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Reproducibility Of Flux Balance Analysis Fba Predi

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Paper Monitoring and modelling the glutamine metabolic pathway: a review and future perspectives
Mirveis, Zohreh; Howe, Orla; Cahill, Paul A. et al. · 2023 · Metabolomics · DOI
Full title: Monitoring and modelling the glutamine metabolic pathway: a review and future perspectives
Authors: Mirveis, Zohreh; Howe, Orla; Cahill, Paul A.; Patil, Nitin; Byrne, Hugh J.
Year: 2023
Venue: Metabolomics
Paper Towards industrial biological hydrogen production: a review
Teke, George M.; Cho, Bovinille Anye; Bosman, Catharine Elizabeth et al. · 2023 · World Journal of Microbiology and Biotechnology · DOI
Full title: Towards industrial biological hydrogen production: a review
Authors: Teke, George M.; Cho, Bovinille Anye; Bosman, Catharine Elizabeth; Mapholi, Zwonaka; Zhang, Dongda; Pott, Robert W. M.
Year: 2023
Venue: World Journal of Microbiology and Biotechnology
Paper Unbiased metabolic flux inference through combined thermodynamic and 13 C flux analysis
Saldida, Joana; Muntoni, Anna Paola; Martino, Daniele De et al. · 2020 · DOI
Full title: Unbiased metabolic flux inference through combined thermodynamic and 13 C flux analysis
Authors: Saldida, Joana; Muntoni, Anna Paola; Martino, Daniele De; Hubmann, Georg; Niebel, Bastian; Schmidt, Anna Mareike; Braunstein, Alfredo; Milias‐Argeitis, Andreas; Heinemann, Matthias
Year: 2020
Paper A graph neural network model to estimate cell-wise metabolic flux using single cell RNA-seq data
Alghamdi, Norah; Chang, Wennan; Dang, Pengtao et al. · 2020 · DOI
Full title: A graph neural network model to estimate cell-wise metabolic flux using single cell RNA-seq data
Authors: Alghamdi, Norah; Chang, Wennan; Dang, Pengtao; Lu, Xiaoyu; Wan, Changlin; Gampala, Silpa; Huang, Zhi; Wang, Jiashi; Ma, Qin; Zang, Yong; Fishel, Melissa L.; Cao, Sha; Zhang, Chi
Year: 2020
Paper Genomic and metabolic plasticity drive alternative scenarios for adapting <i>Pseudomonas putida</i> to non-native substrate D-xylose
Dvořák, Pavel; Burýšková, Barbora; Popelářová, Barbora et al. · 2023 · DOI
Full title: Genomic and metabolic plasticity drive alternative scenarios for adapting <i>Pseudomonas putida</i> to non-native substrate D-xylose
Authors: Dvořák, Pavel; Burýšková, Barbora; Popelářová, Barbora; Ebert, Birgitta E.; Botka, Tibor; Bujdoš, Dalimil; Sánchez-Pascuala, Alberto; Schöttler, Hannah; Hayen, Heiko; Lorenzo, Vı́ctor de; Blank, Lars M.; Benešík, Martin
Year: 2023
Paper A method to identify high consensus predictions of single-cell metabolic flux
Amiss, Michael; Lum, Julian J.; Jabbari, Hosna · 2024 · DOI
Full title: A method to identify high consensus predictions of single-cell metabolic flux
Authors: Amiss, Michael; Lum, Julian J.; Jabbari, Hosna
Year: 2024
Paper A diel multi-tissue genome-scale metabolic model of Vitis vinifera
Sampaio, Marta; Rocha, Miguel; Dias, Óscar · 2024 · DOI
Full title: A diel multi-tissue genome-scale metabolic model of Vitis vinifera
Authors: Sampaio, Marta; Rocha, Miguel; Dias, Óscar
Year: 2024
Paper Simulation of biochemical systems using constraint-based methods and complex networks
Burke, Paulo E. P. · 2021 · DOI
Full title: Simulation of biochemical systems using constraint-based methods and complex networks
Authors: Burke, Paulo E. P.
Year: 2021
Paper A framework for evolutionary systems biology
Loewe, Laurence · 2009 · BMC Systems Biology · DOI
Full title: A framework for evolutionary systems biology
Authors: Loewe, Laurence
Year: 2009
Venue: BMC Systems Biology
Paper Métodos numéricos para modelos de redes metabólicas.
Oliveira, Rafael David de · 2022 · DOI
Full title: Métodos numéricos para modelos de redes metabólicas.
Authors: Oliveira, Rafael David de
Year: 2022
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
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 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
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
Paper Transcriptional landscapes of lipid producing microalgae
Carrères, Benoît M. · 2019 · DOI
Full title: Transcriptional landscapes of lipid producing microalgae
Authors: Carrères, Benoît M.
Year: 2019
Paper Model-driven design of Mycoplasma as a vaccine chassis
Gaspari, Erika · 2021 · DOI
Full title: Model-driven design of Mycoplasma as a vaccine chassis
Authors: Gaspari, Erika
Year: 2021
Paper Microbiome.config : Deciphering microbial lifestyles for rational design of plant growth promoting communities
Poncheewin, Wasin · 2022 · DOI
Full title: Microbiome.config : Deciphering microbial lifestyles for rational design of plant growth promoting communities
Authors: Poncheewin, Wasin
Year: 2022
Paper Enzyme promiscuity approaches to predict metabolic pathways in the human gut microbiota.
Balzerani, Francesco · 2023 · DOI
Full title: Enzyme promiscuity approaches to predict metabolic pathways in the human gut microbiota.
Authors: Balzerani, Francesco
Year: 2023
Paper Metabolic modelling approaches for describing and engineering microbial communities
García-Jiménez, Beatriz; Torres‐Bacete, Jesús; Nogales, Juan · 2020 · Computational and Structural Biotechnology Journal · DOI
Full title: Metabolic modelling approaches for describing and engineering microbial communities
Authors: García-Jiménez, Beatriz; Torres‐Bacete, Jesús; Nogales, Juan
Year: 2020
Venue: Computational and Structural Biotechnology Journal
Paper Microbiome Modeling: A Beginner’s Guide
Lange, Emanuel; Kranert, Lena; Krüger, Jacob et al. · 2024 · Preprints.org · DOI
Full title: Microbiome Modeling: A Beginner’s Guide
Authors: Lange, Emanuel; Kranert, Lena; Krüger, Jacob; Benndorf, Dirk; Heyer, Robert
Year: 2024
Venue: Preprints.org
Paper Experimental Definition and Validation of Protein Coding Transcripts in Chlamydomonas reinhardtii
Salehi‐Ashtiani, Kourosh; Papin, Jason A. · 2012 · DOI
Full title: Experimental Definition and Validation of Protein Coding Transcripts in Chlamydomonas reinhardtii
Authors: Salehi‐Ashtiani, Kourosh; Papin, Jason A.
Year: 2012
Paper Model-Based Hypothesis Testing in Biomedicine : How Systems Biology Can Drive the Growth of Scientific Knowledge
Johansson, Rikard · 2017 · Linköping studies in science and technology. Dissertations · DOI
Full title: Model-Based Hypothesis Testing in Biomedicine : How Systems Biology Can Drive the Growth of Scientific Knowledge
Authors: Johansson, Rikard
Year: 2017
Venue: Linköping studies in science and technology. Dissertations
Paper Developments in the Tools and Methodologies of Synthetic Biology
Kelwick, Richard; MacDonald, James T.; Webb, Alexander J. et al. · 2014 · Frontiers in Bioengineering and Biotechnology · DOI
Full title: Developments in the Tools and Methodologies of Synthetic Biology
Authors: Kelwick, Richard; MacDonald, James T.; Webb, Alexander J.; Freemont, Paul S.
Year: 2014
Venue: Frontiers in Bioengineering and Biotechnology
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
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
Paper Cancer cell growth and survival as a system-level property sustained by enhanced glycolysis and mitochondrial metabolic remodeling
Alberghina, Lilia; Gaglio, Daniela; Gelfi, Cecilia et al. · 2012 · Frontiers in Physiology · DOI
Full title: Cancer cell growth and survival as a system-level property sustained by enhanced glycolysis and mitochondrial metabolic remodeling
Authors: Alberghina, Lilia; Gaglio, Daniela; Gelfi, Cecilia; Moresco, Rosa Maria; Mauri, Giancarlo; Bertolazzi, Paola; Messa, Cristina; Gilardi, Maria Carla; Chiaradonna, Ferdinando; Vanoni, Marco
Year: 2012
Venue: Frontiers in Physiology
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
Paper Genome-Scale Reconstruction of Microbial Dynamic Phenotype: Successes and Challenges
Panikov, Nicolai · 2021 · Microorganisms · DOI
Full title: Genome-Scale Reconstruction of Microbial Dynamic Phenotype: Successes and Challenges
Authors: Panikov, Nicolai
Year: 2021
Venue: Microorganisms
Paper Modelling Cell Metabolism: A Review on Constraint-Based Steady-State and Kinetic Approaches
Yasemi, Mohammadreza; Jolicœur, Mario · 2021 · Processes · DOI
Full title: Modelling Cell Metabolism: A Review on Constraint-Based Steady-State and Kinetic Approaches
Authors: Yasemi, Mohammadreza; Jolicœur, Mario
Year: 2021
Venue: Processes
Paper Computational Studies on Cellular Metabolism : From Biochemical Pathways to Complex Metabolic Networks
Hadadi, Noushin · 2015 · Infoscience (Ecole Polytechnique Fédérale de Lausanne) · DOI
Full title: Computational Studies on Cellular Metabolism : From Biochemical Pathways to Complex Metabolic Networks
Authors: Hadadi, Noushin
Year: 2015
Venue: Infoscience (Ecole Polytechnique Fédérale de Lausanne)
Paper Metabolic flux analysis in Euglena gracilis
Inwongwan, Sahutchai · 2020 · Oxford University Research Archive (ORA) (University of Oxford) · DOI
Full title: Metabolic flux analysis in Euglena gracilis
Authors: Inwongwan, Sahutchai
Year: 2020
Venue: Oxford University Research Archive (ORA) (University of Oxford)
Paper Computational approaches for understanding one-carbon metabolism in cancer
Mehrmohamadi, Mahya · 2017 · eCommons (Cornell University) · DOI
Full title: Computational approaches for understanding one-carbon metabolism in cancer
Authors: Mehrmohamadi, Mahya
Year: 2017
Venue: eCommons (Cornell University)
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
Paper Theoretical Studies of Intracellular Concentration of Micro-organisms’ Metabolites
Yang, Hai-Feng; Zhang, Xiaonan; Li, Yan et al. · 2017 · Scientific Reports · DOI
Full title: Theoretical Studies of Intracellular Concentration of Micro-organisms’ Metabolites
Authors: Yang, Hai-Feng; Zhang, Xiaonan; Li, Yan; Zhang, Yonghong; Xu, Qin; Wei, Dong‐Qing
Year: 2017
Venue: Scientific Reports
Paper Alpha-ketoglutarate utilization in Saccharomyces cerevisiae: transport, compartmentation and catabolism
Zhang, Jinrui; Herik, Bas Mees van den; Wahl, A. · 2020 · Scientific Reports · DOI
Full title: Alpha-ketoglutarate utilization in Saccharomyces cerevisiae: transport, compartmentation and catabolism
Authors: Zhang, Jinrui; Herik, Bas Mees van den; Wahl, A.
Year: 2020
Venue: Scientific Reports
Paper Integrating a dynamic central metabolism model of cancer cells with a hybrid 3D multiscale model for vascular hepatocellular carcinoma growth
Lapin, Alexey; Perfahl, Holger; Jain, Harsh et al. · 2022 · Scientific Reports · DOI
Full title: Integrating a dynamic central metabolism model of cancer cells with a hybrid 3D multiscale model for vascular hepatocellular carcinoma growth
Authors: Lapin, Alexey; Perfahl, Holger; Jain, Harsh; Reuß, Matthias
Year: 2022
Venue: Scientific Reports
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
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
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
Paper Predicting the decision making chemicals used for bacterial growth
Ashino, Kazuha; Sugano, Kenta; Amagasa, Toshiyuki et al. · 2019 · Scientific Reports · DOI
Full title: Predicting the decision making chemicals used for bacterial growth
Authors: Ashino, Kazuha; Sugano, Kenta; Amagasa, Toshiyuki; Ying, Bei‐Wen
Year: 2019
Venue: Scientific Reports
Paper Multi-omics integrative analysis with genome-scale metabolic model simulation reveals global cellular adaptation of Aspergillus niger under industrial enzyme production condition
Lu, Hongzhong; Cao, Weiqiang; Liu, Xiaoyun et al. · 2018 · Scientific Reports · DOI
Full title: Multi-omics integrative analysis with genome-scale metabolic model simulation reveals global cellular adaptation of Aspergillus niger under industrial enzyme production condition
Authors: Lu, Hongzhong; Cao, Weiqiang; Liu, Xiaoyun; Sui, Yufei; Ouyang, Liming; Xia, Jianye; Huang, Mingzhi; Zhuang, Yingping; Zhang, Siliang; Noorman, Henk; Chu, Ju
Year: 2018
Venue: Scientific Reports
Paper A biochemical network modeling of a whole-cell
Burke, Paulo E. P.; Campos, Cláudia Barbosa Ladeira de; Costa, Luciano da Fontoura et al. · 2020 · Scientific Reports · DOI
Full title: A biochemical network modeling of a whole-cell
Authors: Burke, Paulo E. P.; Campos, Cláudia Barbosa Ladeira de; Costa, Luciano da Fontoura; Quiles, Marcos G.
Year: 2020
Venue: Scientific Reports
Paper Logic programming-based Minimal Cut Sets reveal consortium-level therapeutic targets for chronic wound infections
Mahout, Maxime; Carlson, Ross P.; Simon, Laurent et al. · 2024 · npj Systems Biology and Applications · DOI
Full title: Logic programming-based Minimal Cut Sets reveal consortium-level therapeutic targets for chronic wound infections
Authors: Mahout, Maxime; Carlson, Ross P.; Simon, Laurent; Pérès, Sabine
Year: 2024
Venue: npj Systems Biology and Applications
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
Paper Rapid-SL identifies synthetic lethal sets with an arbitrary cardinality
Manshadi, Mehdi Dehghan; Setoodeh, Payam; Zare, Habil · 2022 · Scientific Reports · DOI
Full title: Rapid-SL identifies synthetic lethal sets with an arbitrary cardinality
Authors: Manshadi, Mehdi Dehghan; Setoodeh, Payam; Zare, Habil
Year: 2022
Venue: Scientific Reports
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
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
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
Paper Reliable and efficient solution of genome-scale models of Metabolism and macromolecular Expression
Ma, Ding; Yang, Laurence; Fleming, Ronan M. T. et al. · 2017 · Scientific Reports · 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 Ø.; Saunders, Michael A.
Year: 2017
Venue: Scientific Reports
Paper Diverse classes of constraints enable broader applicability of a linear programming-based dynamic metabolic modeling framework
Lee, Justin Y.; Styczynski, Mark P. · 2021 · Scientific Reports · DOI
Full title: Diverse classes of constraints enable broader applicability of a linear programming-based dynamic metabolic modeling framework
Authors: Lee, Justin Y.; Styczynski, Mark P.
Year: 2021
Venue: Scientific Reports
Paper High Production of 3-Hydroxypropionic Acid in Klebsiella pneumoniae by Systematic Optimization of Glycerol Metabolism
Li, Ying; Wang, Xi; Ge, Xizhen et al. · 2016 · Scientific Reports · DOI
Full title: High Production of 3-Hydroxypropionic Acid in Klebsiella pneumoniae by Systematic Optimization of Glycerol Metabolism
Authors: Li, Ying; Wang, Xi; Ge, Xizhen; Tian, Pingfang
Year: 2016
Venue: Scientific Reports
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
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
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
Paper Genome-wide characterization of Phytophthora infestans metabolism: a systems biology approach
Rodenburg, Sander Y.A.; Seidl, Michael; Ridder, Dick de et al. · 2017 · DOI
Full title: Genome-wide characterization of Phytophthora infestans metabolism: a systems biology approach
Authors: Rodenburg, Sander Y.A.; Seidl, Michael; Ridder, Dick de; Govers, Francine
Year: 2017
Paper A systematic simulation of the effect of salicylic acid on sphingolipid metabolism
Shi, Chao; Yin, Jian; Liu, Zhe et al. · 2014 · 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: 2014
Venue: Frontiers in Plant Science
Paper Simulating Serial-Target Antibacterial Drug Synergies Using Flux Balance Analysis
Krueger, Andrew; Munck, Christian; Dantas, Gautam et al. · 2016 · PLoS ONE · DOI
Full title: Simulating Serial-Target Antibacterial Drug Synergies Using Flux Balance Analysis
Authors: Krueger, Andrew; Munck, Christian; Dantas, Gautam; Church, George M.; Galagan, James E.; Lehár, Joseph; Sommer, Morten Otto Alexander
Year: 2016
Venue: PLoS ONE
Paper 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. · 2016 · 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.; Palsson, Bernhard Ø.
Year: 2016
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 PHENSIM: Phenotype Simulator
Alaimo, Salvatore; Rapicavoli, Rosaria Valentina; Marceca, Gioacchino P. et al. · 2020 · DOI
Full title: PHENSIM: Phenotype Simulator
Authors: Alaimo, Salvatore; Rapicavoli, Rosaria Valentina; Marceca, Gioacchino P.; Ferlita, Alessandro La; Serebrennikova, Oksana B.; Tsichlis, Philip N.; Mishra, Bud; Pulvirenti, Alfredo; Ferro, Alfredo
Year: 2020
Paper Improving Designer Glycan Production in <i>Escherichia coli</i> 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 <i>Escherichia coli</i> through Model-Guided Metabolic Engineering
Authors: Wayman, Joseph A.; Glasscock, Cameron J.; Mansell, Thomas J.; DeLisa, Matthew P.; Varner, Jeffrey D.
Year: 2017
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
Paper Protein allocation and enzymatic constraints explain <i>Escherichia coli</i> wildtype and mutant phenotypes
Alter, Tobias B.; Blank, Lars M.; Ebert, Birgitta E. · 2020 · DOI
Full title: Protein allocation and enzymatic constraints explain <i>Escherichia coli</i> wildtype and mutant phenotypes
Authors: Alter, Tobias B.; Blank, Lars M.; Ebert, Birgitta E.
Year: 2020
Paper Combining multiple functional annotation tools increases coverage of metabolic annotation
Griesemer, Marc; Kimbrel, Jeffrey A.; Zhou, Carol E. et al. · 2018 · BMC Genomics · DOI
Full title: Combining multiple functional annotation tools increases coverage of metabolic annotation
Authors: Griesemer, Marc; Kimbrel, Jeffrey A.; Zhou, Carol E.; Navid, Ali; D’haeseleer, Patrik
Year: 2018
Venue: BMC Genomics
Paper Automated Parameterization of Predictive Kinetic Metabolic Models from Sparse Datasets for Efficient Optimization of Many-Enzyme Heterologous Pathways
Halper, Sean M.; Farasat, Iman; Salis, Howard M. · 2017 · DOI
Full title: Automated Parameterization of Predictive Kinetic Metabolic Models from Sparse Datasets for Efficient Optimization of Many-Enzyme Heterologous Pathways
Authors: Halper, Sean M.; Farasat, Iman; Salis, Howard M.
Year: 2017
Paper The ModelSEED 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. · 2020 · DOI
Full title: The ModelSEED 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 G.; Faria, José P.; Edirisinghe, Janaka N.; Mundy, Michael; Chia, Nicholas; Noor, Εlad; Beber, Moritz E.; Best, Aaron A.; DeJongh, Matthew; Kimbrel, Jeffrey A.; D’haeseleer, Patrik; Pearson, Erik; Canon, Shane; Wood‐Charlson, Elisha M.; Cottingham, Robert W.; Arkin, Adam P.; Henry, Christopher S.
Year: 2020
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 Personalized Genome-Scale Metabolic Models Identify Targets of Redox Metabolism in Radiation-Resistant Tumors
Lewis, Joshua E.; Forshaw, Tom E.; Boothman, David A. et al. · 2020 · DOI
Full title: Personalized Genome-Scale Metabolic Models Identify Targets of Redox Metabolism in Radiation-Resistant Tumors
Authors: Lewis, Joshua E.; Forshaw, Tom E.; Boothman, David A.; Furdui, Cristina M.; Kemp, Melissa L.
Year: 2020
Paper Modeling microbial cross-feeding at intermediate scale portrays community dynamics and species coexistence
Liao, Chen; Wang, Tong; Maslov, Sergei et al. · 2020 · DOI
Full title: Modeling microbial cross-feeding at intermediate scale portrays community dynamics and species coexistence
Authors: Liao, Chen; Wang, Tong; Maslov, Sergei; Xavier, João B.
Year: 2020
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 Systematically gap-filling the genome-scale metabolic model of CHO cells
Fouladiha, Hamideh; Marashi, Sayed-Amir; Li, Shangzhong et al. · 2020 · DOI
Full title: Systematically gap-filling the genome-scale metabolic model of CHO cells
Authors: Fouladiha, Hamideh; Marashi, Sayed-Amir; Li, Shangzhong; Li, Zerong; Masson, Helen O.; Vaziri, Behrouz; Lewis, Nathan E.
Year: 2020
Paper Development of a genome-scale metabolic model of <i>Clostridium thermocellum</i> 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 <i>Clostridium thermocellum</i> 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
Paper Enzyme capacity-based genome scale modelling of CHO cells
Yeo, Hock Chuan; Hong, Jongkwang; Lakshmanan, Meiyappan et al. · 2019 · DOI
Full title: Enzyme capacity-based genome scale modelling of CHO cells
Authors: Yeo, Hock Chuan; Hong, Jongkwang; Lakshmanan, Meiyappan; Lee, Dong‐Yup
Year: 2019
Paper Integration of machine learning and genome-scale metabolic modeling identifies multi-omics biomarkers for radiation resistance
Lewis, Joshua E.; Kemp, Melissa L. · 2021 · Nature Communications · DOI
Full title: Integration of machine learning and genome-scale metabolic modeling identifies multi-omics biomarkers for radiation resistance
Authors: Lewis, Joshua E.; Kemp, Melissa L.
Year: 2021
Venue: Nature Communications
Paper Ecology-guided prediction of cross-feeding interactions in the human gut microbiome
Goyal, Akshit; Wang, Tong; Dubinkina, Veronika et al. · 2020 · DOI
Full title: Ecology-guided prediction of cross-feeding interactions in the human gut microbiome
Authors: Goyal, Akshit; Wang, Tong; Dubinkina, Veronika; Maslov, Sergei
Year: 2020
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
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
Paper Systematic evaluation of parameters for genome-scale metabolic models of cultured mammalian cells
Schinn, Song‐Min; Morrison, Carly; Wei, Wei et al. · 2020 · DOI
Full title: Systematic evaluation of parameters for genome-scale metabolic models of cultured mammalian cells
Authors: Schinn, Song‐Min; Morrison, Carly; Wei, Wei; Zhang, Lin; Lewis, Nathan E.
Year: 2020
Paper Modeling a co-culture of <i>Clostridium autoethanogenum</i> and <i>Clostridium kluyveri</i> 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 <i>Clostridium autoethanogenum</i> and <i>Clostridium kluyveri</i> 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
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
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
Paper Elucidating Human Milk Oligosaccharide biosynthetic genes through network-based multiomics integration
Kellman, Benjamin P.; Richelle, Anne; Yang, Jeong‐Yeh et al. · 2020 · DOI
Full title: Elucidating Human Milk Oligosaccharide biosynthetic genes through network-based multiomics integration
Authors: Kellman, Benjamin P.; Richelle, Anne; Yang, Jeong‐Yeh; Chapla, Digantkumar; Chiang, Austin W.T.; Najera, Julia A.; Bao, Bokan; Koga, Natália Massaco; Mohammad, Mahmoud A.; Bruntse, Anders Bech; Haymond, Morey W.; Moremen, Kelley W.; Bode, Lars; Lewis, Nathan E.
Year: 2020
Paper Analysis of Metabolic Network Disruption in Engineered Microbial Hosts due to Enzyme Promiscuity
Porokhin, Vladimir; Amin, Sara A.; Nicks, Trevor B. et al. · 2020 · DOI
Full title: Analysis of Metabolic Network Disruption in Engineered Microbial Hosts due to Enzyme Promiscuity
Authors: Porokhin, Vladimir; Amin, Sara A.; Nicks, Trevor B.; Gopinarayanan, Venkatesh Endalur; Nair, Nikhil U.; Hassoun, Soha
Year: 2020
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
Paper Emergence of diauxie as an optimal growth strategy under resource allocation constraints in cellular metabolism
Salvy, Pierre; Hatzimanikatis, Vassily · 2021 · Proceedings of the National Academy of Sciences · 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: Proceedings of the National Academy of Sciences
Paper Xylose Metabolism and the Effect of Oxidative Stress on Lipid and Carotenoid Production in <i>Rhodotorula toruloides</i> : Insights for Future Biorefinery
Pinheiro, Marina Julio; Bonturi, Nemailla; Belouah, Isma et al. · 2020 · DOI
Full title: Xylose Metabolism and the Effect of Oxidative Stress on Lipid and Carotenoid Production in <i>Rhodotorula toruloides</i> : Insights for Future Biorefinery
Authors: Pinheiro, Marina Julio; Bonturi, Nemailla; Belouah, Isma; Miranda, Everson Alves; Lahtvee, Petri‐Jaan
Year: 2020
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
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
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
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
Paper Modular Dynamic Biomolecular Modelling with Bond Graphs: The Unification of Stoichiometry, Thermodynamics, Kinetics and Data
Gawthrop, P.J.; Pan, Michael; Crampin, Edmund J. · 2021 · DOI
Full title: Modular Dynamic Biomolecular Modelling with Bond Graphs: The Unification of Stoichiometry, Thermodynamics, Kinetics and Data
Authors: Gawthrop, P.J.; Pan, Michael; Crampin, Edmund J.
Year: 2021
Paper Integrating thermodynamic and enzymatic constraints into genome-scale metabolic models
Yang, Xue; Mao, Zhitao; Zhao, Xin et al. · 2020 · 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; Ma, Hongwu
Year: 2020
Paper <i>In silico</i> analysis of the fast-growing thermophile <i>Geobacillus</i> sp. LC300 using a novel genome-scale metabolic model
Ljungqvist, Emil; Gustavsson, Martin · 2021 · DOI
Full title: <i>In silico</i> analysis of the fast-growing thermophile <i>Geobacillus</i> sp. LC300 using a novel genome-scale metabolic model
Authors: Ljungqvist, Emil; Gustavsson, Martin
Year: 2021
Paper Control and regulation of acetate overflow in Escherichia coli
Millard, Pierre; Enjalbert, Brice; Uttenweiler‐Joseph, Sandrine et al. · 2020 · DOI
Full title: Control and regulation of acetate overflow in Escherichia coli
Authors: Millard, Pierre; Enjalbert, Brice; Uttenweiler‐Joseph, Sandrine; Portais, Jean‐Charles; Létisse, Fabien
Year: 2020
Paper Reconstruction of a catalogue of genome-scale metabolic models with enzymatic constraints using GECKO 2.0
Domenzain, Iván; Sánchez, Benjamín J.; Anton, Mihail et al. · 2022 · Nature Communications · DOI
Full title: Reconstruction of a catalogue of genome-scale metabolic models with enzymatic constraints using GECKO 2.0
Authors: Domenzain, Iván; Sánchez, Benjamín J.; Anton, Mihail; Kerkhoven, Eduard J.; Millán-Oropeza, Aarón; Henry, Céline; Siewers, Verena; Morrissey, John P.; Sonnenschein, Nikolaus; Nielsen, Jens
Year: 2022
Venue: Nature Communications
Paper GPRuler: Metabolic gene-protein-reaction rules automatic reconstruction
Filippo, Marzia Di; Damiani, Chiara; Pescini, Dario · 2021 · PLoS Computational Biology · DOI
Full title: GPRuler: Metabolic gene-protein-reaction rules automatic reconstruction
Authors: Filippo, Marzia Di; Damiani, Chiara; Pescini, Dario
Year: 2021
Venue: PLoS Computational Biology
Paper Elucidating Tumor-stromal Metabolic Crosstalk in Colorectal Cancer through Integration of Constraint-Based Models and LC-MS Metabolomics
Wang, Junmin; Delfarah, Alireza; Gelbach, Patrick E. et al. · 2021 · DOI
Full title: Elucidating Tumor-stromal Metabolic Crosstalk in Colorectal Cancer through Integration of Constraint-Based Models and LC-MS Metabolomics
Authors: Wang, Junmin; Delfarah, Alireza; Gelbach, Patrick E.; Fong, Emma J.; Macklin, Paul; Mumenthaler, Shannon M.; Graham, Nicholas A.; Finley, Stacey D.
Year: 2021
Paper A genome-scale metabolic model of <i>Saccharomyces cerevisiae</i> 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 <i>Saccharomyces cerevisiae</i> that integrates expression constraints and reaction thermodynamics
Authors: Oftadeh, Omid; Salvy, Pierre; Masid, María; Curvat, Maxime; Mišković, Ljubiša; Hatzimanikatis, Vassily
Year: 2021
Paper Genome-scale modeling of <i>Pseudomonas aeruginosa</i> 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 <i>Pseudomonas aeruginosa</i> PA14 unveils its broad metabolic capabilities and role of metabolism in drug potentiation
Authors: Dahal, Sanjeev; Renz, Alina; Dräger, Andreas; Yang, Laurence
Year: 2021
Paper Quantitative prediction of conditional vulnerabilities in regulatory and metabolic networks of <i>Mycobacterium tuberculosis</i>
Immanuel, Selva Rupa Christinal; Arrieta‐Ortiz, Mario L.; Ruiz, Rene A. et al. · 2021 · npj Systems Biology and Applications · DOI
Full title: Quantitative prediction of conditional vulnerabilities in regulatory and metabolic networks of <i>Mycobacterium tuberculosis</i>
Authors: Immanuel, Selva Rupa Christinal; Arrieta‐Ortiz, Mario L.; Ruiz, Rene A.; Pan, Min; Lomana, Adrián López García de; Peterson, Eliza J. R.; Baliga, Nitin S.
Year: 2021
Venue: npj Systems Biology and Applications
Paper Genome-scale metabolic modelling of <i>P. thermoglucosidasius</i> 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 <i>P. thermoglucosidasius</i> 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
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
Paper Diverse classes of constraints enable broader applicability of a linear programming-based dynamic metabolic modeling framework
Lee, Justin Y.; Styczynski, Mark P. · 2021 · DOI
Full title: Diverse classes of constraints enable broader applicability of a linear programming-based dynamic metabolic modeling framework
Authors: Lee, Justin Y.; Styczynski, Mark P.
Year: 2021
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
Paper Increased 3-hydroxypropionic acid production from glycerol, by modification of central metabolism in Escherichia coli
Tokuyama, Kento; Ohno, Satoshi; Yoshikawa, Katsunori 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: Tokuyama, Kento; Ohno, Satoshi; Yoshikawa, Katsunori; Hirasawa, Takashi; Tanaka, Shotaro; Furusawa, Chikara; Shimizu, Hiroshi
Year: 2014
Venue: Microbial Cell Factories
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
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
Paper Improved vanillin production in baker&#x27;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&#x27;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
Paper A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2
Thiele, Ines; Hyduke, Daniel R.; Steeb, Benjamin et al. · 2011 · BMC Systems Biology · DOI
Full title: A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2
Authors: Thiele, Ines; Hyduke, Daniel R.; Steeb, Benjamin; Fankam, Guy; Allen, Doug K.; Bazzani, Susanna; Charusanti, Pep; Chen, Feng‐Chi; Fleming, Ronan M. T.; Hsiung, Chao A.; Keersmaecker, Sigrid C. J. De; Liao, Yu-Chieh; Marchal, Kathleen; Mo, Monica L.; Özdemir, Emre; Raghunathan, Anu; Reed, Jennifer L.; Shin, Sookil; Sigurbjörnsdóttir, Sara; Steinmann, Jonas; Sudarsan, Suresh; Swainston, Neil; Thijs, Inge M; Zengler, Karsten; Palsson, Bernhard Ø.; Adkins, Joshua; Bumann, Dirk
Year: 2011
Venue: BMC Systems Biology
Paper Melhoria experimental por auditoria e alisamento de dados: aplicação em produção de biopolímero..
Gamba, Jessica Rubira · 2023 · Prof. Dr. · DOI
Full title: Melhoria experimental por auditoria e alisamento de dados: aplicação em produção de biopolímero..
Authors: Gamba, Jessica Rubira
Year: 2023
Venue: Prof. Dr.
Paper Modeling and simulation of the main metabolism in Escherichia coli and its several single-gene knockout mutants with experimental verification
Kadir, Tuty Asmawaty Abdul; Mannan, Ahmad A.; Kierzek, Andrzej et al. · 2010 · Microbial Cell Factories · 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, Tuty Asmawaty Abdul; Mannan, Ahmad A.; Kierzek, Andrzej; McFadden, Johnjoe; Shimizu, Kazuyuki
Year: 2010
Venue: Microbial Cell Factories
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
Paper Iterative approach to model identification of biological networks
Gadkar, Kapil; Gunawan, Rudiyanto; Doyle, Francis J. · 2005 · BMC Bioinformatics · DOI
Full title: Iterative approach to model identification of biological networks
Authors: Gadkar, Kapil; Gunawan, Rudiyanto; Doyle, Francis J.
Year: 2005
Venue: BMC Bioinformatics
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
Paper Genome-scale reconstruction and system level investigation of the metabolic network of Methylobacterium extorquensAM1
Peyraud, Rémi; Schneider, Kathrin; Kiefer, Patrick et al. · 2011 · BMC Systems Biology · DOI
Full title: Genome-scale reconstruction and system level investigation of the metabolic network of Methylobacterium extorquensAM1
Authors: Peyraud, Rémi; Schneider, Kathrin; Kiefer, Patrick; Massou, Stéphane; Vorholt, Julia A.; Portais, Jean‐Charles
Year: 2011
Venue: BMC Systems Biology
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
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
Paper A possibilistic framework for constraint-based metabolic flux analysis
Llaneras, Francisco; Sala, Antonio; Picó, Jesús · 2009 · BMC Systems Biology · DOI
Full title: A possibilistic framework for constraint-based metabolic flux analysis
Authors: Llaneras, Francisco; Sala, Antonio; Picó, Jesús
Year: 2009
Venue: BMC Systems Biology
Paper SPABBATS: A pathway-discovery method based on Boolean satisfiability that facilitates the characterization of suppressor mutants
Flórez, Lope A.; Gunka, Katrin; Polanía, Rafael et al. · 2011 · BMC Systems Biology · DOI
Full title: SPABBATS: A pathway-discovery method based on Boolean satisfiability that facilitates the characterization of suppressor mutants
Authors: Flórez, Lope A.; Gunka, Katrin; Polanía, Rafael; Tholen, Stefan; Stülke, Jörg
Year: 2011
Venue: BMC Systems Biology
Paper ChiMera: an easy to use pipeline for bacterial genome based metabolic network reconstruction, evaluation and visualization
Tamasco, Gustavo · 2022 · DOI
Full title: ChiMera: an easy to use pipeline for bacterial genome based metabolic network reconstruction, evaluation and visualization
Authors: Tamasco, Gustavo
Year: 2022
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
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
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
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
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
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
Paper The poly-omics of ageing through individual-based metabolic modelling
Yaneske, Elisabeth; Angione, Claudio · 2018 · BMC Bioinformatics · DOI
Full title: The poly-omics of ageing through individual-based metabolic modelling
Authors: Yaneske, Elisabeth; Angione, Claudio
Year: 2018
Venue: BMC Bioinformatics
Paper Gap-filling analysis of the iJO1366 Escherichia coli metabolic network reconstruction for discovery of metabolic functions
Orth, Jeffrey D.; Palsson, Bernhard Ø. · 2012 · BMC Systems Biology · DOI
Full title: Gap-filling analysis of the iJO1366 Escherichia coli metabolic network reconstruction for discovery of metabolic functions
Authors: Orth, Jeffrey D.; Palsson, Bernhard Ø.
Year: 2012
Venue: BMC Systems Biology
Paper Integrating gene and protein expression data with genome-scale metabolic networks to infer functional pathways
Pey, Jon; Valgepea, Kaspar; Rubio, Ángel et al. · 2013 · BMC Systems Biology · DOI
Full title: Integrating gene and protein expression data with genome-scale metabolic networks to infer functional pathways
Authors: Pey, Jon; Valgepea, Kaspar; Rubio, Ángel; Beasley, J. E.; Planes, Francisco J.
Year: 2013
Venue: BMC Systems Biology
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
Paper Global dynamic optimization approach to predict activation in metabolic pathways
Hijas-Liste, G. M.; Klipp, Edda; Balsa‐Canto, Eva et al. · 2014 · BMC Systems Biology · DOI
Full title: Global dynamic optimization approach to predict activation in metabolic pathways
Authors: Hijas-Liste, G. M.; Klipp, Edda; Balsa‐Canto, Eva; Banga, Julio R.
Year: 2014
Venue: BMC Systems Biology
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
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
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
Paper An objective function exploiting suboptimal solutions in metabolic networks
Wintermute, Edwin H.; Lieberman, Tami D.; Silver, Pamela A. · 2013 · BMC Systems Biology · DOI
Full title: An objective function exploiting suboptimal solutions in metabolic networks
Authors: Wintermute, Edwin H.; Lieberman, Tami D.; Silver, Pamela A.
Year: 2013
Venue: BMC Systems Biology
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
Paper The JBEI quantitative metabolic modeling library (jQMM): a python library for modeling microbial metabolism
Birkel, Garrett W.; Ghosh, Amit; Kumar, Vinay et al. · 2017 · BMC Bioinformatics · 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; Weaver, Daniel; Ando, David; Backman, Tyler W. H.; Arkin, Adam P.; Keasling, Jay D.; Martín, Héctor García
Year: 2017
Venue: BMC Bioinformatics
Paper Non-stationary 13C metabolic flux analysis of Chinese hamster ovary cells in batch culture using extracellular labeling highlights metabolic reversibility and compartmentation
Nicolae, Averina; Wahrheit, Judith; Bahnemann, Janina et al. · 2014 · BMC Systems Biology · DOI
Full title: Non-stationary 13C metabolic flux analysis of Chinese hamster ovary cells in batch culture using extracellular labeling highlights metabolic reversibility and compartmentation
Authors: Nicolae, Averina; Wahrheit, Judith; Bahnemann, Janina; Zeng, An‐Ping; Heinzle, Elmar
Year: 2014
Venue: BMC Systems Biology
Paper Ethylene-forming enzyme and bioethylene production
Eckert, Carrie A.; Xu, Wu; Xiong, Wei et al. · 2014 · Biotechnology for Biofuels · DOI
Full title: Ethylene-forming enzyme and bioethylene production
Authors: Eckert, Carrie A.; Xu, Wu; Xiong, Wei; Lynch, Sean; Ungerer, Justin; Tao, Ling; Gill, Ryan T.; Maness, Pin‐Ching; Yu, Jianping
Year: 2014
Venue: Biotechnology for Biofuels
Paper Parameter-less approaches for interpreting dynamic cellular response
Selvarajoo, Kumar · 2014 · Journal of Biological Engineering · DOI
Full title: Parameter-less approaches for interpreting dynamic cellular response
Authors: Selvarajoo, Kumar
Year: 2014
Venue: Journal of Biological Engineering
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
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
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
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
Paper Exploring the associations between transcript levels and fluxes in constraint-based models of metabolism
Sinha, Neeraj; Schothorst, Evert M. van; Hooiveld, Guido et al. · 2021 · BMC Bioinformatics · DOI
Full title: Exploring the associations between transcript levels and fluxes in constraint-based models of metabolism
Authors: Sinha, Neeraj; Schothorst, Evert M. van; Hooiveld, Guido; Keijer, Jaap; Santos, Vítor A. P. Martins dos; Suárez‐Diez, María
Year: 2021
Venue: BMC Bioinformatics
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
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
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
Paper Identification of critical connectors in the directed reaction-centric graphs of microbial metabolic networks
Kim, Eun-Youn; Ashlock, Daniel; Yoon, Sung Ho · 2019 · BMC Bioinformatics · DOI
Full title: Identification of critical connectors in the directed reaction-centric graphs of microbial metabolic networks
Authors: Kim, Eun-Youn; Ashlock, Daniel; Yoon, Sung Ho
Year: 2019
Venue: BMC Bioinformatics
Paper RELATCH: relative optimality in metabolic networks explains robust metabolic and regulatory responses to perturbations
Kim, Joonhoon; Reed, Jennifer L. · 2012 · Genome biology · DOI
Full title: RELATCH: relative optimality in metabolic networks explains robust metabolic and regulatory responses to perturbations
Authors: Kim, Joonhoon; Reed, Jennifer L.
Year: 2012
Venue: Genome biology
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
Paper CBFA: phenotype prediction integrating metabolic models with constraints derived from experimental data
Carreira, Rafael; Evangelista, Pedro; Maia, Paulo et al. · 2014 · BMC Systems Biology · DOI
Full title: CBFA: phenotype prediction integrating metabolic models with constraints derived from experimental data
Authors: Carreira, Rafael; Evangelista, Pedro; Maia, Paulo; Vilaça, Paulo; Pont, Marcellinus; Tomb, Jean-François; Rocha, Isabel; Rocha, Miguel
Year: 2014
Venue: BMC Systems Biology
Paper Improving the organization and interactivity of metabolic pathfinding with precomputed pathways
Kim, Sarah M.; Peña, Matthew I.; Moll, Mark et al. · 2020 · BMC Bioinformatics · DOI
Full title: Improving the organization and interactivity of metabolic pathfinding with precomputed pathways
Authors: Kim, Sarah M.; Peña, Matthew I.; Moll, Mark; Bennett, George N.; Kavraki, Lydia E.
Year: 2020
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
Paper Combining multiple functional annotation tools increases coverage of metabolic annotation
Griesemer, Marc; Kimbrel, Jeffrey A.; Zhou, Carol E. et al. · 2018 · BMC Genomics · DOI
Full title: Combining multiple functional annotation tools increases coverage of metabolic annotation
Authors: Griesemer, Marc; Kimbrel, Jeffrey A.; Zhou, Carol E.; Navid, Ali; D’haeseleer, Patrik
Year: 2018
Venue: BMC Genomics
Paper Studying metabolic flux adaptations in cancer through integrated experimental-computational approaches
Lagziel, Shoval; Lee, Won Dong; Shlomi, Tomer · 2019 · BMC Biology · DOI
Full title: Studying metabolic flux adaptations in cancer through integrated experimental-computational approaches
Authors: Lagziel, Shoval; Lee, Won Dong; Shlomi, Tomer
Year: 2019
Venue: BMC Biology
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
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
Paper Metabolic modelling in a dynamic evolutionary framework predicts adaptive diversification of bacteria in a long-term evolution experiment
Großkopf, Tobias; Consuegra, Jessika; Gaffé, Joël et al. · 2016 · BMC Evolutionary Biology · DOI
Full title: Metabolic modelling in a dynamic evolutionary framework predicts adaptive diversification of bacteria in a long-term evolution experiment
Authors: Großkopf, Tobias; Consuegra, Jessika; Gaffé, Joël; Willison, John C.; Lenski, Richard E.; Soyer, Orkun S.; Schneider, Dominique
Year: 2016
Venue: BMC Evolutionary Biology
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
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
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
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
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
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
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
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
Paper Heterogeneous oxygen availability affects the titer and topology but not the fidelity of plasmid DNA produced by Escherichia coli
Jaén, Karim E.; Sigala, Juan‐Carlos; Olivares‐Hernández, Roberto et al. · 2017 · BMC Biotechnology · DOI
Full title: Heterogeneous oxygen availability affects the titer and topology but not the fidelity of plasmid DNA produced by Escherichia coli
Authors: Jaén, Karim E.; Sigala, Juan‐Carlos; Olivares‐Hernández, Roberto; Niehaus, Karsten; Lara, Alvaro R.
Year: 2017
Venue: BMC Biotechnology
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, M.; Magni, Paolo; Calvio, Cinzia; Herrgård, Markus J.
Year: 2019
Venue: Microbial Cell Factories
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
Paper Engineering Escherichia coli for the utilization of ethylene glycol
Pandit, Aditya Vikram; Harrison, Emma; Mahadevan, Radhakrishnan · 2021 · Microbial Cell Factories · DOI
Full title: Engineering Escherichia coli for the utilization of ethylene glycol
Authors: Pandit, Aditya Vikram; Harrison, Emma; Mahadevan, Radhakrishnan
Year: 2021
Venue: Microbial Cell Factories
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
Paper Diversity of flux distribution in central carbon metabolism of S. cerevisiae strains from diverse environments
Nidelet, Thibault; Brial, Pascale; Camarasa, Carole et al. · 2016 · Microbial Cell Factories · DOI
Full title: Diversity of flux distribution in central carbon metabolism of S. cerevisiae strains from diverse environments
Authors: Nidelet, Thibault; Brial, Pascale; Camarasa, Carole; Dequin, Sylvie
Year: 2016
Venue: Microbial Cell Factories
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
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
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
Paper Integration of enzyme constraints in a genome-scale metabolic model of Aspergillus niger improves phenotype predictions
Zhou, Jingru; Zhuang, Yingping; Xia, Jianye · 2021 · Microbial Cell Factories · DOI
Full title: Integration of enzyme constraints in a genome-scale metabolic model of Aspergillus niger improves phenotype predictions
Authors: Zhou, Jingru; Zhuang, Yingping; Xia, Jianye
Year: 2021
Venue: Microbial Cell Factories
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 · 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.; Santos, Filipe Branco dos; Özdemir, Emre; Herrgård, Markus J.; França, Lucas; Ferreira, Bruno Sommer; Nielsen, Alex Toftgaard; Guðmundsson, Steinn
Year: 2019
Venue: Microbial Cell Factories
Paper DynamicME: dynamic simulation and refinement of integrated models of metabolism and protein expression
Yang, Laurence; Ebrahim, Ali; Lloyd, Colton J. et al. · 2019 · BMC Systems Biology · 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 Ø.
