al. · 2016 · Bioinformatics · DOI

Full title: BeReTa: a systematic method for identifying target transcriptional regulators to enhance microbial production of chemicals

Authors: Kim, Minsuk; Sun, Gwanggyu; Lee, Dong‐Yup; Kim, Byung‐Gee

Year: 2016

Venue: Bioinformatics

DOI: https://doi.org/10.1093/bioinformatics/btw557

Paper From genotype to phenotype: computational approaches for inferring microbial traits relevant to the food industry

Karlsen, Signe Tang; Rau, Martin Holm; Sánchez, Benjamín J. et al. · 2023 · FEMS Microbiology Reviews · DOI

Full title: From genotype to phenotype: computational approaches for inferring microbial traits relevant to the food industry

Authors: Karlsen, Signe Tang; Rau, Martin Holm; Sánchez, Benjamín J.; Jensen, Kristian; Zeidan, Ahmad A.

Year: 2023

Venue: FEMS Microbiology Reviews

DOI: https://doi.org/10.1093/femsre/fuad030

Paper Genome-scale fluxes predicted under the guidance of enzyme abundance using a novel hyper-cube shrink algorithm

Xie, Zhengwei; Zhang, Tianyu; Ouyang, Qi · 2017 · Bioinformatics · DOI

Full title: Genome-scale fluxes predicted under the guidance of enzyme abundance using a novel hyper-cube shrink algorithm

Authors: Xie, Zhengwei; Zhang, Tianyu; Ouyang, Qi

Year: 2017

Venue: Bioinformatics

DOI: https://doi.org/10.1093/bioinformatics/btx574

Paper A genome-scale metabolic reconstruction provides insight into the metabolism of the thermophilic bacterium Rhodothermus marinus

Kristjansdottir, Thordis; Hreggviðsson, Guðmundur Ó.; Stefánsson, Sigmar K. et al. · 2021 · FEMS Microbiology Ecology · DOI

Full title: A genome-scale metabolic reconstruction provides insight into the metabolism of the thermophilic bacterium Rhodothermus marinus

Year: 2021

Venue: FEMS Microbiology Ecology

DOI: https://doi.org/10.1101/2021.05.17.444423

Paper Gsmodutils: a python based framework for test-driven genome scale metabolic model development

Gilbert, James P.; Pearcy, Nicole; Norman, Rupert et al. · 2019 · Bioinformatics · DOI

Full title: Gsmodutils: a python based framework for test-driven genome scale metabolic model development

Authors: Gilbert, James P.; Pearcy, Nicole; Norman, Rupert; Millat, Thomas; Winzer, Klaus; King, John R.; Hodgman, Charlie; Minton, Nigel P.; Twycross, Jamie

Year: 2019

Venue: Bioinformatics

DOI: https://doi.org/10.1093/bioinformatics/btz088

Paper Elevated energy costs of biomass production in mitochondrial respiration-deficientSaccharomyces cerevisiae

Grigaitis, Pranas; Bogaard, Samira L. van den; Teusink, Bas · 2023 · FEMS Yeast Research · DOI

Full title: Elevated energy costs of biomass production in mitochondrial respiration-deficientSaccharomyces cerevisiae

Authors: Grigaitis, Pranas; Bogaard, Samira L. van den; Teusink, Bas

Year: 2023

Venue: FEMS Yeast Research

DOI: https://doi.org/10.1093/femsyr/foad008

Paper Modelling cyanobacteria: from metabolism to integrative models of phototrophic growth

Steuer, Ralf; Knoop, Henning; Machné, Rainer · 2012 · Journal of Experimental Botany · DOI

Full title: Modelling cyanobacteria: from metabolism to integrative models of phototrophic growth

Authors: Steuer, Ralf; Knoop, Henning; Machné, Rainer

Year: 2012

Venue: Journal of Experimental Botany

DOI: https://doi.org/10.1093/jxb/ers018

Paper Metabolic reconstruction of the human pathogen Candida auris: using a cross-species approach for drug target prediction

Viana, Romeu; Carreiro, Tiago; Couceiro, Diogo et al. · 2023 · FEMS Yeast Research · DOI

Full title: Metabolic reconstruction of the human pathogen Candida auris: using a cross-species approach for drug target prediction

Authors: Viana, Romeu; Carreiro, Tiago; Couceiro, Diogo; Dias, Óscar; Rocha, Isabel; Teixeira, Miguel C.

Year: 2023

Venue: FEMS Yeast Research

DOI: https://doi.org/10.1093/femsyr/foad045

Paper Co-feeding enhances the yield of methyl ketones

Ziegler, Anita L.; Grütering, Carolin; Poduschnick, Leon et al. · 2023 · Journal of Industrial Microbiology & Biotechnology · DOI

Full title: Co-feeding enhances the yield of methyl ketones

Authors: Ziegler, Anita L.; Grütering, Carolin; Poduschnick, Leon; Mitsos, Alexander; Blank, Lars M.

Year: 2023

Venue: Journal of Industrial Microbiology & Biotechnology

DOI: https://doi.org/10.1093/jimb/kuad029

Paper Lifestyle, metabolism and environmental adaptation in Lactococcus lactis

Kleerebezem, Michiel; Bachmann, Herwig; Pelt‐KleinJan, Eunice van et al. · 2020 · FEMS Microbiology Reviews · DOI

Full title: Lifestyle, metabolism and environmental adaptation in Lactococcus lactis

Authors: Kleerebezem, Michiel; Bachmann, Herwig; Pelt‐KleinJan, Eunice van; Douwenga, Sieze; Smid, Eddy J.; Teusink, Bas; Mastrigt, Oscar van

Year: 2020

Venue: FEMS Microbiology Reviews

DOI: https://doi.org/10.1093/femsre/fuaa033

Paper merlin , an improved framework for the reconstruction of high-quality genome-scale metabolic models

Capela, João; Lagoa, Davide; Rodrigues, Rúben et al. · 2022 · Nucleic Acids Research · DOI

Full title: merlin , an improved framework for the reconstruction of high-quality genome-scale metabolic models

Authors: Capela, João; Lagoa, Davide; Rodrigues, Rúben; Cunha, Emanuel; Cruz, Fernando; Barbosa, Ana; Bastos, José Roberto Henrique; Lima, Diogo; Ferreira, Eugénio C.; Rocha, Miguel; Dias, Óscar

Year: 2022

Venue: Nucleic Acids Research

DOI: https://doi.org/10.1093/nar/gkac459

Paper Sucrose and Saccharomyces cerevisiae : a relationship most sweet

Marques, Wesley Leoricy; Raghavendran, Vijayendran; Stambuk, Boris U. et al. · 2015 · FEMS Yeast Research · DOI

Full title: Sucrose and Saccharomyces cerevisiae : a relationship most sweet

Authors: Marques, Wesley Leoricy; Raghavendran, Vijayendran; Stambuk, Boris U.; Gombert, Andreas

Year: 2015

Venue: FEMS Yeast Research

DOI: https://doi.org/10.1093/femsyr/fov107

Paper Genome-scale modeling of yeast: chronology, applications and critical perspectives.

Lopes, Helder; Rocha, Isabel · 2017 · FEMS yeast research · DOI

Full title: Genome-scale modeling of yeast: chronology, applications and critical perspectives.

Authors: Lopes, Helder; Rocha, Isabel

Year: 2017

Venue: FEMS yeast research

DOI: https://doi.org/10.1093/femsyr/fox050

Paper Building the repertoire of dispensable chromosome regions in Bacillus subtilis entails major refinement of cognate large-scale metabolic model

Tanaka, Kosei; Henry, Christopher S.; Zinner, Jenifer F. et al. · 2012 · Nucleic Acids Research · DOI

Full title: Building the repertoire of dispensable chromosome regions in Bacillus subtilis entails major refinement of cognate large-scale metabolic model

Authors: Tanaka, Kosei; Henry, Christopher S.; Zinner, Jenifer F.; Jolivet, Edmond; Cohoon, Matthew; Xia, Fangfang; Bidnenko, Vladimir; Ehrlich, S. Dusko; Stevens, Rick; Noirot, Philippe

Year: 2012

Venue: Nucleic Acids Research

DOI: https://doi.org/10.1093/nar/gks963

Paper BiGG Models: A platform for integrating, standardizing and sharing genome-scale models

King, Zachary A.; Lu, Justin S.; Dräger, Andreas et al. · 2015 · Nucleic Acids Research · DOI

Full title: BiGG Models: A platform for integrating, standardizing and sharing genome-scale models

Authors: King, Zachary A.; Lu, Justin S.; Dräger, Andreas; Miller, Philip; Federowicz, Stephen; Lerman, Joshua A.; Ebrahim, Ali; Palsson, Bernhard Ø.; Lewis, Nathan E.

Year: 2015

Venue: Nucleic Acids Research

DOI: https://doi.org/10.1093/nar/gkv1049

Paper BioMet Toolbox: genome-wide analysis of metabolism

Cvijović, Marija; Olivares‐Hernández, Roberto; Ågren, Rasmus et al. · 2010 · Nucleic Acids Research · DOI

Full title: BioMet Toolbox: genome-wide analysis of metabolism

Authors: Cvijović, Marija; Olivares‐Hernández, Roberto; Ågren, Rasmus; Dahr, N.; Vongsangnak, Wanwipa; Nookaew, Intawat; Patil, Kiran Raosaheb; Nielsen, Jens

Year: 2010

Venue: Nucleic Acids Research

DOI: https://doi.org/10.1093/nar/gkq404

Paper A flux-based machine learning model to simulate the impact of pathogen metabolic heterogeneity on drug interactions

Chung, Carolina H.; Chandrasekaran, Sriram · 2022 · PNAS Nexus · DOI

Full title: A flux-based machine learning model to simulate the impact of pathogen metabolic heterogeneity on drug interactions

Authors: Chung, Carolina H.; Chandrasekaran, Sriram

Year: 2022

Venue: PNAS Nexus

DOI: https://doi.org/10.1093/pnasnexus/pgac132

Paper Phenotypic innovation through recombination in genome-scale metabolic networks

Hosseini, Sayed‐Rzgar; Martin, Olivier; Wagner, Andreas · 2016 · Proceedings of the Royal Society B Biological Sciences · DOI

Full title: Phenotypic innovation through recombination in genome-scale metabolic networks

Authors: Hosseini, Sayed‐Rzgar; Martin, Olivier; Wagner, Andreas

Year: 2016

Venue: Proceedings of the Royal Society B Biological Sciences

DOI: https://doi.org/10.1098/rspb.2016.1536

Paper Discovering Essential Multiple Gene Effects Through Large Scale Optimization: An Application to Human Cancer Metabolism

Occhipinti, Annalisa; Hamadi, Youssef; Kugler, Hillel et al. · 2020 · IEEE/ACM Transactions on Computational Biology and Bioinformatics · DOI

Full title: Discovering Essential Multiple Gene Effects Through Large Scale Optimization: An Application to Human Cancer Metabolism

Authors: Occhipinti, Annalisa; Hamadi, Youssef; Kugler, Hillel; Wintersteiger, Christoph M.; Yordanov, Boyan; Angione, Claudio

Year: 2020

Venue: IEEE/ACM Transactions on Computational Biology and Bioinformatics

DOI: https://doi.org/10.1109/tcbb.2020.2973386

Paper Genome-Based Metabolic Mapping and 13C Flux Analysis Reveal Systematic Properties of an Oleaginous Microalga Chlorella protothecoides

Wu, Chao; Xiong, Wei; Dai, Junbiao et al. · 2014 · PLANT PHYSIOLOGY · DOI

Full title: Genome-Based Metabolic Mapping and 13C Flux Analysis Reveal Systematic Properties of an Oleaginous Microalga Chlorella protothecoides

Authors: Wu, Chao; Xiong, Wei; Dai, Junbiao; Wu, Qingyu

Year: 2014

Venue: PLANT PHYSIOLOGY

DOI: https://doi.org/10.1104/pp.114.250688

Paper The Metabolic Network of Synechocystis sp. PCC 6803: Systemic Properties of Autotrophic Growth

Knoop, Henning; Zilliges, Yvonne; Lockau, Wolfgang et al. · 2010 · PLANT PHYSIOLOGY · DOI

Full title: The Metabolic Network of Synechocystis sp. PCC 6803: Systemic Properties of Autotrophic Growth

Authors: Knoop, Henning; Zilliges, Yvonne; Lockau, Wolfgang; Steuer, Ralf

Year: 2010

Venue: PLANT PHYSIOLOGY

DOI: https://doi.org/10.1104/pp.110.157198

Paper A Genome-Scale Metabolic Model of Arabidopsis and Some of Its Properties

Poolman, Mark G.; Miguet, Laurent; Sweetlove, Lee et al. · 2009 · PLANT PHYSIOLOGY · DOI

Full title: A Genome-Scale Metabolic Model of Arabidopsis and Some of Its Properties

Authors: Poolman, Mark G.; Miguet, Laurent; Sweetlove, Lee; Fell, David A.

Year: 2009

Venue: PLANT PHYSIOLOGY

DOI: https://doi.org/10.1104/pp.109.141267

Paper Genome‐Scale Model of Rhizopus microsporus : Metabolic integration of a fungal holobiont with its bacterial and viral endosymbionts

Valadez‐Cano, Cecilio; Olivares‐Hernández, Roberto; Espino‐Vázquez, Astrid N. et al. · 2023 · Environmental Microbiology · DOI

Full title: Genome‐Scale Model of Rhizopus microsporus : Metabolic integration of a fungal holobiont with its bacterial and viral endosymbionts

Authors: Valadez‐Cano, Cecilio; Olivares‐Hernández, Roberto; Espino‐Vázquez, Astrid N.; Partida‐Martínez, Laila P.

Year: 2023

Venue: Environmental Microbiology

DOI: https://doi.org/10.1111/1462-2920.16551

Paper Fine‐tuning the P. pastoris iMT1026 genome‐scale metabolic model for improved prediction of growth on methanol or glycerol as sole carbon sources

Màrius Tomàs-Gamisans; P. Ferrer; J. Albiol · 2017 · Microbial Biotechnology · DOI

Full title: Fine‐tuning the P. pastoris iMT1026 genome‐scale metabolic model for improved prediction of growth on methanol or glycerol as sole carbon sources

Authors: Màrius Tomàs-Gamisans; P. Ferrer; J. Albiol

Year: 2017

Venue: Microbial Biotechnology

DOI: https://doi.org/10.1111/1751-7915.12871

Paper Competition for nutrients increases invasion resistance during assembly of microbial communities

Wagner, Andreas · 2022 · Molecular Ecology · DOI

Full title: Competition for nutrients increases invasion resistance during assembly of microbial communities

Authors: Wagner, Andreas

Year: 2022

Venue: Molecular Ecology

DOI: https://doi.org/10.1111/mec.16565

Paper High‐quality genome‐scale metabolic modelling of Pseudomonas putida highlights its broad metabolic capabilities

Nogales, Juan; Mueller, Joshua; Guðmundsson, Steinn et al. · 2019 · Environmental Microbiology · DOI

Full title: High‐quality genome‐scale metabolic modelling of Pseudomonas putida highlights its broad metabolic capabilities

Authors: Nogales, Juan; Mueller, Joshua; Guðmundsson, Steinn; Canalejo, Francisco J.; Duque, Estrella; Monk, Jonathan M.; Feist, Adam M.; Ramos, Juan L.; Niu, Wei; Palsson, Bernhard Ø.

Year: 2019

Venue: Environmental Microbiology

DOI: https://doi.org/10.1111/1462-2920.14843

Paper Genome-scale models of bacterial metabolism: reconstruction and applications

Durot, Maxime; Bourguignon, Pierre-Yves; Schächter, Vincent · 2008 · FEMS Microbiology Reviews · DOI

Full title: Genome-scale models of bacterial metabolism: reconstruction and applications

Authors: Durot, Maxime; Bourguignon, Pierre-Yves; Schächter, Vincent

Year: 2008

Venue: FEMS Microbiology Reviews

DOI: https://doi.org/10.1111/j.1574-6976.2008.00146.x

Paper Unveiling the Potential of Lentilactobacillus hilgardii in Malolactic Fermentation: Comparative Genomics and Fermentation Dynamics.

Mantegazza, Giacomo; Mangieri, Nicola; Yazdi, Elnaz Vojoudi et al. · 2025 · Microbial biotechnology · DOI

Full title: Unveiling the Potential of Lentilactobacillus hilgardii in Malolactic Fermentation: Comparative Genomics and Fermentation Dynamics.

Authors: Mantegazza, Giacomo; Mangieri, Nicola; Yazdi, Elnaz Vojoudi; Russo, Pasquale; Mora, Diego; Gargari, Giorgio

Year: 2025

Venue: Microbial biotechnology

DOI: https://doi.org/10.1111/1751-7915.70259

Paper Synthetic biology

Osbourn, Anne; O’Maille, Paul E.; Rosser, Susan J. et al. · 2012 · New Phytologist · DOI

Full title: Synthetic biology

Authors: Osbourn, Anne; O’Maille, Paul E.; Rosser, Susan J.; Lindsey, Keith

Year: 2012

Venue: New Phytologist

DOI: https://doi.org/10.1111/j.1469-8137.2012.04374.x

Paper Enzyme‐constrained models predict the dynamics of Saccharomyces cerevisiae growth in continuous, batch and fed‐batch bioreactors

Moreno‐Paz, Sara; Schmitz, Joep; Santos, Vítor A. P. Martins dos et al. · 2022 · Microbial Biotechnology · DOI

Full title: Enzyme‐constrained models predict the dynamics of Saccharomyces cerevisiae growth in continuous, batch and fed‐batch bioreactors

Authors: Moreno‐Paz, Sara; Schmitz, Joep; Santos, Vítor A. P. Martins dos; Suárez‐Diez, María

Year: 2022

Venue: Microbial Biotechnology

DOI: https://doi.org/10.1111/1751-7915.13995

Paper Modelling metabolic CO 2 evolution – a fresh perspective on respiration

Sweetlove, Lee; Williams, Thomas Christopher Rhys; Cheung, C. Y. Maurice et al. · 2013 · Plant Cell & Environment · DOI

Full title: Modelling metabolic CO 2 evolution – a fresh perspective on respiration

Authors: Sweetlove, Lee; Williams, Thomas Christopher Rhys; Cheung, C. Y. Maurice; Ratcliffe, R. George

Year: 2013

Venue: Plant Cell & Environment

DOI: https://doi.org/10.1111/pce.12105

Paper Environmental systems biology of cold‐tolerant phenotype inSaccharomycesspecies adapted to grow at different temperatures

Paget, Caroline M.; Schwartz, Jean‐Marc; Delneri, Daniela · 2014 · Molecular Ecology · DOI

Full title: Environmental systems biology of cold‐tolerant phenotype inSaccharomycesspecies adapted to grow at different temperatures

Authors: Paget, Caroline M.; Schwartz, Jean‐Marc; Delneri, Daniela

Year: 2014

Venue: Molecular Ecology

DOI: https://doi.org/10.1111/mec.12930

Paper Analysis of metabolic flux using dynamic labelling and metabolic modelling

Fernie, Alisdair R.; Morgan, John A. · 2013 · Plant Cell & Environment · DOI

Full title: Analysis of metabolic flux using dynamic labelling and metabolic modelling

Authors: Fernie, Alisdair R.; Morgan, John A.

Year: 2013

Venue: Plant Cell & Environment

DOI: https://doi.org/10.1111/pce.12083

Paper Nutritional requirements of the BY series ofSaccharomyces cerevisiaestrains for optimum growth

Hanscho, Michael; Ruckerbauer, David E.; Chauhan, Neha et al. · 2012 · FEMS Yeast Research · DOI

Full title: Nutritional requirements of the BY series ofSaccharomyces cerevisiaestrains for optimum growth

Authors: Hanscho, Michael; Ruckerbauer, David E.; Chauhan, Neha; Hofbauer, Harald F.; Krahulec, Stefan; Nidetzky, Bernd; Kohlwein, Sepp D.; Zanghellini, Jürgen; Natter, Klaus

Year: 2012

Venue: FEMS Yeast Research

DOI: https://doi.org/10.1111/j.1567-1364.2012.00830.x

Paper Investigation of Malic Acid Production in Aspergillus oryzae under Nitrogen Starvation Conditions

Knuf, Christoph; Nookaew, Intawat; Brown, Stephen H.M. et al. · 2013 · Applied and Environmental Microbiology · DOI

Full title: Investigation of Malic Acid Production in Aspergillus oryzae under Nitrogen Starvation Conditions

Authors: Knuf, Christoph; Nookaew, Intawat; Brown, Stephen H.M.; McCulloch, Michael; Berry, A.; Nielsen, Jens

Year: 2013

Venue: Applied and Environmental Microbiology

DOI: https://doi.org/10.1128/aem.01445-13

Paper A method for accounting for maintenance costs in flux balance analysis improves the prediction of plant cell metabolic phenotypes under stress conditions

Cheung, C. Y. Maurice; Williams, Thomas Christopher Rhys; Poolman, Mark G. et al. · 2013 · The Plant Journal · DOI

Full title: A method for accounting for maintenance costs in flux balance analysis improves the prediction of plant cell metabolic phenotypes under stress conditions

Authors: Cheung, C. Y. Maurice; Williams, Thomas Christopher Rhys; Poolman, Mark G.; Fell, David A.; Ratcliffe, R. George; Sweetlove, Lee

Year: 2013

Venue: The Plant Journal

DOI: https://doi.org/10.1111/tpj.12252

Paper Development of a genome-scale metabolic model for the lager hybrid yeast S. pastorianus to understand the evolution of metabolic pathways in industrial settings.

Timouma, Soukaina; Balarezo-Cisneros, Laura Natalia; Schwartz, Jean-Marc et al. · 2024 · mSystems · DOI

Full title: Development of a genome-scale metabolic model for the lager hybrid yeast S. pastorianus to understand the evolution of metabolic pathways in industrial settings.

Authors: Timouma, Soukaina; Balarezo-Cisneros, Laura Natalia; Schwartz, Jean-Marc; Delneri, Daniela

Year: 2024

Venue: mSystems

DOI: https://doi.org/10.1128/msystems.00429-24

Paper Zymomonas mobilis as a model system for production of biofuels and biochemicals

Yang, Shihui; Fei, Qiang; Zhang, Yaoping et al. · 2016 · Microbial Biotechnology · DOI

Full title: Zymomonas mobilis as a model system for production of biofuels and biochemicals

Authors: Yang, Shihui; Fei, Qiang; Zhang, Yaoping; Contreras, Lydia M.; Utturkar, Sagar M.; Brown, Steven D.; Himmel, Michael E.; Zhang, Min

Year: 2016

Venue: Microbial Biotechnology

DOI: https://doi.org/10.1111/1751-7915.12408

Paper The genome‐scale metabolic network of Ectocarpus siliculosus (Ecto GEM ): a resource to study brown algal physiology and beyond

Prigent, Sylvain; Collet, Guillaume; Dittami, Simon M. et al. · 2014 · The Plant Journal · DOI

Full title: The genome‐scale metabolic network of Ectocarpus siliculosus (Ecto GEM ): a resource to study brown algal physiology and beyond

Authors: Prigent, Sylvain; Collet, Guillaume; Dittami, Simon M.; Delage, Ludovic; Corny, Floriane Ethis de; Dameron, Olivier; Eveillard, Damien; Thiele, Sven; Cambefort, Jeanne; Boyen, Catherine; Siegel, Anne; Tonon, Thierry

Year: 2014

Venue: The Plant Journal

DOI: https://doi.org/10.1111/tpj.12627

Paper Quantifying Methane and Methanol Metabolism of “ Methylotuvimicrobium buryatense ” 5GB1C under Substrate Limitation

He, Lian; Fu, Yanfen; Lidstrom, Mary E. · 2019 · mSystems · DOI

Full title: Quantifying Methane and Methanol Metabolism of “ Methylotuvimicrobium buryatense ” 5GB1C under Substrate Limitation

Authors: He, Lian; Fu, Yanfen; Lidstrom, Mary E.

Year: 2019

Venue: mSystems

DOI: https://doi.org/10.1128/msystems.00748-19

Paper Dynamic Metabolic Flux Analysis Demonstrated on Cultures Where the Limiting Substrate Is Changed from Carbon to Nitrogen andVice Versa

Lequeux, Gaspard; Beauprez, Joeri; Maertens, Jo et al. · 2010 · Journal of Biomedicine and Biotechnology · DOI

Full title: Dynamic Metabolic Flux Analysis Demonstrated on Cultures Where the Limiting Substrate Is Changed from Carbon to Nitrogen andVice Versa

Authors: Lequeux, Gaspard; Beauprez, Joeri; Maertens, Jo; Horen, Ellen Van; Soetaert, Wim; Vandamme, Erick; Vanrolleghem, Peter A.

Year: 2010

Venue: Journal of Biomedicine and Biotechnology

DOI: https://doi.org/10.1155/2010/621645

Paper Metabolic Engineering for Production of Biorenewable Fuels and Chemicals: Contributions of Synthetic Biology

Jarboe, Laura R.; Zhang, Xueli; Wang, Xuan et al. · 2010 · Journal of Biomedicine and Biotechnology · DOI

Full title: Metabolic Engineering for Production of Biorenewable Fuels and Chemicals: Contributions of Synthetic Biology

Authors: Jarboe, Laura R.; Zhang, Xueli; Wang, Xuan; Moore, Jonathan C.; Shanmugam, K. T.; Ingram, L. O.

Year: 2010

Venue: Journal of Biomedicine and Biotechnology

DOI: https://doi.org/10.1155/2010/761042

Paper Mathematical Modeling: Bridging the Gap between Concept and Realization in Synthetic Biology

Zheng, Yuting; Sriram, Ganesh · 2010 · Journal of Biomedicine and Biotechnology · DOI

Full title: Mathematical Modeling: Bridging the Gap between Concept and Realization in Synthetic Biology

Authors: Zheng, Yuting; Sriram, Ganesh

Year: 2010

Venue: Journal of Biomedicine and Biotechnology

DOI: https://doi.org/10.1155/2010/541609

Paper Modeling the Differences in Biochemical Capabilities of Pseudomonas Species by Flux Balance Analysis: How Good Are Genome-Scale Metabolic Networks at Predicting the Differences?

Babaei, Parizad; Ghasemi-Kahrizsangi, Tahereh; Marashi, Sayed‐Amir · 2014 · The Scientific World JOURNAL · DOI

Full title: Modeling the Differences in Biochemical Capabilities of Pseudomonas Species by Flux Balance Analysis: How Good Are Genome-Scale Metabolic Networks at Predicting the Differences?

Authors: Babaei, Parizad; Ghasemi-Kahrizsangi, Tahereh; Marashi, Sayed‐Amir

Year: 2014

Venue: The Scientific World JOURNAL

DOI: https://doi.org/10.1155/2014/416289

Paper Flux Analysis of the Trypanosoma brucei Glycolysis Based on a Multiobjective-Criteria Bioinformatic Approach

Ghozlane, Amine; Bringaud, Frédéric; Soueidan, Hayssam et al. · 2012 · Advances in Bioinformatics · DOI

Full title: Flux Analysis of the Trypanosoma brucei Glycolysis Based on a Multiobjective-Criteria Bioinformatic Approach

Authors: Ghozlane, Amine; Bringaud, Frédéric; Soueidan, Hayssam; Dutour, Isabelle; Jourdan, Fabien; Thébault, Patricia

Year: 2012

Venue: Advances in Bioinformatics

DOI: https://doi.org/10.1155/2012/159423

Paper Metabolic Modeling of Common Escherichia coli Strains in Human Gut Microbiome

Gao, Yue‐Dong; Zhao, Yuqi; Huang, Jing‐Fei · 2014 · BioMed Research International · DOI

Full title: Metabolic Modeling of Common Escherichia coli Strains in Human Gut Microbiome

Authors: Gao, Yue‐Dong; Zhao, Yuqi; Huang, Jing‐Fei

Year: 2014

Venue: BioMed Research International

DOI: https://doi.org/10.1155/2014/694967

Paper In Silico Analysis of Bioethanol Overproduction by Genetically Modified Microorganisms in Coculture Fermentation

Parambil, Lisha K.; Sarkar, Debasis · 2015 · Biotechnology Research International · DOI

Full title: In Silico Analysis of Bioethanol Overproduction by Genetically Modified Microorganisms in Coculture Fermentation

Authors: Parambil, Lisha K.; Sarkar, Debasis

Year: 2015

Venue: Biotechnology Research International

DOI: https://doi.org/10.1155/2015/238082

Paper Genome-Scale Metabolic Modeling of Archaea Lends Insight into Diversity of Metabolic Function

Thor, ShengShee; Peterson, J.R.; Luthey‐Schulten, Zaida · 2017 · Archaea · DOI

Full title: Genome-Scale Metabolic Modeling of Archaea Lends Insight into Diversity of Metabolic Function

Authors: Thor, ShengShee; Peterson, J.R.; Luthey‐Schulten, Zaida

Year: 2017

Venue: Archaea

DOI: https://doi.org/10.1155/2017/9763848

Paper Gene Knockout Identification Using an Extension of Bees Hill Flux Balance Analysis

Choon, Yee Wen; Mohamad, Mohd Saberi; Deris, Safaai et al. · 2015 · BioMed Research International · DOI

Full title: Gene Knockout Identification Using an Extension of Bees Hill Flux Balance Analysis

Authors: Choon, Yee Wen; Mohamad, Mohd Saberi; Deris, Safaai; Chong, Chuii Khim; Omatu, Sigeru; Corchado, Juan M.

Year: 2015

Venue: BioMed Research International

DOI: https://doi.org/10.1155/2015/124537

Paper Systems biology of the central metabolism of Streptococcus pyogenes

Levering, Jennifer · 2011 · heiDOK (Heidelberg University) · DOI

Full title: Systems biology of the central metabolism of Streptococcus pyogenes

Authors: Levering, Jennifer

Year: 2011

Venue: heiDOK (Heidelberg University)

DOI: https://doi.org/10.11588/heidok.00012488

Paper Reconstruction ofArabidopsismetabolic network models accounting for subcellular compartmentalization and tissue-specificity

Mintz-Oron, Shira; Meir, Sagit; Malitsky, Sergey et al. · 2011 · Proceedings of the National Academy of Sciences · DOI

Full title: Reconstruction ofArabidopsismetabolic network models accounting for subcellular compartmentalization and tissue-specificity

Authors: Mintz-Oron, Shira; Meir, Sagit; Malitsky, Sergey; Ruppin, Eytan; Aharoni, Asaph; Shlomi, Tomer

Year: 2011

Venue: Proceedings of the National Academy of Sciences

DOI: https://doi.org/10.1073/pnas.1100358109

Paper Dynamic flux balance analysis for synthetic microbial communities

Henson, Michael A.; Hanly, Timothy J. · 2014 · IET Systems Biology · DOI

Full title: Dynamic flux balance analysis for synthetic microbial communities

Authors: Henson, Michael A.; Hanly, Timothy J.

Year: 2014

Venue: IET Systems Biology

DOI: https://doi.org/10.1049/iet-syb.2013.0021

Paper Glycerol as a key reactant in the production of 3-hydroxypropanoic acid using engineered microbes

Jeevitha, P.; Elango, K.S.; L., Ganesh Babu et al. · 2021 · AIP conference proceedings · DOI

Full title: Glycerol as a key reactant in the production of 3-hydroxypropanoic acid using engineered microbes

Authors: Jeevitha, P.; Elango, K.S.; L., Ganesh Babu; Ranjitha, J.; Vijayalakshmi, S.

Year: 2021

Venue: AIP conference proceedings

DOI: https://doi.org/10.1063/5.0066423

Paper Kinetic profiling of metabolic specialists demonstrates stability and consistency of in vivo enzyme turnover numbers

Heckmann, David; Campeau, Anaamika; Lloyd, Colton J. et al. · 2020 · Proceedings of the National Academy of Sciences · DOI

Full title: Kinetic profiling of metabolic specialists demonstrates stability and consistency of in vivo enzyme turnover numbers

Authors: Heckmann, David; Campeau, Anaamika; Lloyd, Colton J.; Phaneuf, Patrick V.; Hefner, Ying; Carrillo-Terrazas, Marvic; Feist, Adam M.; Gonzalez, David J.; Palsson, Bernhard Ø.

Year: 2020

Venue: Proceedings of the National Academy of Sciences

DOI: https://doi.org/10.1073/pnas.2001562117

Paper Energy metabolism controls phenotypes by protein efficiency and allocation

Chen, Yu; Nielsen, Jens · 2019 · Proceedings of the National Academy of Sciences · DOI

Full title: Energy metabolism controls phenotypes by protein efficiency and allocation

Authors: Chen, Yu; Nielsen, Jens

Year: 2019

Venue: Proceedings of the National Academy of Sciences

DOI: https://doi.org/10.1073/pnas.1906569116

Paper Multiscale plant modeling: from genome to phenome and beyond

Matthews, Megan L.; Marshall‐Colón, Amy · 2021 · Emerging Topics in Life Sciences · DOI

Full title: Multiscale plant modeling: from genome to phenome and beyond

Authors: Matthews, Megan L.; Marshall‐Colón, Amy

Year: 2021

Venue: Emerging Topics in Life Sciences

DOI: https://doi.org/10.1042/etls20200276

Paper Genome-scale metabolic reconstructions of multiple Escherichia coli strains highlight strain-specific adaptations to nutritional environments

Monk, Jonathan M.; Charusanti, Pep; Aziz, Ramy K. et al. · 2013 · Proceedings of the National Academy of Sciences · DOI

Full title: Genome-scale metabolic reconstructions of multiple Escherichia coli strains highlight strain-specific adaptations to nutritional environments

Authors: Monk, Jonathan M.; Charusanti, Pep; Aziz, Ramy K.; Lerman, Joshua A.; Premyodhin, Ned; Orth, Jeffrey D.; Feist, Adam M.; Palsson, Bernhard Ø.

Year: 2013

Venue: Proceedings of the National Academy of Sciences

DOI: https://doi.org/10.1073/pnas.1307797110

Paper Applications of genome-scale metabolic models to investigate microbial metabolic adaptations in response to genetic or environmental perturbations

Carter, Elena Lucy; Constantinidou, Chrystala; Alam, Mohammad Tauqeer · 2023 · Briefings in Bioinformatics · DOI

Full title: Applications of genome-scale metabolic models to investigate microbial metabolic adaptations in response to genetic or environmental perturbations

Authors: Carter, Elena Lucy; Constantinidou, Chrystala; Alam, Mohammad Tauqeer

Year: 2023

Venue: Briefings in Bioinformatics

DOI: https://doi.org/10.1093/bib/bbad439

Paper Genome Scale Reconstruction of a Salmonella Metabolic Model

AbuOun, Manal; Suthers, Patrick F.; Jones, Gareth I. et al. · 2009 · Journal of Biological Chemistry · DOI

Full title: Genome Scale Reconstruction of a Salmonella Metabolic Model

Authors: AbuOun, Manal; Suthers, Patrick F.; Jones, Gareth I.; Carter, Ben; Saunders, Mark; Maranas, Costas D.; Woodward, Martin J.; Anjum, Muna F.

Year: 2009

Venue: Journal of Biological Chemistry

DOI: https://doi.org/10.1074/jbc.m109.005868

Paper Metabolite Profiling and Integrative Modeling Reveal Metabolic Constraints for Carbon Partitioning under Nitrogen Starvation in the Green Algae Haematococcus pluvialis

Recht, Lee; Töpfer, Nadine; Batushansky, Albert et al. · 2014 · Journal of Biological Chemistry · DOI

Full title: Metabolite Profiling and Integrative Modeling Reveal Metabolic Constraints for Carbon Partitioning under Nitrogen Starvation in the Green Algae Haematococcus pluvialis

Authors: Recht, Lee; Töpfer, Nadine; Batushansky, Albert; Sikron, Noga; Gibon, Yves; Fait, Aaron; Nikoloski, Zoran; Boussiba, Sammy; Zarka, Aliza

Year: 2014

Venue: Journal of Biological Chemistry

DOI: https://doi.org/10.1074/jbc.m114.555144

Paper Genome-scale Reconstruction of Metabolic Network in Bacillus subtilis Based on High-throughput Phenotyping and Gene Essentiality Data

Oh, You‐Kwan; Palsson, Bernhard Ø.; Park, Sung M. et al. · 2007 · Journal of Biological Chemistry · DOI

Full title: Genome-scale Reconstruction of Metabolic Network in Bacillus subtilis Based on High-throughput Phenotyping and Gene Essentiality Data

Authors: Oh, You‐Kwan; Palsson, Bernhard Ø.; Park, Sung M.; Schilling, Christophe H.; Mahadevan, Radhakrishnan

Year: 2007

Venue: Journal of Biological Chemistry

DOI: https://doi.org/10.1074/jbc.m703759200

Paper PYF: a multi-functional algorithm for predicting production and optimizing metabolic engineering strategy in Escherichia coli microbial consortia

Yang, Chen; Zhao, Yingqi; Xue, Boyuan et al. · 2025 · Briefings in Bioinformatics · DOI

Full title: PYF: a multi-functional algorithm for predicting production and optimizing metabolic engineering strategy in Escherichia coli microbial consortia

Authors: Yang, Chen; Zhao, Yingqi; Xue, Boyuan; Wang, Shaojie; Su, Haijia

Year: 2025

Venue: Briefings in Bioinformatics

DOI: https://doi.org/10.1093/bib/bbaf295

Paper Flux balance analysis of biological systems: applications and challenges

Raman, Karthik; Chandra, Nagasuma · 2009 · Briefings in Bioinformatics · DOI

Full title: Flux balance analysis of biological systems: applications and challenges

Authors: Raman, Karthik; Chandra, Nagasuma

Year: 2009

Venue: Briefings in Bioinformatics

DOI: https://doi.org/10.1093/bib/bbp011

Paper Towards dynamic genome-scale models

Gilbert, David; Heiner, Monika; Jayaweera, Yasoda et al. · 2017 · Briefings in Bioinformatics · DOI

Full title: Towards dynamic genome-scale models

Authors: Gilbert, David; Heiner, Monika; Jayaweera, Yasoda; Röhr, Christian

Year: 2017

Venue: Briefings in Bioinformatics

DOI: https://doi.org/10.1093/bib/bbx096

Paper Analysis of Growth of Lactobacillus plantarum WCFS1 on a Complex Medium Using a Genome-scale Metabolic Model

Teusink, Bas; Wiersma, Anne; Molenaar, Douwe et al. · 2006 · Journal of Biological Chemistry · DOI

Full title: Analysis of Growth of Lactobacillus plantarum WCFS1 on a Complex Medium Using a Genome-scale Metabolic Model

Authors: Teusink, Bas; Wiersma, Anne; Molenaar, Douwe; Francke, Christof; Vos, Willem M. de; Siezen, Roland J.; Smid, Eddy J.

Year: 2006

Venue: Journal of Biological Chemistry

DOI: https://doi.org/10.1074/jbc.m606263200

Paper Predicting metabolic engineering knockout strategies for chemical production: accounting for competing pathways

Tepper, Naama; Shlomi, Tomer · 2009 · Bioinformatics · DOI

Full title: Predicting metabolic engineering knockout strategies for chemical production: accounting for competing pathways

Authors: Tepper, Naama; Shlomi, Tomer

Year: 2009

Venue: Bioinformatics

DOI: https://doi.org/10.1093/bioinformatics/btp704

Paper Integrating quantitative proteomics and metabolomics with a genome-scale metabolic network model

Keren Yizhak; Tomer Benyamini; Wolfram Liebermeister et al. · 2010 · Bioinform. · DOI

Full title: Integrating quantitative proteomics and metabolomics with a genome-scale metabolic network model

Authors: Keren Yizhak; Tomer Benyamini; Wolfram Liebermeister; E. Ruppin; T. Shlomi

Year: 2010

Venue: Bioinform.

DOI: https://doi.org/10.1093/bioinformatics/btq183

Paper Fast Reconstruction of Compact Context-Specific Metabolic Network Models

Vlassis, Nikos; Pacheco, Maria Pires; Sauter, Thomas · 2014 · PLoS Computational Biology · DOI

Full title: Fast Reconstruction of Compact Context-Specific Metabolic Network Models

Authors: Vlassis, Nikos; Pacheco, Maria Pires; Sauter, Thomas

Year: 2014

Venue: PLoS Computational Biology

DOI: https://doi.org/10.1371/journal.pcbi.1003424

Paper Correction: Dynamic Analysis of Integrated Signaling, Metabolic, and Regulatory Networks

Lee, Jong Min; Gianchandani, Erwin P.; Eddy, James A. et al. · 2008 · PLoS Computational Biology · DOI

Full title: Correction: Dynamic Analysis of Integrated Signaling, Metabolic, and Regulatory Networks

Authors: Lee, Jong Min; Gianchandani, Erwin P.; Eddy, James A.; Papin, Jason A.

Year: 2008

Venue: PLoS Computational Biology

DOI: https://doi.org/10.1371/annotation/5594348b-de00-446a-bdd0-ec56e70b3553

Paper Correction: Inferring Carbon Sources from Gene Expression Profiles Using Metabolic Flux Models

Brandes, Aaron; Lun, Desmond S.; Ip, Kuhn et al. · 2012 · PLoS ONE · DOI

Full title: Correction: Inferring Carbon Sources from Gene Expression Profiles Using Metabolic Flux Models

Authors: Brandes, Aaron; Lun, Desmond S.; Ip, Kuhn; Zucker, Jeremy; Colijn, Caroline; Weiner, Brian; Galagan, James E.

Year: 2012

Venue: PLoS ONE

DOI: https://doi.org/10.1371/annotation/139857f3-5a05-4a23-9bfe-a77aafbce54d

Paper Genome-Scale Reconstruction and Analysis of the Pseudomonas putida KT2440 Metabolic Network Facilitates Applications in Biotechnology

Puchałka, Jacek; Oberhardt, Matthew; Godinho, Miguel et al. · 2008 · PLoS Computational Biology · DOI

Full title: Genome-Scale Reconstruction and Analysis of the Pseudomonas putida KT2440 Metabolic Network Facilitates Applications in Biotechnology

Authors: Puchałka, Jacek; Oberhardt, Matthew; Godinho, Miguel; Bielecka‐Dąbrowa, Agata; Regenhardt, Daniela; Timmis, Kenneth N.; Papin, Jason A.; Santos, Vítor A. P. Martins dos

Year: 2008

Venue: PLoS Computational Biology

DOI: https://doi.org/10.1371/journal.pcbi.1000210

Paper CO2 to succinic acid – Estimating the potential of biocatalytic routes

Liebal, Ulf W.; Blank, Lars M.; Ebert, Birgitta E. · 2018 · Metabolic Engineering Communications · DOI

Full title: CO2 to succinic acid – Estimating the potential of biocatalytic routes

Authors: Liebal, Ulf W.; Blank, Lars M.; Ebert, Birgitta E.

Year: 2018

Venue: Metabolic Engineering Communications

DOI: https://doi.org/10.1016/j.mec.2018.e00075

Paper Engineering Escherichia coli for methanol conversion

Müller, Jonas E. N.; Meyer, Fabian; Litsanov, Boris et al. · 2015 · Metabolic Engineering · DOI

Full title: Engineering Escherichia coli for methanol conversion

Authors: Müller, Jonas E. N.; Meyer, Fabian; Litsanov, Boris; Kiefer, Patrick; Potthoff, Eva; Heux, Stéphanie; Quax, Wim J.; Wendisch, Volker F.; Brautaset, Trygve; Portais, Jean‐Charles; Vorholt, Julia A.

Year: 2015

Venue: Metabolic Engineering

DOI: https://doi.org/10.1016/j.ymben.2014.12.008

Paper Functional genomics for the oleaginous yeast Yarrowia lipolytica

Patterson, Kurt; Yu, James; Landberg, Jenny et al. · 2018 · Metabolic Engineering · DOI

Full title: Functional genomics for the oleaginous yeast Yarrowia lipolytica

Authors: Patterson, Kurt; Yu, James; Landberg, Jenny; Chang, Ivan; Shavarebi, Farbod; Bilanchone, Virginia; Sandmeyer, Suzanne

Year: 2018

Venue: Metabolic Engineering

DOI: https://doi.org/10.1016/j.ymben.2018.05.008

Paper Metabolic engineering of human gut microbiome: Recent developments and future perspectives

Li, Peishun; Roos, Stefan; Luo, Hao et al. · 2023 · Metabolic Engineering · DOI

Full title: Metabolic engineering of human gut microbiome: Recent developments and future perspectives

Authors: Li, Peishun; Roos, Stefan; Luo, Hao; Ji, Boyang; Nielsen, Jens

Year: 2023

Venue: Metabolic Engineering

DOI: https://doi.org/10.1016/j.ymben.2023.06.006

Paper A genome-scale dynamic constraint-based modelling (gDCBM) framework predicts growth dynamics, medium composition and intracellular flux distributions in CHO clonal variations

Yasemi, Mohammadreza; Jolicœur, Mario · 2023 · Metabolic Engineering · DOI

Full title: A genome-scale dynamic constraint-based modelling (gDCBM) framework predicts growth dynamics, medium composition and intracellular flux distributions in CHO clonal variations

Authors: Yasemi, Mohammadreza; Jolicœur, Mario

Year: 2023

Venue: Metabolic Engineering

DOI: https://doi.org/10.1016/j.ymben.2023.06.005

Paper A dynamic kinetic model captures cell-free metabolism for improved butanol production

Martin, Jacob P.; Rasor, Blake J.; DeBonis, Jonathon et al. · 2023 · Metabolic Engineering · DOI

Full title: A dynamic kinetic model captures cell-free metabolism for improved butanol production

Authors: Martin, Jacob P.; Rasor, Blake J.; DeBonis, Jonathon; Karim, Ashty S.; Jewett, Michael C.; Tyo, Keith E. J.; Broadbelt, Linda J.

Year: 2023

Venue: Metabolic Engineering

DOI: https://doi.org/10.1016/j.ymben.2023.01.009

Paper Engineering Pseudomonas putida for efficient aromatic conversion to bioproduct using high throughput screening in a bioreactor

Eng, Thomas; Banerjee, Deepanwita; Lau, Andrew K. et al. · 2021 · Metabolic Engineering · DOI

Full title: Engineering Pseudomonas putida for efficient aromatic conversion to bioproduct using high throughput screening in a bioreactor

Authors: Eng, Thomas; Banerjee, Deepanwita; Lau, Andrew K.; Bowden, Emily; Herbert, Robin A.; Trinh, Jessica; Prahl, Jan‐Philip; Deutschbauer, Adam M.; Tanjore, Deepti; Mukhopadhyay, Aindrila

Year: 2021

Venue: Metabolic Engineering

DOI: https://doi.org/10.1016/j.ymben.2021.04.015

Paper Self-controlled in silico gene knockdown strategies to enhance the sustainable production of heterologous terpenoid by Saccharomyces cerevisiae

Zhang, Na; Li, Xiaohan; Zhou, Qiang et al. · 2024 · Metabolic Engineering · DOI

Full title: Self-controlled in silico gene knockdown strategies to enhance the sustainable production of heterologous terpenoid by Saccharomyces cerevisiae

Authors: Zhang, Na; Li, Xiaohan; Zhou, Qiang; Zhang, Ying; Lv, Bo; Hu, Bing; Li, Chun

Year: 2024

Venue: Metabolic Engineering

DOI: https://doi.org/10.1016/j.ymben.2024.04.005

Paper Genome-scale dynamic modeling of the competition between Rhodoferax and Geobacter in anoxic subsurface environments

Zhuang, Kai; Izallalen, Mounir; Mouser, Paula et al. · 2010 · The ISME Journal · DOI

Full title: Genome-scale dynamic modeling of the competition between Rhodoferax and Geobacter in anoxic subsurface environments

Authors: Zhuang, Kai; Izallalen, Mounir; Mouser, Paula; Richter, Hanno; Risso, Carla; Mahadevan, Radhakrishnan; Lovley, Derek R.

Year: 2010

Venue: The ISME Journal

DOI: https://doi.org/10.1038/ismej.2010.117

Paper Integrating thermodynamic and enzymatic constraints into genome-scale metabolic models.

Yang, Xue; Mao, Zhitao; Zhao, Xin et al. · 2021 · Metabolic engineering · DOI

Full title: Integrating thermodynamic and enzymatic constraints into genome-scale metabolic models.

Authors: Yang, Xue; Mao, Zhitao; Zhao, Xin; Wang, Ruoyu; Zhang, Peiji; Cai, Jingyi; Xue, Chaoyou; Ma, Hongwu

Year: 2021

Venue: Metabolic engineering

DOI: https://doi.org/10.1016/j.ymben.2021.06.005

Paper A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology

Herrgård, Markus J.; Swainston, Neil; Dobson, Paul D. et al. · 2008 · Nature Biotechnology · DOI

Full title: A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology

Authors: Herrgård, Markus J.; Swainston, Neil; Dobson, Paul D.; Dunn, Warwick B.; Arğa, Kazım Yalçın; Arvas, Mikko; Blüthgen, Nils; Borger, Simon; Costenoble, Roeland; Heinemann, Matthias; Hucka, Michael; Novère, Nicolas Le; Li, Peter; Liebermeister, Wolfram; Mo, Monica L.; Oliveira, Ana Paula; Petranović, Dina; Pettifer, Steve; Simeonidis, Evangelos; Smallbone, Kieran; Spasié, Irena; Weichart, Dieter; Brent, Roger; Broomhead, David S.; Westerhoff, Hans V.; Kürdar, Betül; Penttilä, Merja; Klipp, Edda; Palsson, Bernhard Ø.; Sauer, Uwe; Oliver, Stephen G.; Mendes, Pedro; Nielsen, Jens; Kell, Douglas B.

Year: 2008

Venue: Nature Biotechnology

DOI: https://doi.org/10.1038/nbt1492

Paper Reconstruction of the Fatty Acid Biosynthetic Pathway ofExiguobacterium antarcticumB7 Based on Genomic and Bibliomic Data

Kawasaki, Regiane; Baraúna, Rafael A.; Silva, Artur et al. · 2016 · BioMed Research International · DOI

Full title: Reconstruction of the Fatty Acid Biosynthetic Pathway ofExiguobacterium antarcticumB7 Based on Genomic and Bibliomic Data

Authors: Kawasaki, Regiane; Baraúna, Rafael A.; Silva, Artur; Carepo, Marta S. P.; Oliveira, Rui; Marques, Rodolfo; Ramos, Rommel Thiago Jucá; Schneider, Maria Paula Cruz

Year: 2016

Venue: BioMed Research International

DOI: https://doi.org/10.1155/2016/7863706

Thesis DynamicME: dynamic simulation and refinement of integrated models of metabolism and protein expression

Yang, Laurence; Ebrahim, Ali; Lloyd, Colton J. et al. · 2019 · Technical University of Denmark (DTU) · DOI

Full title: DynamicME: dynamic simulation and refinement of integrated models of metabolism and protein expression

Authors: Yang, Laurence; Ebrahim, Ali; Lloyd, Colton J.; Saunders, Michael A.; Palsson, Bernhard; id_orcid 0000-0003-2357-6785

Year: 2019

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/ec15b607-dcd9-490b-9d3e-ea05a9aec631

Thesis Network Reconstruction and In Silico Metabolic Model of Chinese Hamster Ovary cells

Calmels, Cyrielle · 2018 · Technical University of Denmark (DTU) · DOI

Full title: Network Reconstruction and In Silico Metabolic Model of Chinese Hamster Ovary cells

Authors: Calmels, Cyrielle

Year: 2018

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/e8e79519-7089-44aa-9964-6700b9af9251

Thesis Industrial Systems Biology of Saccharomyces cerevisiae Enables Novel Succinic Acid Cell Factory.

Otero, José Manuel; Cimini, Donatella; Patil, Kiran Raosaheb et al. · 2013 · Technical University of Denmark (DTU) · DOI

Full title: Industrial Systems Biology of Saccharomyces cerevisiae Enables Novel Succinic Acid Cell Factory.

Authors: Otero, José Manuel; Cimini, Donatella; Patil, Kiran Raosaheb; Poulsen, Simon Guldberg; Olsson, Lisbeth; Nielsen, Jens

Year: 2013

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/e7ba99b8-8502-4f6e-9bc4-8084fb3826aa

Thesis Development of a screening approach for exploring cell factory potential through metabolic flux analysis and physiology

Knudsen, Peter Boldsen; Nielsen, Kristian Fog; Thykær, Jette · 2012 · Technical University of Denmark (DTU) · DOI

Full title: Development of a screening approach for exploring cell factory potential through metabolic flux analysis and physiology

Authors: Knudsen, Peter Boldsen; Nielsen, Kristian Fog; Thykær, Jette

Year: 2012

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/e4617fd9-adab-48f9-bfeb-a1e9784d9aff

Thesis Using Genome-scale Models to Predict Biological Capabilities

O’Brien, Edward J.; Monk, Jonathan M.; Palsson, Bernhard O. et al. · 2015 · Technical University of Denmark (DTU) · DOI

Full title: Using Genome-scale Models to Predict Biological Capabilities

Authors: O’Brien, Edward J.; Monk, Jonathan M.; Palsson, Bernhard O.; id_orcid 0000-0003-2357-6785

Year: 2015

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/e3b32d6d-318c-4030-9d2a-0e14edc51a75

Thesis Genome-scale metabolic rewiring improves titers rates and yields of the non-native product indigoidine at scale

Banerjee, Deepanwita; Eng, Thomas; Lau, Andrew K. et al. · 2020 · Technical University of Denmark (DTU) · DOI

Full title: Genome-scale metabolic rewiring improves titers rates and yields of the non-native product indigoidine at scale

Authors: Banerjee, Deepanwita; Eng, Thomas; Lau, Andrew K.; Sasaki, Yusuke; Wang, Brenda; Chen, Yan; Prahl, Jan Philip; Singan, Vasanth R.; Herbert, Robin A.; Liu, Yuzhong; Tanjore, Deepti; Petzold, Christopher J.; Keasling, Jay D.; Mukhopadhyay, Aindrila

Year: 2020

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/f007def8-3e0b-4ed0-8302-e02aa544e164

Thesis Turnover Dependent Phenotypic Simulation: A Quantitative Constraint-Based Simulation Method That Accommodates All Main Strain Design Strategies

Pereira, Rui; Vilaça, Paulo; Maia, Paulo et al. · 2019 · Technical University of Denmark (DTU) · DOI

Full title: Turnover Dependent Phenotypic Simulation: A Quantitative Constraint-Based Simulation Method That Accommodates All Main Strain Design Strategies

Authors: Pereira, Rui; Vilaça, Paulo; Maia, Paulo; Nielsen, Jens; Rocha, Isabel

Year: 2019

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/ebf4708b-30df-48bb-8562-32a31c81b850

Thesis Multi-omics analysis of fatty alcohol production in engineered yeasts saccharomyces cerevisiae and yarrowia lipolytica

Dahlin, Jonathan; Holkenbrink, Carina; Marella, Eko Roy et al. · 2019 · Technical University of Denmark (DTU) · DOI

Full title: Multi-omics analysis of fatty alcohol production in engineered yeasts saccharomyces cerevisiae and yarrowia lipolytica

Authors: Dahlin, Jonathan; Holkenbrink, Carina; Marella, Eko Roy; Wang, Guokun; Liebal, Ulf; Lieven, Christian; Weber, Dieter; McCloskey, Douglas; Ebert, Birgitta E.; Herrgård, Markus J.; Blank, Lars Mathias; Borodina, Irina

Year: 2019

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/ed194746-96c9-44cb-aa39-1307ed519a49

Thesis Machine learning applied to enzyme turnover numbers reveals protein structural correlates and improves metabolic models

Heckmann, David; Lloyd, Colton J.; Mih, Nathan et al. · 2018 · Technical University of Denmark (DTU) · DOI

Full title: Machine learning applied to enzyme turnover numbers reveals protein structural correlates and improves metabolic models

Authors: Heckmann, David; Lloyd, Colton J.; Mih, Nathan; Ha, Yuanchi; Zielinski, Daniel C.; Haiman, Zachary B.; Desouki, Abdelmoneim Amer; Lercher, Martin J.; Palsson, Bernhard O.; id_orcid 0000-0003-2357-6785

Year: 2018

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/f5199711-3cab-4d21-80dc-5ea8676d426d

Thesis Manually curated genome-scale reconstruction of the metabolic network of Bacillus megaterium DSM319

Aminian-Dehkordi, Javad; Mousavi, Seyyed Mohammad; Jafari, Arezou et al. · 2019 · Technical University of Denmark (DTU) · DOI

Full title: Manually curated genome-scale reconstruction of the metabolic network of Bacillus megaterium DSM319

Authors: Aminian-Dehkordi, Javad; Mousavi, Seyyed Mohammad; Jafari, Arezou; Mijakovic, Ivan; Marashi, Sayed Amir

Year: 2019

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/ef4a2309-59e5-4a56-ab9b-10dcbf5985a6

Thesis MARSI: metabolite analogues for rational strain improvement

Cardoso, João G. R.; Zeidan, Ahmad A; Jensen, Kristian et al. · 2018 · Technical University of Denmark (DTU) · DOI

Full title: MARSI: metabolite analogues for rational strain improvement

Authors: Cardoso, João G. R.; Zeidan, Ahmad A; Jensen, Kristian; Sonnenschein, Nikolaus; id_orcid 0000-0002-7581-4936; Neves, Ana Rute; Herrgård, Markus J

Year: 2018

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/f490b237-6e58-42b7-ba63-ad4f8e7ab754

Thesis A Novel Efficient L-Lysine Exporter Identified by Functional Metagenomics

Malla, Sailesh; van der Helm, Eric; Darbani, Behrooz et al. · 2022 · Technical University of Denmark (DTU) · DOI

Full title: A Novel Efficient L-Lysine Exporter Identified by Functional Metagenomics

Authors: Malla, Sailesh; van der Helm, Eric; Darbani, Behrooz; Wieschalka, Stefan; Foerster, Jochen; id_orcid 0000-0003-4045-7905; Borodina, Irina; Sommer, Morten Otto Alexander; id_orcid 0000-0003-4005-5674

Year: 2022

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/eadfcd55-8819-462d-94d2-ebbdee699b15

Thesis Targeting population heterogeneity for optimal cell factories

Heins, Anna-Lena; Carlqvist, Magnus; Helmark, S. et al. · 2011 · Technical University of Denmark (DTU) · DOI

Full title: Targeting population heterogeneity for optimal cell factories

Authors: Heins, Anna-Lena; Carlqvist, Magnus; Helmark, S.; Lencastre Fernandes, Rita; Gernaey, Krist; id_orcid 0000-0002-0364-1773; Eliasson Lantz, Anna

Year: 2011

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/f6330829-57ee-45a2-9c4a-1e6ef89fe66a

Thesis Yeast metabolic innovations emerged via expanded metabolic network and gene positive selection

Lu, Hongzhong; Li, Feiran; Yuan, Le et al. · 2021 · Technical University of Denmark (DTU) · DOI

Full title: Yeast metabolic innovations emerged via expanded metabolic network and gene positive selection

Authors: Lu, Hongzhong; Li, Feiran; Yuan, Le; Domenzain, Iván; Yu, Rosemary; Wang, Hao; Li, Gang; Chen, Yu; Ji, Boyang; Kerkhoven, Eduard J.; Nielsen, Jens

Year: 2021

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/d25d3abb-a2f3-4f03-93e4-c55ccce1667d

Thesis Pangenome reconstruction of Lactobacillaceae metabolism predicts species-specific metabolic traits

Ardalani, O.; id_orcid 0000-0002-0064-3802; Phaneuf, P. V. et al. · 2024 · Technical University of Denmark (DTU) · DOI

Full title: Pangenome reconstruction of Lactobacillaceae metabolism predicts species-specific metabolic traits

Authors: Ardalani, O.; id_orcid 0000-0002-0064-3802; Phaneuf, P. V.; Mohite, O. S.; id_orcid 0000-0002-3240-1656; Nielsen, L. K.; Palsson, B. O.; id_orcid 0000-0003-2357-6785

Year: 2024

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/f0da44fd-f204-4ec1-8c80-8df20ddd87a1

Thesis Current state of genome-scale modeling in filamentous fungi

Brandl, Julian; Andersen, Mikael Rørdam; id_orcid 0000-0003-4794-6808 · 2015 · Technical University of Denmark (DTU) · DOI

Full title: Current state of genome-scale modeling in filamentous fungi

Authors: Brandl, Julian; Andersen, Mikael Rørdam; id_orcid 0000-0003-4794-6808

Year: 2015

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/f66c76b8-e86d-4823-902a-77f9eb2db7be

Thesis Pangenome Scale Reconstruction of Lactobacillaceae family and Escherichia coli Species Metabolism

Ardalani, Omid; id_orcid 0000-0002-0064-3802 · 2024 · Technical University of Denmark (DTU) · DOI

Full title: Pangenome Scale Reconstruction of Lactobacillaceae family and Escherichia coli Species Metabolism

Authors: Ardalani, Omid; id_orcid 0000-0002-0064-3802

Year: 2024

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/fa6f2508-15ed-4b8c-829d-bed44a23cc3e

Thesis Metabolic Engineering and Molecular Tool Development in Yeast for Production of Bulk Chemicals

Fabre, Mathew Malcolm Jessop; id_orcid 0000-0001-7534-2230 · 2018 · Technical University of Denmark (DTU) · DOI

Full title: Metabolic Engineering and Molecular Tool Development in Yeast for Production of Bulk Chemicals

Authors: Fabre, Mathew Malcolm Jessop; id_orcid 0000-0001-7534-2230

Year: 2018

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/fd6dee37-6d3f-49d6-ace9-1d5bd29b3fb4

Thesis Integration of metabolome data with metabolic networks reveals reporter reactions

Çakir, Tunahan; Patil, Kiran Raosaheb; Önsan, Zeynep Ilsen et al. · 2006 · Technical University of Denmark (DTU) · DOI

Full title: Integration of metabolome data with metabolic networks reveals reporter reactions

Authors: Çakir, Tunahan; Patil, Kiran Raosaheb; Önsan, Zeynep Ilsen; Ülgen, Kutlu Özergin; Kirdar, Betül; Nielsen, Jens

Year: 2006

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/fa28a9b7-8cae-4798-a7a9-6a33af7369d2

Thesis Metabolic Trade-offs in Yeast are Caused by F1F0-ATP synthase

Nilsson, Avlant; Nielsen, Jens · 2016 · Technical University of Denmark (DTU) · DOI

Full title: Metabolic Trade-offs in Yeast are Caused by F1F0-ATP synthase

Authors: Nilsson, Avlant; Nielsen, Jens

Year: 2016

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/f1e21ad2-7d0f-4ea4-b415-b38067ef879a

Thesis Proteome constraints reveal targets for improving microbial fitness in nutrient-rich environments

Chen, Yu; van Pelt-KleinJan, Eunice; van Olst, Berdien et al. · 2021 · Technical University of Denmark (DTU) · DOI

Full title: Proteome constraints reveal targets for improving microbial fitness in nutrient-rich environments

Authors: Chen, Yu; van Pelt-KleinJan, Eunice; van Olst, Berdien; Douwenga, Sieze; Boeren, Sjef; Bachmann, Herwig; Molenaar, Douwe; Nielsen, Jens; Teusink, Bas

Year: 2021

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/fc704304-27bc-409f-9c5c-ec6b6e76c4fb

Thesis Laboratory evolution reveals a two-dimensional rate-yield tradeoff in microbial metabolism

Cheng, Chuankai; O'Brien, Edward J.; McCloskey, Douglas et al. · 2019 · Technical University of Denmark (DTU) · DOI

Full title: Laboratory evolution reveals a two-dimensional rate-yield tradeoff in microbial metabolism

Authors: Cheng, Chuankai; O'Brien, Edward J.; McCloskey, Douglas; Utrilla, Jose; Olson, Connor; LaCroix, Ryan A.; Sandberg, Troy E.; Feist, Adam M.; Palsson, Bernhard O.; id_orcid 0000-0003-2357-6785; King, Zachary A.