Year: 2019
Venue: BMC Systems Biology
Paper Systems metabolic engineering for citric acid production by Aspergillus niger in the post-genomic era
Tong, Zhenyu; Zheng, Xiaomei; Tong, Yi et al. · 2019 · Microbial Cell Factories · DOI
Full title: Systems metabolic engineering for citric acid production by Aspergillus niger in the post-genomic era
Authors: Tong, Zhenyu; Zheng, Xiaomei; Tong, Yi; Shi, Yong‐Cheng; Sun, Jibin
Year: 2019
Venue: Microbial Cell Factories
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
Paper Systems biology of the structural proteome
Brunk, Elizabeth; Mih, Nathan; Monk, Jonathan M. et al. · 2016 · BMC Systems Biology · DOI
Full title: Systems biology of the structural proteome
Authors: Brunk, Elizabeth; Mih, Nathan; Monk, Jonathan M.; Zhang, Zhen; O’Brien, Edward J.; Bliven, Spencer; Chen, Ke; Chang, Roger L.; Bourne, Philip E.; Palsson, Bernhard Ø.
Year: 2016
Venue: BMC Systems Biology
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 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
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
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
Paper Theoretical exploration of optimal metabolic flux distributions for extracellular electron transfer by Shewanella oneidensisMR-1
Mao, Longfei; Verwoerd, W.S. · 2014 · Biotechnology for Biofuels · DOI
Full title: Theoretical exploration of optimal metabolic flux distributions for extracellular electron transfer by Shewanella oneidensisMR-1
Authors: Mao, Longfei; Verwoerd, W.S.
Year: 2014
Venue: Biotechnology for Biofuels
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
Paper Computational inference of the structure and regulation of the lignin pathway in Panicum virgatum
Faraji, Mojdeh; Fonseca, Luís L.; Escamilla‐Treviño, Luis L. et al. · 2015 · Biotechnology for Biofuels · DOI
Full title: Computational inference of the structure and regulation of the lignin pathway in Panicum virgatum
Authors: Faraji, Mojdeh; Fonseca, Luís L.; Escamilla‐Treviño, Luis L.; Dixon, Richard A.; Voit, Eberhard O.
Year: 2015
Venue: Biotechnology for Biofuels
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
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
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
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
Paper Investigation of two metabolic engineering approaches for (R,R)-2,3-butanediol production from glycerol in Bacillus subtilis
Vikromvarasiri, Nunthaphan; Noda, Shuhei; Shirai, Tomokazu et al. · 2023 · Journal of Biological Engineering · DOI
Full title: Investigation of two metabolic engineering approaches for (R,R)-2,3-butanediol production from glycerol in Bacillus subtilis
Authors: Vikromvarasiri, Nunthaphan; Noda, Shuhei; Shirai, Tomokazu; Kondo, Akihiko
Year: 2023
Venue: Journal of Biological Engineering
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
Paper Advances in metabolic modeling of oleaginous microalgae
Tibocha‐Bonilla, Juan D.; Zúñiga, Cristal; Godoy‐Silva, Rubén Darío et al. · 2018 · Biotechnology for Biofuels · DOI
Full title: Advances in metabolic modeling of oleaginous microalgae
Authors: Tibocha‐Bonilla, Juan D.; Zúñiga, Cristal; Godoy‐Silva, Rubén Darío; Zengler, Karsten
Year: 2018
Venue: Biotechnology for Biofuels
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
Paper Bridging the gap between non-targeted stable isotope labeling and metabolic flux analysis
Weindl, Daniel; Cordes, Thekla; Battello, Nadia et al. · 2016 · Cancer & Metabolism · DOI
Full title: Bridging the gap between non-targeted stable isotope labeling and metabolic flux analysis
Authors: Weindl, Daniel; Cordes, Thekla; Battello, Nadia; Sapcariu, Sean C.; Dong, Xiangyi; Wegner, André; Hiller, Karsten
Year: 2016
Venue: Cancer & Metabolism
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
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
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
Paper Fast exchange fluxes around the pyruvate node: a leaky cell model to explain the gain and loss of unlabelled and labelled metabolites in a tracer experiment
Quek, Lake‐Ee; Liu, Menghan; Joshi, Sanket et al. · 2016 · Cancer & Metabolism · DOI
Full title: Fast exchange fluxes around the pyruvate node: a leaky cell model to explain the gain and loss of unlabelled and labelled metabolites in a tracer experiment
Authors: Quek, Lake‐Ee; Liu, Menghan; Joshi, Sanket; Turner, Nigel
Year: 2016
Venue: Cancer & Metabolism
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
Paper On the optimality of the enzyme–substrate relationship in bacteria
Dourado, Hugo; Mori, Matteo; Hwa, Terence et al. · 2021 · PLoS Biology · DOI
Full title: On the optimality of the enzyme–substrate relationship in bacteria
Authors: Dourado, Hugo; Mori, Matteo; Hwa, Terence; Lercher, Martin J.
Year: 2021
Venue: PLoS Biology
Paper Drug Off-Target Effects Predicted Using Structural Analysis in the Context of a Metabolic Network Model
Chang, Roger L.; Xie, Li; Xie, Lei et al. · 2010 · PLoS Computational Biology · DOI
Full title: Drug Off-Target Effects Predicted Using Structural Analysis in the Context of a Metabolic Network Model
Authors: Chang, Roger L.; Xie, Li; Xie, Lei; Bourne, Philip E.; Palsson, Bernhard Ø.
Year: 2010
Venue: PLoS Computational Biology
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
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
Paper In silico reconstruction and experimental validation of Saccharopolyspora erythraea genome-scale metabolic model iZZ1342 that accounts for 1685 ORFs
Zhuang, Zhendong; Huang, Mingzhi; Chu, Ju · 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: Zhuang, Zhendong; Huang, Mingzhi; Chu, Ju
Year: 2018
Venue: Bioresources and Bioprocessing
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 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
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
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
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
Paper Integrative Analysis of Transgenic Alfalfa (Medicago sativa L.) Suggests New Metabolic Control Mechanisms for Monolignol Biosynthesis
Lee, Yun; Chen, Fang; Gallego‐Giraldo, Lina et al. · 2011 · PLoS Computational Biology · DOI
Full title: Integrative Analysis of Transgenic Alfalfa (Medicago sativa L.) Suggests New Metabolic Control Mechanisms for Monolignol Biosynthesis
Authors: Lee, Yun; Chen, Fang; Gallego‐Giraldo, Lina; Dixon, Richard A.; Voit, Eberhard O.
Year: 2011
Venue: PLoS Computational Biology
Paper Likelihood-Based Gene Annotations for Gap Filling and Quality Assessment in Genome-Scale Metabolic Models
Benedict, Matthew N.; Mundy, Michael; Henry, Christopher S. et al. · 2014 · PLoS Computational Biology · DOI
Full title: Likelihood-Based Gene Annotations for Gap Filling and Quality Assessment in Genome-Scale Metabolic Models
Authors: Benedict, Matthew N.; Mundy, Michael; Henry, Christopher S.; Chia, Nicholas; Price, Nathan D.
Year: 2014
Venue: PLoS Computational Biology
Paper Reconciliation of Genome-Scale Metabolic Reconstructions for Comparative Systems Analysis
Oberhardt, Matthew; Puchałka, Jacek; Santos, Vítor A. P. Martins dos et al. · 2011 · PLoS Computational Biology · DOI
Full title: Reconciliation of Genome-Scale Metabolic Reconstructions for Comparative Systems Analysis
Authors: Oberhardt, Matthew; Puchałka, Jacek; Santos, Vítor A. P. Martins dos; Papin, Jason A.
Year: 2011
Venue: PLoS Computational Biology
Paper Integrating Cellular Metabolism into a Multiscale Whole-Body Model
Krauß, Markus; Schaller, Stephan; Borchers, Steffen et al. · 2012 · PLoS Computational Biology · DOI
Full title: Integrating Cellular Metabolism into a Multiscale Whole-Body Model
Authors: Krauß, Markus; Schaller, Stephan; Borchers, Steffen; Findeisen, Rolf; Lippert, Jörg; Kuepfer, Lars
Year: 2012
Venue: PLoS Computational Biology
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 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
Paper Integrated Modeling of Gene Regulatory and Metabolic Networks in Mycobacterium tuberculosis
Ma, Shuyi; Minch, K; Rustad, Tige R. et al. · 2015 · PLoS Computational Biology · DOI
Full title: Integrated Modeling of Gene Regulatory and Metabolic Networks in Mycobacterium tuberculosis
Authors: Ma, Shuyi; Minch, K; Rustad, Tige R.; Hobbs, Samuel J.; Zhou, Suk-Lin; Sherman, David R.; Price, Nathan D.
Year: 2015
Venue: PLoS Computational Biology
Paper A Method to Constrain Genome-Scale Models with 13C Labeling Data.
Martín, Héctor García; Kumar, Vinay Satish; 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 Satish; Weaver, Daniel; Ghosh, Amit; Chubukov, Victor; Mukhopadhyay, Aindrila; Arkin, Adam; Keasling, Jay D
Year: 2015
Venue: PLoS computational biology
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
Paper Redirector: Designing Cell Factories by Reconstructing the Metabolic Objective
Rockwell, Graham N.; Guido, Nicholas J.; Church, George M. · 2013 · PLoS Computational Biology · DOI
Full title: Redirector: Designing Cell Factories by Reconstructing the Metabolic Objective
Authors: Rockwell, Graham N.; Guido, Nicholas J.; Church, George M.
Year: 2013
Venue: PLoS Computational Biology
Paper Rapid Prediction of Bacterial Heterotrophic Fluxomics Using Machine Learning and Constraint Programming
Wu, Stephen Gang; Wang, Yuxuan; Wu, Jiang et al. · 2016 · PLoS Computational Biology · DOI
Full title: Rapid Prediction of Bacterial Heterotrophic Fluxomics Using Machine Learning and Constraint Programming
Authors: Wu, Stephen Gang; Wang, Yuxuan; Wu, Jiang; Oyetunde, Tolutola; Yao, Ruilian; Zhang, Xuehong; Shimizu, Kazuyuki; Tang, Yinjie; Bao, Forrest Sheng
Year: 2016
Venue: PLoS Computational Biology
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
Paper A Systems Approach to Predict Oncometabolites via Context-Specific Genome-Scale Metabolic Networks
Nam, Hojung; Campodonico, Miguel A.; Bordbar, Aarash et al. · 2014 · PLoS Computational Biology · DOI
Full title: A Systems Approach to Predict Oncometabolites via Context-Specific Genome-Scale Metabolic Networks
Authors: Nam, Hojung; Campodonico, Miguel A.; Bordbar, Aarash; Hyduke, Daniel R.; Kim, Sangwoo; Zielinski, Daniel C.; Palsson, Bernhard Ø.
Year: 2014
Venue: PLoS Computational Biology
Paper Optimality principles reveal a complex interplay of intermediate toxicity and kinetic efficiency in the regulation of prokaryotic metabolism
Ewald, Jan; Bartl, M.; Dandekar, Thomas et al. · 2017 · PLoS Computational Biology · DOI
Full title: Optimality principles reveal a complex interplay of intermediate toxicity and kinetic efficiency in the regulation of prokaryotic metabolism
Authors: Ewald, Jan; Bartl, M.; Dandekar, Thomas; Kaleta, Christoph
Year: 2017
Venue: PLoS Computational Biology
Paper Efficient Reconstruction of Predictive Consensus Metabolic Network Models
Heck, Ruben; Ganter, Mathias; Santos, Vítor A. P. Martins dos et al. · 2016 · PLoS Computational Biology · DOI
Full title: Efficient Reconstruction of Predictive Consensus Metabolic Network Models
Authors: Heck, Ruben; Ganter, Mathias; Santos, Vítor A. P. Martins dos; Stelling, Joerg
Year: 2016
Venue: PLoS Computational Biology
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
Paper Constrained Allocation Flux Balance Analysis
Mori, Matteo; Hwa, Terence; Martin, Olivier et al. · 2016 · PLoS Computational Biology · DOI
Full title: Constrained Allocation Flux Balance Analysis
Authors: Mori, Matteo; Hwa, Terence; Martin, Olivier; Martino, Andrea De; Marinari, Enzo
Year: 2016
Venue: PLoS Computational Biology
Paper Meneco, a Topology-Based Gap-Filling Tool Applicable to Degraded Genome-Wide Metabolic Networks
Prigent, Sylvain; Frioux, Clémence; Dittami, Simon M. et al. · 2017 · PLoS Computational Biology · DOI
Full title: Meneco, a Topology-Based Gap-Filling Tool Applicable to Degraded Genome-Wide Metabolic Networks
Authors: Prigent, Sylvain; Frioux, Clémence; Dittami, Simon M.; Thiele, Sven; Larhlimi, Abdelhalim; Collet, Guillaume; Gutknecht, Fabien; Got, Jeanne; Eveillard, Damien; Bourdon, Jérémie; Plewniak, Frédéric; Tonon, Thierry; Siegel, Anne
Year: 2017
Venue: PLoS Computational Biology
Paper Estimating Relative Changes of Metabolic Fluxes
Huang, Lei; Kim, Dong-Sung; Liu, Xiaojing et al. · 2014 · PLoS Computational Biology · DOI
Full title: Estimating Relative Changes of Metabolic Fluxes
Authors: Huang, Lei; Kim, Dong-Sung; Liu, Xiaojing; Myers, Christopher R.; Locasale, Jason W.
Year: 2014
Venue: PLoS Computational Biology
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
Paper Predicting proteome allocation, overflow metabolism, and metal requirements in a model acetogen
Liu, Joanne K.; Lloyd, Colton J.; Al‐Bassam, Mahmoud M. et al. · 2019 · PLoS Computational Biology · DOI
Full title: Predicting proteome allocation, overflow metabolism, and metal requirements in a model acetogen
Authors: Liu, Joanne K.; Lloyd, Colton J.; Al‐Bassam, Mahmoud M.; Ebrahim, Ali; Kim, Ji-Nu; Olson, Connor A.; Aksenov, Alexander A.; Dorrestein, Pieter C.; Zengler, Karsten
Year: 2019
Venue: PLoS Computational Biology
Paper Summary of the DREAM8 Parameter Estimation Challenge: Toward Parameter Identification for Whole-Cell Models
Karr, Jonathan R.; Li, Shuai Cheng; Zucker, Jeremy et al. · 2015 · PLoS Computational Biology · DOI
Full title: Summary of the DREAM8 Parameter Estimation Challenge: Toward Parameter Identification for Whole-Cell Models
Authors: Karr, Jonathan R.; Li, Shuai Cheng; Zucker, Jeremy; Raue, Andreas; Steiert, Bernhard; Timmer, Jens; Kreutz, Clemens; Wilkinson, Simon; Allgood, Brandon; Bot, Brian M.; Hoff, Bruce; Kellen, Michael R.; Covert, Markus W.; Stolovitzky, Gustavo A.; Meyer, Pablo
Year: 2015
Venue: PLoS Computational Biology
Paper An enormous potential for niche construction through bacterial cross-feeding in a homogeneous environment
Román, Magdalena San; Wagner, Andreas · 2018 · PLoS Computational Biology · DOI
Full title: An enormous potential for niche construction through bacterial cross-feeding in a homogeneous environment
Authors: Román, Magdalena San; Wagner, Andreas
Year: 2018
Venue: PLoS Computational Biology
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
Paper p13CMFA: Parsimonious 13C metabolic flux analysis
Foguet, Carles; Jayaraman, Anusha; Marín, Silvia et al. · 2019 · PLoS Computational Biology · DOI
Full title: p13CMFA: Parsimonious 13C metabolic flux analysis
Authors: Foguet, Carles; Jayaraman, Anusha; Marín, Silvia; Selivanov, Vitaly A.; Moreno, Pablo; Messeguer, Ramón; Atauri, Pedro de; Cascante, Marta
Year: 2019
Venue: PLoS Computational Biology
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 Fast uncertainty quantification for dynamic flux balance analysis using non-smooth polynomial chaos expansions
Paulson, Joel A.; Martin-Casas, Marc; Mesbah, Ali · 2019 · PLoS Computational Biology · DOI
Full title: Fast uncertainty quantification for dynamic flux balance analysis using non-smooth polynomial chaos expansions
Authors: Paulson, Joel A.; Martin-Casas, Marc; Mesbah, Ali
Year: 2019
Venue: PLoS Computational Biology
Paper OptMDFpathway: Identification of metabolic pathways with maximal thermodynamic driving force and its application for analyzing the endogenous CO2 fixation potential of Escherichia coli
Hädicke, Oliver; Kamp, Axel von; Aydogan, Timur et al. · 2018 · PLoS Computational Biology · DOI
Full title: OptMDFpathway: Identification of metabolic pathways with maximal thermodynamic driving force and its application for analyzing the endogenous CO2 fixation potential of Escherichia coli
Authors: Hädicke, Oliver; Kamp, Axel von; Aydogan, Timur; Klamt, Steffen
Year: 2018
Venue: PLoS Computational Biology
Paper A systematic evaluation of Mycobacterium tuberculosis Genome-Scale Metabolic Networks
López-Agudelo, Víctor A.; Mendum, Tom A.; Laing, Emma et al. · 2020 · PLoS Computational Biology · DOI
Full title: A systematic evaluation of Mycobacterium tuberculosis Genome-Scale Metabolic Networks
Authors: López-Agudelo, Víctor A.; Mendum, Tom A.; Laing, Emma; Wu, Huihai; Baena, Andrés; Barrera, Luis F.; Beste, Dany J. V.; Ríos‐Estepa, Rigoberto
Year: 2020
Venue: PLoS Computational Biology
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, Chen‐Guang; Wang, Zhuo
Year: 2019
Venue: PLoS Computational Biology
Paper Mathematical reconstruction of the metabolic network in an in-vitro multiple myeloma model
Vera-Sigüenza, Elías; Escribano-Gonzalez, Cristina; Serrano‐Gonzalo, Irene et al. · 2023 · PLoS Computational Biology · DOI
Full title: Mathematical reconstruction of the metabolic network in an in-vitro multiple myeloma model
Authors: Vera-Sigüenza, Elías; Escribano-Gonzalez, Cristina; Serrano‐Gonzalo, Irene; Eskla, Kattri‐Liis; Spill, Fabian; Tennant, Daniel A.
Year: 2023
Venue: PLoS Computational Biology
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
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
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
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
Paper In silico co-factor balance estimation using constraint-based modelling informs metabolic engineering in Escherichia coli
Garcia, Laura de Arroyo; Jones, Patrik R. · 2020 · PLoS Computational Biology · DOI
Full title: In silico co-factor balance estimation using constraint-based modelling informs metabolic engineering in Escherichia coli
Authors: Garcia, Laura de Arroyo; Jones, Patrik R.
Year: 2020
Venue: PLoS Computational Biology
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
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
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
Paper Impact of insertion sequences on convergent evolution of Shigella species
Hawkey, Jane; Monk, Jonathan M.; Billman‐Jacobe, Helen et al. · 2020 · PLoS Genetics · DOI
Full title: Impact of insertion sequences on convergent evolution of Shigella species
Authors: Hawkey, Jane; Monk, Jonathan M.; Billman‐Jacobe, Helen; Palsson, Bernhard Ø.; Holt, Kathryn E.
Year: 2020
Venue: PLoS Genetics
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
Paper GPRuler: Metabolic gene-protein-reaction rules automatic reconstruction
Filippo, Marzia Di; Damiani, Chiara; Pescini, Dario · 2021 · PLoS Computational Biology · DOI
Full title: GPRuler: Metabolic gene-protein-reaction rules automatic reconstruction
Authors: Filippo, Marzia Di; Damiani, Chiara; Pescini, Dario
Year: 2021
Venue: PLoS Computational Biology
Paper Maximizing multi-reaction dependencies provides more accurate and precise predictions of intracellular fluxes than the principle of parsimony
Hashemi, Seirana; Razaghi‐Moghadam, Zahra; Nikoloski, Zoran · 2023 · PLoS Computational Biology · DOI
Full title: Maximizing multi-reaction dependencies provides more accurate and precise predictions of intracellular fluxes than the principle of parsimony
Authors: Hashemi, Seirana; Razaghi‐Moghadam, Zahra; Nikoloski, Zoran
Year: 2023
Venue: PLoS Computational Biology
Paper A pipeline for the reconstruction and evaluation of context-specific human metabolic models at a large-scale
Vieira, Vítor; Ferreira, Jorge; Rocha, Miguel · 2022 · PLoS Computational Biology · DOI
Full title: A pipeline for the reconstruction and evaluation of context-specific human metabolic models at a large-scale
Authors: Vieira, Vítor; Ferreira, Jorge; Rocha, Miguel
Year: 2022
Venue: PLoS Computational Biology
Paper The limitations of phenotype prediction in metabolism
Yubero, Pablo; Lavin, Alvar A.; Poyatos, Juan F. · 2023 · PLoS Computational Biology · DOI
Full title: The limitations of phenotype prediction in metabolism
Authors: Yubero, Pablo; Lavin, Alvar A.; Poyatos, Juan F.
Year: 2023
Venue: PLoS Computational Biology
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
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
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
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
Paper Flux balance analysis-based metabolic modeling of microbial secondary metabolism: Current status and outlook
Qiu, Sizhe; Yang, Aidong; Zeng, Hong · 2023 · PLoS Computational Biology · DOI
Full title: Flux balance analysis-based metabolic modeling of microbial secondary metabolism: Current status and outlook
Authors: Qiu, Sizhe; Yang, Aidong; Zeng, Hong
Year: 2023
Venue: PLoS Computational Biology
Paper Reconstruction of Danio rerio Metabolic Model Accounting for Subcellular Compartmentalisation
Bekaert, Michaël · 2012 · PLoS ONE · DOI
Full title: Reconstruction of Danio rerio Metabolic Model Accounting for Subcellular Compartmentalisation
Authors: Bekaert, Michaël
Year: 2012
Venue: PLoS ONE
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
Paper BioMog: A Computational Framework for the De Novo Generation or Modification of Essential Biomass Components
Tervo, Christopher J.; Reed, Jennifer L. · 2013 · PLoS ONE · DOI
Full title: BioMog: A Computational Framework for the De Novo Generation or Modification of Essential Biomass Components
Authors: Tervo, Christopher J.; Reed, Jennifer L.
Year: 2013
Venue: PLoS ONE
Paper Dissecting Leishmania infantum Energy Metabolism - A Systems Perspective
Subramanian, Abhishek; Jhawar, Jitesh; Sarkar, Ram Rup · 2015 · PLoS ONE · DOI
Full title: Dissecting Leishmania infantum Energy Metabolism - A Systems Perspective
Authors: Subramanian, Abhishek; Jhawar, Jitesh; Sarkar, Ram Rup
Year: 2015
Venue: PLoS ONE
Paper 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 · PLoS ONE · DOI
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.
Year: 2016
Venue: PLoS ONE
Paper Flux Balance Analysis with Objective Function Defined by Proteomics Data—Metabolism of Mycobacterium tuberculosis Exposed to Mefloquine
Montezano, Daniel; Meek, Laura; Gupta, Rashmi et al. · 2015 · PLoS ONE · DOI
Full title: Flux Balance Analysis with Objective Function Defined by Proteomics Data—Metabolism of Mycobacterium tuberculosis Exposed to Mefloquine
Authors: Montezano, Daniel; Meek, Laura; Gupta, Rashmi; Bermudez, Luiz E.; Bermudez, J.C.M.
Year: 2015
Venue: PLoS ONE
Paper Predictive Potential of Flux Balance Analysis of Saccharomyces cerevisiae Using as Optimization Function Combinations of Cell Compartmental Objectives
Sánchez, Carlos Eduardo García; Vargas-García, Cesar A.; Torres, Rodrigo · 2012 · PLoS ONE · DOI
Full title: Predictive Potential of Flux Balance Analysis of Saccharomyces cerevisiae Using as Optimization Function Combinations of Cell Compartmental Objectives
Authors: Sánchez, Carlos Eduardo García; Vargas-García, Cesar A.; Torres, Rodrigo
Year: 2012
Venue: PLoS ONE
Paper 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 · PLoS ONE · DOI
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
Year: 2016
Venue: PLoS ONE
Paper Genome-Scale Model Reveals Metabolic Basis of Biomass Partitioning in a Model Diatom
Levering, Jennifer; Broddrick, Jared T.; Dupont, Christopher L. et al. · 2016 · PLoS ONE · DOI
Full title: Genome-Scale Model Reveals Metabolic Basis of Biomass Partitioning in a Model Diatom
Authors: Levering, Jennifer; Broddrick, Jared T.; Dupont, Christopher L.; Peers, Graham; Beeri, Karen; Mayers, Joshua J.; Gallina, Alessandra A.; Allen, Andrew E.; Palsson, Bernhard Ø.; Zengler, Karsten
Year: 2016
Venue: PLoS ONE
Paper Type and capacity of glucose transport influences succinate yield in two-stage cultivations
Kyselova, L.; Kreitmayer, Diana; Kremling, Andreas et al. · 2018 · Microbial Cell Factories · DOI
Full title: Type and capacity of glucose transport influences succinate yield in two-stage cultivations
Authors: Kyselova, L.; Kreitmayer, Diana; Kremling, Andreas; Bettenbrock, Katja
Year: 2018
Venue: Microbial Cell Factories
Paper 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 · PLoS ONE · DOI
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.
Year: 2016
Venue: PLoS ONE
Paper 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 · PLoS ONE · DOI
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
Year: 2015
Venue: PLoS ONE
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
Paper Prediction of reaction knockouts to maximize succinate production by Actinobacillus succinogenes
Nag, Ambarish; John, Peter C. St.; Crowley, Michael F. et al. · 2018 · PLoS ONE · DOI
Full title: Prediction of reaction knockouts to maximize succinate production by Actinobacillus succinogenes
Authors: Nag, Ambarish; John, Peter C. St.; Crowley, Michael F.; Bomble, Yannick J.
Year: 2018
Venue: PLoS ONE
Paper OM-FBA: Integrate Transcriptomics Data with Flux Balance Analysis to Decipher the Cell Metabolism
Weihua Guo; Xueyang Feng · 2016 · PLoS ONE · DOI
Full title: OM-FBA: Integrate Transcriptomics Data with Flux Balance Analysis to Decipher the Cell Metabolism
Authors: Weihua Guo; Xueyang Feng
Year: 2016
Venue: PLoS ONE
Paper Simulating Serial-Target Antibacterial Drug Synergies Using Flux Balance Analysis
Krueger, Andrew; Munck, Christian; Dantas, Gautam et al. · 2016 · PLoS ONE · DOI
Full title: Simulating Serial-Target Antibacterial Drug Synergies Using Flux Balance Analysis
Authors: Krueger, Andrew; Munck, Christian; Dantas, Gautam; Church, George M.; Galagan, James E.; Lehár, Joseph; Sommer, Morten Otto Alexander
Year: 2016
Venue: PLoS ONE
Paper Estimating Metabolic Fluxes Using a Maximum Network Flexibility Paradigm
Megchelenbrink, Wout; Rossell, Sergio; Huynen, Martijn A. et al. · 2015 · PLoS ONE · DOI
Full title: Estimating Metabolic Fluxes Using a Maximum Network Flexibility Paradigm
Authors: Megchelenbrink, Wout; Rossell, Sergio; Huynen, Martijn A.; Notebaart, Richard A.; Marchiori, Elena
Year: 2015
Venue: PLoS ONE
Paper Ethanol production improvement driven by genome-scale metabolic modeling and sensitivity analysis in Scheffersomyces stipitis
Acevedo, Alejandro; Conejeros, Raúl; Aroca, Germán · 2017 · PLoS ONE · DOI
Full title: Ethanol production improvement driven by genome-scale metabolic modeling and sensitivity analysis in Scheffersomyces stipitis
Authors: Acevedo, Alejandro; Conejeros, Raúl; Aroca, Germán
Year: 2017
Venue: PLoS ONE
Paper Distributed flux balance analysis simulations of serial biomass fermentation by two organisms
Vitkin, Edward; Gillis, Amichai; Polikovsky, Mark et al. · 2020 · PLoS ONE · DOI
Full title: Distributed flux balance analysis simulations of serial biomass fermentation by two organisms
Authors: Vitkin, Edward; Gillis, Amichai; Polikovsky, Mark; Bender, Barak; Golberg, Alexander; Yakhini, Zohar
Year: 2020
Venue: PLoS ONE
Paper Metabolic flux configuration determination using information entropy
Rivas‐Astroza, Marcelo; Conejeros, Raúl · 2020 · PLoS ONE · DOI
Full title: Metabolic flux configuration determination using information entropy
Authors: Rivas‐Astroza, Marcelo; Conejeros, Raúl
Year: 2020
Venue: PLoS ONE
Paper Flux prediction using artificial neural network (ANN) for the upper part of glycolysis
Nagaraja, Anamya Ajjolli; Fontaine, Nicolas; Delsaut, Mathieu et al. · 2019 · PLoS ONE · DOI
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
Year: 2019
Venue: PLoS ONE
Paper Osmoregulation in the Halophilic Bacterium Halomonas elongata: A Case Study for Integrative Systems Biology
Kindzierski, Viktoria; Raschke, Silvia; Knabe, Nicole et al. · 2017 · PLoS ONE · DOI
Full title: Osmoregulation in the Halophilic Bacterium Halomonas elongata: A Case Study for Integrative Systems Biology
Authors: Kindzierski, Viktoria; Raschke, Silvia; Knabe, Nicole; Siedler, Frank; Scheffer, Beatrix; Pflüger‐Grau, Katharina; Pfeiffer, Friedhelm; Oesterhelt, Dieter; Marı́n-Sanguino, Alberto; Kunte, Hans‐Jörg
Year: 2017
Venue: PLoS ONE
Paper Metabolic network reconstruction and phenome analysis of the industrial microbe, Escherichia coli BL21(DE3)
Kim, Hanseol; Kim, Sinyeon; Yoon, Sung Ho · 2018 · PLoS ONE · DOI
Full title: Metabolic network reconstruction and phenome analysis of the industrial microbe, Escherichia coli BL21(DE3)
Authors: Kim, Hanseol; Kim, Sinyeon; Yoon, Sung Ho
Year: 2018
Venue: PLoS ONE
Paper Constraints-based analysis identifies NAD+ recycling through metabolic reprogramming in antibiotic resistant Chromobacterium violaceum
Banerjee, Deepanwita; Raghunathan, Anu · 2019 · PLoS ONE · DOI
Full title: Constraints-based analysis identifies NAD+ recycling through metabolic reprogramming in antibiotic resistant Chromobacterium violaceum
Authors: Banerjee, Deepanwita; Raghunathan, Anu
Year: 2019
Venue: PLoS ONE
Paper <i>Vibrio natriegens</i> genome‐scale modeling reveals insights into halophilic adaptations and resource allocation
Coppens, Lucas; Tschirhart, Tanya; Leary, Dagmar H. et al. · 2023 · Molecular Systems Biology · DOI
Full title: <i>Vibrio natriegens</i> 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, W. Judson; Dana, Karl L; Vora, Gary J.; Bordel, Sergio; Ledesma‐Amaro, Rodrigo
Year: 2023
Venue: Molecular Systems Biology
Paper A study of a diauxic growth experiment using an expanded dynamic flux balance framework
Karlsen, Emil; Gylseth, Marianne; Schulz, Christian et al. · 2023 · PLoS ONE · DOI
Full title: A study of a diauxic growth experiment using an expanded dynamic flux balance framework
Authors: Karlsen, Emil; Gylseth, Marianne; Schulz, Christian; Almaas, Eivind
Year: 2023
Venue: PLoS ONE
Paper PyMiner: A method for metabolic pathway design based on the uniform similarity of substrate-product pairs and conditional search
Song, Xinfang; Dong, Mingyu; Liu, Min · 2022 · PLoS ONE · DOI
Full title: PyMiner: A method for metabolic pathway design based on the uniform similarity of substrate-product pairs and conditional search
Authors: Song, Xinfang; Dong, Mingyu; Liu, Min
Year: 2022
Venue: PLoS ONE
Paper Microbiome distribution modeling using gradient descent strategies for mock, in vitro and clinical community distributions
Velasco-Álvarez, Juan Ricardo; Torres, Nimbe; Chaírez, Isaac et al. · 2023 · PLoS ONE · DOI
Full title: Microbiome distribution modeling using gradient descent strategies for mock, in vitro and clinical community distributions
Authors: Velasco-Álvarez, Juan Ricardo; Torres, Nimbe; Chaírez, Isaac; Castrejón-Flores, José Luis
Year: 2023
Venue: PLoS ONE
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
Paper Evaluating <i>E. coli</i> 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 <i>E. coli</i> 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
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
Paper Of (Biological) Models and Simulations
Ling, Maurice HT · 2016 · MOJ Proteomics & Bioinformatics · DOI
Full title: Of (Biological) Models and Simulations
Authors: Ling, Maurice HT
Year: 2016
Venue: MOJ Proteomics & Bioinformatics
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 The Evolution of Cell Free Biomanufacturing
Vilkhovoy, Michael; Adhikari, Abhinav; Vadhin, Sandra et al. · 2020 · Processes · DOI
Full title: The Evolution of Cell Free Biomanufacturing
Authors: Vilkhovoy, Michael; Adhikari, Abhinav; Vadhin, Sandra; Varner, Jeffrey D.
Year: 2020
Venue: Processes
Paper Construction and Analysis of an Enzyme‐constrained Metabolic Model of <em>Corynebacterium glutamicum</em>
Niu, Jinhui; Mao, Zhitao; Mao, Yufeng et al. · 2022 · Preprints.org · DOI
Full title: Construction and Analysis of an Enzyme‐constrained Metabolic Model of <em>Corynebacterium glutamicum</em>
Authors: Niu, Jinhui; Mao, Zhitao; Mao, Yufeng; Wu, Ke; Shi, Zhenkun; Yuan, Qianqian; Cai, Jingyi; Ma, Hongwu
Year: 2022
Venue: Preprints.org
Paper ECMpy, a Simplified Workflow for Constructing Enzymatic Constrained Metabolic Network Model
Mao, Zhitao; Zhao, Xin; Yang, Xue et al. · 2022 · Biomolecules · DOI
Full title: ECMpy, a Simplified Workflow for Constructing Enzymatic Constrained Metabolic Network Model
Authors: Mao, Zhitao; Zhao, Xin; Yang, Xue; Zhang, Peiji; Du, Jiawei; Yuan, Qianqian; Ma, Hongwu
Year: 2022
Venue: Biomolecules
Paper ecBSU1: A Genome-scale Enzyme-constrained Model of <em>Bacillus subtilis</em> 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 <em>Bacillus subtilis</em> 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
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 Ten Quick Tips for Accurate Reconstruction of Prokaryotic and Eukaryotic Genome-Scale Metabolic Models
Canto-Encalada, Gabriela; Armstrong, Jenna L.; Focil-Espinosa, Carlos et al. · 2023 · Preprints.org · DOI
Full title: Ten Quick Tips for Accurate Reconstruction of Prokaryotic and Eukaryotic Genome-Scale Metabolic Models
Authors: Canto-Encalada, Gabriela; Armstrong, Jenna L.; Focil-Espinosa, Carlos; Adekunle-Fiyin, Ademikanra; Peeler, Ila; Gebbie, William; Nuñez‐Garcia, J.; Saldivar, Alexis; Martínez, Diego; Zúñiga, Cristal
Year: 2023
Venue: Preprints.org
Paper A Mechanistic Model for Genome-Scale Estimations of Metabolic Activity
Çubuk, Cankut; Loucera, Carlos; Hidalgo, Marta R. et al. · 2021 · Preprints.org · DOI
Full title: A Mechanistic Model for Genome-Scale Estimations of Metabolic Activity
Authors: Çubuk, Cankut; Loucera, Carlos; Hidalgo, Marta R.; Amadoz, Alicia; Carbonell‐Caballero, José; Peña-Chilet, María; Dopazo, Joaquı́n
Year: 2021
Venue: Preprints.org
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
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
Paper A new metabolic model of<i>Drosophila melanogaster</i>and the integrative analysis of Parkinson’s disease
Cesur, Müberra Fatma; Basile, Arianna; Patil, Kiran Raosaheb et al. · 2023 · Life Science Alliance · DOI
Full title: A new metabolic model of<i>Drosophila melanogaster</i>and the integrative analysis of Parkinson’s disease
Authors: Cesur, Müberra Fatma; Basile, Arianna; Patil, Kiran Raosaheb; Çakır, Tunahan
Year: 2023
Venue: Life Science Alliance
Paper Comprehensive genome-scale metabolic model of the human pathogen Cryptococcus neoformans: A platform for understanding pathogen metabolism and identifying new drug targets
Tezcan, Enes Fahri; Demirtas, Yigit; Çakar, Zeynep Petek et al. · 2023 · Frontiers in Bioinformatics · DOI
Full title: Comprehensive genome-scale metabolic model of the human pathogen Cryptococcus neoformans: A platform for understanding pathogen metabolism and identifying new drug targets
Authors: Tezcan, Enes Fahri; Demirtas, Yigit; Çakar, Zeynep Petek; Ülgen, Kutlu Ö.
Year: 2023
Venue: Frontiers in Bioinformatics
Paper Succinate Overproduction: A Case Study of Computational Strain Design Using a Comprehensive Escherichia coli Kinetic Model
Khodayari, Ali; Chowdhury, Anupam; Maranas, Costas D. · 2015 · Frontiers in Bioengineering and Biotechnology · DOI
Full title: Succinate Overproduction: A Case Study of Computational Strain Design Using a Comprehensive Escherichia coli Kinetic Model
Authors: Khodayari, Ali; Chowdhury, Anupam; Maranas, Costas D.
Year: 2015
Venue: Frontiers in Bioengineering and Biotechnology
Paper Metabolic Network Discovery by Top-Down and Bottom-Up Approaches and Paths for Reconciliation
Çakır, 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: Çakır, Tunahan; Khatibipour, Mohammad Jafar
Year: 2014
Venue: Frontiers in Bioengineering and Biotechnology
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
Paper Toward a systems-level understanding of gene regulatory, protein interaction, and metabolic networks in cyanobacteria
Hernández-Prieto, Miguel A.; Semeniuk, T. A.; Futschik, Matthias E. · 2014 · Frontiers in Genetics · DOI
Full title: Toward a systems-level understanding of gene regulatory, protein interaction, and metabolic networks in cyanobacteria
Authors: Hernández-Prieto, Miguel A.; Semeniuk, T. A.; Futschik, Matthias E.
Year: 2014
Venue: Frontiers in Genetics
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
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
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
Paper Modeling the Th17 and Tregs Paradigm: Implications for Cancer Immunotherapy
Corral‐Jara, Karla Fabiola; Silva, Gonçalo Rosas da; Fierro, Nora A. et al. · 2021 · Frontiers in Cell and Developmental Biology · DOI
Full title: Modeling the Th17 and Tregs Paradigm: Implications for Cancer Immunotherapy
Authors: Corral‐Jara, Karla Fabiola; Silva, Gonçalo Rosas da; Fierro, Nora A.; Soumelis, Vassili
Year: 2021
Venue: Frontiers in Cell and Developmental Biology
Paper Stable Isotopes for Tracing Cardiac Metabolism in Diseases
Karlstaedt, Anja · 2021 · Frontiers in Cardiovascular Medicine · DOI
Full title: Stable Isotopes for Tracing Cardiac Metabolism in Diseases
Authors: Karlstaedt, Anja
Year: 2021
Venue: Frontiers in Cardiovascular Medicine
Paper Dissecting Host-Pathogen Interactions in TB Using Systems-Based Omic Approaches
Borah, Khushboo; Xu, Ye; McFadden, Johnjoe · 2021 · Frontiers in Immunology · DOI
Full title: Dissecting Host-Pathogen Interactions in TB Using Systems-Based Omic Approaches
Authors: Borah, Khushboo; Xu, Ye; McFadden, Johnjoe
Year: 2021
Venue: Frontiers in Immunology
Paper Computer-aided design and implementation of efficient biosynthetic pathways to produce high added-value products derived from tyrosine in Escherichia coli
Ferreira, Sofia; Balola, Alexandra; Sveshnikova, Anastasia et al. · 2024 · Frontiers in Bioengineering and Biotechnology · DOI
Full title: Computer-aided design and implementation of efficient biosynthetic pathways to produce high added-value products derived from tyrosine in Escherichia coli
Authors: Ferreira, Sofia; Balola, Alexandra; Sveshnikova, Anastasia; Hatzimanikatis, Vassily; Vilaça, Paulo; Maia, Paulo; Carreira, Rafael; Stoney, Ruth; Carbonell, Pablo; Souza, Caio Silva; Correia, João; Lousa, Diana; Soares, Cláudio M.; Rocha, Isabel
Year: 2024
Venue: Frontiers in Bioengineering and Biotechnology
Paper Metabolic analyses elucidate non-trivial gene targets for amplifying dihydroartemisinic acid production in yeast
A. Misra; Matthew F. Conway; Joseph Johnnie et al. · 2013 · Frontiers in Microbiology · DOI
Full title: Metabolic analyses elucidate non-trivial gene targets for amplifying dihydroartemisinic acid production in yeast
Authors: A. Misra; Matthew F. Conway; Joseph Johnnie; Tabish Qureshi; Bao Lige; Anne Derrick; E. Agbo; G. Sriram
Year: 2013
Venue: Frontiers in Microbiology
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
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
Paper Mapping the Physiological Response of Oenococcus oeni to Ethanol Stress Using an Extended Genome-Scale Metabolic Model
Contreras, Ángela; Ribbeck, Magdalena; Gutiérrez, Guillermo Dávila et al. · 2018 · Frontiers in Microbiology · DOI
Full title: Mapping the Physiological Response of Oenococcus oeni to Ethanol Stress Using an Extended Genome-Scale Metabolic Model
Authors: Contreras, Ángela; Ribbeck, Magdalena; Gutiérrez, Guillermo Dávila; Cañón, Pablo; Mendoza, Sebastián N.; Agosín, Eduardo
Year: 2018
Venue: Frontiers in Microbiology
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
Paper Microbial Systems Ecology to Understand Cross-Feeding in Microbiomes
Mataigne, Victor; Vannier, Nathan; Vandenkoornhuyse, Philippe et al. · 2021 · Frontiers in Microbiology · DOI
Full title: Microbial Systems Ecology to Understand Cross-Feeding in Microbiomes
Authors: Mataigne, Victor; Vannier, Nathan; Vandenkoornhuyse, Philippe; Hacquard, Stéphane
Year: 2021
Venue: Frontiers in Microbiology
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
Paper From DNA to FBA: How to Build Your Own Genome-Scale Metabolic Model
Cuevas, Daniel; Edirisinghe, Janaka N.; Henry, Chris et al. · 2016 · Frontiers in Microbiology · DOI
Full title: From DNA to FBA: How to Build Your Own Genome-Scale Metabolic Model
Authors: Cuevas, Daniel; Edirisinghe, Janaka N.; Henry, Chris; Overbeek, Ross; O’Connell, Taylor; Edwards, Robert A.
Year: 2016
Venue: Frontiers in Microbiology
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
Paper Constraint-Based Reconstruction and Analyses of Metabolic Models: Open-Source Python Tools and Applications to Cancer
Ng, Raymond T.; Lee, J.; Baloni, Priyanka et al. · 2022 · Frontiers in Oncology · DOI
Full title: Constraint-Based Reconstruction and Analyses of Metabolic Models: Open-Source Python Tools and Applications to Cancer
Authors: Ng, Raymond T.; Lee, J.; Baloni, Priyanka; Diener, Christian; Heath, James R.; Su, Yapeng
Year: 2022
Venue: Frontiers in Oncology
Paper Model-driven approach for the production of butyrate from CO2/H2 by a novel co-culture of C. autoethanogenum and C. beijerinckii
Benito-Vaquerizo, Sara; Nouse, Niels; Schaap, Peter J. et al. · 2022 · Frontiers in Microbiology · DOI
Full title: Model-driven approach for the production of butyrate from CO2/H2 by a novel co-culture of C. autoethanogenum and C. beijerinckii
Authors: Benito-Vaquerizo, Sara; Nouse, Niels; Schaap, Peter J.; Hugenholtz, Jeroen; Brul, Stanley; López‐Contreras, Ana M.; Santos, Vítor A. P. Martins dos; Suárez‐Diez, María
Year: 2022
Venue: Frontiers in Microbiology
Paper Phenotypic response of yeast metabolic network to availability of proteinogenic amino acids
Simensen, Vetle; Seif, Yara; Almaas, Eivind · 2022 · Frontiers in Molecular Biosciences · DOI
Full title: Phenotypic response of yeast metabolic network to availability of proteinogenic amino acids
Authors: Simensen, Vetle; Seif, Yara; Almaas, Eivind
Year: 2022
Venue: Frontiers in Molecular Biosciences
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
Paper MetaboTools: A Comprehensive Toolbox for Analysis of Genome-Scale Metabolic Models
Aurich, Maike K.; Fleming, Ronan M. T.; Thiele, Ines · 2016 · Frontiers in Physiology · DOI
Full title: MetaboTools: A Comprehensive Toolbox for Analysis of Genome-Scale Metabolic Models
Authors: Aurich, Maike K.; Fleming, Ronan M. T.; Thiele, Ines
Year: 2016
Venue: Frontiers in Physiology
Paper A Systematic Strategy to Find Potential Therapeutic Targets for Pseudomonas aeruginosa Using Integrated Computational Models
Filho, Fernando Medeiros; Nascimento, Ana Paula Barbosa do; Costa, Maiana de Oliveira Cerqueira e et al. · 2021 · Frontiers in Molecular Biosciences · DOI
Full title: A Systematic Strategy to Find Potential Therapeutic Targets for Pseudomonas aeruginosa Using Integrated Computational Models
Authors: Filho, Fernando Medeiros; Nascimento, Ana Paula Barbosa do; Costa, Maiana de Oliveira Cerqueira e; Merigueti, Thiago Castanheira; Menezes, Márcio Argollo de; Nicolás, Marisa; Santos, Marcelo Trindade dos; Carvalho-Assef, Ana Paula D’Alincourt; Silva, Fabrício Alves Barbosa da
Year: 2021
Venue: Frontiers in Molecular Biosciences
Paper DataSheet1_Understanding Metabolic Flux Behaviour in Whole-Cell Model Output.pdf
(11849009), Sophie Landon; (10955449), Oliver Chalkley; (11849012), Gus Breese et al. · 2021 · Figshare · DOI
Full title: DataSheet1_Understanding Metabolic Flux Behaviour in Whole-Cell Model Output.pdf
Authors: (11849009), Sophie Landon; (10955449), Oliver Chalkley; (11849012), Gus Breese; (3594455), Claire Grierson; (256269), Lucia Marucci
Year: 2021
Venue: Figshare
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
Paper Integration of a constraint-based metabolic model of Brassica napus developing seeds with 13C-metabolic flux analysis
Hay, Jordan O.; Shi, Hai; Heinzel, Nicolas et al. · 2014 · Frontiers in Plant Science · DOI
Full title: Integration of a constraint-based metabolic model of Brassica napus developing seeds with 13C-metabolic flux analysis
Authors: Hay, Jordan O.; Shi, Hai; Heinzel, Nicolas; Hebbelmann, Inga; Rolletschek, Hardy; Schwender, Jörg
Year: 2014
Venue: Frontiers in Plant Science
Paper Recent Progress in the Development of Metabolome Databases for Plant Systems Biology
Fukushima, Atsushi; Kusano, Miyako · 2013 · Frontiers in Plant Science · DOI
Full title: Recent Progress in the Development of Metabolome Databases for Plant Systems Biology
Authors: Fukushima, Atsushi; Kusano, Miyako
Year: 2013
Venue: Frontiers in Plant Science
Paper Cancer Metabolism: A Modeling Perspective
Ghaffari, Pouyan; Mardinoğlu, Adil; Nielsen, Jens · 2015 · Frontiers in Physiology · DOI
Full title: Cancer Metabolism: A Modeling Perspective
Authors: Ghaffari, Pouyan; Mardinoğlu, Adil; Nielsen, Jens
Year: 2015
Venue: Frontiers in Physiology
Paper Elucidating Plant-Microbe-Environment Interactions Through Omics-Enabled Metabolic Modelling Using Synthetic Communities
Beck, Ashley E.; Kleiner, Manuel; Garrell, Anna-Katharina · 2022 · Frontiers in Plant Science · DOI
Full title: Elucidating Plant-Microbe-Environment Interactions Through Omics-Enabled Metabolic Modelling Using Synthetic Communities
Authors: Beck, Ashley E.; Kleiner, Manuel; Garrell, Anna-Katharina
Year: 2022
Venue: Frontiers in Plant Science
Paper Metabolome-Wide Analysis of Stable Isotope Labeling—Is It Worth the Effort?
Daniel Weindl; A. Wegner; Karsten Hiller · 2015 · Frontiers in Physiology · DOI
Full title: Metabolome-Wide Analysis of Stable Isotope Labeling—Is It Worth the Effort?
Authors: Daniel Weindl; A. Wegner; Karsten Hiller
Year: 2015
Venue: Frontiers in Physiology
Paper Modeling Rice Metabolism: From Elucidating Environmental Effects on Cellular Phenotype to Guiding Crop Improvement
Lakshmanan, Meiyappan; Cheung, C. Y. Maurice; Mohanty, Bijayalaxmi et al. · 2016 · Frontiers in Plant Science · DOI
Full title: Modeling Rice Metabolism: From Elucidating Environmental Effects on Cellular Phenotype to Guiding Crop Improvement
Authors: Lakshmanan, Meiyappan; Cheung, C. Y. Maurice; Mohanty, Bijayalaxmi; Lee, Dong‐Yup
Year: 2016
Venue: Frontiers in Plant Science
Paper Functional genomics tools applied to plant metabolism: a survey on plant respiration, its connections and the annotation of complex gene functions
Araújo, Wagner L.; Nunes‐Nesi, Adriano; Williams, Thomas Christopher Rhys · 2012 · Frontiers in Plant Science · DOI
Full title: Functional genomics tools applied to plant metabolism: a survey on plant respiration, its connections and the annotation of complex gene functions
Authors: Araújo, Wagner L.; Nunes‐Nesi, Adriano; Williams, Thomas Christopher Rhys
Year: 2012
Venue: Frontiers in Plant Science
Paper Understanding Antimicrobial Resistance Using Genome-Scale Metabolic Modeling
Alonso-Vásquez, Tania; Fondi, Marco; Perrin, Elena · 2023 · Antibiotics · DOI
Full title: Understanding Antimicrobial Resistance Using Genome-Scale Metabolic Modeling
Authors: Alonso-Vásquez, Tania; Fondi, Marco; Perrin, Elena
Year: 2023
Venue: Antibiotics
Paper Systematic Multi-Omics Integration (MOI) Approach in Plant Systems Biology
Jamil, Ili Nadhirah; Remali, Juwairiah; Azizan, Kamalrul Azlan et al. · 2020 · Frontiers in Plant Science · DOI
Full title: Systematic Multi-Omics Integration (MOI) Approach in Plant Systems Biology
Authors: Jamil, Ili Nadhirah; Remali, Juwairiah; Azizan, Kamalrul Azlan; Muhammad, Nor Azlan Nor; Arita, Masanori; Goh, Hoe‐Han; Aizat, Wan Mohd
Year: 2020
Venue: Frontiers in Plant Science
Paper ECMpy, a Simplified Workflow for Constructing Enzymatic Constrained Metabolic Network Model
Mao, Zhitao; Zhao, Xin; Yang, Xue et al. · 2022 · Biomolecules · DOI
Full title: ECMpy, a Simplified Workflow for Constructing Enzymatic Constrained Metabolic Network Model
Authors: Mao, Zhitao; Zhao, Xin; Yang, Xue; Zhang, Peiji; Du, Jiawei; Yuan, Qianqian; Ma, Hongwu
Year: 2022
Venue: Biomolecules
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
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
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 Construction and Analysis of an Enzyme-Constrained Metabolic Model of Corynebacterium glutamicum
Niu, Jinhui; Mao, Zhitao; Mao, Yufeng et al. · 2022 · Biomolecules · 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: Biomolecules
Paper Integration of metabolomics data into metabolic networks
Töpfer, Nadine; Kleeßen, Sabrina; Nikoloski, Zoran · 2015 · Frontiers in Plant Science · DOI
Full title: Integration of metabolomics data into metabolic networks
Authors: Töpfer, Nadine; Kleeßen, Sabrina; Nikoloski, Zoran
Year: 2015
Venue: Frontiers in Plant Science
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 Genome-Scale Metabolic Model of the Human Pathogen Candida albicans: A Promising Platform for Drug Target Prediction
Viana, Romeu; Dias, Óscar; Lagoa, Davide et al. · 2020 · Journal of Fungi · DOI
Full title: Genome-Scale Metabolic Model of the Human Pathogen Candida albicans: A Promising Platform for Drug Target Prediction
Authors: Viana, Romeu; Dias, Óscar; Lagoa, Davide; Galocha, Mónica; Rocha, Isabel; Teixeira, Miguel C.
Year: 2020
Venue: Journal of Fungi
Paper Recent Developments in Systems Biology and Metabolic Engineering of Plant–Microbe Interactions
Kumar, Vishal; Baweja, Mehak; Singh, Puneet Kumar et al. · 2016 · Frontiers in Plant Science · DOI
Full title: Recent Developments in Systems Biology and Metabolic Engineering of Plant–Microbe Interactions
Authors: Kumar, Vishal; Baweja, Mehak; Singh, Puneet Kumar; Shukla, Pratyoosh
Year: 2016
Venue: Frontiers in Plant Science
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
Paper Control Theory and Systems Biology: Potential Applications in Neurodegeneration and Search for Therapeutic Targets
Angarita-Rodríguez, Andrea; González‐Giraldo, Yeimy; Rubio-Mesa, Juan J. et al. · 2023 · International Journal of Molecular Sciences · DOI
Full title: Control Theory and Systems Biology: Potential Applications in Neurodegeneration and Search for Therapeutic Targets
Authors: Angarita-Rodríguez, Andrea; González‐Giraldo, Yeimy; Rubio-Mesa, Juan J.; Aristizábal-Pachón, Andrés Felipe; Pinzón, Andrés; González, Janneth
Year: 2023
Venue: International Journal of Molecular Sciences
Paper A Two-Compartment Fermentation System to Quantify Strain-Specific Interactions in Microbial Co-Cultures
Ulmer, Andreas; Veit, Stefan; Erdemann, Florian et al. · 2023 · Bioengineering · DOI
Full title: A Two-Compartment Fermentation System to Quantify Strain-Specific Interactions in Microbial Co-Cultures
Authors: Ulmer, Andreas; Veit, Stefan; Erdemann, Florian; Freund, Andreas; Loesch, Maren; Teleki, Attila; Zeidan, Ahmad A.; Takors, Ralf
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
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
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
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 The Model System Saccharomyces cerevisiae Versus Emerging Non-Model Yeasts for the Production of Biofuels
Lacerda, Maria Priscila Franco; Oh, Eun Joong; Eckert, Carrie A. · 2020 · Life · DOI
Full title: The Model System Saccharomyces cerevisiae Versus Emerging Non-Model Yeasts for the Production of Biofuels
Authors: Lacerda, Maria Priscila Franco; Oh, Eun Joong; Eckert, Carrie A.
Year: 2020
Venue: Life
Paper Integrating Omics Data in Genome-Scale Metabolic Modeling: A Methodological Perspective for Precision Medicine
Sen, Partho; Orešič, Matej · 2023 · Metabolites · DOI
Full title: Integrating Omics Data in Genome-Scale Metabolic Modeling: A Methodological Perspective for Precision Medicine
Authors: Sen, Partho; Orešič, Matej
Year: 2023
Venue: Metabolites
Paper Stoichiometry Based Steady-State Hepatic Flux Analysis: Computational and Experimental Aspects
Orman, Mehmet A.; Mattick, John S.; Androulakis, Ioannis P. et al. · 2012 · Metabolites · DOI
Full title: Stoichiometry Based Steady-State Hepatic Flux Analysis: Computational and Experimental Aspects
Authors: Orman, Mehmet A.; Mattick, John S.; Androulakis, Ioannis P.; Berthiaume, François; Ierapetritou, Marianthi
Year: 2012
Venue: Metabolites
Paper Next-Generation Genome-Scale Metabolic Modeling through Integration of Regulatory Mechanisms
Chung, Carolina H.; Lin, Dawei; Eames, Alec et al. · 2021 · Metabolites · DOI
Full title: Next-Generation Genome-Scale Metabolic Modeling through Integration of Regulatory Mechanisms
Authors: Chung, Carolina H.; Lin, Dawei; Eames, Alec; Chandrasekaran, Sriram
Year: 2021
Venue: Metabolites
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
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
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
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 A Protocol for Generating and Exchanging (Genome-Scale) Metabolic Resource Allocation Models
Reimers, Alexandra-M.; Lindhorst, Henning; Waldherr, Steffen · 2017 · Metabolites · DOI
Full title: A Protocol for Generating and Exchanging (Genome-Scale) Metabolic Resource Allocation Models
Authors: Reimers, Alexandra-M.; Lindhorst, Henning; Waldherr, Steffen
Year: 2017
Venue: Metabolites
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
Paper Context-Specific Genome-Scale Metabolic Modelling and Its Application to the Analysis of COVID-19 Metabolic Signatures
Moškon, Miha; Režen, Tadeja · 2023 · Metabolites · DOI
Full title: Context-Specific Genome-Scale Metabolic Modelling and Its Application to the Analysis of COVID-19 Metabolic Signatures
Authors: Moškon, Miha; Režen, Tadeja
Year: 2023
Venue: Metabolites
Paper Ensemble Kinetic Modeling of Metabolic Networks from Dynamic Metabolic Profiles
Jia, Gengjie; Stephanopoulos, Gregory; Gunawan, Rudiyanto · 2012 · Metabolites · DOI
Full title: Ensemble Kinetic Modeling of Metabolic Networks from Dynamic Metabolic Profiles
Authors: Jia, Gengjie; Stephanopoulos, Gregory; Gunawan, Rudiyanto
Year: 2012
Venue: Metabolites
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
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
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
Paper Dynamic Sequence Specific Constraint-Based Modeling of Cell-Free Protein Synthesis
Dai, David; Horvath, Nicholas; Varner, Jeffrey D. · 2018 · Processes · DOI
Full title: Dynamic Sequence Specific Constraint-Based Modeling of Cell-Free Protein Synthesis
Authors: Dai, David; Horvath, Nicholas; Varner, Jeffrey D.
Year: 2018
Venue: Processes
Paper Time Integrated Flux Analysis: Exploiting the Concentration Measurements Directly for Cost-Effective Metabolic Network Flux Analysis
Portela, Rui M. C.; Richelle, Anne; Dumas, Patrick et al. · 2019 · Microorganisms · DOI
Full title: Time Integrated Flux Analysis: Exploiting the Concentration Measurements Directly for Cost-Effective Metabolic Network Flux Analysis
Authors: Portela, Rui M. C.; Richelle, Anne; Dumas, Patrick; Stosch, Moritz von
Year: 2019
Venue: Microorganisms
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
Paper Integration of Time-Series Transcriptomic Data with Genome-Scale CHO Metabolic Models for mAb Engineering
Huang, Zhuangrong; Yoon, Seongkyu · 2020 · Processes · DOI
Full title: Integration of Time-Series Transcriptomic Data with Genome-Scale CHO Metabolic Models for mAb Engineering
Authors: Huang, Zhuangrong; Yoon, Seongkyu
Year: 2020
Venue: Processes
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
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
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
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
Paper Accelerating Biologics Manufacturing by Upstream Process Modelling
Kornecki, Martin; Strube, Jochen · 2019 · Processes · DOI
Full title: Accelerating Biologics Manufacturing by Upstream Process Modelling
Authors: Kornecki, Martin; Strube, Jochen
Year: 2019
Venue: Processes
Paper The Evolution of Cell Free Biomanufacturing
Vilkhovoy, Michael; Adhikari, Abhinav; Vadhin, Sandra et al. · 2020 · Processes · DOI
Full title: The Evolution of Cell Free Biomanufacturing
Authors: Vilkhovoy, Michael; Adhikari, Abhinav; Vadhin, Sandra; Varner, Jeffrey D.
Year: 2020
Venue: Processes
Paper Production of High Added-Value Chemicals in Basfia succiniciproducens: Role of Medium Composition
Bartos, Hunor; Balázs, Márta; Kuzman, Ildikó Hajnalka et al. · 2021 · Sustainability · DOI
Full title: Production of High Added-Value Chemicals in Basfia succiniciproducens: Role of Medium Composition
Authors: Bartos, Hunor; Balázs, Márta; Kuzman, Ildikó Hajnalka; Lányi, Szabolcs; Miklóssy, Ildikó
Year: 2021
Venue: Sustainability
Paper True and Illusory Benefits of Modeling: Comment on “Genome-Scale Metabolic Network Reconstruction and In Silico Analysis of Hexanoic Acid Producing Megasphaera elsdenii. Microorganisms 2020, 8, 539”
Panikov, Nicolai · 2020 · Microorganisms · DOI
Full title: True and Illusory Benefits of Modeling: Comment on “Genome-Scale Metabolic Network Reconstruction and In Silico Analysis of Hexanoic Acid Producing Megasphaera elsdenii. Microorganisms 2020, 8, 539”
Authors: Panikov, Nicolai
Year: 2020
Venue: Microorganisms
Paper &amp;lt;i&amp;gt;cysA, cysP, and rpoS&amp;lt;/i&amp;gt; mutations increase the power density in &amp;lt;i&amp;gt;P. aeruginosa&amp;lt;/i&amp;gt; microbial fuel cells: Performing enhancement based on metabolic flux analysis
Mejía, Juan Diego; Rojas, Cindy Stephany; Avellaneda-Franco, Laura et al. · 2013 · Advances in Bioscience and Biotechnology · DOI
Full title: &amp;lt;i&amp;gt;cysA, cysP, and rpoS&amp;lt;/i&amp;gt; mutations increase the power density in &amp;lt;i&amp;gt;P. aeruginosa&amp;lt;/i&amp;gt; microbial fuel cells: Performing enhancement based on metabolic flux analysis
Authors: Mejía, Juan Diego; Rojas, Cindy Stephany; Avellaneda-Franco, Laura; Gomez, David; Arias, Beatriz Helena Correa; Velasco, Nubia; Montañez, Maria Teresa Cortes; Vives, Martha J.; Barrios, Andrés Fernando González
Year: 2013
Venue: Advances in Bioscience and Biotechnology
Paper Minimal Cut Sets and the Use of Failure Modes in Metabolic Networks
Clark, Sangaalofa Tooki; Verwoerd, W.S. · 2012 · Metabolites · DOI
Full title: Minimal Cut Sets and the Use of Failure Modes in Metabolic Networks
Authors: Clark, Sangaalofa Tooki; Verwoerd, W.S.
Year: 2012
Venue: Metabolites
Paper How to Tackle Underdeterminacy in Metabolic Flux Analysis? A Tutorial and Critical Review
Bogaerts, Philippe; Wouwer, Alain Vande · 2021 · Processes · DOI
Full title: How to Tackle Underdeterminacy in Metabolic Flux Analysis? A Tutorial and Critical Review
Authors: Bogaerts, Philippe; Wouwer, Alain Vande
Year: 2021
Venue: Processes
Paper Parameter Identification in Metabolic Reaction Networks by Means of Multiple Steady-State Measurements
Palombo, Giovanni; Borri, Alessandro; Papa, Federico et al. · 2023 · Symmetry · DOI
Full title: Parameter Identification in Metabolic Reaction Networks by Means of Multiple Steady-State Measurements
Authors: Palombo, Giovanni; Borri, Alessandro; Papa, Federico; Papi, Marco; Palumbo, Pasquale
Year: 2023
Venue: Symmetry
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
Paper Polyamine-Mediated Growth Regulation in Microalgae: Integrating Redox Balance and Amino Acids Pathway into Metabolic Engineering
Lavandosque, Leandro Luis; Winck, Flávia Vischi · 2025 · SynBio · DOI
Full title: Polyamine-Mediated Growth Regulation in Microalgae: Integrating Redox Balance and Amino Acids Pathway into Metabolic Engineering
Authors: Lavandosque, Leandro Luis; Winck, Flávia Vischi
Year: 2025
Venue: SynBio
Paper Metabolic Network Modelling: Including Stochastic Effects
Ao, Ping · 2005 · arXiv (Cornell University) · DOI
Full title: Metabolic Network Modelling: Including Stochastic Effects
Authors: Ao, Ping
Year: 2005
Venue: arXiv (Cornell University)
Paper Peer Review #1 of &quot;Parameter estimation in tree graph metabolic networks (v0.1)&quot;
Runcie, D · 2016 · DOI
Full title: Peer Review #1 of &quot;Parameter estimation in tree graph metabolic networks (v0.1)&quot;
Authors: Runcie, D
Year: 2016
Paper Optimization of the bioconversion of glycerol to ethanol using &amp;lt;i&amp;gt;Escherichia coli&amp;lt;/i&amp;gt; by implementing a bi-level programming framework for proposing gene transcription control strategies based on genetic algorithms
Barreto-Rodriguez, Carol Milena; Ramirez-Angulo, Jessica Paola; Gómez, Jorge M. et al. · 2012 · Advances in Bioscience and Biotechnology · DOI
Full title: Optimization of the bioconversion of glycerol to ethanol using &amp;lt;i&amp;gt;Escherichia coli&amp;lt;/i&amp;gt; by implementing a bi-level programming framework for proposing gene transcription control strategies based on genetic algorithms
Authors: Barreto-Rodriguez, Carol Milena; Ramirez-Angulo, Jessica Paola; Gómez, Jorge M.; Achenie, Luke E. K.; Barrios, Andrés Fernando González
Year: 2012
Venue: Advances in Bioscience and Biotechnology
Paper Parameter estimation in tree graph metabolic networks
Astola, Laura; Stigter, J.D.; Roldán, Maria Victoria Gómez et al. · 2016 · DOI
Full title: Parameter estimation in tree graph metabolic networks
Authors: Astola, Laura; Stigter, J.D.; Roldán, Maria Victoria Gómez; Eeuwijk, Fred van; Hall, Robert D.; Groenenboom, Marian; Molenaar, J Jaap
Year: 2016
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
Paper Dissecting the Metabolic Reprogramming of Maize Root under Nitrogen Limiting Stress Condition
Chowdhury, Niaz Bahar; Schroeder, Wheaton L.; Sarkar, Debolina et al. · 2021 · DOI
Full title: Dissecting the Metabolic Reprogramming of Maize Root under Nitrogen Limiting Stress Condition
Authors: Chowdhury, Niaz Bahar; Schroeder, Wheaton L.; Sarkar, Debolina; Amiour, Nardjis; Quilleré, Isabelle; Hirel, Bertrand; Maranas, Costas D.; Saha, Rajib
Year: 2021
Paper A pipeline for the reconstruction and evaluation of context-specific human metabolic models at a large-scale
Vieira, Vítor; Ferreira, Jorge; Rocha, Miguel · 2022 · PLoS Computational Biology · DOI
Full title: A pipeline for the reconstruction and evaluation of context-specific human metabolic models at a large-scale
Authors: Vieira, Vítor; Ferreira, Jorge; Rocha, Miguel
Year: 2022
Venue: PLoS Computational Biology
Paper Microbial mutualism generates multistable and oscillatory growth dynamics
Amchin, Daniel B.; Martínez-Calvo, Alejandro; Datta, Sujit S. · 2022 · DOI
Full title: Microbial mutualism generates multistable and oscillatory growth dynamics
Authors: Amchin, Daniel B.; Martínez-Calvo, Alejandro; Datta, Sujit S.
Year: 2022
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 Characterizing the interplay of rubisco and nitrogenase enzymes in anaerobic-photoheterotrophically grown <i>Rhodopseudomonas palustris</i> 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 <i>Rhodopseudomonas palustris</i> CGA009 through a genome-scale metabolic and expression model
Authors: Chowdhury, Niaz Bahar; Alsiyabi, Adil; Saha, Rajib
Year: 2022
Paper CHOmpact: A reduced metabolic model of Chinese hamster ovary cells with enhanced interpretability
Val, Ioscani Jiménez del; Kyriakopoulos, Sarantos; Albrecht, Simone et al. · 2023 · Biotechnology and Bioengineering · DOI
Full title: CHOmpact: A reduced metabolic model of Chinese hamster ovary cells with enhanced interpretability
Authors: Val, Ioscani Jiménez del; Kyriakopoulos, Sarantos; Albrecht, Simone; Stöckmann, Henning; Rudd, Pauline M.; Polizzi, Karen M.; Kontoravdi, Cleo
Year: 2023
Venue: Biotechnology and Bioengineering
Paper A genome-scale metabolic reconstruction provides insight into the metabolism of the thermophilic bacterium <i>Rhodothermus marinus</i>
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 <i>Rhodothermus marinus</i>
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
Paper Quantifying the propagation of parametric uncertainty on flux balance analysis
Dinh, Hoang V.; Sarkar, Debolina; Maranas, Costas D. · 2021 · DOI
Full title: Quantifying the propagation of parametric uncertainty on flux balance analysis
Authors: Dinh, Hoang V.; Sarkar, Debolina; Maranas, Costas D.
Year: 2021
Paper A universal dynamical metabolic model representing mixotrophic growth of Chlorella sp
Pessi, Bruno Assis; Baroukh, Caroline; Bacquet, Anais et al. · 2022 · DOI
Full title: A universal dynamical metabolic model representing mixotrophic growth of Chlorella sp
Authors: Pessi, Bruno Assis; Baroukh, Caroline; Bacquet, Anais; Bernard, Olivier
Year: 2022
Paper A study of a diauxic growth experiment using an expanded dynamic flux balance framework
Karlsen, Emil; Gylseth, Marianne; Schulz, Christian et al. · 2023 · PLoS ONE · DOI
Full title: A study of a diauxic growth experiment using an expanded dynamic flux balance framework
Authors: Karlsen, Emil; Gylseth, Marianne; Schulz, Christian; Almaas, Eivind
Year: 2023
Venue: PLoS ONE
Paper Phenotype-Centric Modeling for Rational Metabolic Engineering
Valderrama-Gómez, Miguel Á.; Savageau, Michael A. · 2021 · DOI
Full title: Phenotype-Centric Modeling for Rational Metabolic Engineering
Authors: Valderrama-Gómez, Miguel Á.; Savageau, Michael A.
Year: 2021
Paper Data-Driven Flow-Map Models for Data-Efficient Discovery of Dynamics and Fast Uncertainty Quantification of Biological and Biochemical Systems
Makrygiorgos, Georgios; Berliner, Aaron J.; Shi, Fengzhe et al. · 2022 · DOI
Full title: Data-Driven Flow-Map Models for Data-Efficient Discovery of Dynamics and Fast Uncertainty Quantification of Biological and Biochemical Systems
Authors: Makrygiorgos, Georgios; Berliner, Aaron J.; Shi, Fengzhe; Clark, Douglas S.; Arkin, Adam P.; Mesbah, Ali
Year: 2022
Paper Integration of physiologically relevant photosynthetic energy flows into whole genome models of light-driven metabolism
Broddrick, Jared T.; Ware, Maxwell A.; Jallet, Denis et al. · 2021 · DOI
Full title: Integration of physiologically relevant photosynthetic energy flows into whole genome models of light-driven metabolism
Authors: Broddrick, Jared T.; Ware, Maxwell A.; Jallet, Denis; Palsson, Bernhard Ø.; Peers, Graham
Year: 2021
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
Paper Dynamic genome-scale modeling of <i>Saccharomyces cerevisiae</i> unravels mechanisms for ester formation during alcoholic fermentation
Scott, William T.; Henriques, David; Smid, Eddy J. et al. · 2022 · DOI
Full title: Dynamic genome-scale modeling of <i>Saccharomyces cerevisiae</i> unravels mechanisms for ester formation during alcoholic fermentation
Authors: Scott, William T.; Henriques, David; Smid, Eddy J.; Notebaart, Richard A.; Balsa‐Canto, Eva
Year: 2022
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
Paper Phenotypic response of yeast metabolic network to availability of proteinogenic amino acids
Simensen, Vetle; Seif, Yara; Almaas, Eivind · 2022 · DOI
Full title: Phenotypic response of yeast metabolic network to availability of proteinogenic amino acids
Authors: Simensen, Vetle; Seif, Yara; Almaas, Eivind
Year: 2022
Paper Mathematical reconstruction of the metabolic network in an in-vitro multiple myeloma model
Vera-Sigüenza, Elías; Escribano-Gonzalez, Cristina; Serrano‐Gonzalo, Irene et al. · 2022 · DOI
Full title: Mathematical reconstruction of the metabolic network in an in-vitro multiple myeloma model
Authors: Vera-Sigüenza, Elías; Escribano-Gonzalez, Cristina; Serrano‐Gonzalo, Irene; Eskla, Kattri‐Liis; Spill, Fabian; Tennant, Daniel A.
Year: 2022
Paper MAMBA: a model-driven, constraint-based multiomic integration method
Ugidos, Manuel; Nuño‐Cabanes, Carme; Tarazona, Sonia et al. · 2022 · DOI
Full title: MAMBA: a model-driven, constraint-based multiomic integration method
Authors: Ugidos, Manuel; Nuño‐Cabanes, Carme; Tarazona, Sonia; Ferrer, Alberto; Nielsen, Lars K.; Rodríguez‐Navarro, Susana; Mas, Igor Marín de; Conesa, Ana
Year: 2022
Paper mergem : merging and comparing genome-scale metabolic models using universal identifiers
Hari, Archana; Lobo, Daniel · 2022 · DOI
Full title: mergem : merging and comparing genome-scale metabolic models using universal identifiers
Authors: Hari, Archana; Lobo, Daniel
Year: 2022
Paper A Novel Algorithm to Calculate Elementary Modes: Analysis of Campylobacter jejuni Metabolism
Said, Yanica; Singh, Dipali; Sebu, Cristiana et al. · 2023 · DOI
Full title: A Novel Algorithm to Calculate Elementary Modes: Analysis of Campylobacter jejuni Metabolism
Authors: Said, Yanica; Singh, Dipali; Sebu, Cristiana; Poolman, Mark G.
Year: 2023
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
Paper Novel Context-Specific Genome-Scale Modelling Explores the Potential of <i>Chlamydomonas reinhardtii</i> for Synthetic Biology Applications
Yao, Herbert; Dahal, Sanjeev; Yang, Laurence · 2022 · DOI
Full title: Novel Context-Specific Genome-Scale Modelling Explores the Potential of <i>Chlamydomonas reinhardtii</i> for Synthetic Biology Applications
Authors: Yao, Herbert; Dahal, Sanjeev; Yang, Laurence
Year: 2022
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
Paper Model-driven approach for the production of butyrate from CO <sub>2</sub> /H <sub>2</sub> by a novel co-culture of <i>C. autoethanogenum</i> and <i>C. beijerinckii</i>
Benito-Vaquerizo, Sara; Nouse, Niels; Schaap, Peter J. et al. · 2022 · DOI
Full title: Model-driven approach for the production of butyrate from CO <sub>2</sub> /H <sub>2</sub> by a novel co-culture of <i>C. autoethanogenum</i> and <i>C. beijerinckii</i>
Authors: Benito-Vaquerizo, Sara; Nouse, Niels; Schaap, Peter J.; Hugenholtz, Jeroen; Brul, Stanley; López‐Contreras, Ana M.; Santos, Vítor A. P. Martins dos; Suárez‐Diez, María
Year: 2022
Paper Analysis of the genome-scale metabolic model of <i>Bacillus subtilis</i> 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 <i>Bacillus subtilis</i> to design novel in-silico strategies for native and recombinant L-asparaginase overproduction
Authors: Barge, Nisha Sanjay; Sahoo, Ansuman; Dasu, Veeranki Venkata
Year: 2023
Paper The limitations of phenotype prediction in metabolism
Yubero, Pablo; Lavin, Alvar A.; Poyatos, Juan F. · 2023 · PLoS Computational Biology · DOI
Full title: The limitations of phenotype prediction in metabolism
Authors: Yubero, Pablo; Lavin, Alvar A.; Poyatos, Juan F.
Year: 2023
Venue: PLoS Computational Biology
Paper Debottlenecking and reformulating feed media for improved CHO cell growth and titer by data-driven and model-guided analyses
Park, Seo‐Young; Choi, Dong‐Hyuk; Song, Jinsung et al. · 2023 · DOI
Full title: Debottlenecking and reformulating feed media for improved CHO cell growth and titer by data-driven and model-guided analyses
Authors: Park, Seo‐Young; Choi, Dong‐Hyuk; Song, Jinsung; Park, Uiseon; Cho, Hyeran; Hong, Bee Hak; Silberberg, Yaron; Lee, Dong‐Yup
Year: 2023
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
Paper Rational strain design with minimal phenotype perturbation
Narayanan, Bharath; Weilandt, Daniel; Masid, María et al. · 2024 · Nature Communications · DOI
Full title: Rational strain design with minimal phenotype perturbation
Authors: Narayanan, Bharath; Weilandt, Daniel; Masid, María; Mišković, Ljubiša; Hatzimanikatis, Vassily
Year: 2024
Venue: Nature Communications
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 A Bayesian model for genomic prediction using metabolic networks
Onogi, Akio · 2023 · DOI
Full title: A Bayesian model for genomic prediction using metabolic networks
Authors: Onogi, Akio
Year: 2023
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
Paper Time-resolved, deuterium-based fluxomics uncovers the hierarchy and dynamics of sugar processing by <i>Pseudomonas putida</i>
Volke, Daniel C.; Gurdo, Nicolás; Milanesi, Riccardo et al. · 2023 · DOI
Full title: Time-resolved, deuterium-based fluxomics uncovers the hierarchy and dynamics of sugar processing by <i>Pseudomonas putida</i>
Authors: Volke, Daniel C.; Gurdo, Nicolás; Milanesi, Riccardo; Nikel, Pablo I.
Year: 2023
Paper Sulfate limitation increases specific plasmid DNA yield and productivity in <i>E. coli</i> fed-batch processes
Gotsmy, Mathias; Strobl, Florian; Weiß, Florian et al. · 2023 · DOI
Full title: Sulfate limitation increases specific plasmid DNA yield and productivity in <i>E. coli</i> fed-batch processes
Authors: Gotsmy, Mathias; Strobl, Florian; Weiß, Florian; Gruber, Petra; Kraus, Barbara; Mairhofer, Juergen; Zanghellini, Jürgen
Year: 2023
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
Paper Proteomics and constraint-based modelling reveal enzyme kinetic properties of <i>Chlamydomonas reinhardtii</i> on a genome scale
Arend, Marius; Zimmer, David; Xu, Rudan et al. · 2022 · DOI
Full title: Proteomics and constraint-based modelling reveal enzyme kinetic properties of <i>Chlamydomonas reinhardtii</i> on a genome scale
Authors: Arend, Marius; Zimmer, David; Xu, Rudan; Sommer, Frederick; Mühlhaus, Timo; Nikoloski, Zoran
Year: 2022
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
Paper Integrated Constraint-Based Modeling of E. coli Cell-Free Protein Synthesis
Vilkhovoy, Michael; Dammalapati, Sruti; Vadhin, Sandra et al. · 2023 · DOI
Full title: Integrated Constraint-Based Modeling of E. coli Cell-Free Protein Synthesis
Authors: Vilkhovoy, Michael; Dammalapati, Sruti; Vadhin, Sandra; Adhikari, Abhinav; Varner, Jeffrey D.
Year: 2023
Paper Stochastic modeling of the dynamics of Salmonella infection of epithelial cells
Hannig, Jennifer; Beygi, Alireza; Ackermann, Jörg et al. · 2023 · DOI
Full title: Stochastic modeling of the dynamics of Salmonella infection of epithelial cells
Authors: Hannig, Jennifer; Beygi, Alireza; Ackermann, Jörg; Amstein, Leonie; Welsch, Christoph; Đikić, Ivan; Koch, Ina
Year: 2023
Paper Improving genome-scale metabolic models of incomplete genomes with deep learning
Boer, Meine D.; Melkonian, Chrats; Zafeiropoulos, Haris et al. · 2023 · DOI
Full title: Improving genome-scale metabolic models of incomplete genomes with deep learning
Authors: Boer, Meine D.; Melkonian, Chrats; Zafeiropoulos, Haris; Haas, Andreas F.; Garza, Daniel; Dutilh, Bas E.
Year: 2023
Paper Targeting metabolic fluxes reverts metastatic transitions in ovarian cancer
Arora, Garhima; Langthasa, Jimpi; Banerjee, Mallar et al. · 2023 · DOI
Full title: Targeting metabolic fluxes reverts metastatic transitions in ovarian cancer
Authors: Arora, Garhima; Langthasa, Jimpi; Banerjee, Mallar; Bhat, Ramray; Chatterjee, Samrat
Year: 2023
Paper ModelSEED v2: High-throughput genome-scale metabolic model reconstruction with enhanced energy biosynthesis pathway prediction
Faria, José P.; Liu, Filipe; Edirisinghe, Janaka N. et al. · 2023 · DOI
Full title: ModelSEED v2: High-throughput genome-scale metabolic model reconstruction with enhanced energy biosynthesis pathway prediction
Authors: Faria, José P.; Liu, Filipe; Edirisinghe, Janaka N.; Gupta, Nidhi; Seaver, Samuel M. D.; Freiburger, Andrew; Zhang, Qizhi; Weisenhorn, Pamela; Conrad, Neal; Zarecki, Raphy; Song, Hyun‐Seob; DeJongh, Matthew; Best, Aaron A.; Cottingham, Robert W.; Arkin, Adam P.; Henry, Christopher S.
Year: 2023
Paper CFSA: Comparative Flux Sampling Analysis as a Guide for Strain Design
Rosmalen, Rik P. van; Moreno‐Paz, Sara; Duman‐Özdamar, Zeynep Efsun et al. · 2023 · DOI
Full title: CFSA: Comparative Flux Sampling Analysis as a Guide for Strain Design
Authors: Rosmalen, Rik P. van; Moreno‐Paz, Sara; Duman‐Özdamar, Zeynep Efsun; Suárez‐Diez, María
Year: 2023
Paper BayFlux: A <i>Bay</i> esian method to quantify metabolic <i>Flux</i> es and their uncertainty at the genome scale
Backman, Tyler W. H.; Schenk, Christina; Radivojević, Tijana et al. · 2023 · DOI
Full title: BayFlux: A <i>Bay</i> esian method to quantify metabolic <i>Flux</i> 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
Paper Genome-scale metabolic models consistently predict <i>in vitro</i> characteristics of <i>Corynebacterium striatum</i>
Bäuerle, Famke; Gusak, Gwendolyn O.; Camus, Laura et al. · 2023 · DOI
Full title: Genome-scale metabolic models consistently predict <i>in vitro</i> characteristics of <i>Corynebacterium striatum</i>
Authors: Bäuerle, Famke; Gusak, Gwendolyn O.; Camus, Laura; Heilbronner, Simon; Dräger, Andreas
Year: 2023
Paper Unraveling principles of thermodynamics for genome-scale metabolic networks using graph neural networks
Fan, Wenchao; Ding, Chuyun; Huang, Dan et al. · 2024 · DOI
Full title: Unraveling principles of thermodynamics for genome-scale metabolic networks using graph neural networks
Authors: Fan, Wenchao; Ding, Chuyun; Huang, Dan; Zheng, Weiyan; Dai, Ziwei
Year: 2024
Paper lista -GEM: the genome-scale metabolic reconstruction of Lipomyces starkeyi
Almeida, Eduardo Luís Menezes de; Ferreira, Maurício Alexander de Moura; Silveira, Wendel Batista da · 2023 · DOI
Full title: lista -GEM: the genome-scale metabolic reconstruction of Lipomyces starkeyi
Authors: Almeida, Eduardo Luís Menezes de; Ferreira, Maurício Alexander de Moura; Silveira, Wendel Batista da
Year: 2023
Paper First Genome-Scale Metabolic Modeling of <i>Brucella abortus</i> Predicts Pathogen Gene Essentiality and New Drug Target
Pinto, Bruno Ribeiro; Oliveira, Filipe Vilaça Guimarães de; Fernandes, Miquéias et al. · 2023 · DOI
Full title: First Genome-Scale Metabolic Modeling of <i>Brucella abortus</i> Predicts Pathogen Gene Essentiality and New Drug Target
Authors: Pinto, Bruno Ribeiro; Oliveira, Filipe Vilaça Guimarães de; Fernandes, Miquéias; Lima, Alex Jerônimo Ranieri; Mendes, Tiago Antônio de Oliveira
Year: 2023
Paper Systematic analysis of microorganisms’ metabolism for selective targeting
Manshadi, Mehdi Dehghan; Setoodeh, Payam; Zare, Habil · 2023 · DOI
Full title: Systematic analysis of microorganisms’ metabolism for selective targeting
Authors: Manshadi, Mehdi Dehghan; Setoodeh, Payam; Zare, Habil
Year: 2023
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
Paper A new genome-scale metabolic model of oleaginous microalgae with refined lipid metabolism elucidates Microchloropsis gaditana mutant phenotypes.
Dupont-Thibert, Clémence; Roy, Sylvaine; Carneiro, Sónia et al. · 2023 · DOI
Full title: A new genome-scale metabolic model of oleaginous microalgae with refined lipid metabolism elucidates Microchloropsis gaditana mutant phenotypes.
Authors: Dupont-Thibert, Clémence; Roy, Sylvaine; Carneiro, Sónia; Pereira, Bruno; Careira, Rafael; Vilaça, Paulo; Collin, Séverine; Maréchal, Éric; Billey, Élodie; Curien, Gilles; Durot, Maxime; Jouhet, Juliette
Year: 2023
Paper Multi-omic characterization of antibody-producing CHO cell lines elucidates metabolic reprogramming and nutrient uptake bottlenecks
Gopalakrishnan, Saratram; Johnson, William; Valderrama-Gomez, Miguel A. et al. · 2023 · DOI
Full title: Multi-omic characterization of antibody-producing CHO cell lines elucidates metabolic reprogramming and nutrient uptake bottlenecks
Authors: Gopalakrishnan, Saratram; Johnson, William; Valderrama-Gomez, Miguel A.; Içten, Elçin; Tat, Jasmine; Lay, Fides D.; Diep, Jonathan; Gómez, Natalia; Stevens, Jennitte; Schlegel, Fabrice; Rolandi, Pablo; Kontoravdi, Cleo; Lewis, Nathan E.
Year: 2023
Paper COSMIC-dFBA: A novel multi-scale hybrid framework for bioprocess modeling
Gopalakrishnan, Saratram; Johnson, William; Valderrama-Gómez, Miguel Á. et al. · 2023 · DOI
Full title: COSMIC-dFBA: A novel multi-scale hybrid framework for bioprocess modeling
Authors: Gopalakrishnan, Saratram; Johnson, William; Valderrama-Gómez, Miguel Á.; Içten, Elçin; Tat, Jasmine; Ingram, Michael; Shek, Coral Fung; Chan, Pik K.; Schlegel, Fabrice; Rolandi, Pablo; Kontoravdi, Cleo; Lewis, Nathan E.
Year: 2023
Paper Understanding systems level metabolic adaptation resulting from osmotic stress
Tremblay, Alexandre; Bekiaris, Pavlos Stephanos; Klamt, Steffen et al. · 2024 · DOI
Full title: Understanding systems level metabolic adaptation resulting from osmotic stress
Authors: Tremblay, Alexandre; Bekiaris, Pavlos Stephanos; Klamt, Steffen; Mahadevan, Radhakrishnan
Year: 2024
Paper Quantitative differences in anaerobic growth and metabolism of three different <i>E. coli</i> strains using <sup>13</sup> C-Metabolic Flux Analysis
Pachauri, Piyush; Desai, Trunil; Ahmad, Ahmad et al. · 2024 · DOI
Full title: Quantitative differences in anaerobic growth and metabolism of three different <i>E. coli</i> strains using <sup>13</sup> C-Metabolic Flux Analysis
Authors: Pachauri, Piyush; Desai, Trunil; Ahmad, Ahmad; Srivastava, Shireesh
Year: 2024
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
Paper A constraint-based framework to reconstruct interaction networks in microbial communities
Oftadeh, Omid; Sahin, Asli; Vayena, Evangelia et al. · 2024 · DOI
Full title: A constraint-based framework to reconstruct interaction networks in microbial communities
Authors: Oftadeh, Omid; Sahin, Asli; Vayena, Evangelia; Hatzimanikatis, Vassily
Year: 2024
Paper BayesianSSA: a Bayesian statistical model based on structural sensitivity analysis for predicting responses to enzyme perturbations in metabolic networks
Hosoda, Shion; Iwata, Hisashi; Miura, Takuya et al. · 2024 · DOI
Full title: BayesianSSA: a Bayesian statistical model based on structural sensitivity analysis for predicting responses to enzyme perturbations in metabolic networks
Authors: Hosoda, Shion; Iwata, Hisashi; Miura, Takuya; Tanabe, Maiko; Okada, Takashi; Mochizuki, Atsushi; Sato, Miwa
Year: 2024
Paper DLTKcat: deep learning based prediction of temperature dependent enzyme turnover rates
Qiu, Sizhe; Zhao, Simiao; Yang, Aidong · 2023 · DOI
Full title: DLTKcat: deep learning based prediction of temperature dependent enzyme turnover rates
Authors: Qiu, Sizhe; Zhao, Simiao; Yang, Aidong
Year: 2023
Paper Entangled stoichiometric objectives shape microbial catabolism
Remeijer, Maaike; Bruggeman, Frank J. · 2025 · DOI
Full title: Entangled stoichiometric objectives shape microbial catabolism
Authors: Remeijer, Maaike; Bruggeman, Frank J.