Year: 2019

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/f4a20dad-892d-4e49-8f9c-5697c6c501e8

Thesis Complex yeast–bacteria interactions affect the yield of industrial ethanol fermentation

Senne de Oliveira Lino, Felipe; Bajic, Djordje; Vila, Jean Celestin Charles et al. · 2021 · Technical University of Denmark (DTU) · DOI

Full title: Complex yeast–bacteria interactions affect the yield of industrial ethanol fermentation

Authors: Senne de Oliveira Lino, Felipe; Bajic, Djordje; Vila, Jean Celestin Charles; Sánchez, Alvaro; Sommer, Morten Otto Alexander; id_orcid 0000-0003-4005-5674

Year: 2021

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/f94bf19e-27e6-4067-9c31-38e7efc31f66

Thesis Compositions and methods for modeling Saccharomyces cerevisiae metabolism

Palsson, Bernard; Famili, Imandokht; Fu, Pengcheng et al. · 2012 · Technical University of Denmark (DTU) · DOI

Full title: Compositions and methods for modeling Saccharomyces cerevisiae metabolism

Authors: Palsson, Bernard; Famili, Imandokht; Fu, Pengcheng; Nielsen, Jens B.; Förster, Jochen; id_orcid 0000-0003-4045-7905

Year: 2012

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/fe4e6ec8-5121-4c9b-98bd-4861e72234a9

Thesis Laboratory evolution reveals regulatory and metabolic trade-offs of glycerol utilization in Saccharomyces cerevisiae

Strucko, Tomas; id_orcid 0000-0003-1947-8138; Zirngibl, Katharina et al. · 2018 · Technical University of Denmark (DTU) · DOI

Full title: Laboratory evolution reveals regulatory and metabolic trade-offs of glycerol utilization in Saccharomyces cerevisiae

Authors: Strucko, Tomas; id_orcid 0000-0003-1947-8138; Zirngibl, Katharina; Pereira, Filipa; Kafkia, Eleni; Mohamed, Elsayed T.; Rettel, Mandy; Stein, Frank; Feist, Adam M; id_orcid 0000-0002-8630-4800; Jouhten, Paula; Patil, Kiran Raosaheb; Forster, Jochen; id_orcid 0000-0003-4045-7905

Year: 2018

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/0aa491a2-33ed-47fe-9519-f8675852207e

Thesis OptCouple: Joint simulation of gene knockouts, insertions and medium modifications for prediction of growth-coupled strain designs

Jensen, Kristian; Broeken, Valentijn; Hansen, Anne Sofie Lærke et al. · 2019 · Technical University of Denmark (DTU) · DOI

Full title: OptCouple: Joint simulation of gene knockouts, insertions and medium modifications for prediction of growth-coupled strain designs

Authors: Jensen, Kristian; Broeken, Valentijn; Hansen, Anne Sofie Lærke; id_orcid 0000-0003-2771-4671; Sonnenschein, Nikolaus; id_orcid 0000-0002-7581-4936; Herrgård, Markus J.

Year: 2019

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/fbfbc117-2665-47ca-8858-589c209247c2

Thesis Application of a genome-scale model in tandem with enzyme assays for identification of metabolic signatures of high and low CHO cell producers

Calmels, Cyrielle; Arnoult, Solène; Ben Yahia, Bassem et al. · 2019 · Technical University of Denmark (DTU) · DOI

Full title: Application of a genome-scale model in tandem with enzyme assays for identification of metabolic signatures of high and low CHO cell producers

Authors: Calmels, Cyrielle; Arnoult, Solène; Ben Yahia, Bassem; Malphettes, Laetitia; Andersen, Mikael Rørdam; id_orcid 0000-0003-4794-6808

Year: 2019

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/07c1b78f-8e1b-4264-8b5a-d74f261ebab9

Thesis Natural computation meta-heuristics for the in silico optimization of microbial strains

Rocha, Miguel; Maia, Paulo; Mendes, Rui et al. · 2008 · Technical University of Denmark (DTU) · DOI

Full title: Natural computation meta-heuristics for the in silico optimization of microbial strains

Authors: Rocha, Miguel; Maia, Paulo; Mendes, Rui; Pinto, José; Ferreira, Euqénio; Nielsen, Jens; Patil, Kiran Raosaheb; Rocha, Isabel

Year: 2008

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/f8e459ca-9581-400e-be54-c8a43b6d97cc

Thesis Whole-cell modeling in yeast predicts compartment-specific proteome constraints that drive metabolic strategies

Elsemman, Ibrahim E.; Rodriguez Prado, Angelica; Grigaitis, Pranas et al. · 2022 · Technical University of Denmark (DTU) · DOI

Full title: Whole-cell modeling in yeast predicts compartment-specific proteome constraints that drive metabolic strategies

Authors: Elsemman, Ibrahim E.; Rodriguez Prado, Angelica; Grigaitis, Pranas; Garcia Albornoz, Manuel; Harman, Victoria; Holman, Stephen W.; van Heerden, Johan; Bruggeman, Frank J.; Bisschops, Mark M.M.; Sonnenschein, Nikolaus; id_orcid 0000-0002-7581-4936; Hubbard, Simon; Beynon, Rob; Daran-Lapujade, Pascale; Nielsen, Jens; Teusink, Bas

Year: 2022

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/f8ac3827-f62d-4c07-8848-b31d93a6586e

Thesis Big data in yeast systems biology

Yu, Rosemary; Nielsen, Jens · 2019 · Technical University of Denmark (DTU) · DOI

Full title: Big data in yeast systems biology

Authors: Yu, Rosemary; Nielsen, Jens

Year: 2019

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/013b49f9-e949-4d09-a1e8-c05af46366f9

Thesis Multi-omics Quantification of Species Variation of Escherichia coli Links Molecular Features with Strain Phenotypes

Monk, Jonathan M; Koza, Anna; Campodonico, Miguel A et al. · 2016 · Technical University of Denmark (DTU) · DOI

Full title: Multi-omics Quantification of Species Variation of Escherichia coli Links Molecular Features with Strain Phenotypes

Authors: Monk, Jonathan M; Koza, Anna; Campodonico, Miguel A; Machado, Daniel; Seoane, Jose Miguel; Palsson, Bernhard; id_orcid 0000-0003-2357-6785; Herrgard, Markus; Feist, Adam; id_orcid 0000-0002-8630-4800

Year: 2016

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/00cda276-05c8-41fd-aa02-cabdeb876216

Thesis Deciphering flux adjustments of engineered E. coli cells during fermentation with changing growth conditions

He, Lian; Xiu, Yu; Jones, J. Andrew et al. · 2017 · Technical University of Denmark (DTU) · DOI

Full title: Deciphering flux adjustments of engineered E. coli cells during fermentation with changing growth conditions

Authors: He, Lian; Xiu, Yu; Jones, J. Andrew; Baidoo, Edward E. K.; Keasling, Jay D.; Tang, Yinjie J; Koffas, Mattheos A. G.

Year: 2017

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/06d07d80-fff5-4b9f-97a1-502d02f2af31

Thesis Escherichia coli B2 strains prevalent in inflammatory bowel disease patients have distinct metabolic capabilities that enable colonization of intestinal mucosa

Fang, Xin; Monk, Jonathan M.; Mih, Nathan et al. · 2018 · Technical University of Denmark (DTU) · DOI

Full title: Escherichia coli B2 strains prevalent in inflammatory bowel disease patients have distinct metabolic capabilities that enable colonization of intestinal mucosa

Authors: Fang, Xin; Monk, Jonathan M.; Mih, Nathan; Du, Bin; Sastry, Anand V.; Kavvas, Erol; Seif, Yara; Smarr, Larry; Palsson, Bernhard O.; id_orcid 0000-0003-2357-6785

Year: 2018

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/175a933b-16a0-4622-a676-cfde406c23b8

Thesis Hybrid dynamic modeling of Escherichia coli central metabolic network combining Michaelis–Menten and approximate kinetic equations

Costa, Rafael S.; Machado, Daniel; Rocha, Isabel et al. · 2010 · Technical University of Denmark (DTU) · DOI

Full title: Hybrid dynamic modeling of Escherichia coli central metabolic network combining Michaelis–Menten and approximate kinetic equations

Authors: Costa, Rafael S.; Machado, Daniel; Rocha, Isabel; Ferreira, Eugénio C.

Year: 2010

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/0eb8ac2f-20d8-4229-90ad-9d26399c1b29

Thesis Model-driven experimental design workflow expands understanding of regulatory role of Nac in Escherichia coli

Park, Joon Young; Lee, Sang-Mok; Ebrahim, Ali et al. · 2023 · Technical University of Denmark (DTU) · DOI

Full title: Model-driven experimental design workflow expands understanding of regulatory role of Nac in Escherichia coli

Authors: Park, Joon Young; Lee, Sang-Mok; Ebrahim, Ali; Scott-Nevros, Zoe K.; Kim, Jaehyung; Yang, Laurence; Sastry, Anand; Seo, Sang Woo; Palsson, Bernhard O; id_orcid 0000-0003-2357-6785; Kim, Donghyuk

Year: 2023

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/15aea79c-c198-4999-abd0-5f4b82f1c715

Thesis Analysis of genetic variation and potential applications in genome-scale metabolic modeling

Cardoso, Joao; Andersen, Mikael Rørdam; id_orcid 0000-0003-4794-6808 et al. · 2015 · Technical University of Denmark (DTU) · DOI

Full title: Analysis of genetic variation and potential applications in genome-scale metabolic modeling

Authors: Cardoso, Joao; Andersen, Mikael Rørdam; id_orcid 0000-0003-4794-6808; Herrgard, Markus; Sonnenschein, Nikolaus; id_orcid 0000-0002-7581-4936

Year: 2015

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/025d0c23-79e4-47f2-a308-0e27609c34fc

Thesis Multi-scale modeling for prediction of distributed cellular properties in response to substrate spatial gradients in a continuously run microreactor

Lencastre Fernandes, Rita; Krühne, Ulrich; id_orcid 0000-0001-7774-7442 et al. · 2012 · Technical University of Denmark (DTU) · DOI

Full title: Multi-scale modeling for prediction of distributed cellular properties in response to substrate spatial gradients in a continuously run microreactor

Authors: Lencastre Fernandes, Rita; Krühne, Ulrich; id_orcid 0000-0001-7774-7442; Nopens, Ingmar; Jensen, Anker Degn; id_orcid 0000-0002-7341-4859; Gernaey, Krist; id_orcid 0000-0002-0364-1773

Year: 2012

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/0cee1ed5-59e8-438f-ae43-806bc60af832

Thesis Flux-Enabled Exploration of the Role of Sip1 in galactose yeast metabolism

Shymansky, Christopher M.; Wang, George; Baidoo, Edward E. K. et al. · 2017 · Technical University of Denmark (DTU) · DOI

Full title: Flux-Enabled Exploration of the Role of Sip1 in galactose yeast metabolism

Authors: Shymansky, Christopher M.; Wang, George; Baidoo, Edward E. K.; Gin, Jennifer; Apel, Amanda Reider; Mukhopadhyay, Aindrila; Martin, Hector Garcia; Keasling, Jay

Year: 2017

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/1bf17655-c24f-48fa-b6cf-7748c1b70623

Thesis Linking high-resolution metabolic flux phenotypes and transcriptional regulation in yeast modulated by the global regulator Gcn4p

Moxley, Joel F.; Jewett, Michael Christopher; Antoniewicz, Maciek R. et al. · 2009 · Technical University of Denmark (DTU) · DOI

Full title: Linking high-resolution metabolic flux phenotypes and transcriptional regulation in yeast modulated by the global regulator Gcn4p

Authors: Moxley, Joel F.; Jewett, Michael Christopher; Antoniewicz, Maciek R.; Villas-Boas, Silas G.; Alper, Hal; Wheeler, Robert T.; Tong, Lily; Hinnebusch, Alan G.; Ideker, Trey; Nielsen, Jens; Stephanopoulos, Gregory

Year: 2009

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/17623919-bea0-458e-b978-e17c5ebaefb4

Thesis Reconstruction and analysis of a Kluyveromyces marxianus genome-scale metabolic model

Marcišauskas, Simonas; Ji, Boyang; Nielsen, Jens · 2019 · Technical University of Denmark (DTU) · DOI

Full title: Reconstruction and analysis of a Kluyveromyces marxianus genome-scale metabolic model

Authors: Marcišauskas, Simonas; Ji, Boyang; Nielsen, Jens

Year: 2019

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/193e0362-799e-434c-853e-01e450c42b2f

Thesis Model-assisted CRISPRi/a library screening reveals central carbon metabolic targets for enhanced recombinant protein production in yeast

Chen, Xin; Li, Feiran; Li, Xiaowei et al. · 2025 · Technical University of Denmark (DTU) · DOI

Full title: Model-assisted CRISPRi/a library screening reveals central carbon metabolic targets for enhanced recombinant protein production in yeast

Authors: Chen, Xin; Li, Feiran; Li, Xiaowei; Otto, Maximilian; Chen, Yu; Siewers, Verena

Year: 2025

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/1f4bb513-1a17-4a08-99c2-a87746baf059

Thesis Toward Synthetic Biology Strategies for Adipic Acid Production: An in Silico Tool for Combined Thermodynamics and Stoichiometric Analysis of Metabolic Networks

Averesch, Nils J. H.; Martínez, Verónica S.; Nielsen, Lars K. et al. · 2018 · Technical University of Denmark (DTU) · DOI

Full title: Toward Synthetic Biology Strategies for Adipic Acid Production: An in Silico Tool for Combined Thermodynamics and Stoichiometric Analysis of Metabolic Networks

Authors: Averesch, Nils J. H.; Martínez, Verónica S.; Nielsen, Lars K.; Krömer, Jens O.

Year: 2018

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/078e97b3-0a4e-40e9-98c4-2e4b4be110ca

Thesis Simulating Serial-Target Antibacterial Drug Synergies Using Flux Balance Analysis

Krueger, Andrew S.; Munck, Christian; Dantas, Gautam et al. · 2016 · Technical University of Denmark (DTU) · DOI

Full title: Simulating Serial-Target Antibacterial Drug Synergies Using Flux Balance Analysis

Authors: Krueger, Andrew S.; Munck, Christian; Dantas, Gautam; Church, George M.; Galagan, James; Lehár, Joseph; Sommer, Morten Otto Alexander; id_orcid 0000-0003-4005-5674

Year: 2016

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/12aaecb6-31d8-4610-b73f-4fe24c8bade9

Thesis Mathematical modeling of proteome constraints within metabolism

Chen, Yu; Nielsen, Jens · 2021 · Technical University of Denmark (DTU) · DOI

Full title: Mathematical modeling of proteome constraints within metabolism

Authors: Chen, Yu; Nielsen, Jens

Year: 2021

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/0c2d4597-c72a-443a-9195-bfd78e7ae259

Thesis Impact of systems biology on metabolic engineering of Saccharomyces cerevisiae

Nielsen, Jens; Jewett, Michael Christopher · 2008 · Technical University of Denmark (DTU) · DOI

Full title: Impact of systems biology on metabolic engineering of Saccharomyces cerevisiae

Authors: Nielsen, Jens; Jewett, Michael Christopher

Year: 2008

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/1a19c010-bc4e-4677-99ec-5f77360af045

Thesis Systems metabolic engineering

Hesselberg-Thomsen, Viktor; id_orcid 0000-0001-6929-3671 · 2024 · Technical University of Denmark (DTU) · DOI

Full title: Systems metabolic engineering

Authors: Hesselberg-Thomsen, Viktor; id_orcid 0000-0001-6929-3671

Year: 2024

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/18523551-e95d-4dca-8278-5501b8e2ec1d

Thesis Comparative metabolic network analysis of two xylose fermenting recombinant Saccharomyses cerevisiae strains

Grotkjær, Thomas; Christakopoulos, Paul; Nielsen, Jens et al. · 2005 · Technical University of Denmark (DTU) · DOI

Full title: Comparative metabolic network analysis of two xylose fermenting recombinant Saccharomyses cerevisiae strains

Authors: Grotkjær, Thomas; Christakopoulos, Paul; Nielsen, Jens; Olsson, Lisbeth

Year: 2005

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/2177120a-6c72-45ff-a7a9-4a0466c8b6cb

Thesis A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology

Herrgard, Markus; Swainston, Neil; Dobson, Paul et al. · 2008 · Technical University of Denmark (DTU) · DOI

Full title: A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology

Authors: Herrgard, Markus; Swainston, Neil; Dobson, Paul; Dunn, Warwick B.; Arga, K Yalçin; Arvas, Mikko; Blüthgen, Nils; Borger, Simon; Costenoble, Roeland; Heinemann, Matthias; Hucka, Michael; Le Novère, Nicolas; Li, Peter; Liebermeister, Wolfram; Mo, Minica L.; Soberano de Oliveira, Ana Paula; Petranovic, Dina; Pettifer, Stephen; Simeonidis, Evangelos; Smallbone, Kieran; Spasić, Irena; Weichart, Dieter; Brent, Roger; Broomhead, David S.; Westerhoff, Hans V.; Kirdar, Betül; Penttilä, Merja; Klipp, Edda; Palsson, Bernhard Ø.; Sauer, Uwe; Oliver, Stephen G.; Mendes, Pedro; Nielsen, Jens; Kell, Douglas B.

Year: 2008

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/185bf1f7-067a-4991-b68b-378738bfcd3b

Thesis Enhancing Saccharomyces cerevisiae Taxane Biosynthesis and Overcoming Nutritional Stress-Induced Pseudohyphal Growth

Walls, Laura Ellen; Martinez, José L; id_orcid 0000-0002-4490-8534 et al. · 2022 · Technical University of Denmark (DTU) · DOI

Full title: Enhancing Saccharomyces cerevisiae Taxane Biosynthesis and Overcoming Nutritional Stress-Induced Pseudohyphal Growth

Authors: Walls, Laura Ellen; Martinez, José L; id_orcid 0000-0002-4490-8534; Rios-Solis, Leonardo

Year: 2022

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/1fe5f10e-3e62-4344-8fce-daaef23aba9a

Thesis Rewiring regulatory networks in Escherichia coli to improve productionof Human Milk Oligosaccharides

Labunskaité, Rugilé; id_orcid 0009-0007-8147-9023 · 2025 · Technical University of Denmark (DTU) · DOI

Full title: Rewiring regulatory networks in Escherichia coli to improve productionof Human Milk Oligosaccharides

Authors: Labunskaité, Rugilé; id_orcid 0009-0007-8147-9023

Year: 2025

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/1d0c2abd-7c3d-4569-9401-f4201d21c190

Thesis Machine learning-guided cell factory optimization

Jensen, Michael Krogh; id_orcid 0000-0001-7574-4707 · 2023 · Technical University of Denmark (DTU) · DOI

Full title: Machine learning-guided cell factory optimization

Authors: Jensen, Michael Krogh; id_orcid 0000-0001-7574-4707

Year: 2023

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/2cf1d067-ce54-4ebe-9df2-9aed79c7f6b4

Thesis Primary Metabolic Pathways and Metabolic Flux Analysis

Villadsen, John; id_orcid 0000-0002-6523-8445 · 2015 · Technical University of Denmark (DTU) · DOI

Full title: Primary Metabolic Pathways and Metabolic Flux Analysis

Authors: Villadsen, John; id_orcid 0000-0002-6523-8445

Year: 2015

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/263c10bd-7f6a-43f9-80e6-1253e3d00d5e

Thesis Reconstruction and Quality Control of a Genome-Scale Metabolic Model for Methylococcus capsulatus

Lieven, Christian · 2018 · Technical University of Denmark (DTU) · DOI

Full title: Reconstruction and Quality Control of a Genome-Scale Metabolic Model for Methylococcus capsulatus

Authors: Lieven, Christian

Year: 2018

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/1c66d29b-56f9-4d49-a60e-33a3a88e11e8

Thesis Linking Genotype and Phenotype of Saccharomyces cerevisiae Strains Reveals Metabolic Engineering Targets and Leads to Triterpene Hyper-Producers

Madsen, Karina Marie; Udatha, Gupta D. B. R. K.; Semba, Saori et al. · 2011 · Technical University of Denmark (DTU) · DOI

Full title: Linking Genotype and Phenotype of Saccharomyces cerevisiae Strains Reveals Metabolic Engineering Targets and Leads to Triterpene Hyper-Producers

Authors: Madsen, Karina Marie; Udatha, Gupta D. B. R. K.; Semba, Saori; Otero, Jose M.; Koetter, Peter; Nielsen, Jens; Ebizuka, Yutaka; Kushiro, Tetsuo; Panagiotou, Gianni

Year: 2011

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/2578f46c-6ae7-4fd2-9c63-2e996ab0d253

Thesis Yeast optimizes metal utilization based on metabolic network and enzyme kinetics

Chen, Yu; Li, Feiran; Mao, Jiwei et al. · 2021 · Technical University of Denmark (DTU) · DOI

Full title: Yeast optimizes metal utilization based on metabolic network and enzyme kinetics

Authors: Chen, Yu; Li, Feiran; Mao, Jiwei; Chen, Yun; Nielsen, Jens

Year: 2021

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/26097f97-3cd4-43e3-9a84-ad5124b70e08

Thesis Maximizing microbial bioproduction from sustainable carbon sources using iterative systems engineering

Eng, Thomas; Banerjee, Deepanwita; Menasalvas, Javier et al. · 2023 · Technical University of Denmark (DTU) · DOI

Full title: Maximizing microbial bioproduction from sustainable carbon sources using iterative systems engineering

Authors: Eng, Thomas; Banerjee, Deepanwita; Menasalvas, Javier; Chen, Yan; Gin, Jennifer; Choudhary, Hemant; Baidoo, Edward; Chen, Jian Hua; Ekman, Axel; Kakumanu, Ramu; Diercks, Yuzhong Liu; Codik, Alex; Larabell, Carolyn; Gladden, John; Simmons, Blake A.; Keasling, Jay D.; Petzold, Christopher J.; Mukhopadhyay, Aindrila

Year: 2023

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/2e007d49-0095-4677-9f1c-18bf73d9ad98

Thesis BOFdat: Generating biomass objective functions for genome-scale metabolic models from experimental data

Lachance, Jean Christophe; Lloyd, Colton J.; Monk, Jonathan M. et al. · 2019 · Technical University of Denmark (DTU) · DOI

Full title: BOFdat: Generating biomass objective functions for genome-scale metabolic models from experimental data

Authors: Lachance, Jean Christophe; Lloyd, Colton J.; Monk, Jonathan M.; Yang, Laurence; Sastry, Anand V.; Seif, Yara; Palsson, Bernhard O.; id_orcid 0000-0003-2357-6785; Rodrigue, Sébastien; Feist, Adam M.; id_orcid 0000-0002-8630-4800; King, Zachary A.; Jacques, Pierre Étienne

Year: 2019

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/231ab331-0114-4d98-86f5-f29b3cd5ed46

Thesis Metabollic Engineering of Saccharomyces Cereviae a,omi acid metabolism for production of products of industrial interest

Chen, Xiao · 2011 · Technical University of Denmark (DTU) · DOI

Full title: Metabollic Engineering of Saccharomyces Cereviae a,omi acid metabolism for production of products of industrial interest

Authors: Chen, Xiao

Year: 2011

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/2131b4b8-7ae6-4e96-bb46-5a0beccef4db

Thesis Generation of an atlas for commodity chemical production in Escherichia coli and a novel pathway prediction algorithm, GEM-Path

Campodonico, Miguel A.; Andrews, Barbara A.; Asenjo, Juan A. et al. · 2014 · Technical University of Denmark (DTU) · DOI

Full title: Generation of an atlas for commodity chemical production in Escherichia coli and a novel pathway prediction algorithm, GEM-Path

Authors: Campodonico, Miguel A.; Andrews, Barbara A.; Asenjo, Juan A.; Palsson, Bernhard; id_orcid 0000-0003-2357-6785; Feist, Adam; id_orcid 0000-0002-8630-4800

Year: 2014

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/26953bc8-15c8-4fba-83ee-d846f3eeec06

Thesis A Methodology for Development of a Pedagogical Simulation Tool used in Fermentation Applications

de las Heras, Simoneta Caño; id_orcid 0000-0002-5436-9001; Mansouri, Seyed Soheil et al. · 2018 · Technical University of Denmark (DTU) · DOI

Full title: A Methodology for Development of a Pedagogical Simulation Tool used in Fermentation Applications

Authors: de las Heras, Simoneta Caño; id_orcid 0000-0002-5436-9001; Mansouri, Seyed Soheil; id_orcid 0000-0002-0924-4947; Cignitti, Stefano; Uellendahl, Hinrich; Weitze, Charlotte Lærke; Gernaey, Krist V.; id_orcid 0000-0002-0364-1773; Rootzén, Helle; id_orcid 0000-0002-2928-7610; Krühne, Ulrich; id_orcid 0000-0001-7774-7442

Year: 2018

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/28f3950f-f0dc-412b-8c43-429d277a1ba3

Thesis Enhancing Biotransformation of Organic Micropollutants by Complex Microbial Communities Using Metabolic Modeling

Pierrelée, M.; id_orcid 0009-0006-4521-0097; Elad, T. et al. · 2025 · Technical University of Denmark (DTU) · DOI

Full title: Enhancing Biotransformation of Organic Micropollutants by Complex Microbial Communities Using Metabolic Modeling

Authors: Pierrelée, M.; id_orcid 0009-0006-4521-0097; Elad, T.; Delgado, A. Santos; Dechesne, A.; id_orcid 0000-0002-6638-2158; Valverde-Pérez, B.; id_orcid 0000-0001-7255-1395

Year: 2025

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/23ab54a9-16cb-4a6c-996e-c4e142c132c8

Thesis Enhancing yeast transcription analysis through integration of heterogeneous data

Grotkjær, Thomas; Nielsen, Jens · 2004 · Technical University of Denmark (DTU) · DOI

Full title: Enhancing yeast transcription analysis through integration of heterogeneous data

Authors: Grotkjær, Thomas; Nielsen, Jens

Year: 2004

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/2a08a149-1d2e-47a5-a5ee-1601d95201c0

Thesis Evolutionary programming as a platform for in silico metabolic engineering

Patil, Kiran Raosaheb; Rocha, Isabel; Förster, Jochen et al. · 2005 · Technical University of Denmark (DTU) · DOI

Full title: Evolutionary programming as a platform for in silico metabolic engineering

Authors: Patil, Kiran Raosaheb; Rocha, Isabel; Förster, Jochen; id_orcid 0000-0003-4045-7905; Nielsen, Jens

Year: 2005

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/2cb39a53-3203-4ab0-ac90-3aadec619dbe

Thesis Rewiring carbon metabolism in yeast for high level production of aromatic chemicals

Liu, Quanli; Yu, Tao; Li, Xiaowei et al. · 2019 · Technical University of Denmark (DTU) · DOI

Full title: Rewiring carbon metabolism in yeast for high level production of aromatic chemicals

Authors: Liu, Quanli; Yu, Tao; Li, Xiaowei; Chen, Yu; Campbell, Kate; Nielsen, Jens; Chen, Yun

Year: 2019

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/2a5826c3-a05b-4089-8592-5c2f6a573dd3

Thesis A Consensus Genome-scale Reconstruction of Chinese Hamster Ovary Cell Metabolism

Hefzi, Hooman; Ang, Kok Siong; Hanscho, Michael et al. · 2016 · Technical University of Denmark (DTU) · DOI

Full title: A Consensus Genome-scale Reconstruction of Chinese Hamster Ovary Cell Metabolism

Authors: Hefzi, Hooman; Ang, Kok Siong; Hanscho, Michael; Bordbar, Aarash; Ruckerbauer, David; Lakshmanan, Meiyappan; Orellana, Camila A.; Baycin-Hizal, Deniz; Huang, Yingxiang; Ley, Daniel; Martinez, Veronica S.; Kyriakopoulos, Sarantos; Jiménez, Natalia E.; Zielinski, Daniel C.; Quek, Lake-Ee; Wulff, Tune; Arnsdorf, Johnny; id_orcid 0000-0002-2738-0811; Li, Shangzhong; Lee, Jae Seong; Paglia, Giuseppe; Loira, Nicolas; Spahn, Philipp N.; Pedersen, Lasse Ebdrup; id_orcid 0000-0002-6064-919X; Gutierrez, Jahir M.; King, Zachary A.; Lund, Anne Mathilde; Nagarajan, Harish; Thomas, Alex; Abdel-Haleem, Alyaa M.; Zanghellini, Juergen; Kildegaard, Helene Faustrup; Voldborg, Bjørn Gunnar; id_orcid 0000-0002-7005-1642; Gerdtzen, Ziomara P.; Betenbaugh, Michael J.; Palsson, Bernhard; id_orcid 0000-0003-2357-6785; Andersen, Mikael Rørdam; id_orcid 0000-0003-4794-6808; Nielsen, Lars K.; Borth, Nicole; Lee, Dong-Yup; Lewis, Nathan E.

Year: 2016

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/2f8bb3cd-eb0c-46f7-b39b-3791d7c86d1d

Thesis Metabolic engineering in Saccharomyces cerevisiae through the use of a reconstructed genome-scale metabolic network leads to improved ethanol production

Bro, Christoffer; Regenberg, Birgitte; Förster, Jochen et al. · 2003 · Technical University of Denmark (DTU) · DOI

Full title: Metabolic engineering in Saccharomyces cerevisiae through the use of a reconstructed genome-scale metabolic network leads to improved ethanol production

Authors: Bro, Christoffer; Regenberg, Birgitte; Förster, Jochen; id_orcid 0000-0003-4045-7905; Nielsen, Jens

Year: 2003

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/2e86f7ed-ed53-4b2f-8253-cd568b4636dc

Thesis Model-driven engineering of microbial metabolism

van Rosmalen, Rik P. · 2022 · Wageningen University & Research · DOI

Full title: Model-driven engineering of microbial metabolism

Authors: van Rosmalen, Rik P.

Year: 2022

Venue: Wageningen University & Research

DOI: https://research.wur.nl/en/publications/model-driven-engineering-of-microbial-metabolism

Thesis Co-evolution of strain design methods based on flux balance and elementary mode analysis

Machado, Daniel; Herrgard, Markus · 2015 · Technical University of Denmark (DTU) · DOI

Full title: Co-evolution of strain design methods based on flux balance and elementary mode analysis

Authors: Machado, Daniel; Herrgard, Markus

Year: 2015

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/2b639a7f-da26-4749-aebd-458a55145056

Thesis Genome-Scale Metabolic Reconstruction of Actinomycetes for Antibiotics Production

Mohite, Omkar Satyavan; id_orcid 0000-0002-3240-1656; Weber, Tilmann et al. · 2019 · Technical University of Denmark (DTU) · DOI

Full title: Genome-Scale Metabolic Reconstruction of Actinomycetes for Antibiotics Production

Authors: Mohite, Omkar Satyavan; id_orcid 0000-0002-3240-1656; Weber, Tilmann; id_orcid 0000-0002-8260-5120; Kim, Hyun Uk; Lee, Sang Yup

Year: 2019

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/31dfc03d-44c1-4afd-b9bf-9e2dd4887426

Thesis Scheffersomyces stipitis: a comparative systems biology study with the Crabtree positive yeast Saccharomyces cerevisiae

Papini, Marta; Nookaew, Intawat; Uhlén, Mathias et al. · 2012 · Technical University of Denmark (DTU) · DOI

Full title: Scheffersomyces stipitis: a comparative systems biology study with the Crabtree positive yeast Saccharomyces cerevisiae

Authors: Papini, Marta; Nookaew, Intawat; Uhlén, Mathias; Nielsen, Jens

Year: 2012

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/29988970-e965-4858-969b-fc92d34c9718

Thesis MID Max: LC–MS/MS Method for Measuring the Precursor and Product Mass Isotopomer Distributions of Metabolic Intermediates and Cofactors for Metabolic Flux Analysis Applications

McCloskey, Douglas; Young, Jamey D.; Xu, Sibei et al. · 2016 · Technical University of Denmark (DTU) · DOI

Full title: MID Max: LC–MS/MS Method for Measuring the Precursor and Product Mass Isotopomer Distributions of Metabolic Intermediates and Cofactors for Metabolic Flux Analysis Applications

Authors: McCloskey, Douglas; Young, Jamey D.; Xu, Sibei; Palsson, Bernhard; id_orcid 0000-0003-2357-6785; Feist, Adam; id_orcid 0000-0002-8630-4800

Year: 2016

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/2fbb60e9-0a2f-4aa6-a879-39dd82df0146

Thesis Optimization of the IPP-bypass mevalonate pathway and fed-batch fermentation for the production of isoprenol in Escherichia coli

Kang, Aram; Mendez-Perez, Daniel; Goh, Ee Been et al. · 2019 · Technical University of Denmark (DTU) · DOI

Full title: Optimization of the IPP-bypass mevalonate pathway and fed-batch fermentation for the production of isoprenol in Escherichia coli

Authors: Kang, Aram; Mendez-Perez, Daniel; Goh, Ee Been; Baidoo, Edward E.K.; Benites, Veronica T.; Beller, Harry R.; Keasling, Jay D.; Adams, Paul D.; Mukhopadhyay, Aindrila; Lee, Taek Soon

Year: 2019

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/304d63cb-a7ca-4bb3-a7dd-b0014f68e46e

Thesis Modelling Enzyme Allocation and Metabolic Adaptation in Cyanobacteria

Firoozabadi, Hossein · 2024 · Technical University of Denmark (DTU) · DOI

Full title: Modelling Enzyme Allocation and Metabolic Adaptation in Cyanobacteria

Authors: Firoozabadi, Hossein

Year: 2024

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/2fb64401-0002-4f64-8992-c6bbacbc0e17

Thesis Multi-scale modeling for sustainable chemical production

Zhuang, Kai; Bakshi, Bhavik R.; Herrgard, Markus · 2013 · Technical University of Denmark (DTU) · DOI

Full title: Multi-scale modeling for sustainable chemical production

Authors: Zhuang, Kai; Bakshi, Bhavik R.; Herrgard, Markus

Year: 2013

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/3a32ab4f-bc60-4ef5-a9c1-9fea574de87b

Thesis Reconstruction and Validation of a Genome-Scale Metabolic Model of Streptococcus oralis (iCJ415), a Human Commensal and Opportunistic Pathogen

Jensen, Christian S.; Norsigian, Charles J.; Fang, Xin et al. · 2020 · Technical University of Denmark (DTU) · DOI

Full title: Reconstruction and Validation of a Genome-Scale Metabolic Model of Streptococcus oralis (iCJ415), a Human Commensal and Opportunistic Pathogen

Authors: Jensen, Christian S.; Norsigian, Charles J.; Fang, Xin; Nielsen, Xiaohui C.; Christensen, Jens Jørgen; Palsson, Bernhard O.; id_orcid 0000-0003-2357-6785; Monk, Jonathan M.

Year: 2020

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/3d0a3070-dfa2-41f1-b3e5-eb835416ff38

Thesis Improved production of Taxol ® precursors in S. cerevisiae using combinatorial in silico design and metabolic engineering

Malcı, Koray; Santibáñez, Rodrigo; Jonguitud-Borrego, Nestor et al. · 2023 · Technical University of Denmark (DTU) · DOI

Full title: Improved production of Taxol ® precursors in S. cerevisiae using combinatorial in silico design and metabolic engineering

Authors: Malcı, Koray; Santibáñez, Rodrigo; Jonguitud-Borrego, Nestor; Santoyo-Garcia, Jorge H.; Kerkhoven, Eduard J.; Rios-Solis, Leonardo

Year: 2023

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/2f11e723-d064-4b2b-8f99-934b2d2b4964

Thesis Computing the functional proteome:recent progress and future prospects for genome-scale models

O'Brien, Edward J.; Palsson, Bernhard; id_orcid 0000-0003-2357-6785 · 2015 · Technical University of Denmark (DTU) · DOI

Full title: Computing the functional proteome:recent progress and future prospects for genome-scale models

Authors: O'Brien, Edward J.; Palsson, Bernhard; id_orcid 0000-0003-2357-6785

Year: 2015

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/3e9a2c17-c486-4cf9-8d3f-3664d6495059

Thesis Early-stage economic and environmental impact assessment for optimized bioprocess development:Monoterpenoid indole alkaloids

Etit, Deniz; Ögmundarson, Ólafur; Zhang, Jie et al. · 2024 · Technical University of Denmark (DTU) · DOI

Full title: Early-stage economic and environmental impact assessment for optimized bioprocess development:Monoterpenoid indole alkaloids

Authors: Etit, Deniz; Ögmundarson, Ólafur; Zhang, Jie; Krogh Jensen, Michael; id_orcid 0000-0001-7574-4707; Sukumara, Sumesh

Year: 2024

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/404a3234-6af0-4e8e-91c6-898c12a05758

Thesis Energy metabolism controls phenotypes by protein efficiency and allocation

Chen, Yu; Nielsen, Jens · 2019 · Technical University of Denmark (DTU) · DOI

Full title: Energy metabolism controls phenotypes by protein efficiency and allocation

Authors: Chen, Yu; Nielsen, Jens

Year: 2019

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/55a57a57-1730-47f1-b7cd-2ee07d03ee1a

Thesis Modelling of microbial interactions in anaerobic digestion:from black to glass box

Basile, Arianna; Zampieri, Guido; Kovalovszki, Adam et al. · 2023 · Technical University of Denmark (DTU) · DOI

Full title: Modelling of microbial interactions in anaerobic digestion:from black to glass box

Authors: Basile, Arianna; Zampieri, Guido; Kovalovszki, Adam; id_orcid 0000-0001-7509-4580; Karkaria, Behzad; Treu, Laura; Patil, Kiran Raosaheb; Campanaro, Stefano

Year: 2023

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/3f0f2bb3-1d09-4a2b-bed8-bc87f1096969

Thesis High-quality genome-scale metabolic network reconstruction of probiotic bacterium Escherichia coli Nissle 1917

van ‘t Hof, Max; Mohite, Omkar S.; id_orcid 0000-0002-3240-1656 et al. · 2022 · Technical University of Denmark (DTU) · DOI

Full title: High-quality genome-scale metabolic network reconstruction of probiotic bacterium Escherichia coli Nissle 1917

Authors: van ‘t Hof, Max; Mohite, Omkar S.; id_orcid 0000-0002-3240-1656; Monk, Jonathan M.; Weber, Tilmann; id_orcid 0000-0002-8260-5120; Palsson, Bernhard O.; id_orcid 0000-0003-2357-6785; Sommer, Morten O. A.; id_orcid 0000-0003-4005-5674

Year: 2022

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/3d4c5d32-3a6f-46cb-9dae-a11a5a18e8dd

Thesis Laboratory Evolution to Alternating Substrate Environments Yields Distinct Phenotypic and Genetic Adaptive Strategies

Sandberg, Troy E.; Lloyd, Colton J.; Palsson, Bernhard O. et al. · 2017 · Technical University of Denmark (DTU) · DOI

Full title: Laboratory Evolution to Alternating Substrate Environments Yields Distinct Phenotypic and Genetic Adaptive Strategies

Authors: Sandberg, Troy E.; Lloyd, Colton J.; Palsson, Bernhard O.; id_orcid 0000-0003-2357-6785; Feist, Adam M.; id_orcid 0000-0002-8630-4800

Year: 2017

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/3f90556a-f9e7-4eb9-9566-8a115da160d8

Thesis Genome-scale metabolic model of Pichia pastoris with native and humanized glycosylation of recombinant proteins

Irani, Zahra Azimzadeh; Kerkhoven, Eduard J.; Shojaosadati, Seyed Abbas et al. · 2016 · Technical University of Denmark (DTU) · DOI

Full title: Genome-scale metabolic model of Pichia pastoris with native and humanized glycosylation of recombinant proteins

Authors: Irani, Zahra Azimzadeh; Kerkhoven, Eduard J.; Shojaosadati, Seyed Abbas; Nielsen, Jens

Year: 2016

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/33e2d41c-b61a-40d7-befe-f48d7a160ca3

Thesis Metabolic growth-coupling strategies for in vivo enzyme selection systems

Alter, Tobias B.; Pieters, Pascal A.; Lloyd, Colton J. et al. · 2025 · Technical University of Denmark (DTU) · DOI

Full title: Metabolic growth-coupling strategies for in vivo enzyme selection systems

Authors: Alter, Tobias B.; Pieters, Pascal A.; Lloyd, Colton J.; Feist, Adam M.; id_orcid 0000-0002-8630-4800; Özdemir, Emre; id_orcid 0000-0001-5548-6720; Palsson, Bernhard O.; id_orcid 0000-0003-2357-6785; Zielinski, Daniel C.

Year: 2025

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/3ea363d8-0894-4535-8fa1-d0f176835782

Thesis Linking genetic, metabolic, and phenotypic diversity among Saccharomyces cerevisiae strains using multi-omics associations

Kang, Kang; Bergdahl, Basti; Machado, Daniel et al. · 2019 · Technical University of Denmark (DTU) · DOI

Full title: Linking genetic, metabolic, and phenotypic diversity among Saccharomyces cerevisiae strains using multi-omics associations

Authors: Kang, Kang; Bergdahl, Basti; Machado, Daniel; Dato, Laura; Han, Ting-Li; Li, Jun; Villas-Boas, Silas; Herrgård, Markus J; Förster, Jochen; id_orcid 0000-0003-4045-7905; Panagiotou, Gianni

Year: 2019

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/4a3146d4-93ff-4761-ab2a-0e10f0522e0b

Thesis Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network

Förster, Jochen; id_orcid 0000-0003-4045-7905; Famili, I. et al. · 2003 · Technical University of Denmark (DTU) · DOI

Full title: Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network

Authors: Förster, Jochen; id_orcid 0000-0003-4045-7905; Famili, I.; Fu, P.; Palsson, B.O.; Nielsen, Jens

Year: 2003

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/4beb590c-7576-48fc-9de9-816edf3138df

Thesis Development and application of computer-aided design methods for cell factory optimization

Cardoso, Joao · 2017 · Technical University of Denmark (DTU) · DOI

Full title: Development and application of computer-aided design methods for cell factory optimization

Authors: Cardoso, Joao

Year: 2017

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/436ef08b-c0d7-43cf-a024-8c78597ed00f

Thesis Metabolic engineering of Saccharomyces cerevisiae microbial cell factories for succinic acid production

Otero, José Manuel; Olsson, Lisbeth; Nielsen, Jens · 2007 · Technical University of Denmark (DTU) · DOI

Full title: Metabolic engineering of Saccharomyces cerevisiae microbial cell factories for succinic acid production

Authors: Otero, José Manuel; Olsson, Lisbeth; Nielsen, Jens

Year: 2007

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/4ce5b2d2-e323-4bf0-ad98-7411b4920a71

Thesis Determining the Control Circuitry of Redox Metabolism at the Genome-Scale

Federowicz, Stephen; Kim, Donghyuk; Ebrahim, Ali et al. · 2014 · Technical University of Denmark (DTU) · DOI

Full title: Determining the Control Circuitry of Redox Metabolism at the Genome-Scale

Authors: Federowicz, Stephen; Kim, Donghyuk; Ebrahim, Ali; Lerman, Joshua; Nagarajan, Harish; Cho, Byung-kwan; Zengler, Karsten; Palsson, Bernhard; id_orcid 0000-0003-2357-6785

Year: 2014

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/423d44f5-d407-46f7-a3a9-a39f7a28fe85

Thesis Computational Methods to Assess the Production Potential of Bio-Based Chemicals

Campodonico, Miguel A; Sukumara, Sumesh; Feist, Adam M. et al. · 2018 · Technical University of Denmark (DTU) · DOI

Full title: Computational Methods to Assess the Production Potential of Bio-Based Chemicals

Authors: Campodonico, Miguel A; Sukumara, Sumesh; Feist, Adam M.; id_orcid 0000-0002-8630-4800; Herrgård, Markus J.

Year: 2018

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/355b663a-56b1-4457-8cfe-881d75909301

Thesis Enhancing Metabolic Models with Genome-Scale Experimental Data

Jensen, Kristian; Gudmundsson, Steinn; Herrgård, Markus · 2018 · Technical University of Denmark (DTU) · DOI

Full title: Enhancing Metabolic Models with Genome-Scale Experimental Data

Authors: Jensen, Kristian; Gudmundsson, Steinn; Herrgård, Markus

Year: 2018

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/4ae0928a-15e0-49bf-85bf-1d9ca6ab10fc

Thesis Harnessing additional metabolic energy during fermentation processes: will the proton-motive force be with you?

Folch, Pauline L. · 2021 · Wageningen University & Research · DOI

Full title: Harnessing additional metabolic energy during fermentation processes: will the proton-motive force be with you?

Authors: Folch, Pauline L.

Year: 2021

Venue: Wageningen University & Research

DOI: https://research.wur.nl/en/publications/harnessing-additional-metabolic-energy-during-fermentation-proces

Thesis Nice T-R-Y : Metabolic engineering of Escherichia coli for improved bio-based ethyl acetate production

Bohnenkamp, Anna C. · 2021 · Wageningen University & Research · DOI

Full title: Nice T-R-Y : Metabolic engineering of Escherichia coli for improved bio-based ethyl acetate production

Authors: Bohnenkamp, Anna C.

Year: 2021

Venue: Wageningen University & Research

DOI: https://research.wur.nl/en/publications/nice-t-r-y-metabolic-engineering-of-escherichia-coli-for-improved

Thesis Evaluating and deploying genome-scale metabolic models for microbial cell factories

Pham, Nhung · 2021 · Wageningen University & Research · DOI

Full title: Evaluating and deploying genome-scale metabolic models for microbial cell factories

Authors: Pham, Nhung

Year: 2021

Venue: Wageningen University & Research

DOI: https://research.wur.nl/en/publications/evaluating-and-deploying-genome-scale-metabolic-models-for-microb

Thesis Analysis of yeast metabolism using metabolic control analysis under uncertainty

Wang, Liqing; Hatzimanikatis, Vassily · 2007 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: Analysis of yeast metabolism using metabolic control analysis under uncertainty

Authors: Wang, Liqing; Hatzimanikatis, Vassily

Year: 2007

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/238817

Thesis Explorations of interlinked energy and redox metabolism in two industrially applied microorganisms

Sreenivas, Krishnan · 2024 · Lund University (LUP) · DOI

Full title: Explorations of interlinked energy and redox metabolism in two industrially applied microorganisms

Authors: Sreenivas, Krishnan

Year: 2024

Venue: Lund University (LUP)

DOI: https://lup.lub.lu.se/record/22abb568-bd1c-4e61-9c1e-4657de0deb3a

Thesis Metabolic modeling to understand and redesign microbial systems

van Heck, Ruben G.A. · 2017 · Wageningen University & Research · DOI

Full title: Metabolic modeling to understand and redesign microbial systems

Authors: van Heck, Ruben G.A.

Year: 2017

Venue: Wageningen University & Research

DOI: https://research.wur.nl/en/publications/metabolic-modeling-to-understand-and-redesign-microbial-systems

Thesis Microbial lifestyle engineering

Kampers, Linde F.C. · 2020 · Wageningen University & Research · DOI

Full title: Microbial lifestyle engineering

Authors: Kampers, Linde F.C.

Year: 2020

Venue: Wageningen University & Research

DOI: https://research.wur.nl/en/publications/microbial-lifestyle-engineering

Thesis Engineering oleaginous yeasts for a bio-based future

Duman-Özdamar, Zeynep Efsun · 2025 · Wageningen University & Research · DOI

Full title: Engineering oleaginous yeasts for a bio-based future

Authors: Duman-Özdamar, Zeynep Efsun

Year: 2025

Venue: Wageningen University & Research

DOI: https://research.wur.nl/en/publications/engineering-oleaginous-yeasts-for-a-bio-based-future

Thesis Engineering of central carbon metabolism in recombinant Saccharomyces cerevisiae for improved production of biopolymers

Bjurman, Nina · 2016 · Lund University Student Papers · DOI

Full title: Engineering of central carbon metabolism in recombinant Saccharomyces cerevisiae for improved production of biopolymers

Authors: Bjurman, Nina

Year: 2016

Venue: Lund University Student Papers

DOI: http://lup.lub.lu.se/student-papers/record/8891516

Thesis Wisdom of crowds for robust gene network inference

Drton, Mathias (as part of the ‘DREAM5 Consortium’) · 2012 · Technical University of Munich (TUM) · DOI

Full title: Wisdom of crowds for robust gene network inference

Authors: Drton, Mathias (as part of the ‘DREAM5 Consortium’)

Year: 2012

Venue: Technical University of Munich (TUM)

DOI: https://mediatum.ub.tum.de/1520318

Thesis Molecular and Computational Methods for Cellular State Control

Michael, Drew Groves · 2015 · Washington University in St. Louis · DOI

Full title: Molecular and Computational Methods for Cellular State Control

Authors: Michael, Drew Groves

Year: 2015

Venue: Washington University in St. Louis

DOI: https://openscholarship.wustl.edu/art_sci_etds/452

Thesis Application of theoretical methods to increase succinate production in engineered strains

M. A. Valderrama-Gomez; D. Kreitmayer; S. Wolf et al. · 2017 · Technical University of Munich (TUM) · DOI

Full title: Application of theoretical methods to increase succinate production in engineered strains

Authors: M. A. Valderrama-Gomez; D. Kreitmayer; S. Wolf; A. Marin-Sanguino; A. Kremling

Year: 2017

Venue: Technical University of Munich (TUM)

DOI: https://mediatum.ub.tum.de/1353855

Thesis Investigating Non-model Microorganisms for Biomanufacturing via Systems Biology and Machine Learning

Czajka, Jeffrey John · 2021 · Washington University in St. Louis · DOI

Full title: Investigating Non-model Microorganisms for Biomanufacturing via Systems Biology and Machine Learning

Authors: Czajka, Jeffrey John

Year: 2021

Venue: Washington University in St. Louis

DOI: https://openscholarship.wustl.edu/eng_etds/722

Thesis Development of 13C Fingerprint Tool and Its Application for Exploring Carbon and Energy Metabolism in Cyanobacterium Synechocystis sp. PCC 6803

You, Le · 2015 · Washington University in St. Louis · DOI

Full title: Development of 13C Fingerprint Tool and Its Application for Exploring Carbon and Energy Metabolism in Cyanobacterium Synechocystis sp. PCC 6803

Authors: You, Le

Year: 2015

Venue: Washington University in St. Louis

DOI: https://openscholarship.wustl.edu/eng_etds/100

Thesis Application of metabolic modeling and machine learning for investigating microbial systems

Wan, Ni · 2018 · Washington University in St. Louis · DOI

Full title: Application of metabolic modeling and machine learning for investigating microbial systems

Authors: Wan, Ni

Year: 2018

Venue: Washington University in St. Louis

DOI: https://openscholarship.wustl.edu/eng_etds/334

Thesis Characterizing nonmodel microorganisms and reconstructing catabolic pathways for bio-productions

Hollinshead, Whitney · 2016 · Washington University in St. Louis · DOI

Full title: Characterizing nonmodel microorganisms and reconstructing catabolic pathways for bio-productions

Authors: Hollinshead, Whitney

Year: 2016

Venue: Washington University in St. Louis

DOI: https://openscholarship.wustl.edu/eng_etds/200

Thesis Development of Steady-State and Dynamic Flux Models for Broad-Scope Microbial Metabolism Analysis

He, Lian · 2016 · Washington University in St. Louis · DOI

Full title: Development of Steady-State and Dynamic Flux Models for Broad-Scope Microbial Metabolism Analysis

Authors: He, Lian

Year: 2016

Venue: Washington University in St. Louis

DOI: https://openscholarship.wustl.edu/eng_etds/159

Thesis Revelation of Yin-Yang Balance in Microbial Cell Factories by Data Mining, Flux Modeling, and Metabolic Engineering

Wu, Gang · 2016 · Washington University in St. Louis · DOI

Full title: Revelation of Yin-Yang Balance in Microbial Cell Factories by Data Mining, Flux Modeling, and Metabolic Engineering

Authors: Wu, Gang

Year: 2016

Venue: Washington University in St. Louis

DOI: https://openscholarship.wustl.edu/eng_etds/163

Thesis Systems Metabolic Engineering of Microbial Cell Factories for the Synthesis of Value-added Chemicals

Varman, Arul Mozhy · 2013 · Washington University in St. Louis · DOI

Full title: Systems Metabolic Engineering of Microbial Cell Factories for the Synthesis of Value-added Chemicals

Authors: Varman, Arul Mozhy

Year: 2013

Venue: Washington University in St. Louis

DOI: https://openscholarship.wustl.edu/etd/1176

Thesis Systematic Metabolic Engineering of Recombinant Xylose-Utilizing S. cerevisiae: Strategies for Improving Xylose Uptake Rate

Miskovic, Ljubisa; Bart, Dorothee; Soh, Keng Cher et al. · 2012 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: Systematic Metabolic Engineering of Recombinant Xylose-Utilizing S. cerevisiae: Strategies for Improving Xylose Uptake Rate

Authors: Miskovic, Ljubisa; Bart, Dorothee; Soh, Keng Cher; Alff-Tuomala, Susanne; Salusjarvi, Laura; Pitkanen, Juha-Pekka; Ruohonen, Laura; Pentilla, Merja; Hatzimanikatis, Vassily

Year: 2012

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/86230

Thesis Constraint-based modelling of metabolic networks incorporating resource allocation

Zeng, H · 2020 · University of Oxford - ORA · DOI

Full title: Constraint-based modelling of metabolic networks incorporating resource allocation

Authors: Zeng, H

Year: 2020

Venue: University of Oxford - ORA

DOI: oai:ora.ox.ac.uk:uuid:805d2cdd-17d8-4863-afe8-701fa66a0947

Thesis Decoding Complexity in Metabolic Networks using Integrated Mechanistic and Machine Learning Approaches

Oyetunde, Tolutola Timothy · 2018 · Washington University in St. Louis · DOI

Full title: Decoding Complexity in Metabolic Networks using Integrated Mechanistic and Machine Learning Approaches

Authors: Oyetunde, Tolutola Timothy

Year: 2018

Venue: Washington University in St. Louis

DOI: https://openscholarship.wustl.edu/eng_etds/400

Thesis ENGINEERING ADVANCED GENETIC TOOLS FOR ENHANCING NATURAL PRODUCT BIOSYNTHESIS

Zou, Yusong · 2025 · University of Georgia - UGA Open Scholar · DOI

Full title: ENGINEERING ADVANCED GENETIC TOOLS FOR ENHANCING NATURAL PRODUCT BIOSYNTHESIS

Authors: Zou, Yusong

Year: 2025

Venue: University of Georgia - UGA Open Scholar

DOI: https://openscholar.uga.edu/record/27075/files/Zou_uga_0077E_16230.pdf

Thesis Development and Application of Fluxomics Tools for Analyzing Metabolisms in Non-Model Microorganisms

Feng, Xueyang · 2012 · Washington University in St. Louis · DOI

Full title: Development and Application of Fluxomics Tools for Analyzing Metabolisms in Non-Model Microorganisms

Authors: Feng, Xueyang

Year: 2012

Venue: Washington University in St. Louis

DOI: https://openscholarship.wustl.edu/etd/574

Thesis Investigating Cyanobacteria Metabolism and Channeling-based Regulations via Isotopic Nonstationary Labeling and Metabolomic Analyses

Abernathy, Mary Helen · 2018 · Washington University in St. Louis · DOI

Full title: Investigating Cyanobacteria Metabolism and Channeling-based Regulations via Isotopic Nonstationary Labeling and Metabolomic Analyses

Authors: Abernathy, Mary Helen

Year: 2018

Venue: Washington University in St. Louis

DOI: https://openscholarship.wustl.edu/eng_etds/396

Thesis Modelling rhizobial metabolism in rhizobium-legume symbioses

Schulte, C · 2021 · University of Oxford - ORA · DOI

Full title: Modelling rhizobial metabolism in rhizobium-legume symbioses

Authors: Schulte, C

Year: 2021

Venue: University of Oxford - ORA

DOI: oai:ora.ox.ac.uk:uuid:49aecfb4-5f17-4e93-a5a4-559608cbfaaf

Thesis Analysis of genetic variation and potential applications in genome-scale metabolic modeling

Cardoso, Joao; Andersen, Mikael Rørdam; id_orcid 0000-0003-4794-6808 et al. · 2015 · Technical University of Denmark (DTU) · DOI

Full title: Analysis of genetic variation and potential applications in genome-scale metabolic modeling

Authors: Cardoso, Joao; Andersen, Mikael Rørdam; id_orcid 0000-0003-4794-6808; Herrgard, Markus; Sonnenschein, Nikolaus; id_orcid 0000-0002-7581-4936

Year: 2015

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/025d0c23-79e4-47f2-a308-0e27609c34fc

Thesis Multi-scale modeling for prediction of distributed cellular properties in response to substrate spatial gradients in a continuously run microreactor

Lencastre Fernandes, Rita; Krühne, Ulrich; id_orcid 0000-0001-7774-7442 et al. · 2012 · Technical University of Denmark (DTU) · DOI

Full title: Multi-scale modeling for prediction of distributed cellular properties in response to substrate spatial gradients in a continuously run microreactor

Authors: Lencastre Fernandes, Rita; Krühne, Ulrich; id_orcid 0000-0001-7774-7442; Nopens, Ingmar; Jensen, Anker Degn; id_orcid 0000-0002-7341-4859; Gernaey, Krist; id_orcid 0000-0002-0364-1773

Year: 2012

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/0cee1ed5-59e8-438f-ae43-806bc60af832

Thesis Metabolic engineering of Clostridium saccharoperbutylacetonicum for improved solvent production

Bones, A · 2022 · University of Oxford - ORA · DOI

Full title: Metabolic engineering of Clostridium saccharoperbutylacetonicum for improved solvent production

Authors: Bones, A

Year: 2022

Venue: University of Oxford - ORA

DOI: oai:ora.ox.ac.uk:uuid:ead19c15-09eb-48bc-bf1f-9eeb0132a5cf

Thesis Multi-omics Quantification of Species Variation of Escherichia coli Links Molecular Features with Strain Phenotypes

Monk, Jonathan M; Koza, Anna; Campodonico, Miguel A et al. · 2016 · Technical University of Denmark (DTU) · DOI

Full title: Multi-omics Quantification of Species Variation of Escherichia coli Links Molecular Features with Strain Phenotypes

Year: 2016

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/00cda276-05c8-41fd-aa02-cabdeb876216

Thesis Application of a genome-scale model in tandem with enzyme assays for identification of metabolic signatures of high and low CHO cell producers

Calmels, Cyrielle; Arnoult, Solène; Ben Yahia, Bassem et al. · 2019 · Technical University of Denmark (DTU) · DOI

Full title: Application of a genome-scale model in tandem with enzyme assays for identification of metabolic signatures of high and low CHO cell producers

Authors: Calmels, Cyrielle; Arnoult, Solène; Ben Yahia, Bassem; Malphettes, Laetitia; Andersen, Mikael Rørdam; id_orcid 0000-0003-4794-6808

Year: 2019

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/07c1b78f-8e1b-4264-8b5a-d74f261ebab9

Thesis Laboratory evolution reveals regulatory and metabolic trade-offs of glycerol utilization in Saccharomyces cerevisiae

Strucko, Tomas; id_orcid 0000-0003-1947-8138; Zirngibl, Katharina et al. · 2018 · Technical University of Denmark (DTU) · DOI

Full title: Laboratory evolution reveals regulatory and metabolic trade-offs of glycerol utilization in Saccharomyces cerevisiae

Year: 2018

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/0aa491a2-33ed-47fe-9519-f8675852207e

Thesis Genome scale metabolic models of plant tissues

Cheung, C · 2013 · University of Oxford - ORA · DOI

Full title: Genome scale metabolic models of plant tissues

Authors: Cheung, C

Year: 2013

Venue: University of Oxford - ORA

DOI: oai:ora.ox.ac.uk:uuid:9a2af288-848c-48fc-94e7-343bbc732645

Thesis Reconstruction and analysis of a Kluyveromyces marxianus genome-scale metabolic model

Marcišauskas, Simonas; Ji, Boyang; Nielsen, Jens · 2019 · Technical University of Denmark (DTU) · DOI

Full title: Reconstruction and analysis of a Kluyveromyces marxianus genome-scale metabolic model

Authors: Marcišauskas, Simonas; Ji, Boyang; Nielsen, Jens

Year: 2019

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/193e0362-799e-434c-853e-01e450c42b2f

Thesis Escherichia coli B2 strains prevalent in inflammatory bowel disease patients have distinct metabolic capabilities that enable colonization of intestinal mucosa

Fang, Xin; Monk, Jonathan M.; Mih, Nathan et al. · 2018 · Technical University of Denmark (DTU) · DOI

Full title: Escherichia coli B2 strains prevalent in inflammatory bowel disease patients have distinct metabolic capabilities that enable colonization of intestinal mucosa

Authors: Fang, Xin; Monk, Jonathan M.; Mih, Nathan; Du, Bin; Sastry, Anand V.; Kavvas, Erol; Seif, Yara; Smarr, Larry; Palsson, Bernhard O.; id_orcid 0000-0003-2357-6785

Year: 2018

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/175a933b-16a0-4622-a676-cfde406c23b8

Thesis Systems metabolic engineering

Hesselberg-Thomsen, Viktor; id_orcid 0000-0001-6929-3671 · 2024 · Technical University of Denmark (DTU) · DOI