Year: 2025
Paper Experiments and simulations on short chain fatty acid production in a colonic bacterial community
Yu, Bea; Dukovski, Ilija; Kong, David S. et al. · 2018 · Mass. Ave. · DOI
Full title: Experiments and simulations on short chain fatty acid production in a colonic bacterial community
Authors: Yu, Bea; Dukovski, Ilija; Kong, David S.; Bobrow, Johanna; Ostrinskaya, Alla; Segrè, Daniel; Thorsen, Todd
Year: 2018
Venue: Mass. Ave.
Paper Emergent sub-population behavior uncovered with a community dynamic metabolic model of <i>Escherichia coli</i> diauxic growth
Succurro, A.; Segrè, Daniel; Ebenhöh, Oliver · 2018 · DOI
Full title: Emergent sub-population behavior uncovered with a community dynamic metabolic model of <i>Escherichia coli</i> diauxic growth
Authors: Succurro, A.; Segrè, Daniel; Ebenhöh, Oliver
Year: 2018
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 Uncovering novel pathways for enhancing hyaluronan synthesis in recombinant <i>Lactococcus lactis</i> : Genome-scale metabolic modelling and experimental validation
Badri, Abinaya; Raman, Karthik; Jayaraman, Guhan · 2018 · DOI
Full title: Uncovering novel pathways for enhancing hyaluronan synthesis in recombinant <i>Lactococcus lactis</i> : Genome-scale metabolic modelling and experimental validation
Authors: Badri, Abinaya; Raman, Karthik; Jayaraman, Guhan
Year: 2018
Paper Cofactors revisited – Predicting the impact of flavoprotein-related diseases on a genome scale
Wegrzyn, Agnieszka B.; Stolle, Sarah; Rienksma, Rienk A. et al. · 2018 · Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease · DOI
Full title: Cofactors revisited – Predicting the impact of flavoprotein-related diseases on a genome scale
Authors: Wegrzyn, Agnieszka B.; Stolle, Sarah; Rienksma, Rienk A.; Santos, Vítor A. P. Martins dos; Bakker, Barbara M.; Suárez‐Diez, María
Year: 2018
Venue: Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease
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
Paper A metabolic reconstruction of <i>Lactobacillus reuteri</i> 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 <i>Lactobacillus reuteri</i> 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
Paper Modeling the Interplay between Photosynthesis, CO <sub>2</sub> 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 <sub>2</sub> Fixation, and the Quinone Pool in a Purple Non-Sulfur Bacterium
Authors: Alsiyabi, Adil; Immethun, Cheryl M.; Saha, Rajib
Year: 2019
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
Paper Laboratory evolution reveals a two-dimensional rate-yield tradeoff in microbial metabolism
Cheng, Chuankai; O’Brien, Edward J.; McCloskey, Douglas et al. · 2018 · 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, José; Olson, Connor A.; LaCroix, Ryan A.; Sandberg, Troy E.; Feist, Adam M.; Palsson, Bernhard Ø.; King, Zachary A.
Year: 2018
Paper Revealing metabolic flexibility of <i>Candidatus</i> Accumulibacter phosphatis through redox cofactor analysis and metabolic network modeling
Silva, Leonor Guedes da; Olavarría, Karel; Gomes, Joana Castro et al. · 2018 · DOI
Full title: Revealing metabolic flexibility of <i>Candidatus</i> Accumulibacter phosphatis through redox cofactor analysis and metabolic network modeling
Authors: Silva, Leonor Guedes da; Olavarría, Karel; Gomes, Joana Castro; Akkermans, Kasper; Welles, Laurens; Abbas, Ben; Loosdrecht, Mark C.M. van; Wahl, A.
Year: 2018
Paper Reconstruction of consensus tissue-specific metabolic models
Correia, Sara; Costa, Bruno M.; Rocha, Miguel · 2018 · DOI
Full title: Reconstruction of consensus tissue-specific metabolic models
Authors: Correia, Sara; Costa, Bruno M.; Rocha, Miguel
Year: 2018
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
Paper A comprehensive genome-scale model for <i>Rhodosporidium toruloides</i> IFO0880 accounting for functional genomics and phenotypic data
Dinh, Hoang V.; Suthers, Patrick F.; Chan, Siu Hung Joshua et al. · 2019 · DOI
Full title: A comprehensive genome-scale model for <i>Rhodosporidium toruloides</i> IFO0880 accounting for functional genomics and phenotypic data
Authors: Dinh, Hoang V.; Suthers, Patrick F.; Chan, Siu Hung Joshua; Shen, Yihui; Xiao, Tianxia; Deewan, Anshu; Jagtap, Sujit Sadashiv; Rabinowitz, Joshua D.; Rao, Christopher V.; Zhao, Huimin; Maranas, Costas D.
Year: 2019
Paper Genome-Scale reconstruction of <i>Paenarthrobacter aurescens</i> 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 <i>Paenarthrobacter aurescens</i> 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
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
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
Paper Flux-based hierarchical organization of Escherichia coli ’s metabolic network
Robaina‐Estévez, Semidán; Nikoloski, Zoran · 2019 · DOI
Full title: Flux-based hierarchical organization of Escherichia coli ’s metabolic network
Authors: Robaina‐Estévez, Semidán; Nikoloski, Zoran
Year: 2019
Paper Charting the metabolic landscape of the facultative methylotroph Bacillus methanolicus
Delépine, Baudoin; López, Marina Gil; Carnicer, Marc et al. · 2019 · DOI
Full title: Charting the metabolic landscape of the facultative methylotroph Bacillus methanolicus
Authors: Delépine, Baudoin; López, Marina Gil; Carnicer, Marc; Vicente, Cláudia M.; Wendisch, Volker F.; Heux, Stéphanie
Year: 2019
Paper Effects of MCHM on yeast metabolism
Pupo, Amaury; Ku, Kang‐Mo; Gallagher, Jennifer E. G. · 2019 · DOI
Full title: Effects of MCHM on yeast metabolism
Authors: Pupo, Amaury; Ku, Kang‐Mo; Gallagher, Jennifer E. G.
Year: 2019
Paper Metabolic Modeling of Cystic Fibrosis Airway Communities Predicts Mechanisms of Pathogen Dominance
Henson, Michael A.; Orazi, Giulia; Phalak, Poonam et al. · 2019 · DOI
Full title: Metabolic Modeling of Cystic Fibrosis Airway Communities Predicts Mechanisms of Pathogen Dominance
Authors: Henson, Michael A.; Orazi, Giulia; Phalak, Poonam; O’Toole, George A.
Year: 2019
Paper A systematic evaluation of Mycobacterium tuberculosis Genome-Scale Metabolic Networks
López-Agudelo, Víctor A.; Laing, Emma; Mendum, Tom A. et al. · 2019 · DOI
Full title: A systematic evaluation of Mycobacterium tuberculosis Genome-Scale Metabolic Networks
Authors: López-Agudelo, Víctor A.; Laing, Emma; Mendum, Tom A.; Baena, Andrés; Barrera, Luis F.; Beste, Dany J. V.; Ríos‐Estepa, Rigoberto
Year: 2019
Paper Reconstruction and Validation of <i>Saccharomyces cerevisiae</i> 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 <i>Saccharomyces cerevisiae</i> iND750, a Fully Compartmentalized Genome-Scale Metabolic Model
Authors: Duarte, Natalie C.; Herrgård, Markus J.; Palsson, Bernhard Ø.
Year: 2004
Venue: Genome Research
Paper Wax ester production in nitrogen-rich conditions by metabolically engineered <i>Acinetobacter baylyi</i> ADP1
Luo, Jin; Efimova, Elena; Losoi, Pauli et al. · 2019 · DOI
Full title: Wax ester production in nitrogen-rich conditions by metabolically engineered <i>Acinetobacter baylyi</i> ADP1
Authors: Luo, Jin; Efimova, Elena; Losoi, Pauli; Santala, Ville; Santala, Suvi
Year: 2019
Paper Pooled CRISPRi screening of the cyanobacterium <i>Synechocystis</i> sp. PCC 6803 for enhanced growth, tolerance, and chemical production
Yao, Lun; Shabestary, Kiyan; Björk, Sara et al. · 2019 · DOI
Full title: Pooled CRISPRi screening of the cyanobacterium <i>Synechocystis</i> sp. PCC 6803 for enhanced growth, tolerance, and chemical production
Authors: Yao, Lun; Shabestary, Kiyan; Björk, Sara; Asplund‐Samuelsson, Johannes; Joensson, Haakan N.; Jahn, Michael; Hudson, Elton P.
Year: 2019
Paper Systems biology tools for toxicology
Geenen, Suzanne; Taylor, Peter N.; Snoep, Jacky L. et al. · 2012 · Archives of Toxicology · DOI
Full title: Systems biology tools for toxicology
Authors: Geenen, Suzanne; Taylor, Peter N.; Snoep, Jacky L.; Wilson, Ian D.; Kenna, J. Gerry; Westerhoff, Hans V.
Year: 2012
Venue: Archives of Toxicology
Paper Pangenome Flux Balance Analysis Toward Panphenomes
Norsigian, Charles J.; Fang, Xin; Palsson, Bernhard Ø. et al. · 2020 · DOI
Full title: Pangenome Flux Balance Analysis Toward Panphenomes
Authors: Norsigian, Charles J.; Fang, Xin; Palsson, Bernhard Ø.; Monk, Jonathan M.
Year: 2020
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
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
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
Paper Substrate type and CO2 addition significantly influence succinic acid production of Basfia succiniciproducens
Balázs, Márta; Bartos, Hunor; Lányi, Szabolcs et al. · 2023 · Biotechnology Letters · DOI
Full title: Substrate type and CO2 addition significantly influence succinic acid production of Basfia succiniciproducens
Authors: Balázs, Márta; Bartos, Hunor; Lányi, Szabolcs; Bodor, Zsolt; Miklóssy, Ildikó
Year: 2023
Venue: Biotechnology Letters
Paper Scaling up genetic circuit design for cellular computing: advances and prospects
Xiang, Yiyu; Dalchau, Neil; Wang, Baojun · 2018 · Natural Computing · DOI
Full title: Scaling up genetic circuit design for cellular computing: advances and prospects
Authors: Xiang, Yiyu; Dalchau, Neil; Wang, Baojun
Year: 2018
Venue: Natural Computing
Paper Mathematical modelling of clostridial acetone-butanol-ethanol fermentation
Millat, Thomas; Winzer, Klaus · 2017 · Applied Microbiology and Biotechnology · DOI
Full title: Mathematical modelling of clostridial acetone-butanol-ethanol fermentation
Authors: Millat, Thomas; Winzer, Klaus
Year: 2017
Venue: Applied Microbiology and Biotechnology
Paper Integrative genome‐scale metabolic analysis of <i>Vibrio vulnificus</i> 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 <i>Vibrio vulnificus</i> 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
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
Paper Genome‐scale engineering for systems and synthetic biology
Esvelt, Kevin M.; Wang, Harris H. · 2013 · Molecular Systems Biology · DOI
Full title: Genome‐scale engineering for systems and synthetic biology
Authors: Esvelt, Kevin M.; Wang, Harris H.
Year: 2013
Venue: Molecular Systems Biology
Paper Multi-omic data integration enables discovery of hidden biological regularities
Ebrahim, Ali; Brunk, Elizabeth; Tan, Justin et al. · 2016 · Nature Communications · DOI
Full title: Multi-omic data integration enables discovery of hidden biological regularities
Authors: Ebrahim, Ali; Brunk, Elizabeth; Tan, Justin; O’Brien, Edward J.; Kim, Donghyuk; Szubin, Richard; Lerman, Joshua A.; Lechner, Anna; Sastry, Anand V.; Bordbar, Aarash; Feist, Adam M.; Palsson, Bernhard Ø.
Year: 2016
Venue: Nature Communications
Paper What is quantitative plant biology?
Autran, Daphné; Bassel, George W.; Chae, Eunyoung et al. · 2021 · Quantitative Plant Biology · DOI
Full title: What is quantitative plant biology?
Authors: Autran, Daphné; Bassel, George W.; Chae, Eunyoung; Ezer, Daphne; Ferjani, Ali; Fleck, Christian; Hamant, Olivier; Hartmann, Félix; Jiao, Yuling; Johnston, Iain G.; Kwiatkowska, Dorota; Lim, Boon Leong; Mähönen, Ari Pekka; Morris, Richard J.; Mulder, Bela M.; Nakayama, Naomi; Sozzani, Rosangela; Strader, Lucia C.; Tusscher, Kirsten ten; Ueda, Minako; Wolf, Sebastian
Year: 2021
Venue: Quantitative Plant Biology
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
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
Paper Multi-omics integration accurately predicts cellular state in unexplored conditions for Escherichia coli
Kim, Minseung; Rai, Navneet; Zorraquino, Violeta et al. · 2016 · Nature Communications · DOI
Full title: Multi-omics integration accurately predicts cellular state in unexplored conditions for Escherichia coli
Authors: Kim, Minseung; Rai, Navneet; Zorraquino, Violeta; Tagkopoulos, Ilias
Year: 2016
Venue: Nature Communications
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
Paper Enzyme I facilitates reverse flux from pyruvate to phosphoenolpyruvate in Escherichia coli
Long, Christopher P.; Au, Jennifer; Sandoval, Nicholas R. et al. · 2017 · Nature Communications · DOI
Full title: Enzyme I facilitates reverse flux from pyruvate to phosphoenolpyruvate in Escherichia coli
Authors: Long, Christopher P.; Au, Jennifer; Sandoval, Nicholas R.; Gebreselassie, Nikodimos A.; Antoniewicz, Maciek R.
Year: 2017
Venue: Nature Communications
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
Paper Artificial neural networks enable genome-scale simulations of intracellular signaling
Nilsson, Avlant; Peters, Joshua M.; Meimetis, Nikolaos et al. · 2022 · Nature Communications · DOI
Full title: Artificial neural networks enable genome-scale simulations of intracellular signaling
Authors: Nilsson, Avlant; Peters, Joshua M.; Meimetis, Nikolaos; Bryson, Bryan D.; Lauffenburger, Douglas A.
Year: 2022
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
Paper Spatial-fluxomics provides a subcellular-compartmentalized view of reductive glutamine metabolism in cancer cells
Lee, Won Dong; Mukha, Dzmitry; Aizenshtein, É. M. et al. · 2019 · Nature Communications · DOI
Full title: Spatial-fluxomics provides a subcellular-compartmentalized view of reductive glutamine metabolism in cancer cells
Authors: Lee, Won Dong; Mukha, Dzmitry; Aizenshtein, É. M.; Shlomi, Tomer
Year: 2019
Venue: Nature Communications
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
Paper The ETFL formulation allows multi-omics integration in thermodynamics-compliant metabolism and expression models
Salvy, Pierre; Hatzimanikatis, Vassily · 2020 · Nature Communications · 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: Nature Communications
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
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 · Nature Communications · 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
Venue: Nature Communications
Paper Methanol-dependent Escherichia coli strains with a complete ribulose monophosphate cycle
Keller, Philipp; Noor, Εlad; Meyer, Fabian et al. · 2020 · Nature Communications · DOI
Full title: Methanol-dependent Escherichia coli strains with a complete ribulose monophosphate cycle
Authors: Keller, Philipp; Noor, Εlad; Meyer, Fabian; Reiter, Michael; Anastassov, Stanislav; Kiefer, Patrick; Vorholt, Julia A.
Year: 2020
Venue: Nature Communications
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
Paper Characterizing cancer metabolism from bulk and single-cell RNA-seq data using METAFlux
Huang, Yuefan; Mohanty, Vakul; Dede, Merve et al. · 2023 · Nature Communications · DOI
Full title: Characterizing cancer metabolism from bulk and single-cell RNA-seq data using METAFlux
Authors: Huang, Yuefan; Mohanty, Vakul; Dede, Merve; Tsai, Kyle; Daher, May; Li, Li; Rezvani, Katayoun; Chen, Ken
Year: 2023
Venue: Nature Communications
Paper The protein translation machinery is expressed for maximal efficiency in Escherichia coli
Hu, Xiao-Pan; Dourado, Hugo; Schubert, Peter et al. · 2020 · Nature Communications · DOI
Full title: The protein translation machinery is expressed for maximal efficiency in Escherichia coli
Authors: Hu, Xiao-Pan; Dourado, Hugo; Schubert, Peter; Lercher, Martin J.
Year: 2020
Venue: Nature Communications
Paper Reconstruction of a catalogue of genome-scale metabolic models with enzymatic constraints using GECKO 2.0
Domenzain, Iván; Sánchez, Benjamín J.; Anton, Mihail et al. · 2022 · Nature Communications · DOI
Full title: Reconstruction of a catalogue of genome-scale metabolic models with enzymatic constraints using GECKO 2.0
Authors: Domenzain, Iván; Sánchez, Benjamín J.; Anton, Mihail; Kerkhoven, Eduard J.; Millán-Oropeza, Aarón; Henry, Céline; Siewers, Verena; Morrissey, John P.; Sonnenschein, Nikolaus; Nielsen, Jens
Year: 2022
Venue: Nature Communications
Paper Integration of machine learning and genome-scale metabolic modeling identifies multi-omics biomarkers for radiation resistance
Lewis, Joshua E.; Kemp, Melissa L. · 2021 · Nature Communications · DOI
Full title: Integration of machine learning and genome-scale metabolic modeling identifies multi-omics biomarkers for radiation resistance
Authors: Lewis, Joshua E.; Kemp, Melissa L.
Year: 2021
Venue: Nature Communications
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 Proteome allocations change linearly with the specific growth rate of Saccharomyces cerevisiae under glucose limitation
Xia, Jianye; Sánchez, Benjamín J.; Chen, Yu et al. · 2022 · Nature Communications · DOI
Full title: Proteome allocations change linearly with the specific growth rate of Saccharomyces cerevisiae under glucose limitation
Authors: Xia, Jianye; Sánchez, Benjamín J.; Chen, Yu; Campbell, Kate; Kasvandik, Sergo; Nielsen, Jens
Year: 2022
Venue: Nature Communications
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
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 Identification of gene function based on models capturing natural variability of Arabidopsis thaliana lipid metabolism
Córdoba, Sandra Correa; Tong, Hao; Burgos, Asdrúbal et al. · 2023 · Nature Communications · DOI
Full title: Identification of gene function based on models capturing natural variability of Arabidopsis thaliana lipid metabolism
Authors: Córdoba, Sandra Correa; Tong, Hao; Burgos, Asdrúbal; Zhu, Feng; Alseekh, Saleh; Fernie, Alisdair R.; Nikoloski, Zoran
Year: 2023
Venue: Nature Communications
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
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 Targeted and high-throughput gene knockdown in diverse bacteria using synthetic sRNAs
Cho, Jae Sung; Yang, Dongsoo; Prabowo, Cindy Pricilia Surya et al. · 2023 · Nature Communications · DOI
Full title: Targeted and high-throughput gene knockdown in diverse bacteria using synthetic sRNAs
Authors: Cho, Jae Sung; Yang, Dongsoo; Prabowo, Cindy Pricilia Surya; Ghiffary, Mohammad Rifqi; Han, Tae-Hee; Choi, Kyeong Rok; Moon, Cheon Woo; Zhou, Hengrui; Ryu, Jae Yong; Kim, Hyun Uk; Lee, Sang Yup
Year: 2023
Venue: Nature Communications
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 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
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 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
Paper Convergence of resistance and evolutionary responses in Escherichia coli and Salmonella enterica co-inhabiting chicken farms in China
Baker, Michelle; Zhang, Xibin; Maciel-Guerra, Alexandre et al. · 2024 · Nature Communications · DOI
Full title: Convergence of resistance and evolutionary responses in Escherichia coli and Salmonella enterica co-inhabiting chicken farms in China
Authors: Baker, Michelle; Zhang, Xibin; Maciel-Guerra, Alexandre; Babaarslan, Kubra; Dong, Yinping; Wang, Wei; Hu, Yujie; Renney, David; Liu, Longhai; Li, Hui; Hossain, Maqsud; Heeb, Stephan; Tong, Zhiqin; Pearcy, Nicole; Zhang, Meimei; Geng, Yingzhi; Zhao, Li; Hao, Zhihui; Senin, Nicola; Chen, Junshi; Peng, Zixin; Li, Fengqin; Dottorini, Tania
Year: 2024
Venue: Nature Communications
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
Paper Proteomics and constraint-based modelling reveal enzyme kinetic properties of Chlamydomonas reinhardtii on a genome scale
Arend, Marius; Zimmer, David; Xu, Rudan et al. · 2023 · Nature Communications · DOI
Full title: Proteomics and constraint-based modelling reveal enzyme kinetic properties of Chlamydomonas reinhardtii on a genome scale
Authors: Arend, Marius; Zimmer, David; Xu, Rudan; Sommer, Frederik; Mühlhaus, Timo; Nikoloski, Zoran
Year: 2023
Venue: Nature Communications
Paper Quantitative prediction of conditional vulnerabilities in regulatory and metabolic networks using PRIME
Immanuel, Selva Rupa Christinal; Arrieta‐Ortiz, Mario L.; Ruiz, Rene A. et al. · 2021 · npj Systems Biology and Applications · DOI
Full title: Quantitative prediction of conditional vulnerabilities in regulatory and metabolic networks using PRIME
Authors: Immanuel, Selva Rupa Christinal; Arrieta‐Ortiz, Mario L.; Ruiz, Rene A.; Pan, Min; Lomana, Adrián López García de; Peterson, Eliza J. R.; Baliga, Nitin S.
Year: 2021
Venue: npj Systems Biology and Applications
Paper Rational strain design with minimal phenotype perturbation
Narayanan, Bharath; Weilandt, Daniel; Masid, María et al. · 2024 · Nature Communications · DOI
Full title: Rational strain design with minimal phenotype perturbation
Authors: Narayanan, Bharath; Weilandt, Daniel; Masid, María; Mišković, Ljubiša; Hatzimanikatis, Vassily
Year: 2024
Venue: Nature Communications
Paper Modelling the pyrenoid-based CO2-concentrating mechanism provides insights into its operating principles and a roadmap for its engineering into crops
Fei, Chenyi; Wilson, Alexandra T.; Mangan, Niall M. et al. · 2022 · Nature Plants · DOI
Full title: Modelling the pyrenoid-based CO2-concentrating mechanism provides insights into its operating principles and a roadmap for its engineering into crops
Authors: Fei, Chenyi; Wilson, Alexandra T.; Mangan, Niall M.; Wingreen, Ned S.; Jonikas, Martin C.
Year: 2022
Venue: Nature Plants
Paper Towards a widespread adoption of metabolic modeling tools in biopharmaceutical industry: a process systems biology engineering perspective
Richelle, Anne; David, Blandine; Demaegd, Didier et al. · 2020 · npj Systems Biology and Applications · DOI
Full title: Towards a widespread adoption of metabolic modeling tools in biopharmaceutical industry: a process systems biology engineering perspective
Authors: Richelle, Anne; David, Blandine; Demaegd, Didier; Dewerchin, Marianne; Kinet, Romain; Morreale, Angelo; Portela, Rui M. C.; Zune, Quentin; Stosch, Moritz von
Year: 2020
Venue: npj Systems Biology and Applications
Paper 13C-metabolic flux analysis of respiratory chain disrupted strain ΔndhF1 of Synechocystis sp. PCC 6803
Wada, Keisuke; Toya, Yoshihiro; Matsuda, Fumio et al. · 2025 · Applied Biochemistry and Biotechnology · DOI
Full title: 13C-metabolic flux analysis of respiratory chain disrupted strain ΔndhF1 of Synechocystis sp. PCC 6803
Authors: Wada, Keisuke; Toya, Yoshihiro; Matsuda, Fumio; Shimizu, Hiroshi
Year: 2025
Venue: Applied Biochemistry and Biotechnology
Paper AGORA2: Large scale reconstruction of the microbiome highlights wide-spread drug-metabolising capacities
Heinken, Almut; Acharya, Geeta; Ravcheev, Dmitry A. et al. · 2020 · DOI
Full title: AGORA2: Large scale reconstruction of the microbiome highlights wide-spread drug-metabolising capacities
Authors: Heinken, Almut; Acharya, Geeta; Ravcheev, Dmitry A.; Hertel, Johannes; Nyga, Malgorzata; Okpala, Onyedika Emmanuel; Hogan, Marcus; Magnúsdóttir, Stefanía; Boneschi, Filippo Martinelli; Preciat, German; Edirisinghe, Janaka N.; Henry, Christopher S.; Fleming, Ronan M. T.; Thiele, Ines
Year: 2020
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
Paper H2 drives metabolic rearrangements in gas-fermenting Clostridium autoethanogenum
Valgepea, Kaspar; Lemgruber, Renato de Souza Pinto; Abdalla, Tanus et al. · 2018 · Biotechnology for Biofuels · DOI
Full title: H2 drives metabolic rearrangements in gas-fermenting Clostridium autoethanogenum
Authors: Valgepea, Kaspar; Lemgruber, Renato de Souza Pinto; Abdalla, Tanus; Binos, Steve; Takemori, Nobuaki; Takemori, Ayako; Tanaka, Yuki; Tappel, Ryan; Köpke, Michael; Simpson, Séan D.; Nielsen, Lars K.; Marcellin, Esteban
Year: 2018
Venue: Biotechnology for Biofuels
Thesis Metabolic modelling and analysis for the optimisation of Escherichia coli as a production host = Metabolische modellering en analyse voor de optimalisatie van Escherichia coli als productiestam
Lequeux, Gaspard · 2008 · Ghent University (Universiteit Gent) · DOI
Full title: Metabolic modelling and analysis for the optimisation of Escherichia coli as a production host = Metabolische modellering en analyse voor de optimalisatie van Escherichia coli als productiestam
Authors: Lequeux, Gaspard
Year: 2008
Venue: Ghent University (Universiteit Gent)
Thesis Using Genome-Scale Metabolic Models to Compare Serovars of the Foodborne Pathogen Listeria monocytogenes
Metz, Zachary · 2016 · University of Minnesota - Digital Conservancy · DOI
Full title: Using Genome-Scale Metabolic Models to Compare Serovars of the Foodborne Pathogen Listeria monocytogenes
Authors: Metz, Zachary
Year: 2016
Venue: University of Minnesota - Digital Conservancy
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
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
Thesis Tracing the fungal carbon metabolic roadmap
Pontes, María Victoria Aguilar · 2018 · Utrecht University · DOI
Full title: Tracing the fungal carbon metabolic roadmap
Authors: Pontes, María Victoria Aguilar
Year: 2018
Venue: Utrecht University
Thesis Evaluating Microbial Community Interactions, using Ecology and Flux Balance Analysis
Seto, Charlie · 2019 · University of Minnesota - Digital Conservancy · DOI
Full title: Evaluating Microbial Community Interactions, using Ecology and Flux Balance Analysis
Authors: Seto, Charlie
Year: 2019
Venue: University of Minnesota - Digital Conservancy
Thesis Unravelling the genetic complexity and redundancy of Aspergillus niger sugar metabolism
Chroumpi, Soultana · 2022 · Utrecht University · DOI
Full title: Unravelling the genetic complexity and redundancy of Aspergillus niger sugar metabolism
Authors: Chroumpi, Soultana
Year: 2022
Venue: Utrecht University
Thesis Simulation, sensitivity analysis, and optimization of bioprocesses using dynamic flux balance analysis
Gomez, Jose Alberto, Ph. D. Massachusetts Institute of Technology · 2018 · Massachusetts Institute of Technology (MIT) · DOI
Full title: Simulation, sensitivity analysis, and optimization of bioprocesses using dynamic flux balance analysis
Authors: Gomez, Jose Alberto, Ph. D. Massachusetts Institute of Technology
Year: 2018
Venue: Massachusetts Institute of Technology (MIT)
Thesis Selection and optimization of gene targets for the metabolic engineering of E. coli
Fischer, Curt R., Ph. D. Massachusetts Institute of Technology · 2010 · Massachusetts Institute of Technology (MIT) · DOI
Full title: Selection and optimization of gene targets for the metabolic engineering of E. coli
Authors: Fischer, Curt R., Ph. D. Massachusetts Institute of Technology
Year: 2010
Venue: Massachusetts Institute of Technology (MIT)
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
Thesis Computational modeling techniques for biological network productivity increases : optimization and rate-limiting reaction detection
Cui, Yuanyuan, Ph.D. Massachusetts Institute of Technology · 2013 · Massachusetts Institute of Technology (MIT) · DOI
Full title: Computational modeling techniques for biological network productivity increases : optimization and rate-limiting reaction detection
Authors: Cui, Yuanyuan, Ph.D. Massachusetts Institute of Technology
Year: 2013
Venue: Massachusetts Institute of Technology (MIT)
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
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)
Thesis Causation in biology : a biomolecular systems view
Lewis, Nathan Enoch · 2012 · University of California, San Diego (UCSD) · DOI
Full title: Causation in biology : a biomolecular systems view
Authors: Lewis, Nathan Enoch
Year: 2012
Venue: University of California, San Diego (UCSD)
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)
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)
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)
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
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)
Thesis Systems Biology of the Human Erythrocyte: Characterizing the Red Blood Cell Proteome Through Metabolic Modeling
Haiman, Zachary Brandon · 2024 · University of California, San Diego (UCSD) · DOI
Full title: Systems Biology of the Human Erythrocyte: Characterizing the Red Blood Cell Proteome Through Metabolic Modeling
Authors: Haiman, Zachary Brandon
Year: 2024
Venue: University of California, San Diego (UCSD)
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)
Thesis A stoichiometric model of Escherichia coli &#x27;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 &#x27;s macromolecular synthesis machinery and its integration with metabolism
Authors: Thiele, Ines
Year: 2009
Venue: University of California, San Diego (UCSD)
Thesis Chronicles of a pathogen’s lifestyle: from a single cell to a population
Seif, Yara · 2020 · University of California, San Diego (UCSD) · DOI
Full title: Chronicles of a pathogen’s lifestyle: from a single cell to a population
Authors: Seif, Yara
Year: 2020
Venue: University of California, San Diego (UCSD)
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)
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)
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
Thesis Monte Carlo simulation in systems biology
Schellenberger, Jan · 2010 · University of California, San Diego (UCSD) · DOI
Full title: Monte Carlo simulation in systems biology
Authors: Schellenberger, Jan
Year: 2010
Venue: University of California, San Diego (UCSD)
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)
Thesis Systems analysis of energy metabolism elucidates the roles of mitochondria in human health and disease
Vo, Thuy D. · 2007 · University of California, San Diego (UCSD) · DOI
Full title: Systems analysis of energy metabolism elucidates the roles of mitochondria in human health and disease
Authors: Vo, Thuy D.
Year: 2007
Venue: University of California, San Diego (UCSD)
Thesis Human platelet metabolic network reconstruction
Rahmaniyan, Sorena · 2012 · University of California, San Diego (UCSD) · DOI
Full title: Human platelet metabolic network reconstruction
Authors: Rahmaniyan, Sorena
Year: 2012
Venue: University of California, San Diego (UCSD)
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)
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)
Thesis Biomass composition: the &quot;elephant in the room&quot; of metabolic modelling.
Dikicioglu, Duygu; Kırdar, Betul; Oliver, Stephen G · 2015 · University of Cambridge · DOI
Full title: Biomass composition: the &quot;elephant in the room&quot; of metabolic modelling.
Authors: Dikicioglu, Duygu; Kırdar, Betul; Oliver, Stephen G
Year: 2015
Venue: University of Cambridge
Thesis Making life difficult for Clostridium difficile: augmenting the pathogen&#x27;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&#x27;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
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
Thesis Integrating Petri Nets and Flux Balance Methods in Computational Biology Models: a Methodological and Computational Practice
Simone, Pernice; Laura, Follia; Gianfranco, Balbo et al. · 2020 · University of Cambridge · DOI
Full title: Integrating Petri Nets and Flux Balance Methods in Computational Biology Models: a Methodological and Computational Practice
Authors: Simone, Pernice; Laura, Follia; Gianfranco, Balbo; Luciano, Milanesi; Giulia, Sartini; Niccoló, Totis; Pietro, Lió; Ivan, Merelli; Francesca, Cordero; Marco, Beccuti
Year: 2020
Venue: University of Cambridge
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
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
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
Thesis metaGEM: reconstruction of genome scale metabolic models directly from metagenomes.
Zorrilla, Francisco; Buric, Filip; Patil, Kiran R et al. · 2025 · University of Cambridge · DOI
Full title: metaGEM: reconstruction of genome scale metabolic models directly from metagenomes.
Authors: Zorrilla, Francisco; Buric, Filip; Patil, Kiran R; Zelezniak, Aleksej
Year: 2025
Venue: University of Cambridge
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
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.
Authors: Jouhten, Paula; Konstantinidis, Dimitrios; Pereira, Filipa; Andrejev, Sergej; Grkovska, Kristina; Castillo, Sandra; Ghiachi, Payam; Beltran, Gemma; Almaas, Eivind; Mas, Albert; Warringer, Jonas; Gonzalez, Ramon; Morales, Pilar; Patil, Kiran R
Year: 2022
Venue: University of Cambridge
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
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)
Thesis Design principles for engineering bacteria to maximise chemical production from batch cultures
Mannan, Ahmad; Darlington, Alexander; Tanaka, Reiko et al. · 2024 · Imperial College London · DOI
Full title: Design principles for engineering bacteria to maximise chemical production from batch cultures
Authors: Mannan, Ahmad; Darlington, Alexander; Tanaka, Reiko; Bates, Declan
Year: 2024
Venue: Imperial College London
Thesis An exact arithmetic toolbox for a consistent and reproducible structural analysis of metabolic network models
Chindelevitch, Leonid; Trigg, Jason; Regev, Aviv et al. · 2020 · Imperial College London · DOI
Full title: An exact arithmetic toolbox for a consistent and reproducible structural analysis of metabolic network models
Authors: Chindelevitch, Leonid; Trigg, Jason; Regev, Aviv; Berger, Bonnie
Year: 2020
Venue: Imperial College London
Thesis Flux-dependent graphs for metabolic networks
Beguerisse, Mariano; Bosque, Gabriel; Oyarzun, DA et al. · 2018 · Imperial College London · DOI
Full title: Flux-dependent graphs for metabolic networks
Authors: Beguerisse, Mariano; Bosque, Gabriel; Oyarzun, DA; Pico, Jesus; Barahona, Mauricio
Year: 2018
Venue: Imperial College London
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
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
Thesis Genome-scale metabolic modeling reveals metabolic alterations of multidrug-resistant acinetobacter Baumannii in a murine bloodstream infection model
Zhao, J; Zhu, Y; Han, J et al. · 2020 · University of Melbourne · DOI
Full title: Genome-scale metabolic modeling reveals metabolic alterations of multidrug-resistant acinetobacter Baumannii in a murine bloodstream infection model
Authors: Zhao, J; Zhu, Y; Han, J; Lin, YW; Aichem, M; Wang, J; Chen, K; Velkov, T; Schreiber, F; Li, J
Year: 2020
Venue: University of Melbourne
Thesis NIBBS-search for fast and accurate prediction of phenotype-biased metabolic systems
Schmidt, MC; Rocha, AM; Padmanabhan, K et al. · 2022 · University of Melbourne · DOI
Full title: NIBBS-search for fast and accurate prediction of phenotype-biased metabolic systems
Authors: Schmidt, MC; Rocha, AM; Padmanabhan, K; Shpanskaya, Y; Banfield, J; Scott, K; Mihelcic, JR; Samatova, NF
Year: 2022
Venue: University of Melbourne
Thesis Strategies for extending metabolomics studies with stable isotope labelling and fluxomics
Srivastava, A; Kowalski, GM; Callahan, DL et al. · 2021 · University of Melbourne · DOI
Full title: Strategies for extending metabolomics studies with stable isotope labelling and fluxomics
Authors: Srivastava, A; Kowalski, GM; Callahan, DL; Meikle, PJ; Creek, DJ
Year: 2021
Venue: University of Melbourne
Thesis Metabolic Responses to Polymyxin Treatment in Acinetobacter baumannii ATCC 19606: Integrating Transcriptomics and Metabolomics with Genome-Scale Metabolic Modeling
Zhu, Y; Zhao, J; Maifiah, MHM et al. · 2019 · University of Melbourne · DOI
Full title: Metabolic Responses to Polymyxin Treatment in Acinetobacter baumannii ATCC 19606: Integrating Transcriptomics and Metabolomics with Genome-Scale Metabolic Modeling
Authors: Zhu, Y; Zhao, J; Maifiah, MHM; Velkov, T; Schreiber, F; Li, J
Year: 2019
Venue: University of Melbourne
Thesis Comparative analysis of metabolic models of microbial communities reconstructed from automated tools and consensus approaches
Hsieh, YE; Tandon, K; Verbruggen, H et al. · 2024 · University of Melbourne · DOI
Full title: Comparative analysis of metabolic models of microbial communities reconstructed from automated tools and consensus approaches
Authors: Hsieh, YE; Tandon, K; Verbruggen, H; Nikoloski, Z
Year: 2024
Venue: University of Melbourne
Thesis Genome-scale metabolic modeling of responses to polymyxins in Pseudomonas aeruginosa
Zhu, Y; Czauderna, T; Zhao, J et al. · 2019 · University of Melbourne · DOI
Full title: Genome-scale metabolic modeling of responses to polymyxins in Pseudomonas aeruginosa
Authors: Zhu, Y; Czauderna, T; Zhao, J; Klapperstueck, M; Maifiah, MHM; Han, ML; Lu, J; Sommer, B; Velkov, T; Lithgow, T; Song, J; Schreiber, F; Li, J
Year: 2019
Venue: University of Melbourne
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
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
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
Thesis Near-optimal experimental design for model selection in systems biology
Busetto, AG; Hauser, A; Krummenacher, G et al. · 2021 · University of Melbourne · DOI
Full title: Near-optimal experimental design for model selection in systems biology
Authors: Busetto, AG; Hauser, A; Krummenacher, G; Sunnåker, M; Dimopoulos, S; Ong, CS; Stelling, J; Buhmann, JM
Year: 2021
Venue: University of Melbourne
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)
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
Thesis Genomic study of Photobacterium marinum strain J15 and development of genome scale metabolic model for cellular metabolism identification
Roslan, Noordiyanah Nadhirah · 2017 · Universiti Putra Malaysia (PSAS IR) · DOI
Full title: Genomic study of Photobacterium marinum strain J15 and development of genome scale metabolic model for cellular metabolism identification
Authors: Roslan, Noordiyanah Nadhirah
Year: 2017
Venue: Universiti Putra Malaysia (PSAS IR)
Thesis Genome-wide characterization of Phytophthora infestans metabolism: a systems biology approach
Rodenburg, Sander Y A; Seidl, Michael F; de Ridder, Dick et al. · 2018 · Utrecht University · DOI
Full title: Genome-wide characterization of Phytophthora infestans metabolism: a systems biology approach
Authors: Rodenburg, Sander Y A; Seidl, Michael F; de Ridder, Dick; Govers, Francine
Year: 2018
Venue: Utrecht University
Thesis Generalized metabolic flux analysis framework provides mechanism-based predictions of ophthalmic complications in type 2 diabetes patients
Batagov, Arsen; Dalan, Rinkoo; Wu, Andrew et al. · 2023 · Nanyang Technological University (NTU) · DOI
Full title: Generalized metabolic flux analysis framework provides mechanism-based predictions of ophthalmic complications in type 2 diabetes patients
Authors: Batagov, Arsen; Dalan, Rinkoo; Wu, Andrew; Lai, Wenbin; Tan, Colin S.; Eisenhaber, Frank
Year: 2023
Venue: Nanyang Technological University (NTU)
Thesis Lipid Metabolic Versatility in Malassezia spp. Yeasts Studied through Metabolic Modeling
Triana, Sergio; de Cock, Hans; Ohm, Robin A et al. · 2017 · Utrecht University · DOI
Full title: Lipid Metabolic Versatility in Malassezia spp. Yeasts Studied through Metabolic Modeling
Authors: Triana, Sergio; de Cock, Hans; Ohm, Robin A; Danies, Giovanna; Wösten, Han A B; Restrepo, Silvia; González Barrios, Andrés F; Celis Ramirez, Adriana
Year: 2017
Venue: Utrecht University
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
Thesis Predictive biology: modelling, understanding and harnessing microbial complexity
Lopatkin, Allison J.; Collins, James J. · 2021 · Massachusetts Institute of Technology (MIT) · DOI
Full title: Predictive biology: modelling, understanding and harnessing microbial complexity
Authors: Lopatkin, Allison J.; Collins, James J.
Year: 2021
Venue: Massachusetts Institute of Technology (MIT)
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)
Thesis Towards a whole-cell modeling approach for synthetic biology
Purcell, Oliver; Jain, Bonny; Karr, Jonathan R. et al. · 2016 · Massachusetts Institute of Technology (MIT) · DOI
Full title: Towards a whole-cell modeling approach for synthetic biology
Authors: Purcell, Oliver; Jain, Bonny; Karr, Jonathan R.; Covert, Markus W.; Lu, Timothy K.
Year: 2016
Venue: Massachusetts Institute of Technology (MIT)
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)
Thesis Design of robust metabolic pathways
Umeton, Renato; Stracquadanio, Giovanni; Sorathiya, Anilkumar et al. · 2016 · Massachusetts Institute of Technology (MIT) · DOI
Full title: Design of robust metabolic pathways
Authors: Umeton, Renato; Stracquadanio, Giovanni; Sorathiya, Anilkumar; Papini, Alessio; Nicosia, Giuseppe; Lio, Pietro
Year: 2016
Venue: Massachusetts Institute of Technology (MIT)
Thesis Efficient solution of ordinary differential equations with a parametric lexicographic linear program embedded
Höffner, Kai; Barton, Paul I.; Harwood, Stuart Maxwell et al. · 2016 · Massachusetts Institute of Technology (MIT) · DOI
Full title: Efficient solution of ordinary differential equations with a parametric lexicographic linear program embedded
Authors: Höffner, Kai; Barton, Paul I.; Harwood, Stuart Maxwell; Hoeffner, Kai
Year: 2016
Venue: Massachusetts Institute of Technology (MIT)
Thesis Nutrition or nature: using elementary flux modes to disentangle the complex forces shaping prokaryote pan-genomes
Garza, Daniel R; von Meijenfeldt, F A Bastiaan; van Dijk, Bram et al. · 2022 · Utrecht University · DOI
Full title: Nutrition or nature: using elementary flux modes to disentangle the complex forces shaping prokaryote pan-genomes
Authors: Garza, Daniel R; von Meijenfeldt, F A Bastiaan; van Dijk, Bram; Boleij, Annemarie; Huynen, Martijn A; Dutilh, Bas E
Year: 2022
Venue: Utrecht University
Thesis Metabolic requirements for cancer cell proliferation
Iliopoulos, Othon; Keibler, Mark Andrew; Wasylenko, Thomas Michael et al. · 2018 · Massachusetts Institute of Technology (MIT) · DOI
Full title: Metabolic requirements for cancer cell proliferation
Authors: Iliopoulos, Othon; Keibler, Mark Andrew; Wasylenko, Thomas Michael; Vander Heiden, Matthew G.; Stephanopoulos, Gregory; Kelleher, Joanne Keene
Year: 2018
Venue: Massachusetts Institute of Technology (MIT)
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
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)
Thesis Reply to &quot;Do genome-scale models need exact solvers or clearer standards?&quot;
Chindelevitch, Leonid; Regev, Aviv; Berger Leighton, Bonnie et al. · 2016 · Massachusetts Institute of Technology (MIT) · DOI
Full title: Reply to &quot;Do genome-scale models need exact solvers or clearer standards?&quot;
Authors: Chindelevitch, Leonid; Regev, Aviv; Berger Leighton, Bonnie; Trigg, Jason
Year: 2016
Venue: Massachusetts Institute of Technology (MIT)
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)
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)
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)
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)
Thesis Recon 2.2: from reconstruction to model of human metabolism
Swainston, Neil; Smallbone, Kieran; Hefzi, Hooman et al. · 2017 · Massachusetts Institute of Technology (MIT) · DOI
Full title: Recon 2.2: from reconstruction to model of human metabolism
Authors: Swainston, Neil; Smallbone, Kieran; Hefzi, Hooman; Hanscho, Michael; Kyriakopoulos, Sarantos; Lakshmanan, Meiyappan; Li, Shangzhong; Quek, Lake-Ee; Thomas, Alex; Zanghellini, Juergen; Borth, Nicole; Lee, Dong-Yup; Mendes, Pedro; Dobson, Paul D.; Zielinski, Daniel C.; Ang, Kok Siong; Gardiner, Natalie J.; Gutierrez, Jahir M.; Liu, Joanne K.; Martínez, Veronica S.; Orellana, Camila A.; Nielsen, Lars K.; Kell, Douglas B.; Lewis, Nathan E.; Brewer, Judith A
Year: 2017
Venue: Massachusetts Institute of Technology (MIT)
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)
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)
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)
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)
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)
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)
Thesis DFBAlab: a fast and reliable MATLAB code for dynamic flux balance analysis
Gomez, Jose Alberto; Hoeffner, Kai; Barton, Paul I. · 2015 · Massachusetts Institute of Technology (MIT) · DOI
Full title: DFBAlab: a fast and reliable MATLAB code for dynamic flux balance analysis
Authors: Gomez, Jose Alberto; Hoeffner, Kai; Barton, Paul I.
Year: 2015
Venue: Massachusetts Institute of Technology (MIT)
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)
Thesis Incremental parameter estimation of kinetic metabolic network models
Jia, Gengjie; Stephanopoulos, Gregory; Gunawan, Rudiyanto · 2013 · Massachusetts Institute of Technology (MIT) · DOI
Full title: Incremental parameter estimation of kinetic metabolic network models
Authors: Jia, Gengjie; Stephanopoulos, Gregory; Gunawan, Rudiyanto
Year: 2013
Venue: Massachusetts Institute of Technology (MIT)
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)
Thesis Statistical Modeling of Sensors and Dials in Metabolic Networks
Hoysala, Swathi Vishwanath · 2018 · University of California, San Diego (UCSD) · DOI
Full title: Statistical Modeling of Sensors and Dials in Metabolic Networks
Authors: Hoysala, Swathi Vishwanath
Year: 2018
Venue: University of California, San Diego (UCSD)
Thesis The Study of Overflow Metabolism and kinetics in a model of metabolism and gene expression of Escherichia coli
Cheng, Chuankai · 2017 · University of California, San Diego (UCSD) · DOI
Full title: The Study of Overflow Metabolism and kinetics in a model of metabolism and gene expression of Escherichia coli
Authors: Cheng, Chuankai
Year: 2017
Venue: University of California, San Diego (UCSD)
Thesis Genome-Scale Reconstruction of the Chlorella vulgaris UTEX 395 Metabolic Network
Huelsman, Tyler Paul · 2015 · University of California, San Diego (UCSD) · DOI
Full title: Genome-Scale Reconstruction of the Chlorella vulgaris UTEX 395 Metabolic Network
Authors: Huelsman, Tyler Paul
Year: 2015
Venue: University of California, San Diego (UCSD)
Thesis The establishment of endosymbiosis: An experimental and computational investigation using the artificial symbiont Synechocystis
Sørensen, Megan · 2015 · White Rose eTheses (Leeds, Sheffield, York) · DOI
Full title: The establishment of endosymbiosis: An experimental and computational investigation using the artificial symbiont Synechocystis
Authors: Sørensen, Megan
Year: 2015
Venue: White Rose eTheses (Leeds, Sheffield, York)
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)
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)
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)
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)
Thesis Essential metabolic pathways in Trypanosoma cruzi
Souza Shiratsubaki, Isabel · 2019 · University of California, San Diego (UCSD) · DOI
Full title: Essential metabolic pathways in Trypanosoma cruzi
Authors: Souza Shiratsubaki, Isabel
Year: 2019
Venue: University of California, San Diego (UCSD)
Thesis Rationally reduced libraries for combinatorial pathway optimization minimizing experimental effort
Jeschek, Markus; Gerngross, Daniel; Panke, Sven · 2025 · École polytechnique fédérale de Lausanne (EPFL) · DOI
Full title: Rationally reduced libraries for combinatorial pathway optimization minimizing experimental effort
Authors: Jeschek, Markus; Gerngross, Daniel; Panke, Sven
Year: 2025
Venue: École polytechnique fédérale de Lausanne (EPFL)
Thesis Uncertainty reduction in biochemical kinetic models: Enforcing desired model properties
Miskovic, Ljubisa; Béal, Jonas; Moret, Michael et al. · 2019 · École polytechnique fédérale de Lausanne (EPFL) · 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: École polytechnique fédérale de Lausanne (EPFL)
Thesis Kinetic models of metabolism that consider alternative steady-state solutions of intracellular fluxes and concentrations
Hameri, Tuure Eelis; Fengos, Georgios; Ataman, Meriç et al. · 2018 · École polytechnique fédérale de Lausanne (EPFL) · DOI
Full title: Kinetic models of metabolism that consider alternative steady-state solutions of intracellular fluxes and concentrations
Authors: Hameri, Tuure Eelis; Fengos, Georgios; Ataman, Meriç; Miskovic, Ljubisa; Hatzimanikatis, Vassily
Year: 2018
Venue: École polytechnique fédérale de Lausanne (EPFL)
Thesis Computational Inference of Metabolic Programs: A Case Study Analyzing the Effect of BRCA1 Loss
Masid, Maria; Rota, Ioanna A.; Barras, David et al. · 2025 · École polytechnique fédérale de Lausanne (EPFL) · DOI
Full title: Computational Inference of Metabolic Programs: A Case Study Analyzing the Effect of BRCA1 Loss
Authors: Masid, Maria; Rota, Ioanna A.; Barras, David; De Carlo, Flavia; Ginefra, Pierpaolo; Desbuisson, Matthieu; Ortiz-Miranda, Yaquelin; Zamarin, Dmitriy; Shah, Sohrab P; Vannini, Nicola; Coukos, George; Laniti, Denarda Dangaj; Hatzimanikatis, Vassily
Year: 2025
Venue: École polytechnique fédérale de Lausanne (EPFL)
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)
Thesis Extending a dynamic mathematical model of metabolism in Trypanosoma brucei
Kerkhoven, Eduard Johannes · 2012 · University of Glasgow · DOI
Full title: Extending a dynamic mathematical model of metabolism in Trypanosoma brucei
Authors: Kerkhoven, Eduard Johannes
Year: 2012
Venue: University of Glasgow
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)
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)
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)
Thesis Analysis of human metabolism by reducing the complexity of the genome-scale models using redHUMAN
Masid, Maria; Ataman, Meric; Hatzimanikatis, Vassily · 2020 · École polytechnique fédérale de Lausanne (EPFL) · DOI
Full title: Analysis of human metabolism by reducing the complexity of the genome-scale models using redHUMAN
Authors: Masid, Maria; Ataman, Meric; Hatzimanikatis, Vassily
Year: 2020
Venue: École polytechnique fédérale de Lausanne (EPFL)
Thesis Quantitative modeling of human metabolism: A call for a community effort
Masid Barcon, Maria; Hatzimanikatis, Vassily · 2021 · École polytechnique fédérale de Lausanne (EPFL) · DOI
Full title: Quantitative modeling of human metabolism: A call for a community effort
Authors: Masid Barcon, Maria; Hatzimanikatis, Vassily
Year: 2021
Venue: École polytechnique fédérale de Lausanne (EPFL)
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)
Thesis MEMOTE for standardized genome-scale metabolic model testing
Lieven, Christian; Beber, Moritz E.; Olivier, Brett G. et al. · 2020 · École polytechnique fédérale de Lausanne (EPFL) · DOI
Full title: MEMOTE for standardized genome-scale metabolic model testing
Authors: Lieven, Christian; Beber, Moritz E.; Olivier, Brett G.; Bergmann, Frank T.; Ataman, Meric; Babaei, Parizad; Bartell, Jennifer A.; Blank, Lars M.; Chauhan, Siddharth; Correia, Kevin; Diener, Christian; Draeger, Andreas; Ebert, Birgitta E.; Edirisinghe, Janaka N.; Faria, Jose P.; Feist, Adam M.; Fengos, Georgios; Fleming, Ronan M. T.; Garcia-Jimenez, Beatriz; Hatzimanikatis, Vassily; van Helvoirt, Wout; Henry, Christopher S.; Hermjakob, Henning; Herrgard, Markus J.; Kaafarani, Ali; Kim, Hyun Uk; King, Zachary; Klamt, Steffen; Klipp, Edda; Koehorst, Jasper J.; Koenig, Matthias; Lakshmanan, Meiyappan; Lee, Dong-Yup; Lee, Sang Yup; Lee, Sunjae; Lewis, Nathan E.; Liu, Filipe; Ma, Hongwu; Machado, Daniel; Mahadevan, Radhakrishnan; Maia, Paulo; Mardinoglu, Adil; Medlock, Gregory L.; Monk, Jonathan M.; Nielsen, Jens; Nielsen, Lars Keld; Nogales, Juan; Nookaew, Intawat; Palsson, Bernhard O.; Papin, Jason A.; Patil, Kiran R.; Poolman, Mark; Price, Nathan D.; Resendis-Antonio, Osbaldo; Richelle, Anne; Rocha, Isabel; Sanchez, Benjamin J.; Schaap, Peter J.; Malik Sheriff, Rahuman S.; Shoaie, Saeed; Sonnenschein, Nikolaus; Teusink, Bas; Vilaca, Paulo; Vik, Jon Olav; Wodke, Judith A. H.; Xavier, Joana C.; Yuan, Qianqian; Zakhartsev, Maksim; Zhang, Cheng
Year: 2020
Venue: École polytechnique fédérale de Lausanne (EPFL)
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)
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)
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)
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)
Thesis Analysis and Design of Biological Circuits and Systems
Koeppl, H.; Setti, G. · 2009 · École polytechnique fédérale de Lausanne (EPFL) · DOI
Full title: Analysis and Design of Biological Circuits and Systems
Authors: Koeppl, H.; Setti, G.
Year: 2009
Venue: École polytechnique fédérale de Lausanne (EPFL)
Thesis Data, Parameters &amp; 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 &amp; 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)
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)
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)
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)
Thesis Rites of passage: requirements and standards for building kinetic models of metabolic phenotypes
Miskovic, Ljubisa; Tokic, Milenko; Fengos, Georgios et al. · 2015 · École polytechnique fédérale de Lausanne (EPFL) · DOI
Full title: Rites of passage: requirements and standards for building kinetic models of metabolic phenotypes
Authors: Miskovic, Ljubisa; Tokic, Milenko; Fengos, Georgios; Hatzimanikatis, Vassily
Year: 2015
Venue: École polytechnique fédérale de Lausanne (EPFL)
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)
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)
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)
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)
Thesis lumpGEM: Systematic generation of subnetworks and elementally balanced lumped reactions for the biosynthesis of target metabolites
Ataman, Meric; Hatzimanikatis, Vassily · 2017 · École polytechnique fédérale de Lausanne (EPFL) · DOI
Full title: lumpGEM: Systematic generation of subnetworks and elementally balanced lumped reactions for the biosynthesis of target metabolites
Authors: Ataman, Meric; Hatzimanikatis, Vassily
Year: 2017
Venue: École polytechnique fédérale de Lausanne (EPFL)
Thesis 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 · École polytechnique fédérale de Lausanne (EPFL) · 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: École polytechnique fédérale de Lausanne (EPFL)
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)
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)
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)
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)
Thesis Understanding genetic variation in the proteome: a multi-scale structural systems biology toolkit
Mih, Nathan Da-Wei · 2018 · University of California, San Diego (UCSD) · DOI
Full title: Understanding genetic variation in the proteome: a multi-scale structural systems biology toolkit
Authors: Mih, Nathan Da-Wei
Year: 2018
Venue: University of California, San Diego (UCSD)
Thesis Biologically-interpretable machine learning for microbial genomics
Kavvas, Erol · 2020 · University of California, San Diego (UCSD) · DOI
Full title: Biologically-interpretable machine learning for microbial genomics
Authors: Kavvas, Erol
Year: 2020
Venue: University of California, San Diego (UCSD)
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)
Thesis On the systems characterization of metabolic networks
Jamshidi, Neema · 2009 · University of California, San Diego (UCSD) · DOI
Full title: On the systems characterization of metabolic networks
Authors: Jamshidi, Neema
Year: 2009
Venue: University of California, San Diego (UCSD)
Thesis Systems biology of the cardiac hypoxia response in Drosophila
Feala, Jacob Daniel · 2008 · University of California, San Diego (UCSD) · DOI
Full title: Systems biology of the cardiac hypoxia response in Drosophila
Authors: Feala, Jacob Daniel
Year: 2008
Venue: University of California, San Diego (UCSD)
Thesis Metabolic systems biology of the malaria parasite
Forth, Thomas · 2012 · White Rose eTheses (Leeds, Sheffield, York) · DOI
Full title: Metabolic systems biology of the malaria parasite
Authors: Forth, Thomas
Year: 2012
Venue: White Rose eTheses (Leeds, Sheffield, York)
Thesis Using metabolic network reconstructions to analyze complex data sets
Zielinski, Daniel Craig · 2015 · University of California, San Diego (UCSD) · DOI
Full title: Using metabolic network reconstructions to analyze complex data sets
Authors: Zielinski, Daniel Craig
Year: 2015
Venue: University of California, San Diego (UCSD)
Thesis Genome-Scale Metabolic Network Reconstruction of Thermotoga sp.Strain RQ7
Gautam, Jyotshana · 2020 · OhioLINK Electronic Theses and Dissertations · DOI
Full title: Genome-Scale Metabolic Network Reconstruction of Thermotoga sp.Strain RQ7
Authors: Gautam, Jyotshana
Year: 2020
Venue: OhioLINK Electronic Theses and Dissertations
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)
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)
Thesis Improved computational model of the malaria metabolic network and flux analysis for drug target prediction
Totanes, Francis Isidore Garcia · 2017 · White Rose eTheses (Leeds, Sheffield, York) · DOI
Full title: Improved computational model of the malaria metabolic network and flux analysis for drug target prediction
Authors: Totanes, Francis Isidore Garcia
Year: 2017
Venue: White Rose eTheses (Leeds, Sheffield, York)
Thesis Validation of drug targets in malaria parasites predicted by metabolic modelling using CRISPR-Cas9
Taweechai, Supannee · 2018 · White Rose eTheses (Leeds, Sheffield, York) · DOI
Full title: Validation of drug targets in malaria parasites predicted by metabolic modelling using CRISPR-Cas9
Authors: Taweechai, Supannee
Year: 2018
Venue: White Rose eTheses (Leeds, Sheffield, York)
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)
Thesis Multi-omics-driven kinetic modeling reveals metabolic vulnerabilities and differential drug-response dynamics in ovarian cancer
Toumpe, Ilias; Masid, Maria; Hatzimanikatis, Vassily et al. · 2025 · École polytechnique fédérale de Lausanne (EPFL) · DOI
Full title: Multi-omics-driven kinetic modeling reveals metabolic vulnerabilities and differential drug-response dynamics in ovarian cancer
Authors: Toumpe, Ilias; Masid, Maria; Hatzimanikatis, Vassily; Miskovic, Ljubisa
Year: 2025
Venue: École polytechnique fédérale de Lausanne (EPFL)
Thesis Analysis of cellular and drug action mechanisms in the malaria parasites using systems biology approaches
Chiappino-Pepe, Anush · 2018 · École polytechnique fédérale de Lausanne (EPFL) · DOI
Full title: Analysis of cellular and drug action mechanisms in the malaria parasites using systems biology approaches
Authors: Chiappino-Pepe, Anush
Year: 2018
Venue: École polytechnique fédérale de Lausanne (EPFL)
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)
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)
Thesis Genome-Scale Identification of Essential Metabolic Processes for Targeting the Plasmodium Liver Stage
Stanway, Rebecca R.; Bushell, Ellen; Chiappino-Pepe, Anush et al. · 2019 · École polytechnique fédérale de Lausanne (EPFL) · DOI
Full title: Genome-Scale Identification of Essential Metabolic Processes for Targeting the Plasmodium Liver Stage
Authors: Stanway, Rebecca R.; Bushell, Ellen; Chiappino-Pepe, Anush; Roques, Magali; Sanderson, Theo; Franke-Fayard, Blandine; Caldelari, Reto; Golomingi, Murielle; Nyonda, Mary; Pandey, Vikash; Schwach, Frank; Chevalley, Severine; Ramesar, Jai; Metcalf, Tom; Herd, Colin; Burda, Paul-Christian; Rayner, Julian C.; Soldati-Favre, Dominique; Janse, Chris J.; Hatzimanikatis, Vassily; Billker, Oliver; Heussler, Volker T.
Year: 2019
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)
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 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)
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)
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)
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)
Thesis Reconstruction and systems analysis of metabolism in apicomplexan parasites Toxoplasma gondii and Plasmodium falciparum
Tymoshenko, Stepan · 2015 · École polytechnique fédérale de Lausanne (EPFL) · DOI
Full title: Reconstruction and systems analysis of metabolism in apicomplexan parasites Toxoplasma gondii and Plasmodium falciparum
Authors: Tymoshenko, Stepan
Year: 2015
Venue: École polytechnique fédérale de Lausanne (EPFL)
Thesis Computational Studies on Cellular Metabolism : From Biochemical Pathways to Complex Metabolic Networks
Hadadi, Noushin · 2015 · École polytechnique fédérale de Lausanne (EPFL) · DOI
Full title: Computational Studies on Cellular Metabolism : From Biochemical Pathways to Complex Metabolic Networks
Authors: Hadadi, Noushin
Year: 2015
Venue: École polytechnique fédérale de Lausanne (EPFL)
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)
Thesis Computational methods and modeling of cellular function for the optimization of protein production and the study of cellular disease states
Pinto Vieira, Joana Raquel · 2017 · École polytechnique fédérale de Lausanne (EPFL) · DOI
Full title: Computational methods and modeling of cellular function for the optimization of protein production and the study of cellular disease states
Authors: Pinto Vieira, Joana Raquel
Year: 2017
Venue: École polytechnique fédérale de Lausanne (EPFL)
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)
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
Thesis Constraint-based analysis of substructures of metabolic networks
Marashi, Sayed-Amir · 2011 · Freie Universität Berlin (Refubium) · DOI
Full title: Constraint-based analysis of substructures of metabolic networks
Authors: Marashi, Sayed-Amir
Year: 2011
Venue: Freie Universität Berlin (Refubium)
Thesis Mathematical Modeling of Metabolic-Genetic Networks
Ali Salem Eshtewy, Neveen · 2020 · Freie Universität Berlin (Refubium) · DOI
Full title: Mathematical Modeling of Metabolic-Genetic Networks
Authors: Ali Salem Eshtewy, Neveen
Year: 2020
Venue: Freie Universität Berlin (Refubium)
Thesis New concepts and tools in constraint-based analysis of metabolic networks
Larhlimi, Abdelhalim · 2009 · Freie Universität Berlin (Refubium) · DOI
Full title: New concepts and tools in constraint-based analysis of metabolic networks
Authors: Larhlimi, Abdelhalim
Year: 2009
Venue: Freie Universität Berlin (Refubium)
Thesis Unifying metabolic networks, regulatory constraints, and resource allocation
Liu, Lin · 2020 · Freie Universität Berlin (Refubium) · DOI
Full title: Unifying metabolic networks, regulatory constraints, and resource allocation
Authors: Liu, Lin
Year: 2020
Venue: Freie Universität Berlin (Refubium)
Thesis Algorithms for the constraint-based analysis of metabolic networks
Dávid, László · 2015 · Freie Universität Berlin (Refubium) · DOI
Full title: Algorithms for the constraint-based analysis of metabolic networks
Authors: Dávid, László
Year: 2015
Venue: Freie Universität Berlin (Refubium)
Thesis Fundamentals and application of metabolic engineering
Wong, Kelvin Wai Wah · 2006 · Hong Kong University of Science and Technology (HKUST) · DOI
Full title: Fundamentals and application of metabolic engineering
Authors: Wong, Kelvin Wai Wah
Year: 2006
Venue: Hong Kong University of Science and Technology (HKUST)
Thesis Bioinformatics tools for cell modeling and metabolomics using Lactococcus lactis as a model organism
Aggio, Raphael · 2013 · University of Auckland · DOI
Full title: Bioinformatics tools for cell modeling and metabolomics using Lactococcus lactis as a model organism
Authors: Aggio, Raphael
Year: 2013
Venue: University of Auckland
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
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
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
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
Thesis Systems Biology in an Imperfect World: Modeling Biological Systems with Incomplete Information
Pokrzywa, Revonda Maria · 2014 · Virginia Tech - VTechWorks · DOI
Full title: Systems Biology in an Imperfect World: Modeling Biological Systems with Incomplete Information
Authors: Pokrzywa, Revonda Maria
Year: 2014
Venue: Virginia Tech - VTechWorks
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
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
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
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
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Metadata only

Paper System-level strategies for studying the metabolism of Mycobacterium tuberculosis
Beste, Dany J. V.; McFadden, Johnjoe · 2010 · Molecular BioSystems · DOI
Full title: System-level strategies for studying the metabolism of Mycobacterium tuberculosis
Authors: Beste, Dany J. V.; McFadden, Johnjoe
Year: 2010
Venue: Molecular BioSystems
Paper Cellular trade-offs and optimal resource allocation during cyanobacterial diurnal growth
Reimers, Alexandra-M.; Knoop, Henning; Bockmayr, Alexander et al. · 2017 · Proceedings of the National Academy of Sciences · DOI
Full title: Cellular trade-offs and optimal resource allocation during cyanobacterial diurnal growth
Authors: Reimers, Alexandra-M.; Knoop, Henning; Bockmayr, Alexander; Steuer, Ralf
Year: 2017
Venue: Proceedings of the National Academy of Sciences
Paper Quantitative analysis of amino acid metabolism in liver cancer links glutamate excretion to nucleotide synthesis
Nilsson, Avlant; Haanstra, Jurgen R.; Engqvist, Martin K. M. et al. · 2020 · Proceedings of the National Academy of Sciences · DOI
Full title: Quantitative analysis of amino acid metabolism in liver cancer links glutamate excretion to nucleotide synthesis
Authors: Nilsson, Avlant; Haanstra, Jurgen R.; Engqvist, Martin K. M.; Gerding, Albert; Bakker, Barbara M.; Klingmüller, Ursula; Teusink, Bas; Nielsen, Jens
Year: 2020
Venue: Proceedings of the National Academy of Sciences
Paper Properties of alternative microbial hosts used in synthetic biology: towards the design of a modular chassis
Kim, Juhyun; Salvador, Manuel; Saunders, Elizabeth et al. · 2016 · Essays in Biochemistry · DOI
Full title: Properties of alternative microbial hosts used in synthetic biology: towards the design of a modular chassis
Authors: Kim, Juhyun; Salvador, Manuel; Saunders, Elizabeth; González, Jaime; Avignone–Rossa, Claudio; Jiménez, José I.
Year: 2016
Venue: Essays in Biochemistry
Paper Emergence of diauxie as an optimal growth strategy under resource allocation constraints in cellular metabolism
Salvy, Pierre; Hatzimanikatis, Vassily · 2021 · Proceedings of the National Academy of Sciences · 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: Proceedings of the National Academy of Sciences
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
Paper Dynamic modelling and analysis of biochemical networks: mechanism-based models and model-based experiments
Riel, N.A.W. van · 2006 · Briefings in Bioinformatics · DOI
Full title: Dynamic modelling and analysis of biochemical networks: mechanism-based models and model-based experiments
Authors: Riel, N.A.W. van
Year: 2006
Venue: Briefings in Bioinformatics
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
Paper Integrating genome-scale metabolic modelling and transfer learning for human gene regulatory network reconstruction
Pio, Gianvito; Mignone, Paolo; Magazzù, Giuseppe et al. · 2021 · Bioinformatics · DOI
Full title: Integrating genome-scale metabolic modelling and transfer learning for human gene regulatory network reconstruction
Authors: Pio, Gianvito; Mignone, Paolo; Magazzù, Giuseppe; Zampieri, Guido; Ceci, Michelangelo; Angione, Claudio
Year: 2021
Venue: Bioinformatics
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
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
Paper Balancing biomass reaction stoichiometry and measured fluxes in flux balance analysis
Kamp, Axel von; Klamt, Steffen · 2023 · Bioinformatics · DOI
Full title: Balancing biomass reaction stoichiometry and measured fluxes in flux balance analysis
Authors: Kamp, Axel von; Klamt, Steffen
Year: 2023
Venue: Bioinformatics
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
Paper Systematic inference of functional phosphorylation events in yeast metabolism
Chen, Yu; Wang, Yonghong; Nielsen, Jens · 2017 · Bioinformatics · DOI
Full title: Systematic inference of functional phosphorylation events in yeast metabolism
Authors: Chen, Yu; Wang, Yonghong; Nielsen, Jens
Year: 2017
Venue: Bioinformatics
Paper Version 6 of the consensus yeast metabolic network refines biochemical coverage and improves model performance
Heavner, Ben; Smallbone, Kieran; Price, Nathan D. et al. · 2013 · Database · DOI
Full title: Version 6 of the consensus yeast metabolic network refines biochemical coverage and improves model performance
Authors: Heavner, Ben; Smallbone, Kieran; Price, Nathan D.; Walker, Larry P.
Year: 2013
Venue: Database
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
Paper Synthetic gene circuits for metabolic control: design trade-offs and constraints
Oyarzún, Diego A.; Stan, Guy‐Bart · 2012 · Journal of The Royal Society Interface · DOI
Full title: Synthetic gene circuits for metabolic control: design trade-offs and constraints
Authors: Oyarzún, Diego A.; Stan, Guy‐Bart
Year: 2012
Venue: Journal of The Royal Society Interface
Paper Model-based media selection to minimize the cost of metabolic cooperation in microbial ecosystems
Zampieri, Mattia; Sauer, Uwe · 2016 · Bioinformatics · DOI
Full title: Model-based media selection to minimize the cost of metabolic cooperation in microbial ecosystems
Authors: Zampieri, Mattia; Sauer, Uwe
Year: 2016
Venue: Bioinformatics
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
Paper CeCaFDB: a curated database for the documentation, visualization and comparative analysis of central carbon metabolic flux distributions explored by 13C-fluxomics
Zhang, Zhengdong; Shen, Tie; Rui, Bin et al. · 2014 · Nucleic Acids Research · DOI
Full title: CeCaFDB: a curated database for the documentation, visualization and comparative analysis of central carbon metabolic flux distributions explored by 13C-fluxomics
Authors: Zhang, Zhengdong; Shen, Tie; Rui, Bin; Zhou, Wenwei; Zhou, Xiangfei; Shang, Chuanyu; Xin, Chenwei; Liu, Xiaoguang; Li, Gang; Jiang, Jiansi; Li, Chao; Li, Ruiyuan; Han, Mengshu; You, Shanping; Yu, Guojun; Yi, Yin; Wen, Han Yun; Liu, Zhijie; Xie, Xiaoyao
Year: 2014
Venue: Nucleic Acids Research
Paper A genome-scale metabolic reconstruction provides insight into the metabolism of the thermophilic bacterium <i>Rhodothermus marinus</i>
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 <i>Rhodothermus marinus</i>
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
Venue: FEMS Microbiology Ecology
Paper 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. · 2020 · Nucleic Acids Research · 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 G.; Faria, José P.; Edirisinghe, Janaka N.; Mundy, Michael; Chia, Nicholas; Noor, Εlad; Beber, Moritz E.; Best, Aaron A.; DeJongh, Matthew; Kimbrel, Jeffrey A.; D’haeseleer, Patrik; McCorkle, S.; Bolton, Jay R; Pearson, Erik; Canon, Shane; Wood‐Charlson, Elisha M.; Cottingham, Robert W.; Arkin, Adam P.; Henry, Christopher S.
Year: 2020
Venue: Nucleic Acids Research
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
Paper Flux Analysis of the <i>Trypanosoma brucei</i> 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 <i>Trypanosoma brucei</i> 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
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
Paper In Silico Knockout Screening of<i> Plasmodium falciparum</i> Reactions and Prediction of Novel Essential Reactions by Analysing the Metabolic Network
Oyelade, Jelili; Isewon, Itunuoluwa; Uwoghiren, Efosa et al. · 2018 · BioMed Research International · DOI
Full title: In Silico Knockout Screening of<i> Plasmodium falciparum</i> Reactions and Prediction of Novel Essential Reactions by Analysing the Metabolic Network
Authors: Oyelade, Jelili; Isewon, Itunuoluwa; Uwoghiren, Efosa; Aromolaran, Olufemi; Oladipupo, Olufunke
Year: 2018
Venue: BioMed Research International
Paper Genome‐scale metabolic modelling of extremophiles and its applications in astrobiological environments
Noirungsee, Nuttapol; Changkhong, Sakunthip; Phinyo, Kittiya et al. · 2024 · Environmental Microbiology Reports · DOI
Full title: Genome‐scale metabolic modelling of extremophiles and its applications in astrobiological environments
Authors: Noirungsee, Nuttapol; Changkhong, Sakunthip; Phinyo, Kittiya; Suwannajak, Chutipong; Tanakul, Nahathai; Inwongwan, Sahutchai
Year: 2024
Venue: Environmental Microbiology Reports
Paper <i>In Silico</i> Analysis of Bioethanol Overproduction by Genetically Modified Microorganisms in Coculture Fermentation
Parambil, Lisha K.; Sarkar, Debasis · 2015 · Biotechnology Research International · DOI
Full title: <i>In Silico</i> Analysis of Bioethanol Overproduction by Genetically Modified Microorganisms in Coculture Fermentation
Authors: Parambil, Lisha K.; Sarkar, Debasis
Year: 2015
Venue: Biotechnology Research International
Paper Human Systems Biology and Metabolic Modelling: A Review—From Disease Metabolism to Precision Medicine
Angione, Claudio · 2019 · BioMed Research International · DOI
Full title: Human Systems Biology and Metabolic Modelling: A Review—From Disease Metabolism to Precision Medicine
Authors: Angione, Claudio
Year: 2019
Venue: BioMed Research International
Paper A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: i JN746 as a cell factory
Nogales, Juan; Palsson, Bernhard Ø.; Thiele, Ines · 2008 · BMC Systems Biology · DOI
Full title: A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: i JN746 as a cell factory
Authors: Nogales, Juan; Palsson, Bernhard Ø.; Thiele, Ines
Year: 2008
Venue: BMC Systems Biology
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
Paper Construction of cental metabolic pathway of riboflavin producer Ashbya gossypii using 13C metabolic flux analysis
Jeong, Bo‐Young · 2014 · Shizuoka University Repository (Shizuoka University) · DOI
Full title: Construction of cental metabolic pathway of riboflavin producer Ashbya gossypii using 13C metabolic flux analysis
Authors: Jeong, Bo‐Young
Year: 2014
Venue: Shizuoka University Repository (Shizuoka University)
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
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
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
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
Paper A multi-level approach to study the metabolic effects of chronic exposure to Aldrin in prostate cancer cells
Bedia, Carmen; Dalmau, Núria; Nielsen, Lars K. et al. · 2022 · Research Square (Research Square) · DOI
Full title: A multi-level approach to study the metabolic effects of chronic exposure to Aldrin in prostate cancer cells
Authors: Bedia, Carmen; Dalmau, Núria; Nielsen, Lars K.; Tauler, Romá; Mas, Igor Marín de
Year: 2022
Venue: Research Square (Research Square)
Paper Reconstruction of a catalogue of genome-scale metabolic models with enzymatic constraints using GECKO 2.0
Domenzain, Iván; Sánchez, Benjamín J.; Anton, Mihail et al. · 2022 · Nature Communications · DOI
Full title: Reconstruction of a catalogue of genome-scale metabolic models with enzymatic constraints using GECKO 2.0
Authors: Domenzain, Iván; Sánchez, Benjamín J.; Anton, Mihail; Kerkhoven, Eduard J.; Millán-Oropeza, Aarón; Henry, Céline; Siewers, Verena; Morrissey, John P.; Sonnenschein, Nikolaus; Nielsen, Jens
Year: 2022
Venue: Nature Communications
Paper Ecology-guided prediction of cross-feeding interactions in the human gut microbiome
Goyal, Akshit; Wang, Tong; Dubinkina, Veronika et al. · 2020 · DOI
Full title: Ecology-guided prediction of cross-feeding interactions in the human gut microbiome
Authors: Goyal, Akshit; Wang, Tong; Dubinkina, Veronika; Maslov, Sergei
Year: 2020
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 · Research Square (Research Square) · 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
Venue: Research Square (Research Square)
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 · Research Square (Research Square) · 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: Research Square (Research Square)
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
Paper Investigation of two metabolic engineering approaches for (R,R)-2,3-butanediol production from glycerol in Bacillus subtilis
Vikromvarasiri, Nunthaphan; Noda, Shuhei; Shirai, Tomokazu et al. · 2023 · Journal of Biological Engineering · DOI
Full title: Investigation of two metabolic engineering approaches for (R,R)-2,3-butanediol production from glycerol in Bacillus subtilis
Authors: Vikromvarasiri, Nunthaphan; Noda, Shuhei; Shirai, Tomokazu; Kondo, Akihiko
Year: 2023
Venue: Journal of Biological Engineering
Paper Genome-Scale Modelling of Chinese Hamster Ovary Cells by Hybrid Semi-Parametric Flux Balance Analysis
Ramos, João R. C.; Poiares‐Oliveira, Gil; Dumas, Patrick et al. · 2022 · DOI
Full title: Genome-Scale Modelling 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
Paper Metabolic modelling of microalgae for wastewater treatment
Pessi, Bruno Assis · 2023 · IWA Publishing eBooks · DOI
Full title: Metabolic modelling of microalgae for wastewater treatment
Authors: Pessi, Bruno Assis
Year: 2023
Venue: IWA Publishing eBooks
Paper Gene Deletion Algorithms for Minimum Reaction Network Design by Mixed-integer Linear Programming for Metabolite Production in Constraint-based Models: gDel_minRN
Tamura, Takeyuki; Muto-Fujita, Ai; Tohsato, Yukako et al. · 2021 · Research Square (Research Square) · DOI
Full title: Gene Deletion Algorithms for Minimum Reaction Network Design by Mixed-integer Linear Programming for Metabolite Production in Constraint-based Models: gDel_minRN
Authors: Tamura, Takeyuki; Muto-Fujita, Ai; Tohsato, Yukako; Kosaka, Tomoyuki
Year: 2021
Venue: Research Square (Research Square)
Paper Engineering Escherichia coli for the utilization of ethylene glycol
Pandit, Aditya Vikram; Harrison, Emma; Mahadevan, Radhakrishnan · 2021 · Microbial Cell Factories · DOI
Full title: Engineering Escherichia coli for the utilization of ethylene glycol
Authors: Pandit, Aditya Vikram; Harrison, Emma; Mahadevan, Radhakrishnan
Year: 2021
Venue: Microbial Cell Factories
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
Paper Towards Rational Design of Biosynthesis Pathways
Alazmi, Meshari · 2018 · King Abdullah University of Science and Technology Repository (King Abdullah University of Science and Technology) · DOI
Full title: Towards Rational Design of Biosynthesis Pathways
Authors: Alazmi, Meshari
Year: 2018
Venue: King Abdullah University of Science and Technology Repository (King Abdullah University of Science and Technology)
Paper A multiscale modelling framework for the processes involved in consolidated bioprocessing
Caul, Kristian Mc · 2017 · Spiral (Imperial College London) · DOI
Full title: A multiscale modelling framework for the processes involved in consolidated bioprocessing
Authors: Caul, Kristian Mc
Year: 2017
Venue: Spiral (Imperial College London)
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
Paper Computationally evaluating high-yield metabolites for sustainable aviation fuel (SAF) using machine learning
Landera, Alexander; Mays, Wittney; Poorey, Kunal et al. · 2024 · DOI
Full title: Computationally evaluating high-yield metabolites for sustainable aviation fuel (SAF) using machine learning
Authors: Landera, Alexander; Mays, Wittney; Poorey, Kunal; Kamruzzaman, Md; Adamczyk, Paul; Carrieri, Damian
Year: 2024
Paper Untitled
Ali, Villayat, Singh, Priyanka, Gupta, Sonu, Muley, Vijaykumar Yogesh, Verma, Malkhey, Moreno-Sanchez, R, Saavedra, E, Rodriguez-Enriquez, S, Sandoval, Olin, V, Kruger, J, Ratcliffe, G, Hahn-Hgerdal, B, Wahlbom, C, Grdonyi, M, H, Van Zyl W, C, Otero R R, Jonsson, L, Boatright, J, Negre, F, Chen, X, Kish, C, Wood, B, Peel, G, Mcneil, S D, Nuccio, M L, Rhodes, D, Shachar-Hill, Y, Hanson, A, Alonso, A P, Vigeolas, H, Raymond, P, Rolin, D, Dieuaide-Noubhani, M, Schwender, J, Goffman, F, Ohlrogge, J B, Hill, Shachar-, Y, Alonso, P, Raymond, P, Rolin, D, Dieuaide-Noubhani, M, Fernie, A, Roscher, A, G, Ratcliffe R, Kruger, N, Junker, B, Lonien, J, Heady, L, Rogers, A, Schwender, J, Rontein, D, Dieuaide-Noubhani, M, Dufourc, E, Raymond, P, Rolin, D, Price, N D, Papin, J, Schilling, C H, Palsson, B, Price, N D, Reed, J L, Palsson, B, Reed, J L, Palsson, B, Varma, A, Palsson, B, Schilling, C, Letscher, H, Palsson, D, B, Schuster, S, Dandekar, T, Fell, D, Schuster, S, Fell, D, Dandekar, T, Poolman, M, Fell, D, Raines, C, Morgan, J A, Rhodes, D, Poolman, M, Assmus, H, Fell, D, Luo, R, Liao, S, Zeng, S, Li, Y, Luo, Q, Heinrich, R, Rapoport, T, Kacser, H, Burns, J, Fell, D, P, Hafner R, Brown, G C, Brand, M, Stephanopoulos, G · 2019 · Research Journal of Life Sciences Bioinformatics Pharmaceutical and Chemical Sciences · DOI
Full title: Untitled
Authors: Ali, Villayat, Singh, Priyanka, Gupta, Sonu, Muley, Vijaykumar Yogesh, Verma, Malkhey, Moreno-Sanchez, R, Saavedra, E, Rodriguez-Enriquez, S, Sandoval, Olin, V, Kruger, J, Ratcliffe, G, Hahn-Hgerdal, B, Wahlbom, C, Grdonyi, M, H, Van Zyl W, C, Otero R R, Jonsson, L, Boatright, J, Negre, F, Chen, X, Kish, C, Wood, B, Peel, G, Mcneil, S D, Nuccio, M L, Rhodes, D, Shachar-Hill, Y, Hanson, A, Alonso, A P, Vigeolas, H, Raymond, P, Rolin, D, Dieuaide-Noubhani, M, Schwender, J, Goffman, F, Ohlrogge, J B, Hill, Shachar-, Y, Alonso, P, Raymond, P, Rolin, D, Dieuaide-Noubhani, M, Fernie, A, Roscher, A, G, Ratcliffe R, Kruger, N, Junker, B, Lonien, J, Heady, L, Rogers, A, Schwender, J, Rontein, D, Dieuaide-Noubhani, M, Dufourc, E, Raymond, P, Rolin, D, Price, N D, Papin, J, Schilling, C H, Palsson, B, Price, N D, Reed, J L, Palsson, B, Reed, J L, Palsson, B, Varma, A, Palsson, B, Schilling, C, Letscher, H, Palsson, D, B, Schuster, S, Dandekar, T, Fell, D, Schuster, S, Fell, D, Dandekar, T, Poolman, M, Fell, D, Raines, C, Morgan, J A, Rhodes, D, Poolman, M, Assmus, H, Fell, D, Luo, R, Liao, S, Zeng, S, Li, Y, Luo, Q, Heinrich, R, Rapoport, T, Kacser, H, Burns, J, Fell, D, P, Hafner R, Brown, G C, Brand, M, Stephanopoulos, G
Year: 2019
Venue: Research Journal of Life Sciences Bioinformatics Pharmaceutical and Chemical Sciences
Paper Application of metabolic flux and transcript analyses to understanding the physiology of engineered Geobacillus thermoglucosidasius
Ward, Charlotte · 2014 · Spiral (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: 2014
Venue: Spiral (Imperial College London)
Paper Integration of enzyme constraints in a genome-scale metabolic model of Aspergillus niger improves phenotype predictions
Zhou, Jingru; Zhuang, Yingping; Xia, Jianye · 2021 · Microbial Cell Factories · DOI
Full title: Integration of enzyme constraints in a genome-scale metabolic model of Aspergillus niger improves phenotype predictions
Authors: Zhou, Jingru; Zhuang, Yingping; Xia, Jianye
Year: 2021
Venue: Microbial Cell Factories
Paper Algal Systems for Resource Recovery from Waste and Wastewater
Lens, Piet N.L.; Khandelwal, Amitap; Khandelwal, Amitap et al. · 2023 · IWA Publishing eBooks · DOI
Full title: Algal Systems for Resource Recovery from Waste and Wastewater
Authors: Lens, Piet N.L.; Khandelwal, Amitap; Khandelwal, Amitap; Lens, Piet N.L.; Pessi, Bruno Assis; Rada-Ariza, A.M.; López-Vázquez, Carlos M.; Steen, Peter; Lens, Piet N.L.; Lawrence, James F.; Oliva, Armando; Murphy, Jerry D.; Lens, Piet N.L.; Acién, F.G.; Gómez-Serrano, Cintia; Morillas, A.; Arbib, Zouhayr; Sanchez, A.; Nordio, Rebecca; Rodríguez, Enrique; Guzmán, José Luís; Fernández‐Sevilla, J.M.; Wang, Jin; He, Q. Peter; Mishra, Archana; Chhabra, Meenu; Calijuri, Maria Lúcia; Assemany, Paula Peixoto; Lorentz, Juliana Ferreira; Castro, J.S.; Pereira, Alexia Saleme Aona de Paula; Marangon, Bianca Barros; Magalhães, Iara Barbosa; Silva, Thiago A.; Ferreira, Jéssica; Gama, Rafael Carvalho Nogueira da; Braga, Matheus Quintão; Velasquez‐Orta, Sharon B.; Saxena, Pallavi; Majhi, Pritikrishna; Pithania, Ruchi; Tarigholizadeh, Sarieh; Mangesh, Harish; Minkina, Tatiana; Sakarika, Myrsini; Sventzouri, Eirini; Pispas, Konstantinos; Ali, Sameh S.; Kornaros, Michael; Chandra, Rashmi; Hooshmand, Masoomeh
Year: 2023
Venue: IWA Publishing eBooks
Paper In silico patient: systems medicine approach to inborn errors of metabolism
Wegrzyn, Agnieszka B. · 2020 · DOI
Full title: In silico patient: systems medicine approach to inborn errors of metabolism
Authors: Wegrzyn, Agnieszka B.
Year: 2020
Paper A multi-tissue genome-scale metabolic modeling framework for the analysis of whole plant systems
Dal’Molin, Cristiana Gomes de Oliveira; Quek, Lake‐Ee; Saa, Pedro A. et al. · 2015 · Frontiers in Plant Science · DOI
Full title: A multi-tissue genome-scale metabolic modeling framework for the analysis of whole plant systems
Authors: Dal’Molin, Cristiana Gomes de Oliveira; Quek, Lake‐Ee; Saa, Pedro A.; Nielsen, Lars K.