Full title: Systems metabolic engineering

Authors: Hesselberg-Thomsen, Viktor; id_orcid 0000-0001-6929-3671

Year: 2024

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/18523551-e95d-4dca-8278-5501b8e2ec1d

Thesis Mathematical modeling of proteome constraints within metabolism

Chen, Yu; Nielsen, Jens · 2021 · Technical University of Denmark (DTU) · DOI

Full title: Mathematical modeling of proteome constraints within metabolism

Authors: Chen, Yu; Nielsen, Jens

Year: 2021

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/0c2d4597-c72a-443a-9195-bfd78e7ae259

Thesis Rewiring regulatory networks in Escherichia coli to improve productionof Human Milk Oligosaccharides

Labunskaité, Rugilé; id_orcid 0009-0007-8147-9023 · 2025 · Technical University of Denmark (DTU) · DOI

Full title: Rewiring regulatory networks in Escherichia coli to improve productionof Human Milk Oligosaccharides

Authors: Labunskaité, Rugilé; id_orcid 0009-0007-8147-9023

Year: 2025

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/1d0c2abd-7c3d-4569-9401-f4201d21c190

Thesis Simulating Serial-Target Antibacterial Drug Synergies Using Flux Balance Analysis

Krueger, Andrew S.; Munck, Christian; Dantas, Gautam et al. · 2016 · Technical University of Denmark (DTU) · DOI

Full title: Simulating Serial-Target Antibacterial Drug Synergies Using Flux Balance Analysis

Authors: Krueger, Andrew S.; Munck, Christian; Dantas, Gautam; Church, George M.; Galagan, James; Lehár, Joseph; Sommer, Morten Otto Alexander; id_orcid 0000-0003-4005-5674

Year: 2016

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/12aaecb6-31d8-4610-b73f-4fe24c8bade9

Thesis Model-assisted CRISPRi/a library screening reveals central carbon metabolic targets for enhanced recombinant protein production in yeast

Chen, Xin; Li, Feiran; Li, Xiaowei et al. · 2025 · Technical University of Denmark (DTU) · DOI

Full title: Model-assisted CRISPRi/a library screening reveals central carbon metabolic targets for enhanced recombinant protein production in yeast

Authors: Chen, Xin; Li, Feiran; Li, Xiaowei; Otto, Maximilian; Chen, Yu; Siewers, Verena

Year: 2025

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/1f4bb513-1a17-4a08-99c2-a87746baf059

Thesis Enhancing Saccharomyces cerevisiae Taxane Biosynthesis and Overcoming Nutritional Stress-Induced Pseudohyphal Growth

Walls, Laura Ellen; Martinez, José L; id_orcid 0000-0002-4490-8534 et al. · 2022 · Technical University of Denmark (DTU) · DOI

Full title: Enhancing Saccharomyces cerevisiae Taxane Biosynthesis and Overcoming Nutritional Stress-Induced Pseudohyphal Growth

Authors: Walls, Laura Ellen; Martinez, José L; id_orcid 0000-0002-4490-8534; Rios-Solis, Leonardo

Year: 2022

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/1fe5f10e-3e62-4344-8fce-daaef23aba9a

Thesis Metabollic Engineering of Saccharomyces Cereviae a,omi acid metabolism for production of products of industrial interest

Chen, Xiao · 2011 · Technical University of Denmark (DTU) · DOI

Full title: Metabollic Engineering of Saccharomyces Cereviae a,omi acid metabolism for production of products of industrial interest

Authors: Chen, Xiao

Year: 2011

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/2131b4b8-7ae6-4e96-bb46-5a0beccef4db

Thesis Model-driven experimental design workflow expands understanding of regulatory role of Nac in Escherichia coli

Park, Joon Young; Lee, Sang-Mok; Ebrahim, Ali et al. · 2023 · Technical University of Denmark (DTU) · DOI

Full title: Model-driven experimental design workflow expands understanding of regulatory role of Nac in Escherichia coli

Year: 2023

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/15aea79c-c198-4999-abd0-5f4b82f1c715

Thesis Flux-Enabled Exploration of the Role of Sip1 in galactose yeast metabolism

Shymansky, Christopher M.; Wang, George; Baidoo, Edward E. K. et al. · 2017 · Technical University of Denmark (DTU) · DOI

Full title: Flux-Enabled Exploration of the Role of Sip1 in galactose yeast metabolism

Authors: Shymansky, Christopher M.; Wang, George; Baidoo, Edward E. K.; Gin, Jennifer; Apel, Amanda Reider; Mukhopadhyay, Aindrila; Martin, Hector Garcia; Keasling, Jay

Year: 2017

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/1bf17655-c24f-48fa-b6cf-7748c1b70623

Thesis Linking Genotype and Phenotype of Saccharomyces cerevisiae Strains Reveals Metabolic Engineering Targets and Leads to Triterpene Hyper-Producers

Madsen, Karina Marie; Udatha, Gupta D. B. R. K.; Semba, Saori et al. · 2011 · Technical University of Denmark (DTU) · DOI

Full title: Linking Genotype and Phenotype of Saccharomyces cerevisiae Strains Reveals Metabolic Engineering Targets and Leads to Triterpene Hyper-Producers

Authors: Madsen, Karina Marie; Udatha, Gupta D. B. R. K.; Semba, Saori; Otero, Jose M.; Koetter, Peter; Nielsen, Jens; Ebizuka, Yutaka; Kushiro, Tetsuo; Panagiotou, Gianni

Year: 2011

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/2578f46c-6ae7-4fd2-9c63-2e996ab0d253

Thesis Reconstruction and Quality Control of a Genome-Scale Metabolic Model for Methylococcus capsulatus

Lieven, Christian · 2018 · Technical University of Denmark (DTU) · DOI

Full title: Reconstruction and Quality Control of a Genome-Scale Metabolic Model for Methylococcus capsulatus

Authors: Lieven, Christian

Year: 2018

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/1c66d29b-56f9-4d49-a60e-33a3a88e11e8

Thesis Yeast optimizes metal utilization based on metabolic network and enzyme kinetics

Chen, Yu; Li, Feiran; Mao, Jiwei et al. · 2021 · Technical University of Denmark (DTU) · DOI

Full title: Yeast optimizes metal utilization based on metabolic network and enzyme kinetics

Authors: Chen, Yu; Li, Feiran; Mao, Jiwei; Chen, Yun; Nielsen, Jens

Year: 2021

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/26097f97-3cd4-43e3-9a84-ad5124b70e08

Thesis Scheffersomyces stipitis: a comparative systems biology study with the Crabtree positive yeast Saccharomyces cerevisiae

Papini, Marta; Nookaew, Intawat; Uhlén, Mathias et al. · 2012 · Technical University of Denmark (DTU) · DOI

Full title: Scheffersomyces stipitis: a comparative systems biology study with the Crabtree positive yeast Saccharomyces cerevisiae

Authors: Papini, Marta; Nookaew, Intawat; Uhlén, Mathias; Nielsen, Jens

Year: 2012

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/29988970-e965-4858-969b-fc92d34c9718

Thesis Optimization of the IPP-bypass mevalonate pathway and fed-batch fermentation for the production of isoprenol in Escherichia coli

Kang, Aram; Mendez-Perez, Daniel; Goh, Ee Been et al. · 2019 · Technical University of Denmark (DTU) · DOI

Full title: Optimization of the IPP-bypass mevalonate pathway and fed-batch fermentation for the production of isoprenol in Escherichia coli

Authors: Kang, Aram; Mendez-Perez, Daniel; Goh, Ee Been; Baidoo, Edward E.K.; Benites, Veronica T.; Beller, Harry R.; Keasling, Jay D.; Adams, Paul D.; Mukhopadhyay, Aindrila; Lee, Taek Soon

Year: 2019

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/304d63cb-a7ca-4bb3-a7dd-b0014f68e46e

Thesis Improved production of Taxol ® precursors in S. cerevisiae using combinatorial in silico design and metabolic engineering

Malcı, Koray; Santibáñez, Rodrigo; Jonguitud-Borrego, Nestor et al. · 2023 · Technical University of Denmark (DTU) · DOI

Full title: Improved production of Taxol ® precursors in S. cerevisiae using combinatorial in silico design and metabolic engineering

Authors: Malcı, Koray; Santibáñez, Rodrigo; Jonguitud-Borrego, Nestor; Santoyo-Garcia, Jorge H.; Kerkhoven, Eduard J.; Rios-Solis, Leonardo

Year: 2023

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/2f11e723-d064-4b2b-8f99-934b2d2b4964

Thesis BOFdat: Generating biomass objective functions for genome-scale metabolic models from experimental data

Lachance, Jean Christophe; Lloyd, Colton J.; Monk, Jonathan M. et al. · 2019 · Technical University of Denmark (DTU) · DOI

Full title: BOFdat: Generating biomass objective functions for genome-scale metabolic models from experimental data

Year: 2019

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/231ab331-0114-4d98-86f5-f29b3cd5ed46

Thesis Rewiring carbon metabolism in yeast for high level production of aromatic chemicals

Liu, Quanli; Yu, Tao; Li, Xiaowei et al. · 2019 · Technical University of Denmark (DTU) · DOI

Full title: Rewiring carbon metabolism in yeast for high level production of aromatic chemicals

Authors: Liu, Quanli; Yu, Tao; Li, Xiaowei; Chen, Yu; Campbell, Kate; Nielsen, Jens; Chen, Yun

Year: 2019

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/2a5826c3-a05b-4089-8592-5c2f6a573dd3

Thesis A Consensus Genome-scale Reconstruction of Chinese Hamster Ovary Cell Metabolism

Hefzi, Hooman; Ang, Kok Siong; Hanscho, Michael et al. · 2016 · Technical University of Denmark (DTU) · DOI

Full title: A Consensus Genome-scale Reconstruction of Chinese Hamster Ovary Cell Metabolism

Year: 2016

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/2f8bb3cd-eb0c-46f7-b39b-3791d7c86d1d

Thesis Machine learning-guided cell factory optimization

Jensen, Michael Krogh; id_orcid 0000-0001-7574-4707 · 2023 · Technical University of Denmark (DTU) · DOI

Full title: Machine learning-guided cell factory optimization

Authors: Jensen, Michael Krogh; id_orcid 0000-0001-7574-4707

Year: 2023

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/2cf1d067-ce54-4ebe-9df2-9aed79c7f6b4

Thesis Maximizing microbial bioproduction from sustainable carbon sources using iterative systems engineering

Eng, Thomas; Banerjee, Deepanwita; Menasalvas, Javier et al. · 2023 · Technical University of Denmark (DTU) · DOI

Full title: Maximizing microbial bioproduction from sustainable carbon sources using iterative systems engineering

Year: 2023

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/2e007d49-0095-4677-9f1c-18bf73d9ad98

Thesis Evolutionary programming as a platform for in silico metabolic engineering

Patil, Kiran Raosaheb; Rocha, Isabel; Förster, Jochen et al. · 2005 · Technical University of Denmark (DTU) · DOI

Full title: Evolutionary programming as a platform for in silico metabolic engineering

Authors: Patil, Kiran Raosaheb; Rocha, Isabel; Förster, Jochen; id_orcid 0000-0003-4045-7905; Nielsen, Jens

Year: 2005

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/2cb39a53-3203-4ab0-ac90-3aadec619dbe

Thesis Modelling Enzyme Allocation and Metabolic Adaptation in Cyanobacteria

Firoozabadi, Hossein · 2024 · Technical University of Denmark (DTU) · DOI

Full title: Modelling Enzyme Allocation and Metabolic Adaptation in Cyanobacteria

Authors: Firoozabadi, Hossein

Year: 2024

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/2fb64401-0002-4f64-8992-c6bbacbc0e17

Thesis Engineering Saccharomyces cerevisiae cells for production of fatty acid-derived biofuels and chemicals

Hu, Yating; Zhu, Zhiwei; Nielsen, Jens et al. · 2019 · Technical University of Denmark (DTU) · DOI

Full title: Engineering Saccharomyces cerevisiae cells for production of fatty acid-derived biofuels and chemicals

Authors: Hu, Yating; Zhu, Zhiwei; Nielsen, Jens; Siewers, Verena

Year: 2019

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/4307d50e-cd16-47d3-9b4f-c849c89aad59

Thesis Reconstruction and Validation of a Genome-Scale Metabolic Model of Streptococcus oralis (iCJ415), a Human Commensal and Opportunistic Pathogen

Jensen, Christian S.; Norsigian, Charles J.; Fang, Xin et al. · 2020 · Technical University of Denmark (DTU) · DOI

Full title: Reconstruction and Validation of a Genome-Scale Metabolic Model of Streptococcus oralis (iCJ415), a Human Commensal and Opportunistic Pathogen

Authors: Jensen, Christian S.; Norsigian, Charles J.; Fang, Xin; Nielsen, Xiaohui C.; Christensen, Jens Jørgen; Palsson, Bernhard O.; id_orcid 0000-0003-2357-6785; Monk, Jonathan M.

Year: 2020

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/3d0a3070-dfa2-41f1-b3e5-eb835416ff38

Thesis Modelling of microbial interactions in anaerobic digestion:from black to glass box

Basile, Arianna; Zampieri, Guido; Kovalovszki, Adam et al. · 2023 · Technical University of Denmark (DTU) · DOI

Full title: Modelling of microbial interactions in anaerobic digestion:from black to glass box

Authors: Basile, Arianna; Zampieri, Guido; Kovalovszki, Adam; id_orcid 0000-0001-7509-4580; Karkaria, Behzad; Treu, Laura; Patil, Kiran Raosaheb; Campanaro, Stefano

Year: 2023

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/3f0f2bb3-1d09-4a2b-bed8-bc87f1096969

Thesis Metabolic growth-coupling strategies for in vivo enzyme selection systems

Alter, Tobias B.; Pieters, Pascal A.; Lloyd, Colton J. et al. · 2025 · Technical University of Denmark (DTU) · DOI

Full title: Metabolic growth-coupling strategies for in vivo enzyme selection systems

Year: 2025

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/3ea363d8-0894-4535-8fa1-d0f176835782

Thesis Determining the Control Circuitry of Redox Metabolism at the Genome-Scale

Federowicz, Stephen; Kim, Donghyuk; Ebrahim, Ali et al. · 2014 · Technical University of Denmark (DTU) · DOI

Full title: Determining the Control Circuitry of Redox Metabolism at the Genome-Scale

Authors: Federowicz, Stephen; Kim, Donghyuk; Ebrahim, Ali; Lerman, Joshua; Nagarajan, Harish; Cho, Byung-kwan; Zengler, Karsten; Palsson, Bernhard; id_orcid 0000-0003-2357-6785

Year: 2014

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/423d44f5-d407-46f7-a3a9-a39f7a28fe85

Thesis Bacterial fitness landscapes stratify based on proteome allocation associated with discrete aero-types

Chen, Ke; Anand, Amitesh; Olson, Connor et al. · 2021 · Technical University of Denmark (DTU) · DOI

Full title: Bacterial fitness landscapes stratify based on proteome allocation associated with discrete aero-types

Authors: Chen, Ke; Anand, Amitesh; Olson, Connor; Sandberg, Troy E.; Gao, Ye; Mih, Nathan; Palsson, Bernhard O.; id_orcid 0000-0003-2357-6785

Year: 2021

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/3f263cdd-32d7-4df3-94b3-ed7e2b467de7

Thesis Enzyme-constrained metabolic model and in silico metabolic engineering of Clostridium ljungdahlii for the development of sustainable production processes

Caivano, Antonio; id_orcid 0000-0001-6296-5383; van Winden, Wouter et al. · 2023 · Technical University of Denmark (DTU) · DOI

Full title: Enzyme-constrained metabolic model and in silico metabolic engineering of Clostridium ljungdahlii for the development of sustainable production processes

Authors: Caivano, Antonio; id_orcid 0000-0001-6296-5383; van Winden, Wouter; Dragone, Giuliano; id_orcid 0000-0002-5555-8381; Mussatto, Solange I; id_orcid 0000-0002-7182-6198

Year: 2023

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/4cb1ff43-f4f3-4085-b209-6c57bcb0480d

Thesis High-quality genome-scale metabolic network reconstruction of probiotic bacterium Escherichia coli Nissle 1917

van ‘t Hof, Max; Mohite, Omkar S.; id_orcid 0000-0002-3240-1656 et al. · 2022 · Technical University of Denmark (DTU) · DOI

Full title: High-quality genome-scale metabolic network reconstruction of probiotic bacterium Escherichia coli Nissle 1917

Year: 2022

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/3d4c5d32-3a6f-46cb-9dae-a11a5a18e8dd

Thesis Development and application of computer-aided design methods for cell factory optimization

Cardoso, Joao · 2017 · Technical University of Denmark (DTU) · DOI

Full title: Development and application of computer-aided design methods for cell factory optimization

Authors: Cardoso, Joao

Year: 2017

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/436ef08b-c0d7-43cf-a024-8c78597ed00f

Thesis Improving the phenotype predictions of a yeast genome-scale metabolic model by incorporating enzymatic constraints

Sanchez, Benjamin J.; Zhang, Xi-Cheng; Nilsson, Avlant et al. · 2017 · Technical University of Denmark (DTU) · DOI

Full title: Improving the phenotype predictions of a yeast genome-scale metabolic model by incorporating enzymatic constraints

Authors: Sanchez, Benjamin J.; Zhang, Xi-Cheng; Nilsson, Avlant; Lahtvee, Petri-Jaan; Kerkhoven, Eduard J.; Nielsen, Jens

Year: 2017

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/58026a68-5f76-4b48-979d-3068258c577c

Thesis Linking genetic, metabolic, and phenotypic diversity among Saccharomyces cerevisiae strains using multi-omics associations

Kang, Kang; Bergdahl, Basti; Machado, Daniel et al. · 2019 · Technical University of Denmark (DTU) · DOI

Full title: Linking genetic, metabolic, and phenotypic diversity among Saccharomyces cerevisiae strains using multi-omics associations

Authors: Kang, Kang; Bergdahl, Basti; Machado, Daniel; Dato, Laura; Han, Ting-Li; Li, Jun; Villas-Boas, Silas; Herrgård, Markus J; Förster, Jochen; id_orcid 0000-0003-4045-7905; Panagiotou, Gianni

Year: 2019

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/4a3146d4-93ff-4761-ab2a-0e10f0522e0b

Thesis Early-stage economic and environmental impact assessment for optimized bioprocess development:Monoterpenoid indole alkaloids

Etit, Deniz; Ögmundarson, Ólafur; Zhang, Jie et al. · 2024 · Technical University of Denmark (DTU) · DOI

Full title: Early-stage economic and environmental impact assessment for optimized bioprocess development:Monoterpenoid indole alkaloids

Authors: Etit, Deniz; Ögmundarson, Ólafur; Zhang, Jie; Krogh Jensen, Michael; id_orcid 0000-0001-7574-4707; Sukumara, Sumesh

Year: 2024

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/404a3234-6af0-4e8e-91c6-898c12a05758

Thesis Reconstructing organisms in silico: genome-scale models and their emerging applications

Fang, Xin; Lloyd, Colton J.; Palsson, Bernhard O. et al. · 2020 · Technical University of Denmark (DTU) · DOI

Full title: Reconstructing organisms in silico: genome-scale models and their emerging applications

Authors: Fang, Xin; Lloyd, Colton J.; Palsson, Bernhard O.; id_orcid 0000-0003-2357-6785

Year: 2020

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/575aa54d-59ad-4b61-a171-369c7dbbdd9c

Thesis 13 C Metabolic Flux Analysis for Systematic Metabolic Engineering of S. cerevisiae for Overproduction of Fatty Acids

Ghosh, Amit; Ando, David; Gin, Jennifer et al. · 2016 · Technical University of Denmark (DTU) · DOI

Full title: 13 C Metabolic Flux Analysis for Systematic Metabolic Engineering of S. cerevisiae for Overproduction of Fatty Acids

Authors: Ghosh, Amit; Ando, David; Gin, Jennifer; Runguphan, Weerawat; Denby, Charles; Wang, George; Baidoo, Edward E. K.; Shymansky, Chris; Keasling, Jay; García Martín, Héctor

Year: 2016

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/4b2157b3-0f83-4553-bae4-d6f4dc3300ca

Thesis Co-evolution of strain design methods based on flux balance and elementary mode analysis

Machado, Daniel; Herrgard, Markus · 2015 · Technical University of Denmark (DTU) · DOI

Full title: Co-evolution of strain design methods based on flux balance and elementary mode analysis

Authors: Machado, Daniel; Herrgard, Markus

Year: 2015

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/2b639a7f-da26-4749-aebd-458a55145056

Thesis Engineering of Saccharomyces cerevisiae for enhanced metabolic robustness and L-lactic acid production from lignocellulosic biomass

Choi, Bohyun; Tafur Rangel, Albert; Kerkhoven, Eduard J. et al. · 2024 · Technical University of Denmark (DTU) · DOI

Full title: Engineering of Saccharomyces cerevisiae for enhanced metabolic robustness and L-lactic acid production from lignocellulosic biomass

Authors: Choi, Bohyun; Tafur Rangel, Albert; Kerkhoven, Eduard J.; Nygård, Yvonne

Year: 2024

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/52700d2e-e6df-40b2-99af-c91e5b38ae23

Thesis The topology of genome-scale metabolic reconstructions unravels independent modules and high network flexibility

Martínez, Verónica S.; Saa, Pedro A.; Jooste, Jason et al. · 2022 · Technical University of Denmark (DTU) · DOI

Full title: The topology of genome-scale metabolic reconstructions unravels independent modules and high network flexibility

Authors: Martínez, Verónica S.; Saa, Pedro A.; Jooste, Jason; Tiwari, Kanupriya; Quek, Lake Ee; Nielsen, Lars K.

Year: 2022

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/596e366c-6a99-477e-bcd6-e0168d6325b4

Thesis Cell culture process dynamics and metabolic flux distributions using hybrid models

Kailasanathan, Rajiv; Sivaram, Abhishek; Mansouri, Seyed Soheil et al. · 2025 · Technical University of Denmark (DTU) · DOI

Full title: Cell culture process dynamics and metabolic flux distributions using hybrid models

Authors: Kailasanathan, Rajiv; Sivaram, Abhishek; Mansouri, Seyed Soheil; id_orcid 0000-0002-0924-4947

Year: 2025

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/572e7d61-3351-4ced-b2f5-6b9e4ceab22f

Thesis Systematic Evaluation of Methods for Integration of Transcriptomic Data into Constraint-Based Models of Metabolism.

Machado, Daniel; Herrgard, Markus · 2014 · Technical University of Denmark (DTU) · DOI

Full title: Systematic Evaluation of Methods for Integration of Transcriptomic Data into Constraint-Based Models of Metabolism.

Authors: Machado, Daniel; Herrgard, Markus

Year: 2014

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/52005488-21bb-4253-9872-6d37eda149f7

Thesis Energy metabolism controls phenotypes by protein efficiency and allocation

Chen, Yu; Nielsen, Jens · 2019 · Technical University of Denmark (DTU) · DOI

Full title: Energy metabolism controls phenotypes by protein efficiency and allocation

Authors: Chen, Yu; Nielsen, Jens

Year: 2019

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/55a57a57-1730-47f1-b7cd-2ee07d03ee1a

Thesis Application of a curated genome-scale metabolic model of CHO DG44 to an industrial fed-batch process

Calmels, Cyrielle; McCann, Andréa; Malphettes, Laetitia et al. · 2018 · Technical University of Denmark (DTU) · DOI

Full title: Application of a curated genome-scale metabolic model of CHO DG44 to an industrial fed-batch process

Authors: Calmels, Cyrielle; McCann, Andréa; Malphettes, Laetitia; Andersen, Mikael Rørdam; id_orcid 0000-0003-4794-6808

Year: 2018

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/59c3f8ac-571d-4312-969f-4d6d5689e961

Thesis Omics data for sampling thermodynamically feasible kinetic models

de Leeuw, Marina; Matos, Marta R.A.; Nielsen, Lars Keld · 2023 · Technical University of Denmark (DTU) · DOI

Full title: Omics data for sampling thermodynamically feasible kinetic models

Authors: de Leeuw, Marina; Matos, Marta R.A.; Nielsen, Lars Keld

Year: 2023

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/5985722c-e25c-4611-ab4e-fc5b5c8fdf8c

Thesis pyTFA and matTFA: a Python package and a Matlab toolbox for Thermodynamics-based Flux Analysis

Salvy, Pierre; Fengos, Georgios; Ataman, Meric et al. · 2018 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: pyTFA and matTFA: a Python package and a Matlab toolbox for Thermodynamics-based Flux Analysis

Authors: Salvy, Pierre; Fengos, Georgios; Ataman, Meric; Pathier, Thomas; Soh, Keng C; Hatzimanikatis, Vassily

Year: 2018

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/147677

Thesis ETFL: A Formulation of ME-Models Accounting for Expression and Thermodynamics in Constraint-Based Models

Salvy, Pierre Guy Rémy · 2018 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: ETFL: A Formulation of ME-Models Accounting for Expression and Thermodynamics in Constraint-Based Models

Authors: Salvy, Pierre Guy Rémy

Year: 2018

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/149618

Thesis Mapping the diverse phenotypic states of yeast lipid metabolism to enzymes using mechanistic kinetic models

Tsouka, Sofia · 2018 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: Mapping the diverse phenotypic states of yeast lipid metabolism to enzymes using mechanistic kinetic models

Authors: Tsouka, Sofia

Year: 2018

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/149683

Thesis Generative machine learning produces kinetic models that accurately characterize intracellular metabolic states

Choudhury, Subham; Narayanan, Bharath; Moret, Michael et al. · 2023 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: Generative machine learning produces kinetic models that accurately characterize intracellular metabolic states

Authors: Choudhury, Subham; Narayanan, Bharath; Moret, Michael; Hatzimanikatis, Vassily; Miskovic, Ljubisa

Year: 2023

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/198254

Thesis Computational Analysis of Xylose-Utilizing Saccharomyces cerevisiae

Miskovic, Ljubisa; Hatzimanikatis, Vassily · 2010 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: Computational Analysis of Xylose-Utilizing Saccharomyces cerevisiae

Authors: Miskovic, Ljubisa; Hatzimanikatis, Vassily

Year: 2010

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/51528

Thesis A workflow for annotating the knowledge gaps in metabolic reconstructions using known and hypothetical reactions

Vayena, Evangelia; Chiappino-Pepe, Anush; MohammadiPeyhani, Homa et al. · 2023 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: A workflow for annotating the knowledge gaps in metabolic reconstructions using known and hypothetical reactions

Authors: Vayena, Evangelia; Chiappino-Pepe, Anush; MohammadiPeyhani, Homa; Francioli, Yannick; Hadadi, Noushin; Ataman, Meric; Hafner, Jasmin; Pavlou, Stavros; Hatzimanikatis, Vassily

Year: 2023

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/198489

Thesis Thermodynamics-Based Metabolic Flux Analysis

Henry, Christopher S.; Broadbelt, Linda J.; Hatzimanikatis, Vassily · 2007 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: Thermodynamics-Based Metabolic Flux Analysis

Authors: Henry, Christopher S.; Broadbelt, Linda J.; Hatzimanikatis, Vassily

Year: 2007

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/10291

Thesis Quantitative Analysis of Metabolic Networks Through the Explicit Consideration of Kinetic Mechanisms

Miskovic, Ljubisa; Hatzimanikatis, Vassily · 2010 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: Quantitative Analysis of Metabolic Networks Through the Explicit Consideration of Kinetic Mechanisms

Authors: Miskovic, Ljubisa; Hatzimanikatis, Vassily

Year: 2010

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/51526

Thesis Group contribution method for thermodynamic analysis of complex metabolic networks

Jankowski, Matthew D.; Henry, Christopher S.; Broadbelt, Linda J. et al. · 2010 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: Group contribution method for thermodynamic analysis of complex metabolic networks

Authors: Jankowski, Matthew D.; Henry, Christopher S.; Broadbelt, Linda J.; Hatzimanikatis, Vassily

Year: 2010

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/61196

Thesis Kinetic modeling of the central carbon metabolism of Escherichia Coli

Miskovic, Ljubisa; Hatzimanikatis, Vassily · 2011 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: Kinetic modeling of the central carbon metabolism of Escherichia Coli

Authors: Miskovic, Ljubisa; Hatzimanikatis, Vassily

Year: 2011

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/64770

Thesis Improving Ethanol Production of Xylose-Utilizing Saccharomyces cerevisiae

Miskovic, Ljubisa; Hatzimanikatis, Vassily · 2011 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: Improving Ethanol Production of Xylose-Utilizing Saccharomyces cerevisiae

Authors: Miskovic, Ljubisa; Hatzimanikatis, Vassily

Year: 2011

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/64771

Thesis Modeling and analysis of ethanol production in Escherichia coli

Mettraux, Yannick · 2010 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: Modeling and analysis of ethanol production in Escherichia coli

Authors: Mettraux, Yannick

Year: 2010

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/58220

Thesis Large-scale dynamic models of metabolic networks

Chakrabarti, Anirikh; Soh, Keng Cher; Miskovic, Ljubisa et al. · 2012 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: Large-scale dynamic models of metabolic networks

Authors: Chakrabarti, Anirikh; Soh, Keng Cher; Miskovic, Ljubisa; Hatzimanikatis, Vassily

Year: 2012

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/86231

Thesis Metabolic control analysis of the central carbon pathway in optimally grown E. coli

Andreozzi, Stefano; Miskovic, Ljubisa; Soh, Keng Cher et al. · 2012 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: Metabolic control analysis of the central carbon pathway in optimally grown E. coli

Authors: Andreozzi, Stefano; Miskovic, Ljubisa; Soh, Keng Cher; Hatzimanikatis, Vassily

Year: 2012

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/81480

Thesis Computational Studies on Cellular Bioenergetics

Soh, Keng Cher · 2013 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: Computational Studies on Cellular Bioenergetics

Authors: Soh, Keng Cher

Year: 2013

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/90595

Thesis Manipulating redox and ATP balancing for improved production of succinate in E. coli

Singh, Amarjeet; Soh, Keng Cher; Hatzimanikatis, Vassily et al. · 2010 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: Manipulating redox and ATP balancing for improved production of succinate in E. coli

Authors: Singh, Amarjeet; Soh, Keng Cher; Hatzimanikatis, Vassily; Gill, Ryan T.

Year: 2010

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/62333

Thesis Systematic characterization of flux and network thermodynamic states for identification of metabolic engineering targets

Soh, Keng Cher; Miskovic, Ljubisa; Hatzimanikatis, Vassily · 2012 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: Systematic characterization of flux and network thermodynamic states for identification of metabolic engineering targets

Authors: Soh, Keng Cher; Miskovic, Ljubisa; Hatzimanikatis, Vassily

Year: 2012

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/81481

Thesis Unraveling the inhibitory effects of acetate on ethanol production in CEN.PK

Chakrabarti, Anirikh; Soh, Keng Cher; Kiparissides, Alexandros et al. · 2014 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: Unraveling the inhibitory effects of acetate on ethanol production in CEN.PK

Authors: Chakrabarti, Anirikh; Soh, Keng Cher; Kiparissides, Alexandros; van Rijsewijk, Haverkorn; Bart, R. B.; Hickman, Jason W.; Najdi, Tarek S.; Halim, D.; Portnoy, Vasiliy A.; Osequera, R.; Burja, Adam R.; Miskovic, Ljubisa; Hatzimanikatis, Vassily

Year: 2014

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/104997

Thesis Implications of the Assumptions on Intracellular Metabolic Operational States in Metabolic Control Analysis

Fengos, Georgios; Chakrabarti, Anirikh; Soh, Keng Cher et al. · 2014 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: Implications of the Assumptions on Intracellular Metabolic Operational States in Metabolic Control Analysis

Authors: Fengos, Georgios; Chakrabarti, Anirikh; Soh, Keng Cher; Miskovic, Ljubisa; Hatzimanikatis, Vassily

Year: 2014

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/104999

Thesis Unlocking Yeast Metabolism: Identification of optimal flux directionalities

Kiparissides, Alexandros; Soh, Keng Cher; Chakrabarti, Anirikh et al. · 2014 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: Unlocking Yeast Metabolism: Identification of optimal flux directionalities

Authors: Kiparissides, Alexandros; Soh, Keng Cher; Chakrabarti, Anirikh; Miskovic, Ljubisa; Hatzimanikatis, Vassily

Year: 2014

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/108120

Thesis Engineering improved productivity of 1,4-butanediol in E. coli – a kinetic modeling approach

Andreozzi, Stefano; Chakrabarti, Anirikh; Soh, Keng Cher et al. · 2014 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: Engineering improved productivity of 1,4-butanediol in E. coli – a kinetic modeling approach

Authors: Andreozzi, Stefano; Chakrabarti, Anirikh; Soh, Keng Cher; Burgard, Anthony; Van Dien, Steve; Miskovic, Ljubisa; Hatzimanikatis, Vassily; Yang, Tae Hoon

Year: 2014

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/104995

Thesis Computational studies on Escherichia coli metabolism : from constitutive bricks to large-scale behaviour

Andreozzi, Stefano · 2015 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: Computational studies on Escherichia coli metabolism : from constitutive bricks to large-scale behaviour

Authors: Andreozzi, Stefano

Year: 2015

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/115141

Thesis The design of “Super E. coli” through automated reaction network generation and genome scale models

Hadadi, N.; Ataman, A.; Soh, K. C. et al. · 2014 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: The design of “Super E. coli” through automated reaction network generation and genome scale models

Authors: Hadadi, N.; Ataman, A.; Soh, K. C.; Hatzimanikatis, V.

Year: 2014

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/108154

Thesis In silico analysis of the interplay between P/O ratio and physiological states of the optimally grown Escherichia coli

Ataman, Meriç; Andreozzi, Stefano; Soh, Keng Cher et al. · 2014 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: In silico analysis of the interplay between P/O ratio and physiological states of the optimally grown Escherichia coli

Authors: Ataman, Meriç; Andreozzi, Stefano; Soh, Keng Cher; Miskovic, Ljubisa

Year: 2014

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/104998

Thesis Towards a kinetic model of the phospholipids biosynthesis of the yeast Saccharomyces cerevisiae

Oikonomidi, Iro; Savoglidis, Georgios; Ataman, Meriç et al. · 2014 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: Towards a kinetic model of the phospholipids biosynthesis of the yeast Saccharomyces cerevisiae

Authors: Oikonomidi, Iro; Savoglidis, Georgios; Ataman, Meriç; Hatzimanikatis, Vassily

Year: 2014

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/108117

Thesis Kinetic models in industrial biotechnology - Improving cell factory performance

Almquist, Joachim; Cvijovic, Marija; Hatzimanikatis, Vassily et al. · 2014 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: Kinetic models in industrial biotechnology - Improving cell factory performance

Authors: Almquist, Joachim; Cvijovic, Marija; Hatzimanikatis, Vassily; Nielsen, Jens; Jirstrand, Mats

Year: 2014

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/106350

Thesis iSCHRUNK – in Silico Approach to Characterization and Reduction of Uncertainty in the Kinetic Models of Genome-scale Metabolic Networks

Andreozzi, Stefano; Miskovic, Ljubisa; Hatzimanikatis, Vassily · 2015 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: iSCHRUNK – in Silico Approach to Characterization and Reduction of Uncertainty in the Kinetic Models of Genome-scale Metabolic Networks

Authors: Andreozzi, Stefano; Miskovic, Ljubisa; Hatzimanikatis, Vassily

Year: 2015

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/117575

Thesis Systematic Reduction of Genome Scale Metabolic Reconstructions - redGEM

Ataman, Meriç; Hernandez Gardiol, Daniel Federico; Fengos, Georgios et al. · 2015 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: Systematic Reduction of Genome Scale Metabolic Reconstructions - redGEM

Authors: Ataman, Meriç; Hernandez Gardiol, Daniel Federico; Fengos, Georgios; Soh, Keng Cher; Hatzimanikatis, Vassily

Year: 2015

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/119806

Thesis Exploring enhancement of 1,4-butanediol production in recombinant E. coli using large-scale kinetic models

Andreozzi, Stefano; Chakrabarti, Anirikh; Soh, Keng Cher et al. · 2015 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: Exploring enhancement of 1,4-butanediol production in recombinant E. coli using large-scale kinetic models

Authors: Andreozzi, Stefano; Chakrabarti, Anirikh; Soh, Keng Cher; Burgard, Anthony; Yang, T. H.; van Dien, Stephen; Miskovic, Ljubisa; Hatzimanikatis, Vassily

Year: 2015

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/117566

Thesis A Study of Dynamic Responses of E. coli Metabolism Upon Large Perturbations Using Large-Scale Kinetic Models

Tokic, Milenko; Fengos, Georgios; Miskovic, Ljubisa et al. · 2015 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: A Study of Dynamic Responses of E. coli Metabolism Upon Large Perturbations Using Large-Scale Kinetic Models

Authors: Tokic, Milenko; Fengos, Georgios; Miskovic, Ljubisa; Hatzimanikatis, Vassily

Year: 2015

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/119791

Thesis Heading in the right direction: thermodynamics-based network analysis and pathway engineering

Ataman, Meriç; Hatzimanikatis, Vassily · 2015 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: Heading in the right direction: thermodynamics-based network analysis and pathway engineering

Authors: Ataman, Meriç; Hatzimanikatis, Vassily

Year: 2015

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/119809

Thesis Analysis and Design of Metabolic Engineering and Synthetic Biology Strategies using Large Scale Dynamic Models of Metabolism

Fengos, Georgios; Miskovic, Ljubisa; Hatzimanikatis, Vassily · 2016 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: Analysis and Design of Metabolic Engineering and Synthetic Biology Strategies using Large Scale Dynamic Models of Metabolism

Authors: Fengos, Georgios; Miskovic, Ljubisa; Hatzimanikatis, Vassily

Year: 2016

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/127103

Thesis Study on how underlying uncertainty in the flux values affects metabolic control analysis of optimally grown E. coli

Hameri, Tuure Eelis; Fengos, Georgios; Ataman, Meriç et al. · 2015 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: Study on how underlying uncertainty in the flux values affects metabolic control analysis of optimally grown E. coli

Authors: Hameri, Tuure Eelis; Fengos, Georgios; Ataman, Meriç; Miskovic, Ljubisa

Year: 2015

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/119830

Thesis Integrating Transcriptomic Data with Thermodynamically Consistent Metabolic Models

Hernandez Gardiol, Daniel Federico; Pandey, Vikash Kumar · 2015 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: Integrating Transcriptomic Data with Thermodynamically Consistent Metabolic Models

Authors: Hernandez Gardiol, Daniel Federico; Pandey, Vikash Kumar

Year: 2015

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/119805

Thesis Developing a Reconciled Genome-Scale Model of the Malaria Parasite Plasmodium falciparum and its Thermodynamics-based Flux Balance Analysis

Chiappino Pepe, Anush; Tymoshenko, Stepan; Ataman, Meriç et al. · 2015 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: Developing a Reconciled Genome-Scale Model of the Malaria Parasite Plasmodium falciparum and its Thermodynamics-based Flux Balance Analysis

Authors: Chiappino Pepe, Anush; Tymoshenko, Stepan; Ataman, Meriç; Soldati-Favre, Dominique; Hatzimanikatis, Vassily

Year: 2015

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/119807

Thesis iSCHRUNK – In Silico Approach to Characterization and Reduction of Uncertainty in the Kinetic Models of Genome-scale Metabolic Networks

Andreozzi, Stefano; Miskovic, Ljubisa; Hatzimanikatis, Vassily · 2015 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: iSCHRUNK – In Silico Approach to Characterization and Reduction of Uncertainty in the Kinetic Models of Genome-scale Metabolic Networks

Authors: Andreozzi, Stefano; Miskovic, Ljubisa; Hatzimanikatis, Vassily

Year: 2015

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/120408

Thesis Discovery and Evaluation of Novel Pathways for Production of the Second Generation of Biofuels

Tokic, Milenko; Hadadi, Noushin; Ataman, Meriç et al. · 2016 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: Discovery and Evaluation of Novel Pathways for Production of the Second Generation of Biofuels

Authors: Tokic, Milenko; Hadadi, Noushin; Ataman, Meriç; Miskovic, Ljubisa; Neves, Dario; Ebert, Birgitta; Blank, Lars; Hatzimanikatis, Vassily

Year: 2016

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/127104

Thesis A method for analysis and design of metabolism using metabolomics data and kinetic models: Application on lipidomics using a novel kinetic model of sphingolipid metabolism

Savoglidis, Georgios; Dos Santos, Aline Xavier Da Silveira; Riezman, Isabelle et al. · 2016 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: A method for analysis and design of metabolism using metabolomics data and kinetic models: Application on lipidomics using a novel kinetic model of sphingolipid metabolism

Authors: Savoglidis, Georgios; Dos Santos, Aline Xavier Da Silveira; Riezman, Isabelle; Angelino, Paolo; Riezman, Howard; Hatzimanikatis, Vassily

Year: 2016

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/127505

Thesis Exploring enhancement of 1,4-butanediol production in recombinant E. coli using Large-scale kinetic models

Andreozzi, Stefano; Chakrabarti, Anirikh; Burgard, A. et al. · 2016 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: Exploring enhancement of 1,4-butanediol production in recombinant E. coli using Large-scale kinetic models

Authors: Andreozzi, Stefano; Chakrabarti, Anirikh; Burgard, A.; Yang, T. H.; Van Dien, S.; Miskovic, Ljubisa; Hatzimanikatis, Vassily

Year: 2016

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/127105

Thesis Large Scale Dynamic Models of Metabolism as a Tool for Analysis and Design of Metabolic Engineering and Synthetic Biology Strategies

Fengos, Georgios; Miskovic, Ljubisa; Hatzimanikatis, Vassily · 2016 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: Large Scale Dynamic Models of Metabolism as a Tool for Analysis and Design of Metabolic Engineering and Synthetic Biology Strategies

Authors: Fengos, Georgios; Miskovic, Ljubisa; Hatzimanikatis, Vassily

Year: 2016

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/127107

Thesis iSCHRUNK – In Silico Approach to Characterization and Reduction of Uncertainty in the Kinetic Models of Genome-scale Metabolic Networks

Andreozzi, Stefano; Miskovic, Ljubisa; Hatzimanikatis, Vassily · 2016 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: iSCHRUNK – In Silico Approach to Characterization and Reduction of Uncertainty in the Kinetic Models of Genome-scale Metabolic Networks

Authors: Andreozzi, Stefano; Miskovic, Ljubisa; Hatzimanikatis, Vassily

Year: 2016

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/127106

Thesis Systematic Reduction of Genome Scale Metabolic Reconstructions - redGEM

Ataman, Meriç; Hernandez Gardiol, Daniel Federico; Fengos, Georgios et al. · 2015 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: Systematic Reduction of Genome Scale Metabolic Reconstructions - redGEM

Authors: Ataman, Meriç; Hernandez Gardiol, Daniel Federico; Fengos, Georgios; Soh, Keng Cher; Hatzimanikatis, Vassily

Year: 2015

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/117586

Thesis Application of mathematical tools for metabolic design of microbial ethanol production

Hatzimanikatis, Vassily; Emmerling, Marcel; Sauer, Uwe et al. · 2007 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: Application of mathematical tools for metabolic design of microbial ethanol production

Authors: Hatzimanikatis, Vassily; Emmerling, Marcel; Sauer, Uwe; Bailey, James E.

Year: 2007

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/238783

Thesis Identification of the enzymes that determine the robustness of lipid profiles in yeast

Tsouka, Sofia; Savoglidis, Georgios; Riezman, Howard et al. · 2017 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: Identification of the enzymes that determine the robustness of lipid profiles in yeast

Authors: Tsouka, Sofia; Savoglidis, Georgios; Riezman, Howard; Hatzimanikatis, Vassily

Year: 2017

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/140975

Thesis Deciphering ambiguous control over fluxes through characterization and reduction of uncertainty

Miskovic, Ljubisa; Béal, Jonas; Moret, Michaël Roger Germain et al. · 2017 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: Deciphering ambiguous control over fluxes through characterization and reduction of uncertainty

Authors: Miskovic, Ljubisa; Béal, Jonas; Moret, Michaël Roger Germain; Hatzimanikatis, Vassily

Year: 2017

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/140960

Thesis Toward fully characterized knowledge gaps in metabolic networks: discovery of missing biochemistry in Escherichia coli

Chiappino Pepe, Anush; Ataman, Meriç; Hadadi, Noushin et al. · 2017 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: Toward fully characterized knowledge gaps in metabolic networks: discovery of missing biochemistry in Escherichia coli

Authors: Chiappino Pepe, Anush; Ataman, Meriç; Hadadi, Noushin; Hatzimanikatis, Vassily

Year: 2017

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/141419

Thesis Facing The Unknown: Suggesting Alternative Novel Biochemistry in Escherichia coli and Saccharomyces cerevisiae

Chiappino Pepe, Anush; Ataman, Meriç; Hadadi, Noushin et al. · 2017 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: Facing The Unknown: Suggesting Alternative Novel Biochemistry in Escherichia coli and Saccharomyces cerevisiae

Authors: Chiappino Pepe, Anush; Ataman, Meriç; Hadadi, Noushin; Hatzimanikatis, Vassily

Year: 2017

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/141421

Thesis Generation and Analysis of Large-Scale Dynamic Non-Linear Models of Metabolism

Fengos, Georgios; Miskovic, Ljubisa; Hatzimanikatis, Vassily · 2017 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: Generation and Analysis of Large-Scale Dynamic Non-Linear Models of Metabolism

Authors: Fengos, Georgios; Miskovic, Ljubisa; Hatzimanikatis, Vassily

Year: 2017

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/141044

Thesis Analysis and Design of Metabolic Engineering and Synthetic Biology Strategies using Large Scale Dynamic Models of Metabolism

Fengos, Georgios; Miskovic, Ljubisa; Hatzimanikatis, Vassily · 2017 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: Analysis and Design of Metabolic Engineering and Synthetic Biology Strategies using Large Scale Dynamic Models of Metabolism

Authors: Fengos, Georgios; Miskovic, Ljubisa; Hatzimanikatis, Vassily

Year: 2017

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/141045

Thesis Quantitative comparison of transient growth of Saccharomyces cerevisiae, Saccharomyces kluyveri, and Kluyveromyces lactis

Herwig, Christoph; von Stockar, Urs · 2006 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: Quantitative comparison of transient growth of Saccharomyces cerevisiae, Saccharomyces kluyveri, and Kluyveromyces lactis

Authors: Herwig, Christoph; von Stockar, Urs

Year: 2006

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/226082

Thesis Optimization of the production of methyl ethyl ketone in recombinant Pseudomonas putida using large-scale kinetic models

Tokic, Milenko; Ataman, Meriç; Miskovic, Ljubisa et al. · 2017 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: Optimization of the production of methyl ethyl ketone in recombinant Pseudomonas putida using large-scale kinetic models

Authors: Tokic, Milenko; Ataman, Meriç; Miskovic, Ljubisa; Hatzimanikatis, Vassily

Year: 2017

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/140977

Thesis Toward the identification of cellular mechanisms behind the lethal phenotypes in malaria parasites blood stages with PlasmoGEM and metabolic modeling

Chiappino Pepe, Anush; Bushell, Ellen; Rayner, Julian C. et al. · 2017 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: Toward the identification of cellular mechanisms behind the lethal phenotypes in malaria parasites blood stages with PlasmoGEM and metabolic modeling

Authors: Chiappino Pepe, Anush; Bushell, Ellen; Rayner, Julian C.; Billker, Oliver; Hatzimanikatis, Vassily

Year: 2017

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/141423

Thesis Analysis of free energy change and thermodynamic feasibility in a genome scale metabolic model

Henry, Christopher S.; Jankowski, Matthew; Broadbelt, Linda J. et al. · 2007 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: Analysis of free energy change and thermodynamic feasibility in a genome scale metabolic model

Authors: Henry, Christopher S.; Jankowski, Matthew; Broadbelt, Linda J.; Hatzimanikatis, Vassily

Year: 2007

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/238811

Thesis A small metabolic flux model to identify transient metabolic regulations in Saccharomyces cerevisiae

Herwig, Christoph; von Stockar, Urs · 2006 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: A small metabolic flux model to identify transient metabolic regulations in Saccharomyces cerevisiae

Authors: Herwig, Christoph; von Stockar, Urs

Year: 2006

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/226059

Thesis Quantification and characterization of uncertainty in metabolic engineering

Hatzimanikatis, Vassily; Birol, Inanc; Shi, Jiaxiao et al. · 2007 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: Quantification and characterization of uncertainty in metabolic engineering

Authors: Hatzimanikatis, Vassily; Birol, Inanc; Shi, Jiaxiao; Wang, Liqing

Year: 2007

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/238799

Thesis Generally applicable fed-batch culture concept based on the detection of metabolic state by on-line balancing

Jobe, Anna Marya; Herwig, Christoph; Surzyn, Martin et al. · 2006 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: Generally applicable fed-batch culture concept based on the detection of metabolic state by on-line balancing

Authors: Jobe, Anna Marya; Herwig, Christoph; Surzyn, Martin; Walker, Bernhard; Marison, Ian; von Stockar, Urs

Year: 2006

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/226095

Thesis Fusing Individual-based Models with Genome-scale Metabolic Networks - a Novel Approach for Quantifying Emergent Microbial Community Spatiotemporal Dynamics

Ataman, Meriç; Borer, Benedict; Or, Dani et al. · 2017 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: Fusing Individual-based Models with Genome-scale Metabolic Networks - a Novel Approach for Quantifying Emergent Microbial Community Spatiotemporal Dynamics

Authors: Ataman, Meriç; Borer, Benedict; Or, Dani; Hatzimanikatis, Vassily

Year: 2017

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/141049

Thesis Toward the identification of cellular mechanisms behind the lethal phenotypes in Plasmodium berghei blood stages with PlasmoGEM and metabolic modeling

Chiappino Pepe, Anush; Bushell, Ellen; Rayner, Julian C. et al. · 2017 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: Toward the identification of cellular mechanisms behind the lethal phenotypes in Plasmodium berghei blood stages with PlasmoGEM and metabolic modeling

Authors: Chiappino Pepe, Anush; Bushell, Ellen; Rayner, Julian C.; Billker, Oliver; Hatzimanikatis, Vassily

Year: 2017

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/141420

Thesis On-line stoichiometry and identification of metabolic state under dynamic process conditions

Herwig, Christoph; Marison, Ian; Von Stockar, Urs · 2006 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: On-line stoichiometry and identification of metabolic state under dynamic process conditions

Authors: Herwig, Christoph; Marison, Ian; Von Stockar, Urs

Year: 2006

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/226052

Thesis Genome-scale thermodynamic analysis of Escherichia coli metabolism

Henry, Christopher S.; Jankowski, Matthew D.; Broadbelt, Linda J. et al. · 2007 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: Genome-scale thermodynamic analysis of Escherichia coli metabolism

Authors: Henry, Christopher S.; Jankowski, Matthew D.; Broadbelt, Linda J.; Hatzimanikatis, Vassily

Year: 2007

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/238818

Thesis Metabolic engineering under uncertainty-II: Analysis of yeast metabolism

Wang, Liqing; Hatzimanikatis, Vassily · 2007 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: Metabolic engineering under uncertainty-II: Analysis of yeast metabolism

Authors: Wang, Liqing; Hatzimanikatis, Vassily

Year: 2007

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/238821

Thesis Derivative processes for modelling metabolic fluxes

Žurauskiene, J; Kirk, P; Thorne, T et al. · 2020 · University of Melbourne · DOI

Full title: Derivative processes for modelling metabolic fluxes

Authors: Žurauskiene, J; Kirk, P; Thorne, T; Pinney, J; Stumpf, M

Year: 2020

Venue: University of Melbourne

DOI: https://hdl.handle.net/11343/244308

Thesis Uncertainty reduction in biochemical kinetic models: Enforcing desired model properties

Miskovic, Ljubisa; Béal, Jonas; Moret, Michael et al. · 2019 · ETH Zurich (Swiss Federal Institute of Technology in Zurich) · DOI

Full title: Uncertainty reduction in biochemical kinetic models: Enforcing desired model properties

Authors: Miskovic, Ljubisa; Béal, Jonas; Moret, Michael; Hatzimanikatis, Vassily

Year: 2019

Venue: ETH Zurich (Swiss Federal Institute of Technology in Zurich)

DOI: http://hdl.handle.net/20.500.11850/372256

Thesis Metabolic enzyme cost explains variable trade-offs between microbial growth rate and yield

Wortel, Meike T.; Noor, Elad; Ferris, Michael et al. · 2018 · ETH Zurich (Swiss Federal Institute of Technology in Zurich) · DOI

Full title: Metabolic enzyme cost explains variable trade-offs between microbial growth rate and yield

Authors: Wortel, Meike T.; Noor, Elad; Ferris, Michael; Bruggeman, Frank J.; Liebermeister, Wolfram

Year: 2018

Venue: ETH Zurich (Swiss Federal Institute of Technology in Zurich)

DOI: http://hdl.handle.net/20.500.11850/250012

Thesis System-Level Insights into Yeast Metabolism by Thermodynamic Analysis of Elementary Flux Modes

Jol, Stefan J.; Kümmel, Anne; Terzer, Marco et al. · 2012 · ETH Zurich (Swiss Federal Institute of Technology in Zurich) · DOI

Full title: System-Level Insights into Yeast Metabolism by Thermodynamic Analysis of Elementary Flux Modes

Authors: Jol, Stefan J.; Kümmel, Anne; Terzer, Marco; Stelling, Jörg; Heinemann, Matthias

Year: 2012

Venue: ETH Zurich (Swiss Federal Institute of Technology in Zurich)

DOI: http://hdl.handle.net/20.500.11850/47855

Thesis Microbial Community Decision Making Models in Batch and Chemostat Cultures

Theorell, Axel; Stelling, Jörg · 2021 · ETH Zurich (Swiss Federal Institute of Technology in Zurich) · DOI

Full title: Microbial Community Decision Making Models in Batch and Chemostat Cultures

Authors: Theorell, Axel; Stelling, Jörg

Year: 2021

Venue: ETH Zurich (Swiss Federal Institute of Technology in Zurich)

DOI: http://hdl.handle.net/20.500.11850/523461

Thesis Metabolomics-Driven Identification of the Rate-Limiting Steps in 1-Propanol Production

Ohtake, Toshiyuki; Kawase, Naoki; Pontrelli, Sammy et al. · 2022 · ETH Zurich (Swiss Federal Institute of Technology in Zurich) · DOI

Full title: Metabolomics-Driven Identification of the Rate-Limiting Steps in 1-Propanol Production

Authors: Ohtake, Toshiyuki; Kawase, Naoki; Pontrelli, Sammy; Nitta, Katsuaki; Laviña, Walter A.; Shen, Claire R.; Putri, Sastia P.; Liao, James C.; Fukusaki, Eiichiro

Year: 2022

Venue: ETH Zurich (Swiss Federal Institute of Technology in Zurich)

DOI: http://hdl.handle.net/20.500.11850/547737

Thesis A Genome-Scale Metabolic Model of Marine Heterotroph Vibrio splendidus Strain 1A01

Iffland-Stettner, Arion; Okano, Hiroyuki; Gralka, Matti et al. · 2023 · ETH Zurich (Swiss Federal Institute of Technology in Zurich) · DOI

Full title: A Genome-Scale Metabolic Model of Marine Heterotroph Vibrio splendidus Strain 1A01

Authors: Iffland-Stettner, Arion; Okano, Hiroyuki; Gralka, Matti; Guessous, Ghita; Amarnath, Kapil; Cordero, Otto X.; Hwa, Terence; Bonhoeffer, Sebastian; id_orcid0000-0001-8052-3925

Year: 2023

Venue: ETH Zurich (Swiss Federal Institute of Technology in Zurich)

DOI: http://hdl.handle.net/20.500.11850/603876

Thesis MCF2Chem: A manually curated knowledge base of biosynthetic compound production

Cai, Pengli; Liu, Sheng; Zhang, Dachuan et al. · 2023 · ETH Zurich (Swiss Federal Institute of Technology in Zurich) · DOI

Full title: MCF2Chem: A manually curated knowledge base of biosynthetic compound production

Authors: Cai, Pengli; Liu, Sheng; Zhang, Dachuan; id_orcid0000-0003-2467-6286; Hu, Qian-Nan

Year: 2023

Venue: ETH Zurich (Swiss Federal Institute of Technology in Zurich)

DOI: http://hdl.handle.net/20.500.11850/641512

Thesis Integration of time-resolved transcriptomics data with flux-based methods reveals stress-induced metabolic adaptation in Escherichia coli

Töpfer, Nadine; Jozefczuk, Szymon; Nikoloski, Zoran · 2012 · ETH Zurich (Swiss Federal Institute of Technology in Zurich) · DOI

Full title: Integration of time-resolved transcriptomics data with flux-based methods reveals stress-induced metabolic adaptation in Escherichia coli

Authors: Töpfer, Nadine; Jozefczuk, Szymon; Nikoloski, Zoran

Year: 2012

Venue: ETH Zurich (Swiss Federal Institute of Technology in Zurich)

DOI: http://hdl.handle.net/20.500.11850/64536

Thesis Scalable enumeration and sampling of minimal metabolic pathways for organisms and communities

Øyås, Ove; Theorell, Axel; Stelling, Jörg · 2024 · ETH Zurich (Swiss Federal Institute of Technology in Zurich) · DOI

Full title: Scalable enumeration and sampling of minimal metabolic pathways for organisms and communities

Authors: Øyås, Ove; Theorell, Axel; Stelling, Jörg

Year: 2024

Venue: ETH Zurich (Swiss Federal Institute of Technology in Zurich)

DOI: http://hdl.handle.net/20.500.11850/718827

Thesis Functional comparison of metabolic networks across species

Ramon, Charlotte; Stelling, Jörg · 2023 · ETH Zurich (Swiss Federal Institute of Technology in Zurich) · DOI

Full title: Functional comparison of metabolic networks across species

Authors: Ramon, Charlotte; Stelling, Jörg

Year: 2023

Venue: ETH Zurich (Swiss Federal Institute of Technology in Zurich)

DOI: http://hdl.handle.net/20.500.11850/606194

Thesis Bioprocess in-line monitoring using Raman spectroscopy and Indirect Hard Modeling (IHM): A simple calibration yields a robust model

Müller, David Heinrich; Flake, Carsten; Brands, Thorsten et al. · 2023 · ETH Zurich (Swiss Federal Institute of Technology in Zurich) · DOI

Full title: Bioprocess in-line monitoring using Raman spectroscopy and Indirect Hard Modeling (IHM): A simple calibration yields a robust model

Authors: Müller, David Heinrich; Flake, Carsten; Brands, Thorsten; Koß, Hans-Jürgen

Year: 2023

Venue: ETH Zurich (Swiss Federal Institute of Technology in Zurich)

DOI: http://hdl.handle.net/20.500.11850/614575

Thesis Functional and computational genomics reveal unprecedented flexibility in stage-specific toxoplasma metabolism

Krishnan, Aarti; Kloehn, Joachim; Lunghi, Matteo et al. · 2020 · Vetsuisse Faculty Bern and Zurich · DOI

Full title: Functional and computational genomics reveal unprecedented flexibility in stage-specific toxoplasma metabolism

Authors: Krishnan, Aarti; Kloehn, Joachim; Lunghi, Matteo; Chiappino-Pepe, Anush; Waldman, Benjamin S; Nicolas, Damien; Varesio, Emmanuel; Hehl, Adrian B; https://orcid.org/0000-0002-2110-4445; Lourido, Sebastian; Hatzimanikatis, Vassily; Soldati-Favre, Dominique

Year: 2020

Venue: Vetsuisse Faculty Bern and Zurich

DOI: oai:www.zora.uzh.ch:20.500.14742/175105

Thesis Machine learning reveals novel compound for the improved production of chitooligosaccharides in Escherichia coli

Mey, Friederike; De Waele, Gaetan; Demeester, Wouter et al. · 2025 · ETH Zurich (Swiss Federal Institute of Technology in Zurich) · DOI

Full title: Machine learning reveals novel compound for the improved production of chitooligosaccharides in Escherichia coli

Authors: Mey, Friederike; De Waele, Gaetan; Demeester, Wouter; Guidi, Chiara; Duchi, Dries; Diederen, Tomek; id_orcid0000-0003-4772-2484; Kochuyt, Hanne; Van Huffel, Kirsten; Zamboni, Nicola; id_orcid0000-0003-4772-2484; Waegeman, Willem; De Mey, Marjan

Year: 2025

Venue: ETH Zurich (Swiss Federal Institute of Technology in Zurich)

DOI: http://hdl.handle.net/20.500.11850/721101

Thesis Fedbatchdesigner: A User-Friendly Dashboard for Modeling and Optimizing Growth-Arrested Fed-Batch Processes

Graf, Andrea C.; Libiseller-Egger, Julian; Gotsmy, Mathias et al. · 2025 · ETH Zurich (Swiss Federal Institute of Technology in Zurich) · DOI

Full title: Fedbatchdesigner: A User-Friendly Dashboard for Modeling and Optimizing Growth-Arrested Fed-Batch Processes

Authors: Graf, Andrea C.; Libiseller-Egger, Julian; Gotsmy, Mathias; id_orcid0000-0003-1333-4870; Zanghellini, Jürgen

Year: 2025

Venue: ETH Zurich (Swiss Federal Institute of Technology in Zurich)

DOI: http://hdl.handle.net/20.500.11850/748681

Thesis Current state of genome-scale modeling in filamentous fungi

Brandl, Julian; Andersen, Mikael Rørdam; id_orcid 0000-0003-4794-6808 · 2015 · Technical University of Denmark (DTU) · DOI

Full title: Current state of genome-scale modeling in filamentous fungi

Authors: Brandl, Julian; Andersen, Mikael Rørdam; id_orcid 0000-0003-4794-6808

Year: 2015

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/f66c76b8-e86d-4823-902a-77f9eb2db7be

Thesis Dynamic control of gene expression in Saccharomyces cerevisiae engineered for the production of plant sesquitepene α-santalene in a fed-batch mode

Scalcinati, Gionata; Knuf, Christoph; Partow, Siavash et al. · 2012 · Technical University of Denmark (DTU) · DOI

Full title: Dynamic control of gene expression in Saccharomyces cerevisiae engineered for the production of plant sesquitepene α-santalene in a fed-batch mode

Authors: Scalcinati, Gionata; Knuf, Christoph; Partow, Siavash; Chen, Yun; Maury, Jerome; Schalk, Michel; Daviet, Laurent; Nielsen, Jens; Siewers, Verena

Year: 2012

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/f55f5326-7cb5-4bcf-b074-76fdf9dfe301

Thesis Physiological characterization of the high malic acid-producing Aspergillus oryzae strain 2103a-68

Knuf, Christoph; Nookaew, Intawat; Remmers, Ilse et al. · 2014 · Technical University of Denmark (DTU) · DOI

Full title: Physiological characterization of the high malic acid-producing Aspergillus oryzae strain 2103a-68

Authors: Knuf, Christoph; Nookaew, Intawat; Remmers, Ilse; Khoomrung, Sakda; Brown, Stephen; Berry, Alan; Nielsen, Jens

Year: 2014

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/f38a07b4-7e4b-4a39-a395-29200109773a

Thesis MARSI: metabolite analogues for rational strain improvement

Cardoso, João G. R.; Zeidan, Ahmad A; Jensen, Kristian et al. · 2018 · Technical University of Denmark (DTU) · DOI

Full title: MARSI: metabolite analogues for rational strain improvement

Authors: Cardoso, João G. R.; Zeidan, Ahmad A; Jensen, Kristian; Sonnenschein, Nikolaus; id_orcid 0000-0002-7581-4936; Neves, Ana Rute; Herrgård, Markus J

Year: 2018

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/f490b237-6e58-42b7-ba63-ad4f8e7ab754

Thesis Machine learning applied to enzyme turnover numbers reveals protein structural correlates and improves metabolic models

Heckmann, David; Lloyd, Colton J.; Mih, Nathan et al. · 2018 · Technical University of Denmark (DTU) · DOI

Full title: Machine learning applied to enzyme turnover numbers reveals protein structural correlates and improves metabolic models

Year: 2018

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/f5199711-3cab-4d21-80dc-5ea8676d426d

Thesis Proteome constraints reveal targets for improving microbial fitness in nutrient-rich environments

Chen, Yu; van Pelt-KleinJan, Eunice; van Olst, Berdien et al. · 2021 · Technical University of Denmark (DTU) · DOI

Full title: Proteome constraints reveal targets for improving microbial fitness in nutrient-rich environments

Authors: Chen, Yu; van Pelt-KleinJan, Eunice; van Olst, Berdien; Douwenga, Sieze; Boeren, Sjef; Bachmann, Herwig; Molenaar, Douwe; Nielsen, Jens; Teusink, Bas

Year: 2021

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/fc704304-27bc-409f-9c5c-ec6b6e76c4fb

Thesis Targeting population heterogeneity for optimal cell factories

Heins, Anna-Lena; Carlqvist, Magnus; Helmark, S. et al. · 2011 · Technical University of Denmark (DTU) · DOI

Full title: Targeting population heterogeneity for optimal cell factories

Authors: Heins, Anna-Lena; Carlqvist, Magnus; Helmark, S.; Lencastre Fernandes, Rita; Gernaey, Krist; id_orcid 0000-0002-0364-1773; Eliasson Lantz, Anna

Year: 2011

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/f6330829-57ee-45a2-9c4a-1e6ef89fe66a

Thesis Laboratory evolution reveals a two-dimensional rate-yield tradeoff in microbial metabolism

Cheng, Chuankai; O'Brien, Edward J.; McCloskey, Douglas et al. · 2019 · Technical University of Denmark (DTU) · DOI

Full title: Laboratory evolution reveals a two-dimensional rate-yield tradeoff in microbial metabolism

Year: 2019

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/f4a20dad-892d-4e49-8f9c-5697c6c501e8

Thesis Pangenome Scale Reconstruction of Lactobacillaceae family and Escherichia coli Species Metabolism

Ardalani, Omid; id_orcid 0000-0002-0064-3802 · 2024 · Technical University of Denmark (DTU) · DOI

Full title: Pangenome Scale Reconstruction of Lactobacillaceae family and Escherichia coli Species Metabolism

Authors: Ardalani, Omid; id_orcid 0000-0002-0064-3802

Year: 2024

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/fa6f2508-15ed-4b8c-829d-bed44a23cc3e

Thesis An automated workflow for multi-omics screening of microbial model organisms

Donati, Stefano; id_orcid 0000-0001-9946-0346; Mattanovich, Matthias et al. · 2023 · Technical University of Denmark (DTU) · DOI

Full title: An automated workflow for multi-omics screening of microbial model organisms

Authors: Donati, Stefano; id_orcid 0000-0001-9946-0346; Mattanovich, Matthias; Hjort, Pernille; Baallal Jacobsen, Simo Abdessamad; Blomquist, Sarah Dina; Mangaard, Drude; Gurdo, Nicolas; Pacheco Pastor, Felix; Maury, Jerome; Hanke, René; Herrgård, Markus J; Wulff, Tune; Jakociunas, Tadas; id_orcid 0000-0003-1264-173X; Nielsen, Lars Keld; McCloskey, Douglas

Year: 2023

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/ef757ea8-8d70-4985-a645-94d6cb70d635

Thesis OptCouple: Joint simulation of gene knockouts, insertions and medium modifications for prediction of growth-coupled strain designs

Jensen, Kristian; Broeken, Valentijn; Hansen, Anne Sofie Lærke et al. · 2019 · Technical University of Denmark (DTU) · DOI

Full title: OptCouple: Joint simulation of gene knockouts, insertions and medium modifications for prediction of growth-coupled strain designs

Authors: Jensen, Kristian; Broeken, Valentijn; Hansen, Anne Sofie Lærke; id_orcid 0000-0003-2771-4671; Sonnenschein, Nikolaus; id_orcid 0000-0002-7581-4936; Herrgård, Markus J.

Year: 2019

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/fbfbc117-2665-47ca-8858-589c209247c2

Thesis Integration of metabolome data with metabolic networks reveals reporter reactions

Çakir, Tunahan; Patil, Kiran Raosaheb; Önsan, Zeynep Ilsen et al. · 2006 · Technical University of Denmark (DTU) · DOI

Full title: Integration of metabolome data with metabolic networks reveals reporter reactions

Authors: Çakir, Tunahan; Patil, Kiran Raosaheb; Önsan, Zeynep Ilsen; Ülgen, Kutlu Özergin; Kirdar, Betül; Nielsen, Jens

Year: 2006

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/fa28a9b7-8cae-4798-a7a9-6a33af7369d2

Thesis Natural computation meta-heuristics for the in silico optimization of microbial strains

Rocha, Miguel; Maia, Paulo; Mendes, Rui et al. · 2008 · Technical University of Denmark (DTU) · DOI

Full title: Natural computation meta-heuristics for the in silico optimization of microbial strains

Authors: Rocha, Miguel; Maia, Paulo; Mendes, Rui; Pinto, José; Ferreira, Euqénio; Nielsen, Jens; Patil, Kiran Raosaheb; Rocha, Isabel

Year: 2008

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/f8e459ca-9581-400e-be54-c8a43b6d97cc

Thesis Complex yeast–bacteria interactions affect the yield of industrial ethanol fermentation

Senne de Oliveira Lino, Felipe; Bajic, Djordje; Vila, Jean Celestin Charles et al. · 2021 · Technical University of Denmark (DTU) · DOI

Full title: Complex yeast–bacteria interactions affect the yield of industrial ethanol fermentation

Authors: Senne de Oliveira Lino, Felipe; Bajic, Djordje; Vila, Jean Celestin Charles; Sánchez, Alvaro; Sommer, Morten Otto Alexander; id_orcid 0000-0003-4005-5674

Year: 2021

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/f94bf19e-27e6-4067-9c31-38e7efc31f66

Thesis Applying mechanistic models in bioprocess development.

Lencastre Fernandes, Rita; Bodla, Vijaya Krishna; Carlquist, Magnus et al. · 2013 · Technical University of Denmark (DTU) · DOI

Full title: Applying mechanistic models in bioprocess development.

Authors: Lencastre Fernandes, Rita; Bodla, Vijaya Krishna; Carlquist, Magnus; Heins, Anna-Lena; Eliasson Lantz, Anna; Sin, Gürkan; id_orcid 0000-0003-0513-4502; Gernaey, Krist V; id_orcid 0000-0002-0364-1773

Year: 2013

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/fe2c6796-3008-4384-b8ce-953dce98e3d9

Thesis The future of genome-scale modeling of yeast through integration of a transcriptional regulatory network

Liu, Guodong; Marras, Antonio; Nielsen, Jens · 2014 · Technical University of Denmark (DTU) · DOI

Full title: The future of genome-scale modeling of yeast through integration of a transcriptional regulatory network

Authors: Liu, Guodong; Marras, Antonio; Nielsen, Jens

Year: 2014

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/fc8c28d1-dff1-41e4-8cf4-021e2aea387b

Thesis Whole-cell modeling in yeast predicts compartment-specific proteome constraints that drive metabolic strategies

Elsemman, Ibrahim E.; Rodriguez Prado, Angelica; Grigaitis, Pranas et al. · 2022 · Technical University of Denmark (DTU) · DOI

Full title: Whole-cell modeling in yeast predicts compartment-specific proteome constraints that drive metabolic strategies

Year: 2022

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/f8ac3827-f62d-4c07-8848-b31d93a6586e

Thesis Effects of introducing heterologous pathways on microbial metabolism with respect to metabolic optimality

Kim, Hyun Uk; Kim, Byoungjin; Seung, Do Young et al. · 2014 · Technical University of Denmark (DTU) · DOI

Full title: Effects of introducing heterologous pathways on microbial metabolism with respect to metabolic optimality

Authors: Kim, Hyun Uk; Kim, Byoungjin; Seung, Do Young; Yup Lee, Sang

Year: 2014

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/feac96ee-3b11-4b9e-9113-b9a2d35da5df

Thesis Application of synthetic biology for production of chemicals in yeast Saccharomyces cerevisiae

Borodina, Irina; Li, Mingji · 2015 · Technical University of Denmark (DTU) · DOI

Full title: Application of synthetic biology for production of chemicals in yeast Saccharomyces cerevisiae

Authors: Borodina, Irina; Li, Mingji

Year: 2015

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/fe2cdd83-cee6-4bee-b7d1-2e9695809830

Thesis Towards a full genome-scale model of yeast metabolism

Stanford, Natalie · 2011 · University of Manchester · DOI

Full title: Towards a full genome-scale model of yeast metabolism

Authors: Stanford, Natalie

Year: 2011

Venue: University of Manchester

DOI: https://research.manchester.ac.uk/en/studentTheses/1c1c018e-3679-4807-ae1b-79d316e09a22

Thesis A case study in flux balance analysis: Lysine, a cephamycin C precursor, can also increase clavulanic acid production

Cavallieri, André Pastrelo [UNESP]; Baptista, Amanda Salvador [UNESP]; Leite, Carla Andréa [UNESP] et al. · 2018 · Universidade Estadual Paulista (UNESP) · DOI

Full title: A case study in flux balance analysis: Lysine, a cephamycin C precursor, can also increase clavulanic acid production

Authors: Cavallieri, André Pastrelo [UNESP]; Baptista, Amanda Salvador [UNESP]; Leite, Carla Andréa [UNESP]; Araujo, Maria Lucia Gonsales da Costa [UNESP]

Year: 2018

Venue: Universidade Estadual Paulista (UNESP)

DOI: http://dx.doi.org/10.1016/j.bej.2016.03.012

Thesis Extending knowledge of Escherichia coli metabolism by modeling and experiment

Voit, Eberhard O.; Riley, Monica · 2006 · Georgia Institute of Technology · DOI

Full title: Extending knowledge of Escherichia coli metabolism by modeling and experiment

Authors: Voit, Eberhard O.; Riley, Monica

Year: 2006

Venue: Georgia Institute of Technology

DOI: http://hdl.handle.net/1853/12277

Thesis COMPUTATIONAL MODELING OF METABOLIC PATHWAYS TOWARD PREDICTING DYNAMIC PHENOTYPES

Lee, Justin Y. · 2021 · Georgia Institute of Technology · DOI

Full title: COMPUTATIONAL MODELING OF METABOLIC PATHWAYS TOWARD PREDICTING DYNAMIC PHENOTYPES

Authors: Lee, Justin Y.

Year: 2021

Venue: Georgia Institute of Technology

DOI: http://hdl.handle.net/1853/65039

Thesis First- and second-generation integrated process for bioethanol production: Fermentation of molasses diluted with hemicellulose hydrolysate by recombinant Saccharomyces cerevisiae

de Oliveira Pereira, Isabela; dos Santos, Ângela A.; Guimarães, Nick C. et al. · 2025 · Universidade Estadual Paulista (UNESP) · DOI

Full title: First- and second-generation integrated process for bioethanol production: Fermentation of molasses diluted with hemicellulose hydrolysate by recombinant Saccharomyces cerevisiae

Authors: de Oliveira Pereira, Isabela; dos Santos, Ângela A.; Guimarães, Nick C.; Lima, Cleilton S.; Zanella, Eduardo; Matsushika, Akinori; Rabelo, Sarita C. [UNESP]; Stambuk, Boris U.; Ienczak, Jaciane L.

Year: 2025

Venue: Universidade Estadual Paulista (UNESP)

DOI: http://dx.doi.org/10.1002/bit.28648

Thesis Incorporating Protein Biosynthesis into the Saccharomyces cerevisiae Genome-scale Metabolic Model

Olivares Hernandez, Roberto · 2006 · Technical University of Denmark (DTU) · DOI

Full title: Incorporating Protein Biosynthesis into the Saccharomyces cerevisiae Genome-scale Metabolic Model

Authors: Olivares Hernandez, Roberto

Year: 2006

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/ff21a8d2-4762-4b6f-aa76-d1f752477046

Thesis Comparative metabolic modeling of multiple sulfate‐reducing prokaryotes reveals versatile energy conservation mechanisms

Tang, Wentao; Hao, Tianwei; Chen, Guanghao · 2021 · Hong Kong University of Science and Technology (HKUST) · DOI

Full title: Comparative metabolic modeling of multiple sulfate‐reducing prokaryotes reveals versatile energy conservation mechanisms

Authors: Tang, Wentao; Hao, Tianwei; Chen, Guanghao

Year: 2021

Venue: Hong Kong University of Science and Technology (HKUST)

DOI: http://repository.hkust.edu.hk/ir/Record/1783.1-110300

Thesis Computational methods for integrating metabolomics data with metabolic engineering strain design

Dromms, Robert A. · 2019 · Georgia Institute of Technology · DOI

Full title: Computational methods for integrating metabolomics data with metabolic engineering strain design

Authors: Dromms, Robert A.

Year: 2019

Venue: Georgia Institute of Technology

DOI: http://hdl.handle.net/1853/61595

Thesis Genome-Based Metabolic Modelling of CHO Cells

Chen, Ning · 2013 · Imperial College London · DOI

Full title: Genome-Based Metabolic Modelling of CHO Cells

Authors: Chen, Ning

Year: 2013

Venue: Imperial College London

DOI: http://hdl.handle.net/10044/1/11054

Thesis Derivative processes for modelling metabolic fluxes

Zurauskiene, J; Kirk, P; Thorne, T et al. · 2016 · Imperial College London · DOI

Full title: Derivative processes for modelling metabolic fluxes

Authors: Zurauskiene, J; Kirk, P; Thorne, T; Pinney, J; Stumpf, M

Year: 2016

Venue: Imperial College London

DOI: http://hdl.handle.net/10044/1/39921

Thesis Genome-scale models as a vehicle for knowledge transfer from microbial to mammalian cell systems

Strain, Benjamin; Morrissey, Richard; Antonakoudis, Athanasios et al. · 2023 · Imperial College London · DOI

Full title: Genome-scale models as a vehicle for knowledge transfer from microbial to mammalian cell systems

Authors: Strain, Benjamin; Morrissey, Richard; Antonakoudis, Athanasios; Kontoravdi, Kleio

Year: 2023

Venue: Imperial College London

DOI: https://www.sciencedirect.com/science/article/pii/S2001037023000600

Thesis Probing Genomic, Metabolic, And Phenotypic Evolution In Microbes Using Comparative And Experimental Evolution Data

Castro Gordillo, Juan Camilo Camilo · 2024 · Georgia Institute of Technology · DOI

Full title: Probing Genomic, Metabolic, And Phenotypic Evolution In Microbes Using Comparative And Experimental Evolution Data

Authors: Castro Gordillo, Juan Camilo Camilo

Year: 2024

Venue: Georgia Institute of Technology

DOI: https://hdl.handle.net/1853/75069

Thesis Application of metabolic flux and transcript analyses to understanding the physiology of engineered Geobacillus thermoglucosidasius

Ward, Charlotte · 2015 · Imperial College London · DOI

Full title: Application of metabolic flux and transcript analyses to understanding the physiology of engineered Geobacillus thermoglucosidasius

Authors: Ward, Charlotte

Year: 2015

Venue: Imperial College London

DOI: http://hdl.handle.net/10044/1/25514

Thesis Understanding and engineering cofactor metabolism: a quest for improved biochemical production

de Arroyo Garcia, Laura · 2022 · Imperial College London · DOI

Full title: Understanding and engineering cofactor metabolism: a quest for improved biochemical production

Authors: de Arroyo Garcia, Laura

Year: 2022

Venue: Imperial College London

DOI: http://hdl.handle.net/10044/1/100259

Thesis NEXT-FBA: a hybrid stoichiometric/data-driven approach to improve intracellular flux predictions

Morrissey, James; Barberi, Gianmarco; Strain, Benjamin et al. · 2025 · Imperial College London · DOI

Full title: NEXT-FBA: a hybrid stoichiometric/data-driven approach to improve intracellular flux predictions

Authors: Morrissey, James; Barberi, Gianmarco; Strain, Benjamin; Facco, Pierantonio; Kontoravdi, Cleo

Year: 2025

Venue: Imperial College London

DOI: https://hdl.handle.net/10044/1/118593

Thesis Modeling and simulation of the main metabolism in Escherichia coli and its several single-gene knockout mutants with experimental verification.

Kadir, TA; Mannan, AA; Kierzek, AM et al. · 2015 · Imperial College London · DOI

Full title: Modeling and simulation of the main metabolism in Escherichia coli and its several single-gene knockout mutants with experimental verification.

Authors: Kadir, TA; Mannan, AA; Kierzek, AM; McFadden, J; Shimizu, K

Year: 2015

Venue: Imperial College London

DOI: http://hdl.handle.net/10044/1/26892

Thesis Metabolic adaptation of two in silico mutants of Mycobacterium tuberculosis during infection

Lopez-Agudelo, Victor A; Baena, Andres; Ramirez-Malule, Howard et al. · 2017 · Imperial College London · DOI

Full title: Metabolic adaptation of two in silico mutants of Mycobacterium tuberculosis during infection

Authors: Lopez-Agudelo, Victor A; Baena, Andres; Ramirez-Malule, Howard; Ochoa, Silvia; Barrera, Luis F; Rios-Estepa, Rigoberto

Year: 2017

Venue: Imperial College London

DOI: http://hdl.handle.net/10044/1/55356

Thesis Utilising a genome scale metabolic model to design high-producing CHO cell lines through bi-level optimisation

Antonakoudis, Athanasios · 2024 · Imperial College London · DOI

Full title: Utilising a genome scale metabolic model to design high-producing CHO cell lines through bi-level optimisation

Authors: Antonakoudis, Athanasios

Year: 2024

Venue: Imperial College London

DOI: http://hdl.handle.net/10044/1/110783

Thesis Vibrio natriegens genome-scale modeling reveals insights into halophilic adaptations and resource allocation

Coppens, Lucas; Tschirhart, Tanya; Leary, Dagmar H et al. · 2023 · Imperial College London · DOI

Full title: Vibrio natriegens genome-scale modeling reveals insights into halophilic adaptations and resource allocation

Authors: Coppens, Lucas; Tschirhart, Tanya; Leary, Dagmar H; Colston, Sophie M; Compton, Jaimee R; Hervey, William Judson; Dana, Karl L; Vora, Gary J; Bordel, Sergio; Ledesma-Amaro, Rodrigo

Year: 2023

Venue: Imperial College London

DOI: https://www.ncbi.nlm.nih.gov/pubmed/36847213

Thesis Metabolic modeling and engineering of Escherichia coli to reduce acetate formation in recombinant DNA-fermentations

De Mey, Marjan · 2007 · Ghent University (Universiteit Gent) · DOI

Full title: Metabolic modeling and engineering of Escherichia coli to reduce acetate formation in recombinant DNA-fermentations

Authors: De Mey, Marjan

Year: 2007

Venue: Ghent University (Universiteit Gent)

DOI: https://biblio.ugent.be/publication/470130

Thesis Genome-based kinetic modeling of cytosolic glucose metabolism in industrially relevant cell lines - Saccharomyces cerevisiae and Chinese hamster ovary cells

Chen, N; Koumpouras, GC; Polizzi, KM et al. · 2014 · Imperial College London · DOI

Full title: Genome-based kinetic modeling of cytosolic glucose metabolism in industrially relevant cell lines - Saccharomyces cerevisiae and Chinese hamster ovary cells

Authors: Chen, N; Koumpouras, GC; Polizzi, KM; Kontoravdi, C

Year: 2014

Venue: Imperial College London

DOI: http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=000305211100017&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=1ba7043ffcc86c417c072aa74d649202

Thesis Towards next-generation model microorganism chassis for biomanufacturing

Liu, Yanfeng; Su, Anqi; Li, Jianghua et al. · 2020 · Imperial College London · DOI

Full title: Towards next-generation model microorganism chassis for biomanufacturing

Authors: Liu, Yanfeng; Su, Anqi; Li, Jianghua; Ledesma-Amaro, Rodrigo; Xu, Peng; Du, Guocheng; Liu, Long

Year: 2020

Venue: Imperial College London

DOI: http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000572607200001&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=1ba7043ffcc86c417c072aa74d649202

Thesis A multiscale modelling framework for the processes involved in consolidated bioprocessing

Mc Caul, Kristian · 2018 · Imperial College London · DOI

Full title: A multiscale modelling framework for the processes involved in consolidated bioprocessing

Authors: Mc Caul, Kristian

Year: 2018

Venue: Imperial College London

DOI: http://hdl.handle.net/10044/1/59706

Thesis Development and application of genome-scale models in chinese hamster ovary cell culture

Morrissey, Richard James · 2025 · Imperial College London · DOI

Full title: Development and application of genome-scale models in chinese hamster ovary cell culture

Authors: Morrissey, Richard James

Year: 2025

Venue: Imperial College London

DOI: https://hdl.handle.net/10044/1/122460

Thesis Dynamic optimization of metabolic networks coupled with gene expression

Waldherr, S; Oyarzun, DA; Bockmayr, A · 2015 · Imperial College London · DOI

Full title: Dynamic optimization of metabolic networks coupled with gene expression

Authors: Waldherr, S; Oyarzun, DA; Bockmayr, A

Year: 2015

Venue: Imperial College London

DOI: http://hdl.handle.net/10044/1/21664

Thesis The era of big data: Genome-scale modelling meets machine learning

Antonakoudis, Athanasios; Barbosa, Rodrigo; Kotidis, Pavlos et al. · 2020 · Imperial College London · DOI

Full title: The era of big data: Genome-scale modelling meets machine learning

Authors: Antonakoudis, Athanasios; Barbosa, Rodrigo; Kotidis, Pavlos; Kontoravdi, Kleio

Year: 2020

Venue: Imperial College London

DOI: http://hdl.handle.net/10044/1/84715

Thesis Understanding and engineering the factors that control fatty acid biosynthesis in escherichia coli

Gallagher, Danielle · 2021 · Imperial College London · DOI

Full title: Understanding and engineering the factors that control fatty acid biosynthesis in escherichia coli

Authors: Gallagher, Danielle

Year: 2021

Venue: Imperial College London

DOI: http://hdl.handle.net/10044/1/86387

Thesis Dynamic metabolic control: towards precision engineering of metabolism

Liu, D; Mannan, AA; Han, Y et al. · 2018 · Imperial College London · DOI

Full title: Dynamic metabolic control: towards precision engineering of metabolism

Authors: Liu, D; Mannan, AA; Han, Y; Oyarzun, DA; Zhang, F

Year: 2018

Venue: Imperial College London

DOI: http://hdl.handle.net/10044/1/56656

Thesis Unraveling the potential of non-conventional yeasts in biotechnology.

Geijer, C; Ledesma-Amaro, R; Tomás-Pejó, E · 2022 · Imperial College London · DOI

Full title: Unraveling the potential of non-conventional yeasts in biotechnology.

Authors: Geijer, C; Ledesma-Amaro, R; Tomás-Pejó, E

Year: 2022

Venue: Imperial College London

DOI: https://www.ncbi.nlm.nih.gov/pubmed/35040953

Thesis How reliable are Chinese hamster ovary (CHO) cell genome-scale metabolic models?

Strain, Benjamin; Morrissey, richard; Antonakoudis, Athanasios et al. · 2023 · Imperial College London · DOI

Full title: How reliable are Chinese hamster ovary (CHO) cell genome-scale metabolic models?

Authors: Strain, Benjamin; Morrissey, richard; Antonakoudis, Athanasios; Kontoravdi, Kleio

Year: 2023

Venue: Imperial College London

DOI: https://onlinelibrary.wiley.com/doi/full/10.1002/bit.28366

Thesis Making life difficult for Clostridium difficile: augmenting the pathogen's metabolic model with transcriptomic and codon usage data for better therapeutic target characterization.

Kashaf, SS; Angione, C; Lió, P · 2017 · University of Cambridge · DOI

Full title: Making life difficult for Clostridium difficile: augmenting the pathogen's metabolic model with transcriptomic and codon usage data for better therapeutic target characterization.

Authors: Kashaf, SS; Angione, C; Lió, P

Year: 2017

Venue: University of Cambridge

DOI: https://www.repository.cam.ac.uk/handle/1810/262645

Thesis Integrating highly quantitative proteomics and genome-scale metabolic modeling to study pH adaptation in the human pathogen Enterococcus faecalis

Grosseholz, Ruth; Koh, Ching Chiek; Veith, Nadine et al. · 2016 · ETH Zurich (Swiss Federal Institute of Technology in Zurich) · DOI

Full title: Integrating highly quantitative proteomics and genome-scale metabolic modeling to study pH adaptation in the human pathogen Enterococcus faecalis

Authors: Grosseholz, Ruth; Koh, Ching Chiek; Veith, Nadine; Fiedler, Tomas; Strauss, Madlen; Olivier, Brett; Collins, Ben C.; Schubert, Olga T.; Bergmann, Frank; Kreikemeyer, Bernd; Aebersold, Ruedi; Kummer, Ursula

Year: 2016

Venue: ETH Zurich (Swiss Federal Institute of Technology in Zurich)

DOI: http://hdl.handle.net/20.500.11850/228084

Thesis Integrated in silico analysis of pathway designs for synthetic photo-electro-autotrophy

Volpers, Michael; Claassens, Nico J.; Noor, Elad et al. · 2016 · ETH Zurich (Swiss Federal Institute of Technology in Zurich) · DOI

Full title: Integrated in silico analysis of pathway designs for synthetic photo-electro-autotrophy

Authors: Volpers, Michael; Claassens, Nico J.; Noor, Elad; id_orcid0000-0001-8776-4799; Oost, John van der; de Vos, Willem M.; Kengen, Servé W.M.; Dos Santos, Vitor A.P.M.

Year: 2016

Venue: ETH Zurich (Swiss Federal Institute of Technology in Zurich)

DOI: http://hdl.handle.net/20.500.11850/118129

Thesis An analytic and systematic framework for estimating metabolic flux ratios from ¹³C tracer experiments

Rantanen, Ari; Rousu, Juho; Jouhten, Paula et al. · 2008 · ETH Zurich (Swiss Federal Institute of Technology in Zurich) · DOI

Full title: An analytic and systematic framework for estimating metabolic flux ratios from ¹³C tracer experiments

Authors: Rantanen, Ari; Rousu, Juho; Jouhten, Paula; Zamboni, Nicola; id_orcid0000-0003-1271-1021; Maaheimo, Hannu; Ukkonen, Esko

Year: 2008

Venue: ETH Zurich (Swiss Federal Institute of Technology in Zurich)

DOI: http://hdl.handle.net/20.500.11850/287441

Thesis Efficient Reconstruction of Predictive Consensus Metabolic Network Models

Heck, Ruben G.A. van; Ganter, Mathias; Martins Dos Santos, Vítor A.P. et al. · 2016 · ETH Zurich (Swiss Federal Institute of Technology in Zurich) · DOI

Full title: Efficient Reconstruction of Predictive Consensus Metabolic Network Models

Authors: Heck, Ruben G.A. van; Ganter, Mathias; Martins Dos Santos, Vítor A.P.; Stelling, Jörg

Year: 2016

Venue: ETH Zurich (Swiss Federal Institute of Technology in Zurich)

DOI: http://hdl.handle.net/20.500.11850/120906

Thesis Constrained Allocation Flux Balance Analysis

Mori, Matteo; Hwa, Terence; Martin, Olivier C. et al. · 2016 · ETH Zurich (Swiss Federal Institute of Technology in Zurich) · DOI

Full title: Constrained Allocation Flux Balance Analysis

Authors: Mori, Matteo; Hwa, Terence; Martin, Olivier C.; De Martino, Andrea; Marinari, Enzo

Year: 2016

Venue: ETH Zurich (Swiss Federal Institute of Technology in Zurich)

DOI: http://hdl.handle.net/20.500.11850/118868

Thesis Evolutionary programming as a platform for in silico metabolic engineering.

Patil, Kiran Raosaheb; Rocha, Isabel; Förster, Jochen et al. · 2020 · University of Cambridge · DOI

Full title: Evolutionary programming as a platform for in silico metabolic engineering.

Authors: Patil, Kiran Raosaheb; Rocha, Isabel; Förster, Jochen; Nielsen, Jens

Year: 2020

Venue: University of Cambridge

DOI: https://www.repository.cam.ac.uk/handle/1810/303272

Thesis Unraveling condition-dependent networks of transcription factors that control metabolic pathway activity in yeast

Fendt, Sarah-Maria; Oliveira, Ana Paula; Christen, Stefan et al. · 2010 · ETH Zurich (Swiss Federal Institute of Technology in Zurich) · DOI

Full title: Unraveling condition-dependent networks of transcription factors that control metabolic pathway activity in yeast

Authors: Fendt, Sarah-Maria; Oliveira, Ana Paula; Christen, Stefan; Picotti, Paola; Dechant, Reinhard Christoph; Sauer, Uwe

Year: 2010

Venue: ETH Zurich (Swiss Federal Institute of Technology in Zurich)

DOI: http://hdl.handle.net/20.500.11850/26918

Thesis FiatFlux – a software for metabolic flux analysis from ¹³C-glucose experiments

Zamboni, Nicola; id_orcid0000-0003-1271-1021; Fischer, Eliane et al. · 2005 · ETH Zurich (Swiss Federal Institute of Technology in Zurich) · DOI

Full title: FiatFlux – a software for metabolic flux analysis from ¹³C-glucose experiments

Authors: Zamboni, Nicola; id_orcid0000-0003-1271-1021; Fischer, Eliane; Sauer, Uwe; id_orcid0000-0003-1271-1021

Year: 2005

Venue: ETH Zurich (Swiss Federal Institute of Technology in Zurich)

DOI: http://hdl.handle.net/20.500.11850/287426

Thesis Comprehensive quantitative analysis of central carbon and amino-acid metabolism in Saccharomyces cerevisiae under multiple conditions by targeted proteomics

Costenoble, Roeland; Picotti, Paola; Reiter, Lukas et al. · 2011 · ETH Zurich (Swiss Federal Institute of Technology in Zurich) · DOI

Full title: Comprehensive quantitative analysis of central carbon and amino-acid metabolism in Saccharomyces cerevisiae under multiple conditions by targeted proteomics

Authors: Costenoble, Roeland; Picotti, Paola; Reiter, Lukas; Stallmach, Robert; Heinemann, Matthias; Sauer, Uwe; Aebersold, Ruedi

Year: 2011

Venue: ETH Zurich (Swiss Federal Institute of Technology in Zurich)

DOI: http://hdl.handle.net/20.500.11850/41335

Thesis Large-scale 13C-flux analysis reveals mechanistic principles of metabolic network robustness to null mutations in yeast

Blank, Lars M.; Kuepfer, Lars; Sauer, Uwe et al. · 2005 · ETH Zurich (Swiss Federal Institute of Technology in Zurich) · DOI

Full title: Large-scale 13C-flux analysis reveals mechanistic principles of metabolic network robustness to null mutations in yeast

Authors: Blank, Lars M.; Kuepfer, Lars; Sauer, Uwe; id_orcid0000-0002-5923-0770

Year: 2005

Venue: ETH Zurich (Swiss Federal Institute of Technology in Zurich)

DOI: http://hdl.handle.net/20.500.11850/32325

Thesis The Protein Cost of Metabolic Fluxes: Prediction from Enzymatic Rate Laws and Cost Minimization

Noor, Elad; id_orcid0000-0001-8776-4799; Flamholz, Avi, I et al. · 2016 · ETH Zurich (Swiss Federal Institute of Technology in Zurich) · DOI

Full title: The Protein Cost of Metabolic Fluxes: Prediction from Enzymatic Rate Laws and Cost Minimization

Authors: Noor, Elad; id_orcid0000-0001-8776-4799; Flamholz, Avi, I; Bar-Even, Arren; Davidi, Dan; Milo, Ron; Liebermeister, Wolfram

Year: 2016

Venue: ETH Zurich (Swiss Federal Institute of Technology in Zurich)

DOI: http://hdl.handle.net/20.500.11850/123705

Thesis Systematic assignment of thermodynamic constraints in metabolic network models

Kümmel, Anne; Panke, Sven; Heinemann, Matthias · 2006 · ETH Zurich (Swiss Federal Institute of Technology in Zurich) · DOI

Full title: Systematic assignment of thermodynamic constraints in metabolic network models

Authors: Kümmel, Anne; Panke, Sven; Heinemann, Matthias

Year: 2006

Venue: ETH Zurich (Swiss Federal Institute of Technology in Zurich)

DOI: http://hdl.handle.net/20.500.11850/286994

Thesis Large-scale 13C-flux analysis reveals distinct transcriptional control of respiratory and fermentative metabolism in Escherichia coli

Haverkorn van Rijsewijk, Bart R.B.; Nanchen, Annik; Nallet, Sophie et al. · 2011 · ETH Zurich (Swiss Federal Institute of Technology in Zurich) · DOI

Full title: Large-scale 13C-flux analysis reveals distinct transcriptional control of respiratory and fermentative metabolism in Escherichia coli

Authors: Haverkorn van Rijsewijk, Bart R.B.; Nanchen, Annik; Nallet, Sophie; Kleijn, Roelco J.; Sauer, Uwe

Year: 2011

Venue: ETH Zurich (Swiss Federal Institute of Technology in Zurich)

DOI: http://hdl.handle.net/20.500.11850/268321

Thesis Identifying the Preferred Subset of Enzymatic Profiles in Nonlinear Kinetic Metabolic Models via Multiobjective Global Optimization and Pareto Filters

Pozo, Carlos; Guillén Gosálbez, Gonzalo; id_orcid0000-0001-6074-8473 et al. · 2012 · ETH Zurich (Swiss Federal Institute of Technology in Zurich) · DOI

Full title: Identifying the Preferred Subset of Enzymatic Profiles in Nonlinear Kinetic Metabolic Models via Multiobjective Global Optimization and Pareto Filters

Authors: Pozo, Carlos; Guillén Gosálbez, Gonzalo; id_orcid0000-0001-6074-8473; Sorribas, Albert; Jiménez, Laureano

Year: 2012

Venue: ETH Zurich (Swiss Federal Institute of Technology in Zurich)

DOI: http://hdl.handle.net/20.500.11850/431145

Thesis Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli

Schuetz, Robert; Kuepfer, Lars; Sauer, Uwe · 2007 · ETH Zurich (Swiss Federal Institute of Technology in Zurich) · DOI

Full title: Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli

Authors: Schuetz, Robert; Kuepfer, Lars; Sauer, Uwe

Year: 2007

Venue: ETH Zurich (Swiss Federal Institute of Technology in Zurich)

DOI: http://hdl.handle.net/20.500.11850/4128

Thesis Regulatory mechanisms underlying coordination of amino acid and glucose catabolism in Escherichia coli

Zampieri, Mattia; Hörl, Manuel; Hotz, Florian et al. · 2019 · ETH Zurich (Swiss Federal Institute of Technology in Zurich) · DOI

Full title: Regulatory mechanisms underlying coordination of amino acid and glucose catabolism in Escherichia coli

Authors: Zampieri, Mattia; Hörl, Manuel; Hotz, Florian; Müller, Nicola F.; Sauer, Uwe; id_orcid0000-0002-5923-0770

Year: 2019

Venue: ETH Zurich (Swiss Federal Institute of Technology in Zurich)

DOI: http://hdl.handle.net/20.500.11850/356441

Thesis Model reduction of genome-scale metabolic models as a basis for targeted kinetic models

van Rosmalen, Rik P.; Smith R.W.; Martins Dos Santos, Vítor A.P. et al. · 2021 · ETH Zurich (Swiss Federal Institute of Technology in Zurich) · DOI

Full title: Model reduction of genome-scale metabolic models as a basis for targeted kinetic models

Authors: van Rosmalen, Rik P.; Smith R.W.; Martins Dos Santos, Vítor A.P.; Fleck, Christian; Suarez-Diez, María

Year: 2021

Venue: ETH Zurich (Swiss Federal Institute of Technology in Zurich)

DOI: http://hdl.handle.net/20.500.11850/467924

Thesis Prediction of Microbial Growth Rate versus Biomass Yield by a Metabolic Network with Kinetic Parameters

Shlomi, Tomer; Adadi, Roi; Volkmer, Benjamin et al. · 2012 · ETH Zurich (Swiss Federal Institute of Technology in Zurich) · DOI

Full title: Prediction of Microbial Growth Rate versus Biomass Yield by a Metabolic Network with Kinetic Parameters

Authors: Shlomi, Tomer; Adadi, Roi; Volkmer, Benjamin; Milo, Ron; Heinemann, Matthias

Year: 2012

Venue: ETH Zurich (Swiss Federal Institute of Technology in Zurich)

DOI: http://hdl.handle.net/20.500.11850/54657

Thesis Enhancing Microbiome Research through Genome-Scale Metabolic Modeling

Ankrah, Nana Y. D.; Bernstein, David B.; Biggs, Matthew et al. · 2021 · ETH Zurich (Swiss Federal Institute of Technology in Zurich) · DOI

Full title: Enhancing Microbiome Research through Genome-Scale Metabolic Modeling

Authors: Ankrah, Nana Y. D.; Bernstein, David B.; Biggs, Matthew; Carey, Maureen; Engevik, Melinda; García-Jiménez, Beatriz; Lakshmanan, Meiyappan; Pacheco, Alan R.; Sulheim, Snorre; Medlock, Gregory L.

Year: 2021

Venue: ETH Zurich (Swiss Federal Institute of Technology in Zurich)

DOI: http://hdl.handle.net/20.500.11850/523735

Thesis Delta FBA-Predicting metabolic flux alterations using genome-scale metabolic models and differential transcriptomic data

Ravi, Sudharshan A.; Gunawan, Rudiyanto · 2021 · ETH Zurich (Swiss Federal Institute of Technology in Zurich) · DOI

Full title: Delta FBA-Predicting metabolic flux alterations using genome-scale metabolic models and differential transcriptomic data

Authors: Ravi, Sudharshan A.; Gunawan, Rudiyanto

Year: 2021

Venue: ETH Zurich (Swiss Federal Institute of Technology in Zurich)

DOI: http://hdl.handle.net/20.500.11850/517069

Thesis Combining omics data and genome-scale models to understand metabolic adaptations in lactic acid bacteria to changing environments

Loghmani, Seyed Babak · 2022 · Heidelberg University · DOI

Full title: Combining omics data and genome-scale models to understand metabolic adaptations in lactic acid bacteria to changing environments

Authors: Loghmani, Seyed Babak

Year: 2022

Venue: Heidelberg University

DOI: https://archiv.ub.uni-heidelberg.de/volltextserver/31896/1/Loghmani_Dissertation.pdf

Thesis Network-Scale Engineering: Systems Approaches to Synthetic Biology

Boyle, Patrick M. · 2012 · Harvard University - DASH · DOI

Full title: Network-Scale Engineering: Systems Approaches to Synthetic Biology

Authors: Boyle, Patrick M.

Year: 2012

Venue: Harvard University - DASH

DOI: http://dissertations.umi.com/gsas.harvard:10298

Thesis Probabilistic Reconstruction and Comparative Systems Biology of Microbial Metabolism

Plata Caviedes, German · 2013 · Columbia University · DOI

Full title: Probabilistic Reconstruction and Comparative Systems Biology of Microbial Metabolism

Authors: Plata Caviedes, German

Year: 2013

Venue: Columbia University

DOI: https://doi.org/10.7916/D80C534R

Thesis Adaptability of metabolic networks in evolution and disease

Zirngibl, Katharina · 2021 · Heidelberg University · DOI

Full title: Adaptability of metabolic networks in evolution and disease

Authors: Zirngibl, Katharina

Year: 2021

Venue: Heidelberg University

DOI: https://archiv.ub.uni-heidelberg.de/volltextserver/27941/1/KatharinaZirngibl_PhdThesis.pdf

Thesis Pathway engineering and metabolic flux analysis of acetyl-coA biosynthesis.

Hee, Kai Sheng. · 2011 · Nanyang Technological University (NTU) · DOI

Full title: Pathway engineering and metabolic flux analysis of acetyl-coA biosynthesis.

Authors: Hee, Kai Sheng.

Year: 2011

Venue: Nanyang Technological University (NTU)

DOI: https://hdl.handle.net/10356/46134

Thesis Adaptation of a genome-scale metabolic model to study Saccharomyces cerevisiae anaerobic metabolism

Basso, Thiago Olitta · 2019 · Universidade de São Paulo – USP Digital Library · DOI

Full title: Adaptation of a genome-scale metabolic model to study Saccharomyces cerevisiae anaerobic metabolism

Authors: Basso, Thiago Olitta

Year: 2019

Venue: Universidade de São Paulo – USP Digital Library

DOI: https://proceedings.science/sinaferm/sinaferm-sheb-2019/papers/adaptation-of-a-genome-scale-metabolic-model-to-study-saccharomyces-cerevisiae-anaerobic-metabolism

Thesis Developing an unstructured model to investigate the effect of ethanol on product yields for glucose and xylose cofermentation in Saccharomyces cerevisiae 424A (LNH-ST)

Clingenpeel, Shane D. · 2014 · Purdue University · DOI

Full title: Developing an unstructured model to investigate the effect of ethanol on product yields for glucose and xylose cofermentation in Saccharomyces cerevisiae 424A (LNH-ST)

Authors: Clingenpeel, Shane D.

Year: 2014

Venue: Purdue University

DOI: https://docs.lib.purdue.edu/open_access_theses/450

Thesis A community-driven reconstruction of the Aspergillus niger metabolic network

Brandl, Julian; Aguilar-Pontes, Maria Victoria; Schäpe, Paul et al. · 2018 · Utrecht University · DOI

Full title: A community-driven reconstruction of the Aspergillus niger metabolic network

Authors: Brandl, Julian; Aguilar-Pontes, Maria Victoria; Schäpe, Paul; Noerregaard, Anders; Arvas, Mikko; Ram, Arthur F J; Meyer, Vera; Tsang, Adrian; de Vries, Ronald P; Andersen, Mikael R

Year: 2018

Venue: Utrecht University

DOI: https://dspace.library.uu.nl/handle/1874/376160

Thesis Systems-level characterization and reconstitution of genetic regulatory networks in Escherichia coli for rational strain optimization : towards improved bioprocesses

Kang, A Ram · 2012 · Nanyang Technological University (NTU) · DOI

Full title: Systems-level characterization and reconstitution of genetic regulatory networks in Escherichia coli for rational strain optimization : towards improved bioprocesses

Authors: Kang, A Ram

Year: 2012

Venue: Nanyang Technological University (NTU)

DOI: https://hdl.handle.net/10356/50704

Thesis Understanding the regulation of the metabolic network associated with fermentative hydrogen production in Clostridium butyricum.

Cai, Guiqin · 2012 · University of Adelaide · DOI

Full title: Understanding the regulation of the metabolic network associated with fermentative hydrogen production in Clostridium butyricum.

Authors: Cai, Guiqin

Year: 2012

Venue: University of Adelaide

DOI: http://hdl.handle.net/2440/79589

Thesis Heterologous expression and characterization of bacterial 2-C-methyl-d-erythritol-4-phosphate pathway in Saccharomyces cerevisiae

Formenti, Luca Riccardo; Phon, Too Heng; Nielsen, Michael Lynge et al. · 2017 · Massachusetts Institute of Technology (MIT) · DOI

Full title: Heterologous expression and characterization of bacterial 2-C-methyl-d-erythritol-4-phosphate pathway in Saccharomyces cerevisiae

Authors: Formenti, Luca Riccardo; Phon, Too Heng; Nielsen, Michael Lynge; Lantz, Anna Eliasson; Kielland-Brandt, Morten C.; Carlsen, Simon; Zhou, Kang; Stephanopoulos, Gregory; Parayil Kumaran, Ajikumar

Year: 2017

Venue: Massachusetts Institute of Technology (MIT)

DOI: http://hdl.handle.net/1721.1/107177

Thesis Genome-Scale Reconstruction and Analysis of Eukaryotic Metabolic Networks

Hurlen, Natalie Christine · 2016 · University of California, San Diego (UCSD) · DOI

Full title: Genome-Scale Reconstruction and Analysis of Eukaryotic Metabolic Networks

Authors: Hurlen, Natalie Christine

Year: 2016

Venue: University of California, San Diego (UCSD)

DOI: https://escholarship.org/uc/item/5rq7d96x

Thesis Prediction Without Training: Expanding Mechanistic Models for Microbial Insight

Neal, Maxwell Julian · 2025 · University of California, San Diego (UCSD) · DOI

Full title: Prediction Without Training: Expanding Mechanistic Models for Microbial Insight

Authors: Neal, Maxwell Julian

Year: 2025

Venue: University of California, San Diego (UCSD)

DOI: https://escholarship.org/uc/item/4010k919

Thesis Enhancing the Reconstruction and Application of Models of Metabolism and Gene Expression

Tibocha Bonilla, Juan David · 2024 · University of California, San Diego (UCSD) · DOI

Full title: Enhancing the Reconstruction and Application of Models of Metabolism and Gene Expression

Authors: Tibocha Bonilla, Juan David

Year: 2024

Venue: University of California, San Diego (UCSD)

DOI: https://escholarship.org/uc/item/1mn937c1

Thesis Applications of Metabolic Modelling: Understanding Energy Production in Electricity-Producing Shewanella oneidensis MR-1 and Lipid-Producing Nannochloropsis gaditana

Gao, Mengyu · 2015 · White Rose eTheses (Leeds, Sheffield, York) · DOI

Full title: Applications of Metabolic Modelling: Understanding Energy Production in Electricity-Producing Shewanella oneidensis MR-1 and Lipid-Producing Nannochloropsis gaditana

Authors: Gao, Mengyu

Year: 2015

Venue: White Rose eTheses (Leeds, Sheffield, York)

DOI: https://etheses.whiterose.ac.uk/id/eprint/8871/1/Gao_thesis_2015_2.docx

Thesis Computational Methods for Reconstruction and Analysis of Genome-Scale Metabolic Networks

Pitkänen, Esa · 2010 · University of Helsinki (HELDA) · DOI

Full title: Computational Methods for Reconstruction and Analysis of Genome-Scale Metabolic Networks

Authors: Pitkänen, Esa

Year: 2010

Venue: University of Helsinki (HELDA)

DOI: http://hdl.handle.net/10138/21328

Thesis Transcriptome and proteome analysis of xylose-metabolising Saccharomyces cerevisiae

Salusjärvi, Laura · 2010 · University of Helsinki (HELDA) · DOI

Full title: Transcriptome and proteome analysis of xylose-metabolising Saccharomyces cerevisiae

Authors: Salusjärvi, Laura

Year: 2010

Venue: University of Helsinki (HELDA)

DOI: http://hdl.handle.net/10138/22385

Thesis Machine Learning for Uncertainty Reduction in Biochemical Kinetic Models

Miskovic, Ljubisa; Beal, Jonas; Moret, Michael et al. · 2018 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: Machine Learning for Uncertainty Reduction in Biochemical Kinetic Models

Authors: Miskovic, Ljubisa; Beal, Jonas; Moret, Michael; Hatzimanikatis, Vassily

Year: 2018

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/149573

Thesis Predicted responses of a large-scale Pseudomonas putida KT2440 kinetic metabolic model to several single-gene knockouts are consistent with experimental observations

Tokic, Milenko; Miskovic, Ljubisa; Hatzimanikatis, Vassily · 2018 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: Predicted responses of a large-scale Pseudomonas putida KT2440 kinetic metabolic model to several single-gene knockouts are consistent with experimental observations

Authors: Tokic, Milenko; Miskovic, Ljubisa; Hatzimanikatis, Vassily

Year: 2018

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/149575

Thesis Computational analysis of Pseudomonas Putida metabolism Using Large-scale Kinetic Models

Tokic, Milenko; Miskovic, Ljubisa; Hatzimanikatis, Vassily · 2018 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: Computational analysis of Pseudomonas Putida metabolism Using Large-scale Kinetic Models

Authors: Tokic, Milenko; Miskovic, Ljubisa; Hatzimanikatis, Vassily

Year: 2018

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/147813

Thesis Identification of the enzymes responsible for diverse phenotypic states of yeast lipid metabolism using comprehensive mechanistic models

Tsouka, Sofia · 2018 · École polytechnique fédérale de Lausanne (EPFL) · DOI

Full title: Identification of the enzymes responsible for diverse phenotypic states of yeast lipid metabolism using comprehensive mechanistic models

Authors: Tsouka, Sofia

Year: 2018

Venue: École polytechnique fédérale de Lausanne (EPFL)

DOI: https://infoscience.epfl.ch/handle/20.500.14299/149684

Thesis Systems assessment of transcriptional regulation on central carbon metabolism by Cra and CRP

Kim, Donghyuk; Seo, Sang Woo; Gao, Ye et al. · 2018 · Technical University of Denmark (DTU) · DOI

Full title: Systems assessment of transcriptional regulation on central carbon metabolism by Cra and CRP

Authors: Kim, Donghyuk; Seo, Sang Woo; Gao, Ye; Nam, Hojung; Guzman, Gabriela I.; Cho, Byung-Kwan; Palsson, Bernhard O.; id_orcid 0000-0003-2357-6785

Year: 2018

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/599dc867-877a-464c-9ac8-6d9de9a7520b

Thesis The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes

Seaver, Samuel M. D.; Liu, Filipe; Zhang, Qizhi et al. · 2021 · Technical University of Denmark (DTU) · DOI

Full title: The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes

Authors: Seaver, Samuel M. D.; Liu, Filipe; Zhang, Qizhi; Jeffryes, James; Faria, José P.; Edirisinghe, Janaka N.; Mundy, Michael; Chia, Nicholas; Noor, Elad; Beber, Moritz E.; id_orcid 0000-0003-2406-1978; Best, Aaron A.; DeJongh, Matthew; Kimbrel, Jeffrey A.; D'haeseleer, Patrik; McCorkle, Sean R.; Bolton, Jay R.; Pearson, Erik; Canon, Shane; Wood-Charlson, Elisha M.; Cottingham, Robert W.; Arkin, Adam P.; Henry, Christopher S.

Year: 2021

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/5d855a28-cf61-4734-8b32-d3eafa52424c

Thesis Adaptations in metabolism and protein translation give rise to the Crabtree effect in yeast

Malina, Carl; Yu, Rosemary; Bjorkeroth, Johan et al. · 2021 · Technical University of Denmark (DTU) · DOI

Full title: Adaptations in metabolism and protein translation give rise to the Crabtree effect in yeast

Authors: Malina, Carl; Yu, Rosemary; Bjorkeroth, Johan; Kerkhoven, Eduard J.; Nielsen, Jens

Year: 2021

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/60146c8d-be0d-4f08-bab0-fd4cc21686cb

Thesis The Expanding Computational Toolbox for Engineering Microbial Phenotypes at the Genome Scale

Zielinski, Daniel Craig; Patel, Arjun; Palsson, Bernhard O et al. · 2020 · Technical University of Denmark (DTU) · DOI

Full title: The Expanding Computational Toolbox for Engineering Microbial Phenotypes at the Genome Scale

Authors: Zielinski, Daniel Craig; Patel, Arjun; Palsson, Bernhard O; id_orcid 0000-0003-2357-6785

Year: 2020

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/5c4ece29-33bb-4954-92aa-2b7734453cb4

Thesis BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree

Norsigian, Charles J.; Pusarla, Neha; McConn, John Luke et al. · 2020 · Technical University of Denmark (DTU) · DOI

Full title: BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree

Authors: Norsigian, Charles J.; Pusarla, Neha; McConn, John Luke; Yurkovich, James T.; Dräger, Andreas; Palsson, Bernhard O.; id_orcid 0000-0003-2357-6785; King, Zachary

Year: 2020

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/66e6b978-0bab-43c5-b81b-f9ab14993d9d

Thesis Reliable and efficient solution of genome-scale models of Metabolism and macromolecular Expression

Ma, Ding; Yang, Laurence; Fleming, Ronan M. T. et al. · 2017 · Technical University of Denmark (DTU) · DOI

Full title: Reliable and efficient solution of genome-scale models of Metabolism and macromolecular Expression

Authors: Ma, Ding; Yang, Laurence; Fleming, Ronan M. T.; Thiele, Ines; Palsson, Bernhard; id_orcid 0000-0003-2357-6785; Saunders, Michael A.

Year: 2017

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/5c6e0bb8-7db3-4934-9d71-484bc0d18d15

Thesis Mass Action Stoichiometric. Simulation for Cell Factory Design

Matos, Marta R. A. · 2018 · Technical University of Denmark (DTU) · DOI

Full title: Mass Action Stoichiometric. Simulation for Cell Factory Design

Authors: Matos, Marta R. A.

Year: 2018

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/5dca35ef-9f63-41d1-b780-3c50e6bd0bf4

Thesis Constraining genome-scale models to represent the bow tie structure of metabolism for 13C metabolic flux analysis

Backman, Tyler W.H.; Ando, David; Singh, Jahnavi et al. · 2018 · Technical University of Denmark (DTU) · DOI

Full title: Constraining genome-scale models to represent the bow tie structure of metabolism for 13C metabolic flux analysis

Authors: Backman, Tyler W.H.; Ando, David; Singh, Jahnavi; Keasling, Jay D.; Martín, Héctor García

Year: 2018

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/5c6aa2d9-4d5b-41ed-a760-91d6f1098c13

Thesis Development, Validation and Comprehensive Sensitivity Analysis of a Fermentation Model Expediting the Process Design of a Biorefinery

Vollmer, Nikolaus I.; id_orcid 0000-0002-5604-3099; Gernaey, Krist V. et al. · 2019 · Technical University of Denmark (DTU) · DOI

Full title: Development, Validation and Comprehensive Sensitivity Analysis of a Fermentation Model Expediting the Process Design of a Biorefinery

Authors: Vollmer, Nikolaus I.; id_orcid 0000-0002-5604-3099; Gernaey, Krist V.; id_orcid 0000-0002-0364-1773; Mussatto, Solange I.; id_orcid 0000-0002-7182-6198; Sin, Gürkan; id_orcid 0000-0003-0513-4502

Year: 2019

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/63b64ec8-ca7b-45fe-8088-d6c242d7abad

Thesis Heterologous expression and characterization of bacterial 2-C-methyl-d-erythritol-4-phosphate pathway in Saccharomyces cerevisiae

Carlsen, Simon; Ajikumar, Parayil Kumaran; Formenti, Luca Riccardo et al. · 2013 · Technical University of Denmark (DTU) · DOI

Full title: Heterologous expression and characterization of bacterial 2-C-methyl-d-erythritol-4-phosphate pathway in Saccharomyces cerevisiae

Authors: Carlsen, Simon; Ajikumar, Parayil Kumaran; Formenti, Luca Riccardo; Zhou, Kang; Phon, Too Heng; Nielsen, Michael Lynge; Eliasson Lantz, Anna; Kielland-Brandt, Morten; id_orcid 0000-0002-1272-3877; Stephanopoulos, Gregory

Year: 2013

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/60357545-6000-49a6-8a45-e4c54d451922

Thesis Genome-scale metabolic modeling of P. thermoglucosidasius NCIMB 11955 reveals metabolic bottlenecks in anaerobic metabolism

Mol, Viviënne; Bennett, Martyn; Sánchez, Benjamín J. et al. · 2021 · Technical University of Denmark (DTU) · DOI

Full title: Genome-scale metabolic modeling of P. thermoglucosidasius NCIMB 11955 reveals metabolic bottlenecks in anaerobic metabolism

Authors: Mol, Viviënne; Bennett, Martyn; Sánchez, Benjamín J.; Lisowska, Beata K.; Herrgård, Markus J.; Nielsen, Alex Toftgaard; Leak, David J.; Sonnenschein, Nikolaus; id_orcid 0000-0002-7581-4936

Year: 2021

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/5fd1a4cc-3aed-41ea-887a-78bdac847b3f

Thesis Simultaneous application of enzyme and thermodynamic constraints to metabolic models using an updated Python implementation of GECKO

Carrasco Muriel, Jorge; Long, Christopher; Sonnenschein, Nikolaus et al. · 2023 · Technical University of Denmark (DTU) · DOI

Full title: Simultaneous application of enzyme and thermodynamic constraints to metabolic models using an updated Python implementation of GECKO

Authors: Carrasco Muriel, Jorge; Long, Christopher; Sonnenschein, Nikolaus; id_orcid 0000-0002-7581-4936

Year: 2023

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/66ca6afb-ca5d-4f6c-a301-8dc2ec9d4491

Thesis Genome-scale metabolic reconstructions of multiple Salmonella strains reveal serovar-specific metabolic traits

Seif, Yara; Kavvas, Erol; Lachance, Jean-Christophe et al. · 2018 · Technical University of Denmark (DTU) · DOI

Full title: Genome-scale metabolic reconstructions of multiple Salmonella strains reveal serovar-specific metabolic traits

Authors: Seif, Yara; Kavvas, Erol; Lachance, Jean-Christophe; Yurkovich, James T.; Nuccio, Sean-Paul; Fang, Xin; Catoiu, Edward; Raffatellu, Manuela; Palsson, Bernhard O.; id_orcid 0000-0003-2357-6785; Monk, Jonathan M.