Year: 2015
Venue: Frontiers in Plant Science
Paper Desenvolvimento de métodos de análises e integração de dados de ômicas aplicados à construção de leveduras industriais para produção de bioetanol de segunda geração
Carvalho, Lucas Miguel de · 2019 · DOI
Full title: Desenvolvimento de métodos de análises e integração de dados de ômicas aplicados à construção de leveduras industriais para produção de bioetanol de segunda geração
Authors: Carvalho, Lucas Miguel de
Year: 2019
Paper Network Modeling and Control of Dynamic Disease Pathways, Review and Perspectives
Hsiao, Yen-Che; Dutta, Abhishek · 2023 · DOI
Full title: Network Modeling and Control of Dynamic Disease Pathways, Review and Perspectives
Authors: Hsiao, Yen-Che; Dutta, Abhishek
Year: 2023
Paper Unraveling redox metabolism in Escherichia coli
Alvarez, M.I. Velasco · 2021 · Research Repository (Delft University of Technology) · DOI
Full title: Unraveling redox metabolism in Escherichia coli
Authors: Alvarez, M.I. Velasco
Year: 2021
Venue: Research Repository (Delft University of Technology)
Paper Analyzing Intracellular flux Distributions of Thermoanaerobacter sp.X514 under Various Substrate Conditions by Gibbs Sampling
Yang, Jing · 2013 · Journal of Biometrics & Biostatistics · DOI
Full title: Analyzing Intracellular flux Distributions of Thermoanaerobacter sp.X514 under Various Substrate Conditions by Gibbs Sampling
Authors: Yang, Jing
Year: 2013
Venue: Journal of Biometrics & Biostatistics
Paper A Novel Method for the Integration of Stochastic Petri Net Simulation and Transcriptomic Data Applied to a Metabolic Pathway
LM, Carvalho; GV, Meirelles; GAG, Pereira et al. · 2019 · Journal of Computer Science & Systems Biology · DOI
Full title: A Novel Method for the Integration of Stochastic Petri Net Simulation and Transcriptomic Data Applied to a Metabolic Pathway
Authors: LM, Carvalho; GV, Meirelles; GAG, Pereira; MF, Carazzolle
Year: 2019
Venue: Journal of Computer Science & Systems Biology
Paper Systems biology in Bacillus subtilis
Weidinger, Lope Andrés Flórez · 2010 · DOI
Full title: Systems biology in Bacillus subtilis
Authors: Weidinger, Lope Andrés Flórez
Year: 2010
Paper Design and analysis of amino acid supplementation in hepatocyte culture using in vitro experiment and mathematical modeling
Yang, Hong · 2010 · Rutgers University Community Repository (Rutgers University) · DOI
Full title: Design and analysis of amino acid supplementation in hepatocyte culture using in vitro experiment and mathematical modeling
Authors: Yang, Hong
Year: 2010
Venue: Rutgers University Community Repository (Rutgers University)
Paper Reviewer #3 (Public Review): 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: Reviewer #3 (Public Review): 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
Paper Constrain and conquer
Grigaitis, Pranas · 2023 · DOI
Full title: Constrain and conquer
Authors: Grigaitis, Pranas
Year: 2023
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
Paper Systems Biology Methods to Model Cancer Metabolism and Epigenetics for Drug Discovery
Campit, Scott · 2022 · Deep Blue (University of Michigan) · DOI
Full title: Systems Biology Methods to Model Cancer Metabolism and Epigenetics for Drug Discovery
Authors: Campit, Scott
Year: 2022
Venue: Deep Blue (University of Michigan)
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 Application of 13C and fluorescence labeling in metabolic studies of Saccharomyces spp. 13C- ja fluoressentsmärgise kasutamine Saccharomyces spp. ainevahetuse uurimisel
Nisamedtinov, Ildar · 2006
Full title: Application of 13C and fluorescence labeling in metabolic studies of Saccharomyces spp. 13C- ja fluoressentsmärgise kasutamine Saccharomyces spp. ainevahetuse uurimisel
Authors: Nisamedtinov, Ildar
Year: 2006
Paper Allocation of Proteome Resources in E. coli
Hui, Sheng · 2014 · eScholarship (California Digital Library)
Full title: Allocation of Proteome Resources in E. coli
Authors: Hui, Sheng
Year: 2014
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 Decoding Complexity in Metabolic Networks using Integrated Mechanistic and Machine Learning Approaches
Oyetunde, Tolutola · 2019 · Open Scholarship Institutional Repository (Washington University in St. Louis) · DOI
Full title: Decoding Complexity in Metabolic Networks using Integrated Mechanistic and Machine Learning Approaches
Authors: Oyetunde, Tolutola
Year: 2019
Venue: Open Scholarship Institutional Repository (Washington University in St. Louis)
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
Paper Comprehensive Characterization of an Inducible Mammalian Expression System Using 13C-Metabolic Flux Analysis
Sheikholeslami, Zahra · 2013 · PolyPublie (École Polytechnique de Montréal)
Full title: Comprehensive Characterization of an Inducible Mammalian Expression System Using 13C-Metabolic Flux Analysis
Authors: Sheikholeslami, Zahra
Year: 2013
Venue: PolyPublie (École Polytechnique de Montréal)
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 Constraint-based modeling of metabolism - interpreting predictions of growth and ATP synthesis in human and yeast
Nilsson, Avlant · 2019 · Chalmers Research (Chalmers University of Technology)
Full title: Constraint-based modeling of metabolism - interpreting predictions of growth and ATP synthesis in human and yeast
Authors: Nilsson, Avlant
Year: 2019
Venue: Chalmers Research (Chalmers University of Technology)
Paper Comparative Systems Biology Analysis of Microbial Pathogens
Jonathan M. Monk · 2015 · eScholarship (California Digital Library)
Full title: Comparative Systems Biology Analysis of Microbial Pathogens
Authors: Jonathan M. Monk
Year: 2015
Venue: eScholarship (California Digital Library)
Paper Computing abundance constraints in Saccharomyces cerevisiae’s metabolism
Sánchez, Benjamín J. · 2019 · Chalmers Research (Chalmers University of Technology)
Full title: Computing abundance constraints in Saccharomyces cerevisiae’s metabolism
Authors: Sánchez, Benjamín J.
Year: 2019
Venue: Chalmers Research (Chalmers University of Technology)
Paper Genome-scale Models of Metabolism and Gene Expression: Construction and Use for Growth Phenotype Prediction
Lerman, Joshua A. · 2014 · eScholarship (California Digital Library)
Full title: Genome-scale Models of Metabolism and Gene Expression: Construction and Use for Growth Phenotype Prediction
Authors: Lerman, Joshua A.
Year: 2014
Venue: eScholarship (California Digital Library)
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 Minimal Cut Sets and Their Use in Modelling Flavonoid Metabolism
Clark, Sangaalofa Tooki · 2014 · Lincoln University Research Archive (Lincoln University)
Full title: Minimal Cut Sets and Their Use in Modelling Flavonoid Metabolism
Authors: Clark, Sangaalofa Tooki
Year: 2014
Venue: Lincoln University Research Archive (Lincoln University)
Paper Developing synthetic consortia for industrial biofuel production from lignocellulose
Tc, Reid · 2019 · Open Research Exeter (University of Exeter)
Full title: Developing synthetic consortia for industrial biofuel production from lignocellulose
Authors: Tc, Reid
Year: 2019
Venue: Open Research Exeter (University of Exeter)
Paper Dissecting the Regulatory Network of Sphingolipid Biosynthesis in Plants
González‐Solís, Ariadna · 2020 · Insecta mundi
Full title: Dissecting the Regulatory Network of Sphingolipid Biosynthesis in Plants
Authors: González‐Solís, Ariadna
Year: 2020
Venue: Insecta mundi
Paper Causation in Biology: A Biomolecular Systems View
Lewis, Nathan E. · 2012 · eScholarship (California Digital Library)
Full title: Causation in Biology: A Biomolecular Systems View
Authors: Lewis, Nathan E.
Year: 2012
Venue: eScholarship (California Digital Library)
Paper Evaluating And Improving Stoichiometrically Constrained Models Of Yeast Metabolism For Application To Design Of Metabolic Engineering Strategies
Heavner, Ben · 2012 · eCommons (Cornell University)
Full title: Evaluating And Improving Stoichiometrically Constrained Models Of Yeast Metabolism For Application To Design Of Metabolic Engineering Strategies
Authors: Heavner, Ben
Year: 2012
Venue: eCommons (Cornell University)
Paper Mass-balanced randomization : a significance measure for metabolic networks
Basler, Georg · 2012 · publish.UP (University of Potsdam)
Full title: Mass-balanced randomization : a significance measure for metabolic networks
Authors: Basler, Georg
Year: 2012
Venue: publish.UP (University of Potsdam)
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 Engineering Molecules, Mineralization and Magnetism in Biology by Directed Evolution and Computation
Liu, Xueliang · 2017 · Digital Access to Scholarship at Harvard (DASH) (Harvard University)
Full title: Engineering Molecules, Mineralization and Magnetism in Biology by Directed Evolution and Computation
Authors: Liu, Xueliang
Year: 2017
Venue: Digital Access to Scholarship at Harvard (DASH) (Harvard University)
Paper Modeling photosynthesis and related metabolic processes : from detailed examination to consideration of the metabolic context
Arnold, Anne · 2014 · publish.UP (University of Potsdam)
Full title: Modeling photosynthesis and related metabolic processes : from detailed examination to consideration of the metabolic context
Authors: Arnold, Anne
Year: 2014
Venue: publish.UP (University of Potsdam)
Paper Metabolic modelling and 13C flux analysis application to biotechnologically important yeasts and a fungus
Jouhten, Paula · 2009 · Aaltodoc (Aalto University)
Full title: Metabolic modelling and 13C flux analysis application to biotechnologically important yeasts and a fungus
Authors: Jouhten, Paula
Year: 2009
Venue: Aaltodoc (Aalto University)
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 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 Investigation of Metabolic Modeling Strategies to Predict Phenotypes of Microbial Mutants Under Data Scarcity
Anturan, Ece · 2020 · Hacettepe University Institutional Repository (hacettepe.edu.tr)
Full title: Investigation of Metabolic Modeling Strategies to Predict Phenotypes of Microbial Mutants Under Data Scarcity
Authors: Anturan, Ece
Year: 2020
Venue: Hacettepe University Institutional Repository (hacettepe.edu.tr)
Paper New Algorithms for Mining Network Datasets: Applications to Phenotype and Pathway Modeling
Jin, Ying · 2009 · VTechWorks (Virginia Tech)
Full title: New Algorithms for Mining Network Datasets: Applications to Phenotype and Pathway Modeling
Authors: Jin, Ying
Year: 2009
Venue: VTechWorks (Virginia Tech)
Paper Systematic Metabolic Engineering of Recombinant Xylose-Utilizing S. cerevisiae: Strategies for Improving Xylose Uptake Rate
L. Miskovic; D. Bart; Keng C. Soh et al. · 2012 · Infoscience (Ecole Polytechnique Fédérale de Lausanne)
Full title: Systematic Metabolic Engineering of Recombinant Xylose-Utilizing S. cerevisiae: Strategies for Improving Xylose Uptake Rate
Authors: L. Miskovic; D. Bart; Keng C. Soh; Susanne Alff-Tuomala; Laura Salusjärvi; Juha-Pekka Pitkänen; L. Ruohonen; M. Pentillä; V. Hatzimanikatis
Year: 2012
Venue: Infoscience (Ecole Polytechnique Fédérale de Lausanne)
Paper Model-guided Analysis of Plant Metabolism and Design of Metabolic Engineering Strategies
Yen, Jiun Y. · 2017 · VTechWorks (Virginia Tech)
Full title: Model-guided Analysis of Plant Metabolism and Design of Metabolic Engineering Strategies
Authors: Yen, Jiun Y.
Year: 2017
Venue: VTechWorks (Virginia Tech)
Paper Prioritisation of candidate disease genes via multi-omics data integration
Zampieri, Guido · 2018 · Padua@research (University of Padova)
Full title: Prioritisation of candidate disease genes via multi-omics data integration
Authors: Zampieri, Guido
Year: 2018
Venue: Padua@research (University of Padova)
Paper Systems Biology Of Thermotoga Neapolitana For Biological Hydrogen Production
Munro, Sarah · 2010 · eCommons (Cornell University)
Full title: Systems Biology Of Thermotoga Neapolitana For Biological Hydrogen Production
Authors: Munro, Sarah
Year: 2010
Venue: eCommons (Cornell University)
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 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
Paper Genome-Based Metabolic Mapping and 13C Flux Analysis Reveal Systematic Properties of an Oleaginous Microalga Chlorella protothecoides1[OPEN]
Chao Wu; Wei Xiong; Junbiao Dai et al. · 2014 · Plant Physiology · DOI
Full title: Genome-Based Metabolic Mapping and 13C Flux Analysis Reveal Systematic Properties of an Oleaginous Microalga Chlorella protothecoides1[OPEN]
Authors: Chao Wu; Wei Xiong; Junbiao Dai; Qingyu Wu
Year: 2014
Venue: Plant Physiology
Paper Improved production of 2,3‐butanediol and isobutanol by engineering electron transport chain in Escherichia coli
Jung, Hwapyung; Han, Jae‐Ho; Oh, Min‐Kyu · 2020 · Microbial Biotechnology · DOI
Full title: Improved production of 2,3‐butanediol and isobutanol by engineering electron transport chain in Escherichia coli
Authors: Jung, Hwapyung; Han, Jae‐Ho; Oh, Min‐Kyu
Year: 2020
Venue: Microbial Biotechnology
Paper Integration of omics data: how well does it work for bacteria?
Keersmaecker, Sigrid C. J. De; Thijs, Inge M; Vanderleyden, Jos et al. · 2006 · Molecular Microbiology · DOI
Full title: Integration of omics data: how well does it work for bacteria?
Authors: Keersmaecker, Sigrid C. J. De; Thijs, Inge M; Vanderleyden, Jos; Marchal, Kathleen
Year: 2006
Venue: Molecular Microbiology
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
Paper Cross‐compartment metabolic coupling enables flexible photoprotective mechanisms in the diatom<i>Phaeodactylum tricornutum</i>
Broddrick, Jared T.; Du, Niu; Smith, Sarah R. et al. · 2019 · New Phytologist · DOI
Full title: Cross‐compartment metabolic coupling enables flexible photoprotective mechanisms in the diatom<i>Phaeodactylum tricornutum</i>
Authors: Broddrick, Jared T.; Du, Niu; Smith, Sarah R.; Tsuji, Yoshinori; Jallet, Denis; Ware, Maxwell A.; Peers, Graham; Matsuda, Yusuke; Dupont, Christopher L.; Mitchell, B. Greg; Palsson, Bernhard Ø.; Allen, Andrew E.
Year: 2019
Venue: New Phytologist
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
Paper Assessment of Zymomonas mobilis biotechnological potential in ethanol production by flux variability analysis
Pentjuss, Agris; Kalnenieks, Uldis · 2013 · Biosystems and Information technology · DOI
Full title: Assessment of Zymomonas mobilis biotechnological potential in ethanol production by flux variability analysis
Authors: Pentjuss, Agris; Kalnenieks, Uldis
Year: 2013
Venue: Biosystems and Information technology
Paper Models and molecular mechanisms for trade‐offs in the context of metabolism
Hashemi, Seirana; Laitinen, Roosa A. E.; Nikoloski, Zoran · 2023 · Molecular Ecology · DOI
Full title: Models and molecular mechanisms for trade‐offs in the context of metabolism
Authors: Hashemi, Seirana; Laitinen, Roosa A. E.; Nikoloski, Zoran
Year: 2023
Venue: Molecular Ecology
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
Paper Assessing Escherichia coli metabolism models and simulation approaches in phenotype predictions: Validation against experimental data
Rafael S. Costa; S. Vinga · 2018 · Biotechnology progress (Print) · DOI
Full title: Assessing Escherichia coli metabolism models and simulation approaches in phenotype predictions: Validation against experimental data
Authors: Rafael S. Costa; S. Vinga
Year: 2018
Venue: Biotechnology progress (Print)
Paper CHOmpact: A reduced metabolic model of Chinese hamster ovary cells with enhanced interpretability
Val, Ioscani Jiménez del; Kyriakopoulos, Sarantos; Albrecht, Simone et al. · 2023 · Biotechnology and Bioengineering · DOI
Full title: CHOmpact: A reduced metabolic model of Chinese hamster ovary cells with enhanced interpretability
Authors: Val, Ioscani Jiménez del; Kyriakopoulos, Sarantos; Albrecht, Simone; Stöckmann, Henning; Rudd, Pauline M.; Polizzi, Karen M.; Kontoravdi, Cleo
Year: 2023
Venue: Biotechnology and Bioengineering
Paper Systems‐level approaches for understanding and engineering of the oleaginous cell factory <i>Yarrowia lipolytica</i>
Poorinmohammad, Naghmeh; Kerkhoven, Eduard J. · 2021 · Biotechnology and Bioengineering · DOI
Full title: Systems‐level approaches for understanding and engineering of the oleaginous cell factory <i>Yarrowia lipolytica</i>
Authors: Poorinmohammad, Naghmeh; Kerkhoven, Eduard J.
Year: 2021
Venue: Biotechnology and Bioengineering
Paper Systems biology for crop improvement
Pazhamala, Lekha T.; Kudapa, Himabindu; Weckwerth, Wolfram et al. · 2021 · The Plant Genome · DOI
Full title: Systems biology for crop improvement
Authors: Pazhamala, Lekha T.; Kudapa, Himabindu; Weckwerth, Wolfram; Millar, A. Harvey; Varshney, Rajeev K.
Year: 2021
Venue: The Plant Genome
Paper Trade‐offs between the instantaneous growth rate and long‐term fitness: Consequences for microbial physiology and predictive computational models
Bruggeman, Frank J.; Teusink, Bas; Steuer, Ralf · 2023 · BioEssays · DOI
Full title: Trade‐offs between the instantaneous growth rate and long‐term fitness: Consequences for microbial physiology and predictive computational models
Authors: Bruggeman, Frank J.; Teusink, Bas; Steuer, Ralf
Year: 2023
Venue: BioEssays
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
Paper Harnessing metabolic plasticity in CHO cells for enhanced perfusion cultivation
Nöbel, Matthias; Barry, Craig; MacDonald, M. A. et al. · 2023 · Biotechnology and Bioengineering · DOI
Full title: Harnessing metabolic plasticity in CHO cells for enhanced perfusion cultivation
Authors: Nöbel, Matthias; Barry, Craig; MacDonald, M. A.; Baker, Kym; Shave, Evan; Mahler, Stephen M.; Munro, Trent P.; Martínez, Verónica S.; Nielsen, Lars K.; Marcellin, Esteban
Year: 2023
Venue: Biotechnology and Bioengineering
Paper Synthesizing Systems Biology Knowledge from Omics Using Genome‐Scale Models
Dahal, Sanjeev; Yurkovich, James T.; Xu, Hao et al. · 2020 · PROTEOMICS · DOI
Full title: Synthesizing Systems Biology Knowledge from Omics Using Genome‐Scale Models
Authors: Dahal, Sanjeev; Yurkovich, James T.; Xu, Hao; Palsson, Bernhard Ø.; Yang, Laurence
Year: 2020
Venue: PROTEOMICS
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
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
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
Paper Multi‐omic data integration and exploiting metabolic models using systems biology approach increase precision in subtyping and early diagnosis of cancer
Tanıl, Ezgi; Nıkerel, Emrah · 2025 · Quantitative Biology · DOI
Full title: Multi‐omic data integration and exploiting metabolic models using systems biology approach increase precision in subtyping and early diagnosis of cancer
Authors: Tanıl, Ezgi; Nıkerel, Emrah
Year: 2025
Venue: Quantitative Biology
Paper <i>Clostridioides difficile</i> 630Δ<i>erm in silico</i> and <i>in vivo</i> – quantitative growth and extensive polysaccharide secretion
Dannheim, Henning; Will, Sabine; Schomburg, Dietmar et al. · 2017 · FEBS Open Bio · DOI
Full title: <i>Clostridioides difficile</i> 630Δ<i>erm in silico</i> and <i>in vivo</i> – quantitative growth and extensive polysaccharide secretion
Authors: Dannheim, Henning; Will, Sabine; Schomburg, Dietmar; Neumann‐Schaal, Meina
Year: 2017
Venue: FEBS Open Bio
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
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
Paper Optimized elemental sulfur recovery from sulfide-containing streams applying systems biology and genome-scale metabolic model of Thioalkalivibrio versutus D301.
Peighami, Reza; Motamedian, Ehsan; Rasekh, Behnam et al. · 2026 · Bioprocess and biosystems engineering · DOI
Full title: Optimized elemental sulfur recovery from sulfide-containing streams applying systems biology and genome-scale metabolic model of Thioalkalivibrio versutus D301.
Authors: Peighami, Reza; Motamedian, Ehsan; Rasekh, Behnam; Buguña, David Gabriel; Ghaffari, Mohammadreza; Yazdian, Fatemeh
Year: 2026
Venue: Bioprocess and biosystems engineering
Paper Genome-scale modeling enables metabolic engineering of Saccharomyces cerevisiae for succinic acid production.
Agren, Rasmus; Otero, José Manuel; Nielsen, Jens · 2013 · Journal of industrial microbiology & biotechnology · DOI
Full title: Genome-scale modeling enables metabolic engineering of Saccharomyces cerevisiae for succinic acid production.
Authors: Agren, Rasmus; Otero, José Manuel; Nielsen, Jens
Year: 2013
Venue: Journal of industrial microbiology & biotechnology
Paper In silico model-driven cofactor engineering strategies for improving the overall NADP(H) turnover in microbial cell factories
Lakshmanan, Meiyappan; Yu, Kai; Koduru, Lokanand et al. · 2015 · Journal of Industrial Microbiology & Biotechnology · DOI
Full title: In silico model-driven cofactor engineering strategies for improving the overall NADP(H) turnover in microbial cell factories
Authors: Lakshmanan, Meiyappan; Yu, Kai; Koduru, Lokanand; Lee, Dong‐Yup
Year: 2015
Venue: Journal of Industrial Microbiology & Biotechnology
Paper Lysine overproducing Corynebacterium glutamicum is characterized by a robust linear combination of two optimal phenotypic states
Rajvanshi, Meghna; Gayen, Kalyan; Venkatesh, K. V. · 2013 · Systems and Synthetic Biology · DOI
Full title: Lysine overproducing Corynebacterium glutamicum is characterized by a robust linear combination of two optimal phenotypic states
Authors: Rajvanshi, Meghna; Gayen, Kalyan; Venkatesh, K. V.
Year: 2013
Venue: Systems and Synthetic Biology
Paper Flux analysis and metabolomics for systematic metabolic engineering of microorganisms.
Toya, Yoshihiro; Shimizu, Hiroshi · 2013 · Biotechnology advances · DOI
Full title: Flux analysis and metabolomics for systematic metabolic engineering of microorganisms.
Authors: Toya, Yoshihiro; Shimizu, Hiroshi
Year: 2013
Venue: Biotechnology advances
Paper Mitigating biomass composition uncertainties in flux balance analysis using ensemble representations
Choi, Yoon-Mi; Choi, Dong‐Hyuk; Lee, Yi Qing et al. · 2023 · Computational and Structural Biotechnology Journal · DOI
Full title: Mitigating biomass composition uncertainties in flux balance analysis using ensemble representations
Authors: Choi, Yoon-Mi; Choi, Dong‐Hyuk; Lee, Yi Qing; Koduru, Lokanand; Lewis, Nathan E.; Lakshmanan, Meiyappan; Lee, Dong‐Yup
Year: 2023
Venue: Computational and Structural Biotechnology Journal
Paper Synthetic biology tools for environmental protection
Aminian-Dehkordi, Javad; Rahimi, Shadi; Golzar-Ahmadi, Mehdi et al. · 2023 · Biotechnology Advances · DOI
Full title: Synthetic biology tools for environmental protection
Authors: Aminian-Dehkordi, Javad; Rahimi, Shadi; Golzar-Ahmadi, Mehdi; Singh, Amritpal; López, Javiera; Ledesma‐Amaro, Rodrigo; Mijakovic̀, Ivan
Year: 2023
Venue: Biotechnology Advances
Paper Retrosynthetic design of metabolic pathways to chemicals not found in nature
Lin, Geng-Min; Warden‐Rothman, Robert; Voigt, Christopher A. · 2019 · Current Opinion in Systems Biology · DOI
Full title: Retrosynthetic design of metabolic pathways to chemicals not found in nature
Authors: Lin, Geng-Min; Warden‐Rothman, Robert; Voigt, Christopher A.
Year: 2019
Venue: Current Opinion in Systems Biology
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
Paper Systems biology&#x27;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&#x27;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
Paper A model-driven approach to upcycling recalcitrant feedstocks in Pseudomonas putida by decoupling PHA production from nutrient limitation
Manoli, Maria‐Tsampika; Becerra, A. Gargantilla; Cerro, Carlos del et al. · 2024 · Cell Reports · DOI
Full title: A model-driven approach to upcycling recalcitrant feedstocks in Pseudomonas putida by decoupling PHA production from nutrient limitation
Authors: Manoli, Maria‐Tsampika; Becerra, A. Gargantilla; Cerro, Carlos del; Rivero‐Buceta, Virginia; Prieto, M. Auxiliadora; Nogales, Juan
Year: 2024
Venue: Cell Reports
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
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
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
Paper Unstructured kinetic models to simulate an arabinose switch that decouples cell growth from metabolite production
Edwards, Harley; Xu, Peng · 2020 · Synthetic and Systems Biotechnology · DOI
Full title: Unstructured kinetic models to simulate an arabinose switch that decouples cell growth from metabolite production
Authors: Edwards, Harley; Xu, Peng
Year: 2020
Venue: Synthetic and Systems Biotechnology
Paper Automated generation of bacterial resource allocation models
Bulović, Ana; Fischer, Stephan; Dinh, Marc et al. · 2019 · Metabolic Engineering · DOI
Full title: Automated generation of bacterial resource allocation models
Authors: Bulović, Ana; Fischer, Stephan; Dinh, Marc; Golib, Felipe; Liebermeister, Wolfram; Poirier, Christian; Tournier, Laurent; Klipp, Edda; Fromion, Vincent; Goelzer, Anne
Year: 2019
Venue: Metabolic Engineering
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
Paper Improving the flux distributions simulated with genome-scale metabolic models of Saccharomyces cerevisiae
Pereira, Rui; Nielsen, Jens; Rocha, Isabel · 2016 · Metabolic Engineering Communications · DOI
Full title: Improving the flux distributions simulated with genome-scale metabolic models of Saccharomyces cerevisiae
Authors: Pereira, Rui; Nielsen, Jens; Rocha, Isabel
Year: 2016
Venue: Metabolic Engineering Communications
Paper Synthetic Microbial Cocultivation for Targeted Production of Odd-Chain Carboxylates and Alcohols from Carbon Monoxide
Olm, Ivette Parera; Benito-Vaquerizo, Sara; Dubaere, Charles et al. · 2025 · Environmental Science & Technology · DOI
Full title: Synthetic Microbial Cocultivation for Targeted Production of Odd-Chain Carboxylates and Alcohols from Carbon Monoxide
Authors: Olm, Ivette Parera; Benito-Vaquerizo, Sara; Dubaere, Charles; Santos, Vítor A. P. Martins dos; Suárez‐Diez, María; Sousa, Diana Z.
Year: 2025
Venue: Environmental Science & Technology
Paper Computational Framework for Machine-Learning-Enabled 13C Fluxomics.
Wu, Chao; Yu, Jianping; Guarnieri, Michael et al. · 2022 · ACS synthetic biology · DOI
Full title: Computational Framework for Machine-Learning-Enabled 13C Fluxomics.
Authors: Wu, Chao; Yu, Jianping; Guarnieri, Michael; Xiong, Wei
Year: 2022
Venue: ACS synthetic biology
Paper Systems analysis of minimal metabolic networks In prokaryotes
Xavier, Joana R. · 2016 · RepositóriUM (Universidade do Minho)
Full title: Systems analysis of minimal metabolic networks In prokaryotes
Authors: Xavier, Joana R.
Year: 2016
Venue: RepositóriUM (Universidade do Minho)
Paper Predicting metabolic strategies in Saccharomyces cerevisiae with a kinetically constrained FBA model
Nilsson, Avlant · 2014 · Chalmers Publication Library (Chalmers University of Technology)
Full title: Predicting metabolic strategies in Saccharomyces cerevisiae with a kinetically constrained FBA model
Authors: Nilsson, Avlant
Year: 2014
Venue: Chalmers Publication Library (Chalmers University of Technology)
Paper Towards predictive metabolic engineering: kinetic modeling and experimental analysis of a heterologous mevalonate pathway in E. coli
Weaver, Lane J. · 2013 · eScholarship (California Digital Library)
Full title: Towards predictive metabolic engineering: kinetic modeling and experimental analysis of a heterologous mevalonate pathway in E. coli
Authors: Weaver, Lane J.
Year: 2013
Venue: eScholarship (California Digital Library)
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 The application of metabolic network analysis in understanding and targeting metabolism for drug discovery
Liu, Jiangxia · 2010 · D-Scholarship@Pitt (University of Pittsburgh)
Full title: The application of metabolic network analysis in understanding and targeting metabolism for drug discovery
Authors: Liu, Jiangxia
Year: 2010
Venue: D-Scholarship@Pitt (University of Pittsburgh)
Paper Validation of a Saccharomyces cerevisiae Dynamic Flux Balance Model
Hjersted, Jared L.; Henson, Michael A. · 2008 · ScholarWorks@UMassAmherst (University of Massachusetts Amherst)
Full title: Validation of a Saccharomyces cerevisiae Dynamic Flux Balance Model
Authors: Hjersted, Jared L.; Henson, Michael A.
Year: 2008
Venue: ScholarWorks@UMassAmherst (University of Massachusetts Amherst)
Paper Using metabolic network reconstructions to analyze complex data sets
Zielinski, Daniel C. · 2015 · eScholarship (California Digital Library)
Full title: Using metabolic network reconstructions to analyze complex data sets
Authors: Zielinski, Daniel C.
Year: 2015
Venue: eScholarship (California Digital Library)
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)
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)
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)
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)
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)
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)
Thesis Systems biology definition of the core proteome of metabolism and expression is consistent with high-throughput data
Yang, Laurence; Tan, Justin; O'Brien, Edward J. et al. · 2015 · Technical University of Denmark (DTU) · DOI
Full title: Systems biology definition of the core proteome of metabolism and expression is consistent with high-throughput data
Authors: Yang, Laurence; Tan, Justin; O'Brien, Edward J.; Monk, Jonathan M.; Kim, Donghyuk; Li, Howard J.; Charusanti, Pep; Ebrahim, Ali; Lloyd, Colton J.; Yurkovich, James T.; Du, Bin; Draeger, Andreas; Thomas, Alex; Sun, Yuekai; Saunders, Michael A.; Palsson, Bernhard O.; id_orcid 0000-0003-2357-6785
Year: 2015
Venue: Technical University of Denmark (DTU)
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)
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)
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)
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)
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)
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)
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)
Thesis Improved vanillin production in baker&#x27;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&#x27;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)
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)
Thesis Reframing gene essentiality in terms of adaptive flexibility
Guzmán, Gabriela I.; Olson, Connor A.; Hefner, Ying et al. · 2018 · Technical University of Denmark (DTU) · DOI
Full title: Reframing gene essentiality in terms of adaptive flexibility
Authors: Guzmán, Gabriela I.; Olson, Connor A.; Hefner, Ying; Phaneuf, Patrick V.; Catoiu, Edward; Crepaldi, Lais B.; Micas, Lucas Goldschmidt; 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)
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)
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)
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)
Thesis Antibiotic Overproduction in Steptomyces coelicolor A3(2) Mediated by Phosphofructokinase Deletion
Borodina, Irina; Siebring, Jeroen; Zhang, Jie et al. · 2008 · Technical University of Denmark (DTU) · DOI
Full title: Antibiotic Overproduction in Steptomyces coelicolor A3(2) Mediated by Phosphofructokinase Deletion
Authors: Borodina, Irina; Siebring, Jeroen; Zhang, Jie; Smith, Colin P.; van Keulen, Geertje; Dijkhuizen, Lubbert; Nielsen, Jens
Year: 2008
Venue: Technical University of Denmark (DTU)
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)
Thesis Synthetic biology and metabolic engineering of actinomycetes for natural product discovery
Palazzotto, Emilia; Tong, Yaojun; Lee, Sang Yup et al. · 2019 · Technical University of Denmark (DTU) · DOI
Full title: Synthetic biology and metabolic engineering of actinomycetes for natural product discovery
Authors: Palazzotto, Emilia; Tong, Yaojun; Lee, Sang Yup; Weber, Tilmann; id_orcid 0000-0002-8260-5120
Year: 2019
Venue: Technical University of Denmark (DTU)
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)
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)
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)
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)
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)
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)
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)
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)
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)
Thesis MEMOTE for standardized genome-scale metabolic model testing
Lieven, Christian; Beber, Moritz Emanuel; id_orcid 0000-0003-2406-1978 et al. · 2020 · Technical University of Denmark (DTU) · DOI
Full title: MEMOTE for standardized genome-scale metabolic model testing
Authors: Lieven, Christian; Beber, Moritz Emanuel; id_orcid 0000-0003-2406-1978; Olivier, Brett G.; Bergmann, Frank T.; Ataman, Meric; Babaei, Parizad; Bartell, Jennifer A.; Blank, Lars M.; Chauhan, Siddharth; Correia, Kevin; Diener, Christian; Dräger, Andreas; Ebert, Birgitta E.; Edirisinghe, Janaka N.; Faria, José P.; Feist, Adam M.; id_orcid 0000-0002-8630-4800; Fengos, Georgios; Fleming, Ronan M. T.; García-Jiménez, Beatriz; Hatzimanikatis, Vassily; van Helvoirt, Wout; Henry, Christopher S.; Hermjakob, Henning; Herrgard, Markus J.; Kaafarani, Ali; Kim, Hyun Uk; King, Zachary; Klamt, Steffen; Klipp, Edda; Koehorst, Jasper J.; König, Matthias; Lakshmanan, Meiyappan; Lee, Dong-Yup; Lee, Sang Yup; Lee, Sunjae; Lewis, Nathan E.; Liu, Filipe; Ma, Hongwu; Machado, Daniel; Mahadevan, Radhakrishnan; Maia, Paulo; Mardinoglu, Adil; Medlock, Gregory L.; Monk, Jonathan M.; Nielsen, Jens; Nielsen, Lars Keld; Nogales, Juan; Nookaew, Intawat; Palsson, Bernhard O.; id_orcid 0000-0003-2357-6785; Papin, Jason A.; Patil, Kiran Raosaheb; Poolman, Mark; Price, Nathan D.; Resendis-Antonio, Osbaldo; Richelle, Anne; Rocha, Isabel; Sánchez, Benjamín José; Schaap, Peter J.; Malik Sheriff, Rahuman S.; Shoaie, Saeed; Sonnenschein, Nikolaus; id_orcid 0000-0002-7581-4936; Teusink, Bas; Vilaca, Paulo; Vik, Jon Olav; Wodke, Judith A. H.; Xavier, Joana C.; Yuan, Qianqian; Zakhartsev, Maksim; Zhang, Cheng
Year: 2020
Venue: Technical University of Denmark (DTU)
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)
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)
Thesis Strategies and challenges for metabolic rewiring
Yu, Tao; Dabirian, Yasaman; Liu, Quanli et al. · 2019 · Technical University of Denmark (DTU) · DOI
Full title: Strategies and challenges for metabolic rewiring
Authors: Yu, Tao; Dabirian, Yasaman; Liu, Quanli; Siewers, Verena; Nielsen, Jens
Year: 2019
Venue: Technical University of Denmark (DTU)
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)
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)
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)
Thesis Prediction, Precision, and Safety In Advanced Microbial Therapeutics
van 't Hof, Max · 2022 · Technical University of Denmark (DTU) · DOI
Full title: Prediction, Precision, and Safety In Advanced Microbial Therapeutics
Authors: van 't Hof, Max
Year: 2022
Venue: Technical University of Denmark (DTU)
Thesis Systems Biology of Metabolism: Annual Review of Biochemistry
Nielsen, Jens · 2017 · Technical University of Denmark (DTU) · DOI
Full title: Systems Biology of Metabolism: Annual Review of Biochemistry
Authors: Nielsen, Jens
Year: 2017
Venue: Technical University of Denmark (DTU)
Thesis Reflections on the aerobic fermentation stoichiometry of crabtree positive yeasts
Villadsen, John; id_orcid 0000-0002-6523-8445; Jørgensen, Sten Bay et al. · 2014 · Technical University of Denmark (DTU) · DOI
Full title: Reflections on the aerobic fermentation stoichiometry of crabtree positive yeasts
Authors: Villadsen, John; id_orcid 0000-0002-6523-8445; Jørgensen, Sten Bay; id_orcid 0000-0002-3179-972X
Year: 2014
Venue: Technical University of Denmark (DTU)
Thesis GRASP:A computational platform for building kinetic models of cellular metabolism
Matos, Marta R.A.; Saa, Pedro A.; Cowie, Nicholas et al. · 2022 · Technical University of Denmark (DTU) · DOI
Full title: GRASP:A computational platform for building kinetic models of cellular metabolism
Authors: Matos, Marta R.A.; Saa, Pedro A.; Cowie, Nicholas; Volkova, Svetlana; De Leeuw, Marina; Nielsen, Lars K.
Year: 2022
Venue: Technical University of Denmark (DTU)
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)
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)
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)
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)
Thesis Understanding flux switching in metabolic networks through an analysis of synthetic lethals
Narasimha, Sowmya Manojna; Malpani, Tanisha; Mohite, Omkar S. et al. · 2024 · Technical University of Denmark (DTU) · DOI
Full title: Understanding flux switching in metabolic networks through an analysis of synthetic lethals
Authors: Narasimha, Sowmya Manojna; Malpani, Tanisha; Mohite, Omkar S.; id_orcid 0000-0002-3240-1656; Nath, J. Saketha; Raman, Karthik
Year: 2024
Venue: Technical University of Denmark (DTU)
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)
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)
Thesis Harnessing the metabolic potential of thermophilic bacteria:Systems metabolic engineering tools for the production of volatile biochemicals
Mol, Viviënne · 2022 · Technical University of Denmark (DTU) · DOI
Full title: Harnessing the metabolic potential of thermophilic bacteria:Systems metabolic engineering tools for the production of volatile biochemicals
Authors: Mol, Viviënne
Year: 2022
Venue: Technical University of Denmark (DTU)
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)
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)
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)
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)
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)
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)
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)
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)
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)
Thesis multiTFA:A python package for multi-variate thermodynamics-based flux analysis
Mahamkali, Vishnuvardhan; McCubbin, Tim; Beber, Moritz Emanuel et al. · 2021 · Technical University of Denmark (DTU) · DOI
Full title: multiTFA:A python package for multi-variate thermodynamics-based flux analysis
Authors: Mahamkali, Vishnuvardhan; McCubbin, Tim; Beber, Moritz Emanuel; id_orcid 0000-0003-2406-1978; Noor, Elad; Marcellin, Esteban; Nielsen, Lars Keld
Year: 2021
Venue: Technical University of Denmark (DTU)
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)
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)
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)
Thesis Identifying anti-growth factors for human cancer cell lines through genome-scale metabolic modeling
Ghaffari, Pouyan; Mardinoglu, Adil; Asplund, Anna et al. · 2015 · Technical University of Denmark (DTU) · DOI
Full title: Identifying anti-growth factors for human cancer cell lines through genome-scale metabolic modeling
Authors: Ghaffari, Pouyan; Mardinoglu, Adil; Asplund, Anna; Shoaie, Saeed; Kampf, Caroline; Uhlén, Mathias; Nielsen, Jens
Year: 2015
Venue: Technical University of Denmark (DTU)
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)
Thesis Application of a Mechanistic Model as a Tool for On-line Monitoring of Pilot Scale Filamentous Fungal Fermentation Processes - The Importance of Evaporation Effects:Mechanistic model for pilot scale monitoring
Mears, Lisa; Stocks, Stuart M.; Albæk, Mads Orla et al. · 2017 · Technical University of Denmark (DTU) · DOI
Full title: Application of a Mechanistic Model as a Tool for On-line Monitoring of Pilot Scale Filamentous Fungal Fermentation Processes - The Importance of Evaporation Effects:Mechanistic model for pilot scale monitoring
Authors: Mears, Lisa; Stocks, Stuart M.; Albæk, Mads Orla; Sin, Gürkan; id_orcid 0000-0003-0513-4502; Gernaey, Krist V.; id_orcid 0000-0002-0364-1773
Year: 2017
Venue: Technical University of Denmark (DTU)
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)
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)
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)
Thesis Community standards to facilitate development and address challenges in metabolic modeling
Carey, Maureen A.; Dräger, Andreas; Beber, Moritz E. et al. · 2020 · Technical University of Denmark (DTU) · DOI
Full title: Community standards to facilitate development and address challenges in metabolic modeling
Authors: Carey, Maureen A.; Dräger, Andreas; Beber, Moritz E.; id_orcid 0000-0003-2406-1978; Papin, Jason A.; Yurkovich, James T.
Year: 2020
Venue: Technical University of Denmark (DTU)
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)
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)
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)
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)
Thesis Reconstruction of genome-scale human metabolic models using omics data
Ryu, Jae Yong; Kim, Hyun Uk; Lee, Sang Yup · 2015 · Technical University of Denmark (DTU) · DOI
Full title: Reconstruction of genome-scale human metabolic models using omics data
Authors: Ryu, Jae Yong; Kim, Hyun Uk; Lee, Sang Yup
Year: 2015
Venue: Technical University of Denmark (DTU)
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)
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)
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)
Thesis Recent advances in microbial production of fuels and chemicals using tools and strategies of systems metabolic engineering
Cho, Changhee; Choi, So Young; Luo, Zi Wei et al. · 2015 · Technical University of Denmark (DTU) · DOI
Full title: Recent advances in microbial production of fuels and chemicals using tools and strategies of systems metabolic engineering
Authors: Cho, Changhee; Choi, So Young; Luo, Zi Wei; Lee, Sang Yup
Year: 2015
Venue: Technical University of Denmark (DTU)
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)
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)
Thesis Modeling genome-wide enzyme evolution predicts strong epistasis underlying catalytic turnover rates
Heckmann, David; Zielinski, Daniel C.; Palsson, Bernhard O. et al. · 2018 · Technical University of Denmark (DTU) · DOI
Full title: Modeling genome-wide enzyme evolution predicts strong epistasis underlying catalytic turnover rates
Authors: Heckmann, David; Zielinski, Daniel C.; Palsson, Bernhard O.; id_orcid 0000-0003-2357-6785
Year: 2018
Venue: Technical University of Denmark (DTU)
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)
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)
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)
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)
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)
Thesis Putting computational modeling at the fingertips of bench biologists
Sonnenschein, Nikolaus; id_orcid 0000-0002-7581-4936; Herrgard, Markus · 2014 · Technical University of Denmark (DTU) · DOI
Full title: Putting computational modeling at the fingertips of bench biologists
Authors: Sonnenschein, Nikolaus; id_orcid 0000-0002-7581-4936; Herrgard, Markus
Year: 2014
Venue: Technical University of Denmark (DTU)
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)
Thesis Identifying therapeutic weak spots in cancer using network analysis
Thiel, Denise Anna · 2022 · Imperial College London · DOI
Full title: Identifying therapeutic weak spots in cancer using network analysis
Authors: Thiel, Denise Anna
Year: 2022
Venue: Imperial College London
Thesis SUMOFLUX: A Generalized Method for Targeted 13C Metabolic Flux Ratio Analysis
Kogadeeva, Maria; Zamboni, Nicola; id_orcid0000-0003-1271-1021 · 2016 · ETH Zurich (Swiss Federal Institute of Technology in Zurich) · DOI
Full title: SUMOFLUX: A Generalized Method for Targeted 13C Metabolic Flux Ratio Analysis
Authors: Kogadeeva, Maria; Zamboni, Nicola; id_orcid0000-0003-1271-1021
Year: 2016
Venue: ETH Zurich (Swiss Federal Institute of Technology in Zurich)
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
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)
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)
Thesis Assessing and Resolving Model Misspecifications in Metabolic Flux Analysis
Gunawan, Rudiyanto; Hutter, Sandro · 2017 · ETH Zurich (Swiss Federal Institute of Technology in Zurich) · DOI
Full title: Assessing and Resolving Model Misspecifications in Metabolic Flux Analysis
Authors: Gunawan, Rudiyanto; Hutter, Sandro
Year: 2017
Venue: ETH Zurich (Swiss Federal Institute of Technology in Zurich)
Thesis Methanol-essential growth of Escherichia coli
Meyer, Fabian; Keller, Philipp; Hartl, Johannes et al. · 2018 · ETH Zurich (Swiss Federal Institute of Technology in Zurich) · DOI
Full title: Methanol-essential growth of Escherichia coli
Authors: Meyer, Fabian; Keller, Philipp; Hartl, Johannes; Gröninger, Olivier G.; Kiefer, Patrick; Vorholt, Julia A.
Year: 2018
Venue: ETH Zurich (Swiss Federal Institute of Technology in Zurich)
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)
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)
Thesis anNET: a tool for network-embedded thermodynamic analysis of quantitative metabolome data
Zamboni, Nicola; id_orcid0000-0003-1271-1021; Kümmel, Anne et al. · 2008 · ETH Zurich (Swiss Federal Institute of Technology in Zurich) · DOI
Full title: anNET: a tool for network-embedded thermodynamic analysis of quantitative metabolome data
Authors: Zamboni, Nicola; id_orcid0000-0003-1271-1021; Kümmel, Anne; Heinemann, Matthias
Year: 2008
Venue: ETH Zurich (Swiss Federal Institute of Technology in Zurich)
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)
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)
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)
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)
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)
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)
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)
Thesis Genome-scale reconstruction and system level investigation of the metabolic network of Methylobacterium extorquens AM1
Peyraud, Rémi; Schneider, Kathrin; Kiefer, Patrick et al. · 2011 · ETH Zurich (Swiss Federal Institute of Technology in Zurich) · DOI
Full title: Genome-scale reconstruction and system level investigation of the metabolic network of Methylobacterium extorquens AM1
Authors: Peyraud, Rémi; Schneider, Kathrin; Kiefer, Patrick; Massou, Stéphane; Vorholt, Julia A.; Portais, Jean-Charles
Year: 2011
Venue: ETH Zurich (Swiss Federal Institute of Technology in Zurich)
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)
Thesis ScalaFlux: A scalable approach to quantify fluxes in metabolic subnetworks
Millard, Pierre; Schmitt, Uwe; Kiefer, Patrick et al. · 2020 · ETH Zurich (Swiss Federal Institute of Technology in Zurich) · DOI
Full title: ScalaFlux: A scalable approach to quantify fluxes in metabolic subnetworks
Authors: Millard, Pierre; Schmitt, Uwe; Kiefer, Patrick; Vorholt, Julia A.; Heux, Stéphanie; Portais, Jean-Charles
Year: 2020
Venue: ETH Zurich (Swiss Federal Institute of Technology in Zurich)
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)
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)
Thesis Ensemble Kinetic Modeling of Metabolic Networks from Dynamic Metabolic Profiles
Jia, Gengjie; Stephanopoulos, Gregory; Gunawan, Rudiyanto · 2012 · ETH Zurich (Swiss Federal Institute of Technology in Zurich) · DOI
Full title: Ensemble Kinetic Modeling of Metabolic Networks from Dynamic Metabolic Profiles
Authors: Jia, Gengjie; Stephanopoulos, Gregory; Gunawan, Rudiyanto
Year: 2012
Venue: ETH Zurich (Swiss Federal Institute of Technology in Zurich)
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)
Thesis Combinatorial pathway optimization for streamlined metabolic engineering
Jeschek, Markus; Gerngross, Daniel; Panke, Sven · 2017 · ETH Zurich (Swiss Federal Institute of Technology in Zurich) · DOI
Full title: Combinatorial pathway optimization for streamlined metabolic engineering
Authors: Jeschek, Markus; Gerngross, Daniel; Panke, Sven
Year: 2017
Venue: ETH Zurich (Swiss Federal Institute of Technology in Zurich)
Thesis Modeling metabolic networks of individual bacterial agents in heterogeneous and dynamic soil habitats (IndiMeSH)
Borer, Benedict; Ataman, Meric; Hatzimanikatis, Vassily et al. · 2019 · ETH Zurich (Swiss Federal Institute of Technology in Zurich) · DOI
Full title: Modeling metabolic networks of individual bacterial agents in heterogeneous and dynamic soil habitats (IndiMeSH)
Authors: Borer, Benedict; Ataman, Meric; Hatzimanikatis, Vassily; Or, Dani
Year: 2019
Venue: ETH Zurich (Swiss Federal Institute of Technology in Zurich)
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)
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)
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 · ETH Zurich (Swiss Federal Institute of Technology in Zurich) · 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; id_orcid0000-0001-8776-4799; Beber, Moritz E.; Best, Aaron A.; DeJongh, Matthew; Kimbrel, Jeffrey A.; 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: ETH Zurich (Swiss Federal Institute of Technology in Zurich)
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)
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)
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)
Thesis Integration of Metabolomics and Transcriptomics Reveals a Complex Diet of Mycobacterium tuberculosis during Early Macrophage Infection
Zimmermann, Michael; Kogadeeva, Maria; Gengenbacher, Martin et al. · 2017 · ETH Zurich (Swiss Federal Institute of Technology in Zurich) · DOI
Full title: Integration of Metabolomics and Transcriptomics Reveals a Complex Diet of Mycobacterium tuberculosis during Early Macrophage Infection
Authors: Zimmermann, Michael; Kogadeeva, Maria; Gengenbacher, Martin; McEwen, Gayle; Mollenkopf, Hans-Joachim; Zamboni, Nicola; id_orcid0000-0003-1271-1021; Kaufmann, Stefan Hugo Ernst
Year: 2017
Venue: ETH Zurich (Swiss Federal Institute of Technology in Zurich)
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)
Thesis Assumptions on decision making and environment can yield multiple steady states in microbial community models
Theorell, Axel; Stelling, Jörg · 2023 · ETH Zurich (Swiss Federal Institute of Technology in Zurich) · 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: ETH Zurich (Swiss Federal Institute of Technology in Zurich)
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)
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)
Thesis Minimal Metabolic Exchanges for Microbial Communities in a Chemostat at Steady State
Moawad, Alix; Stelling, Jörg O.O. · 2026 · ETH Zurich (Swiss Federal Institute of Technology in Zurich) · DOI
Full title: Minimal Metabolic Exchanges for Microbial Communities in a Chemostat at Steady State
Authors: Moawad, Alix; Stelling, Jörg O.O.