Year: 2018

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/6265b868-ba4f-442b-ad03-65a5c465af90

Thesis Genome‐scale metabolic modeling reveals key features of a minimal gene set

Lachance, Jean‐Christophe; Matteau, Dominick; Brodeur, Joëlle et al. · 2021 · Technical University of Denmark (DTU) · DOI

Full title: Genome‐scale metabolic modeling reveals key features of a minimal gene set

Authors: Lachance, Jean‐Christophe; Matteau, Dominick; Brodeur, Joëlle; Lloyd, Colton J; Mih, Nathan; King, Zachary A; Knight, Thomas F; Feist, Adam M; id_orcid 0000-0002-8630-4800; Monk, Jonathan M; Palsson, Bernhard O; id_orcid 0000-0003-2357-6785; Jacques, Pierre‐Étienne; Rodrigue, Sébastien

Year: 2021

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/6c5fb099-d5ce-4372-8b47-e669ebfea949

Thesis Methods for predictable and accelerated engineering of metabolism in eukaryotes

Petersen, Søren Dalsgård; id_orcid 0000-0003-4104-5144 · 2019 · Technical University of Denmark (DTU) · DOI

Full title: Methods for predictable and accelerated engineering of metabolism in eukaryotes

Authors: Petersen, Søren Dalsgård; id_orcid 0000-0003-4104-5144

Year: 2019

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/697b48dd-33be-40fb-b1be-16a108f71163

Thesis Principles of proteome allocation are revealed using proteomic data and genome-scale models

Yang, Laurence; Yurkovich, James T.; Lloyd, Colton J. et al. · 2016 · Technical University of Denmark (DTU) · DOI

Full title: Principles of proteome allocation are revealed using proteomic data and genome-scale models

Authors: Yang, Laurence; Yurkovich, James T.; Lloyd, Colton J.; Ebrahim, Ali; Saunders, Michael A.; Palsson, Bernhard; id_orcid 0000-0003-2357-6785

Year: 2016

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/6d11117c-622a-46f0-bb23-c40d91539dda

Thesis Computational tools and analytical methods for effective metabolic engineering of microbial cell factories

Taylor Parkins, Shannara Kayleigh; id_orcid 0000-0003-4728-2159 · 2023 · Technical University of Denmark (DTU) · DOI

Full title: Computational tools and analytical methods for effective metabolic engineering of microbial cell factories

Authors: Taylor Parkins, Shannara Kayleigh; id_orcid 0000-0003-4728-2159

Year: 2023

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/6ced90b7-de9c-4445-bb8d-c0a58b4959c8

Thesis Identification of growth-coupled production strains considering protein costs and kinetic variability

Dinh, Hoang V.; King, Zachary A.; Palsson, Bernhard O. et al. · 2018 · Technical University of Denmark (DTU) · DOI

Full title: Identification of growth-coupled production strains considering protein costs and kinetic variability

Authors: Dinh, Hoang V.; King, Zachary A.; Palsson, Bernhard O.; id_orcid 0000-0003-2357-6785; Feist, Adam M.; id_orcid 0000-0002-8630-4800

Year: 2018

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/6c666f6f-48e9-45a7-9228-24af7d38552a

Thesis A community-driven reconstruction of the Aspergillus niger metabolic network

Brandl, Julian; Aguilar-Pontes, Maria Victoria; Schäpe, Paul et al. · 2018 · Technical University of Denmark (DTU) · DOI

Full title: A community-driven reconstruction of the Aspergillus niger metabolic network

Authors: Brandl, Julian; Aguilar-Pontes, Maria Victoria; Schäpe, Paul; Nørregaard, Anders; Arvas, Mikko; Ram, Arthur F. J.; Meyer, Vera; Tsang, Adrian; de Vries, Ronald P.; Andersen, Mikael Rørdam; id_orcid 0000-0003-4794-6808

Year: 2018

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/700a4b31-b046-49c7-896e-bf25567a5b40

Thesis Development of an intracellular glycolytic flux sensor for high throughput applications in E.coli

Lehning, Christina Eva · 2017 · Technical University of Denmark (DTU) · DOI

Full title: Development of an intracellular glycolytic flux sensor for high throughput applications in E.coli

Authors: Lehning, Christina Eva

Year: 2017

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/6d1af514-be4e-4301-b52a-4525f8639c5d

Thesis Modeling for understanding and engineering metabolism

Nielsen, Jens; Petranovic, Dina · 2025 · Technical University of Denmark (DTU) · DOI

Full title: Modeling for understanding and engineering metabolism

Authors: Nielsen, Jens; Petranovic, Dina

Year: 2025

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/75fb593d-049b-4d93-84f8-7653d7e4da90

Thesis Computation of condition-dependent proteome allocation reveals variability in the macro and micro nutrient requirements for growth

Lloyd, Colton J.; Monk, Jonathan; Yang, Laurence et al. · 2021 · Technical University of Denmark (DTU) · DOI

Full title: Computation of condition-dependent proteome allocation reveals variability in the macro and micro nutrient requirements for growth

Authors: Lloyd, Colton J.; Monk, Jonathan; Yang, Laurence; Ebrahim, Ali; Palsson, Bernhard O.; id_orcid 0000-0003-2357-6785

Year: 2021

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/6b77a1ef-cf52-45a0-b100-265d61b42ad3

Thesis BiGG Models: A platform for integrating, standardizing and sharing genome-scale models

King, Zachary A.; Lu, Justin; Dräger, Andreas et al. · 2016 · Technical University of Denmark (DTU) · DOI

Full title: BiGG Models: A platform for integrating, standardizing and sharing genome-scale models

Authors: King, Zachary A.; Lu, Justin; Dräger, Andreas; Miller, Philip; Federowicz, Stephen; Lerman, Joshua A.; Ebrahim, Ali; Palsson, Bernhard; id_orcid 0000-0003-2357-6785; Lewis, Nathan

Year: 2016

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/71799399-3bf7-430d-88a8-ff1a1c3d4c94

Thesis Genome-scale model of metabolism and gene expression provides a multi-scale description of acid stress responses in Escherichia coli

Du, Bin; Yang, Laurence; Lloyd, Colton J. et al. · 2019 · Technical University of Denmark (DTU) · DOI

Full title: Genome-scale model of metabolism and gene expression provides a multi-scale description of acid stress responses in Escherichia coli

Authors: Du, Bin; Yang, Laurence; Lloyd, Colton J.; Fang, Xin; Palsson, Bernhard ; id_orcid 0000-0003-2357-6785

Year: 2019

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/7ad7a238-5b96-4b00-9916-d419015e26fd

Thesis Genome scale models of yeast: towards standardized evaluation and consistent omic integration

Sanchez, Benjamin J.; Nielsen, Jens · 2015 · Technical University of Denmark (DTU) · DOI

Full title: Genome scale models of yeast: towards standardized evaluation and consistent omic integration

Authors: Sanchez, Benjamin J.; Nielsen, Jens

Year: 2015

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/6faa78ce-0fbc-43d4-a40a-635c5ecf43c3

Thesis Improved vanillin production in baker's yeast through in silico design

Brochado, Ana Rita; Matos, Cláudia; Møller, Birger L. et al. · 2010 · Technical University of Denmark (DTU) · DOI

Full title: Improved vanillin production in baker's yeast through in silico design

Authors: Brochado, Ana Rita; Matos, Cláudia; Møller, Birger L.; Hansen, Jørgen; Mortensen, Uffe H.; Patil, Kiran Raosaheb

Year: 2010

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/7eeeb11a-5367-4e03-b5d6-f34785c588c1

Thesis CRISPRi-mediated metabolic switch enables concurrent aerobic and synthetic anaerobic fermentations in engineered consortium

Rong, Yixin; Frey, Adrian; id_orcid 0009-0008-7716-4042 et al. · 2024 · Technical University of Denmark (DTU) · DOI

Full title: CRISPRi-mediated metabolic switch enables concurrent aerobic and synthetic anaerobic fermentations in engineered consortium

Authors: Rong, Yixin; Frey, Adrian; id_orcid 0009-0008-7716-4042; Özdemir, Emre; id_orcid 0000-0001-5548-6720; Sainz de la Maza Larrea, Arrate; Li, Songyuan; Nielsen, Alex Toftgaard; Jensen, Sheila Ingemann; id_orcid 0000-0001-8277-5907

Year: 2024

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/7415d711-3048-4df6-af78-a3fbfc720dad

Thesis Yeast Systems Biology: Model organism and Cell Factory

Nielsen, Jens · 2019 · Technical University of Denmark (DTU) · DOI

Full title: Yeast Systems Biology: Model organism and Cell Factory

Authors: Nielsen, Jens

Year: 2019

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/7e1c5273-9c1e-4048-a7e3-5adb5644906d

Thesis Mapping condition-dependent regulation of metabolism in yeast through genome-scale modeling

Österlund, Tobias; Nookaew, Intawat; Bordel, Sergio et al. · 2013 · Technical University of Denmark (DTU) · DOI

Full title: Mapping condition-dependent regulation of metabolism in yeast through genome-scale modeling

Authors: Österlund, Tobias; Nookaew, Intawat; Bordel, Sergio; Nielsen, Jens

Year: 2013

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/83e87b72-797f-4ed6-9818-866298439307

Thesis Probing efficient microbial CO 2 utilisation through metabolic and process modelling

Gorter de Vries, Philip J.; id_orcid 0000-0002-0311-5634; Mol, Viviënne et al. · 2024 · Technical University of Denmark (DTU) · DOI

Full title: Probing efficient microbial CO 2 utilisation through metabolic and process modelling

Authors: Gorter de Vries, Philip J.; id_orcid 0000-0002-0311-5634; Mol, Viviënne; Sonnenschein, Nikolaus; id_orcid 0000-0002-7581-4936; Jensen, Torbjørn Ølshøj; Nielsen, Alex Toftgaard

Year: 2024

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/74c8b1ed-ec94-49f6-b08a-22dbb6f7cef4

Thesis Systems biology solutions for biochemical production challenges

Hansen, Anne Sofie Lærke; id_orcid 0000-0003-2771-4671; Lennen, Rebecca M et al. · 2017 · Technical University of Denmark (DTU) · DOI

Full title: Systems biology solutions for biochemical production challenges

Authors: Hansen, Anne Sofie Lærke; id_orcid 0000-0003-2771-4671; Lennen, Rebecca M; Sonnenschein, Nikolaus; id_orcid 0000-0002-7581-4936; Herrgard, Markus

Year: 2017

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/82d70d8f-916a-4617-916e-00b48a0029a9

Thesis Acetol biosynthesis enables NADPH balance during nitrogen limitation in engineered Escherichia coli

Sudarsan, Suresh; Demling, Philipp; Ozdemir, Emre et al. · 2025 · Technical University of Denmark (DTU) · DOI

Full title: Acetol biosynthesis enables NADPH balance during nitrogen limitation in engineered Escherichia coli

Authors: Sudarsan, Suresh; Demling, Philipp; Ozdemir, Emre; id_orcid 0000-0001-5548-6720; Ben Ammar, Aziz; Mennicken, Philip; Buescher, Joerg M.; Meurer, Guido; Ebert, Birgitta E.; Blank, Lars M.

Year: 2025

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/84d966a5-cdaf-4ddc-9e4e-b614305b2a46

Thesis Diagnosis and mitigation of the systemic impact of genome reduction in Escherichia coli DGF-298

Champie, Antoine; Lachance, Jean Christophe; Sastry, Anand et al. · 2024 · Technical University of Denmark (DTU) · DOI

Full title: Diagnosis and mitigation of the systemic impact of genome reduction in Escherichia coli DGF-298

Authors: Champie, Antoine; Lachance, Jean Christophe; Sastry, Anand; Matteau, Dominick; Lloyd, Colton J.; Grenier, Frédéric; Lamoureux, Cameron R.; Jeanneau, Simon; Feist, Adam M.; id_orcid 0000-0002-8630-4800; Jacques, Pierre Étienne; Palsson, Bernhard O.; id_orcid 0000-0003-2357-6785; Rodrigue, Sébastien

Year: 2024

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/82c5ebb6-c054-4d59-98fe-d3f38249c717

Thesis Bayesian genome scale modelling identifies thermal determinants of yeast metabolism

Li, Gang; Hu, Yating; Jan Zrimec, Zrimec et al. · 2021 · Technical University of Denmark (DTU) · DOI

Full title: Bayesian genome scale modelling identifies thermal determinants of yeast metabolism

Authors: Li, Gang; Hu, Yating; Jan Zrimec, Zrimec; Luo, Hao; Wang, Hao; Zelezniak, Aleksej; Ji, Boyang; Nielsen, Jens

Year: 2021

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/8acf09fc-5d06-471b-8507-8b89e1488a90

Thesis The JBEI quantitative metabolic modeling library (jQMM): a python library for modeling microbial metabolism

Birkel, Garrett W.; Ghosh, Amit; Kumar, Vinay S. et al. · 2017 · Technical University of Denmark (DTU) · DOI

Full title: The JBEI quantitative metabolic modeling library (jQMM): a python library for modeling microbial metabolism

Authors: Birkel, Garrett W.; Ghosh, Amit; Kumar, Vinay S.; Weaver, Daniel; Ando, David; Backman, Tyler W. H.; Arkin, Adam Paul; Keasling, Jay D.; Martin, Hector Garcia

Year: 2017

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/91bbd75c-084f-4a30-9c06-bc0a9f5d5d65

Thesis Systems biology-guided identification of synthetic lethal gene pairs and its potential use to discover antibiotic combinations

Aziz, Ramy K.; Monk, Jonathan M.; Lewis, R. M. et al. · 2015 · Technical University of Denmark (DTU) · DOI

Full title: Systems biology-guided identification of synthetic lethal gene pairs and its potential use to discover antibiotic combinations

Authors: Aziz, Ramy K.; Monk, Jonathan M.; Lewis, R. M.; Loh, Suh I.; Mishra, A.; Nagle, A. A.; Satyanarayana, C.; Dhakshinamoorthy, S.; Luche, M.; Kitchen, D. B.; Andrews, K. A.; Fong, N. L.; Li, H. J.; Palsson, B. O.; Charusanti, Pep; id_orcid 0000-0003-0009-6615

Year: 2015

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/7c5e19b9-eaa1-44b3-8192-c422d98a88fc

Thesis Analysis of Aspergillus nidulans metabolism at the genome-scale

David, Helga; Ozcelik, İlknur Ş; Hofmann, Gerald et al. · 2008 · Technical University of Denmark (DTU) · DOI

Full title: Analysis of Aspergillus nidulans metabolism at the genome-scale

Authors: David, Helga; Ozcelik, İlknur Ş; Hofmann, Gerald; Nielsen, Jens

Year: 2008

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/7b849e31-36e5-46d7-b20f-8b4ee2d906e3

Thesis Constraint-based modeling of yeast mitochondria reveals the dynamics of protein import and iron-sulfur cluster biogenesis

Malina, Carl; Di Bartolomeo, Francesca; Kerkhoven, Eduard J. et al. · 2021 · Technical University of Denmark (DTU) · DOI

Full title: Constraint-based modeling of yeast mitochondria reveals the dynamics of protein import and iron-sulfur cluster biogenesis

Authors: Malina, Carl; Di Bartolomeo, Francesca; Kerkhoven, Eduard J.; Nielsen, Jens

Year: 2021

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/9066bc6b-8a30-46c5-96ff-5bba81b65bc2

Thesis A workflow for generating multi-strain genome-scale metabolic models of prokaryotes

Norsigian, Charles J.; Fang, Xin; Seif, Yara et al. · 2020 · Technical University of Denmark (DTU) · DOI

Full title: A workflow for generating multi-strain genome-scale metabolic models of prokaryotes

Authors: Norsigian, Charles J.; Fang, Xin; Seif, Yara; Monk, Jonathan M.; Palsson, Bernhard O.; id_orcid 0000-0003-2357-6785

Year: 2020

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/915c349a-70f1-4f54-88c9-b33047aa535a

Thesis SLIMEr: probing flexibility of lipid metabolism in yeast with an improved constraint-based modeling framework

Sanchez, Benjamin J.; Li, Feiran; Kerkhoven, Eduard J. et al. · 2019 · Technical University of Denmark (DTU) · DOI

Full title: SLIMEr: probing flexibility of lipid metabolism in yeast with an improved constraint-based modeling framework

Authors: Sanchez, Benjamin J.; Li, Feiran; Kerkhoven, Eduard J.; Nielsen, Jens

Year: 2019

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/9cc81ad1-011f-467e-8566-d9b9a74f57ad

Thesis In vitro turnover numbers do not reflect in vivo activities of yeast enzymes

Chen, Yu; Nielsen, Jens · 2021 · Technical University of Denmark (DTU) · DOI

Full title: In vitro turnover numbers do not reflect in vivo activities of yeast enzymes

Authors: Chen, Yu; Nielsen, Jens

Year: 2021

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/a71b968f-b161-44c7-af91-1bc507b13684

Thesis Metabolic Fluxes Using Deep Learning Based on Enzyme Variations:Application to Glycolysis in Entamoeba histolytica

Oulia, Freddy; Charton, Philippe; Lo-Thong-Viramoutou, Ophélie et al. · 2024 · Technical University of Denmark (DTU) · DOI

Full title: Metabolic Fluxes Using Deep Learning Based on Enzyme Variations:Application to Glycolysis in Entamoeba histolytica

Authors: Oulia, Freddy; Charton, Philippe; Lo-Thong-Viramoutou, Ophélie; Acevedo-Rocha, Carlos G.; Liu, Wei; Huynh, Du; Damour, Cédric; Wang, Jingbo; Cadet, Frederic

Year: 2024

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/93851283-2e55-4d7f-9262-5504188d9642

Thesis Digital models in biotechnology: Towards multi-scale integration and implementation

Hartmann, Fabian S.F.; id_orcid 0000-0001-5394-1865; Udugama, Isuru A. et al. · 2022 · Technical University of Denmark (DTU) · DOI

Full title: Digital models in biotechnology: Towards multi-scale integration and implementation

Authors: Hartmann, Fabian S.F.; id_orcid 0000-0001-5394-1865; Udugama, Isuru A.; Seibold, Gerd M.; id_orcid 0000-0002-9823-8134; Sugiyama, Hirokazu; Gernaey, Krist V.; id_orcid 0000-0002-0364-1773

Year: 2022

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/a9e1d47f-53b8-41c4-993c-fc97c01d2690

Thesis Scale-down study of adaptation in Saccharomyces cerevisiae chemostat cultures for heterologous protein production

Wright, Naia Risager · 2021 · Technical University of Denmark (DTU) · DOI

Full title: Scale-down study of adaptation in Saccharomyces cerevisiae chemostat cultures for heterologous protein production

Authors: Wright, Naia Risager

Year: 2021

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/8d73173b-041b-4ee7-8665-29be40d6cdd1

Thesis BioMet Toolbox: genome-wide analysis of metabolism

Cvijovic, M.; Olivares Hernandez, Roberto; Agren, R. et al. · 2010 · Technical University of Denmark (DTU) · DOI

Full title: BioMet Toolbox: genome-wide analysis of metabolism

Authors: Cvijovic, M.; Olivares Hernandez, Roberto; Agren, R.; Dahr, N.; Vongsangnak, Wanwipa; Nookaew, I.; Patil, Kiran Raosaheb; Nielsen, J.

Year: 2010

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/937fc86a-f9c2-43e5-817b-30b3fbe09ac3

Thesis Improved annotation through genome-scale metabolic modeling of Aspergillus oryzae

Vongsangnak, Wanwipa; Olsen, Peter; Hansen, Kim et al. · 2008 · Technical University of Denmark (DTU) · DOI

Full title: Improved annotation through genome-scale metabolic modeling of Aspergillus oryzae

Authors: Vongsangnak, Wanwipa; Olsen, Peter; Hansen, Kim; Krogsgaard, Steen; Nielsen, Jens

Year: 2008

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/89736fe7-a0e9-47ef-8355-50bae04e65b2

Thesis Fast growth phenotype of E. coli K-12 from adaptive laboratory evolution does not require intracellular flux rewiring

Long, Christopher P.; Gonzalez, Jacqueline E.; Feist, Adam M. et al. · 2017 · Technical University of Denmark (DTU) · DOI

Full title: Fast growth phenotype of E. coli K-12 from adaptive laboratory evolution does not require intracellular flux rewiring

Authors: Long, Christopher P.; Gonzalez, Jacqueline E.; Feist, Adam M.; id_orcid 0000-0002-8630-4800; Palsson, Bernhard O; id_orcid 0000-0003-2357-6785; Antoniewicz, Maciek R.

Year: 2017

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/8c86285a-7d95-413e-95b6-70c1af73ecd4

Thesis Metabolic Engineering of Saccharomyces cerevisiae:From p-Coumaric Acid to Rosmarinic Acid

Borja Zamfir, Gheorghe Manuel · 2024 · Technical University of Denmark (DTU) · DOI

Full title: Metabolic Engineering of Saccharomyces cerevisiae:From p-Coumaric Acid to Rosmarinic Acid

Authors: Borja Zamfir, Gheorghe Manuel

Year: 2024

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/a46ad662-7158-4f6c-8685-c1fbdd6b3bcd

Thesis A Genome-Scale Metabolic Model for Methylococcus capsulatus (Bath) Suggests Reduced Efficiency Electron Transfer to the Particulate Methane Monooxygenase

Lieven, Christian; Petersen, Leander A. H.; Jørgensen, Sten Bay et al. · 2018 · Technical University of Denmark (DTU) · DOI

Full title: A Genome-Scale Metabolic Model for Methylococcus capsulatus (Bath) Suggests Reduced Efficiency Electron Transfer to the Particulate Methane Monooxygenase

Authors: Lieven, Christian; Petersen, Leander A. H.; Jørgensen, Sten Bay; id_orcid 0000-0002-3179-972X; Gernaey, Krist V.; id_orcid 0000-0002-0364-1773; Herrgard, Markus J.; Sonnenschein, Nikolaus; id_orcid 0000-0002-7581-4936

Year: 2018

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/a0369532-98e5-4c0b-a399-b06e4ebf379b

Thesis COBRAme: A computational framework for genome-scale models of metabolism and gene expression

Lloyd, Colton J.; Ebrahim, Ali; Yang, Laurence et al. · 2018 · Technical University of Denmark (DTU) · DOI

Full title: COBRAme: A computational framework for genome-scale models of metabolism and gene expression

Authors: Lloyd, Colton J.; Ebrahim, Ali; Yang, Laurence; King, Zachary A.; Catoiu, Edward; O'Brien, Edward J.; Liu, Joanne K.; Polsson, Bernhard O.; id_orcid 0000-0003-2357-6785

Year: 2018

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/a93a304b-3cfe-4cd9-adf3-d9062e8bd1f7

Thesis A metabolic reconstruction of Lactobacillus reuteri JCM 1112 and analysis of its potential as a cell factory

Kristjansdottir, Thordis; Bosma, Elleke Fenna; Branco Dos Santos, Filipe et al. · 2019 · Technical University of Denmark (DTU) · DOI

Full title: A metabolic reconstruction of Lactobacillus reuteri JCM 1112 and analysis of its potential as a cell factory

Authors: Kristjansdottir, Thordis; Bosma, Elleke Fenna; Branco Dos Santos, Filipe; Özdemir, Emre; id_orcid 0000-0001-5548-6720; Herrgård, Markus J.; França, Lucas; Ferreira, Bruno; Toftgaard Nielsen, Alex; Gudmundsson, Steinn

Year: 2019

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/b7a7d549-8eec-4b68-a47c-7b1c17553b5d

Thesis Characterizing Strain Variation in Engineered E. coli Using a Multi-Omics-Based Workflow

Brunk, Elizabeth; George, Kevin W.; Alonso-Gutierrez, Jorge et al. · 2016 · Technical University of Denmark (DTU) · DOI

Full title: Characterizing Strain Variation in Engineered E. coli Using a Multi-Omics-Based Workflow

Authors: Brunk, Elizabeth; George, Kevin W.; Alonso-Gutierrez, Jorge; Tjompson, Mitchell; Baidoo, Edward; Wang, George; Petzold, Christopher J.; McCloskey , Douglas; Monk, Jonathan; Yang, Laurence; O’Brien, Edward J.; Batth , Tanveer S.; Garcia Martin, Hector; Feist, Adam; id_orcid 0000-0002-8630-4800; Adams, Paul D.; Keasling , Jay D.; Palsson, Bernhard; id_orcid 0000-0003-2357-6785; Soon Lee, Taek

Year: 2016

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/acd86d0f-dae6-4d90-b52a-40794dfe31ac

Thesis Assessing glycolytic flux alterations resulting from genetic perturbations in E. coli using a biosensor

Lehning, Christina Eva; Siedler, Solvej; Ellabaan, Mostafa M Hashim et al. · 2017 · Technical University of Denmark (DTU) · DOI

Full title: Assessing glycolytic flux alterations resulting from genetic perturbations in E. coli using a biosensor

Authors: Lehning, Christina Eva; Siedler, Solvej; Ellabaan, Mostafa M Hashim; Sommer, Morten Otto Alexander; id_orcid 0000-0003-4005-5674

Year: 2017

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/b3fa1244-3799-477e-8c82-aff5ce21c5af

Thesis The transcriptome and flux profiling of Crabtree-negative hydroxy acid producing strains of Saccharomyces cerevisiae reveals changes in the central carbon metabolism

Jessop-Fabre, Mathew M; id_orcid 0000-0001-7534-2230; Dahlin, Jonathan et al. · 2019 · Technical University of Denmark (DTU) · DOI

Full title: The transcriptome and flux profiling of Crabtree-negative hydroxy acid producing strains of Saccharomyces cerevisiae reveals changes in the central carbon metabolism

Authors: Jessop-Fabre, Mathew M; id_orcid 0000-0001-7534-2230; Dahlin, Jonathan; Biron, Mathias Bernfried; Stovicek, Vratislav; Ebert, Birgitta E; Blank, Lars M; Budin, Itay; Keasling, Jay D; Borodina, Irina

Year: 2019

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/ad991126-8644-4edf-88b2-acb9dfe73436

Thesis A consensus S. cerevisiae metabolic model Yeast8 and its ecosystem for comprehensively probing cellular metabolism

Lu, Hongzhong; Li, Feiran; Sánchez, Benjamín J et al. · 2019 · Technical University of Denmark (DTU) · DOI

Full title: A consensus S. cerevisiae metabolic model Yeast8 and its ecosystem for comprehensively probing cellular metabolism

Authors: Lu, Hongzhong; Li, Feiran; Sánchez, Benjamín J; Zhu, Zhengming; Li, Gang; Domenzain, Iván; Marcišauskas, Simonas; Anton, Petre Mihail; Lappa, Dimitra; Lieven, Christian; Beber, Moritz Emanuel; id_orcid 0000-0003-2406-1978; Sonnenschein, Nikolaus; id_orcid 0000-0002-7581-4936; Kerkhoven, Eduard J; Nielsen, Jens

Year: 2019

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/b99607d4-a4c6-4dc3-a3bd-f0417f3f9694

Thesis Escher-FBA: a web application for interactive flux balance analysis

Rowe, Elliot; Palsson, Bernhard O.; id_orcid 0000-0003-2357-6785 et al. · 2018 · Technical University of Denmark (DTU) · DOI

Full title: Escher-FBA: a web application for interactive flux balance analysis

Authors: Rowe, Elliot; Palsson, Bernhard O.; id_orcid 0000-0003-2357-6785; King, Zachary A.

Year: 2018

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/9f8b6eaf-b4e0-43c2-8a1f-1eb31d500f77

Thesis Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0

Heirendt, Laurent; Arreckx, Sylvain; Pfau, Thomas et al. · 2019 · Technical University of Denmark (DTU) · DOI

Full title: Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0

Authors: Heirendt, Laurent; Arreckx, Sylvain; Pfau, Thomas; Mendoza, Sebastian N.; Richelle, Anne; Heinken, Almut; Haraldsdottir, Hulda S.; Wachowiak, Jacek; Keating, Sarah M.; Vlasov, Vanja; Magnusdottir, Stefania; Ng, Chiam Yu; Preciat, German; Zagare, Alise; Chan, Siu Hung Joshua; Aurich, Maike K.; Clancy, Catherine M.; Modamio, Jennifer; Sauls, John T.; Noronha, Alberto; Bordbar, Aarash; Cousins, Benjamin; El Assal, Diana C.; Valcarcel, Luis V.; Apaolaza, Inigo; Ghaderi, Susan; Ahookhosh, Masoud; Ben Guebila, Marouen; Kostromins, Andrejs; Sompairac, Nicolas; Le, Hoai M.; Ma, Ding; Sun, Yuekai; Wang, Lin; Yurkovich, James T.; Oliveira, Miguel A. P.; Vuong, Phan T.; El Assal, Lemmer P.; Kuperstein, Inna; Zinovyev, Andrei; Hinton, H. Scott; Bryant, William A.; Aragon Artacho, Francisco J.; Planes, Francisco J.; Stalidzans, Egils; Maass, Alejandro; Vempala, Santosh; Hucka, Michael; Saunders, Michael A.; Maranas, Costas D.; Lewis, Nathan E.; Sauter, Thomas; Palsson, Bernhard O.; id_orcid 0000-0003-2357-6785; Thiele, Ines; Fleming, Ronan M. T.

Year: 2019

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/abc86310-0a40-40be-9530-faf60fc05c99

Thesis Yeast9: a consensus genome-scale metabolic model for S. cerevisiae curated by the community

Zhang, Chengyu; Sánchez, Benjamín J.; Li, Feiran et al. · 2024 · Technical University of Denmark (DTU) · DOI

Full title: Yeast9: a consensus genome-scale metabolic model for S. cerevisiae curated by the community

Authors: Zhang, Chengyu; Sánchez, Benjamín J.; Li, Feiran; Eiden, Cheng Wei Quan; Scott, William T.; Liebal, Ulf W.; Blank, Lars M.; Mengers, Hendrik G.; Anton, Mihail; Rangel, Albert Tafur; Mendoza, Sebastián N.; Zhang, Lixin; Nielsen, Jens; Lu, Hongzhong; Kerkhoven, Eduard J.

Year: 2024

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/c006865f-270c-4551-a78a-684270c8ab2f

Thesis Genome-scale modeling drives 70-fold improvement of intracellular heme production in Saccharomyces cerevisiae

Ishchuka, Olena P.; Domenzain, Ivan; Sanchez, Benjamín J. et al. · 2022 · Technical University of Denmark (DTU) · DOI

Full title: Genome-scale modeling drives 70-fold improvement of intracellular heme production in Saccharomyces cerevisiae

Authors: Ishchuka, Olena P.; Domenzain, Ivan; Sanchez, Benjamín J.; Muñiz-Paredes, Facundo; Martínez, Jose L.; id_orcid 0000-0002-4490-8534; Nielsen, Jens; Petranovic, Dina

Year: 2022

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/abd35e2e-92e5-4feb-b08c-8c4d4483e8b2

Thesis The genome-scale metabolic model iIN800 of Saccharomyces cerevisiae and its validation: a scaffold to query lipid metabolism

Nookaew, Intawat; Jewett, Michael Christopher; Meechai, Asawin et al. · 2008 · Technical University of Denmark (DTU) · DOI

Full title: The genome-scale metabolic model iIN800 of Saccharomyces cerevisiae and its validation: a scaffold to query lipid metabolism

Authors: Nookaew, Intawat; Jewett, Michael Christopher; Meechai, Asawin; Thammarongtham, Chinae; Laoteng, Kobkul; Cheevadhanarak, Supapon; Nielsen, Jens; Bhumiratana, Sakarindr

Year: 2008

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/c49f3413-3a84-4d2e-8ee5-144646199e99

Thesis Applying omics and synthetic biology tools for improving the production of sustainable industrial biochemicals

Chandrasekaran, Priyadharshini · 2023 · Technical University of Denmark (DTU) · DOI

Full title: Applying omics and synthetic biology tools for improving the production of sustainable industrial biochemicals

Authors: Chandrasekaran, Priyadharshini

Year: 2023

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/b7dbfe52-e7fa-4aa6-918f-a9bb255d4938

Thesis Rewiring Saccharomyces cerevisiae metabolism for optimised Taxol® precursors production

Nowrouzi, Behnaz; Torres-Montero, Pablo; id_orcid 0000-0002-5970-1907 et al. · 2024 · Technical University of Denmark (DTU) · DOI

Full title: Rewiring Saccharomyces cerevisiae metabolism for optimised Taxol® precursors production

Authors: Nowrouzi, Behnaz; Torres-Montero, Pablo; id_orcid 0000-0002-5970-1907; Kerkhoven, Eduard J.; Martínez, José L.; id_orcid 0000-0002-4490-8534; Rios-Solis, Leonardo

Year: 2024

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/b0710034-bbe0-4347-82a7-f16fface96df

Thesis OptFlux: an open-source software platform for in silico metabolic engineering

Rocha, I.; Maia, P.; Evangelista, P. et al. · 2010 · Technical University of Denmark (DTU) · DOI

Full title: OptFlux: an open-source software platform for in silico metabolic engineering

Authors: Rocha, I.; Maia, P.; Evangelista, P.; Vilaca, P.; Soares, S.; Pinto, J.P.; Nielsen, J.; Patil, Kiran Raosaheb; Ferreira, E.C.; Rocha, M.

Year: 2010

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/bdbb867e-17e6-40fc-ac4c-cb09dd72eac7

Thesis Kinetic profiling of metabolic specialists demonstrates stability and consistency of in vivo enzyme turnover numbers

Heckmann, David; Campeau, Anaamika; Lloyd, Colton J. et al. · 2020 · Technical University of Denmark (DTU) · DOI

Full title: Kinetic profiling of metabolic specialists demonstrates stability and consistency of in vivo enzyme turnover numbers

Authors: Heckmann, David; Campeau, Anaamika; Lloyd, Colton J.; Phaneuf, Patrick V.; Hefner, Ying; Carrillo-Terrazas, Marvic; Feist, Adam M.; id_orcid 0000-0002-8630-4800; Gonzalez, David J.; Palsson, Bernhard O.; id_orcid 0000-0003-2357-6785

Year: 2020

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/c1bd7310-f207-4760-9827-91b1b450c87a

Thesis Establishing a synthetic pathway for high-level production of 3-hydroxypropionic acid in Saccharomyces cerevisiae via β-alanine

Borodina, Irina; Kildegaard, Kanchana Rueksomtawin; Jensen, Niels Bjerg et al. · 2015 · Technical University of Denmark (DTU) · DOI

Full title: Establishing a synthetic pathway for high-level production of 3-hydroxypropionic acid in Saccharomyces cerevisiae via β-alanine

Authors: Borodina, Irina; Kildegaard, Kanchana Rueksomtawin; Jensen, Niels Bjerg; Blicher, Thomas H.; Maury, Jerome; Sherstyk, Svetlana; Schneider, Konstantin; Lamosa, Pedro; Herrgard, Markus; Rosenstand, Inger; Öberg, Fredrik; Förster, Jochen; id_orcid 0000-0003-4045-7905; Nielsen, Jens

Year: 2015

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/c3fbec62-077f-403f-bd01-1514ba663bdd

Thesis Metabolic modelling as a framework for metabolomics data integration and analysis

Volkova, Svetlana; Matos, Marta R. A.; Mattanovich, Matthias et al. · 2020 · Technical University of Denmark (DTU) · DOI

Full title: Metabolic modelling as a framework for metabolomics data integration and analysis

Authors: Volkova, Svetlana; Matos, Marta R. A.; Mattanovich, Matthias; Marín de Mas, Igor

Year: 2020

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/c7fe0f0a-1834-46aa-ab97-a28bc2500124

Thesis Modeling Lactococcus lactis using a genome-scale flux model

Soberano de Oliveira, Ana Paula; Nielsen, Jens; Förster, Jochen et al. · 2005 · Technical University of Denmark (DTU) · DOI

Full title: Modeling Lactococcus lactis using a genome-scale flux model

Authors: Soberano de Oliveira, Ana Paula; Nielsen, Jens; Förster, Jochen; id_orcid 0000-0003-4045-7905

Year: 2005

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/c512b848-0fc5-4b06-95a0-b76b1e07557a

Thesis Controlling Central Carbon Metabolism for Improved Pathway Yields in Saccharomyces cerevisiae

Tan, Sue Zanne; Manchester, Shawn; Prather, Kristala L · 2017 · Massachusetts Institute of Technology (MIT) · DOI

Full title: Controlling Central Carbon Metabolism for Improved Pathway Yields in Saccharomyces cerevisiae

Authors: Tan, Sue Zanne; Manchester, Shawn; Prather, Kristala L

Year: 2017

Venue: Massachusetts Institute of Technology (MIT)

DOI: http://hdl.handle.net/1721.1/106893

Thesis RAVEN 2.0: A versatile toolbox for metabolic network reconstruction and a case study on Streptomyces coelicolor

Wang, Hao; Marcisauskas, Simonas; Sanchez, Benjamin J. et al. · 2018 · Technical University of Denmark (DTU) · DOI

Full title: RAVEN 2.0: A versatile toolbox for metabolic network reconstruction and a case study on Streptomyces coelicolor

Authors: Wang, Hao; Marcisauskas, Simonas; Sanchez, Benjamin J.; Domenzain, Ivan; Hermansson, Daniel; Agren, Rasmus; Nielsen, Jens; Kerkhoven, Eduard J.

Year: 2018

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/ccb1a039-b82f-429e-9d47-3e7cea8902b8

Thesis Basic and applied uses of genome-scale metabolic network reconstructions of Escherichia coli.

McCloskey, Douglas; Palsson, Bernhard; id_orcid 0000-0003-2357-6785 et al. · 2013 · Technical University of Denmark (DTU) · DOI

Full title: Basic and applied uses of genome-scale metabolic network reconstructions of Escherichia coli.

Authors: McCloskey, Douglas; Palsson, Bernhard; id_orcid 0000-0003-2357-6785; Feist, Adam; id_orcid 0000-0002-8630-4800

Year: 2013

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/bea0c9bb-a503-493b-8847-4315678a7dbd

Thesis Model guided design of microbial consortia for mixed-culture fermentations

Bras, Jildau Emma · 2023 · Technical University of Denmark (DTU) · DOI

Full title: Model guided design of microbial consortia for mixed-culture fermentations

Authors: Bras, Jildau Emma

Year: 2023

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/cd886c17-324b-4ddc-83d3-adfa75e6b8e9

Thesis Identification of potential drug targets in Salmonella enterica sv. Typhimurium using metabolic modelling and experimental validation

Hartman, Hassan B.; Fell, David A.; Rossell, Sergio et al. · 2014 · Technical University of Denmark (DTU) · DOI

Full title: Identification of potential drug targets in Salmonella enterica sv. Typhimurium using metabolic modelling and experimental validation

Authors: Hartman, Hassan B.; Fell, David A.; Rossell, Sergio; Jensen, Peter Ruhdal; id_orcid 0000-0003-2080-2070; Woodward, Martin J.; Thorndahl, Lotte; Jelsbak, Lotte; Elmerdahl Olsen, John; Raghunathan, Anu; Daefler, Simon; Poolman, Mark G.

Year: 2014

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/c485152d-7329-47aa-a593-04a0788b7037

Thesis Diverse genetic error modes constrain large-scale bio-based production

Rugbjerg, Peter; Myling-Petersen, Nils; Porse, Andreas et al. · 2018 · Technical University of Denmark (DTU) · DOI

Full title: Diverse genetic error modes constrain large-scale bio-based production

Authors: Rugbjerg, Peter; Myling-Petersen, Nils; Porse, Andreas; Sarup-Lytzen, Kira; Sommer, Morten Otto Alexander; id_orcid 0000-0003-4005-5674

Year: 2018

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/bab65aeb-c915-4327-890b-81b6ecda5e24

Thesis Integration of enzymatic data in Bacillus subtilis genome-scale metabolic model improves phenotype predictions and enables in silico design of poly-γ-glutamic acid production strains

Massaiu, Ilaria; Pasotti, Lorenzo; Sonnenschein, Nikolaus et al. · 2019 · Technical University of Denmark (DTU) · DOI

Full title: Integration of enzymatic data in Bacillus subtilis genome-scale metabolic model improves phenotype predictions and enables in silico design of poly-γ-glutamic acid production strains

Authors: Massaiu, Ilaria; Pasotti, Lorenzo; Sonnenschein, Nikolaus; id_orcid 0000-0002-7581-4936; Rama, Erlinda; Cavaletti, Matteo; Magni, Paolo; Calvio, Cinzia; Herrgård, Markus J.

Year: 2019

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/d5caa610-5ed4-400f-8f04-4c37a606a8a9

Thesis Hybrid Modeling for On-Line Fermentation Optimization and Scale-Up:A Review

Albino, Mariana; Gargalo, Carina L.; id_orcid 0000-0002-8740-9591 et al. · 2024 · Technical University of Denmark (DTU) · DOI

Full title: Hybrid Modeling for On-Line Fermentation Optimization and Scale-Up:A Review

Authors: Albino, Mariana; Gargalo, Carina L.; id_orcid 0000-0002-8740-9591; Nadal-Rey, Gisela; Albæk, Mads O.; Krühne, Ulrich; id_orcid 0000-0001-7774-7442; Gernaey, Krist V.; id_orcid 0000-0002-0364-1773

Year: 2024

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/da2224b1-251a-47ea-abc0-1b523e3fb360

Thesis Elucidating dynamic metabolic physiology through network integration of quantitative time-course metabolomics

Bordbar, Aarash; Yurkovich, James T.; Paglia, Giuseppe et al. · 2017 · Technical University of Denmark (DTU) · DOI

Full title: Elucidating dynamic metabolic physiology through network integration of quantitative time-course metabolomics

Authors: Bordbar, Aarash; Yurkovich, James T.; Paglia, Giuseppe; Rolfsson, Ottar; Sigurjónsson, Olafur E.; Palsson, Bernhard; id_orcid 0000-0003-2357-6785

Year: 2017

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/cfb96acb-b500-427f-a8fe-d0f32465a2d7

Thesis CRI-SPA mediated screening for metabolic engineering targets to improve small molecule production in Saccharomyces cerevisiae

Vestergaard, Andreas M.; id_orcid 0000-0002-5042-1474; Cachera, Paul Pierre-Yves Jean et al. · 2023 · Technical University of Denmark (DTU) · DOI

Full title: CRI-SPA mediated screening for metabolic engineering targets to improve small molecule production in Saccharomyces cerevisiae

Authors: Vestergaard, Andreas M.; id_orcid 0000-0002-5042-1474; Cachera, Paul Pierre-Yves Jean; Mortensen, Uffe Hasbro; id_orcid 0000-0002-7794-7273

Year: 2023

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/d734ee1d-b231-411f-97a4-1d5626bab4af

Thesis Investigating genotype-phenotype relationships in Saccharomyces cerevisiae metabolic network through stoichiometric modeling

Brochado, Ana Rita · 2012 · Technical University of Denmark (DTU) · DOI

Full title: Investigating genotype-phenotype relationships in Saccharomyces cerevisiae metabolic network through stoichiometric modeling

Authors: Brochado, Ana Rita

Year: 2012

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/de6f64b4-c567-4671-a580-dc2184e485aa

Thesis In silico-guided engineering of Pseudomonas putida towards growth under micro-oxic conditions

Kampers, Linde F.C.; Van Heck, Ruben G.A.; Donati, Stefano et al. · 2019 · Technical University of Denmark (DTU) · DOI

Full title: In silico-guided engineering of Pseudomonas putida towards growth under micro-oxic conditions

Authors: Kampers, Linde F.C.; Van Heck, Ruben G.A.; Donati, Stefano; Saccenti, Edoardo; Volkers, Rita J.M.; Schaap, Peter J.; Suarez-Diez, Maria; Nikel, Pablo I.; id_orcid 0000-0002-9313-7481; Martins Dos Santos, Vitor A.P.

Year: 2019

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/c9b06315-7ba5-485c-a683-9173957c4612

Thesis Saccharomyces cerevisiae phenotypes can be predicted using constraint based analysis of a genome-scale reconstructed metabolic network

Famili, I.; Förster, Jochen; id_orcid 0000-0003-4045-7905 et al. · 2003 · Technical University of Denmark (DTU) · DOI

Full title: Saccharomyces cerevisiae phenotypes can be predicted using constraint based analysis of a genome-scale reconstructed metabolic network

Authors: Famili, I.; Förster, Jochen; id_orcid 0000-0003-4045-7905; Nielsen, Jens; Palsson, B.O.

Year: 2003

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/ce2e5d37-808b-41be-85cb-d7b067c173fb

Thesis Reprogramming Yeast Metabolism from Alcoholic Fermentation to Lipogenesis

Yu, Tao; Zhou, Yongjin J.; Huang, Mingtao et al. · 2018 · Technical University of Denmark (DTU) · DOI

Full title: Reprogramming Yeast Metabolism from Alcoholic Fermentation to Lipogenesis

Authors: Yu, Tao; Zhou, Yongjin J.; Huang, Mingtao; Liu, Quanli; Pereira, Rui; David, Florian; Nielsen, Jens

Year: 2018

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/e2d68087-fc93-4b81-8d72-1b67f1449334

Thesis Production of 3-Hydroxypropanoic Acid From Glycerol by Metabolically Engineered Bacteria

Jers, Carsten; id_orcid 0000-0002-9930-3137; Kalantari, Aida et al. · 2019 · Technical University of Denmark (DTU) · DOI

Full title: Production of 3-Hydroxypropanoic Acid From Glycerol by Metabolically Engineered Bacteria

Authors: Jers, Carsten; id_orcid 0000-0002-9930-3137; Kalantari, Aida; Garg, Abhroop; Mijakovic, Ivan

Year: 2019

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/dd7921d1-bf8d-4658-86e7-26d0b103aef8

Thesis Modeling the Contribution of Allosteric Regulation for Flux Control in the Central Carbon Metabolism of E. coli

Machado, Daniel; Herrgard, Markus; Rocha, Isabel · 2015 · Technical University of Denmark (DTU) · DOI

Full title: Modeling the Contribution of Allosteric Regulation for Flux Control in the Central Carbon Metabolism of E. coli

Authors: Machado, Daniel; Herrgard, Markus; Rocha, Isabel

Year: 2015

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/dabee1a2-fe3a-4c6a-8841-33d18b5b6717

Thesis Reconstruction of a catalogue of genome-scale metabolic models with enzymatic constraints using GECKO 2.0

Domenzain, Iván; Sánchez, Benjamín; Anton, Mihail et al. · 2022 · Technical University of Denmark (DTU) · DOI

Full title: Reconstruction of a catalogue of genome-scale metabolic models with enzymatic constraints using GECKO 2.0

Authors: Domenzain, Iván; Sánchez, Benjamín; Anton, Mihail; Kerkhoven, Eduard J.; Millán-Oropeza, Aarón; Henry, Céline; Siewers, Verena; Morrissey, John P.; Sonnenschein, Nikolaus; id_orcid 0000-0002-7581-4936; Nielsen, Jens

Year: 2022

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/df6e83e4-1f36-41d2-b699-d64e6d8b405c

Thesis Model-Assisted Fine-Tuning of Central Carbon Metabolism in Yeast through dCas9-Based Regulation

Ferreira, Raphael; Skrekas, Christos; Hedin, Alex et al. · 2019 · Technical University of Denmark (DTU) · DOI

Full title: Model-Assisted Fine-Tuning of Central Carbon Metabolism in Yeast through dCas9-Based Regulation

Authors: Ferreira, Raphael; Skrekas, Christos; Hedin, Alex; Sánchez, Benjamín José; Siewers, Verena; Nielsen, Jens; David, Florian

Year: 2019

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/e453310b-2bf1-47bb-a4c0-7e11c9bb7c96

Thesis Optimizing cultivation of Cordyceps militaris for fast growth and cordycepin overproduction using rational design of synthetic media

Raethong, Nachon; Wang, Hao; Nielsen, Jens et al. · 2020 · Technical University of Denmark (DTU) · DOI

Full title: Optimizing cultivation of Cordyceps militaris for fast growth and cordycepin overproduction using rational design of synthetic media

Authors: Raethong, Nachon; Wang, Hao; Nielsen, Jens; Vongsangnak, Wanwipa

Year: 2020

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/e3060451-18d5-4b01-aff0-9d02cf847900

Thesis Combining mechanistic and machine learning models for predictive engineering and optimization of tryptophan metabolism

Zhang, Jie; Petersen, Søren D.; id_orcid 0000-0003-4104-5144 et al. · 2020 · Technical University of Denmark (DTU) · DOI

Full title: Combining mechanistic and machine learning models for predictive engineering and optimization of tryptophan metabolism

Authors: Zhang, Jie; Petersen, Søren D.; id_orcid 0000-0003-4104-5144; Radivojevic, Tijana; Ramirez, Andrés; Pérez-Manríquez, Andrés; Abeliuk, Eduardo; Sánchez, Benjamín J.; Costello, Zak; Chen, Yu; Fero, Michael J.; Martin, Hector Garcia; Nielsen, Jens; Keasling, Jay D.; Jensen, Michael K.; id_orcid 0000-0001-7574-4707

Year: 2020

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/d3f43470-1242-4282-8114-549377408fd6

Thesis Systems Biology of Metabolic Networks: Uncovering Regulatory and stoichiometric Principles

Patil, Kiran Raosaheb · 2007 · Technical University of Denmark (DTU) · DOI

Full title: Systems Biology of Metabolic Networks: Uncovering Regulatory and stoichiometric Principles

Authors: Patil, Kiran Raosaheb

Year: 2007

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/e5586576-a479-4569-a0da-8d0542a9f448

Thesis Genome-scale metabolic representation of Amycolatopsis balhimycina

Vongsangnak, Wanwipa; Figueiredo, L. F.; Förster, Jochen et al. · 2012 · Technical University of Denmark (DTU) · DOI

Full title: Genome-scale metabolic representation of Amycolatopsis balhimycina

Authors: Vongsangnak, Wanwipa; Figueiredo, L. F.; Förster, Jochen; id_orcid 0000-0003-4045-7905; Weber, Tilmann; id_orcid 0000-0002-8260-5120; Thykær, Jette; Stegmann, E.; Wohlleben, W.; Nielsen, Jens

Year: 2012

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/e1eaad0e-10fd-4378-9c1e-9b7b39397a5d

Thesis Online estimation of changing metabolic capacities in continuous Corynebacterium glutamicum cultivations growing on a complex sugar mixture

Sinner, Peter; Stiegler, Marlene; Goldbeck, Oliver et al. · 2022 · Technical University of Denmark (DTU) · DOI

Full title: Online estimation of changing metabolic capacities in continuous Corynebacterium glutamicum cultivations growing on a complex sugar mixture

Authors: Sinner, Peter; Stiegler, Marlene; Goldbeck, Oliver; Seibold, Gerd M.; id_orcid 0000-0002-9823-8134; Herwig, Christoph; Kager, Julian; id_orcid 0000-0001-7274-6678

Year: 2022

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/e1d47952-5939-40df-b5d8-a033a58e8745

Thesis Output uncertainty of dynamic growth models: Effect of uncertain parameter estimates on model reliability

Anane, Emmanuel; López C, Diana C.; Barz, Tilman et al. · 2019 · Technical University of Denmark (DTU) · DOI

Full title: Output uncertainty of dynamic growth models: Effect of uncertain parameter estimates on model reliability

Authors: Anane, Emmanuel; López C, Diana C.; Barz, Tilman; Sin, Gürkan; id_orcid 0000-0003-0513-4502; Gernaey, Krist V.; id_orcid 0000-0002-0364-1773; Neubauer, Peter; Cruz Bournazou, Mariano Nicolas

Year: 2019

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/e2b40834-81af-4e34-9475-5a085aedbd5d

Thesis Impact of stoichiometry representation on simulation of genotype-phenotype relationships in metabolic networks.

Brochado, Ana Rita; Andrejev, Sergej; Maranas, Costas D. et al. · 2012 · Technical University of Denmark (DTU) · DOI

Full title: Impact of stoichiometry representation on simulation of genotype-phenotype relationships in metabolic networks.

Authors: Brochado, Ana Rita; Andrejev, Sergej; Maranas, Costas D.; Patil, Kiran R.

Year: 2012

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/e98be4c6-510e-4c08-9145-f929cb4e8440

Thesis An automated workflow for multi-omics screening of microbial model organisms

Donati, Stefano; id_orcid 0000-0001-9946-0346; Mattanovich, Matthias et al. · 2023 · Technical University of Denmark (DTU) · DOI

Full title: An automated workflow for multi-omics screening of microbial model organisms

Year: 2023

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/ef757ea8-8d70-4985-a645-94d6cb70d635

Thesis Stoichiometric Representation of Gene–Protein–Reaction Associations Leverages Constraint-Based Analysis from Reaction to Gene-Level Phenotype Prediction

Machado, Daniel; Herrgard, Markus; Rocha, Isabel · 2016 · Technical University of Denmark (DTU) · DOI

Full title: Stoichiometric Representation of Gene–Protein–Reaction Associations Leverages Constraint-Based Analysis from Reaction to Gene-Level Phenotype Prediction

Authors: Machado, Daniel; Herrgard, Markus; Rocha, Isabel

Year: 2016

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/e4208a96-0c33-48f2-8ac5-da96aa1ea44c

Thesis Cell culture process dynamics and metabolic flux distributions using hybrid models

Kailasanathan, Rajiv; Sivaram, Abhishek; Mansouri, Seyed Soheil et al. · 2025 · Technical University of Denmark (DTU) · DOI

Full title: Cell culture process dynamics and metabolic flux distributions using hybrid models

Authors: Kailasanathan, Rajiv; Sivaram, Abhishek; Mansouri, Seyed Soheil; id_orcid 0000-0002-0924-4947

Year: 2025

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/572e7d61-3351-4ced-b2f5-6b9e4ceab22f

Thesis Engineering Saccharomyces cerevisiae cells for production of fatty acid-derived biofuels and chemicals

Hu, Yating; Zhu, Zhiwei; Nielsen, Jens et al. · 2019 · Technical University of Denmark (DTU) · DOI

Full title: Engineering Saccharomyces cerevisiae cells for production of fatty acid-derived biofuels and chemicals

Authors: Hu, Yating; Zhu, Zhiwei; Nielsen, Jens; Siewers, Verena

Year: 2019

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/4307d50e-cd16-47d3-9b4f-c849c89aad59

Thesis Bacterial fitness landscapes stratify based on proteome allocation associated with discrete aero-types

Chen, Ke; Anand, Amitesh; Olson, Connor et al. · 2021 · Technical University of Denmark (DTU) · DOI

Full title: Bacterial fitness landscapes stratify based on proteome allocation associated with discrete aero-types

Authors: Chen, Ke; Anand, Amitesh; Olson, Connor; Sandberg, Troy E.; Gao, Ye; Mih, Nathan; Palsson, Bernhard O.; id_orcid 0000-0003-2357-6785

Year: 2021

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/3f263cdd-32d7-4df3-94b3-ed7e2b467de7

Thesis Enzyme-constrained metabolic model and in silico metabolic engineering of Clostridium ljungdahlii for the development of sustainable production processes

Caivano, Antonio; id_orcid 0000-0001-6296-5383; van Winden, Wouter et al. · 2023 · Technical University of Denmark (DTU) · DOI

Full title: Enzyme-constrained metabolic model and in silico metabolic engineering of Clostridium ljungdahlii for the development of sustainable production processes

Authors: Caivano, Antonio; id_orcid 0000-0001-6296-5383; van Winden, Wouter; Dragone, Giuliano; id_orcid 0000-0002-5555-8381; Mussatto, Solange I; id_orcid 0000-0002-7182-6198

Year: 2023

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/4cb1ff43-f4f3-4085-b209-6c57bcb0480d

Thesis 13 C Metabolic Flux Analysis for Systematic Metabolic Engineering of S. cerevisiae for Overproduction of Fatty Acids

Ghosh, Amit; Ando, David; Gin, Jennifer et al. · 2016 · Technical University of Denmark (DTU) · DOI

Full title: 13 C Metabolic Flux Analysis for Systematic Metabolic Engineering of S. cerevisiae for Overproduction of Fatty Acids

Authors: Ghosh, Amit; Ando, David; Gin, Jennifer; Runguphan, Weerawat; Denby, Charles; Wang, George; Baidoo, Edward E. K.; Shymansky, Chris; Keasling, Jay; García Martín, Héctor

Year: 2016

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/4b2157b3-0f83-4553-bae4-d6f4dc3300ca

Thesis The Impact of Systems Biology on Bioprocessing

Campbell, Kate; Xia, Jianye; Nielsen, Jens · 2017 · Technical University of Denmark (DTU) · DOI

Full title: The Impact of Systems Biology on Bioprocessing

Authors: Campbell, Kate; Xia, Jianye; Nielsen, Jens

Year: 2017

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/5a1b35f6-8710-4563-b1aa-c2e9c09b96b0

Thesis Reconstructing organisms in silico: genome-scale models and their emerging applications

Fang, Xin; Lloyd, Colton J.; Palsson, Bernhard O. et al. · 2020 · Technical University of Denmark (DTU) · DOI

Full title: Reconstructing organisms in silico: genome-scale models and their emerging applications

Authors: Fang, Xin; Lloyd, Colton J.; Palsson, Bernhard O.; id_orcid 0000-0003-2357-6785

Year: 2020

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/575aa54d-59ad-4b61-a171-369c7dbbdd9c

Thesis Systematic Evaluation of Methods for Integration of Transcriptomic Data into Constraint-Based Models of Metabolism.

Machado, Daniel; Herrgard, Markus · 2014 · Technical University of Denmark (DTU) · DOI

Full title: Systematic Evaluation of Methods for Integration of Transcriptomic Data into Constraint-Based Models of Metabolism.

Authors: Machado, Daniel; Herrgard, Markus

Year: 2014

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/52005488-21bb-4253-9872-6d37eda149f7

Thesis Application of a curated genome-scale metabolic model of CHO DG44 to an industrial fed-batch process

Calmels, Cyrielle; McCann, Andréa; Malphettes, Laetitia et al. · 2018 · Technical University of Denmark (DTU) · DOI

Full title: Application of a curated genome-scale metabolic model of CHO DG44 to an industrial fed-batch process

Authors: Calmels, Cyrielle; McCann, Andréa; Malphettes, Laetitia; Andersen, Mikael Rørdam; id_orcid 0000-0003-4794-6808

Year: 2018

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/59c3f8ac-571d-4312-969f-4d6d5689e961

Thesis Omics data for sampling thermodynamically feasible kinetic models

de Leeuw, Marina; Matos, Marta R.A.; Nielsen, Lars Keld · 2023 · Technical University of Denmark (DTU) · DOI

Full title: Omics data for sampling thermodynamically feasible kinetic models

Authors: de Leeuw, Marina; Matos, Marta R.A.; Nielsen, Lars Keld

Year: 2023

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/5985722c-e25c-4611-ab4e-fc5b5c8fdf8c

Thesis The topology of genome-scale metabolic reconstructions unravels independent modules and high network flexibility

Martínez, Verónica S.; Saa, Pedro A.; Jooste, Jason et al. · 2022 · Technical University of Denmark (DTU) · DOI

Full title: The topology of genome-scale metabolic reconstructions unravels independent modules and high network flexibility

Authors: Martínez, Verónica S.; Saa, Pedro A.; Jooste, Jason; Tiwari, Kanupriya; Quek, Lake Ee; Nielsen, Lars K.

Year: 2022

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/596e366c-6a99-477e-bcd6-e0168d6325b4

Thesis Improving the phenotype predictions of a yeast genome-scale metabolic model by incorporating enzymatic constraints

Sanchez, Benjamin J.; Zhang, Xi-Cheng; Nilsson, Avlant et al. · 2017 · Technical University of Denmark (DTU) · DOI

Full title: Improving the phenotype predictions of a yeast genome-scale metabolic model by incorporating enzymatic constraints

Authors: Sanchez, Benjamin J.; Zhang, Xi-Cheng; Nilsson, Avlant; Lahtvee, Petri-Jaan; Kerkhoven, Eduard J.; Nielsen, Jens

Year: 2017

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/58026a68-5f76-4b48-979d-3068258c577c

Thesis Engineering of Saccharomyces cerevisiae for enhanced metabolic robustness and L-lactic acid production from lignocellulosic biomass

Choi, Bohyun; Tafur Rangel, Albert; Kerkhoven, Eduard J. et al. · 2024 · Technical University of Denmark (DTU) · DOI

Full title: Engineering of Saccharomyces cerevisiae for enhanced metabolic robustness and L-lactic acid production from lignocellulosic biomass

Authors: Choi, Bohyun; Tafur Rangel, Albert; Kerkhoven, Eduard J.; Nygård, Yvonne

Year: 2024

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/52700d2e-e6df-40b2-99af-c91e5b38ae23

Thesis The Expanding Computational Toolbox for Engineering Microbial Phenotypes at the Genome Scale

Zielinski, Daniel Craig; Patel, Arjun; Palsson, Bernhard O et al. · 2020 · Technical University of Denmark (DTU) · DOI

Full title: The Expanding Computational Toolbox for Engineering Microbial Phenotypes at the Genome Scale

Authors: Zielinski, Daniel Craig; Patel, Arjun; Palsson, Bernhard O; id_orcid 0000-0003-2357-6785

Year: 2020

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/5c4ece29-33bb-4954-92aa-2b7734453cb4

Thesis Constraining genome-scale models to represent the bow tie structure of metabolism for 13C metabolic flux analysis

Backman, Tyler W.H.; Ando, David; Singh, Jahnavi et al. · 2018 · Technical University of Denmark (DTU) · DOI

Full title: Constraining genome-scale models to represent the bow tie structure of metabolism for 13C metabolic flux analysis

Authors: Backman, Tyler W.H.; Ando, David; Singh, Jahnavi; Keasling, Jay D.; Martín, Héctor García

Year: 2018

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/5c6aa2d9-4d5b-41ed-a760-91d6f1098c13

Thesis C-13 Tracer experiments and metabolite balancing for metabolic flux analysis:Comparing two approaches

Schmidt, Karsten; Marx, A.; de Graaf, A. A. et al. · 1998 · Technical University of Denmark (DTU) · DOI

Full title: C-13 Tracer experiments and metabolite balancing for metabolic flux analysis:Comparing two approaches

Authors: Schmidt, Karsten; Marx, A.; de Graaf, A. A.; Wiechert, W.; Sahm, H.; Nielsen, Jens Bredal; Villadsen, John; id_orcid 0000-0002-6523-8445

Year: 1998

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/5cdd9f29-0342-42de-b333-8c721016f183

Thesis Genome-scale metabolic modeling of P. thermoglucosidasius NCIMB 11955 reveals metabolic bottlenecks in anaerobic metabolism

Mol, Viviënne; Bennett, Martyn; Sánchez, Benjamín J. et al. · 2021 · Technical University of Denmark (DTU) · DOI

Full title: Genome-scale metabolic modeling of P. thermoglucosidasius NCIMB 11955 reveals metabolic bottlenecks in anaerobic metabolism

Year: 2021

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/5fd1a4cc-3aed-41ea-887a-78bdac847b3f

Thesis Reliable and efficient solution of genome-scale models of Metabolism and macromolecular Expression

Ma, Ding; Yang, Laurence; Fleming, Ronan M. T. et al. · 2017 · Technical University of Denmark (DTU) · DOI

Full title: Reliable and efficient solution of genome-scale models of Metabolism and macromolecular Expression

Authors: Ma, Ding; Yang, Laurence; Fleming, Ronan M. T.; Thiele, Ines; Palsson, Bernhard; id_orcid 0000-0003-2357-6785; Saunders, Michael A.

Year: 2017

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/5c6e0bb8-7db3-4934-9d71-484bc0d18d15

Thesis Improving methyl ketone production in Escherichia coli by heterologous expression of NADH-dependent FabG

Goh, Ee Been; Chen, Yan; Petzold, Christopher J. et al. · 2018 · Technical University of Denmark (DTU) · DOI

Full title: Improving methyl ketone production in Escherichia coli by heterologous expression of NADH-dependent FabG

Authors: Goh, Ee Been; Chen, Yan; Petzold, Christopher J.; Keasling, Jay D.; Beller, Harry R.

Year: 2018

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/59368c46-d536-4672-b215-dd47253e678b

Thesis Systems assessment of transcriptional regulation on central carbon metabolism by Cra and CRP

Kim, Donghyuk; Seo, Sang Woo; Gao, Ye et al. · 2018 · Technical University of Denmark (DTU) · DOI

Full title: Systems assessment of transcriptional regulation on central carbon metabolism by Cra and CRP

Authors: Kim, Donghyuk; Seo, Sang Woo; Gao, Ye; Nam, Hojung; Guzman, Gabriela I.; Cho, Byung-Kwan; Palsson, Bernhard O.; id_orcid 0000-0003-2357-6785

Year: 2018

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/599dc867-877a-464c-9ac8-6d9de9a7520b

Thesis Adaptations in metabolism and protein translation give rise to the Crabtree effect in yeast

Malina, Carl; Yu, Rosemary; Bjorkeroth, Johan et al. · 2021 · Technical University of Denmark (DTU) · DOI

Full title: Adaptations in metabolism and protein translation give rise to the Crabtree effect in yeast

Authors: Malina, Carl; Yu, Rosemary; Bjorkeroth, Johan; Kerkhoven, Eduard J.; Nielsen, Jens

Year: 2021

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/60146c8d-be0d-4f08-bab0-fd4cc21686cb

Thesis Single-cell omics analysis with genome-scale metabolic modeling

Chen, Yu; Gustafsson, Johan; Yang, Jingyu et al. · 2024 · Technical University of Denmark (DTU) · DOI

Full title: Single-cell omics analysis with genome-scale metabolic modeling

Authors: Chen, Yu; Gustafsson, Johan; Yang, Jingyu; Nielsen, Jens; Kerkhoven, Eduard J.

Year: 2024

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/5c9dbec0-a3c5-47e5-8257-7977cc6cb44c

Thesis Genome-scale metabolic reconstructions of multiple Salmonella strains reveal serovar-specific metabolic traits

Seif, Yara; Kavvas, Erol; Lachance, Jean-Christophe et al. · 2018 · Technical University of Denmark (DTU) · DOI

Full title: Genome-scale metabolic reconstructions of multiple Salmonella strains reveal serovar-specific metabolic traits

Year: 2018

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/6265b868-ba4f-442b-ad03-65a5c465af90

Thesis The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes

Seaver, Samuel M. D.; Liu, Filipe; Zhang, Qizhi et al. · 2021 · Technical University of Denmark (DTU) · DOI

Full title: The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes

Year: 2021

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/5d855a28-cf61-4734-8b32-d3eafa52424c

Thesis Mass Action Stoichiometric. Simulation for Cell Factory Design

Matos, Marta R. A. · 2018 · Technical University of Denmark (DTU) · DOI

Full title: Mass Action Stoichiometric. Simulation for Cell Factory Design

Authors: Matos, Marta R. A.

Year: 2018

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/5dca35ef-9f63-41d1-b780-3c50e6bd0bf4

Thesis Incorporating Protein Biosynthesis into the Saccharomyces cerevisiae Genome-scale Metabolic Model

Olivares Hernandez, Roberto · 2006 · Technical University of Denmark (DTU) · DOI

Full title: Incorporating Protein Biosynthesis into the Saccharomyces cerevisiae Genome-scale Metabolic Model

Authors: Olivares Hernandez, Roberto

Year: 2006

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/60b61498-7202-47d7-a8a6-eec09162be49

Thesis Impact of synthetic biology and metabolic engineering on industrial production of fine chemicals

Jullesson, David; David, Florian; Pfleger, Brian et al. · 2015 · Technical University of Denmark (DTU) · DOI

Full title: Impact of synthetic biology and metabolic engineering on industrial production of fine chemicals

Authors: Jullesson, David; David, Florian; Pfleger, Brian; Nielsen, Jens

Year: 2015

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/65daa91c-cdeb-41e5-8e6c-2f81ccbed041

Thesis Heterologous expression and characterization of bacterial 2-C-methyl-d-erythritol-4-phosphate pathway in Saccharomyces cerevisiae

Carlsen, Simon; Ajikumar, Parayil Kumaran; Formenti, Luca Riccardo et al. · 2013 · Technical University of Denmark (DTU) · DOI

Full title: Heterologous expression and characterization of bacterial 2-C-methyl-d-erythritol-4-phosphate pathway in Saccharomyces cerevisiae

Year: 2013

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/60357545-6000-49a6-8a45-e4c54d451922

Thesis Toward genome-scale models of the Chinese hamster ovary cells: incentives, status and perspectives

Kaas, Christian Schrøder; Fan, Yuzhou; Weilguny, Dietmar et al. · 2014 · Technical University of Denmark (DTU) · DOI

Full title: Toward genome-scale models of the Chinese hamster ovary cells: incentives, status and perspectives

Authors: Kaas, Christian Schrøder; Fan, Yuzhou; Weilguny, Dietmar; Kristensen, Claus; Kildegaard, Helene Faustrup; Andersen, Mikael Rørdam; id_orcid 0000-0003-4794-6808

Year: 2014

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/6067dd57-c31e-41f2-9225-4c51754db14a

Thesis Model-driven discovery of underground metabolic functions in Escherichia coli

Guzmán, Gabriela I.; Utrilla, José; Nurk, Sergey et al. · 2015 · Technical University of Denmark (DTU) · DOI

Full title: Model-driven discovery of underground metabolic functions in Escherichia coli

Authors: Guzmán, Gabriela I.; Utrilla, José; Nurk, Sergey; Brunk, Elizabeth; Monk, Jonathan M.; Ebrahim, Ali; Palsson, Bernhard O.; id_orcid 0000-0003-2357-6785; Feist, Adam M.; id_orcid 0000-0002-8630-4800

Year: 2015

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/627aac50-c31f-4313-a265-1d3898de367a

Thesis Methods for predictable and accelerated engineering of metabolism in eukaryotes

Petersen, Søren Dalsgård; id_orcid 0000-0003-4104-5144 · 2019 · Technical University of Denmark (DTU) · DOI

Full title: Methods for predictable and accelerated engineering of metabolism in eukaryotes

Authors: Petersen, Søren Dalsgård; id_orcid 0000-0003-4104-5144

Year: 2019

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/697b48dd-33be-40fb-b1be-16a108f71163

Thesis In Silico Genome-Scale Reconstruction and Validation of the Corynebacterium glutamicum Metabolic Network

Kjeldsen, Kjeld Raunkjær; Nielsen, J. · 2009 · Technical University of Denmark (DTU) · DOI

Full title: In Silico Genome-Scale Reconstruction and Validation of the Corynebacterium glutamicum Metabolic Network

Authors: Kjeldsen, Kjeld Raunkjær; Nielsen, J.

Year: 2009

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/638ade8b-47c1-44ce-b0ea-b3c723dbb6a1

Thesis BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree

Norsigian, Charles J.; Pusarla, Neha; McConn, John Luke et al. · 2020 · Technical University of Denmark (DTU) · DOI

Full title: BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree

Authors: Norsigian, Charles J.; Pusarla, Neha; McConn, John Luke; Yurkovich, James T.; Dräger, Andreas; Palsson, Bernhard O.; id_orcid 0000-0003-2357-6785; King, Zachary

Year: 2020

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/66e6b978-0bab-43c5-b81b-f9ab14993d9d

Thesis Current state and applications of microbial genome-scale metabolic models

Kim, Won Jun; Kim, Hyun Uk; Lee, Sang Yup · 2017 · Technical University of Denmark (DTU) · DOI

Full title: Current state and applications of microbial genome-scale metabolic models

Authors: Kim, Won Jun; Kim, Hyun Uk; Lee, Sang Yup

Year: 2017

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/6336b8a2-2367-4a41-b020-58a601f6b5ed

Thesis Production efficiency of the bacterial non-ribosomal peptide indigoidine relies on the respiratory metabolic state in S. cerevisiae

Wehrs, Maren; Prahl, Jan-Philip; Moon, Jadie et al. · 2018 · Technical University of Denmark (DTU) · DOI

Full title: Production efficiency of the bacterial non-ribosomal peptide indigoidine relies on the respiratory metabolic state in S. cerevisiae

Authors: Wehrs, Maren; Prahl, Jan-Philip; Moon, Jadie; Li, Yuchen; Tanjore, Deepti; Keasling, Jay D.; Pray, Todd; Mukhopadhyay, Aindrila

Year: 2018

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/67e08ff4-8d3f-4c32-a48f-749172086dc0

Thesis Principles of proteome allocation are revealed using proteomic data and genome-scale models

Yang, Laurence; Yurkovich, James T.; Lloyd, Colton J. et al. · 2016 · Technical University of Denmark (DTU) · DOI

Full title: Principles of proteome allocation are revealed using proteomic data and genome-scale models

Authors: Yang, Laurence; Yurkovich, James T.; Lloyd, Colton J.; Ebrahim, Ali; Saunders, Michael A.; Palsson, Bernhard; id_orcid 0000-0003-2357-6785

Year: 2016

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/6d11117c-622a-46f0-bb23-c40d91539dda

Thesis Genome‐scale metabolic modeling reveals key features of a minimal gene set

Lachance, Jean‐Christophe; Matteau, Dominick; Brodeur, Joëlle et al. · 2021 · Technical University of Denmark (DTU) · DOI

Full title: Genome‐scale metabolic modeling reveals key features of a minimal gene set

Year: 2021

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/6c5fb099-d5ce-4372-8b47-e669ebfea949

Thesis Computational tools and analytical methods for effective metabolic engineering of microbial cell factories

Taylor Parkins, Shannara Kayleigh; id_orcid 0000-0003-4728-2159 · 2023 · Technical University of Denmark (DTU) · DOI

Full title: Computational tools and analytical methods for effective metabolic engineering of microbial cell factories

Authors: Taylor Parkins, Shannara Kayleigh; id_orcid 0000-0003-4728-2159

Year: 2023

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/6ced90b7-de9c-4445-bb8d-c0a58b4959c8

Thesis Genome scale models of yeast: towards standardized evaluation and consistent omic integration

Sanchez, Benjamin J.; Nielsen, Jens · 2015 · Technical University of Denmark (DTU) · DOI

Full title: Genome scale models of yeast: towards standardized evaluation and consistent omic integration

Authors: Sanchez, Benjamin J.; Nielsen, Jens

Year: 2015

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/6faa78ce-0fbc-43d4-a40a-635c5ecf43c3

Thesis BiGG Models: A platform for integrating, standardizing and sharing genome-scale models

King, Zachary A.; Lu, Justin; Dräger, Andreas et al. · 2016 · Technical University of Denmark (DTU) · DOI

Full title: BiGG Models: A platform for integrating, standardizing and sharing genome-scale models

Authors: King, Zachary A.; Lu, Justin; Dräger, Andreas; Miller, Philip; Federowicz, Stephen; Lerman, Joshua A.; Ebrahim, Ali; Palsson, Bernhard; id_orcid 0000-0003-2357-6785; Lewis, Nathan

Year: 2016

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/71799399-3bf7-430d-88a8-ff1a1c3d4c94

Thesis A community-driven reconstruction of the Aspergillus niger metabolic network

Brandl, Julian; Aguilar-Pontes, Maria Victoria; Schäpe, Paul et al. · 2018 · Technical University of Denmark (DTU) · DOI

Full title: A community-driven reconstruction of the Aspergillus niger metabolic network

Year: 2018

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/700a4b31-b046-49c7-896e-bf25567a5b40

Thesis Simultaneous application of enzyme and thermodynamic constraints to metabolic models using an updated Python implementation of GECKO

Carrasco Muriel, Jorge; Long, Christopher; Sonnenschein, Nikolaus et al. · 2023 · Technical University of Denmark (DTU) · DOI

Full title: Simultaneous application of enzyme and thermodynamic constraints to metabolic models using an updated Python implementation of GECKO

Authors: Carrasco Muriel, Jorge; Long, Christopher; Sonnenschein, Nikolaus; id_orcid 0000-0002-7581-4936

Year: 2023

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/66ca6afb-ca5d-4f6c-a301-8dc2ec9d4491

Thesis The use of in silico genome-scale models for the rational design of minimal cells

Lachance, Jean-Christophe; Rodrigue, Sébastien; Palsson, Bernhard O. et al. · 2019 · Technical University of Denmark (DTU) · DOI

Full title: The use of in silico genome-scale models for the rational design of minimal cells

Authors: Lachance, Jean-Christophe; Rodrigue, Sébastien; Palsson, Bernhard O.; id_orcid 0000-0003-2357-6785

Year: 2019

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/70e04a82-5782-4bae-a371-9f17ebf3a9f9

Thesis Development, Validation and Comprehensive Sensitivity Analysis of a Fermentation Model Expediting the Process Design of a Biorefinery

Vollmer, Nikolaus I.; id_orcid 0000-0002-5604-3099; Gernaey, Krist V. et al. · 2019 · Technical University of Denmark (DTU) · DOI

Full title: Development, Validation and Comprehensive Sensitivity Analysis of a Fermentation Model Expediting the Process Design of a Biorefinery

Year: 2019

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/63b64ec8-ca7b-45fe-8088-d6c242d7abad

Thesis Identification of growth-coupled production strains considering protein costs and kinetic variability

Dinh, Hoang V.; King, Zachary A.; Palsson, Bernhard O. et al. · 2018 · Technical University of Denmark (DTU) · DOI

Full title: Identification of growth-coupled production strains considering protein costs and kinetic variability

Authors: Dinh, Hoang V.; King, Zachary A.; Palsson, Bernhard O.; id_orcid 0000-0003-2357-6785; Feist, Adam M.; id_orcid 0000-0002-8630-4800

Year: 2018

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/6c666f6f-48e9-45a7-9228-24af7d38552a

Thesis Engineering high-level production of fatty alcohols by Saccharomyces cerevisiae from lignocellulosic feedstocks

d'Espaux, Leo; Ghosh, Amit; Runguphan, Weerawat et al. · 2017 · Technical University of Denmark (DTU) · DOI

Full title: Engineering high-level production of fatty alcohols by Saccharomyces cerevisiae from lignocellulosic feedstocks

Authors: d'Espaux, Leo; Ghosh, Amit; Runguphan, Weerawat; Wehrs, Maren; Xu, Feng; Konzock, Oliver; Dev, Ishaan; Nhan, Melissa; Gin, Jennifer; Apel, Amanda Reider; Petzold, Christopher J.; Singh, Seema; Simmons, Blake A.; Mukhopadhyay, Aindrila; Martín, Hector García; Keasling, Jay D.

Year: 2017

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/78f7cfe2-da0e-4919-b845-71961ce44d06

Thesis Modeling for understanding and engineering metabolism

Nielsen, Jens; Petranovic, Dina · 2025 · Technical University of Denmark (DTU) · DOI

Full title: Modeling for understanding and engineering metabolism

Authors: Nielsen, Jens; Petranovic, Dina

Year: 2025

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/75fb593d-049b-4d93-84f8-7653d7e4da90

Thesis Increasing galactose consumption by Saccharomyces cerevisiae through metabolic engineering of the GAL gene regulatory network

Østergaard, Simon; Olsson, Lisbeth; Johnston, M. et al. · 2000 · Technical University of Denmark (DTU) · DOI

Full title: Increasing galactose consumption by Saccharomyces cerevisiae through metabolic engineering of the GAL gene regulatory network

Authors: Østergaard, Simon; Olsson, Lisbeth; Johnston, M.; Nielsen, Jens

Year: 2000

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/7489c400-a9c9-4816-8162-73cc7a488adc

Thesis Genome-scale model of metabolism and gene expression provides a multi-scale description of acid stress responses in Escherichia coli

Du, Bin; Yang, Laurence; Lloyd, Colton J. et al. · 2019 · Technical University of Denmark (DTU) · DOI

Full title: Genome-scale model of metabolism and gene expression provides a multi-scale description of acid stress responses in Escherichia coli

Authors: Du, Bin; Yang, Laurence; Lloyd, Colton J.; Fang, Xin; Palsson, Bernhard ; id_orcid 0000-0003-2357-6785

Year: 2019

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/7ad7a238-5b96-4b00-9916-d419015e26fd

Thesis Development of an intracellular glycolytic flux sensor for high throughput applications in E.coli

Lehning, Christina Eva · 2017 · Technical University of Denmark (DTU) · DOI

Full title: Development of an intracellular glycolytic flux sensor for high throughput applications in E.coli

Authors: Lehning, Christina Eva

Year: 2017

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/6d1af514-be4e-4301-b52a-4525f8639c5d

Thesis CRISPRi-mediated metabolic switch enables concurrent aerobic and synthetic anaerobic fermentations in engineered consortium

Rong, Yixin; Frey, Adrian; id_orcid 0009-0008-7716-4042 et al. · 2024 · Technical University of Denmark (DTU) · DOI

Full title: CRISPRi-mediated metabolic switch enables concurrent aerobic and synthetic anaerobic fermentations in engineered consortium

Year: 2024

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/7415d711-3048-4df6-af78-a3fbfc720dad

Thesis Genome-scale models in human metabologenomics

Mardinoglu, Adil; Palsson, Bernhard; id_orcid 0000-0003-2357-6785 · 2025 · Technical University of Denmark (DTU) · DOI

Full title: Genome-scale models in human metabologenomics

Authors: Mardinoglu, Adil; Palsson, Bernhard; id_orcid 0000-0003-2357-6785

Year: 2025

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/7244a17a-8723-4662-b867-2084d25f7b92

Thesis Engineering yeast metabolism for production of fuels and chemicals

Nielsen, Jens · 2016 · Technical University of Denmark (DTU) · DOI

Full title: Engineering yeast metabolism for production of fuels and chemicals

Authors: Nielsen, Jens

Year: 2016

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/815379a3-c9a7-470f-a809-7fc556e18245

Thesis Systems biology-guided identification of synthetic lethal gene pairs and its potential use to discover antibiotic combinations

Aziz, Ramy K.; Monk, Jonathan M.; Lewis, R. M. et al. · 2015 · Technical University of Denmark (DTU) · DOI

Full title: Systems biology-guided identification of synthetic lethal gene pairs and its potential use to discover antibiotic combinations

Year: 2015

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/7c5e19b9-eaa1-44b3-8192-c422d98a88fc

Thesis Analysis of Aspergillus nidulans metabolism at the genome-scale

David, Helga; Ozcelik, İlknur Ş; Hofmann, Gerald et al. · 2008 · Technical University of Denmark (DTU) · DOI

Full title: Analysis of Aspergillus nidulans metabolism at the genome-scale

Authors: David, Helga; Ozcelik, İlknur Ş; Hofmann, Gerald; Nielsen, Jens

Year: 2008

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/7b849e31-36e5-46d7-b20f-8b4ee2d906e3

Thesis Probing efficient microbial CO 2 utilisation through metabolic and process modelling

Gorter de Vries, Philip J.; id_orcid 0000-0002-0311-5634; Mol, Viviënne et al. · 2024 · Technical University of Denmark (DTU) · DOI

Full title: Probing efficient microbial CO 2 utilisation through metabolic and process modelling

Authors: Gorter de Vries, Philip J.; id_orcid 0000-0002-0311-5634; Mol, Viviënne; Sonnenschein, Nikolaus; id_orcid 0000-0002-7581-4936; Jensen, Torbjørn Ølshøj; Nielsen, Alex Toftgaard

Year: 2024

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/74c8b1ed-ec94-49f6-b08a-22dbb6f7cef4

Thesis Improved vanillin production in baker's yeast through in silico design

Brochado, Ana Rita; Matos, Cláudia; Møller, Birger L. et al. · 2010 · Technical University of Denmark (DTU) · DOI

Full title: Improved vanillin production in baker's yeast through in silico design

Authors: Brochado, Ana Rita; Matos, Cláudia; Møller, Birger L.; Hansen, Jørgen; Mortensen, Uffe H.; Patil, Kiran Raosaheb

Year: 2010

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/7eeeb11a-5367-4e03-b5d6-f34785c588c1

Thesis Integration of gene expression data into genome-scale metabolic models

Åkesson, M.; Förster, Jochen; id_orcid 0000-0003-4045-7905 et al. · 2004 · Technical University of Denmark (DTU) · DOI

Full title: Integration of gene expression data into genome-scale metabolic models

Authors: Åkesson, M.; Förster, Jochen; id_orcid 0000-0003-4045-7905; Nielsen, Jens

Year: 2004

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/829490ac-b29d-4ea8-9d32-32a7da4aab9d

Thesis Optimal cofactor swapping can increase the theoretical yield for chemical production in Escherichia coli and Saccharomyces cerevisiae

King, Zachary A.; Feist, Adam; id_orcid 0000-0002-8630-4800 · 2014 · Technical University of Denmark (DTU) · DOI

Full title: Optimal cofactor swapping can increase the theoretical yield for chemical production in Escherichia coli and Saccharomyces cerevisiae

Authors: King, Zachary A.; Feist, Adam; id_orcid 0000-0002-8630-4800

Year: 2014

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/7d8e9435-082b-4e4f-a1ab-5d6b655c1e76

Thesis Modeling Method for Increased Precision and Scope of Directly Measurable Fluxes at a Genome-Scale

McCloskey, Douglas; Young, Jamey D.; Xu, Sibei et al. · 2016 · Technical University of Denmark (DTU) · DOI

Full title: Modeling Method for Increased Precision and Scope of Directly Measurable Fluxes at a Genome-Scale

Authors: McCloskey, Douglas; Young, Jamey D.; Xu, Sibei; Palsson, Bernhard; id_orcid 0000-0003-2357-6785; Feist, Adam; id_orcid 0000-0002-8630-4800

Year: 2016

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/81f2369d-78d4-4487-8c5b-9c710249b079

Thesis Separation and recovery of intracellular betacarotene using a process synthesis framework

Sabol, Alexander M.; Bertran, Maria-Ona; Raftery, Jonathan P. et al. · 2017 · Technical University of Denmark (DTU) · DOI

Full title: Separation and recovery of intracellular betacarotene using a process synthesis framework

Authors: Sabol, Alexander M.; Bertran, Maria-Ona; Raftery, Jonathan P.; Woodley, John M.; id_orcid 0000-0002-7976-2483; Gani, Rafiqul; Nazmul Karima, M.

Year: 2017

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/8153983c-f26a-4d7b-9859-946a60a7ff92

Thesis Yeast Systems Biology: Model organism and Cell Factory

Nielsen, Jens · 2019 · Technical University of Denmark (DTU) · DOI

Full title: Yeast Systems Biology: Model organism and Cell Factory

Authors: Nielsen, Jens

Year: 2019

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/7e1c5273-9c1e-4048-a7e3-5adb5644906d

Thesis Acetol biosynthesis enables NADPH balance during nitrogen limitation in engineered Escherichia coli

Sudarsan, Suresh; Demling, Philipp; Ozdemir, Emre et al. · 2025 · Technical University of Denmark (DTU) · DOI

Full title: Acetol biosynthesis enables NADPH balance during nitrogen limitation in engineered Escherichia coli

Authors: Sudarsan, Suresh; Demling, Philipp; Ozdemir, Emre; id_orcid 0000-0001-5548-6720; Ben Ammar, Aziz; Mennicken, Philip; Buescher, Joerg M.; Meurer, Guido; Ebert, Birgitta E.; Blank, Lars M.

Year: 2025

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/84d966a5-cdaf-4ddc-9e4e-b614305b2a46

Thesis Reprogramming methanol utilization pathways to convert Saccharomyces cerevisiae to a synthetic methylotroph

Zhan, Chunjun; Li, Xiaowei; Lan, Guangxu et al. · 2023 · Technical University of Denmark (DTU) · DOI

Full title: Reprogramming methanol utilization pathways to convert Saccharomyces cerevisiae to a synthetic methylotroph

Authors: Zhan, Chunjun; Li, Xiaowei; Lan, Guangxu; Baidoo, Edward E.K.; Yang, Yankun; Liu, Yuzhong; Sun, Yang; Wang, Shijie; Wang, Yanyan; Wang, Guokun; Nielsen, Jens; Keasling, Jay D.; Chen, Yun; Bai, Zhonghu

Year: 2023

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/86664e7d-39a3-4655-8134-f98d619e47b5

Thesis Bringing a scalable adaptive hybrid modeling framework closer to industrial use: Application on a multiscale fungal fermentation

Rydal, Thomas; Frandsen, Jesper; Nadal-Rey, Gisela et al. · 2024 · Technical University of Denmark (DTU) · DOI

Full title: Bringing a scalable adaptive hybrid modeling framework closer to industrial use: Application on a multiscale fungal fermentation

Authors: Rydal, Thomas; Frandsen, Jesper; Nadal-Rey, Gisela; Albæk, Mads Orla; Ramin, Pedram; id_orcid 0000-0001-7245-072X

Year: 2024

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/818c461a-a4db-4668-9732-9f02791c25c7

Thesis Mapping condition-dependent regulation of metabolism in yeast through genome-scale modeling

Österlund, Tobias; Nookaew, Intawat; Bordel, Sergio et al. · 2013 · Technical University of Denmark (DTU) · DOI

Full title: Mapping condition-dependent regulation of metabolism in yeast through genome-scale modeling

Authors: Österlund, Tobias; Nookaew, Intawat; Bordel, Sergio; Nielsen, Jens

Year: 2013

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/83e87b72-797f-4ed6-9818-866298439307

Thesis Reconstruction of the central carbon metabolism of Aspergillus niger

David, Helga; Åkesson, Mats Fredrik; Nielsen, Jens · 2003 · Technical University of Denmark (DTU) · DOI

Full title: Reconstruction of the central carbon metabolism of Aspergillus niger

Authors: David, Helga; Åkesson, Mats Fredrik; Nielsen, Jens

Year: 2003

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/8142aeab-168c-4202-b34e-e53b8206409c

Thesis Systems biology solutions for biochemical production challenges

Hansen, Anne Sofie Lærke; id_orcid 0000-0003-2771-4671; Lennen, Rebecca M et al. · 2017 · Technical University of Denmark (DTU) · DOI

Full title: Systems biology solutions for biochemical production challenges

Authors: Hansen, Anne Sofie Lærke; id_orcid 0000-0003-2771-4671; Lennen, Rebecca M; Sonnenschein, Nikolaus; id_orcid 0000-0002-7581-4936; Herrgard, Markus

Year: 2017

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/82d70d8f-916a-4617-916e-00b48a0029a9

Thesis Diagnosis and mitigation of the systemic impact of genome reduction in Escherichia coli DGF-298

Champie, Antoine; Lachance, Jean Christophe; Sastry, Anand et al. · 2024 · Technical University of Denmark (DTU) · DOI

Full title: Diagnosis and mitigation of the systemic impact of genome reduction in Escherichia coli DGF-298

Year: 2024

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/82c5ebb6-c054-4d59-98fe-d3f38249c717

Thesis Constraint-based modeling of yeast mitochondria reveals the dynamics of protein import and iron-sulfur cluster biogenesis

Malina, Carl; Di Bartolomeo, Francesca; Kerkhoven, Eduard J. et al. · 2021 · Technical University of Denmark (DTU) · DOI

Full title: Constraint-based modeling of yeast mitochondria reveals the dynamics of protein import and iron-sulfur cluster biogenesis

Authors: Malina, Carl; Di Bartolomeo, Francesca; Kerkhoven, Eduard J.; Nielsen, Jens

Year: 2021

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/9066bc6b-8a30-46c5-96ff-5bba81b65bc2

Thesis Bayesian genome scale modelling identifies thermal determinants of yeast metabolism

Li, Gang; Hu, Yating; Jan Zrimec, Zrimec et al. · 2021 · Technical University of Denmark (DTU) · DOI

Full title: Bayesian genome scale modelling identifies thermal determinants of yeast metabolism

Authors: Li, Gang; Hu, Yating; Jan Zrimec, Zrimec; Luo, Hao; Wang, Hao; Zelezniak, Aleksej; Ji, Boyang; Nielsen, Jens

Year: 2021

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/8acf09fc-5d06-471b-8507-8b89e1488a90

Thesis Reconstruction, simulation and analysis of enzyme-constrained metabolic models using GECKO Toolbox 3.0

Chen, Yu; Gustafsson, Johan; Tafur Rangel, Albert et al. · 2024 · Technical University of Denmark (DTU) · DOI

Full title: Reconstruction, simulation and analysis of enzyme-constrained metabolic models using GECKO Toolbox 3.0

Authors: Chen, Yu; Gustafsson, Johan; Tafur Rangel, Albert; Anton, Mihail; Domenzain, Iván; Kittikunapong, Cheewin; Li, Feiran; Yuan, Le; Nielsen, Jens; Kerkhoven, Eduard J.

Year: 2024

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/8d0ab070-6b59-4944-98c1-40598638748d

Thesis Improved annotation through genome-scale metabolic modeling of Aspergillus oryzae

Vongsangnak, Wanwipa; Olsen, Peter; Hansen, Kim et al. · 2008 · Technical University of Denmark (DTU) · DOI

Full title: Improved annotation through genome-scale metabolic modeling of Aspergillus oryzae

Authors: Vongsangnak, Wanwipa; Olsen, Peter; Hansen, Kim; Krogsgaard, Steen; Nielsen, Jens

Year: 2008

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/89736fe7-a0e9-47ef-8355-50bae04e65b2

Thesis Phenotypic characterization of glucose repression mutants of Saccharomyce cerevisiae usinge experiments with C-13-labelled glucose

Vijayendran, Raghevendran; Gombert, A.K.; Christensen, B. et al. · 2004 · Technical University of Denmark (DTU) · DOI

Full title: Phenotypic characterization of glucose repression mutants of Saccharomyce cerevisiae usinge experiments with C-13-labelled glucose

Authors: Vijayendran, Raghevendran; Gombert, A.K.; Christensen, B.; Kotter, P.; Nielsen, Jens

Year: 2004

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/9136a327-1556-418e-af14-295a7e588f44

Thesis From genomes to in silico cells via metabolic networks

Borodina, Irina; Nielsen, Jens · 2005 · Technical University of Denmark (DTU) · DOI

Full title: From genomes to in silico cells via metabolic networks

Authors: Borodina, Irina; Nielsen, Jens

Year: 2005

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/9191950b-4f7e-4e4d-bd4d-2950c92ac5fe

Thesis Scale-down study of adaptation in Saccharomyces cerevisiae chemostat cultures for heterologous protein production

Wright, Naia Risager · 2021 · Technical University of Denmark (DTU) · DOI

Full title: Scale-down study of adaptation in Saccharomyces cerevisiae chemostat cultures for heterologous protein production

Authors: Wright, Naia Risager

Year: 2021

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/8d73173b-041b-4ee7-8665-29be40d6cdd1

Thesis The yeastGemMap: A process diagram to assist yeast systems-metabolic studies

Caspeta, Luis; Kerkhoven, Eduard J.; Martinez, Alfredo et al. · 2021 · Technical University of Denmark (DTU) · DOI

Full title: The yeastGemMap: A process diagram to assist yeast systems-metabolic studies

Authors: Caspeta, Luis; Kerkhoven, Eduard J.; Martinez, Alfredo; Nielsen, Jens

Year: 2021

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/92bf7b05-c6fd-41c7-9568-905e21572ab5

Thesis Toward systems metabolic engineering of Aspergillus and Pichia species for the production of chemicals and biofuels

Caspeta, Luis; Nielsen, Jens · 2013 · Technical University of Denmark (DTU) · DOI

Full title: Toward systems metabolic engineering of Aspergillus and Pichia species for the production of chemicals and biofuels

Authors: Caspeta, Luis; Nielsen, Jens

Year: 2013

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/99f7154d-d8d1-49ce-9651-6903e74e89a8

Thesis Metabolic Fluxes Using Deep Learning Based on Enzyme Variations:Application to Glycolysis in Entamoeba histolytica

Oulia, Freddy; Charton, Philippe; Lo-Thong-Viramoutou, Ophélie et al. · 2024 · Technical University of Denmark (DTU) · DOI

Full title: Metabolic Fluxes Using Deep Learning Based on Enzyme Variations:Application to Glycolysis in Entamoeba histolytica

Authors: Oulia, Freddy; Charton, Philippe; Lo-Thong-Viramoutou, Ophélie; Acevedo-Rocha, Carlos G.; Liu, Wei; Huynh, Du; Damour, Cédric; Wang, Jingbo; Cadet, Frederic

Year: 2024

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/93851283-2e55-4d7f-9262-5504188d9642

Thesis Production of a heterologous proteinase A by Saccharomyces kluyveri

Møller, Kasper; Tidemand, L.D.; Winther, J.R. et al. · 2001 · Technical University of Denmark (DTU) · DOI

Full title: Production of a heterologous proteinase A by Saccharomyces kluyveri

Authors: Møller, Kasper; Tidemand, L.D.; Winther, J.R.; Olsson, Lisbeth; Piskur, Jure; Nielsen, Jens

Year: 2001

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/94b98234-01f8-4160-ac95-93a411773d18

Thesis A workflow for generating multi-strain genome-scale metabolic models of prokaryotes

Norsigian, Charles J.; Fang, Xin; Seif, Yara et al. · 2020 · Technical University of Denmark (DTU) · DOI

Full title: A workflow for generating multi-strain genome-scale metabolic models of prokaryotes

Authors: Norsigian, Charles J.; Fang, Xin; Seif, Yara; Monk, Jonathan M.; Palsson, Bernhard O.; id_orcid 0000-0003-2357-6785

Year: 2020

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/915c349a-70f1-4f54-88c9-b33047aa535a

Thesis Fast growth phenotype of E. coli K-12 from adaptive laboratory evolution does not require intracellular flux rewiring

Long, Christopher P.; Gonzalez, Jacqueline E.; Feist, Adam M. et al. · 2017 · Technical University of Denmark (DTU) · DOI

Full title: Fast growth phenotype of E. coli K-12 from adaptive laboratory evolution does not require intracellular flux rewiring

Authors: Long, Christopher P.; Gonzalez, Jacqueline E.; Feist, Adam M.; id_orcid 0000-0002-8630-4800; Palsson, Bernhard O; id_orcid 0000-0003-2357-6785; Antoniewicz, Maciek R.

Year: 2017

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/8c86285a-7d95-413e-95b6-70c1af73ecd4

Thesis BioMet Toolbox: genome-wide analysis of metabolism

Cvijovic, M.; Olivares Hernandez, Roberto; Agren, R. et al. · 2010 · Technical University of Denmark (DTU) · DOI

Full title: BioMet Toolbox: genome-wide analysis of metabolism

Authors: Cvijovic, M.; Olivares Hernandez, Roberto; Agren, R.; Dahr, N.; Vongsangnak, Wanwipa; Nookaew, I.; Patil, Kiran Raosaheb; Nielsen, J.

Year: 2010

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/937fc86a-f9c2-43e5-817b-30b3fbe09ac3

Thesis Challenges in modeling the human gut microbiome

Babaei, Parizad; Shoaie, Saeed; Ji, Boyang et al. · 2018 · Technical University of Denmark (DTU) · DOI

Full title: Challenges in modeling the human gut microbiome

Authors: Babaei, Parizad; Shoaie, Saeed; Ji, Boyang; Nielsen, Jens

Year: 2018

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/989b644f-b86c-4430-8f73-b0b05ecf155c

Thesis Systems strategies for developing industrial microbial strains.

Lee, Sang Yup; Kim, Hyun Uk · 2015 · Technical University of Denmark (DTU) · DOI

Full title: Systems strategies for developing industrial microbial strains.

Authors: Lee, Sang Yup; Kim, Hyun Uk

Year: 2015

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/91cede05-5ec3-4c2a-87d7-e804778b9d3d

Thesis The JBEI quantitative metabolic modeling library (jQMM): a python library for modeling microbial metabolism

Birkel, Garrett W.; Ghosh, Amit; Kumar, Vinay S. et al. · 2017 · Technical University of Denmark (DTU) · DOI

Full title: The JBEI quantitative metabolic modeling library (jQMM): a python library for modeling microbial metabolism

Authors: Birkel, Garrett W.; Ghosh, Amit; Kumar, Vinay S.; Weaver, Daniel; Ando, David; Backman, Tyler W. H.; Arkin, Adam Paul; Keasling, Jay D.; Martin, Hector Garcia

Year: 2017

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/91bbd75c-084f-4a30-9c06-bc0a9f5d5d65

Thesis Genome-Scale Metabolic Modeling from Yeast to Human Cell Models of Complex Diseases: Latest Advances and Challenges

Chen, Yu; Li, Gang; Nielsen, Jens · 2019 · Technical University of Denmark (DTU) · DOI

Full title: Genome-Scale Metabolic Modeling from Yeast to Human Cell Models of Complex Diseases: Latest Advances and Challenges

Authors: Chen, Yu; Li, Gang; Nielsen, Jens

Year: 2019

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/954b2a62-2f06-4f60-9a0e-10acf08649a0

Thesis Metabolic Engineering of Saccharomyces cerevisiae:From p-Coumaric Acid to Rosmarinic Acid

Borja Zamfir, Gheorghe Manuel · 2024 · Technical University of Denmark (DTU) · DOI

Full title: Metabolic Engineering of Saccharomyces cerevisiae:From p-Coumaric Acid to Rosmarinic Acid

Authors: Borja Zamfir, Gheorghe Manuel

Year: 2024

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/a46ad662-7158-4f6c-8685-c1fbdd6b3bcd

Thesis Optimizing Cofactor Specificity of Oxidoreductase Enzymes for the Generation of Microbial Production Strains—OptSwap

King, Zachary A.; Feist, Adam; id_orcid 0000-0002-8630-4800 · 2013 · Technical University of Denmark (DTU) · DOI

Full title: Optimizing Cofactor Specificity of Oxidoreductase Enzymes for the Generation of Microbial Production Strains—OptSwap

Authors: King, Zachary A.; Feist, Adam; id_orcid 0000-0002-8630-4800

Year: 2013

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/9a26e696-e9a9-4736-9bb9-e8b69aa1d54c

Thesis Production of farnesene and santalene by Saccharomyces cerevisiae using fed-batch cultivations with RQ- controlled feed

Tippmann, Stefan; Scalcinati, Gionata; Siewers, Verena et al. · 2016 · Technical University of Denmark (DTU) · DOI

Full title: Production of farnesene and santalene by Saccharomyces cerevisiae using fed-batch cultivations with RQ- controlled feed

Authors: Tippmann, Stefan; Scalcinati, Gionata; Siewers, Verena; Nielsen, Jens

Year: 2016

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/9fd50bb7-99ff-4169-8505-cd5d37b70e61

Thesis SLIMEr: probing flexibility of lipid metabolism in yeast with an improved constraint-based modeling framework

Sanchez, Benjamin J.; Li, Feiran; Kerkhoven, Eduard J. et al. · 2019 · Technical University of Denmark (DTU) · DOI

Full title: SLIMEr: probing flexibility of lipid metabolism in yeast with an improved constraint-based modeling framework

Authors: Sanchez, Benjamin J.; Li, Feiran; Kerkhoven, Eduard J.; Nielsen, Jens

Year: 2019

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/9cc81ad1-011f-467e-8566-d9b9a74f57ad

Thesis Modular Pathway Rewiring of Yeast for Amino Acid Production

Liu, Quanli; Yu, Tao; Campbell, Kate et al. · 2018 · Technical University of Denmark (DTU) · DOI

Full title: Modular Pathway Rewiring of Yeast for Amino Acid Production

Authors: Liu, Quanli; Yu, Tao; Campbell, Kate; Nielsen, Jens; Chen, Yun

Year: 2018

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/93a3e0e6-9093-4b9f-89d9-7d51b9aff931

Thesis Multi-scale Exploration of the Technical, Economic, and Environmental Dimensions of Bio-based Chemical Production

Zhuang, Kai; Herrgard, Markus · 2014 · Technical University of Denmark (DTU) · DOI

Full title: Multi-scale Exploration of the Technical, Economic, and Environmental Dimensions of Bio-based Chemical Production

Authors: Zhuang, Kai; Herrgard, Markus

Year: 2014

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/9e073411-8d1d-4e51-820a-f0b8969ff3b6

Thesis A model‐driven quantitative metabolomics analysis of aerobic and anaerobic metabolism in E. coli K‐12 MG1655 that is biochemically and thermodynamically consistent

McCloskey, Douglas; Gangoiti, Jon A.; King, Zachary A. et al. · 2014 · Technical University of Denmark (DTU) · DOI

Full title: A model‐driven quantitative metabolomics analysis of aerobic and anaerobic metabolism in E. coli K‐12 MG1655 that is biochemically and thermodynamically consistent

Authors: McCloskey, Douglas; Gangoiti, Jon A.; King, Zachary A.; Naviaux, Robert K.; Barshop, Bruce A.; Palsson, Bernhard; id_orcid 0000-0003-2357-6785; Feist, Adam; id_orcid 0000-0002-8630-4800

Year: 2014

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/9f2adcc4-f0c5-4792-bd37-27e34dbac563

Thesis Multi-scale exploration of the technical, economic, and environmental dimensions of bio-based chemical production

Zhuang, Kai; Herrgard, Markus · 2015 · Technical University of Denmark (DTU) · DOI

Full title: Multi-scale exploration of the technical, economic, and environmental dimensions of bio-based chemical production

Authors: Zhuang, Kai; Herrgard, Markus

Year: 2015

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/a8b986e3-46df-4344-bf3b-8d7bf2ef0a21

Thesis Escher-FBA: a web application for interactive flux balance analysis

Rowe, Elliot; Palsson, Bernhard O.; id_orcid 0000-0003-2357-6785 et al. · 2018 · Technical University of Denmark (DTU) · DOI

Full title: Escher-FBA: a web application for interactive flux balance analysis

Authors: Rowe, Elliot; Palsson, Bernhard O.; id_orcid 0000-0003-2357-6785; King, Zachary A.

Year: 2018

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/9f8b6eaf-b4e0-43c2-8a1f-1eb31d500f77

Thesis Digital models in biotechnology: Towards multi-scale integration and implementation

Hartmann, Fabian S.F.; id_orcid 0000-0001-5394-1865; Udugama, Isuru A. et al. · 2022 · Technical University of Denmark (DTU) · DOI

Full title: Digital models in biotechnology: Towards multi-scale integration and implementation

Authors: Hartmann, Fabian S.F.; id_orcid 0000-0001-5394-1865; Udugama, Isuru A.; Seibold, Gerd M.; id_orcid 0000-0002-9823-8134; Sugiyama, Hirokazu; Gernaey, Krist V.; id_orcid 0000-0002-0364-1773

Year: 2022

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/a9e1d47f-53b8-41c4-993c-fc97c01d2690

Thesis In silico aided metabolic engineering of Saccharomyces cerevisiae for improved bioethanol production.

Bro, Christoffer; Regenberg, Birgitte; Förster, Jochen et al. · 2006 · Technical University of Denmark (DTU) · DOI

Full title: In silico aided metabolic engineering of Saccharomyces cerevisiae for improved bioethanol production.

Authors: Bro, Christoffer; Regenberg, Birgitte; Förster, Jochen; id_orcid 0000-0003-4045-7905; Nielsen, Jens

Year: 2006

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/a5bc802a-0ef2-4e20-87ac-b3292251ef36

Thesis A Genome-Scale Metabolic Model for Methylococcus capsulatus (Bath) Suggests Reduced Efficiency Electron Transfer to the Particulate Methane Monooxygenase

Lieven, Christian; Petersen, Leander A. H.; Jørgensen, Sten Bay et al. · 2018 · Technical University of Denmark (DTU) · DOI

Full title: A Genome-Scale Metabolic Model for Methylococcus capsulatus (Bath) Suggests Reduced Efficiency Electron Transfer to the Particulate Methane Monooxygenase

Year: 2018

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/a0369532-98e5-4c0b-a399-b06e4ebf379b

Thesis Literature mining supports a next-generation modeling approach to predict cellular byproduct secretion

King, Zachary A.; O'Brien, Edward J.; Feist, Adam M. et al. · 2017 · Technical University of Denmark (DTU) · DOI

Full title: Literature mining supports a next-generation modeling approach to predict cellular byproduct secretion

Authors: King, Zachary A.; O'Brien, Edward J.; Feist, Adam M.; id_orcid 0000-0002-8630-4800; Palsson, Bernhard O.; id_orcid 0000-0003-2357-6785

Year: 2017

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/a9e23bc3-cf78-46ad-a4cf-8601c6a0a96d

Thesis The transcriptome and flux profiling of Crabtree-negative hydroxy acid producing strains of Saccharomyces cerevisiae reveals changes in the central carbon metabolism

Jessop-Fabre, Mathew M; id_orcid 0000-0001-7534-2230; Dahlin, Jonathan et al. · 2019 · Technical University of Denmark (DTU) · DOI

Full title: The transcriptome and flux profiling of Crabtree-negative hydroxy acid producing strains of Saccharomyces cerevisiae reveals changes in the central carbon metabolism

Year: 2019

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/ad991126-8644-4edf-88b2-acb9dfe73436

Thesis Advances in metabolic engineering of yeast Saccharomyces cerevisiae for production of chemicals

Borodina, Irina; Nielsen, Jens · 2014 · Technical University of Denmark (DTU) · DOI

Full title: Advances in metabolic engineering of yeast Saccharomyces cerevisiae for production of chemicals

Authors: Borodina, Irina; Nielsen, Jens

Year: 2014

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/ab1d20a3-0fcd-483e-8fe8-e92ee9fe22bb

Thesis In vitro turnover numbers do not reflect in vivo activities of yeast enzymes

Chen, Yu; Nielsen, Jens · 2021 · Technical University of Denmark (DTU) · DOI

Full title: In vitro turnover numbers do not reflect in vivo activities of yeast enzymes

Authors: Chen, Yu; Nielsen, Jens

Year: 2021

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/a71b968f-b161-44c7-af91-1bc507b13684

Thesis Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0

Heirendt, Laurent; Arreckx, Sylvain; Pfau, Thomas et al. · 2019 · Technical University of Denmark (DTU) · DOI

Full title: Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0

Year: 2019

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/abc86310-0a40-40be-9530-faf60fc05c99

Thesis Integrated multilaboratory systems biology reveals differences in protein metabolism between two reference yeast strains

Canelas, Andre B.; Harrison, Nicola; Fazio, Alessandro et al. · 2010 · Technical University of Denmark (DTU) · DOI

Full title: Integrated multilaboratory systems biology reveals differences in protein metabolism between two reference yeast strains

Authors: Canelas, Andre B.; Harrison, Nicola; Fazio, Alessandro; Zhang, Jie; Pitkanen, Juha-Pekka; van den Brink, Joost; Bakker, Barbara M.; Bogner, Lara; Bouwman, Jildau; Castrillo, Juan I.; Cankorur, Ayca; Chumnanpuen, Pramote; Daran-Lapujade, Pascale; Dikicioglu, Duygu; van Eunen, Karen; Ewald, Jennifer C.; Heijnen, Joseph J.; Kirdar, Betul; Mattila, Ismo; Mensonides, Femke I. C.; Niebel, Anja; Penttila, Merja; Pronk, Jack T.; Reuss, Matthias; Salusjarvi, Laura; Sauer, Uwe; Sherman, David; Siemann-Herzberg, Martin; Westerhoff, Hans; de Winde, Johannes; Petranovic, Dina; Oliver, Stephen G.; Workman, Christopher; id_orcid 0000-0002-2210-3743; Zamboni, Nicola; Nielsen, Jens

Year: 2010

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/abe5d1ac-570c-4912-8a0a-c959efb55b97

Thesis Towards a quantitative prediction of the fluxome from the proteome

Rossell, Sergio; Solem, Christian; id_orcid 0000-0002-3898-280X et al. · 2011 · Technical University of Denmark (DTU) · DOI

Full title: Towards a quantitative prediction of the fluxome from the proteome

Authors: Rossell, Sergio; Solem, Christian; id_orcid 0000-0002-3898-280X; Jensen, Peter Ruhdal; id_orcid 0000-0003-2080-2070; Heijnen, Joseph J.

Year: 2011

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/b5444c69-4be9-4ca0-82da-3b67db486b99

Thesis Characterizing Strain Variation in Engineered E. coli Using a Multi-Omics-Based Workflow

Brunk, Elizabeth; George, Kevin W.; Alonso-Gutierrez, Jorge et al. · 2016 · Technical University of Denmark (DTU) · DOI

Full title: Characterizing Strain Variation in Engineered E. coli Using a Multi-Omics-Based Workflow

Year: 2016

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/acd86d0f-dae6-4d90-b52a-40794dfe31ac

Thesis Design of homo-organic acid producing strains using multi-objective optimization

Kim, Tae Yong; Park, Jong Myoung; Kim, Hyun Uk et al. · 2015 · Technical University of Denmark (DTU) · DOI

Full title: Design of homo-organic acid producing strains using multi-objective optimization

Authors: Kim, Tae Yong; Park, Jong Myoung; Kim, Hyun Uk; Cho, Kwang Myung; Lee, Sang Yup

Year: 2015

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/b27be36b-dd70-4d89-9026-c24415e13545

Thesis Fuel ethanol production from lignocellulose: a challenge for metabolic engineering and process integration

Zaldivar, Jesus; Nielsen, Jens; Olsson, Lisbeth · 2001 · Technical University of Denmark (DTU) · DOI

Full title: Fuel ethanol production from lignocellulose: a challenge for metabolic engineering and process integration

Authors: Zaldivar, Jesus; Nielsen, Jens; Olsson, Lisbeth

Year: 2001

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/b01b9888-3e1e-4d04-9d2e-d38c10e2bed1

Thesis A biochemically structured model for ethanol fermentation by Kluyveromyces marxianus: A batch fermentation and kinetic study

Sansonetti, Sascha; Hobley, Timothy John; id_orcid 0000-0002-1355-6214 et al. · 2011 · Technical University of Denmark (DTU) · DOI

Full title: A biochemically structured model for ethanol fermentation by Kluyveromyces marxianus: A batch fermentation and kinetic study

Authors: Sansonetti, Sascha; Hobley, Timothy John; id_orcid 0000-0002-1355-6214; Calabrò, V.; Villadsen, John; id_orcid 0000-0002-6523-8445; Sin, Gürkan; id_orcid 0000-0003-0513-4502

Year: 2011

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/aee3c068-1c5d-467f-aad0-8edbfdbfe7dd

Thesis Genome-scale modeling drives 70-fold improvement of intracellular heme production in Saccharomyces cerevisiae

Ishchuka, Olena P.; Domenzain, Ivan; Sanchez, Benjamín J. et al. · 2022 · Technical University of Denmark (DTU) · DOI

Full title: Genome-scale modeling drives 70-fold improvement of intracellular heme production in Saccharomyces cerevisiae

Authors: Ishchuka, Olena P.; Domenzain, Ivan; Sanchez, Benjamín J.; Muñiz-Paredes, Facundo; Martínez, Jose L.; id_orcid 0000-0002-4490-8534; Nielsen, Jens; Petranovic, Dina

Year: 2022

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/abd35e2e-92e5-4feb-b08c-8c4d4483e8b2

Thesis Aerobic glucose metabolism of Saccharomyces kluyveri: Growth, metabolite production, and quantification of metabolic fluxes

Møller, Kasper; Christensen, B.; Förster, Jochen et al. · 2002 · Technical University of Denmark (DTU) · DOI

Full title: Aerobic glucose metabolism of Saccharomyces kluyveri: Growth, metabolite production, and quantification of metabolic fluxes

Authors: Møller, Kasper; Christensen, B.; Förster, Jochen; id_orcid 0000-0003-4045-7905; Piskur, Jure; Nielsen, Jens; Olsson, Lisbeth

Year: 2002

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/b99578a7-af0e-4c5c-9952-f16304d9cc0c

Thesis A metabolic reconstruction of Lactobacillus reuteri JCM 1112 and analysis of its potential as a cell factory

Kristjansdottir, Thordis; Bosma, Elleke Fenna; Branco Dos Santos, Filipe et al. · 2019 · Technical University of Denmark (DTU) · DOI

Full title: A metabolic reconstruction of Lactobacillus reuteri JCM 1112 and analysis of its potential as a cell factory

Year: 2019

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/b7a7d549-8eec-4b68-a47c-7b1c17553b5d

Thesis OptFlux: an open-source software platform for in silico metabolic engineering

Rocha, I.; Maia, P.; Evangelista, P. et al. · 2010 · Technical University of Denmark (DTU) · DOI

Full title: OptFlux: an open-source software platform for in silico metabolic engineering

Authors: Rocha, I.; Maia, P.; Evangelista, P.; Vilaca, P.; Soares, S.; Pinto, J.P.; Nielsen, J.; Patil, Kiran Raosaheb; Ferreira, E.C.; Rocha, M.

Year: 2010

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/bdbb867e-17e6-40fc-ac4c-cb09dd72eac7

Thesis Assessing glycolytic flux alterations resulting from genetic perturbations in E. coli using a biosensor

Lehning, Christina Eva; Siedler, Solvej; Ellabaan, Mostafa M Hashim et al. · 2017 · Technical University of Denmark (DTU) · DOI

Full title: Assessing glycolytic flux alterations resulting from genetic perturbations in E. coli using a biosensor

Authors: Lehning, Christina Eva; Siedler, Solvej; Ellabaan, Mostafa M Hashim; Sommer, Morten Otto Alexander; id_orcid 0000-0003-4005-5674

Year: 2017

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/b3fa1244-3799-477e-8c82-aff5ce21c5af

Thesis Glycerol metabolism of Pichia pastoris ( Komagataella spp. ) characterised by 13 C-based metabolic flux analysis

Tomàs-Gamisans, Màrius; Ødum, Anders Sebastian Rosenkrans; Workman, Mhairi et al. · 2019 · Technical University of Denmark (DTU) · DOI

Full title: Glycerol metabolism of Pichia pastoris ( Komagataella spp. ) characterised by 13 C-based metabolic flux analysis

Authors: Tomàs-Gamisans, Màrius; Ødum, Anders Sebastian Rosenkrans; Workman, Mhairi; Ferrer, Pau; Albiol, Joan

Year: 2019

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/b3f31fe3-4b88-493f-b5f5-924182598049

Thesis Pharmaceutical protein production by yeast: towards production of human blood proteins by microbial fermentation

Martinez Ruiz, José Luis; id_orcid 0000-0002-4490-8534; Liu, Lifang et al. · 2012 · Technical University of Denmark (DTU) · DOI

Full title: Pharmaceutical protein production by yeast: towards production of human blood proteins by microbial fermentation

Authors: Martinez Ruiz, José Luis; id_orcid 0000-0002-4490-8534; Liu, Lifang; Petranovic, Dina; Nielsen, Jens

Year: 2012

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/bfa687b7-2f80-4728-b767-9d8d2c0a272c

Thesis Applying omics and synthetic biology tools for improving the production of sustainable industrial biochemicals

Chandrasekaran, Priyadharshini · 2023 · Technical University of Denmark (DTU) · DOI

Full title: Applying omics and synthetic biology tools for improving the production of sustainable industrial biochemicals

Authors: Chandrasekaran, Priyadharshini

Year: 2023

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/b7dbfe52-e7fa-4aa6-918f-a9bb255d4938

Thesis Basic and applied uses of genome-scale metabolic network reconstructions of Escherichia coli.

McCloskey, Douglas; Palsson, Bernhard; id_orcid 0000-0003-2357-6785 et al. · 2013 · Technical University of Denmark (DTU) · DOI

Full title: Basic and applied uses of genome-scale metabolic network reconstructions of Escherichia coli.

Authors: McCloskey, Douglas; Palsson, Bernhard; id_orcid 0000-0003-2357-6785; Feist, Adam; id_orcid 0000-0002-8630-4800

Year: 2013

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/bea0c9bb-a503-493b-8847-4315678a7dbd

Thesis Metabolic impact of an NADH-producing glucose-6-phosphate dehydrogenase in Escherichia coli.

Olavarria, K.; De Ingeniis, J.; Zielinski, D. C. et al. · 2014 · Technical University of Denmark (DTU) · DOI

Full title: Metabolic impact of an NADH-producing glucose-6-phosphate dehydrogenase in Escherichia coli.

Authors: Olavarria, K.; De Ingeniis, J.; Zielinski, D. C.; Fuentealba, M.; Muñoz, R.; McCloskey, D.; Feist, Adam; id_orcid 0000-0002-8630-4800; Cabrera, R.

Year: 2014

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/be239d76-0dee-4dde-a6a9-cb26ba1725ab

Thesis Rewiring Saccharomyces cerevisiae metabolism for optimised Taxol® precursors production

Nowrouzi, Behnaz; Torres-Montero, Pablo; id_orcid 0000-0002-5970-1907 et al. · 2024 · Technical University of Denmark (DTU) · DOI

Full title: Rewiring Saccharomyces cerevisiae metabolism for optimised Taxol® precursors production

Authors: Nowrouzi, Behnaz; Torres-Montero, Pablo; id_orcid 0000-0002-5970-1907; Kerkhoven, Eduard J.; Martínez, José L.; id_orcid 0000-0002-4490-8534; Rios-Solis, Leonardo

Year: 2024

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/b0710034-bbe0-4347-82a7-f16fface96df

Thesis Harnessing xylose pathways for biofuels production

Li, Xiaowei; Chen, Yun; Nielsen, Jens · 2019 · Technical University of Denmark (DTU) · DOI

Full title: Harnessing xylose pathways for biofuels production

Authors: Li, Xiaowei; Chen, Yun; Nielsen, Jens

Year: 2019

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/b864de3a-1b9c-4c48-8186-cb1faf512585

Thesis In silico analysis of human metabolism: Reconstruction, contextualization and application of genome-scale models

Geng, Jun; Nielsen, Jens · 2017 · Technical University of Denmark (DTU) · DOI

Full title: In silico analysis of human metabolism: Reconstruction, contextualization and application of genome-scale models

Authors: Geng, Jun; Nielsen, Jens

Year: 2017

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/c9ce86c7-79ea-4ec2-bb49-ca4b354352b4

Thesis Establishing a synthetic pathway for high-level production of 3-hydroxypropionic acid in Saccharomyces cerevisiae via β-alanine

Borodina, Irina; Kildegaard, Kanchana Rueksomtawin; Jensen, Niels Bjerg et al. · 2015 · Technical University of Denmark (DTU) · DOI

Full title: Establishing a synthetic pathway for high-level production of 3-hydroxypropionic acid in Saccharomyces cerevisiae via β-alanine

Year: 2015

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/c3fbec62-077f-403f-bd01-1514ba663bdd

Thesis Metabolic modelling as a framework for metabolomics data integration and analysis

Volkova, Svetlana; Matos, Marta R. A.; Mattanovich, Matthias et al. · 2020 · Technical University of Denmark (DTU) · DOI

Full title: Metabolic modelling as a framework for metabolomics data integration and analysis

Authors: Volkova, Svetlana; Matos, Marta R. A.; Mattanovich, Matthias; Marín de Mas, Igor

Year: 2020

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/c7fe0f0a-1834-46aa-ab97-a28bc2500124

Thesis Advancing metabolic engineering through systems biology of industrial microorganisms

Dai, Zongjie; Nielsen, Jens · 2015 · Technical University of Denmark (DTU) · DOI

Full title: Advancing metabolic engineering through systems biology of industrial microorganisms

Authors: Dai, Zongjie; Nielsen, Jens

Year: 2015

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/c5f01453-3af2-4a13-960d-fc47f2a8a982

Thesis Saccharomyces cerevisiae phenotypes can be predicted using constraint based analysis of a genome-scale reconstructed metabolic network

Famili, I.; Förster, Jochen; id_orcid 0000-0003-4045-7905 et al. · 2003 · Technical University of Denmark (DTU) · DOI

Full title: Saccharomyces cerevisiae phenotypes can be predicted using constraint based analysis of a genome-scale reconstructed metabolic network

Authors: Famili, I.; Förster, Jochen; id_orcid 0000-0003-4045-7905; Nielsen, Jens; Palsson, B.O.

Year: 2003

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/ce2e5d37-808b-41be-85cb-d7b067c173fb

Thesis Identification of potential drug targets in Salmonella enterica sv. Typhimurium using metabolic modelling and experimental validation

Hartman, Hassan B.; Fell, David A.; Rossell, Sergio et al. · 2014 · Technical University of Denmark (DTU) · DOI

Full title: Identification of potential drug targets in Salmonella enterica sv. Typhimurium using metabolic modelling and experimental validation

Year: 2014

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/c485152d-7329-47aa-a593-04a0788b7037

Thesis In silico-guided engineering of Pseudomonas putida towards growth under micro-oxic conditions

Kampers, Linde F.C.; Van Heck, Ruben G.A.; Donati, Stefano et al. · 2019 · Technical University of Denmark (DTU) · DOI

Full title: In silico-guided engineering of Pseudomonas putida towards growth under micro-oxic conditions

Year: 2019

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/c9b06315-7ba5-485c-a683-9173957c4612

Thesis Model guided design of microbial consortia for mixed-culture fermentations

Bras, Jildau Emma · 2023 · Technical University of Denmark (DTU) · DOI

Full title: Model guided design of microbial consortia for mixed-culture fermentations

Authors: Bras, Jildau Emma

Year: 2023

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/cd886c17-324b-4ddc-83d3-adfa75e6b8e9

Thesis Use of genome-scale microbial models for metabolic engineering

Patil, Kiran Raosaheb; Åkesson, M.; Nielsen, Jens · 2004 · Technical University of Denmark (DTU) · DOI

Full title: Use of genome-scale microbial models for metabolic engineering

Authors: Patil, Kiran Raosaheb; Åkesson, M.; Nielsen, Jens

Year: 2004

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/c78f2a41-4129-478e-9dd5-8eafec68a5b5

Thesis Kinetic profiling of metabolic specialists demonstrates stability and consistency of in vivo enzyme turnover numbers

Heckmann, David; Campeau, Anaamika; Lloyd, Colton J. et al. · 2020 · Technical University of Denmark (DTU) · DOI

Full title: Kinetic profiling of metabolic specialists demonstrates stability and consistency of in vivo enzyme turnover numbers

Year: 2020

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/c1bd7310-f207-4760-9827-91b1b450c87a

Thesis A consensus S. cerevisiae metabolic model Yeast8 and its ecosystem for comprehensively probing cellular metabolism

Lu, Hongzhong; Li, Feiran; Sánchez, Benjamín J et al. · 2019 · Technical University of Denmark (DTU) · DOI

Full title: A consensus S. cerevisiae metabolic model Yeast8 and its ecosystem for comprehensively probing cellular metabolism

Year: 2019

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/b99607d4-a4c6-4dc3-a3bd-f0417f3f9694

Thesis Flux control through protein phosphorylation in yeast

Chen, Yu; Nielsen, Jens · 2016 · Technical University of Denmark (DTU) · DOI

Full title: Flux control through protein phosphorylation in yeast

Authors: Chen, Yu; Nielsen, Jens

Year: 2016

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/c7a72cba-fd47-4beb-a6dc-8c70b1d3bc90

Thesis Choosing the right platform for the right product: Sustainable production of chemicals in microbial cell factories

Herrgard, Markus · 2012 · Technical University of Denmark (DTU) · DOI

Full title: Choosing the right platform for the right product: Sustainable production of chemicals in microbial cell factories

Authors: Herrgard, Markus

Year: 2012

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/c79a469b-8662-49b0-b2b5-7207c608ab1f

Thesis Diverse genetic error modes constrain large-scale bio-based production

Rugbjerg, Peter; Myling-Petersen, Nils; Porse, Andreas et al. · 2018 · Technical University of Denmark (DTU) · DOI

Full title: Diverse genetic error modes constrain large-scale bio-based production

Authors: Rugbjerg, Peter; Myling-Petersen, Nils; Porse, Andreas; Sarup-Lytzen, Kira; Sommer, Morten Otto Alexander; id_orcid 0000-0003-4005-5674

Year: 2018

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/bab65aeb-c915-4327-890b-81b6ecda5e24

Thesis Combining mechanistic and machine learning models for predictive engineering and optimization of tryptophan metabolism

Zhang, Jie; Petersen, Søren D.; id_orcid 0000-0003-4104-5144 et al. · 2020 · Technical University of Denmark (DTU) · DOI

Full title: Combining mechanistic and machine learning models for predictive engineering and optimization of tryptophan metabolism

Year: 2020

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/d3f43470-1242-4282-8114-549377408fd6

Thesis iML1515, a knowledgebase that computes Escherichia coli traits

Monk, Jonathan M.; Lloyd, Colton J.; Brunk, Elizabeth et al. · 2017 · Technical University of Denmark (DTU) · DOI

Full title: iML1515, a knowledgebase that computes Escherichia coli traits

Authors: Monk, Jonathan M.; Lloyd, Colton J.; Brunk, Elizabeth; Mih, Nathan; Sastry, Anand; King, Zachary; Takeuchi, Rikiya; Nomura, Wataru; Zhang, Zhen; Mori, Hirotada; Feist, Adam M.; id_orcid 0000-0002-8630-4800; Palsson, Bernhard O.; id_orcid 0000-0003-2357-6785

Year: 2017

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/d96be10d-36ec-46ed-be4c-0a2f8653938f

Thesis Yeast metabolic innovations emerged via expanded metabolic network and gene positive selection

Lu, Hongzhong; Li, Feiran; Yuan, Le et al. · 2021 · Technical University of Denmark (DTU) · DOI

Full title: Yeast metabolic innovations emerged via expanded metabolic network and gene positive selection

Authors: Lu, Hongzhong; Li, Feiran; Yuan, Le; Domenzain, Iván; Yu, Rosemary; Wang, Hao; Li, Gang; Chen, Yu; Ji, Boyang; Kerkhoven, Eduard J.; Nielsen, Jens

Year: 2021

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/d25d3abb-a2f3-4f03-93e4-c55ccce1667d

Thesis Large-scale evaluation of in silico gene deletions in Saccharomyces cerevisiae

Förster, Jochen; id_orcid 0000-0003-4045-7905; Famili, Iman et al. · 2003 · Technical University of Denmark (DTU) · DOI

Full title: Large-scale evaluation of in silico gene deletions in Saccharomyces cerevisiae

Authors: Förster, Jochen; id_orcid 0000-0003-4045-7905; Famili, Iman; Palsson, Bernhard Ø; Nielsen, Jens

Year: 2003

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/d60ad36d-d295-4343-9528-a563b10c2086

Thesis Untargeted GC-MS Metabolomics Reveals Changes in the Metabolite Dynamics of Industrial Scale Batch Fermentations of Streptoccoccus thermophilus Broth

Khakimov, Bekzod; Christiansen, Lene D.; Heins, Anna-Lena et al. · 2017 · Technical University of Denmark (DTU) · DOI

Full title: Untargeted GC-MS Metabolomics Reveals Changes in the Metabolite Dynamics of Industrial Scale Batch Fermentations of Streptoccoccus thermophilus Broth

Authors: Khakimov, Bekzod; Christiansen, Lene D.; Heins, Anna-Lena; Sørensen, Klavs M.; Schöller, Charlotte Elisabeth Grüner; Clausen, Anders; Skov, Thomas; Gernaey, Krist V.; id_orcid 0000-0002-0364-1773; Engelsen, Søren B.