Year: 2026
Venue: ETH Zurich (Swiss Federal Institute of Technology in Zurich)
Thesis Simulation-based metabolic flux inference
Diederen, Thomas H. M. · 2023 · ETH Zurich Research Collection · DOI
Full title: Simulation-based metabolic flux inference
Authors: Diederen, Thomas H. M.
Year: 2023
Venue: ETH Zurich Research Collection
Thesis Metabolic network reconstruction as a resource for analyzing Salmonella Typhimurium SL1344 growth in the mouse intestine
Vayena, Evangelia; Fuchs, Lea; Mohammadi Peyhani, Homa et al. · 2025 · ETH Zurich (Swiss Federal Institute of Technology in Zurich) · DOI
Full title: Metabolic network reconstruction as a resource for analyzing Salmonella Typhimurium SL1344 growth in the mouse intestine
Authors: Vayena, Evangelia; Fuchs, Lea; Mohammadi Peyhani, Homa; Lagoda, Konrad; Nguyen, Bidong; Hardt, Wolf-Dietrich; id_orcid0000-0002-9892-6420; Hatzimanikatis, Vassily
Year: 2025
Venue: ETH Zurich (Swiss Federal Institute of Technology in Zurich)
Thesis All Driven by Energy Demand? Integrative Comparison of Metabolism of Enterococcus faecalis Wildtype and a Glutamine Synthase Mutant
Loghmani, Seyed Babak; Zitzow, Eric; Koh, Gene Ching Chiek et al. · 2022 · ETH Zurich (Swiss Federal Institute of Technology in Zurich) · DOI
Full title: All Driven by Energy Demand? Integrative Comparison of Metabolism of Enterococcus faecalis Wildtype and a Glutamine Synthase Mutant
Authors: Loghmani, Seyed Babak; Zitzow, Eric; Koh, Gene Ching Chiek; Ulmer, Andreas; Veith, Nadine; Großeholz, Ruth; Rossnagel, Madlen; Loesch, Maren; Aebersold, Reudi; Kreikemeyer, Bernd; Fiedler, Tomas; Kummer, Ursula
Year: 2022
Venue: ETH Zurich (Swiss Federal Institute of Technology in Zurich)
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)
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)
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)
Thesis Engineering central metabolism – a grand challenge for plant biologists
Sweetlove, Lee J.; Nielsen, Jens; Fernie, Alisdair R. · 2017 · Technical University of Denmark (DTU) · DOI
Full title: Engineering central metabolism – a grand challenge for plant biologists
Authors: Sweetlove, Lee J.; Nielsen, Jens; Fernie, Alisdair R.
Year: 2017
Venue: Technical University of Denmark (DTU)
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)
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)
Thesis Integrated metabolic modeling, culturing, and transcriptomics explain enhanced virulence of Vibrio cholerae during coinfection with enterotoxigenic Escherichia coli
Abdel-Haleem, Alyaa M.; Ravikumar, Vaishnavi; Ji, Boyang et al. · 2020 · Technical University of Denmark (DTU) · DOI
Full title: Integrated metabolic modeling, culturing, and transcriptomics explain enhanced virulence of Vibrio cholerae during coinfection with enterotoxigenic Escherichia coli
Authors: Abdel-Haleem, Alyaa M.; Ravikumar, Vaishnavi; Ji, Boyang; Mineta, Katsuhiko; Gao, Xin; Nielsen, Jens; Gojobori, Takashi; Mijakovic, Ivan
Year: 2020
Venue: Technical University of Denmark (DTU)
Thesis Predicting growth of the healthy infant using a genome scale metabolic model
Nilsson, Avlant; Mardinoglu, Adil; Nielsen, Jens · 2017 · Technical University of Denmark (DTU) · DOI
Full title: Predicting growth of the healthy infant using a genome scale metabolic model
Authors: Nilsson, Avlant; Mardinoglu, Adil; Nielsen, Jens
Year: 2017
Venue: Technical University of Denmark (DTU)
Thesis Integrated modelling of metabolic and regulatory networks
Palinkas, Aljoscha · 2015 · Freie Universität Berlin (Refubium) · DOI
Full title: Integrated modelling of metabolic and regulatory networks
Authors: Palinkas, Aljoscha
Year: 2015
Venue: Freie Universität Berlin (Refubium)
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)
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)
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)
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)
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)
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)
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)
Thesis Genome-scale metabolic models highlight stage-specific differences in essential metabolic pathways in Trypanosoma cruzi
Shiratsubaki, Isabel S.; Fang, Xin; Souza, Rodolpho O.O. et al. · 2020 · Technical University of Denmark (DTU) · DOI
Full title: Genome-scale metabolic models highlight stage-specific differences in essential metabolic pathways in Trypanosoma cruzi
Authors: Shiratsubaki, Isabel S.; Fang, Xin; Souza, Rodolpho O.O.; Palsson, Bernhard O.; id_orcid 0000-0003-2357-6785; Silber, Ariel M.; Siqueira-Neto, Jair L.
Year: 2020
Venue: Technical University of Denmark (DTU)
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)
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)
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)
Thesis Updated and standardized genome-scale reconstruction of Mycobacterium tuberculosis H37Rv, iEK1011, simulates flux states indicative of physiological conditions
Kavvas, Erol S.; Seif, Yara; Yurkovich, James T. et al. · 2018 · Technical University of Denmark (DTU) · DOI
Full title: Updated and standardized genome-scale reconstruction of Mycobacterium tuberculosis H37Rv, iEK1011, simulates flux states indicative of physiological conditions
Authors: Kavvas, Erol S.; Seif, Yara; Yurkovich, James T.; Norsigian, Charles; Poudel, Saugat; Greenwald, William W.; Ghatak, Sankha; Palsson, Bernhard O.; id_orcid 0000-0003-2357-6785; Monk, Jonathan M.
Year: 2018
Venue: Technical University of Denmark (DTU)
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)
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)
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)
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)
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)
Thesis Gene deletion of cytosolic ATP: citrate lyase leads to altered organic acid production in Aspergillus niger
Meijer, Susan Lisette; Nielsen, Michael Lynge; Olsson, Lisbeth et al. · 2009 · Technical University of Denmark (DTU) · DOI
Full title: Gene deletion of cytosolic ATP: citrate lyase leads to altered organic acid production in Aspergillus niger
Authors: Meijer, Susan Lisette; Nielsen, Michael Lynge; Olsson, Lisbeth; Nielsen, Jens
Year: 2009
Venue: Technical University of Denmark (DTU)
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)
Thesis Quantification of intracellular metabolic fluxes from fractional enrichment and 13 C- 13 C coupling constraints on the isotopomer distribution in labeled biomass components
Schmidt, Karsten; Nørregaard, L.C.; Pedersen, B. et al. · 1999 · Technical University of Denmark (DTU) · DOI
Full title: Quantification of intracellular metabolic fluxes from fractional enrichment and 13 C- 13 C coupling constraints on the isotopomer distribution in labeled biomass components
Authors: Schmidt, Karsten; Nørregaard, L.C.; Pedersen, B.; Meissner, A.; Duus, Jens Øllgaard; id_orcid 0000-0003-3625-1250; Nielsen, Jens Bredal; Villadsen, John; id_orcid 0000-0002-6523-8445
Year: 1999
Venue: Technical University of Denmark (DTU)
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)
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)
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)
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)
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)
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)
Thesis Estimating biological elementary flux modes that decompose a flux distribution by the minimal branching property
Chan, Siu Hung Joshua; Solem, Christian; id_orcid 0000-0002-3898-280X et al. · 2014 · Technical University of Denmark (DTU) · DOI
Full title: Estimating biological elementary flux modes that decompose a flux distribution by the minimal branching property
Authors: Chan, Siu Hung Joshua; Solem, Christian; id_orcid 0000-0002-3898-280X; Jensen, Peter Ruhdal; id_orcid 0000-0003-2080-2070; Ji, P.
Year: 2014
Venue: Technical University of Denmark (DTU)
Thesis Reproducibility of oligonucleotide microarray transcriptome analyses - An interlaboratory comparison using chemostat cultures of Saccharomyces cerevisiae
Piper, M.D.W.; Daran-Lapujade, P.; Bro, Christoffer et al. · 2002 · Technical University of Denmark (DTU) · DOI
Full title: Reproducibility of oligonucleotide microarray transcriptome analyses - An interlaboratory comparison using chemostat cultures of Saccharomyces cerevisiae
Authors: Piper, M.D.W.; Daran-Lapujade, P.; Bro, Christoffer; Regenberg, Birgitte; Knudsen, Steen; Nielsen, Jens; Pronk, J.T.
Year: 2002
Venue: Technical University of Denmark (DTU)
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)
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)
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)
Thesis Flux cones of metabolic networks
Wieder, Frederik Laszlo · 2024 · Freie Universität Berlin (Refubium) · DOI
Full title: Flux cones of metabolic networks
Authors: Wieder, Frederik Laszlo
Year: 2024
Venue: Freie Universität Berlin (Refubium)
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)
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)
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)
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)
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)
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)
Thesis Parameter estimation and network identification in metabolic pathway systems
Chou, I-Chun · 2009 · Georgia Institute of Technology · DOI
Full title: Parameter estimation and network identification in metabolic pathway systems
Authors: Chou, I-Chun
Year: 2009
Venue: Georgia Institute of Technology
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)
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)
Thesis Dynamic flux estimation - a novel framework for metabolic pathway analysis
Goel, Gautam · 2010 · Georgia Institute of Technology · DOI
Full title: Dynamic flux estimation - a novel framework for metabolic pathway analysis
Authors: Goel, Gautam
Year: 2010
Venue: Georgia Institute of Technology
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
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
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)
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
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)
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
Thesis Development of hybrid platforms for antibody manufacturing optimisation
Barbosa, Rodrigo · 2024 · Imperial College London · DOI
Full title: Development of hybrid platforms for antibody manufacturing optimisation
Authors: Barbosa, Rodrigo
Year: 2024
Venue: Imperial College London
Thesis Metabolic modeling of different degrees of steatohepatitis in mice
Pandey, Vikash · 2014 · Freie Universität Berlin (Refubium) · DOI
Full title: Metabolic modeling of different degrees of steatohepatitis in mice
Authors: Pandey, Vikash
Year: 2014
Venue: Freie Universität Berlin (Refubium)
Thesis Minimal cut sets and their use in modelling flavonoid metabolism
Clark, Sangaalofa Tooki · 2012 · Lincoln University New Zealand - Research Archive · DOI
Full title: Minimal cut sets and their use in modelling flavonoid metabolism
Authors: Clark, Sangaalofa Tooki
Year: 2012
Venue: Lincoln University New Zealand - Research Archive
Thesis Flux balance analysis to model microbial metabolism for electricity generation
Mao, Longfei · 2013 · Lincoln University New Zealand - Research Archive · DOI
Full title: Flux balance analysis to model microbial metabolism for electricity generation
Authors: Mao, Longfei
Year: 2013
Venue: Lincoln University New Zealand - Research Archive
Thesis Prediction of gene essentiality using machine learning and genome-scale metabolic models
Freischem, Lilli J; Barahona, Mauricio; Oyarzún, Diego A · 2023 · Imperial College London · DOI
Full title: Prediction of gene essentiality using machine learning and genome-scale metabolic models
Authors: Freischem, Lilli J; Barahona, Mauricio; Oyarzún, Diego A
Year: 2023
Venue: Imperial College London
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
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
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)
Thesis Genome-scale modeling of redox metabolism and therapeutic response in radiation-resistant tumors
Lewis, Joshua Elliott · 2021 · Georgia Institute of Technology · DOI
Full title: Genome-scale modeling of redox metabolism and therapeutic response in radiation-resistant tumors
Authors: Lewis, Joshua Elliott
Year: 2021
Venue: Georgia Institute of Technology
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
Thesis Methods for the refinement of genome-scale metabolic networks
Liberal Fernandes, Rodrigo · 2014 · Imperial College London · DOI
Full title: Methods for the refinement of genome-scale metabolic networks
Authors: Liberal Fernandes, Rodrigo
Year: 2014
Venue: Imperial College London
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
Thesis Genome scale metabolic network modelling for metabolic profile predictions
Cooke, Juliette; Delmas, Maxime; Wieder, Cecilia et al. · 2024 · Imperial College London · DOI
Full title: Genome scale metabolic network modelling for metabolic profile predictions
Authors: Cooke, Juliette; Delmas, Maxime; Wieder, Cecilia; Rodríguez Mier, Pablo; Frainay, Clément; Vinson, Florence; Ebbels, Timothy; Poupin, Nathalie; Jourdan, Fabien
Year: 2024
Venue: Imperial College London
Thesis Interrogation of global mutagenesis data with a genome scale model of Neisseria meningitidis to assess gene fitness in vitro and in sera.
Mendum, TA; Newcombe, J; Mannan, AA et al. · 2015 · Imperial College London · 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, TA; Newcombe, J; Mannan, AA; Kierzek, AM; McFadden, J
Year: 2015
Venue: Imperial College London
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
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
Thesis Quantifying Diet-Induced Metabolic Changes of the Human Gut Microbiome
Shoaie, S; Ghaffari, P; Kovatcheva-Datchary, P et al. · 2015 · Imperial College London · DOI
Full title: Quantifying Diet-Induced Metabolic Changes of the Human Gut Microbiome
Authors: Shoaie, S; Ghaffari, P; Kovatcheva-Datchary, P; Mardinoglu, A; Sen, P; Pujos-Guillot, E; de Wouters, T; Juste, C; Rizkalla, S; Chilloux, J; Hoyles, L; Nicholson, JK; MICRO-Obes consortium; Dore, J; Dumas, ME; Clement, K; Bäckhed, F; Nielsen, J
Year: 2015
Venue: Imperial College London
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
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
Thesis Integrating Kinetic Model of E. coli with Genome Scale Metabolic Fluxes Overcomes Its Open System Problem and Reveals Bistability in Central Metabolism
Mannan, AA; Toya, Y; Shimizu, K et al. · 2015 · Imperial College London · 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, AA; Toya, Y; Shimizu, K; McFadden, J; Kierzek, AM; Rocco, A
Year: 2015
Venue: Imperial College London
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
Thesis MUFINS: multi-formalism interaction network simulator.
Wu, H; von Kamp, A; Leoncikas, V et al. · 2017 · Imperial College London · DOI
Full title: MUFINS: multi-formalism interaction network simulator.
Authors: Wu, H; von Kamp, A; Leoncikas, V; Mori, W; Sahin, N; Gevorgyan, A; Linley, C; Grabowski, M; Mannan, AA; Stoy, N; Stewart, GR; Ward, LT; Lewis, DJM; Sroka, J; Matsuno, H; Klamt, S; Westerhoff, HV; McFadden, J; Plant, NJ; Kierzek, AM
Year: 2017
Venue: Imperial College London
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
Thesis dynamic Flux Balance Analysis of the Metabolism of Microalgae under a Diurnal Light Cycle
Baroukh, C; Steyer, JP; Bernard, O et al. · 2016 · Imperial College London · DOI
Full title: dynamic Flux Balance Analysis of the Metabolism of Microalgae under a Diurnal Light Cycle
Authors: Baroukh, C; Steyer, JP; Bernard, O; Chachuat, B
Year: 2016
Venue: Imperial College London
Thesis Modelling and engineering anabaena sp. PCC 7120 for nitrogen excretion
Malatinszky, David · 2020 · Imperial College London · DOI
Full title: Modelling and engineering anabaena sp. PCC 7120 for nitrogen excretion
Authors: Malatinszky, David
Year: 2020
Venue: Imperial College London
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
Thesis Analysis of complex metabolic behavior through pathway decomposition
Ip, K; Colijn, C; Lun, DS · 2017 · Imperial College London · DOI
Full title: Analysis of complex metabolic behavior through pathway decomposition
Authors: Ip, K; Colijn, C; Lun, DS
Year: 2017
Venue: Imperial College London
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
Thesis Computational Analysis of Metabolic Pathway Balance Using Flux Balance Analysis and the iNS142 Stoichiometric Model of Escherichia coli
de Arroyo Garcia, Laura; de Arroyo Garcia, Laura · 2017 · Imperial College London · DOI
Full title: Computational Analysis of Metabolic Pathway Balance Using Flux Balance Analysis and the iNS142 Stoichiometric Model of Escherichia coli
Authors: de Arroyo Garcia, Laura; de Arroyo Garcia, Laura
Year: 2017
Venue: Imperial College London
Thesis Synergising stoichiometric modelling with artificial neural networks to predict antibody glycosylation patterns in Chinese hamster ovary cells
Antonakoudis, Athanasios; Strain, Benjamin; Barbosa, Rodrigo et al. · 2021 · Imperial College London · DOI
Full title: Synergising stoichiometric modelling with artificial neural networks to predict antibody glycosylation patterns in Chinese hamster ovary cells
Authors: Antonakoudis, Athanasios; Strain, Benjamin; Barbosa, Rodrigo; Jimenez del Val, Ioscani; Kontoravdi, Kleio
Year: 2021
Venue: Imperial College London
Thesis Mathematical modelling and experimental validation for optimisation and control of mammalian cell culture systems
Quiroga Campano, Ana · 2019 · Imperial College London · DOI
Full title: Mathematical modelling and experimental validation for optimisation and control of mammalian cell culture systems
Authors: Quiroga Campano, Ana
Year: 2019
Venue: Imperial College London
Thesis A duality-based method for identifying elemental balance violations in metabolic network models
Zabeti, Hooman; Tamon, Stephen; Berger, Bonnie et al. · 2021 · Imperial College London · DOI
Full title: A duality-based method for identifying elemental balance violations in metabolic network models
Authors: Zabeti, Hooman; Tamon, Stephen; Berger, Bonnie; Chindelevitch, Leonid
Year: 2021
Venue: Imperial College London
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
Thesis Metabolic Changes in Astrocytes Following Traumatic Brain Injury
Parker, Brian Christopher · 2025 · Virginia Tech - VTechWorks · DOI
Full title: Metabolic Changes in Astrocytes Following Traumatic Brain Injury
Authors: Parker, Brian Christopher
Year: 2025
Venue: Virginia Tech - VTechWorks
Thesis BRIDGING EXPERIMENTAL AND IN-SILICO METHODS FOR ADVANCED MAMMALIAN BIOMANUFACTURING OPTIMIZATION
Ndahiro, Nelson · 2025 · Johns Hopkins University · DOI
Full title: BRIDGING EXPERIMENTAL AND IN-SILICO METHODS FOR ADVANCED MAMMALIAN BIOMANUFACTURING OPTIMIZATION
Authors: Ndahiro, Nelson
Year: 2025
Venue: Johns Hopkins University
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
Thesis Systems analysis of Mycoplasma hyopneumoniae to improve vaccine production
Kamminga, Tjerko · 2017 · Wageningen University & Research · DOI
Full title: Systems analysis of Mycoplasma hyopneumoniae to improve vaccine production
Authors: Kamminga, Tjerko
Year: 2017
Venue: Wageningen University & Research
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
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)
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
Thesis Design Principles as a Guide for Constraint Based and Dynamic Modeling: Towards an Integrative Workflow
Sehr, Christiana; Kremling, Andreas; Marin-Sanguino, Alberto · 2015 · Technical University of Munich (TUM) · DOI
Full title: Design Principles as a Guide for Constraint Based and Dynamic Modeling: Towards an Integrative Workflow
Authors: Sehr, Christiana; Kremling, Andreas; Marin-Sanguino, Alberto
Year: 2015
Venue: Technical University of Munich (TUM)
Thesis Modeling metabolism of Mycobacterium tuberculosis
Rienksma, Rienk A. · 2019 · Wageningen University & Research · DOI
Full title: Modeling metabolism of Mycobacterium tuberculosis
Authors: Rienksma, Rienk A.
Year: 2019
Venue: Wageningen University & Research
Thesis Improvement of Constraint-Based Flux Estimation During L-Phenylalanine Production with Escherichia coli Using Targeted Knock-out Mutants
Michael Weiner, Julia Tröndle, Christoph Albermann, Georg A. Sprenger, Dirk Weuster-Botz · 2014 · Technical University of Munich (TUM) · DOI
Full title: Improvement of Constraint-Based Flux Estimation During L-Phenylalanine Production with Escherichia coli Using Targeted Knock-out Mutants
Authors: Michael Weiner, Julia Tröndle, Christoph Albermann, Georg A. Sprenger, Dirk Weuster-Botz
Year: 2014
Venue: Technical University of Munich (TUM)
Thesis Metabolic-flux analysis of mammalian-cell culture
Bonarius, H.P.J. · 1998 · Wageningen University & Research · DOI
Full title: Metabolic-flux analysis of mammalian-cell culture
Authors: Bonarius, H.P.J.
Year: 1998
Venue: Wageningen University & Research
Thesis Intelligent host engineering for metabolic flux optimisation in biotechnology
Munro, Lachlan J; Kell, Douglas B · 2021 · University of Liverpool · DOI
Full title: Intelligent host engineering for metabolic flux optimisation in biotechnology
Authors: Munro, Lachlan J; Kell, Douglas B
Year: 2021
Venue: University of Liverpool
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)
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
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
Thesis Computer-Guided Metabolic Engineering
M. A. Valderrama-Gomez; S. G. Wagner; A. Kremling · 2016 · Technical University of Munich (TUM) · DOI
Full title: Computer-Guided Metabolic Engineering
Authors: M. A. Valderrama-Gomez; S. G. Wagner; A. Kremling
Year: 2016
Venue: Technical University of Munich (TUM)
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
Thesis Osmoregulation in the Halophilic Bacterium Halomonas elongata: A Case Study for Integrative Systems Biology
V. Kindzierski, S. Raschke, N. Knabe, F. Siedler, B. Scheffer, K. Pflüger-Grau, .F Pfeiffer, D. Oesterhelt, A. Marin-Sanguino, H-J. Kunte · 2017 · Technical University of Munich (TUM) · DOI
Full title: Osmoregulation in the Halophilic Bacterium Halomonas elongata: A Case Study for Integrative Systems Biology
Authors: V. Kindzierski, S. Raschke, N. Knabe, F. Siedler, B. Scheffer, K. Pflüger-Grau, .F Pfeiffer, D. Oesterhelt, A. Marin-Sanguino, H-J. Kunte
Year: 2017
Venue: Technical University of Munich (TUM)
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
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
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
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
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
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
Thesis Metabolic flux analysis in Euglena gracilis
Inwongwan, S · 2020 · University of Oxford - ORA · DOI
Full title: Metabolic flux analysis in Euglena gracilis
Authors: Inwongwan, S
Year: 2020
Venue: University of Oxford - ORA
Thesis Proteome allocation based metabolic modelling of lactic acid bacteria under environmental stress
Qiu, S · 2024 · University of Oxford - ORA · DOI
Full title: Proteome allocation based metabolic modelling of lactic acid bacteria under environmental stress
Authors: Qiu, S
Year: 2024
Venue: University of Oxford - ORA
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
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
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
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
Thesis Integrated modelling of whole-plant metabolism and growth
Konuntakiet, T · 2020 · University of Oxford - ORA · DOI
Full title: Integrated modelling of whole-plant metabolism and growth
Authors: Konuntakiet, T
Year: 2020
Venue: University of Oxford - ORA
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
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
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)
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
Thesis Scalable computation of intracellular metabolite concentrations
Akbari, Amir; Palsson, Bernhard O.; id_orcid 0000-0003-2357-6785 · 2021 · Technical University of Denmark (DTU) · DOI
Full title: Scalable computation of intracellular metabolite concentrations
Authors: Akbari, Amir; Palsson, Bernhard O.; id_orcid 0000-0003-2357-6785
Year: 2021
Venue: Technical University of Denmark (DTU)
Thesis Metabolic and genetic basis for auxotrophies in Gram-negative species
Seif, Yara; Choudhary, Kumari Sonal; Hefner, Ying et al. · 2020 · Technical University of Denmark (DTU) · DOI
Full title: Metabolic and genetic basis for auxotrophies in Gram-negative species
Authors: Seif, Yara; Choudhary, Kumari Sonal; Hefner, Ying; Anand, Amitesh; Yang, Laurence; Palsson, Bernhard O.; id_orcid 0000-0003-2357-6785
Year: 2020
Venue: Technical University of Denmark (DTU)
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)
Thesis Characterizing posttranslational modifications in prokaryotic metabolism using a multiscale workflow
Brunk, Elizabeth; Chang, Roger L.; Xia, Jing et al. · 2018 · Technical University of Denmark (DTU) · DOI
Full title: Characterizing posttranslational modifications in prokaryotic metabolism using a multiscale workflow
Authors: Brunk, Elizabeth; Chang, Roger L.; Xia, Jing; Hefzi, Hooman; Yurkovich, James T.; Kim, Donghyuk; Buckmiller, Evan; Wang, Harris H.; Cho, Byung-Kwan; Yang, Chen; Palsson, Bernhard O.; id_orcid 0000-0003-2357-6785; Church, George M.; Lewis, Nathan E.
Year: 2018
Venue: Technical University of Denmark (DTU)
Thesis Metabolic modelling of tomato fruit ripening
Hawari, AH · 2014 · University of Oxford - ORA · DOI
Full title: Metabolic modelling of tomato fruit ripening
Authors: Hawari, AH
Year: 2014
Venue: University of Oxford - ORA
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)
Thesis Multigene metabolic engineering for the increase of photosynthetic efficiency
Moreno Garcia, B · 2020 · University of Oxford - ORA · DOI
Full title: Multigene metabolic engineering for the increase of photosynthetic efficiency
Authors: Moreno Garcia, B
Year: 2020
Venue: University of Oxford - ORA
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)
Thesis Metabolic interactions affect the biomass of synthetic bacterial biofilm communities
Sun, Xinli; Xie, Jiyu; Zheng, Daoyue et al. · 2023 · Technical University of Denmark (DTU) · DOI
Full title: Metabolic interactions affect the biomass of synthetic bacterial biofilm communities
Authors: Sun, Xinli; Xie, Jiyu; Zheng, Daoyue; Xia, Riyan; Wang, Wei; Xun, Weibing; Huang, Qiwei; Zhang, Ruifu; Kovács, Ákos T.; Xu, Zhihui; Shen, Qirong
Year: 2023
Venue: Technical University of Denmark (DTU)
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)
Thesis solveME: fast and reliable solution of nonlinear ME models
Yang, Laurence; Ma, Ding; Ebrahim, Ali et al. · 2016 · Technical University of Denmark (DTU) · DOI
Full title: solveME: fast and reliable solution of nonlinear ME models
Authors: Yang, Laurence; Ma, Ding; Ebrahim, Ali; Lloyd, Colton J.; Saunders, Michael A.; Palsson, Bernhard; id_orcid 0000-0003-2357-6785
Year: 2016
Venue: Technical University of Denmark (DTU)
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)
Thesis Domestication Of Pantoea Sp. Through Genome-Scale Metabolic Modelling And A Genetic Toolbox
van der Heijden, Lies; van der Maas, Lucas Nicolaas Ludovic; id_orcid 0000-0002-2468-7850 et al. · 2023 · Technical University of Denmark (DTU) · DOI
Full title: Domestication Of Pantoea Sp. Through Genome-Scale Metabolic Modelling And A Genetic Toolbox
Authors: van der Heijden, Lies; van der Maas, Lucas Nicolaas Ludovic; id_orcid 0000-0002-2468-7850; Gorter de Vries, Philip Johannes; id_orcid 0000-0002-0311-5634; Özdemir, Emre; id_orcid 0000-0001-5548-6720; Ingemann Jensen, Sheila; id_orcid 0000-0001-8277-5907
Year: 2023
Venue: Technical University of Denmark (DTU)
Thesis LooplessFluxSampler:an efficient toolbox for sampling the loopless flux solution space of metabolic models
Saa, Pedro A.; Zapararte, Sebastian; Drovandi, Christopher C. et al. · 2024 · Technical University of Denmark (DTU) · DOI
Full title: LooplessFluxSampler:an efficient toolbox for sampling the loopless flux solution space of metabolic models
Authors: Saa, Pedro A.; Zapararte, Sebastian; Drovandi, Christopher C.; Nielsen, Lars K.
Year: 2024
Venue: Technical University of Denmark (DTU)
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)
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)
Thesis Cameo: A Python Library for Computer Aided Metabolic Engineering and Optimization of Cell Factories
Cardoso, Joao G.R.; Jensen, Kristian; Lieven, Christian et al. · 2018 · Technical University of Denmark (DTU) · DOI
Full title: Cameo: A Python Library for Computer Aided Metabolic Engineering and Optimization of Cell Factories
Authors: Cardoso, Joao G.R.; Jensen, Kristian; Lieven, Christian; Hansen, Anne Sofie Lærke; id_orcid 0000-0003-2771-4671; Galkina, Svetlana; Beber, Moritz; id_orcid 0000-0003-2406-1978; Özdemir, Emre; id_orcid 0000-0001-5548-6720; Herrgård, Markus J.; Redestig, Henning; Sonnenschein, Nikolaus; id_orcid 0000-0002-7581-4936
Year: 2018
Venue: Technical University of Denmark (DTU)
Thesis Ustilago maydis Metabolic Characterization and Growth Quantification with a Genome-Scale Metabolic Model
Liebal, Ulf W.; Ullmann, Lena; Lieven, Christian et al. · 2022 · Technical University of Denmark (DTU) · DOI
Full title: Ustilago maydis Metabolic Characterization and Growth Quantification with a Genome-Scale Metabolic Model
Authors: Liebal, Ulf W.; Ullmann, Lena; Lieven, Christian; Kohl, Philipp; Wibberg, Daniel; Zambanini, Thiemo; Blank, Lars M.
Year: 2022
Venue: Technical University of Denmark (DTU)
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)
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)
Thesis Reconstruction of the metabolic network of Pseudomonas aeruginosa to interrogate virulence factor synthesis
Bartell, Jennifer; Blazier, Anna S; Yen, Phillip et al. · 2017 · Technical University of Denmark (DTU) · DOI
Full title: Reconstruction of the metabolic network of Pseudomonas aeruginosa to interrogate virulence factor synthesis
Authors: Bartell, Jennifer; Blazier, Anna S; Yen, Phillip; Thøgersen, Juliane Charlotte; Jelsbak, Lars; id_orcid 0000-0002-5759-9769; Goldberg, Joanna B; Papin, Jason A
Year: 2017
Venue: Technical University of Denmark (DTU)
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)
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)
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)
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)
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)
Thesis 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 · Technical University of Denmark (DTU) · 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 O.; id_orcid 0000-0003-2357-6785
Year: 2021
Venue: Technical University of Denmark (DTU)
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)
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)
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)
Thesis Formulation, construction and analysis of kinetic models of metabolism: A review of modelling frameworks
Saa, Pedro A.; Nielsen, Lars K. · 2017 · Technical University of Denmark (DTU) · DOI
Full title: Formulation, construction and analysis of kinetic models of metabolism: A review of modelling frameworks
Authors: Saa, Pedro A.; Nielsen, Lars K.
Year: 2017
Venue: Technical University of Denmark (DTU)
Thesis A systems analysis of NADH dehydrogenase mutants reveals flexibility and limits of Pseudomonas taiwanensis VLB120&#x27;s metabolism
Nies, Salome C; Dinger, Robert; Chen, Yan et al. · 2020 · Technical University of Denmark (DTU) · DOI
Full title: A systems analysis of NADH dehydrogenase mutants reveals flexibility and limits of Pseudomonas taiwanensis VLB120&#x27;s metabolism
Authors: Nies, Salome C; Dinger, Robert; Chen, Yan; Wordofa, Gossa Garedew; Kristensen, Mette; Schneider, Konstantin; Büchs, Jochen; Petzold, Christopher J.; Keasling, Jay D.; Blank, Lars M; Ebert, Birgitta E.
Year: 2020
Venue: Technical University of Denmark (DTU)
Thesis Intelligent host engineering for metabolic flux optimisation in biotechnology
Munro, Lachlan J; Kell, Douglas B · 2021 · Technical University of Denmark (DTU) · DOI
Full title: Intelligent host engineering for metabolic flux optimisation in biotechnology
Authors: Munro, Lachlan J; Kell, Douglas B
Year: 2021
Venue: Technical University of Denmark (DTU)
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)
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)
Thesis Revealing metabolic mechanisms of interaction in the anaerobic digestion microbiome by flux balance analysis
Basile, Arianna; Campanaro, Stefano; Kovalovszki, Adam et al. · 2020 · Technical University of Denmark (DTU) · DOI
Full title: Revealing metabolic mechanisms of interaction in the anaerobic digestion microbiome by flux balance analysis
Authors: Basile, Arianna; Campanaro, Stefano; Kovalovszki, Adam; id_orcid 0000-0001-7509-4580; Zampieri, Guido; Rossi, Alessandro; Angelidaki, Irini; id_orcid 0000-0002-6357-578X; Valle, Giorgio; Treu, Laura
Year: 2020
Venue: Technical University of Denmark (DTU)
Thesis Do genome-scale models need exact solvers or clearer standards?
Ebrahim, A.; Almaas, E.; Bauer, E. et al. · 2015 · Technical University of Denmark (DTU) · DOI
Full title: Do genome-scale models need exact solvers or clearer standards?
Authors: Ebrahim, A.; Almaas, E.; Bauer, E.; Bordbar, A.; Burgard, A. P.; Chang, R. L.; Drager, A.; Famili, I.; Feist, A. M.; Fleming, R. M.; Fong, S. S.; Hatzimanikatis, V.; Herrgard, M. J.; Holder, A.; Hucka, M.; Hyduke, D.; Jamshidi, N.; Lee, Sang Yup; Le Novere, N.; Lerman, J. A.; Lewis, Nathan; Ma, D.; Mahadevan, R.; Maranas, C.; Nagarajan, H.; Navid, A.; Nielsen, Jens; Nielsen, L. K.; Nogales, J.; Noronha, A.; Pal, C.; Palsson, Bernhard; id_orcid 0000-0003-2357-6785; Papin, J. A.; Patil, Kiran R.; Price, N. D.; Reed, J. L.; Saunders, M.; Senger, R. S.; Sonnenschein, Nikolaus; id_orcid 0000-0002-7581-4936; Sun, Yuekai; Thiele, I.
Year: 2015
Venue: Technical University of Denmark (DTU)
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)
Thesis Combined Rapid Injection NMR and Simulation Approach to Probe Redox-Dependent Pathway Control in Living Cells
Jensen, Pernille Rose; id_orcid 0000-0003-4359-848X; Matos, Marta et al. · 2019 · Technical University of Denmark (DTU) · DOI
Full title: Combined Rapid Injection NMR and Simulation Approach to Probe Redox-Dependent Pathway Control in Living Cells
Authors: Jensen, Pernille Rose; id_orcid 0000-0003-4359-848X; Matos, Marta; Sonnenschein, Nikolaus; id_orcid 0000-0002-7581-4936; Meier, Sebastian; id_orcid 0000-0003-3761-3217
Year: 2019
Venue: Technical University of Denmark (DTU)
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)
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)
Thesis Engineering Bacterial Genomes throughout the Central Dogma of Molecular Biology
Bayer, Carolyn Nicole · 2022 · Technical University of Denmark (DTU) · DOI
Full title: Engineering Bacterial Genomes throughout the Central Dogma of Molecular Biology
Authors: Bayer, Carolyn Nicole
Year: 2022
Venue: Technical University of Denmark (DTU)
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)
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)
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)
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)
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)
Thesis Systematic engineering for production of anti-aging sunscreen compound in Pseudomonas putida
Yunus, Ian S.; Hudson, Graham A.; Chen, Yan et al. · 2024 · Technical University of Denmark (DTU) · DOI
Full title: Systematic engineering for production of anti-aging sunscreen compound in Pseudomonas putida
Authors: Yunus, Ian S.; Hudson, Graham A.; Chen, Yan; Gin, Jennifer W.; Kim, Joonhoon; Baidoo, Edward E.K.; Petzold, Christopher J.; Adams, Paul D.; Simmons, Blake A.; Mukhopadhyay, Aindrila; Keasling, Jay D.; Lee, Taek Soon
Year: 2024
Venue: Technical University of Denmark (DTU)
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)
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
Thesis Computational Analysis of the Metabolic Network of Microorganisms to Detect Potential Drug Targets
Plaimas, Kitiporn · 2011 · Heidelberg University · DOI
Full title: Computational Analysis of the Metabolic Network of Microorganisms to Detect Potential Drug Targets
Authors: Plaimas, Kitiporn
Year: 2011
Venue: Heidelberg University
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
Thesis Enhanced triacylglycerol production in chlorella vulgaris by flux balance analysis on metabolic network
Kaothong, Issalapap · 2022 · Chulalongkorn University · DOI
Full title: Enhanced triacylglycerol production in chlorella vulgaris by flux balance analysis on metabolic network
Authors: Kaothong, Issalapap
Year: 2022
Venue: Chulalongkorn University
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
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
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
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)
Thesis Functional and Computational Genomics Reveal Unprecedented Flexibility in Stage-Specific Toxoplasma Metabolism
Krishnan, Aarti; Kloehn, Joachim; Lunghi, Matteo et al. · 2021 · Massachusetts Institute of Technology (MIT) · 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; Lourido, Sebastian; Hatzimanikatis, Vassily; Soldati-Favre, Dominique
Year: 2021
Venue: Massachusetts Institute of Technology (MIT)
Thesis Methodologies and analysis of metabolic flux in mammalian systems
Liu, Shiyu · 2022 · Duke University · DOI
Full title: Methodologies and analysis of metabolic flux in mammalian systems
Authors: Liu, Shiyu
Year: 2022
Venue: Duke University
Thesis An exact arithmetic toolbox for a consistent and reproducible structural analysis of metabolic network models
Chindelevitch, Leonid; Trigg, Jason; Regev, Aviv et al. · 2014 · Massachusetts Institute of Technology (MIT) · DOI
Full title: An exact arithmetic toolbox for a consistent and reproducible structural analysis of metabolic network models
Authors: Chindelevitch, Leonid; Trigg, Jason; Regev, Aviv; Berger Leighton, Bonnie
Year: 2014
Venue: Massachusetts Institute of Technology (MIT)
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)
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)
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)
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)
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)
Thesis Generative machine learning produces kinetic models that accurately characterize intracellular metabolic states
Choudhury, Subham; Narayanan, Bharath; Moret, Michael et al. · 2024 · 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: 2024
Venue: École polytechnique fédérale de Lausanne (EPFL)
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)
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)
Thesis Metabolic network reconstruction as a resource for analyzing Salmonella Typhimurium SL1344 growth in the mouse intestine
Vayena, Evangelia; Fuchs, Lea; Peyhani, Homa Mohammadi et al. · 2025 · École polytechnique fédérale de Lausanne (EPFL) · DOI
Full title: Metabolic network reconstruction as a resource for analyzing Salmonella Typhimurium SL1344 growth in the mouse intestine
Authors: Vayena, Evangelia; Fuchs, Lea; Peyhani, Homa Mohammadi; Lagoda, Konrad; Nguyen, Bidong; Hardt, Wolf-Dietrich; Hatzimanikatis, Vassily
Year: 2025
Venue: École polytechnique fédérale de Lausanne (EPFL)
Thesis Combinatorial pathway optimization for streamlined metabolic engineering
Jeschek, Markus; Gerngross, Daniel; Panke, Sven · 2025 · École polytechnique fédérale de Lausanne (EPFL) · DOI
Full title: Combinatorial pathway optimization for streamlined metabolic engineering
Authors: Jeschek, Markus; Gerngross, Daniel; Panke, Sven
Year: 2025
Venue: École polytechnique fédérale de Lausanne (EPFL)
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)
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)
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)
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)
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)
Thesis Studying cancer cells phenotypes integrating omics data in human reduced genome-scale metabolic models.
Masid Barcon, Maria; Pandey, Vikash Kumar; Hatzimanikatis, Vassily · 2018 · École polytechnique fédérale de Lausanne (EPFL) · DOI
Full title: Studying cancer cells phenotypes integrating omics data in human reduced genome-scale metabolic models.
Authors: Masid Barcon, Maria; Pandey, Vikash Kumar; Hatzimanikatis, Vassily
Year: 2018
Venue: École polytechnique fédérale de Lausanne (EPFL)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
Thesis Dissecting the genetic and metabolic mechanisms of adaptation to the knockout of a major metabolic enzyme in Escherichia coli
Long, Christopher P.; Gonzalez, Jacqueline E.; Feist, Adam M. et al. · 2018 · Technical University of Denmark (DTU) · DOI
Full title: Dissecting the genetic and metabolic mechanisms of adaptation to the knockout of a major metabolic enzyme in Escherichia coli
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: 2018
Venue: Technical University of Denmark (DTU)
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)
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)
Thesis Adaptive Evolution of Phosphorus Metabolism in Prochlorococcus
Casey, John R; Mardinoglu, Adil; Nielsen, Jens et al. · 2016 · Technical University of Denmark (DTU) · DOI
Full title: Adaptive Evolution of Phosphorus Metabolism in Prochlorococcus
Authors: Casey, John R; Mardinoglu, Adil; Nielsen, Jens; Karl, David M.