Year: 2017

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/d827018b-3bce-4f35-99c1-6e7cc3578e10

Thesis Integration of enzymatic data in Bacillus subtilis genome-scale metabolic model improves phenotype predictions and enables in silico design of poly-γ-glutamic acid production strains

Massaiu, Ilaria; Pasotti, Lorenzo; Sonnenschein, Nikolaus et al. · 2019 · Technical University of Denmark (DTU) · DOI

Full title: Integration of enzymatic data in Bacillus subtilis genome-scale metabolic model improves phenotype predictions and enables in silico design of poly-γ-glutamic acid production strains

Authors: Massaiu, Ilaria; Pasotti, Lorenzo; Sonnenschein, Nikolaus; id_orcid 0000-0002-7581-4936; Rama, Erlinda; Cavaletti, Matteo; Magni, Paolo; Calvio, Cinzia; Herrgård, Markus J.

Year: 2019

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/d5caa610-5ed4-400f-8f04-4c37a606a8a9

Thesis Next-generation genome-scale models for metabolic engineering

King, Zachary A.; Lloyd, Colton J.; Feist, Adam M. et al. · 2015 · Technical University of Denmark (DTU) · DOI

Full title: Next-generation genome-scale models for metabolic engineering

Authors: King, Zachary A.; Lloyd, Colton J.; Feist, Adam M.; id_orcid 0000-0002-8630-4800; Palsson, Bernhard O.; id_orcid 0000-0003-2357-6785

Year: 2015

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/dd2bf76b-e701-4acd-8207-ab716c6ecdc8

Thesis Reconstruction of 24 Penicillium genome-scale metabolic models shows diversity based on their secondary metabolism

Prigent, Sylvain; Nielsen, Jens C.; Frisvad, Jens C. et al. · 2018 · Technical University of Denmark (DTU) · DOI

Full title: Reconstruction of 24 Penicillium genome-scale metabolic models shows diversity based on their secondary metabolism

Authors: Prigent, Sylvain; Nielsen, Jens C.; Frisvad, Jens C.; id_orcid 0000-0002-0573-4340; Nielsen, Jens

Year: 2018

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/d7a700eb-9cab-4541-a148-73e8e200face

Thesis Hybrid Modeling for On-Line Fermentation Optimization and Scale-Up:A Review

Albino, Mariana; Gargalo, Carina L.; id_orcid 0000-0002-8740-9591 et al. · 2024 · Technical University of Denmark (DTU) · DOI

Full title: Hybrid Modeling for On-Line Fermentation Optimization and Scale-Up:A Review

Year: 2024

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/da2224b1-251a-47ea-abc0-1b523e3fb360

Thesis RAVEN 2.0: A versatile toolbox for metabolic network reconstruction and a case study on Streptomyces coelicolor

Wang, Hao; Marcisauskas, Simonas; Sanchez, Benjamin J. et al. · 2018 · Technical University of Denmark (DTU) · DOI

Full title: RAVEN 2.0: A versatile toolbox for metabolic network reconstruction and a case study on Streptomyces coelicolor

Authors: Wang, Hao; Marcisauskas, Simonas; Sanchez, Benjamin J.; Domenzain, Ivan; Hermansson, Daniel; Agren, Rasmus; Nielsen, Jens; Kerkhoven, Eduard J.

Year: 2018

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/ccb1a039-b82f-429e-9d47-3e7cea8902b8

Thesis Yeast9: a consensus genome-scale metabolic model for S. cerevisiae curated by the community

Zhang, Chengyu; Sánchez, Benjamín J.; Li, Feiran et al. · 2024 · Technical University of Denmark (DTU) · DOI

Full title: Yeast9: a consensus genome-scale metabolic model for S. cerevisiae curated by the community

Year: 2024

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/c006865f-270c-4551-a78a-684270c8ab2f

Thesis Modeling the Contribution of Allosteric Regulation for Flux Control in the Central Carbon Metabolism of E. coli

Machado, Daniel; Herrgard, Markus; Rocha, Isabel · 2015 · Technical University of Denmark (DTU) · DOI

Full title: Modeling the Contribution of Allosteric Regulation for Flux Control in the Central Carbon Metabolism of E. coli

Authors: Machado, Daniel; Herrgard, Markus; Rocha, Isabel

Year: 2015

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/dabee1a2-fe3a-4c6a-8841-33d18b5b6717

Thesis Elucidating dynamic metabolic physiology through network integration of quantitative time-course metabolomics

Bordbar, Aarash; Yurkovich, James T.; Paglia, Giuseppe et al. · 2017 · Technical University of Denmark (DTU) · DOI

Full title: Elucidating dynamic metabolic physiology through network integration of quantitative time-course metabolomics

Authors: Bordbar, Aarash; Yurkovich, James T.; Paglia, Giuseppe; Rolfsson, Ottar; Sigurjónsson, Olafur E.; Palsson, Bernhard; id_orcid 0000-0003-2357-6785

Year: 2017

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/cfb96acb-b500-427f-a8fe-d0f32465a2d7

Thesis A Mathematical Model for Simultaneous Saccharification and Co-fermentation (SSCF) of C6 and C5 Sugars

Morales Rodriguez, Ricardo; Gernaey, Krist; id_orcid 0000-0002-0364-1773 et al. · 2011 · Technical University of Denmark (DTU) · DOI

Full title: A Mathematical Model for Simultaneous Saccharification and Co-fermentation (SSCF) of C6 and C5 Sugars

Authors: Morales Rodriguez, Ricardo; Gernaey, Krist; id_orcid 0000-0002-0364-1773; Meyer, Anne S.; id_orcid 0000-0001-8910-9931; Sin, Gürkan; id_orcid 0000-0003-0513-4502

Year: 2011

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/cddb0135-e218-446b-aa8c-be2eda208384

Thesis Investigating genotype-phenotype relationships in Saccharomyces cerevisiae metabolic network through stoichiometric modeling

Brochado, Ana Rita · 2012 · Technical University of Denmark (DTU) · DOI

Full title: Investigating genotype-phenotype relationships in Saccharomyces cerevisiae metabolic network through stoichiometric modeling

Authors: Brochado, Ana Rita

Year: 2012

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/de6f64b4-c567-4671-a580-dc2184e485aa

Thesis CRI-SPA mediated screening for metabolic engineering targets to improve small molecule production in Saccharomyces cerevisiae

Vestergaard, Andreas M.; id_orcid 0000-0002-5042-1474; Cachera, Paul Pierre-Yves Jean et al. · 2023 · Technical University of Denmark (DTU) · DOI

Full title: CRI-SPA mediated screening for metabolic engineering targets to improve small molecule production in Saccharomyces cerevisiae

Authors: Vestergaard, Andreas M.; id_orcid 0000-0002-5042-1474; Cachera, Paul Pierre-Yves Jean; Mortensen, Uffe Hasbro; id_orcid 0000-0002-7794-7273

Year: 2023

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/d734ee1d-b231-411f-97a4-1d5626bab4af

Thesis Production of 3-Hydroxypropanoic Acid From Glycerol by Metabolically Engineered Bacteria

Jers, Carsten; id_orcid 0000-0002-9930-3137; Kalantari, Aida et al. · 2019 · Technical University of Denmark (DTU) · DOI

Full title: Production of 3-Hydroxypropanoic Acid From Glycerol by Metabolically Engineered Bacteria

Authors: Jers, Carsten; id_orcid 0000-0002-9930-3137; Kalantari, Aida; Garg, Abhroop; Mijakovic, Ivan

Year: 2019

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/dd7921d1-bf8d-4658-86e7-26d0b103aef8

Thesis Pan-reactome analysis of Streptomyces strains reveals association and disconnection between primary and secondary metabolism

Lee, Byung Tae; Mohite, Omkar S.; id_orcid 0000-0002-3240-1656 et al. · 2025 · Technical University of Denmark (DTU) · DOI

Full title: Pan-reactome analysis of Streptomyces strains reveals association and disconnection between primary and secondary metabolism

Authors: Lee, Byung Tae; Mohite, Omkar S.; id_orcid 0000-0002-3240-1656; Kwon, Mun Su; Kang, Hahk Soo; Weber, Tilmann; id_orcid 0000-0002-8260-5120; Lee, Sang Yup; Kim, Hyun Uk

Year: 2025

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/df34f08c-c052-4faf-bfbf-4773ac94e79f

Thesis Enhancing sesquiterpene production in Saccharomyces cerevisiae through in silico driven metabolic engineering

Asadollahi, Mohammadali; Maury, Jerome; Patil, Kiran Raosaheb et al. · 2009 · Technical University of Denmark (DTU) · DOI

Full title: Enhancing sesquiterpene production in Saccharomyces cerevisiae through in silico driven metabolic engineering

Authors: Asadollahi, Mohammadali; Maury, Jerome; Patil, Kiran Raosaheb; schalk, Michel; Clark, Anthony; Nielsen, Jens

Year: 2009

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/dda6bc9b-1517-42c3-8cdb-078b066f3114

Thesis Simple and robust method for estimation of the split between the oxidative pentose phosphate pathway and the Embden- Meyerhof-Parnas pathway in microorganisms

Christensen, J.; Christiansen, Torben; Gombert, Andreas Karoly et al. · 2001 · Technical University of Denmark (DTU) · DOI

Full title: Simple and robust method for estimation of the split between the oxidative pentose phosphate pathway and the Embden- Meyerhof-Parnas pathway in microorganisms

Authors: Christensen, J.; Christiansen, Torben; Gombert, Andreas Karoly; Thykær, Jette; Nielsen, Jens

Year: 2001

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/dba3da4a-2be5-4492-b616-1746b12d2984

Thesis Basics of genome-scale metabolic modeling and applications on C1-utilization

Kabimoldayev, Ilyas; Nguyen, Anh Duc; Yang, Laurence et al. · 2018 · Technical University of Denmark (DTU) · DOI

Full title: Basics of genome-scale metabolic modeling and applications on C1-utilization

Authors: Kabimoldayev, Ilyas; Nguyen, Anh Duc; Yang, Laurence; Park, Sunghoon; Lee, Eun Yeol; Kim, Donghyuk

Year: 2018

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/e1a6c838-a65e-4780-911d-1749e70dd71e

Thesis Reconstruction of a catalogue of genome-scale metabolic models with enzymatic constraints using GECKO 2.0

Domenzain, Iván; Sánchez, Benjamín; Anton, Mihail et al. · 2022 · Technical University of Denmark (DTU) · DOI

Full title: Reconstruction of a catalogue of genome-scale metabolic models with enzymatic constraints using GECKO 2.0

Year: 2022

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/df6e83e4-1f36-41d2-b699-d64e6d8b405c

Thesis Optimizing cultivation of Cordyceps militaris for fast growth and cordycepin overproduction using rational design of synthetic media

Raethong, Nachon; Wang, Hao; Nielsen, Jens et al. · 2020 · Technical University of Denmark (DTU) · DOI

Full title: Optimizing cultivation of Cordyceps militaris for fast growth and cordycepin overproduction using rational design of synthetic media

Authors: Raethong, Nachon; Wang, Hao; Nielsen, Jens; Vongsangnak, Wanwipa

Year: 2020

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/e3060451-18d5-4b01-aff0-9d02cf847900

Thesis Reprogramming Yeast Metabolism from Alcoholic Fermentation to Lipogenesis

Yu, Tao; Zhou, Yongjin J.; Huang, Mingtao et al. · 2018 · Technical University of Denmark (DTU) · DOI

Full title: Reprogramming Yeast Metabolism from Alcoholic Fermentation to Lipogenesis

Authors: Yu, Tao; Zhou, Yongjin J.; Huang, Mingtao; Liu, Quanli; Pereira, Rui; David, Florian; Nielsen, Jens

Year: 2018

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/e2d68087-fc93-4b81-8d72-1b67f1449334

Thesis Online estimation of changing metabolic capacities in continuous Corynebacterium glutamicum cultivations growing on a complex sugar mixture

Sinner, Peter; Stiegler, Marlene; Goldbeck, Oliver et al. · 2022 · Technical University of Denmark (DTU) · DOI

Full title: Online estimation of changing metabolic capacities in continuous Corynebacterium glutamicum cultivations growing on a complex sugar mixture

Authors: Sinner, Peter; Stiegler, Marlene; Goldbeck, Oliver; Seibold, Gerd M.; id_orcid 0000-0002-9823-8134; Herwig, Christoph; Kager, Julian; id_orcid 0000-0001-7274-6678

Year: 2022

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/e1d47952-5939-40df-b5d8-a033a58e8745

Thesis Genome-scale metabolic representation of Amycolatopsis balhimycina

Vongsangnak, Wanwipa; Figueiredo, L. F.; Förster, Jochen et al. · 2012 · Technical University of Denmark (DTU) · DOI

Full title: Genome-scale metabolic representation of Amycolatopsis balhimycina

Year: 2012

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/e1eaad0e-10fd-4378-9c1e-9b7b39397a5d

Thesis Metabolic impact of redox cofactor perturbations in Saccharomyces cerevisiae

Hou, Jin; Lages, Nuno; Oldiges, M. et al. · 2009 · Technical University of Denmark (DTU) · DOI

Full title: Metabolic impact of redox cofactor perturbations in Saccharomyces cerevisiae

Authors: Hou, Jin; Lages, Nuno; Oldiges, M.; Vemuri, Goutham

Year: 2009

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/e43248a5-2bd3-4dcf-a4bd-1156053f2237

Thesis Flux coupling and transcriptional regulation within the metabolic network of the photosynthetic bacterium Synechocystis sp. PCC6803

Montagud, Arnau; Zelezniak, Aleksej; Navarro, Emilio et al. · 2011 · Technical University of Denmark (DTU) · DOI

Full title: Flux coupling and transcriptional regulation within the metabolic network of the photosynthetic bacterium Synechocystis sp. PCC6803

Authors: Montagud, Arnau; Zelezniak, Aleksej; Navarro, Emilio; de Córdoba, Pedro Fernández; Urchueguía, Javier F.; Patil, Kiran Raosaheb

Year: 2011

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/e2facd88-4fc5-42bf-b3d5-b72eb238520d

Thesis Modeling the growth and proteinase A production in continuous cultures of recombinant Saccharomyces cerevisiae

Carlsen, Morten; Jochumsen, Kirsten Væver; Emborg, Claus et al. · 1997 · Technical University of Denmark (DTU) · DOI

Full title: Modeling the growth and proteinase A production in continuous cultures of recombinant Saccharomyces cerevisiae

Authors: Carlsen, Morten; Jochumsen, Kirsten Væver; Emborg, Claus; Nielsen, Jens Bredal

Year: 1997

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/e11d825c-a743-4b15-97a6-96608eeb420a

Thesis Network Reconstruction and In Silico Metabolic Model of Chinese Hamster Ovary cells

Calmels, Cyrielle · 2018 · Technical University of Denmark (DTU) · DOI

Full title: Network Reconstruction and In Silico Metabolic Model of Chinese Hamster Ovary cells

Authors: Calmels, Cyrielle

Year: 2018

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/e8e79519-7089-44aa-9964-6700b9af9251

Thesis Output uncertainty of dynamic growth models: Effect of uncertain parameter estimates on model reliability

Anane, Emmanuel; López C, Diana C.; Barz, Tilman et al. · 2019 · Technical University of Denmark (DTU) · DOI

Full title: Output uncertainty of dynamic growth models: Effect of uncertain parameter estimates on model reliability

Year: 2019

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/e2b40834-81af-4e34-9475-5a085aedbd5d

Thesis Development of a screening approach for exploring cell factory potential through metabolic flux analysis and physiology

Knudsen, Peter Boldsen; Nielsen, Kristian Fog; Thykær, Jette · 2012 · Technical University of Denmark (DTU) · DOI

Full title: Development of a screening approach for exploring cell factory potential through metabolic flux analysis and physiology

Authors: Knudsen, Peter Boldsen; Nielsen, Kristian Fog; Thykær, Jette

Year: 2012

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/e4617fd9-adab-48f9-bfeb-a1e9784d9aff

Thesis Using Genome-scale Models to Predict Biological Capabilities

O’Brien, Edward J.; Monk, Jonathan M.; Palsson, Bernhard O. et al. · 2015 · Technical University of Denmark (DTU) · DOI

Full title: Using Genome-scale Models to Predict Biological Capabilities

Authors: O’Brien, Edward J.; Monk, Jonathan M.; Palsson, Bernhard O.; id_orcid 0000-0003-2357-6785

Year: 2015

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/e3b32d6d-318c-4030-9d2a-0e14edc51a75

Thesis Systems Biology of Metabolic Networks: Uncovering Regulatory and stoichiometric Principles

Patil, Kiran Raosaheb · 2007 · Technical University of Denmark (DTU) · DOI

Full title: Systems Biology of Metabolic Networks: Uncovering Regulatory and stoichiometric Principles

Authors: Patil, Kiran Raosaheb

Year: 2007

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/e5586576-a479-4569-a0da-8d0542a9f448

Thesis Model-Assisted Fine-Tuning of Central Carbon Metabolism in Yeast through dCas9-Based Regulation

Ferreira, Raphael; Skrekas, Christos; Hedin, Alex et al. · 2019 · Technical University of Denmark (DTU) · DOI

Full title: Model-Assisted Fine-Tuning of Central Carbon Metabolism in Yeast through dCas9-Based Regulation

Authors: Ferreira, Raphael; Skrekas, Christos; Hedin, Alex; Sánchez, Benjamín José; Siewers, Verena; Nielsen, Jens; David, Florian

Year: 2019

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/e453310b-2bf1-47bb-a4c0-7e11c9bb7c96

Thesis Application of mechanistic models to fermentation and biocatalysis for next-generation processes

Gernaey, Krist; id_orcid 0000-0002-0364-1773; Eliasson Lantz, Anna et al. · 2010 · Technical University of Denmark (DTU) · DOI

Full title: Application of mechanistic models to fermentation and biocatalysis for next-generation processes

Authors: Gernaey, Krist; id_orcid 0000-0002-0364-1773; Eliasson Lantz, Anna; Tufvesson, Pär; Woodley, John; id_orcid 0000-0002-7976-2483; Sin, Gürkan; id_orcid 0000-0003-0513-4502

Year: 2010

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/e312d8f3-fb95-4662-9f06-4fcdce484b93

Thesis Stoichiometric Representation of Gene–Protein–Reaction Associations Leverages Constraint-Based Analysis from Reaction to Gene-Level Phenotype Prediction

Machado, Daniel; Herrgard, Markus; Rocha, Isabel · 2016 · Technical University of Denmark (DTU) · DOI

Full title: Stoichiometric Representation of Gene–Protein–Reaction Associations Leverages Constraint-Based Analysis from Reaction to Gene-Level Phenotype Prediction

Authors: Machado, Daniel; Herrgard, Markus; Rocha, Isabel

Year: 2016

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/e4208a96-0c33-48f2-8ac5-da96aa1ea44c

Thesis Impact of stoichiometry representation on simulation of genotype-phenotype relationships in metabolic networks.

Brochado, Ana Rita; Andrejev, Sergej; Maranas, Costas D. et al. · 2012 · Technical University of Denmark (DTU) · DOI

Full title: Impact of stoichiometry representation on simulation of genotype-phenotype relationships in metabolic networks.

Authors: Brochado, Ana Rita; Andrejev, Sergej; Maranas, Costas D.; Patil, Kiran R.

Year: 2012

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/e98be4c6-510e-4c08-9145-f929cb4e8440

Thesis Gradient simulation experiments for targeting population heterogeneity in continuous Saccharomyces cerevisiae fermentation

Heins, Anna-Lena; Lencastre Fernandes, Rita; Lundin, L. et al. · 2011 · Technical University of Denmark (DTU) · DOI

Full title: Gradient simulation experiments for targeting population heterogeneity in continuous Saccharomyces cerevisiae fermentation

Authors: Heins, Anna-Lena; Lencastre Fernandes, Rita; Lundin, L.; Carlquist, M.; Sörensen, S.; Gernaey, Krist; id_orcid 0000-0002-0364-1773; Eliasson Lantz, Anna

Year: 2011

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/e6800b62-baa8-4684-b4ec-a06400be2ad8

Thesis Expression of the E.coli pntA and pntB genes encoding nicotinamide nucleotide transhydrogenase in Saccharomyces cerevisiae and its effect on product formation during anaerobic glucose fermentation

Anderlund, M.; Nissen, Torben Lauesgaard; Nielsen, Jens Bredal et al. · 1999 · Technical University of Denmark (DTU) · DOI

Full title: Expression of the E.coli pntA and pntB genes encoding nicotinamide nucleotide transhydrogenase in Saccharomyces cerevisiae and its effect on product formation during anaerobic glucose fermentation

Authors: Anderlund, M.; Nissen, Torben Lauesgaard; Nielsen, Jens Bredal; Villadsen, John; id_orcid 0000-0002-6523-8445; Rydström, J.; Hahn-Hägerdal, B.; Kielland-Brandt, M.C.

Year: 1999

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/eb98a724-2338-40c1-b72b-5aa32e0262bd

Thesis A Novel Efficient L-Lysine Exporter Identified by Functional Metagenomics

Malla, Sailesh; van der Helm, Eric; Darbani, Behrooz et al. · 2022 · Technical University of Denmark (DTU) · DOI

Full title: A Novel Efficient L-Lysine Exporter Identified by Functional Metagenomics

Year: 2022

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/eadfcd55-8819-462d-94d2-ebbdee699b15

Thesis Industrial Systems Biology of Saccharomyces cerevisiae Enables Novel Succinic Acid Cell Factory.

Otero, José Manuel; Cimini, Donatella; Patil, Kiran Raosaheb et al. · 2013 · Technical University of Denmark (DTU) · DOI

Full title: Industrial Systems Biology of Saccharomyces cerevisiae Enables Novel Succinic Acid Cell Factory.

Authors: Otero, José Manuel; Cimini, Donatella; Patil, Kiran Raosaheb; Poulsen, Simon Guldberg; Olsson, Lisbeth; Nielsen, Jens

Year: 2013

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/e7ba99b8-8502-4f6e-9bc4-8084fb3826aa

Thesis Turnover Dependent Phenotypic Simulation: A Quantitative Constraint-Based Simulation Method That Accommodates All Main Strain Design Strategies

Pereira, Rui; Vilaça, Paulo; Maia, Paulo et al. · 2019 · Technical University of Denmark (DTU) · DOI

Full title: Turnover Dependent Phenotypic Simulation: A Quantitative Constraint-Based Simulation Method That Accommodates All Main Strain Design Strategies

Authors: Pereira, Rui; Vilaça, Paulo; Maia, Paulo; Nielsen, Jens; Rocha, Isabel

Year: 2019

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/ebf4708b-30df-48bb-8562-32a31c81b850

Thesis DynamicME: dynamic simulation and refinement of integrated models of metabolism and protein expression

Yang, Laurence; Ebrahim, Ali; Lloyd, Colton J. et al. · 2019 · Technical University of Denmark (DTU) · DOI

Full title: DynamicME: dynamic simulation and refinement of integrated models of metabolism and protein expression

Authors: Yang, Laurence; Ebrahim, Ali; Lloyd, Colton J.; Saunders, Michael A.; Palsson, Bernhard; id_orcid 0000-0003-2357-6785

Year: 2019

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/ec15b607-dcd9-490b-9d3e-ea05a9aec631

Thesis Genome-scale metabolic rewiring improves titers rates and yields of the non-native product indigoidine at scale

Banerjee, Deepanwita; Eng, Thomas; Lau, Andrew K. et al. · 2020 · Technical University of Denmark (DTU) · DOI

Full title: Genome-scale metabolic rewiring improves titers rates and yields of the non-native product indigoidine at scale

Year: 2020

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/f007def8-3e0b-4ed0-8302-e02aa544e164

Thesis Metabolic Trade-offs in Yeast are Caused by F1F0-ATP synthase

Nilsson, Avlant; Nielsen, Jens · 2016 · Technical University of Denmark (DTU) · DOI

Full title: Metabolic Trade-offs in Yeast are Caused by F1F0-ATP synthase

Authors: Nilsson, Avlant; Nielsen, Jens

Year: 2016

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/f1e21ad2-7d0f-4ea4-b415-b38067ef879a

Thesis Industrial systems biology and its impact on synthetic biology of yeast cell factories

Fletcher, Eugene; Krivoruchko, Anastasia; Nielsen, Jens · 2016 · Technical University of Denmark (DTU) · DOI

Full title: Industrial systems biology and its impact on synthetic biology of yeast cell factories

Authors: Fletcher, Eugene; Krivoruchko, Anastasia; Nielsen, Jens

Year: 2016

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/f04c84e9-7839-4db7-8952-abdf62e28719

Thesis Analysis of flux estimates based on C-13-labelling experiments

Christensen, Bjarke; Gombert, Andreas Karoly; Nielsen, Jens · 2002 · Technical University of Denmark (DTU) · DOI

Full title: Analysis of flux estimates based on C-13-labelling experiments

Authors: Christensen, Bjarke; Gombert, Andreas Karoly; Nielsen, Jens

Year: 2002

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/edb42e55-34b1-43dc-b779-f99bcf27e2a6

Thesis Manually curated genome-scale reconstruction of the metabolic network of Bacillus megaterium DSM319

Aminian-Dehkordi, Javad; Mousavi, Seyyed Mohammad; Jafari, Arezou et al. · 2019 · Technical University of Denmark (DTU) · DOI

Full title: Manually curated genome-scale reconstruction of the metabolic network of Bacillus megaterium DSM319

Authors: Aminian-Dehkordi, Javad; Mousavi, Seyyed Mohammad; Jafari, Arezou; Mijakovic, Ivan; Marashi, Sayed Amir

Year: 2019

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/ef4a2309-59e5-4a56-ab9b-10dcbf5985a6

Thesis Model-based optimization of a recombinant E. coli fed-batch process for best time-space yield and conversion efficiency

Kager, Julian; id_orcid 0000-0001-7274-6678; Horst, Nora et al. · 2023 · Technical University of Denmark (DTU) · DOI

Full title: Model-based optimization of a recombinant E. coli fed-batch process for best time-space yield and conversion efficiency

Authors: Kager, Julian; id_orcid 0000-0001-7274-6678; Horst, Nora; Herwig, Christoph; Skiadas, Ioannis V.; id_orcid 0000-0001-6183-4592

Year: 2023

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/ede3ad48-f54e-44ca-ba10-d7fda23e5c9f

Thesis Multi-omics analysis of fatty alcohol production in engineered yeasts saccharomyces cerevisiae and yarrowia lipolytica

Dahlin, Jonathan; Holkenbrink, Carina; Marella, Eko Roy et al. · 2019 · Technical University of Denmark (DTU) · DOI

Full title: Multi-omics analysis of fatty alcohol production in engineered yeasts saccharomyces cerevisiae and yarrowia lipolytica

Year: 2019

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/ed194746-96c9-44cb-aa39-1307ed519a49

Thesis Pangenome reconstruction of Lactobacillaceae metabolism predicts species-specific metabolic traits

Ardalani, O.; id_orcid 0000-0002-0064-3802; Phaneuf, P. V. et al. · 2024 · Technical University of Denmark (DTU) · DOI

Full title: Pangenome reconstruction of Lactobacillaceae metabolism predicts species-specific metabolic traits

Authors: Ardalani, O.; id_orcid 0000-0002-0064-3802; Phaneuf, P. V.; Mohite, O. S.; id_orcid 0000-0002-3240-1656; Nielsen, L. K.; Palsson, B. O.; id_orcid 0000-0003-2357-6785

Year: 2024

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/f0da44fd-f204-4ec1-8c80-8df20ddd87a1

Thesis Promoting the co-utilisation of glucose and xylose in lignocellulosic ethanol fermentations using a data-driven feed-back controller

Lopez, Pau Cabañeros; Abeykoon Udugama, Isuru; Thomsen, Sune Tjalfe et al. · 2020 · Technical University of Denmark (DTU) · DOI

Full title: Promoting the co-utilisation of glucose and xylose in lignocellulosic ethanol fermentations using a data-driven feed-back controller

Authors: Lopez, Pau Cabañeros; Abeykoon Udugama, Isuru; Thomsen, Sune Tjalfe; Bayer, Christoph; Junicke, Helena; id_orcid 0000-0002-2513-2486; Gernaey, Krist V.; id_orcid 0000-0002-0364-1773

Year: 2020

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/52e631db-264f-403b-9e37-ad67def34c63

Thesis COBRAme: A computational framework for genome-scale models of metabolism and gene expression

Lloyd, Colton J.; Ebrahim, Ali; Yang, Laurence et al. · 2018 · Technical University of Denmark (DTU) · DOI

Full title: COBRAme: A computational framework for genome-scale models of metabolism and gene expression

Authors: Lloyd, Colton J.; Ebrahim, Ali; Yang, Laurence; King, Zachary A.; Catoiu, Edward; O'Brien, Edward J.; Liu, Joanne K.; Polsson, Bernhard O.; id_orcid 0000-0003-2357-6785

Year: 2018

Venue: Technical University of Denmark (DTU)

DOI: https://orbit.dtu.dk/en/publications/a93a304b-3cfe-4cd9-adf3-d9062e8bd1f7

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Computational Analysis of Reciprocal Association of Metabolism and Epigenetics in the Budding Yeast: A Genome-Scale Metabolic Model (GSMM) Approach

Salehzadeh‐Yazdi, Ali; Asgari, Yazdan; Saboury, Ali Akbar et al. · 2014

Full title: Computational Analysis of Reciprocal Association of Metabolism and Epigenetics in the Budding Yeast: A Genome-Scale Metabolic Model (GSMM) Approach

Authors: Salehzadeh‐Yazdi, Ali; Asgari, Yazdan; Saboury, Ali Akbar; Masoudi‐Nejad, Ali

DOI: https://doi.org/10.1371/journal.pone.0111686

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MediaDB: A Database of Microbial Growth Conditions in Defined Media

Richards, Matthew A.; Cassen, Victor; Heavner, Ben et al. · 2014

Full title: MediaDB: A Database of Microbial Growth Conditions in Defined Media

Authors: Richards, Matthew A.; Cassen, Victor; Heavner, Ben; Ajami, Nassim E.; Herrmann, Andrea; Simeonidis, Evangelos; Price, Nathan D.

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Differential Bees Flux Balance Analysis with OptKnock for In Silico Microbial Strains Optimization

Yee Wen Choon; M. S. Mohamad; S. Deris et al. · 2014

Full title: Differential Bees Flux Balance Analysis with OptKnock for In Silico Microbial Strains Optimization

Authors: Yee Wen Choon; M. S. Mohamad; S. Deris; R. Illias; Chuii Khim Chong; Lian En Chai; S. Omatu; J. Corchado

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Construction of a Genome-Scale Metabolic Model of Arthrospira platensis NIES-39 and Metabolic Design for Cyanobacterial Bioproduction

Yoshikawa, Katsunori; Aikawa, Shimpei; Kojima, Yuta et al. · 2015

Full title: Construction of a Genome-Scale Metabolic Model of Arthrospira platensis NIES-39 and Metabolic Design for Cyanobacterial Bioproduction

Authors: Yoshikawa, Katsunori; Aikawa, Shimpei; Kojima, Yuta; Toya, Yoshihiro; Furusawa, Chikara; Kondo, Akihiko; Shimizu, Hiroshi

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Prediction of reaction knockouts to maximize succinate production by Actinobacillus succinogenes

Nag, Ambarish; John, Peter C. St.; Crowley, Michael F. et al. · 2018

Full title: Prediction of reaction knockouts to maximize succinate production by Actinobacillus succinogenes

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Dissecting Leishmania infantum Energy Metabolism - A Systems Perspective

Subramanian, Abhishek; Jhawar, Jitesh; Sarkar, Ram Rup · 2015

Full title: Dissecting Leishmania infantum Energy Metabolism - A Systems Perspective

Authors: Subramanian, Abhishek; Jhawar, Jitesh; Sarkar, Ram Rup

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Integration and Validation of the Genome-Scale Metabolic Models of Pichia pastoris: A Comprehensive Update of Protein Glycosylation Pathways, Lipid and Energy Metabolism

Tomàs‐Gamisans, Màrius; Ferrer, Pau; Albiol, Joan · 2016

Full title: Integration and Validation of the Genome-Scale Metabolic Models of Pichia pastoris: A Comprehensive Update of Protein Glycosylation Pathways, Lipid and Energy Metabolism

Authors: Tomàs‐Gamisans, Màrius; Ferrer, Pau; Albiol, Joan

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OM-FBA: Integrate Transcriptomics Data with Flux Balance Analysis to Decipher the Cell Metabolism

Guo, Weihua; Feng, Xueyang · 2016

Full title: OM-FBA: Integrate Transcriptomics Data with Flux Balance Analysis to Decipher the Cell Metabolism

Authors: Guo, Weihua; Feng, Xueyang

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Ethanol production improvement driven by genome-scale metabolic modeling and sensitivity analysis in Scheffersomyces stipitis

Acevedo, Alejandro; Conejeros, Raúl; Aroca, Germán · 2017

Full title: Ethanol production improvement driven by genome-scale metabolic modeling and sensitivity analysis in Scheffersomyces stipitis

Authors: Acevedo, Alejandro; Conejeros, Raúl; Aroca, Germán

DOI: https://doi.org/10.1371/journal.pone.0180074

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Prediction of Metabolic Flux Distribution from Gene Expression Data Based on the Flux Minimization Principle

Song, Hyun‐Seob; Reifman, Jaques; Wallqvist, Anders · 2014

Full title: Prediction of Metabolic Flux Distribution from Gene Expression Data Based on the Flux Minimization Principle

Authors: Song, Hyun‐Seob; Reifman, Jaques; Wallqvist, Anders

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Metabolic network reconstruction and phenome analysis of the industrial microbe, Escherichia coli BL21(DE3)

Kim, Hanseol; Kim, Sinyeon; Yoon, Sung Ho · 2018

Full title: Metabolic network reconstruction and phenome analysis of the industrial microbe, Escherichia coli BL21(DE3)

Authors: Kim, Hanseol; Kim, Sinyeon; Yoon, Sung Ho

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Constraints-based analysis identifies NAD+ recycling through metabolic reprogramming in antibiotic resistant Chromobacterium violaceum

Banerjee, Deepanwita; Raghunathan, Anu · 2019

Full title: Constraints-based analysis identifies NAD+ recycling through metabolic reprogramming in antibiotic resistant Chromobacterium violaceum

Authors: Banerjee, Deepanwita; Raghunathan, Anu

DOI: https://doi.org/10.1371/journal.pone.0210008

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Multiscale Metabolic Modeling of C4 Plants: Connecting Nonlinear Genome-Scale Models to Leaf-Scale Metabolism in Developing Maize Leaves

Bogart, Eli; Myers, Christopher R. · 2016

Full title: Multiscale Metabolic Modeling of C4 Plants: Connecting Nonlinear Genome-Scale Models to Leaf-Scale Metabolism in Developing Maize Leaves

Authors: Bogart, Eli; Myers, Christopher R.

DOI: https://doi.org/10.1371/journal.pone.0151722

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Using genome-scale metabolic models to compare serovars of the foodborne pathogen Listeria monocytogenes

Zachary P. Metz; T. Ding; David J. Baumler · 2018

Full title: Using genome-scale metabolic models to compare serovars of the foodborne pathogen Listeria monocytogenes

Authors: Zachary P. Metz; T. Ding; David J. Baumler

DOI: https://doi.org/10.1371/journal.pone.0198584

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E-Flux2 and SPOT: Validated Methods for Inferring Intracellular Metabolic Flux Distributions from Transcriptomic Data.

Kim, Min Kyung; Lane, Anatoliy; Kelley, James J et al. · 2016

Full title: E-Flux2 and SPOT: Validated Methods for Inferring Intracellular Metabolic Flux Distributions from Transcriptomic Data.

Authors: Kim, Min Kyung; Lane, Anatoliy; Kelley, James J; Lun, Desmond S

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Flux prediction using artificial neural network (ANN) for the upper part of glycolysis

Nagaraja, Anamya Ajjolli; Fontaine, Nicolas; Delsaut, Mathieu et al. · 2019

Full title: Flux prediction using artificial neural network (ANN) for the upper part of glycolysis

Authors: Nagaraja, Anamya Ajjolli; Fontaine, Nicolas; Delsaut, Mathieu; Charton, Philippe; Damour, Cédric; Offmann, Bernard; Grondin-Pérez, Brigitte; Cadet, Frédéric

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Metabolic flux configuration determination using information entropy

Rivas‐Astroza, Marcelo; Conejeros, Raúl · 2020

Full title: Metabolic flux configuration determination using information entropy

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Improving the phenotype predictions of a yeast genome‐scale metabolic model by incorporating enzymatic constraints

Benjamín J. Sánchez; Cheng Zhang; Avlant Nilsson et al. · 2017

Full title: Improving the phenotype predictions of a yeast genome‐scale metabolic model by incorporating enzymatic constraints

Authors: Benjamín J. Sánchez; Cheng Zhang; Avlant Nilsson; Petri-Jaan Lahtvee; E. Kerkhoven; J. Nielsen

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Comparative genomic analysis of Methylocystis sp. MJC1 as a platform strain for polyhydroxybutyrate biosynthesis

Naizabekov, Sanzhar; Hyun, Seung Woon; Na, Jeong‐Geol et al. · 2023

Full title: Comparative genomic analysis of Methylocystis sp. MJC1 as a platform strain for polyhydroxybutyrate biosynthesis

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Distributed flux balance analysis simulations of serial biomass fermentation by two organisms

Vitkin, Edward; Gillis, Amichai; Polikovsky, Mark et al. · 2020

Full title: Distributed flux balance analysis simulations of serial biomass fermentation by two organisms

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Yizhak, Keren; Chaneton, Barbara; Gottlieb, Eyal et al. · 2015

Full title: Modeling cancer metabolism on a genome scale

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Nazarshodeh, Elmira; Marashi, Sayed‐Amir; Gharaghani, Sajjad · 2021

Full title: Structural systems pharmacology: A framework for integrating metabolic network and structure-based virtual screening for drug discovery against bacteria

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Daud, Kauthar Mohd; Ananda, Ridho; Zainudin, Suhaila et al. · 2023

Full title: Optimizing the Production of Valuable Metabolites using a Hybrid of Constraint-based Model and Machine Learning Algorithms: A Review

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Emil Karlsen; Marianne Gylseth; C. Schulz et al. · 2022

Full title: A study of a diauxic growth experiment using an expanded dynamic flux balance framework

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Jouhten, Paula; Konstantinidis, Dimitrios; Pereira, Filipa et al. · 2022

Full title: Predictive evolution of metabolic phenotypes using model-designed environments.

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Chen, Yu; Pelt‐KleinJan, Eunice van; Olst, Berdien van et al. · 2021

Full title: Proteome constraints reveal targets for improving microbial fitness in nutrient‐rich environments

Authors: Chen, Yu; Pelt‐KleinJan, Eunice van; Olst, Berdien van; Douwenga, Sieze; Boeren, Sjef; Bachmann, Herwig; Molenaar, Douwe; Nielsen, Jens; Teusink, Bas

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Full title: Machine learning methods for predicting essential metabolic genes from Plasmodium falciparum genome-scale metabolic network

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Full title: Comparison of Optimization-Modelling Methods for Metabolites Production in Escherichia coli

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Full title: Model‐guided development of an evolutionarily stable yeast chassis

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Steeb, Benjamin; Claudi, Beatrice; Burton, Neil A. et al. · 2013

Full title: Parallel Exploitation of Diverse Host Nutrients Enhances Salmonella Virulence

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Full title: Genome‐scale metabolic modeling reveals key features of a minimal gene set

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Full title: In silico Evaluation of the Effect of Pfl Gene Knockout on the Production of D-lactate by Escherichia coli Genome Scale Model Using the Optflux Software Platform

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Full title: Evaluating E. coli genome‐scale metabolic model accuracy with high‐throughput mutant fitness data

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Full title: Vibrio natriegens genome‐scale modeling reveals insights into halophilic adaptations and resource allocation

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Full title: Development of a Stoichiometric Model for Estimation of Metabolic Fluxes in Saccharomyces cerevisiae during Tequila Production

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Full title: Genetic Optimization Algorithm for Metabolic Engineering Revisited

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Full title: Bridging the gap between mechanistic biological models and machine learning surrogates

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Full title: Construction and Analysis of an Enzyme‐constrained Metabolic Model of Corynebacterium glutamicum

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Full title: ecBSU1: A Genome-scale Enzyme-constrained Model of Bacillus subtilis based on the ECMpy Workflow

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Full title: From Observational to Actionable: Rethinking Omics in Biologics Production

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Full title: A Guide for the Bioinformatic Analysis of Metabolomics Data

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Full title: From Shallow to Deep Bioprocess Hybrid Modeling: Advances and Future Perspectives

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Full title: Designing metabolic engineering strategies with genome-scale metabolic flux modeling

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Full title: Genome-Scale Metabolic Network Models of Bacillus Species Suggest that Model Improvement is Necessary for Biotechnological Applications

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Full title: Metabolic pathway reconstruction strategies for central metabolism and natural product biosynthesis

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Full title: NCMW: A Python Package to Analyze Metabolic Interactions in the Nasal Microbiome

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Full title: Estimation of biomass composition from genomic and transcriptomic information

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Metabolic Network Discovery by Top-Down and Bottom-Up Approaches and Paths for Reconciliation

Ã‡akÄ±r, Tunahan; Khatibipour, Mohammad Jafar · 2014

Full title: Metabolic Network Discovery by Top-Down and Bottom-Up Approaches and Paths for Reconciliation

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Full title: Editorial: Current Challenges in Modeling Cellular Metabolism

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Full title: Conceptos básicos de análisis de fluxes metabólicos

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Cardoso, João · 2015

Full title: Analysis of genetic variation and potential applications in genome-scale metabolic modeling

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Full title: Computer-Aided Whole-Cell Design: Taking a Holistic Approach by Integrating Synthetic With Systems Biology

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Full title: METABOLIC MODELLING AS A POWERFUL TOOL TO IDENTIFY CRITICAL COMPONENTS OF PNEUMOCYSTIS GROWTH MEDIUM

Authors: Nev, Olga A.; Zamaraeva, Elena; Oliveira, Romain De; Duvenage, Lucian; Abou-Jaoudé, Wassim; Ouattara, Djomangan Adama; Hoving, J. Claire; Gudelj, Ivana; Brown, Alistair J. P.

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Full title: Genome-scale metabolic models reveal determinants of phenotypic differences in non-Saccharomyces yeasts

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Liu, Zhihao; Chen, Minghao; Hu, Jingmin et al. · 2024

Full title: Minimization of proteome reallocation explains metabolic transition in hierarchical utilization of carbon sources

Authors: Liu, Zhihao; Chen, Minghao; Hu, Jingmin; Wang, Yonghong; Chen, Yu

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Full title: DLTKcat: deep learning-based prediction of temperature-dependent enzyme turnover rates

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Full title: Exploring the metabolic profiling of A. baumannii for antimicrobial development using genome-scale modelling

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Full title: Machine learning predicts system-wide metabolic flux control in cyanobacteria

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Full title: Genome-Scale Modeling of Rothia mucilaginosa Reveals Insights into Metabolic Capabilities and Therapeutic Strategies for Cystic Fibrosis

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Full title: Improved Production of Taxol® Precursors in S. cerevisiae using Combinatorial in silico Design and Metabolic Engineering

Authors: Malcı, Koray; Santibáñez, Rodrigo; Jonguitud‐Borrego, Nestor; Santoyo‐Garcia, Jorge H.; Kherkoven, Eduard J.; Rios‐Solis, Leonardo

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Full title: Inferring Metabolic States from Single Cell Transcriptomic Data via Geometric Deep Learning

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Full title: Dynamic Flux Balance Analysis Models in SBML

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Full title: Flux modelling analysis reveals the metabolic impact of cryptic plasmids and environmental conditions in probiotic Escherichia coli Nissle 1917

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Full title: Modelling dynamic host-pathway interactions at the genome scale with machine learning

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Full title: MINN: A METABOLIC-INFORMED NEURAL NETWORK FOR INTEGRATING OMICS DATA INTO GENOME-SCALE METABOLIC MODELING

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Full title: Yeast9: A Consensus Yeast Metabolic Model Enables Quantitative Analysis of Cellular Metabolism By Incorporating Big Data

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Full title: Robustness encoded across essential and accessory replicons in an ecologically versatile bacterium

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DOI: https://doi.org/10.1101/209916

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Full title: Machine Learning and Metabolic Model Guided CRISPRi Reveals a Central Role for Phosphoglycerate Mutase in Chlamydia trachomatis Persistence

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Full title: Genome-scale metabolic modelling of trimethoprim’s mode of action reveals free ATP salvaged to restore purine pool

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Lachance, Jean‐Christophe; Monk, Jonathan M.; Lloyd, Colton J. et al. · 2018

Full title: BOFdat: generating biomass objective function stoichiometric coefficients from experimental data

Authors: Lachance, Jean‐Christophe; Monk, Jonathan M.; Lloyd, Colton J.; Seif, Yara; Palsson, Bernhard Ø.; Rodrigue, Sébastien; Feist, Adam M.; King, Zachary A.; Jacques, Pierre‐Étienne

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diCenzo, George C.; Mengoni, Alessio; Fondi, Marco · 2017

Full title: Tn-Core: context-specific reconstruction of core metabolic models using Tn-seq data

Authors: diCenzo, George C.; Mengoni, Alessio; Fondi, Marco

DOI: https://doi.org/10.1101/221325

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Machado, Daniel; Andrejev, Sergej; Tramontano, Melanie et al. · 2018

Full title: Fast automated reconstruction of genome-scale metabolic models for microbial species and communities

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Full title: MIMEco: Multi-objective metabolic modeling to predict and explain pairwise interactions

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Lieven, Christian; Petersen, Leander A. H.; Jørgensen, Sten Bay et al. · 2018

Full title: A genome-scale metabolic model for Methylococcus capsulatus predicts reduced efficiency uphill electron transfer to pMMO

Authors: Lieven, Christian; Petersen, Leander A. H.; Jørgensen, Sten Bay; Gernaey, Krist V.; Herrgård, Markus J.; Sonnenschein, Nikolaus

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Żołędowska, Sabina; Presta, Luana; Fondi, Marco et al. · 2018

Full title: Metabolic modeling of Pectobacterium parmentieri SCC3193 provides insights into metabolic pathways of plant pathogenic bacteria

Authors: Żołędowska, Sabina; Presta, Luana; Fondi, Marco; Decorosi, Francesca; Giovannetti, Luciana; Mengoni, Alessio; Łojkowska, Ewa

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Jijakli, Kenan; Jensen, Paul A. · 2018

Full title: Metabolic modeling of Streptococcus mutans reveals complex nutrient requirements of an oral pathogen

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Heckmann, David; Zielinski, Daniel C.; Palsson, Bernhard Ø. · 2018

Full title: Modeling genome-wide evolution of catalytic turnover rates: Strong epistasis shaped modern enzyme kinetics

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Navid, Ali; Jiao, Yongqin; Wong, Sergio et al. · 2019

Full title: System-level analysis of metabolic trade-offs during anaerobic photoheterotrophic growth in Rhodopseudomonas palustris

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Sánchez, Benjamín J.; Li, Feiran; Kerkhoven, Eduard J. et al. · 2019

Full title: SLIMEr: probing flexibility of lipid metabolism in yeast with an improved constraint-based modeling framework

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Correia, Kevin; Khusnutdinova, Anna N.; Li, Peter Yan et al. · 2018

Full title: Flux balance analysis predicts NADP phosphatase and NADH kinase are critical to balancing redox during xylose fermentation in Scheffersomyces stipitis

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Tokic, Milenko; Mišković, Ljubiša; Hatzimanikatis, Vassily · 2019

Full title: Large-scale kinetic metabolic models of Pseudomonas putida for a consistent design of metabolic engineering strategies

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Groot, Daan H. de; Hulshof, Josephus; Teusink, Bas et al. · 2019

Full title: Elementary Growth Modes provide a molecular description of cellular self-fabrication

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Correia, Kevin; Ho, Han‐Chen; Mahadevan, Radhakrishnan · 2018

Full title: Genome-scale metabolic network reconstruction of the chloroform-respiring Dehalobacter restrictus strain CF

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Ebenhöh, Oliver; Ebeling, Josha; Meyer, R J et al. · 2024

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Volkova, Svetlana; Matos, Marta R. A.; Mattanovich, Matthias et al. · 2020

Full title: Metabolic Modelling as a Framework for Metabolomics Data Integration and Analysis

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Full title: Genome-Scale Metabolic Modeling Enables In-Depth Understanding of Big Data

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Full title: Towards Predicting Gut Microbial Metabolism: Integration of Flux Balance Analysis and Untargeted Metabolomics

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Full title: Drought Stress Responses in Context-Specific Genome-Scale Metabolic Models of Arabidopsis thaliana

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Fu, Weiqi; Chaiboonchoe, Amphun; Khraiwesh, Basel et al. · 2016

Full title: Algal Cell Factories: Approaches, Applications, and Potentials

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Full title: State-of-the-Art Genetic Modalities to Engineer Cyanobacteria for Sustainable Biosynthesis of Biofuel and Fine-Chemicals to Meet Bio–Economy Challenges

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Full title: Reconstruction of a Genome-Scale Metabolic Model of Streptomyces albus J1074: Improved Engineering Strategies in Natural Product Synthesis

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Full title: Revealing the Metabolic Alterations during Biofilm Development of Burkholderia cenocepacia Based on Genome-Scale Metabolic Modeling

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Full title: Optimality Principles in the Regulation of Metabolic Networks

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Full title: Metabolic Modeling of Hermetia illucens Larvae Resource Allocation for High-Value Fatty Acid Production

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Full title: Genome-Scale Metabolic Modelling Approach to Understand the Metabolism of the Opportunistic Human Pathogen Staphylococcus epidermidis RP62A

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Full title: Construction of a Genome-Scale Kinetic Model of Mycobacterium Tuberculosis Using Generic Rate Equations

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Full title: Achieving Metabolic Flux Analysis for S. cerevisiae at a Genome-Scale: Challenges, Requirements, and Considerations

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Full title: Metabolism at Evolutionary Optimal States

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Full title: Extracellular Microbial Metabolomics: The State of the Art

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Full title: An Improved Genome-Scale Metabolic Model of Arthrospira platensis C1 (iAK888) and Its Application in Glycogen Overproduction

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Full title: A Genome-Scale Metabolic Model of Thalassiosira pseudonana CCMP 1335 for a Systems-Level Understanding of Its Metabolism and Biotechnological Potential

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Full title: Thermochemical hydrolysis of macroalgae Ulva for biorefinery: Taguchi robust design method

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Full title: Revisiting the chlorophyll biosynthesis pathway using genome scale metabolic model of Oryza sativa japonica

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Full title: An Automated Scientist to Design and Optimize Microbial Strains for the Industrial Production of Small Molecules

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Full title: Statistical prediction of microbial metabolic traits from genomes

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Full title: A genome-scale metabolic flux model of Escherichia coli K–12 derived from the EcoCyc database

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Full title: gapseq: informed prediction of bacterial metabolic pathways and reconstruction of accurate metabolic models

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Full title: Systems biology elucidates the distinctive metabolic niche filled by the human gut microbe Eggerthella lenta

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Full title: Integrating Kinetic Model of E. coli with Genome Scale Metabolic Fluxes Overcomes Its Open System Problem and Reveals Bistability in Central Metabolism

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Full title: Systems analysis of Mycoplasma hyopneumoniae to improve vaccine production

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Full title: Metabolic Network Modeling of Microbial Interactions in Natural and Engineered Environmental Systems

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Full title: Fungal Alcohol Dehydrogenases: Physiological Function, Molecular Properties, Regulation of Their Production, and Biotechnological Potential

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Full title: Metabolic Engineering of Model Microorganisms for the Production of Xanthophyll

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Full title: Inferring Metabolic States in Uncharacterized Environments Using Gene-Expression Measurements

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Full title: Flux Balance Analysis of Cyanobacterial Metabolism: The Metabolic Network of Synechocystis sp. PCC 6803

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Full title: Swimming in Light: A Large-Scale Computational Analysis of the Metabolism of Dinoroseobacter shibae

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Full title: Semi-automated Curation of Metabolic Models via Flux Balance Analysis: A Case Study with Mycoplasma gallisepticum

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Full title: Reconstruction and Validation of a Genome-Scale Metabolic Model for the Filamentous Fungus Neurospora crassa Using FARM

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Full title: A Method to Constrain Genome-Scale Models with 13C Labeling Data

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Full title: Systematic Evaluation of Methods for Integration of Transcriptomic Data into Constraint-Based Models of Metabolism

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Full title: A Novel Nutritional Predictor Links Microbial Fastidiousness with Lowered Ubiquity, Growth Rate, and Cooperativeness

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Full title: Metabolic fluxes-oriented control of bioreactors: a novel approach to tune micro-aeration and substrate feeding in fermentations

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Full title: Visualization of Metabolic Interaction Networks in Microbial Communities Using VisANT 5.0

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Yang, Hong; Krumholz, Elias W.; Brutinel, Evan D. et al. · 2014

Full title: Genome-Scale Metabolic Network Validation of Shewanella oneidensis Using Transposon Insertion Frequency Analysis

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Chiu, Hsuan; Levy, Roie; Borenstein, Elhanan · 2014

Full title: Emergent Biosynthetic Capacity in Simple Microbial Communities

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Full title: Stoichiometric Representation of Gene–Protein–Reaction Associations Leverages Constraint-Based Analysis from Reaction to Gene-Level Phenotype Prediction

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Full title: lumpGEM: Systematic generation of subnetworks and elementally balanced lumped reactions for the biosynthesis of target metabolites

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Millard, Pierre; Smallbone, Kieran; Mendes, Pedro · 2017

Full title: Metabolic regulation is sufficient for global and robust coordination of glucose uptake, catabolism, energy production and growth in Escherichia coli

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Full title: Combining inferred regulatory and reconstructed metabolic networks enhances phenotype prediction in yeast

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Full title: Metabolic dynamics restricted by conserved carriers: Jamming and feedback

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Full title: Managing uncertainty in metabolic network structure and improving predictions using EnsembleFBA

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Full title: OptRAM: In-silico strain design via integrative regulatory-metabolic network modeling.

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Full title: redGEM: Systematic reduction and analysis of genome-scale metabolic reconstructions for development of consistent core metabolic models

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Full title: Characterizing steady states of genome-scale metabolic networks in continuous cell cultures

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Quantification and Classification of E. coli Proteome Utilization and Unused Protein Costs across Environments

O’Brien, Edward J.; Utrilla, José; Palsson, Bernhard Ø. · 2016

Full title: Quantification and Classification of E. coli Proteome Utilization and Unused Protein Costs across Environments

Authors: O’Brien, Edward J.; Utrilla, José; Palsson, Bernhard Ø.

DOI: https://doi.org/10.1371/journal.pcbi.1004998

Paper

The number of active metabolic pathways is bounded by the number of cellular constraints at maximal metabolic rates

Groot, Daan H. de; Boxtel, Coco van; Planqué, Robert et al. · 2019

Full title: The number of active metabolic pathways is bounded by the number of cellular constraints at maximal metabolic rates

Authors: Groot, Daan H. de; Boxtel, Coco van; Planqué, Robert; Bruggeman, Frank J.; Teusink, Bas

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Machine and deep learning meet genome-scale metabolic modeling

Zampieri, Guido; Vijayakumar, Supreeta; Yaneske, Elisabeth et al. · 2019

Full title: Machine and deep learning meet genome-scale metabolic modeling

Authors: Zampieri, Guido; Vijayakumar, Supreeta; Yaneske, Elisabeth; Angione, Claudio

DOI: https://doi.org/10.1371/journal.pcbi.1007084

Paper

From Escherichia coli mutant 13C labeling data to a core kinetic model: A kinetic model parameterization pipeline

Foster, Charles; Gopalakrishnan, Saratram; Antoniewicz, Maciek R. et al. · 2019

Full title: From Escherichia coli mutant 13C labeling data to a core kinetic model: A kinetic model parameterization pipeline

Authors: Foster, Charles; Gopalakrishnan, Saratram; Antoniewicz, Maciek R.; Maranas, Costas D.

DOI: https://doi.org/10.1371/journal.pcbi.1007319

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Enhanced flux prediction by integrating relative expression and relative metabolite abundance into thermodynamically consistent metabolic models

Pandey, Vikash; Hadadi, Noushin; Hatzimanikatis, Vassily · 2019

Full title: Enhanced flux prediction by integrating relative expression and relative metabolite abundance into thermodynamically consistent metabolic models

Authors: Pandey, Vikash; Hadadi, Noushin; Hatzimanikatis, Vassily

DOI: https://doi.org/10.1371/journal.pcbi.1007036

Paper

A steady-state model of microbial acclimation to substrate limitation

Casey, John R.; Follows, Michael J. · 2020

Full title: A steady-state model of microbial acclimation to substrate limitation

Authors: Casey, John R.; Follows, Michael J.

DOI: https://doi.org/10.1371/journal.pcbi.1008140

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Statistical inference in ensemble modeling of cellular metabolism

Tuure, Hameri; Boldi, Marc‐Olivier; Hatzimanikatis, Vassily · 2019

Full title: Statistical inference in ensemble modeling of cellular metabolism

Authors: Tuure, Hameri; Boldi, Marc‐Olivier; Hatzimanikatis, Vassily

DOI: https://doi.org/10.1371/journal.pcbi.1007536

Paper

Bayesian inference of metabolic kinetics from genome-scale multiomics data

John, Peter C. St.; Strutz, Jonathan; Broadbelt, Linda J. et al. · 2019

Full title: Bayesian inference of metabolic kinetics from genome-scale multiomics data

Authors: John, Peter C. St.; Strutz, Jonathan; Broadbelt, Linda J.; Tyo, Keith E. J.; Bomble, Yannick J.

DOI: https://doi.org/10.1371/journal.pcbi.1007424

Paper

Dissecting the regulatory roles of ORM proteins in the sphingolipid pathway of plants

Alsiyabi, Adil; González‐Solís, Ariadna; Cahoon, Edgar B. et al. · 2021

Full title: Dissecting the regulatory roles of ORM proteins in the sphingolipid pathway of plants

Authors: Alsiyabi, Adil; González‐Solís, Ariadna; Cahoon, Edgar B.; Saha, Rajib

DOI: https://doi.org/10.1371/journal.pcbi.1008284

Paper

BayFlux: A Bayesian method to quantify metabolic Fluxes and their uncertainty at the genome scale

Backman, Tyler W. H.; Schenk, Christina; Radivojević, Tijana et al. · 2023

Full title: BayFlux: A Bayesian method to quantify metabolic Fluxes and their uncertainty at the genome scale

DOI: https://doi.org/10.1371/journal.pcbi.1011111

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Physicochemical and metabolic constraints for thermodynamics-based stoichiometric modelling under mesophilic growth conditions

Tomi-Andrino, Claudio; Norman, Rupert; Millat, Thomas et al. · 2021

Full title: Physicochemical and metabolic constraints for thermodynamics-based stoichiometric modelling under mesophilic growth conditions

Authors: Tomi-Andrino, Claudio; Norman, Rupert; Millat, Thomas; Soucaille, Philippe; Winzer, Klaus; Barrett, David A.; King, John R.; Kim, Dong‐Hyun

DOI: https://doi.org/10.1371/journal.pcbi.1007694

Paper

Genetic buffering and potentiation in metabolism

Poyatos, Juan F. · 2020

Full title: Genetic buffering and potentiation in metabolism

Authors: Poyatos, Juan F.

DOI: https://doi.org/10.1371/journal.pcbi.1008185

Paper

MASSpy: Building, simulating, and visualizing dynamic biological models in Python using mass action kinetics

Haiman, Zachary B.; Zielinski, Daniel C.; Koike, Yuko et al. · 2021

Full title: MASSpy: Building, simulating, and visualizing dynamic biological models in Python using mass action kinetics

Authors: Haiman, Zachary B.; Zielinski, Daniel C.; Koike, Yuko; Yurkovich, James T.; Palsson, Bernhard Ø.

DOI: https://doi.org/10.1371/journal.pcbi.1008208

Paper

Computation of condition-dependent proteome allocation reveals variability in the macro and micro nutrient requirements for growth

Lloyd, Colton J.; Monk, Jonathan M.; Yang, Laurence et al. · 2021

Full title: Computation of condition-dependent proteome allocation reveals variability in the macro and micro nutrient requirements for growth

Authors: Lloyd, Colton J.; Monk, Jonathan M.; Yang, Laurence; Ebrahim, Ali; Palsson, Bernhard Ø.

Paper

Model-driven analysis of mutant fitness experiments improves genome-scale metabolic models of Zymomonas mobilis ZM4

Ong, Wai Kit; Courtney, Dylan K.; Pan, Shu et al. · 2020

Full title: Model-driven analysis of mutant fitness experiments improves genome-scale metabolic models of Zymomonas mobilis ZM4

Authors: Ong, Wai Kit; Courtney, Dylan K.; Pan, Shu; Andrade, Ramon Bonela; Kiley, Patricia J.; Pfleger, Brian F.; Reed, Jennifer L.

DOI: https://doi.org/10.1371/journal.pcbi.1008137

Paper

Strain design optimization using reinforcement learning

Sabzevari, Maryam; Szedmák, Sándor; Penttilä, Merja et al. · 2022

Full title: Strain design optimization using reinforcement learning

Authors: Sabzevari, Maryam; Szedmák, Sándor; Penttilä, Merja; Jouhten, Paula; Rousu, Juho

Paper

Bacterial fitness landscapes stratify based on proteome allocation associated with discrete aero-types

Chen, Ke; Anand, Amitesh; Olson, Connor A. et al. · 2021

Full title: Bacterial fitness landscapes stratify based on proteome allocation associated with discrete aero-types

Authors: Chen, Ke; Anand, Amitesh; Olson, Connor A.; Sandberg, Troy E.; Gao, Ye; Mih, Nathan; Palsson, Bernhard Ø.

DOI: https://doi.org/10.1371/journal.pcbi.1008596

Paper

Bridging the gap between mechanistic biological models and machine learning surrogates

Gherman, Ioana M.; Abdallah, Zahraa S.; Pang, Wei et al. · 2023

Full title: Bridging the gap between mechanistic biological models and machine learning surrogates

Authors: Gherman, Ioana M.; Abdallah, Zahraa S.; Pang, Wei; Gorochowski, Thomas E.; Grierson, Claire; Marucci, Lucia

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Flux balance analysis of the ammonia-oxidizing bacterium Nitrosomonas europaea ATCC19718 unravels specific metabolic activities while degrading toxic compounds

Gabriela Canto-Encalada; Diego Tec-Campos; Juan D. Tibocha-Bonilla et al. · 2022

Full title: Flux balance analysis of the ammonia-oxidizing bacterium Nitrosomonas europaea ATCC19718 unravels specific metabolic activities while degrading toxic compounds

Authors: Gabriela Canto-Encalada; Diego Tec-Campos; Juan D. Tibocha-Bonilla; K. Zengler; A. Zepeda; C. Zúñiga

DOI: https://doi.org/10.1371/journal.pcbi.1009828

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Genome-scale metabolic modeling of the human gut bacterium Bacteroides fragilis strain 638R

Neal, M J; Thiruppathy, Deepan; Zengler, Karsten · 2023

Full title: Genome-scale metabolic modeling of the human gut bacterium Bacteroides fragilis strain 638R

Authors: Neal, M J; Thiruppathy, Deepan; Zengler, Karsten

DOI: https://doi.org/10.1371/journal.pcbi.1011594

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Harnessing the optimization of enzyme catalytic rates in engineering of metabolic phenotypes

Zahra Razaghi-Moghadam; Fayaz Soleymani Babadi; Z. Nikoloski · 2024

Full title: Harnessing the optimization of enzyme catalytic rates in engineering of metabolic phenotypes

Authors: Zahra Razaghi-Moghadam; Fayaz Soleymani Babadi; Z. Nikoloski

DOI: https://doi.org/10.1371/journal.pcbi.1012576

Paper

Epistatic Interaction Maps Relative to Multiple Metabolic Phenotypes

Snitkin, Evan S.; Segrè, Daniel · 2011

Full title: Epistatic Interaction Maps Relative to Multiple Metabolic Phenotypes

Authors: Snitkin, Evan S.; Segrè, Daniel

DOI: https://doi.org/10.1371/journal.pgen.1001294

Paper

Flux balance analysis-based metabolic modeling of microbial secondary metabolism: Current status and outlook

Sizhe Qiu; Ai-ying Yang; H. Zeng · 2023

Full title: Flux balance analysis-based metabolic modeling of microbial secondary metabolism: Current status and outlook

Authors: Sizhe Qiu; Ai-ying Yang; H. Zeng

DOI: https://doi.org/10.1371/journal.pcbi.1011391

Paper

The genome-scale metabolic model for the purple non-sulfur bacterium Rhodopseudomonas palustris Bis A53 accurately predicts phenotypes under chemoheterotrophic, chemoautotrophic, photoheterotrophic, and photoautotrophic growth conditions

Tec-Campos, Diego; Posadas, Camila; Tibocha‐Bonilla, Juan D. et al. · 2023

Authors: Tec-Campos, Diego; Posadas, Camila; Tibocha‐Bonilla, Juan D.; Thiruppathy, Deepan; Glonek, Nathan; Zúñiga, Cristal; Zepeda, Alejandro; Zengler, Karsten

DOI: https://doi.org/10.1371/journal.pcbi.1011371

Paper

Inferring Carbon Sources from Gene Expression Profiles Using Metabolic Flux Models

Brandes, Aaron; Lun, Desmond S.; Ip, Kuhn et al. · 2012

Full title: Inferring Carbon Sources from Gene Expression Profiles Using Metabolic Flux Models

Authors: Brandes, Aaron; Lun, Desmond S.; Ip, Kuhn; Zucker, Jeremy; Colijn, Caroline; Weiner, Brian; Galagan, James E.

DOI: https://doi.org/10.1371/journal.pone.0036947

Paper

Zea mays iRS1563: A Comprehensive Genome-Scale Metabolic Reconstruction of Maize Metabolism

Saha, Rajib; Suthers, Patrick F.; Maranas, Costas D. · 2011

Full title: Zea mays iRS1563: A Comprehensive Genome-Scale Metabolic Reconstruction of Maize Metabolism

Authors: Saha, Rajib; Suthers, Patrick F.; Maranas, Costas D.

DOI: https://doi.org/10.1371/journal.pone.0021784

Paper

Exploring Metabolic Pathway Reconstruction and Genome-Wide Expression Profiling in Lactobacillus reuteri to Define Functional Probiotic Features

Saulnier, Delphine; Santos, Filipe Duarte; Roos, Stefan et al. · 2011

Full title: Exploring Metabolic Pathway Reconstruction and Genome-Wide Expression Profiling in Lactobacillus reuteri to Define Functional Probiotic Features

Authors: Saulnier, Delphine; Santos, Filipe Duarte; Roos, Stefan; Mistretta, Toni-Ann; Spinler, Jennifer K.; Molenaar, Douwe; Teusink, Bas; Versalovic, James

DOI: https://doi.org/10.1371/journal.pone.0018783

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Evolutionary Systems Biology of Amino Acid Biosynthetic Cost in Yeast

Barton, Michael D.; Delneri, Daniela; Oliver, Stephen G. et al. · 2010

Full title: Evolutionary Systems Biology of Amino Acid Biosynthetic Cost in Yeast

Authors: Barton, Michael D.; Delneri, Daniela; Oliver, Stephen G.; Rattray, Magnus; Bergman, Casey

DOI: https://doi.org/10.1371/journal.pone.0011935

Paper

A genome-scale metabolic model for the denitrifying bacterium Thauera sp. MZ1T accurately predicts degradation of pollutants and production of polymers

Tec-Campos, Diego; Tibocha‐Bonilla, Juan D.; Jiang, Chunguo et al. · 2025

Full title: A genome-scale metabolic model for the denitrifying bacterium Thauera sp. MZ1T accurately predicts degradation of pollutants and production of polymers

Authors: Tec-Campos, Diego; Tibocha‐Bonilla, Juan D.; Jiang, Chunguo; Passi, Anurag; Thiruppathy, Deepan; Zúñiga, Cristal; Posadas, Camila; Zepeda, Alejandro; Zengler, Karsten

DOI: https://doi.org/10.1371/journal.pcbi.1012736

Paper

Genome-Scale Consequences of Cofactor Balancing in Engineered Pentose Utilization Pathways in Saccharomyces cerevisiae

Ghosh, Amit; Zhao, Huimin; Price, Nathan D. · 2011

Full title: Genome-Scale Consequences of Cofactor Balancing in Engineered Pentose Utilization Pathways in Saccharomyces cerevisiae

Authors: Ghosh, Amit; Zhao, Huimin; Price, Nathan D.

DOI: https://doi.org/10.1371/journal.pone.0027316

Paper

Characterization of the Metabolic Requirements in Yeast Meiosis

Ray, Debjit; Ye, Ping · 2013

Full title: Characterization of the Metabolic Requirements in Yeast Meiosis

Authors: Ray, Debjit; Ye, Ping

DOI: https://doi.org/10.1371/journal.pone.0063707

Paper

Genome-Scale Reconstruction and Analysis of the Metabolic Network in the Hyperthermophilic Archaeon Sulfolobus Solfataricus

Ulas, Thomas; Riemer, S. Alexander; Zaparty, Melanie et al. · 2012

Full title: Genome-Scale Reconstruction and Analysis of the Metabolic Network in the Hyperthermophilic Archaeon Sulfolobus Solfataricus

Authors: Ulas, Thomas; Riemer, S. Alexander; Zaparty, Melanie; Siebers, Bettina; Schomburg, Dietmar

DOI: https://doi.org/10.1371/journal.pone.0043401

Paper

Reconstruction and In Silico Analysis of Metabolic Network for an Oleaginous Yeast, Yarrowia lipolytica

Pan, Pengcheng; Hua, Qiang · 2012

Full title: Reconstruction and In Silico Analysis of Metabolic Network for an Oleaginous Yeast, Yarrowia lipolytica

Authors: Pan, Pengcheng; Hua, Qiang

DOI: https://doi.org/10.1371/journal.pone.0051535

Paper

Identification of Metabolic Engineering Targets through Analysis of Optimal and Sub-Optimal Routes

Soons, Zita; Ferreira, Eugénio C.; Patil, Kiran Raosaheb et al. · 2013

Full title: Identification of Metabolic Engineering Targets through Analysis of Optimal and Sub-Optimal Routes

Authors: Soons, Zita; Ferreira, Eugénio C.; Patil, Kiran Raosaheb; Rocha, Isabel

DOI: https://doi.org/10.1371/journal.pone.0061648

Paper

Fumaric Acid Production in Saccharomyces cerevisiae by In Silico Aided Metabolic Engineering

Xu, Guoqiang; Zou, Wei; Chen, Xiulai et al. · 2012

Full title: Fumaric Acid Production in Saccharomyces cerevisiae by In Silico Aided Metabolic Engineering

Authors: Xu, Guoqiang; Zou, Wei; Chen, Xiulai; Xu, Nan; Liu, Li; Chen, Jian

DOI: https://doi.org/10.1371/journal.pone.0052086

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ReacKnock: Identifying Reaction Deletion Strategies for Microbial Strain Optimization Based on Genome-Scale Metabolic Network

Xu, Zixiang; Zheng, Ping; Sun, Jibin et al. · 2013

Full title: ReacKnock: Identifying Reaction Deletion Strategies for Microbial Strain Optimization Based on Genome-Scale Metabolic Network

Authors: Xu, Zixiang; Zheng, Ping; Sun, Jibin; Ma, Yanhe

DOI: https://doi.org/10.1371/journal.pone.0072150

Paper

Multiscale Modeling of Metabolism and Macromolecular Synthesis in E. coli and Its Application to the Evolution of Codon Usage

Thiele, Ines; Fleming, Ronan M. T.; Que, Richard et al. · 2012

Full title: Multiscale Modeling of Metabolism and Macromolecular Synthesis in E. coli and Its Application to the Evolution of Codon Usage

Authors: Thiele, Ines; Fleming, Ronan M. T.; Que, Richard; Bordbar, Aarash; Diep, Dinh; Palsson, Bernhard Ø.

DOI: https://doi.org/10.1371/journal.pone.0045635

Paper

Construction and Analysis of the Model of Energy Metabolism in E. coli

Xu, Zixiang; Sun, Xiao; Sun, Jibin · 2013

Full title: Construction and Analysis of the Model of Energy Metabolism in E. coli

Authors: Xu, Zixiang; Sun, Xiao; Sun, Jibin

DOI: https://doi.org/10.1371/journal.pone.0055137

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Maximal Sum of Metabolic Exchange Fluxes Outperforms Biomass Yield as a Predictor of Growth Rate of Microorganisms

Zarecki, Raphy; Oberhardt, Matthew; Yizhak, Keren et al. · 2014

Full title: Maximal Sum of Metabolic Exchange Fluxes Outperforms Biomass Yield as a Predictor of Growth Rate of Microorganisms

Authors: Zarecki, Raphy; Oberhardt, Matthew; Yizhak, Keren; Wagner, Allon; Segal, E.; Freilich, Shiri; Henry, Christopher S.; Gophna, Uri; Ruppin, Eytan

DOI: https://doi.org/10.1371/journal.pone.0098372

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Genome-Scale NAD(H/+) Availability Patterns as a Differentiating Feature between Saccharomyces cerevisiae and Scheffersomyces stipitis in Relation to Fermentative Metabolism

Acevedo, Alejandro; Aroca, Germán; Conejeros, Raúl · 2014

Full title: Genome-Scale NAD(H/+) Availability Patterns as a Differentiating Feature between Saccharomyces cerevisiae and Scheffersomyces stipitis in Relation to Fermentative Metabolism

Authors: Acevedo, Alejandro; Aroca, Germán; Conejeros, Raúl

DOI: https://doi.org/10.1371/journal.pone.0087494

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Rapid Countermeasure Discovery against Francisella tularensis Based on a Metabolic Network Reconstruction

Chaudhury, Sidhartha; AbdulHameed, Mohamed Diwan M.; Singh, Narender et al. · 2013

Full title: Rapid Countermeasure Discovery against Francisella tularensis Based on a Metabolic Network Reconstruction

DOI: https://doi.org/10.1371/journal.pone.0063369

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Combining Chemoinformatics with Bioinformatics: In Silico Prediction of Bacterial Flavor-Forming Pathways by a Chemical Systems Biology Approach “Reverse Pathway Engineering”

Liu, Mengjin; Bienfait, Bruno; Sacher, Oliver et al. · 2014

Full title: Combining Chemoinformatics with Bioinformatics: In Silico Prediction of Bacterial Flavor-Forming Pathways by a Chemical Systems Biology Approach “Reverse Pathway Engineering”

Authors: Liu, Mengjin; Bienfait, Bruno; Sacher, Oliver; Gasteiger, Johann; Siezen, Roland J.; Nauta, Arjen; Geurts, Jan M.W.

DOI: https://doi.org/10.1371/journal.pone.0084769

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Industrial Systems Biology of Saccharomyces cerevisiae Enables Novel Succinic Acid Cell Factory

Otero, José M.; Cimini, Donatella; Patil, Kiran Raosaheb et al. · 2013

Full title: Industrial Systems Biology of Saccharomyces cerevisiae Enables Novel Succinic Acid Cell Factory

Authors: Otero, José M.; Cimini, Donatella; Patil, Kiran Raosaheb; Poulsen, Simon G.; Olsson, Lisbeth; Nielsen, Jens

DOI: https://doi.org/10.1371/journal.pone.0054144

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Reconstruction and Comparison of the Metabolic Potential of Cyanobacteria Cyanothece sp. ATCC 51142 and Synechocystis sp. PCC 6803

Saha, Rajib; Verseput, Alex T.; Berla, Bertram M. et al. · 2012

Full title: Reconstruction and Comparison of the Metabolic Potential of Cyanobacteria Cyanothece sp. ATCC 51142 and Synechocystis sp. PCC 6803

Authors: Saha, Rajib; Verseput, Alex T.; Berla, Bertram M.; Mueller, Thomas J. J.; Pakrasi, Himadri B.; Maranas, Costas D.

DOI: https://doi.org/10.1371/journal.pone.0048285

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Integration of enzymatic data in Bacillus subtilis genome-scale metabolic model improves phenotype predictions and enables in silico design of poly-γ-glutamic acid production strains.

Massaiu, Ilaria; Pasotti, Lorenzo; Sonnenschein, Nikolaus et al. · 2019

Full title: Integration of enzymatic data in Bacillus subtilis genome-scale metabolic model improves phenotype predictions and enables in silico design of poly-γ-glutamic acid production strains.

Authors: Massaiu, Ilaria; Pasotti, Lorenzo; Sonnenschein, Nikolaus; Rama, Erlinda; Cavaletti, Matteo; Magni, Paolo; Calvio, Cinzia; Herrgård, Markus J

DOI: https://doi.org/10.1186/s12934-018-1052-2

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Engineering microbial consortia by division of labor

Roell, Garrett W.; Zha, Jian; Carr, Rhiannon et al. · 2019

Full title: Engineering microbial consortia by division of labor

Authors: Roell, Garrett W.; Zha, Jian; Carr, Rhiannon; Koffas, Mattheos; Fong, Stephen S.; Tang, Yinjie

DOI: https://doi.org/10.1186/s12934-019-1083-3

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Metabolic role of pyrophosphate-linked phosphofructokinase pfk for C1 assimilation in Methylotuvimicrobium alcaliphilum 20Z

Nguyen, Anh Duc; Nam, Gayoung; Kim, Donghyuk et al. · 2020

Full title: Metabolic role of pyrophosphate-linked phosphofructokinase pfk for C1 assimilation in Methylotuvimicrobium alcaliphilum 20Z

Authors: Nguyen, Anh Duc; Nam, Gayoung; Kim, Donghyuk; Lee, Eun Yeol

DOI: https://doi.org/10.1186/s12934-020-01382-5

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Strain engineering and metabolic flux analysis of a probiotic yeast Saccharomyces boulardii for metabolizing l-fucose, a mammalian mucin component

Kim, Jungyeon; Cheong, Yu Eun; Yu, Sora et al. · 2022

Full title: Strain engineering and metabolic flux analysis of a probiotic yeast Saccharomyces boulardii for metabolizing l-fucose, a mammalian mucin component

Authors: Kim, Jungyeon; Cheong, Yu Eun; Yu, Sora; Jin, Yong-Su; Kim, Kyoung Heon

DOI: https://doi.org/10.1186/s12934-022-01926-x

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Improved production of Taxol® precursors in S. cerevisiae using combinatorial in silico design and metabolic engineering

Malcı, Koray; Santibáñez, Rodrigo; Jonguitud‐Borrego, Nestor et al. · 2023

Full title: Improved production of Taxol® precursors in S. cerevisiae using combinatorial in silico design and metabolic engineering

Authors: Malcı, Koray; Santibáñez, Rodrigo; Jonguitud‐Borrego, Nestor; Santoyo‐Garcia, Jorge H.; Kerkhoven, Eduard J.; Rios‐Solis, Leonardo

DOI: https://doi.org/10.1186/s12934-023-02251-7

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Metabolic engineering design to enhance (R,R)-2,3-butanediol production from glycerol in Bacillus subtilis based on flux balance analysis

Vikromvarasiri, Nunthaphan; Shirai, Tomokazu; Kondo, Akihiko · 2021

Full title: Metabolic engineering design to enhance (R,R)-2,3-butanediol production from glycerol in Bacillus subtilis based on flux balance analysis

Authors: Vikromvarasiri, Nunthaphan; Shirai, Tomokazu; Kondo, Akihiko

DOI: https://doi.org/10.1186/s12934-021-01688-y

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Resource-aware whole-cell model of division of labour in a microbial consortium for complex-substrate degradation

Atkinson, Eliza; Tuza, Zoltán A.; Perrino, Giansimone et al. · 2022

Full title: Resource-aware whole-cell model of division of labour in a microbial consortium for complex-substrate degradation

Authors: Atkinson, Eliza; Tuza, Zoltán A.; Perrino, Giansimone; Stan, Guy‐Bart; Ledesma‐Amaro, Rodrigo

DOI: https://doi.org/10.1186/s12934-022-01842-0

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Automation assisted anaerobic phenotyping for metabolic engineering

Raj, Kaushik; Venayak, Naveen; Diep, Patrick et al. · 2021

Full title: Automation assisted anaerobic phenotyping for metabolic engineering

Authors: Raj, Kaushik; Venayak, Naveen; Diep, Patrick; Golla, Sai Akhil; Yakunin, Alexander F.; Mahadevan, Radhakrishnan

DOI: https://doi.org/10.1186/s12934-021-01675-3

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Adaptation of central metabolite pools to variations in growth rate and cultivation conditions in Saccharomyces cerevisiae

Kumar, Kanhaiya; Venkatraman, Vishwesh; Bruheim, Per · 2021

Full title: Adaptation of central metabolite pools to variations in growth rate and cultivation conditions in Saccharomyces cerevisiae

Authors: Kumar, Kanhaiya; Venkatraman, Vishwesh; Bruheim, Per

DOI: https://doi.org/10.1186/s12934-021-01557-8

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High throughput 13C-metabolic flux analysis of 3-hydroxypropionic acid producing Pichia pastoris reveals limited availability of acetyl-CoA and ATP due to tight control of the glycolytic flux

Fina, Albert; Millard, Pierre; Albiol, Joan et al. · 2023

Authors: Fina, Albert; Millard, Pierre; Albiol, Joan; Ferrer, Pau; Heux, Stéphanie

DOI: https://doi.org/10.1186/s12934-023-02123-0

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FastKnock: an efficient next-generation approach to identify all knockout strategies for strain optimization

Hassani, Leila; Moosavi, Mohammad R.; Setoodeh, Payam et al. · 2024

Full title: FastKnock: an efficient next-generation approach to identify all knockout strategies for strain optimization

Authors: Hassani, Leila; Moosavi, Mohammad R.; Setoodeh, Payam; Zare, Habil

DOI: https://doi.org/10.1186/s12934-023-02277-x

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A novel engineered strain of Methylorubrum extorquens for methylotrophic production of glycolic acid

Dietz, K.-J.; Sagstetter, Carina; Speck, Melanie et al. · 2024

Full title: A novel engineered strain of Methylorubrum extorquens for methylotrophic production of glycolic acid

Authors: Dietz, K.-J.; Sagstetter, Carina; Speck, Melanie; Roth, Arne; Klamt, Steffen; Fabarius, Jonathan Thomas

DOI: https://doi.org/10.1186/s12934-024-02583-y

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Designing minimal microbial strains of desired functionality using a genetic algorithm

Nair, Govind; Jungreuthmayer, Christian; Hanscho, Michael et al. · 2015

Full title: Designing minimal microbial strains of desired functionality using a genetic algorithm

Authors: Nair, Govind; Jungreuthmayer, Christian; Hanscho, Michael; Zanghellini, Jürgen

DOI: https://doi.org/10.1186/s13015-015-0060-6

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Sulfate limitation increases specific plasmid DNA yield and productivity in E. coli fed-batch processes

Gotsmy, Mathias; Strobl, Florian; Weiß, Florian et al. · 2023

Full title: Sulfate limitation increases specific plasmid DNA yield and productivity in E. coli fed-batch processes

Authors: Gotsmy, Mathias; Strobl, Florian; Weiß, Florian; Gruber, Petra; Kraus, Barbara; Mairhofer, Juergen; Zanghellini, Jürgen

DOI: https://doi.org/10.1186/s12934-023-02248-2

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Engineering the synthetic β-alanine pathway in Komagataella phaffii for conversion of methanol into 3-hydroxypropionic acid

Àvila-Cabré, Sílvia; Pérez‐Trujillo, Míriam; Albiol, Joan et al. · 2023

Full title: Engineering the synthetic β-alanine pathway in Komagataella phaffii for conversion of methanol into 3-hydroxypropionic acid

Authors: Àvila-Cabré, Sílvia; Pérez‐Trujillo, Míriam; Albiol, Joan; Ferrer, Pau

DOI: https://doi.org/10.1186/s12934-023-02241-9

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Construction of an enzyme-constrained metabolic network model for Myceliophthora thermophila using machine learning-based kcat data.

Wang, Yutao; Mao, Zhitao; Dong, Jiacheng et al. · 2024

Full title: Construction of an enzyme-constrained metabolic network model for Myceliophthora thermophila using machine learning-based kcat data.

Authors: Wang, Yutao; Mao, Zhitao; Dong, Jiacheng; Zhang, Peiji; Gao, Qiang; Liu, Defei; Tian, Chaoguang; Ma, Hongwu

DOI: https://doi.org/10.1186/s12934-024-02415-z

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Mapping the landscape of metabolic goals of a cell

Zhao, Qi; Stettner, Arion; Reznik, Ed et al. · 2016

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Full title: Microbial production of vitamin B12: a review and future perspectives

Authors: Fang, Huan; Kang, Jie; Zhang, Dawei

DOI: https://doi.org/10.1186/s12934-017-0631-y

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SLIMEr: probing flexibility of lipid metabolism in yeast with an improved constraint-based modeling framework

Sánchez, Benjamín J.; Li, Feiran; Kerkhoven, Eduard J. et al. · 2019

Full title: SLIMEr: probing flexibility of lipid metabolism in yeast with an improved constraint-based modeling framework

Authors: Sánchez, Benjamín J.; Li, Feiran; Kerkhoven, Eduard J.; Nielsen, Jens

DOI: https://doi.org/10.3390/bioengineering10060744

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Flux measurements and maintenance energy for carbon dioxide utilization by Methanococcus maripaludis

Goyal, Nishu; Padhiary, Mrutyunjay; Karimi, Iftekhar A. et al. · 2015

Full title: Flux measurements and maintenance energy for carbon dioxide utilization by Methanococcus maripaludis

Authors: Goyal, Nishu; Padhiary, Mrutyunjay; Karimi, Iftekhar A.; Zhou, Zhi

DOI: https://doi.org/10.1186/s12934-015-0336-z

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Full title: A scalable metabolite supplementation strategy against antibiotic resistant pathogen Chromobacterium violaceum induced by NAD+/NADH+ imbalance

Authors: Banerjee, Deepanwita; Parmar, Dharmeshkumar; Bhattacharya, Nivedita; Ghanate, Avinash; Panchagnula, Venkateswarlu; Raghunathan, Anu

DOI: https://doi.org/10.1186/s12918-017-0427-z

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Full title: Production of β-ionone by combined expression of carotenogenic and plant CCD1 genes in Saccharomyces cerevisiae

Authors: López, Javiera; Essus, Karen; Kim, Il‐Kwon; Pereira, Rui; Herzog, Jan; Siewers, Verena; Nielsen, Jens; Agosín, Eduardo

DOI: https://doi.org/10.1186/s12934-015-0273-x

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In silico model-guided identification of transcriptional regulator targets for efficient strain design

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Full title: In silico model-guided identification of transcriptional regulator targets for efficient strain design

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DOI: https://doi.org/10.1186/s12934-018-1015-7

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Lü, Yao; Ye, Chao; Che, Jinxin et al. · 2019

Full title: Genomic sequencing, genome-scale metabolic network reconstruction, and in silico flux analysis of the grape endophytic fungus Alternaria sp. MG1

Authors: Lü, Yao; Ye, Chao; Che, Jinxin; Xu, Xiaoguang; Shao, Dongyan; Jiang, Chunmei; Liu, Yanlin; Shi, Junling

DOI: https://doi.org/10.1186/s12934-019-1063-7

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OptPipe - a pipeline for optimizing metabolic engineering targets

Hartmann, András; Vila-Santa, Ana; Kallscheuer, Nicolai et al. · 2017

Full title: OptPipe - a pipeline for optimizing metabolic engineering targets

Authors: Hartmann, András; Vila-Santa, Ana; Kallscheuer, Nicolai; Vogt, Michael; Julien-Laferrière, Alice; Sagot, Marie-France; Marienhagen, Jan; Vinga, Susana

DOI: https://doi.org/10.1186/s12918-017-0515-0

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Metabolic engineering of Synechococcus elongatus PCC 7942 for improvement of 1,3-propanediol and glycerol production based on in silico simulation of metabolic flux distribution

Hirokawa, Yasutaka; Matsuo, Shingo; Hamada, Hiroyuki et al. · 2017

Full title: Metabolic engineering of Synechococcus elongatus PCC 7942 for improvement of 1,3-propanediol and glycerol production based on in silico simulation of metabolic flux distribution

Authors: Hirokawa, Yasutaka; Matsuo, Shingo; Hamada, Hiroyuki; Matsuda, Fumio; Hanai, Taizo

DOI: https://doi.org/10.1186/s12934-017-0824-4

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Role of phosphate limitation and pyruvate decarboxylase in rewiring of the metabolic network for increasing flux towards isoprenoid pathway in a TATA binding protein mutant of Saccharomyces cerevisiae

Wadhwa, Manisha; Srinivasan, Sumana; Bachhawat, Anand et al. · 2018

Authors: Wadhwa, Manisha; Srinivasan, Sumana; Bachhawat, Anand; Venkatesh, K. V.

DOI: https://doi.org/10.1186/s12934-018-1000-1

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Genome-scale metabolic reconstructions and theoretical investigation of methane conversion in Methylomicrobium buryatense strain 5G(B1)

Torre, Andrea De La; Metivier, Aisha; Chu, Frances et al. · 2015

Full title: Genome-scale metabolic reconstructions and theoretical investigation of methane conversion in Methylomicrobium buryatense strain 5G(B1)

Authors: Torre, Andrea De La; Metivier, Aisha; Chu, Frances; Laurens, Lieve M. L.; Beck, David A. C.; Pienkos, Philip T.; Lidstrom, Mary E.; Kalyuzhnaya, Marina

DOI: https://doi.org/10.1186/s12934-015-0377-3

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Wang, Junhua; Wang, Cheng; Song, Kejing et al. · 2017

Full title: Metabolic network model guided engineering ethylmalonyl-CoA pathway to improve ascomycin production in Streptomyces hygroscopicus var. ascomyceticus

Authors: Wang, Junhua; Wang, Cheng; Song, Kejing; Wen, Jianping

DOI: https://doi.org/10.1186/s12934-017-0787-5

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Metabolic engineering of Corynebacterium glutamicum for anthocyanin production

Zha, Jian; Zang, Ying; Mattozzi, Matthew D. et al. · 2018

Full title: Metabolic engineering of Corynebacterium glutamicum for anthocyanin production

Authors: Zha, Jian; Zang, Ying; Mattozzi, Matthew D.; Plassmeier, Jens; Gupta, Mamta; Wu, Xia; Clarkson, Sonya M.; Koffas, Mattheos

DOI: https://doi.org/10.1186/s12934-018-0990-z

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Integration of enzyme constraints in a genome-scale metabolic model of Aspergillus niger improves phenotype predictions

Jingru Zhou; Y. Zhuang; Jianye Xia · 2021

Full title: Integration of enzyme constraints in a genome-scale metabolic model of Aspergillus niger improves phenotype predictions

Authors: Jingru Zhou; Y. Zhuang; Jianye Xia

DOI: https://doi.org/10.1186/s12934-021-01614-2

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Shikimic Acid Production in Escherichia coli: From Classical Metabolic Engineering Strategies to Omics Applied to Improve Its Production

Martínez, Juan A.; Bolívar, Francisco; Escalante, Adelfo · 2015

Full title: Shikimic Acid Production in Escherichia coli: From Classical Metabolic Engineering Strategies to Omics Applied to Improve Its Production

Authors: Martínez, Juan A.; Bolívar, Francisco; Escalante, Adelfo

DOI: https://doi.org/10.3389/fbioe.2015.00145

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Systems Biology of Microbial Exopolysaccharides Production

Duru, Özlem Ateş · 2015

Full title: Systems Biology of Microbial Exopolysaccharides Production

Authors: Duru, Özlem Ateş

DOI: https://doi.org/10.3389/fbioe.2015.00200

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Production of 3-Hydroxypropanoic Acid From Glycerol by Metabolically Engineered Bacteria

Carsten Jers; Aida Kalantari; Abhroop Garg et al. · 2019

Full title: Production of 3-Hydroxypropanoic Acid From Glycerol by Metabolically Engineered Bacteria

Authors: Carsten Jers; Aida Kalantari; Abhroop Garg; I. Mijakovic

DOI: https://doi.org/10.3389/fbioe.2019.00124

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Combining metabolite doping and metabolic engineering to improve 2-phenylethanol production by engineered cyanobacteria

Usai, Giulia; Cordara, Alessandro; Re, Angela et al. · 2022

Full title: Combining metabolite doping and metabolic engineering to improve 2-phenylethanol production by engineered cyanobacteria

Authors: Usai, Giulia; Cordara, Alessandro; Re, Angela; Polli, Maria Francesca; Mannino, Giuseppe; Bertea, Cinzia M.; Fino, Debora; Pirri, Candido Fabrizio; Menin, Barbara

DOI: https://doi.org/10.3389/fbioe.2022.1005960

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Engineering Saccharomyces cerevisiae for the Overproduction of β-Ionone and Its Precursor β-Carotene

López, Javiera; Bustos, D.P. Jaramillo; Camilo, Conrado et al. · 2020

Full title: Engineering Saccharomyces cerevisiae for the Overproduction of β-Ionone and Its Precursor β-Carotene

Authors: López, Javiera; Bustos, D.P. Jaramillo; Camilo, Conrado; Arenas, N; Saa, Pedro A.; Agosín, Eduardo

DOI: https://doi.org/10.3389/fbioe.2020.578793

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Microbial Biosynthesis of L-Malic Acid and Related Metabolic Engineering Strategies: Advances and Prospects

Wei, Zhen; Xu, Yongxue; Xu, Qing et al. · 2021

Full title: Microbial Biosynthesis of L-Malic Acid and Related Metabolic Engineering Strategies: Advances and Prospects

Authors: Wei, Zhen; Xu, Yongxue; Xu, Qing; Cao, Wei; Huang, He; Liu, Hao

DOI: https://doi.org/10.3389/fbioe.2021.765685

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Construction and application of the genome-scale metabolic model of Streptomyces radiopugnans

Zhidong Zhang; Qi Guo; Jinyi Qian et al. · 2023

Full title: Construction and application of the genome-scale metabolic model of Streptomyces radiopugnans

Authors: Zhidong Zhang; Qi Guo; Jinyi Qian; Chao Ye; He Huang

DOI: https://doi.org/10.3389/fbioe.2023.1108412

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Opportunities at the Interface of Network Science and Metabolic Modeling

Dusad, Varshit; Thiel, Denise; Barahona, Mauricio et al. · 2021

Full title: Opportunities at the Interface of Network Science and Metabolic Modeling

Authors: Dusad, Varshit; Thiel, Denise; Barahona, Mauricio; Keun, Hector C.; Oyarzún, Diego A.

DOI: https://doi.org/10.3389/fbioe.2020.591049

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Production of biopolymer precursors beta-alanine and L-lactic acid from CO2 with metabolically versatile Rhodococcus opacus DSM 43205

Salusjärvi, Laura; Ojala, Leo S.; Gopalacharyulu, Peddinti et al. · 2022

Full title: Production of biopolymer precursors beta-alanine and L-lactic acid from CO2 with metabolically versatile Rhodococcus opacus DSM 43205

Authors: Salusjärvi, Laura; Ojala, Leo S.; Gopalacharyulu, Peddinti; Lienemann, Michael; Jouhten, Paula; Pitkänen, Juha‐Pekka; Toivari, Mervi

DOI: https://doi.org/10.3389/fbioe.2022.989481

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Perspectives and Challenges in Microbial Communities Metabolic Modeling

Bosi, Emanuele; Bacci, Giovanni; Mengoni, Alessio et al. · 2017

Full title: Perspectives and Challenges in Microbial Communities Metabolic Modeling

Authors: Bosi, Emanuele; Bacci, Giovanni; Mengoni, Alessio; Fondi, Marco

DOI: https://doi.org/10.3389/fgene.2017.00088

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Multi-scale models of whole cells: progress and challenges

Georgouli, Konstantia; Yeom, Jae-Seung; Blake, Robert C. et al. · 2023

Full title: Multi-scale models of whole cells: progress and challenges

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DOI: https://doi.org/10.3389/fcell.2023.1260507

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Integration of Proteomics and Metabolomics Into the Design, Build, Test, Learn Cycle to Improve 3-Hydroxypropionic Acid Production in Aspergillus pseudoterreus

Pomraning, Kyle; Dai, Ziyu; Munoz, Nathalie Munoz et al. · 2021

Full title: Integration of Proteomics and Metabolomics Into the Design, Build, Test, Learn Cycle to Improve 3-Hydroxypropionic Acid Production in Aspergillus pseudoterreus

DOI: https://doi.org/10.3389/fbioe.2021.603832

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Characterization of the enzyme kinetics of EMP and HMP pathway in Corynebacterium glutamicum: reference for modeling metabolic networks

Liu, Yang; Li, Xia; Zhang, Yaping et al. · 2023

Full title: Characterization of the enzyme kinetics of EMP and HMP pathway in Corynebacterium glutamicum: reference for modeling metabolic networks

Authors: Liu, Yang; Li, Xia; Zhang, Yaping; Chen, Linlin; Ouyang, Zhilin; Liao, Daocheng; Zhao, Fengguang; Han, Shuangyan

DOI: https://doi.org/10.3389/fbioe.2023.1296880

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RobOKoD: microbial strain design for (over)production of target compounds

Stanford, Natalie; Millard, Pierre; Swainston, Neil · 2015

Full title: RobOKoD: microbial strain design for (over)production of target compounds

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DOI: https://doi.org/10.3389/fcell.2015.00017

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Modeling the Metabolism of Arabidopsis thaliana: Application of Network Decomposition and Network Reduction in the Context of Petri Nets

Koch, Ina; Nöthen, J.; Schleiff, Enrico · 2017

Full title: Modeling the Metabolism of Arabidopsis thaliana: Application of Network Decomposition and Network Reduction in the Context of Petri Nets

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DOI: https://doi.org/10.3389/fgene.2017.00085

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Metabolic analyses elucidate non-trivial gene targets for amplifying dihydroartemisinic acid production in yeast

Misra, Ashish; Conway, Matthew F.; Johnnie, Joseph et al. · 2013

Full title: Metabolic analyses elucidate non-trivial gene targets for amplifying dihydroartemisinic acid production in yeast

Authors: Misra, Ashish; Conway, Matthew F.; Johnnie, Joseph; Qureshi, Tabish M.; Lige, Bao; Derrick, Anne M.; Agbo, Eddy C.; Sriram, Ganesh

DOI: https://doi.org/10.3389/fmicb.2013.00200

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Data-driven integration of genome-scale regulatory and metabolic network models

Imam, Saheed; Schäuble, Sascha; Brooks, Aaron N. et al. · 2015

Full title: Data-driven integration of genome-scale regulatory and metabolic network models

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DOI: https://doi.org/10.3389/fmicb.2015.00409

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Synthetic biology of cyanobacteria: unique challenges and opportunities

Berla, Bertram M.; Saha, Rajib; Immethun, Cheryl M. et al. · 2013

Full title: Synthetic biology of cyanobacteria: unique challenges and opportunities

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DOI: https://doi.org/10.3389/fmicb.2013.00246

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Challenges and Advances for Genetic Engineering of Non-model Bacteria and Uses in Consolidated Bioprocessing

Yan, Qiang; Fong, Stephen S. · 2017

Full title: Challenges and Advances for Genetic Engineering of Non-model Bacteria and Uses in Consolidated Bioprocessing

Authors: Yan, Qiang; Fong, Stephen S.

DOI: https://doi.org/10.3389/fmicb.2017.02060

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Modeling of Zymomonas mobilis central metabolism for novel metabolic engineering strategies

Kalnenieks, Uldis; Pentjuss, Agris; Rutkis, Reinis et al. · 2014

Full title: Modeling of Zymomonas mobilis central metabolism for novel metabolic engineering strategies

Authors: Kalnenieks, Uldis; Pentjuss, Agris; Rutkis, Reinis; Stalidzāns, Egils; Fell, David A.

DOI: https://doi.org/10.3389/fmicb.2014.00042

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Wang, Yali; Xu, Nan; Ye, Chao et al. · 2015

Full title: Reconstruction and in silico analysis of an Actinoplanes sp. SE50/110 genome-scale metabolic model for acarbose production

Authors: Wang, Yali; Xu, Nan; Ye, Chao; Liu, Li; Shi, Zhongping; Wu, Jing

DOI: https://doi.org/10.3389/fmicb.2015.00632

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Genome-Scale Reconstruction of the Metabolic Network in Oenococcus oeni to Assess Wine Malolactic Fermentation

Mendoza, Sebastián N.; Cañón, Pablo; Contreras, Ángela et al. · 2017

Full title: Genome-Scale Reconstruction of the Metabolic Network in Oenococcus oeni to Assess Wine Malolactic Fermentation

Authors: Mendoza, Sebastián N.; Cañón, Pablo; Contreras, Ángela; Ribbeck, Magdalena; Agosín, Eduardo

DOI: https://doi.org/10.3389/fmicb.2017.00534

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Timm, Collin M.; Campbell, Alisha G.; Utturkar, Sagar M. et al. · 2015

Full title: Metabolic functions of Pseudomonas fluorescens strains from Populus deltoides depend on rhizosphere or endosphere isolation compartment

DOI: https://doi.org/10.3389/fmicb.2015.01118

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A Bayesian Framework for the Classification of Microbial Gene Activity States

Disselkoen, Craig; Greco, Brian; Cook, Kaitlyn et al. · 2016

Full title: A Bayesian Framework for the Classification of Microbial Gene Activity States

DOI: https://doi.org/10.3389/fmicb.2016.01191

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Metabolic Engineering of Oleaginous Yeasts for Production of Fuels and Chemicals

Shi, Shuobo; Zhao, Huimin · 2017

Full title: Metabolic Engineering of Oleaginous Yeasts for Production of Fuels and Chemicals

Authors: Shi, Shuobo; Zhao, Huimin

DOI: https://doi.org/10.3389/fmicb.2017.02185

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Network Analyses in Plant Pathogens

Botero, David; Alvarado, Camilo; Bernal, Adriana et al. · 2018

Full title: Network Analyses in Plant Pathogens

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DOI: https://doi.org/10.3389/fmicb.2018.00035

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Simulation of Escherichia coli Dynamics in Biofilms and Submerged Colonies with an Individual-Based Model Including Metabolic Network Information

Tack, Ignace; Nimmegeers, Philippe; Akkermans, Simen et al. · 2017

Full title: Simulation of Escherichia coli Dynamics in Biofilms and Submerged Colonies with an Individual-Based Model Including Metabolic Network Information

Authors: Tack, Ignace; Nimmegeers, Philippe; Akkermans, Simen; Hashem, Ihab; Impe, Jan Van

DOI: https://doi.org/10.3389/fmicb.2017.02509

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Lipid Metabolic Versatility in Malassezia spp. Yeasts Studied through Metabolic Modeling

Triana, Sergio; Cock, Hans de; Ohm, Robin A. et al. · 2017

Full title: Lipid Metabolic Versatility in Malassezia spp. Yeasts Studied through Metabolic Modeling

Authors: Triana, Sergio; Cock, Hans de; Ohm, Robin A.; Danies, Giovanna; Wösten, Han A. B.; Restrepo, Silvia; Barrios, Andrés Fernando González; Ramírez, Adriana Marcela Celis

DOI: https://doi.org/10.3389/fmicb.2017.01772

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Time-Resolved Transcriptomics and Constraint-Based Modeling Identify System-Level Metabolic Features and Overexpression Targets to Increase Spiramycin Production in Streptomyces ambofaciens

Fondi, Marco; Pinatel, Eva; Talà, Adelfia et al. · 2017

DOI: https://doi.org/10.3389/fmicb.2017.00835

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Identification of FadAB Complexes Involved in Fatty Acid β-Oxidation in Streptomyces coelicolor and Construction of a Triacylglycerol Overproducing strain

Menéndez-Bravo, Simón; Paganini, Julián; Avignone–Rossa, Claudio et al. · 2017

Full title: Identification of FadAB Complexes Involved in Fatty Acid β-Oxidation in Streptomyces coelicolor and Construction of a Triacylglycerol Overproducing strain

Authors: Menéndez-Bravo, Simón; Paganini, Julián; Avignone–Rossa, Claudio; Gramajo, Hugo; Arabolaza, Ana

DOI: https://doi.org/10.3389/fmicb.2017.01428

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Cortés, María Paz; Mendoza, Sebastián N.; Travisany, Dante et al. · 2017

Full title: Analysis of Piscirickettsia salmonis Metabolism Using Genome-Scale Reconstruction, Modeling, and Testing

Authors: Cortés, María Paz; Mendoza, Sebastián N.; Travisany, Dante; Gaete, Alexis; Siegel, Anne; Cambiazo, Verónica; Maass, Alejandro

DOI: https://doi.org/10.3389/fmicb.2017.02462

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Joseph, Jewel Ann; Akkermans, Simen; Nimmegeers, Philippe et al. · 2019

Full title: Bioproduction of the Recombinant Sweet Protein Thaumatin: Current State of the Art and Perspectives

Authors: Joseph, Jewel Ann; Akkermans, Simen; Nimmegeers, Philippe; Impe, Jan Van

DOI: https://doi.org/10.3389/fmicb.2019.00695

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Physiological Response of Corynebacterium glutamicum to Increasingly Nutrient-Rich Growth Conditions

Graf, Michaela; Zieringer, Julia; Haas, Thorsten et al. · 2018

Full title: Physiological Response of Corynebacterium glutamicum to Increasingly Nutrient-Rich Growth Conditions

Authors: Graf, Michaela; Zieringer, Julia; Haas, Thorsten; Nieß, Alexander; Blombach, Bastian; Takors, Ralf

DOI: https://doi.org/10.3389/fmicb.2018.02058

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The Genome-Scale Integrated Networks in Microorganisms

Hao, Tong; Wu, Dan; Zhao, Lingxuan et al. · 2018

Full title: The Genome-Scale Integrated Networks in Microorganisms

Authors: Hao, Tong; Wu, Dan; Zhao, Lingxuan; Wang, Qian; Wang, Edwin; Sun, Jinsheng

DOI: https://doi.org/10.3389/fmicb.2018.00296

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Bryant, William A; Stentz, Régis; Gall, Gwénaëlle Le et al. · 2017

Full title: In Silico Analysis of the Small Molecule Content of Outer Membrane Vesicles Produced by Bacteroides thetaiotaomicron Indicates an Extensive Metabolic Link between Microbe and Host

Authors: Bryant, William A; Stentz, Régis; Gall, Gwénaëlle Le; Sternberg, Michael J.E.; Carding, Simon R.; Wilhelm, Thomas

DOI: https://doi.org/10.3389/fmicb.2017.02440

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Ponce-de-León, Miguel; Tamarit, Daniel; Calle-Espinosa, Jorge et al. · 2017

Full title: Determinism and Contingency Shape Metabolic Complementation in an Endosymbiotic Consortium

Authors: Ponce-de-León, Miguel; Tamarit, Daniel; Calle-Espinosa, Jorge; Mori, Matteo; Latorre, Amparo; Montero, Francisco; Peretό, Juli

DOI: https://doi.org/10.3389/fmicb.2017.02290

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Ma, Zhongbao; Ye, Chao; Deng, Wei‐Wei et al. · 2018

Full title: Reconstruction and Analysis of a Genome-Scale Metabolic Model of Ganoderma lucidum for Improved Extracellular Polysaccharide Production

Authors: Ma, Zhongbao; Ye, Chao; Deng, Wei‐Wei; Xu, Mengmeng; Wang, Qiong; Liu, Gao‐Qiang; Wang, Feng; Liu, Li; Xu, Zhenghong; Shi, Guiyang; Ding, Zhongyang

DOI: https://doi.org/10.3389/fmicb.2018.03076

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Approaches to Computational Strain Design in the Multiomics Era

John, Peter C. St.; Bomble, Yannick J. · 2019

Full title: Approaches to Computational Strain Design in the Multiomics Era

Authors: John, Peter C. St.; Bomble, Yannick J.

DOI: https://doi.org/10.3389/fmicb.2019.00597

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Störiko, Anna; Pagel, Holger; Mellage, Adrian et al. · 2021

Full title: Does It Pay Off to Explicitly Link Functional Gene Expression to Denitrification Rates in Reaction Models?

Authors: Störiko, Anna; Pagel, Holger; Mellage, Adrian; Cirpka, Olaf A.

DOI: https://doi.org/10.3389/fmicb.2021.684146

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Dias, Óscar; Saraiva, J.; Faria, Cristiana et al. · 2019

Full title: iDS372, a Phenotypically Reconciled Model for the Metabolism of Streptococcus pneumoniae Strain R6

Authors: Dias, Óscar; Saraiva, J.; Faria, Cristiana; Ramirez, Mário; Pinto, Francisco; Rocha, Isabel

DOI: https://doi.org/10.3389/fmicb.2019.01283

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Fang, Xin; Monk, Jonathan M.; Nurk, Sergey et al. · 2018

Full title: Metagenomics-Based, Strain-Level Analysis of Escherichia coli From a Time-Series of Microbiome Samples From a Crohn's Disease Patient

DOI: https://doi.org/10.3389/fmicb.2018.02559

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Ezzamouri, Bouchra; Shoaie, Saeed; Ledesma‐Amaro, Rodrigo · 2021

Full title: Synergies of Systems Biology and Synthetic Biology in Human Microbiome Studies

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DOI: https://doi.org/10.3389/fmicb.2021.681982

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Rizvi, Arshad; Shankar, Arvind Jaya; Chatterjee, A. et al. · 2019

Full title: Rewiring of Metabolic Network in Mycobacterium tuberculosis During Adaptation to Different Stresses

DOI: https://doi.org/10.3389/fmicb.2019.02417

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Liu, Jianming; Chan, Siu Hung Joshua; Chen, Jun et al. · 2019

Full title: Systems Biology – A Guide for Understanding and Developing Improved Strains of Lactic Acid Bacteria

Authors: Liu, Jianming; Chan, Siu Hung Joshua; Chen, Jun; Solem, Christian; Jensen, Peter Ruhdal

DOI: https://doi.org/10.3389/fmicb.2019.00876

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Full title: Uncovering the Role of Metabolism in Oomycete–Host Interactions Using Genome-Scale Metabolic Models

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DOI: https://doi.org/10.3389/fmicb.2021.748178

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Reconstructed Metabolic Network Models Predict Flux-Level Metabolic Reprogramming in Glioblastoma

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Full title: Reconstructed Metabolic Network Models Predict Flux-Level Metabolic Reprogramming in Glioblastoma

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Authors: Sun, Jun; Sayyar, Bahareh; Butler, Jessica; Pharkya, Priti; Fahland, Tom R; Famili, Iman; Schilling, Christophe H.; Lovley, Derek R.; Mahadevan, Radhakrishnan

DOI: https://doi.org/10.1186/1752-0509-3-15

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Park, Jong Myoung; Kim, Tae Yong; Lee, Sang Yup · 2011

Full title: Genome-scale reconstruction and in silico analysis of the Ralstonia eutropha H16 for polyhydroxyalkanoate synthesis, lithoautotrophic growth, and 2-methyl citric acid production

Authors: Park, Jong Myoung; Kim, Tae Yong; Lee, Sang Yup

DOI: https://doi.org/10.1186/1752-0509-5-101

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Full title: Reconstruction and analysis of genome-scale metabolic model of a photosynthetic bacterium

Authors: Montagud, Arnau; Navarro, Emilio; Córdoba, Pedro Fernández de; Urchueguía, Javier F.; Patil, Kiran Raosaheb

DOI: https://doi.org/10.1186/1752-0509-4-156

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Zomorrodi, Ali R.; Maranas, Costas D. · 2010

Full title: Improving the iMM904 S. cerevisiae metabolic model using essentiality and synthetic lethality data

Authors: Zomorrodi, Ali R.; Maranas, Costas D.

DOI: https://doi.org/10.1186/1752-0509-4-178

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Radrich, Karin; Tsuruoka, Yoshimasa; Dobson, Paul D. et al. · 2010

Full title: Integration of metabolic databases for the reconstruction of genome-scale metabolic networks

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Sun, Jun; Haveman, Shelley A.; Bui, Olivia et al. · 2010

Full title: Constraint-based modeling analysis of the metabolism of two Pelobacter species

Authors: Sun, Jun; Haveman, Shelley A.; Bui, Olivia; Fahland, Tom R; Lovley, Derek R.

DOI: https://doi.org/10.1186/1752-0509-4-174

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Mo, Monica L.; Palsson, Bernhard Ø.; Herrgård, Markus J. · 2009

Full title: Connecting extracellular metabolomic measurements to intracellular flux states in yeast

Authors: Mo, Monica L.; Palsson, Bernhard Ø.; Herrgård, Markus J.

DOI: https://doi.org/10.1186/1752-0509-3-37

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Plaimas, Kitiporn; Mallm, Jan‐Philipp; Oswald, Marcus et al. · 2008

Full title: Machine learning based analyses on metabolic networks supports high-throughput knockout screens

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DOI: https://doi.org/10.1186/1752-0509-2-67

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Fang, Xin; Wallqvist, Anders; Reifman, Jaques · 2009

Full title: A systems biology framework for modeling metabolic enzyme inhibition of Mycobacterium tuberculosis

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DOI: https://doi.org/10.1186/1752-0509-3-92

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Imam, Saheed; Yılmaz, Şafak; Sohmen, Ugur et al. · 2011

Full title: iRsp1095: A genome-scale reconstruction of the Rhodobacter sphaeroides metabolic network

Authors: Imam, Saheed; Yılmaz, Şafak; Sohmen, Ugur; Gorzalski, Alexander S.; Reed, Jennifer L.; Noguera, Daniel R.; Donohue, Timothy J.

DOI: https://doi.org/10.1186/1752-0509-5-116

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Tzamali, Eleftheria; Poirazi, Panayiota; Tollis, Ioannis G. et al. · 2011

Full title: A computational exploration of bacterial metabolic diversity identifying metabolic interactions and growth-efficient strain communities

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DOI: https://doi.org/10.1186/1752-0509-5-167

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Rocha, Isabel; Maia, Paulo; Evangelista, Pedro et al. · 2010

Full title: OptFlux: an open-source software platform for in silico metabolic engineering

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DOI: https://doi.org/10.1186/1752-0509-4-45

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Duru, Özlem Ateş; Öner, Ebru Toksoy; Arğa, Kazım Yalçın · 2011

Full title: Genome-scale reconstruction of metabolic network for a halophilic extremophile, Chromohalobacter salexigens DSM 3043

Authors: Duru, Özlem Ateş; Öner, Ebru Toksoy; Arğa, Kazım Yalçın

DOI: https://doi.org/10.1186/1752-0509-5-12

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Boyle, Nanette; Morgan, John A. · 2009

Full title: Flux balance analysis of primary metabolism in Chlamydomonas reinhardtii

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DOI: https://doi.org/10.1186/1752-0509-3-4

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Sigurðsson, Martin I.; Jamshidi, Neema; Steingrı́msson, Eirı́kur et al. · 2010

Full title: A detailed genome-wide reconstruction of mouse metabolism based on human Recon 1

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DOI: https://doi.org/10.1186/1752-0509-4-140

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Raghunathan, Anu; Shin, Sookil; Daefler, Simon · 2010

Full title: Systems approach to investigating host-pathogen interactions in infections with the biothreat agent Francisella. Constraints-based model of Francisella tularensis

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DOI: https://doi.org/10.1186/1752-0509-4-118

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Roberts, Seth B.; Gowen, Christopher M.; Brooks, J. Paul et al. · 2010

Full title: Genome-scale metabolic analysis of Clostridium thermocellum for bioethanol production

Authors: Roberts, Seth B.; Gowen, Christopher M.; Brooks, J. Paul; Fong, Stephen S.

DOI: https://doi.org/10.1186/1752-0509-4-31

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Roberts, Seth B.; Robichaux, Jennifer L; Chavali, Arvind K. et al. · 2009

Full title: Proteomic and network analysis characterize stage-specific metabolism in Trypanosoma cruzi

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DOI: https://doi.org/10.1186/1752-0509-3-52

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Fang, Xin; Wallqvist, Anders; Reifman, Jaques · 2010

Full title: Development and analysis of an in vivo-compatible metabolic network of Mycobacterium tuberculosis

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DOI: https://doi.org/10.1186/1752-0509-4-160

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Full title: Microarray data can predict diurnal changes of starch content in the picoalga Ostreococcus

Authors: Sorokina, Oksana; Corellou, Florence; Dauvillée, David; Sorokin, Anatoly; Goryanin, Igor; Ball, Steven; Bouget, François‐Yves; Millar, Andrew J.

DOI: https://doi.org/10.1186/1752-0509-5-36

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Milne, Caroline B.; Eddy, James A.; Raju, Ravali et al. · 2011

Full title: Metabolic network reconstruction and genome-scale model of butanol-producing strain Clostridium beijerinckii NCIMB 8052

Authors: Milne, Caroline B.; Eddy, James A.; Raju, Ravali; Ardekani, Soroush; Kim, Pan‐Jun; Senger, Ryan S.; Jin, Yong‐Su; Blaschek, Hans P.; Price, Nathan D.

DOI: https://doi.org/10.1186/1752-0509-5-130

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Full title: Expanding a dynamic flux balance model of yeast fermentation to genome-scale

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DOI: https://doi.org/10.1186/1752-0509-5-75

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Full title: Systems biology of bacterial nitrogen fixation: High-throughput technology and its integrative description with constraint-based modeling

Authors: Reséndis-Antonio, Osbaldo; Hernández, Magdalena; Salazar, Emmanuel; Contreras, Sandra; Batallar, G. Martínez; Mora, Yolanda; Encarnación‐Guevara, Sergio

DOI: https://doi.org/10.1186/1752-0509-5-120

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Byrne, David; Dumitriu, Alexandra; Segrè, Daniel · 2012

Full title: Comparative multi-goal tradeoffs in systems engineering of microbial metabolism

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DOI: https://doi.org/10.1186/1752-0509-6-127

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Baumler, David J.; Peplinski, Roman G; Reed, Jennifer L. et al. · 2011

Full title: The evolution of metabolic networks of E. coli

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DOI: https://doi.org/10.1186/1752-0509-5-182

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Carbonell, Pablo; Planson, Anne‐Gaëlle; Fichera, Davide et al. · 2011

Full title: A retrosynthetic biology approach to metabolic pathway design for therapeutic production

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DOI: https://doi.org/10.1186/1752-0509-5-122

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Fang, Kechi; Zhao, Hansheng; Sun, Changyue et al. · 2011

Full title: Exploring the metabolic network of the epidemic pathogen Burkholderia cenocepacia J2315 via genome-scale reconstruction

Authors: Fang, Kechi; Zhao, Hansheng; Sun, Changyue; Lam, Carolyn MC; Chang, Suhua; Zhang, Kunlin; Panda, Gurudutta; Godinho, Miguel; Santos, Vítor A. P. Martins dos; Wang, Jing

DOI: https://doi.org/10.1186/1752-0509-5-83

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Full title: Flux variability scanning based on enforced objective flux for identifying gene amplification targets

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DOI: https://doi.org/10.1186/1752-0509-6-106

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Kleeßen, Sabrina; Nikoloski, Zoran · 2012

Full title: Dynamic regulatory on/off minimization for biological systems under internal temporal perturbations

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DOI: https://doi.org/10.1186/1752-0509-6-16

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Heavner, Ben; Smallbone, Kieran; Barker, Brandon et al. · 2012

Full title: Yeast 5 – an expanded reconstruction of the Saccharomyces cerevisiae metabolic network

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DOI: https://doi.org/10.1186/1752-0509-6-55

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Rohn, Hendrik; Junker, Astrid; Hartmann, Anja et al. · 2012

Full title: VANTED v2: a framework for systems biology applications

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DOI: https://doi.org/10.1186/1752-0509-6-139

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Hoek, Milan JA van; Merks, Roeland M. H. · 2012

Full title: Redox balance is key to explaining full vs. partial switching to low-yield metabolism

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DOI: https://doi.org/10.1186/1752-0509-6-22

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Töpfer, Nadine; Jozefczuk, Szymon; Nikoloski, Zoran · 2012

Full title: Integration of time-resolved transcriptomics data with flux-based methods reveals stress-induced metabolic adaptation in Escherichia coli

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DOI: https://doi.org/10.1186/1752-0509-6-148

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Navid, Ali; Almaas, Eivind · 2012

Full title: Genome-level transcription data of Yersinia pestis analyzed with a New metabolic constraint-based approach

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DOI: https://doi.org/10.1186/1752-0509-6-150

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Loira, Nicolás; Dulermo, Thierry; Nicaud, Jean‐Marc et al. · 2012

Full title: A genome-scale metabolic model of the lipid-accumulating yeast Yarrowia lipolytica

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DOI: https://doi.org/10.1186/1752-0509-6-35

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McAnulty, Michael J.; Yen, Jiun Y.; Freedman, Benjamin G. et al. · 2012

Full title: Genome-scale modeling using flux ratio constraints to enable metabolic engineering of clostridial metabolism in silico

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DOI: https://doi.org/10.1186/1752-0509-6-42

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Carinhas, Nuno; Bernal, Vicente; Teixeira, Ana P. et al. · 2011

Full title: Hybrid metabolic flux analysis: combining stoichiometric and statistical constraints to model the formation of complex recombinant products

Authors: Carinhas, Nuno; Bernal, Vicente; Teixeira, Ana P.; Carrondo, Manuel J.T.; Alves, Paula M.; Oliveira, Rui

DOI: https://doi.org/10.1186/1752-0509-5-34

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DOI: https://doi.org/10.1186/1752-0509-6-33

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Bazzani, Susanna; Hoppe, Andreas; Holzhütter, Hermann−Georg · 2012

Full title: Network-based assessment of the selectivity of metabolic drug targets in Plasmodium falciparum with respect to human liver metabolism

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DOI: https://doi.org/10.1186/1752-0509-6-118

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Full title: Genome-scale metabolic model of the fission yeast Schizosaccharomyces pombe and the reconciliation of in silico/in vivo mutant growth

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DOI: https://doi.org/10.1186/1752-0509-6-49

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Riemer, S. Alexander; Rex, René; Schomburg, Dietmar · 2013

Full title: A metabolite-centric view on flux distributions in genome-scale metabolic models

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DOI: https://doi.org/10.1186/1752-0509-7-33

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Lee, Dave; Smallbone, Kieran; Dunn, Warwick B et al. · 2012

Full title: Improving metabolic flux predictions using absolute gene expression data.

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DOI: https://doi.org/10.1186/1752-0509-6-73

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Full title: MC3: a steady-state model and constraint consistency checker for biochemical networks

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DOI: https://doi.org/10.1186/1752-0509-7-129

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Full title: Mapping global effects of the anti-sigma factor MucA in Pseudomonas fluorescens SBW25 through genome-scale metabolic modeling

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DOI: https://doi.org/10.1186/1752-0509-7-19

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Full title: Genome-scale metabolic reconstructions of Pichia stipitis and Pichia pastoris and in silico evaluation of their potentials

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DOI: https://doi.org/10.1186/1752-0509-6-24

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Full title: MicrobesFlux: a web platform for drafting metabolic models from the KEGG database

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DOI: https://doi.org/10.1186/1752-0509-6-94

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Full title: Glucose-methanol co-utilization in Pichia pastoris studied by metabolomics and instationary 13C flux analysis

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DOI: https://doi.org/10.1186/1752-0509-7-17

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Full title: i AK692: A genome-scale metabolic model of Spirulina platensis C1

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DOI: https://doi.org/10.1186/1752-0509-6-71

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Full title: Inferring ancient metabolism using ancestral core metabolic models of enterobacteria

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DOI: https://doi.org/10.1186/1752-0509-7-46

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Full title: Understanding the metabolism of the tetralin degrader Sphingopyxis granuli strain TFA through genome-scale metabolic modelling

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