Year: 2016
Venue: Technical University of Denmark (DTU)
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)
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)
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)
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)
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)
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)
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)
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)
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)
Thesis Reframing gene essentiality in terms of adaptive flexibility
Guzmán, Gabriela I.; Olson, Connor A.; Hefner, Ying et al. · 2018 · Technical University of Denmark (DTU) · DOI
Full title: Reframing gene essentiality in terms of adaptive flexibility
Authors: Guzmán, Gabriela I.; Olson, Connor A.; Hefner, Ying; Phaneuf, Patrick V.; Catoiu, Edward; Crepaldi, Lais B.; Micas, Lucas Goldschmidt; 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)
Thesis Modelling challenges to unlock the power of phototrophic systems for wastewater valorization
Casagli, Francesca; Turolla, Andrea; Batstone, Damien J. et al. · 2025 · Technical University of Denmark (DTU) · DOI
Full title: Modelling challenges to unlock the power of phototrophic systems for wastewater valorization
Authors: Casagli, Francesca; Turolla, Andrea; Batstone, Damien J.; Capson-Tojo, Gabriel; Ficara, Elena; García, Joan; González-Flo, Eva; Laurent, Julien; Lorenz, Tatjana; Pierrelée, Michaël; id_orcid 0009-0006-4521-0097; Plósz, Benedek Gy.; Da Silva, Gustavo Henrique Ribero; Robles, Ángel; Rossi, Simone; Rueda, Estel; Stegemüller, Lars; id_orcid 0000-0001-8978-8882; Steyer, Jean-Philippe; Bernard, Olivier; Valverde-Pérez, Borja; id_orcid 0000-0001-7255-1395
Year: 2025
Venue: Technical University of Denmark (DTU)
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)
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)
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)
Thesis Improved vanillin production in baker&#x27;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&#x27;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)
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)
Thesis MEMOTE for standardized genome-scale metabolic model testing
Lieven, Christian; Beber, Moritz Emanuel; id_orcid 0000-0003-2406-1978 et al. · 2020 · Technical University of Denmark (DTU) · DOI
Full title: MEMOTE for standardized genome-scale metabolic model testing
Authors: Lieven, Christian; Beber, Moritz Emanuel; id_orcid 0000-0003-2406-1978; Olivier, Brett G.; Bergmann, Frank T.; Ataman, Meric; Babaei, Parizad; Bartell, Jennifer A.; Blank, Lars M.; Chauhan, Siddharth; Correia, Kevin; Diener, Christian; Dräger, Andreas; Ebert, Birgitta E.; Edirisinghe, Janaka N.; Faria, José P.; Feist, Adam M.; id_orcid 0000-0002-8630-4800; Fengos, Georgios; Fleming, Ronan M. T.; García-Jiménez, Beatriz; Hatzimanikatis, Vassily; van Helvoirt, Wout; Henry, Christopher S.; Hermjakob, Henning; Herrgard, Markus J.; Kaafarani, Ali; Kim, Hyun Uk; King, Zachary; Klamt, Steffen; Klipp, Edda; Koehorst, Jasper J.; König, Matthias; Lakshmanan, Meiyappan; Lee, Dong-Yup; Lee, Sang Yup; Lee, Sunjae; Lewis, Nathan E.; Liu, Filipe; Ma, Hongwu; Machado, Daniel; Mahadevan, Radhakrishnan; Maia, Paulo; Mardinoglu, Adil; Medlock, Gregory L.; Monk, Jonathan M.; Nielsen, Jens; Nielsen, Lars Keld; Nogales, Juan; Nookaew, Intawat; Palsson, Bernhard O.; id_orcid 0000-0003-2357-6785; Papin, Jason A.; Patil, Kiran Raosaheb; Poolman, Mark; Price, Nathan D.; Resendis-Antonio, Osbaldo; Richelle, Anne; Rocha, Isabel; Sánchez, Benjamín José; Schaap, Peter J.; Malik Sheriff, Rahuman S.; Shoaie, Saeed; Sonnenschein, Nikolaus; id_orcid 0000-0002-7581-4936; Teusink, Bas; Vilaca, Paulo; Vik, Jon Olav; Wodke, Judith A. H.; Xavier, Joana C.; Yuan, Qianqian; Zakhartsev, Maksim; Zhang, Cheng
Year: 2020
Venue: Technical University of Denmark (DTU)
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)
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)
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)
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)
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)
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)
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)
Thesis Predicting growth of the healthy infant using a genome scale metabolic model
Nilsson, Avlant; Mardinoglu, Adil; Nielsen, Jens · 2017 · Technical University of Denmark (DTU) · DOI
Full title: Predicting growth of the healthy infant using a genome scale metabolic model
Authors: Nilsson, Avlant; Mardinoglu, Adil; Nielsen, Jens
Year: 2017
Venue: Technical University of Denmark (DTU)
Thesis Prediction, Precision, and Safety In Advanced Microbial Therapeutics
van 't Hof, Max · 2022 · Technical University of Denmark (DTU) · DOI
Full title: Prediction, Precision, and Safety In Advanced Microbial Therapeutics
Authors: van 't Hof, Max
Year: 2022
Venue: Technical University of Denmark (DTU)
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)
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)
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)
Thesis GRASP:A computational platform for building kinetic models of cellular metabolism
Matos, Marta R.A.; Saa, Pedro A.; Cowie, Nicholas et al. · 2022 · Technical University of Denmark (DTU) · DOI
Full title: GRASP:A computational platform for building kinetic models of cellular metabolism
Authors: Matos, Marta R.A.; Saa, Pedro A.; Cowie, Nicholas; Volkova, Svetlana; De Leeuw, Marina; Nielsen, Lars K.
Year: 2022
Venue: Technical University of Denmark (DTU)
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)
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)
Thesis Understanding flux switching in metabolic networks through an analysis of synthetic lethals
Narasimha, Sowmya Manojna; Malpani, Tanisha; Mohite, Omkar S. et al. · 2024 · Technical University of Denmark (DTU) · DOI
Full title: Understanding flux switching in metabolic networks through an analysis of synthetic lethals
Authors: Narasimha, Sowmya Manojna; Malpani, Tanisha; Mohite, Omkar S.; id_orcid 0000-0002-3240-1656; Nath, J. Saketha; Raman, Karthik
Year: 2024
Venue: Technical University of Denmark (DTU)
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)
Thesis Harnessing the metabolic potential of thermophilic bacteria:Systems metabolic engineering tools for the production of volatile biochemicals
Mol, Viviënne · 2022 · Technical University of Denmark (DTU) · DOI
Full title: Harnessing the metabolic potential of thermophilic bacteria:Systems metabolic engineering tools for the production of volatile biochemicals
Authors: Mol, Viviënne
Year: 2022
Venue: Technical University of Denmark (DTU)
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)
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)
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)
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)
Thesis multiTFA:A python package for multi-variate thermodynamics-based flux analysis
Mahamkali, Vishnuvardhan; McCubbin, Tim; Beber, Moritz Emanuel et al. · 2021 · Technical University of Denmark (DTU) · DOI
Full title: multiTFA:A python package for multi-variate thermodynamics-based flux analysis
Authors: Mahamkali, Vishnuvardhan; McCubbin, Tim; Beber, Moritz Emanuel; id_orcid 0000-0003-2406-1978; Noor, Elad; Marcellin, Esteban; Nielsen, Lars Keld
Year: 2021
Venue: Technical University of Denmark (DTU)
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)
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)
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)
Thesis Identifying anti-growth factors for human cancer cell lines through genome-scale metabolic modeling
Ghaffari, Pouyan; Mardinoglu, Adil; Asplund, Anna et al. · 2015 · Technical University of Denmark (DTU) · DOI
Full title: Identifying anti-growth factors for human cancer cell lines through genome-scale metabolic modeling
Authors: Ghaffari, Pouyan; Mardinoglu, Adil; Asplund, Anna; Shoaie, Saeed; Kampf, Caroline; Uhlén, Mathias; Nielsen, Jens
Year: 2015
Venue: Technical University of Denmark (DTU)
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)
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)
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)
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)
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)
Thesis Putting computational modeling at the fingertips of bench biologists
Sonnenschein, Nikolaus; id_orcid 0000-0002-7581-4936; Herrgard, Markus · 2014 · Technical University of Denmark (DTU) · DOI
Full title: Putting computational modeling at the fingertips of bench biologists
Authors: Sonnenschein, Nikolaus; id_orcid 0000-0002-7581-4936; Herrgard, Markus
Year: 2014
Venue: Technical University of Denmark (DTU)
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)
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)
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)
Thesis Community standards to facilitate development and address challenges in metabolic modeling
Carey, Maureen A.; Dräger, Andreas; Beber, Moritz E. et al. · 2020 · Technical University of Denmark (DTU) · DOI
Full title: Community standards to facilitate development and address challenges in metabolic modeling
Authors: Carey, Maureen A.; Dräger, Andreas; Beber, Moritz E.; id_orcid 0000-0003-2406-1978; Papin, Jason A.; Yurkovich, James T.
Year: 2020
Venue: Technical University of Denmark (DTU)
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)
Thesis Updated and standardized genome-scale reconstruction of Mycobacterium tuberculosis H37Rv, iEK1011, simulates flux states indicative of physiological conditions
Kavvas, Erol S.; Seif, Yara; Yurkovich, James T. et al. · 2018 · Technical University of Denmark (DTU) · DOI
Full title: Updated and standardized genome-scale reconstruction of Mycobacterium tuberculosis H37Rv, iEK1011, simulates flux states indicative of physiological conditions
Authors: Kavvas, Erol S.; Seif, Yara; Yurkovich, James T.; Norsigian, Charles; Poudel, Saugat; Greenwald, William W.; Ghatak, Sankha; Palsson, Bernhard O.; id_orcid 0000-0003-2357-6785; Monk, Jonathan M.
Year: 2018
Venue: Technical University of Denmark (DTU)
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)
Thesis Modeling genome-wide enzyme evolution predicts strong epistasis underlying catalytic turnover rates
Heckmann, David; Zielinski, Daniel C.; Palsson, Bernhard O. et al. · 2018 · Technical University of Denmark (DTU) · DOI
Full title: Modeling genome-wide enzyme evolution predicts strong epistasis underlying catalytic turnover rates
Authors: Heckmann, David; Zielinski, Daniel C.; Palsson, Bernhard O.; id_orcid 0000-0003-2357-6785
Year: 2018
Venue: Technical University of Denmark (DTU)
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)
Thesis Application of a Mechanistic Model as a Tool for On-line Monitoring of Pilot Scale Filamentous Fungal Fermentation Processes - The Importance of Evaporation Effects:Mechanistic model for pilot scale monitoring
Mears, Lisa; Stocks, Stuart M.; Albæk, Mads Orla et al. · 2017 · Technical University of Denmark (DTU) · DOI
Full title: Application of a Mechanistic Model as a Tool for On-line Monitoring of Pilot Scale Filamentous Fungal Fermentation Processes - The Importance of Evaporation Effects:Mechanistic model for pilot scale monitoring
Authors: Mears, Lisa; Stocks, Stuart M.; Albæk, Mads Orla; Sin, Gürkan; id_orcid 0000-0003-0513-4502; Gernaey, Krist V.; id_orcid 0000-0002-0364-1773
Year: 2017
Venue: Technical University of Denmark (DTU)
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)
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)
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)
Thesis Integrated metabolic modeling, culturing, and transcriptomics explain enhanced virulence of Vibrio cholerae during coinfection with enterotoxigenic Escherichia coli
Abdel-Haleem, Alyaa M.; Ravikumar, Vaishnavi; Ji, Boyang et al. · 2020 · Technical University of Denmark (DTU) · DOI
Full title: Integrated metabolic modeling, culturing, and transcriptomics explain enhanced virulence of Vibrio cholerae during coinfection with enterotoxigenic Escherichia coli
Authors: Abdel-Haleem, Alyaa M.; Ravikumar, Vaishnavi; Ji, Boyang; Mineta, Katsuhiko; Gao, Xin; Nielsen, Jens; Gojobori, Takashi; Mijakovic, Ivan
Year: 2020
Venue: Technical University of Denmark (DTU)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
Thesis Genome-scale metabolic models highlight stage-specific differences in essential metabolic pathways in Trypanosoma cruzi
Shiratsubaki, Isabel S.; Fang, Xin; Souza, Rodolpho O.O. et al. · 2020 · Technical University of Denmark (DTU) · DOI
Full title: Genome-scale metabolic models highlight stage-specific differences in essential metabolic pathways in Trypanosoma cruzi
Authors: Shiratsubaki, Isabel S.; Fang, Xin; Souza, Rodolpho O.O.; Palsson, Bernhard O.; id_orcid 0000-0003-2357-6785; Silber, Ariel M.; Siqueira-Neto, Jair L.
Year: 2020
Venue: Technical University of Denmark (DTU)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
Thesis Metabolic interactions affect the biomass of synthetic bacterial biofilm communities
Sun, Xinli; Xie, Jiyu; Zheng, Daoyue et al. · 2023 · Technical University of Denmark (DTU) · DOI
Full title: Metabolic interactions affect the biomass of synthetic bacterial biofilm communities
Authors: Sun, Xinli; Xie, Jiyu; Zheng, Daoyue; Xia, Riyan; Wang, Wei; Xun, Weibing; Huang, Qiwei; Zhang, Ruifu; Kovács, Ákos T.; Xu, Zhihui; Shen, Qirong
Year: 2023
Venue: Technical University of Denmark (DTU)
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)
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)
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)
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)
Thesis solveME: fast and reliable solution of nonlinear ME models
Yang, Laurence; Ma, Ding; Ebrahim, Ali et al. · 2016 · Technical University of Denmark (DTU) · DOI
Full title: solveME: fast and reliable solution of nonlinear ME models
Authors: Yang, Laurence; Ma, Ding; Ebrahim, Ali; Lloyd, Colton J.; Saunders, Michael A.; Palsson, Bernhard; id_orcid 0000-0003-2357-6785
Year: 2016
Venue: Technical University of Denmark (DTU)
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)
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)
Thesis LooplessFluxSampler:an efficient toolbox for sampling the loopless flux solution space of metabolic models
Saa, Pedro A.; Zapararte, Sebastian; Drovandi, Christopher C. et al. · 2024 · Technical University of Denmark (DTU) · DOI
Full title: LooplessFluxSampler:an efficient toolbox for sampling the loopless flux solution space of metabolic models
Authors: Saa, Pedro A.; Zapararte, Sebastian; Drovandi, Christopher C.; Nielsen, Lars K.
Year: 2024
Venue: Technical University of Denmark (DTU)
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)
Thesis Multiomic Data Integration and Analysis via Model-Driven Approaches
Marín de Mas, Igor Batolomé · 2018 · Technical University of Denmark (DTU) · DOI
Full title: Multiomic Data Integration and Analysis via Model-Driven Approaches
Authors: Marín de Mas, Igor Batolomé
Year: 2018
Venue: Technical University of Denmark (DTU)
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)
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)
Thesis Scalable computation of intracellular metabolite concentrations
Akbari, Amir; Palsson, Bernhard O.; id_orcid 0000-0003-2357-6785 · 2021 · Technical University of Denmark (DTU) · DOI
Full title: Scalable computation of intracellular metabolite concentrations
Authors: Akbari, Amir; Palsson, Bernhard O.; id_orcid 0000-0003-2357-6785
Year: 2021
Venue: Technical University of Denmark (DTU)
Thesis Characterizing posttranslational modifications in prokaryotic metabolism using a multiscale workflow
Brunk, Elizabeth; Chang, Roger L.; Xia, Jing et al. · 2018 · Technical University of Denmark (DTU) · DOI
Full title: Characterizing posttranslational modifications in prokaryotic metabolism using a multiscale workflow
Authors: Brunk, Elizabeth; Chang, Roger L.; Xia, Jing; Hefzi, Hooman; Yurkovich, James T.; Kim, Donghyuk; Buckmiller, Evan; Wang, Harris H.; Cho, Byung-Kwan; Yang, Chen; Palsson, Bernhard O.; id_orcid 0000-0003-2357-6785; Church, George M.; Lewis, Nathan E.
Year: 2018
Venue: Technical University of Denmark (DTU)
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)
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)
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)
Thesis Domestication Of Pantoea Sp. Through Genome-Scale Metabolic Modelling And A Genetic Toolbox
van der Heijden, Lies; van der Maas, Lucas Nicolaas Ludovic; id_orcid 0000-0002-2468-7850 et al. · 2023 · Technical University of Denmark (DTU) · DOI
Full title: Domestication Of Pantoea Sp. Through Genome-Scale Metabolic Modelling And A Genetic Toolbox
Authors: van der Heijden, Lies; van der Maas, Lucas Nicolaas Ludovic; id_orcid 0000-0002-2468-7850; Gorter de Vries, Philip Johannes; id_orcid 0000-0002-0311-5634; Özdemir, Emre; id_orcid 0000-0001-5548-6720; Ingemann Jensen, Sheila; id_orcid 0000-0001-8277-5907
Year: 2023
Venue: Technical University of Denmark (DTU)
Thesis Metabolic and genetic basis for auxotrophies in Gram-negative species
Seif, Yara; Choudhary, Kumari Sonal; Hefner, Ying et al. · 2020 · Technical University of Denmark (DTU) · DOI
Full title: Metabolic and genetic basis for auxotrophies in Gram-negative species
Authors: Seif, Yara; Choudhary, Kumari Sonal; Hefner, Ying; Anand, Amitesh; Yang, Laurence; Palsson, Bernhard O.; id_orcid 0000-0003-2357-6785
Year: 2020
Venue: Technical University of Denmark (DTU)
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)
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)
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)
Thesis New paradigms for metabolic modeling of human cells
Mardinoglu, Adil; Nielsen, Jens · 2015 · Technical University of Denmark (DTU) · DOI
Full title: New paradigms for metabolic modeling of human cells
Authors: Mardinoglu, Adil; Nielsen, Jens
Year: 2015
Venue: Technical University of Denmark (DTU)
Thesis Cameo: A Python Library for Computer Aided Metabolic Engineering and Optimization of Cell Factories
Cardoso, Joao G.R.; Jensen, Kristian; Lieven, Christian et al. · 2018 · Technical University of Denmark (DTU) · DOI
Full title: Cameo: A Python Library for Computer Aided Metabolic Engineering and Optimization of Cell Factories
Authors: Cardoso, Joao G.R.; Jensen, Kristian; Lieven, Christian; Hansen, Anne Sofie Lærke; id_orcid 0000-0003-2771-4671; Galkina, Svetlana; Beber, Moritz; id_orcid 0000-0003-2406-1978; Özdemir, Emre; id_orcid 0000-0001-5548-6720; Herrgård, Markus J.; Redestig, Henning; Sonnenschein, Nikolaus; id_orcid 0000-0002-7581-4936
Year: 2018
Venue: Technical University of Denmark (DTU)
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)
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)
Thesis Ustilago maydis Metabolic Characterization and Growth Quantification with a Genome-Scale Metabolic Model
Liebal, Ulf W.; Ullmann, Lena; Lieven, Christian et al. · 2022 · Technical University of Denmark (DTU) · DOI
Full title: Ustilago maydis Metabolic Characterization and Growth Quantification with a Genome-Scale Metabolic Model
Authors: Liebal, Ulf W.; Ullmann, Lena; Lieven, Christian; Kohl, Philipp; Wibberg, Daniel; Zambanini, Thiemo; Blank, Lars M.
Year: 2022
Venue: Technical University of Denmark (DTU)
Thesis Reconstruction of the metabolic network of Pseudomonas aeruginosa to interrogate virulence factor synthesis
Bartell, Jennifer; Blazier, Anna S; Yen, Phillip et al. · 2017 · Technical University of Denmark (DTU) · DOI
Full title: Reconstruction of the metabolic network of Pseudomonas aeruginosa to interrogate virulence factor synthesis
Authors: Bartell, Jennifer; Blazier, Anna S; Yen, Phillip; Thøgersen, Juliane Charlotte; Jelsbak, Lars; id_orcid 0000-0002-5759-9769; Goldberg, Joanna B; Papin, Jason A
Year: 2017
Venue: Technical University of Denmark (DTU)
Thesis Revealing metabolic mechanisms of interaction in the anaerobic digestion microbiome by flux balance analysis
Basile, Arianna; Campanaro, Stefano; Kovalovszki, Adam et al. · 2020 · Technical University of Denmark (DTU) · DOI
Full title: Revealing metabolic mechanisms of interaction in the anaerobic digestion microbiome by flux balance analysis
Authors: Basile, Arianna; Campanaro, Stefano; Kovalovszki, Adam; id_orcid 0000-0001-7509-4580; Zampieri, Guido; Rossi, Alessandro; Angelidaki, Irini; id_orcid 0000-0002-6357-578X; Valle, Giorgio; Treu, Laura
Year: 2020
Venue: Technical University of Denmark (DTU)
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)
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)
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)
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)
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)
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)
Thesis Genome scale metabolic modeling of cancer
Nilsson, Avlant; Nielsen, Jens · 2017 · Technical University of Denmark (DTU) · DOI
Full title: Genome scale metabolic modeling of cancer
Authors: Nilsson, Avlant; Nielsen, Jens
Year: 2017
Venue: Technical University of Denmark (DTU)
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)
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)
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)
Thesis Genome-Scale Models
Bergdahl, Basti; Sonnenschein, Nikolaus; id_orcid 0000-0002-7581-4936 et al. · 2016 · Technical University of Denmark (DTU) · DOI
Full title: Genome-Scale Models
Authors: Bergdahl, Basti; Sonnenschein, Nikolaus; id_orcid 0000-0002-7581-4936; Machado, Daniel; Herrgard, Markus; Förster, Jochen; id_orcid 0000-0003-4045-7905
Year: 2016
Venue: Technical University of Denmark (DTU)
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)
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)
Thesis Formulation, construction and analysis of kinetic models of metabolism: A review of modelling frameworks
Saa, Pedro A.; Nielsen, Lars K. · 2017 · Technical University of Denmark (DTU) · DOI
Full title: Formulation, construction and analysis of kinetic models of metabolism: A review of modelling frameworks
Authors: Saa, Pedro A.; Nielsen, Lars K.
Year: 2017
Venue: Technical University of Denmark (DTU)
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)
Thesis 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 · Technical University of Denmark (DTU) · 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 O.; id_orcid 0000-0003-2357-6785
Year: 2021
Venue: Technical University of Denmark (DTU)
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)
Thesis Essential pathway identification: from in silico analysis to potential antifungal targets in Aspergillus fumigatus
Thykær, Jette; Andersen, Mikael Rørdam; id_orcid 0000-0003-4794-6808 et al. · 2009 · Technical University of Denmark (DTU) · DOI
Full title: Essential pathway identification: from in silico analysis to potential antifungal targets in Aspergillus fumigatus
Authors: Thykær, Jette; Andersen, Mikael Rørdam; id_orcid 0000-0003-4794-6808; Baker, S. E.
Year: 2009
Venue: Technical University of Denmark (DTU)
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)
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)
Thesis A systems analysis of NADH dehydrogenase mutants reveals flexibility and limits of Pseudomonas taiwanensis VLB120&#x27;s metabolism
Nies, Salome C; Dinger, Robert; Chen, Yan et al. · 2020 · Technical University of Denmark (DTU) · DOI
Full title: A systems analysis of NADH dehydrogenase mutants reveals flexibility and limits of Pseudomonas taiwanensis VLB120&#x27;s metabolism
Authors: Nies, Salome C; Dinger, Robert; Chen, Yan; Wordofa, Gossa Garedew; Kristensen, Mette; Schneider, Konstantin; Büchs, Jochen; Petzold, Christopher J.; Keasling, Jay D.; Blank, Lars M; Ebert, Birgitta E.
Year: 2020
Venue: Technical University of Denmark (DTU)
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)
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)
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)
Thesis Intelligent host engineering for metabolic flux optimisation in biotechnology
Munro, Lachlan J; Kell, Douglas B · 2021 · Technical University of Denmark (DTU) · DOI
Full title: Intelligent host engineering for metabolic flux optimisation in biotechnology
Authors: Munro, Lachlan J; Kell, Douglas B
Year: 2021
Venue: Technical University of Denmark (DTU)
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)
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)
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)
Thesis Systematic engineering for production of anti-aging sunscreen compound in Pseudomonas putida
Yunus, Ian S.; Hudson, Graham A.; Chen, Yan et al. · 2024 · Technical University of Denmark (DTU) · DOI
Full title: Systematic engineering for production of anti-aging sunscreen compound in Pseudomonas putida
Authors: Yunus, Ian S.; Hudson, Graham A.; Chen, Yan; Gin, Jennifer W.; Kim, Joonhoon; Baidoo, Edward E.K.; Petzold, Christopher J.; Adams, Paul D.; Simmons, Blake A.; Mukhopadhyay, Aindrila; Keasling, Jay D.; Lee, Taek Soon
Year: 2024
Venue: Technical University of Denmark (DTU)
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)
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)
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)
Thesis Do genome-scale models need exact solvers or clearer standards?
Ebrahim, A.; Almaas, E.; Bauer, E. et al. · 2015 · Technical University of Denmark (DTU) · DOI
Full title: Do genome-scale models need exact solvers or clearer standards?
Authors: Ebrahim, A.; Almaas, E.; Bauer, E.; Bordbar, A.; Burgard, A. P.; Chang, R. L.; Drager, A.; Famili, I.; Feist, A. M.; Fleming, R. M.; Fong, S. S.; Hatzimanikatis, V.; Herrgard, M. J.; Holder, A.; Hucka, M.; Hyduke, D.; Jamshidi, N.; Lee, Sang Yup; Le Novere, N.; Lerman, J. A.; Lewis, Nathan; Ma, D.; Mahadevan, R.; Maranas, C.; Nagarajan, H.; Navid, A.; Nielsen, Jens; Nielsen, L. K.; Nogales, J.; Noronha, A.; Pal, C.; Palsson, Bernhard; id_orcid 0000-0003-2357-6785; Papin, J. A.; Patil, Kiran R.; Price, N. D.; Reed, J. L.; Saunders, M.; Senger, R. S.; Sonnenschein, Nikolaus; id_orcid 0000-0002-7581-4936; Sun, Yuekai; Thiele, I.
Year: 2015
Venue: Technical University of Denmark (DTU)
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)
Thesis Modulating bacterial function utilizing A knowledge base of transcriptional regulatory modules
Shin, Jongoh; Zielinski, Daniel C.; Palsson, Bernhard O. et al. · 2024 · Technical University of Denmark (DTU) · DOI
Full title: Modulating bacterial function utilizing A knowledge base of transcriptional regulatory modules
Authors: Shin, Jongoh; Zielinski, Daniel C.; Palsson, Bernhard O.; id_orcid 0000-0003-2357-6785
Year: 2024
Venue: Technical University of Denmark (DTU)
Thesis Combined Rapid Injection NMR and Simulation Approach to Probe Redox-Dependent Pathway Control in Living Cells
Jensen, Pernille Rose; id_orcid 0000-0003-4359-848X; Matos, Marta et al. · 2019 · Technical University of Denmark (DTU) · DOI
Full title: Combined Rapid Injection NMR and Simulation Approach to Probe Redox-Dependent Pathway Control in Living Cells
Authors: Jensen, Pernille Rose; id_orcid 0000-0003-4359-848X; Matos, Marta; Sonnenschein, Nikolaus; id_orcid 0000-0002-7581-4936; Meier, Sebastian; id_orcid 0000-0003-3761-3217
Year: 2019
Venue: Technical University of Denmark (DTU)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
Thesis Dissecting the genetic and metabolic mechanisms of adaptation to the knockout of a major metabolic enzyme in Escherichia coli
Long, Christopher P.; Gonzalez, Jacqueline E.; Feist, Adam M. et al. · 2018 · Technical University of Denmark (DTU) · DOI
Full title: Dissecting the genetic and metabolic mechanisms of adaptation to the knockout of a major metabolic enzyme in Escherichia coli
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: 2018
Venue: Technical University of Denmark (DTU)
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)
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)
Thesis Adaptive Evolution of Phosphorus Metabolism in Prochlorococcus
Casey, John R; Mardinoglu, Adil; Nielsen, Jens et al. · 2016 · Technical University of Denmark (DTU) · DOI
Full title: Adaptive Evolution of Phosphorus Metabolism in Prochlorococcus
Authors: Casey, John R; Mardinoglu, Adil; Nielsen, Jens; Karl, David M.
Year: 2016
Venue: Technical University of Denmark (DTU)
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)
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)
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)
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)
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)
Thesis Modelling challenges to unlock the power of phototrophic systems for wastewater valorization
Casagli, Francesca; Turolla, Andrea; Batstone, Damien J. et al. · 2025 · Technical University of Denmark (DTU) · DOI
Full title: Modelling challenges to unlock the power of phototrophic systems for wastewater valorization
Authors: Casagli, Francesca; Turolla, Andrea; Batstone, Damien J.; Capson-Tojo, Gabriel; Ficara, Elena; García, Joan; González-Flo, Eva; Laurent, Julien; Lorenz, Tatjana; Pierrelée, Michaël; id_orcid 0009-0006-4521-0097; Plósz, Benedek Gy.; Da Silva, Gustavo Henrique Ribero; Robles, Ángel; Rossi, Simone; Rueda, Estel; Stegemüller, Lars; id_orcid 0000-0001-8978-8882; Steyer, Jean-Philippe; Bernard, Olivier; Valverde-Pérez, Borja; id_orcid 0000-0001-7255-1395
Year: 2025
Venue: Technical University of Denmark (DTU)
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)
Thesis Systematic reduction of genome-scale models for the study of metabolic phenotypes of human cells
Masid Barcon, Maria; Ataman, Meriç; Hatzimanikatis, Vassily · 2018 · École polytechnique fédérale de Lausanne (EPFL) · DOI
Full title: Systematic reduction of genome-scale models for the study of metabolic phenotypes of human cells
Authors: Masid Barcon, Maria; Ataman, Meriç; Hatzimanikatis, Vassily
Year: 2018
Venue: École polytechnique fédérale de Lausanne (EPFL)
Thesis Functional and Computational Genomics Reveal Unprecedented Flexibility in Stage-Specific Toxoplasma Metabolism
Krishnan, Aarti; Kloehn, Joachim; Lunghi, Matteo et al. · 2020 · École polytechnique fédérale de Lausanne (EPFL) · 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; Lourido, Sebastian; Hatzimanikatis, Vassily; Soldati-Favre, Dominique
Year: 2020
Venue: École polytechnique fédérale de Lausanne (EPFL)
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)
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)
Thesis Can we assess the model complexity for a bioprocess: theory and example of the anaerobic digestion process
Bernard, Olivier; Chachuat, Benoit; Helias, Arnaud et al. · 2007 · École polytechnique fédérale de Lausanne (EPFL) · DOI
Full title: Can we assess the model complexity for a bioprocess: theory and example of the anaerobic digestion process
Authors: Bernard, Olivier; Chachuat, Benoit; Helias, Arnaud; Rodriguez, Jorge
Year: 2007
Venue: École polytechnique fédérale de Lausanne (EPFL)
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)
Thesis Quantification of uncertainty in metabolic networks through the sampling of kinetic data space
Miskovic, Ljubisa; Hatzimanikatis, Vassily · 2009 · École polytechnique fédérale de Lausanne (EPFL) · DOI
Full title: Quantification of uncertainty in metabolic networks through the sampling of kinetic data space
Authors: Miskovic, Ljubisa; Hatzimanikatis, Vassily
Year: 2009
Venue: École polytechnique fédérale de Lausanne (EPFL)
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)
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)
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)
Thesis Influence of Uncertainties in pH, pMg, Activity Coefficients, Metabolite Concentrations, and Other Factors on the Analysis of the Thermodynamic Feasibility of Metabolic Pathways
Vojinovic, Vojislav; von Stockar, Urs · 2010 · École polytechnique fédérale de Lausanne (EPFL) · DOI
Full title: Influence of Uncertainties in pH, pMg, Activity Coefficients, Metabolite Concentrations, and Other Factors on the Analysis of the Thermodynamic Feasibility of Metabolic Pathways
Authors: Vojinovic, Vojislav; von Stockar, Urs
Year: 2010
Venue: École polytechnique fédérale de Lausanne (EPFL)
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)
Thesis Metabolic modeling and experimental studies on carbon and energy metabolism of Mycobacterium tuberculosis
Özdemir, Muhittin Emre · 2013 · École polytechnique fédérale de Lausanne (EPFL) · DOI
Full title: Metabolic modeling and experimental studies on carbon and energy metabolism of Mycobacterium tuberculosis
Authors: Özdemir, Muhittin Emre
Year: 2013
Venue: École polytechnique fédérale de Lausanne (EPFL)
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)
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)
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)
Thesis Deciphering thermodynamics in metabolic networks: A priority list of candidates for metabolomics
Kiparissides, Alexandros; Hatzimanikatis, Vassily · 2014 · École polytechnique fédérale de Lausanne (EPFL) · DOI
Full title: Deciphering thermodynamics in metabolic networks: A priority list of candidates for metabolomics
Authors: Kiparissides, Alexandros; Hatzimanikatis, Vassily
Year: 2014
Venue: École polytechnique fédérale de Lausanne (EPFL)
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)
Thesis Thermodynamics-Based Significance Ranking of Candidates for Metabolomics
Kiparissides, Alexandros; Hatzimanikatis, Vassily · 2014 · École polytechnique fédérale de Lausanne (EPFL) · DOI
Full title: Thermodynamics-Based Significance Ranking of Candidates for Metabolomics
Authors: Kiparissides, Alexandros; Hatzimanikatis, Vassily
Year: 2014
Venue: École polytechnique fédérale de Lausanne (EPFL)
Thesis Thermodynamics-based Significance Ranking of Candidates for Metabolomics
Kiparissides, Alexandros; Hatzimanikatis, Vassily · 2014 · École polytechnique fédérale de Lausanne (EPFL) · DOI
Full title: Thermodynamics-based Significance Ranking of Candidates for Metabolomics
Authors: Kiparissides, Alexandros; Hatzimanikatis, Vassily
Year: 2014
Venue: École polytechnique fédérale de Lausanne (EPFL)
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)
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)
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)
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)
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)
Thesis A Novel Approach to Design of Metabolic Engineering Strategiesa
Chakrabarti, Anirikh; Fengos, Georgios; Ataman, Meriç et al. · 2014 · École polytechnique fédérale de Lausanne (EPFL) · DOI
Full title: A Novel Approach to Design of Metabolic Engineering Strategiesa
Authors: Chakrabarti, Anirikh; Fengos, Georgios; Ataman, Meriç; Soh, Keng Cher; Miskovic, Ljubisa; Hatzimanikatis, Vassily
Year: 2014
Venue: École polytechnique fédérale de Lausanne (EPFL)
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)
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)
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)
Thesis Characterisation of intracellular metabolic states in cells presenting the Warburg phenotype
Pinto Vieira, Joana Raquel; Kiparissides, Alex; Hatzimanikatis, Vassily · 2014 · École polytechnique fédérale de Lausanne (EPFL) · DOI
Full title: Characterisation of intracellular metabolic states in cells presenting the Warburg phenotype
Authors: Pinto Vieira, Joana Raquel; Kiparissides, Alex; Hatzimanikatis, Vassily
Year: 2014
Venue: École polytechnique fédérale de Lausanne (EPFL)
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)
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)
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)
Thesis Investigation of network flexibility and identification of reaction essentiality of human host cells infected by S. flexneri
Chakrabarti, Anirikh; Miskovic, Ljubisa; Soh, Keng Cher et al. · 2013 · École polytechnique fédérale de Lausanne (EPFL) · DOI
Full title: Investigation of network flexibility and identification of reaction essentiality of human host cells infected by S. flexneri
Authors: Chakrabarti, Anirikh; Miskovic, Ljubisa; Soh, Keng Cher; Hatzimanikatis, Vassily
Year: 2013
Venue: École polytechnique fédérale de Lausanne (EPFL)
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)
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)
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)
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)
Thesis Identifying patterns in kinetic parameters that determine the impact of rate-limiting enzymes
Miskovic, Ljubisa; Moret, Michaël Roger Germain; Hatzimanikatis, Vassily · 2016 · École polytechnique fédérale de Lausanne (EPFL) · DOI
Full title: Identifying patterns in kinetic parameters that determine the impact of rate-limiting enzymes
Authors: Miskovic, Ljubisa; Moret, Michaël Roger Germain; Hatzimanikatis, Vassily
Year: 2016
Venue: École polytechnique fédérale de Lausanne (EPFL)
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)
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)
Thesis Toward the identification of new cancer therapy targets using metabolic modeling in a human genome scale
Masid, Maria; Ataman, Meriç; Fengos, Georgios et al. · 2017 · École polytechnique fédérale de Lausanne (EPFL) · DOI
Full title: Toward the identification of new cancer therapy targets using metabolic modeling in a human genome scale
Authors: Masid, Maria; Ataman, Meriç; Fengos, Georgios; Hatzimanikatis, Vassily
Year: 2017
Venue: École polytechnique fédérale de Lausanne (EPFL)
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)
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)
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)
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)
Thesis How uncertainty in kinetic parameters affects metabolic control analysis of optimally grown E.coli
Hameri, Tuure Eelis; Fengos, Georgios; Ataman, Meriç et al. · 2016 · École polytechnique fédérale de Lausanne (EPFL) · DOI
Full title: How uncertainty in kinetic parameters affects metabolic control analysis of optimally grown E.coli
Authors: Hameri, Tuure Eelis; Fengos, Georgios; Ataman, Meriç; Miskovic, Ljubisa; Hatzimanikatis, Vassily
Year: 2016
Venue: École polytechnique fédérale de Lausanne (EPFL)
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)
Thesis Characterization of intracellular metabolic states in cells presenting the Warburg phenotype
Pinto Vieira, Joana Raquel; Kiparissides, Alex; Hatzimanikatis, Vassily · 2017 · École polytechnique fédérale de Lausanne (EPFL) · DOI
Full title: Characterization of intracellular metabolic states in cells presenting the Warburg phenotype
Authors: Pinto Vieira, Joana Raquel; Kiparissides, Alex; Hatzimanikatis, Vassily
Year: 2017
Venue: École polytechnique fédérale de Lausanne (EPFL)
Thesis A kinetic model of the lipid network in yeast
Tsouka, Sofia; Savoglidis, Georgios; Hatzimanikatis, Vassily · 2017 · École polytechnique fédérale de Lausanne (EPFL) · DOI
Full title: A kinetic model of the lipid network in yeast
Authors: Tsouka, Sofia; Savoglidis, Georgios; Hatzimanikatis, Vassily
Year: 2017
Venue: École polytechnique fédérale de Lausanne (EPFL)
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)
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)
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)
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)
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)
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)
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)
Thesis Identifying and targeting key cellular mechanisms for proliferation in Plasmodium parasites: a combined experimental and computational strategy
Chiappino Pepe, Anush; Bushell, Ellen; Limenitakis, Rebecca et al. · 2017 · École polytechnique fédérale de Lausanne (EPFL) · DOI
Full title: Identifying and targeting key cellular mechanisms for proliferation in Plasmodium parasites: a combined experimental and computational strategy
Authors: Chiappino Pepe, Anush; Bushell, Ellen; Limenitakis, Rebecca; Rayner, Julian C.; Heussler, Volker; Billker, Oliver; Hatzimanikatis, Vassily
Year: 2017
Venue: École polytechnique fédérale de Lausanne (EPFL)
Thesis Identifying and targeting key cellular mechanisms for proliferation in Plasmodium parasites: a combined experimental and computational strategy
Chiappino Pepe, Anush; Bushell, Ellen; Limenitakis, Rebecca et al. · 2017 · École polytechnique fédérale de Lausanne (EPFL) · DOI
Full title: Identifying and targeting key cellular mechanisms for proliferation in Plasmodium parasites: a combined experimental and computational strategy
Authors: Chiappino Pepe, Anush; Bushell, Ellen; Limenitakis, Rebecca; Rayner, Julian C.; Heussler, Volker; Billker, Oliver; Hatzimanikatis, Vassily
Year: 2017
Venue: École polytechnique fédérale de Lausanne (EPFL)
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)
Thesis Thermodynamics-based Metabolite Sensitivity Analysis in metabolic networks
Kiparissides, A.; Hatzimanikatis, V. · 2017 · École polytechnique fédérale de Lausanne (EPFL) · DOI
Full title: Thermodynamics-based Metabolite Sensitivity Analysis in metabolic networks
Authors: Kiparissides, A.; Hatzimanikatis, V.
Year: 2017
Venue: École polytechnique fédérale de Lausanne (EPFL)
Thesis Analysis and design of metabolic reaction networks via mixed-integer linear optimization
Hatzimanikatis, Vassily; Floudas, Christodoulos A.; Bailey, James E. · 2007 · École polytechnique fédérale de Lausanne (EPFL) · DOI
Full title: Analysis and design of metabolic reaction networks via mixed-integer linear optimization
Authors: Hatzimanikatis, Vassily; Floudas, Christodoulos A.; Bailey, James E.
Year: 2007
Venue: École polytechnique fédérale de Lausanne (EPFL)
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)
Thesis Metabolic fluxes in riboflavin-producing Bacillus subtilis
Sauer, Uwe; Hatzimanikatis, Vassily; Bailey, James E. et al. · 2007 · École polytechnique fédérale de Lausanne (EPFL) · DOI
Full title: Metabolic fluxes in riboflavin-producing Bacillus subtilis
Authors: Sauer, Uwe; Hatzimanikatis, Vassily; Bailey, James E.; Hochuli, Michel; Szyperski, Thomas; Wuthrich, Kurt
Year: 2007
Venue: École polytechnique fédérale de Lausanne (EPFL)
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)
Thesis Metabolomics, Standards, and Metabolic Modeling for Synthetic Biology in Plants
Hill, CB; Czauderna, T; Klapperstück, M et al. · 2016 · University of Melbourne · DOI
Full title: Metabolomics, Standards, and Metabolic Modeling for Synthetic Biology in Plants
Authors: Hill, CB; Czauderna, T; Klapperstück, M; Roessner, U; Schreiber, F
Year: 2016
Venue: University of Melbourne
Thesis Metabolic control analysis under uncertainty: Framework development and case studies
Wang, Liqing; Birol, Inanc; Hatzimanikatis, Vassily · 2007 · École polytechnique fédérale de Lausanne (EPFL) · DOI
Full title: Metabolic control analysis under uncertainty: Framework development and case studies
Authors: Wang, Liqing; Birol, Inanc; Hatzimanikatis, Vassily
Year: 2007
Venue: École polytechnique fédérale de Lausanne (EPFL)
Thesis Metabolic fluxes in central carbon metabolism of Bacillus subtilis
Sauer, U.; Hatzimanikatis, V.; Szyperski, T. et al. · 2007 · École polytechnique fédérale de Lausanne (EPFL) · DOI
Full title: Metabolic fluxes in central carbon metabolism of Bacillus subtilis
Authors: Sauer, U.; Hatzimanikatis, V.; Szyperski, T.; Wuthrich, K.; Bailey, J. E.
Year: 2007
Venue: École polytechnique fédérale de Lausanne (EPFL)
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)
Thesis Metabolic engineering under uncertainty. I: Framework development
Wang, Liqing; Hatzimanikatis, Vassily · 2007 · École polytechnique fédérale de Lausanne (EPFL) · DOI
Full title: Metabolic engineering under uncertainty. I: Framework development
Authors: Wang, Liqing; Hatzimanikatis, Vassily
Year: 2007
Venue: École polytechnique fédérale de Lausanne (EPFL)
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2. Data Extraction

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Paper
Monitoring and modelling the glutamine metabolic pathway: a review and future perspectives
Mirveis, Zohreh; Howe, Orla; Cahill, Paul A. et al. · 2023
Full title: Monitoring and modelling the glutamine metabolic pathway: a review and future perspectives
Authors: Mirveis, Zohreh; Howe, Orla; Cahill, Paul A.; Patil, Nitin; Byrne, Hugh J.
Paper
Towards industrial biological hydrogen production: a review
Teke, George M.; Cho, Bovinille Anye; Bosman, Catharine Elizabeth et al. · 2023
Full title: Towards industrial biological hydrogen production: a review
Authors: Teke, George M.; Cho, Bovinille Anye; Bosman, Catharine Elizabeth; Mapholi, Zwonaka; Zhang, Dongda; Pott, Robert W. M.
Paper
Unbiased metabolic flux inference through combined thermodynamic and 13 C flux analysis
Saldida, Joana; Muntoni, Anna Paola; Martino, Daniele De et al. · 2020
Full title: Unbiased metabolic flux inference through combined thermodynamic and 13 C flux analysis
Authors: Saldida, Joana; Muntoni, Anna Paola; Martino, Daniele De; Hubmann, Georg; Niebel, Bastian; Schmidt, Anna Mareike; Braunstein, Alfredo; Milias‐Argeitis, Andreas; Heinemann, Matthias
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A graph neural network model to estimate cell-wise metabolic flux using single cell RNA-seq data
Alghamdi, Norah; Chang, Wennan; Dang, Pengtao et al. · 2020
Full title: A graph neural network model to estimate cell-wise metabolic flux using single cell RNA-seq data
Authors: Alghamdi, Norah; Chang, Wennan; Dang, Pengtao; Lu, Xiaoyu; Wan, Changlin; Gampala, Silpa; Huang, Zhi; Wang, Jiashi; Ma, Qin; Zang, Yong; Fishel, Melissa L.; Cao, Sha; Zhang, Chi
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Genomic and metabolic plasticity drive alternative scenarios for adapting <i>Pseudomonas putida</i> to non-native substrate D-xylose
Dvořák, Pavel; Burýšková, Barbora; Popelářová, Barbora et al. · 2023
Full title: Genomic and metabolic plasticity drive alternative scenarios for adapting <i>Pseudomonas putida</i> to non-native substrate D-xylose
Authors: Dvořák, Pavel; Burýšková, Barbora; Popelářová, Barbora; Ebert, Birgitta E.; Botka, Tibor; Bujdoš, Dalimil; Sánchez-Pascuala, Alberto; Schöttler, Hannah; Hayen, Heiko; Lorenzo, Vı́ctor de; Blank, Lars M.; Benešík, Martin
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A method to identify high consensus predictions of single-cell metabolic flux
Amiss, Michael; Lum, Julian J.; Jabbari, Hosna · 2024
Full title: A method to identify high consensus predictions of single-cell metabolic flux
Authors: Amiss, Michael; Lum, Julian J.; Jabbari, Hosna
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A diel multi-tissue genome-scale metabolic model of Vitis vinifera
Sampaio, Marta; Rocha, Miguel; Dias, Óscar · 2024
Full title: A diel multi-tissue genome-scale metabolic model of Vitis vinifera
Authors: Sampaio, Marta; Rocha, Miguel; Dias, Óscar
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Simulation of biochemical systems using constraint-based methods and complex networks
Burke, Paulo E. P. · 2021
Full title: Simulation of biochemical systems using constraint-based methods and complex networks
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A framework for evolutionary systems biology
Loewe, Laurence · 2009
Full title: A framework for evolutionary systems biology
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Métodos numéricos para modelos de redes metabólicas.
Oliveira, Rafael David de · 2022
Full title: Métodos numéricos para modelos de redes metabólicas.
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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
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.
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gapseq: informed prediction of bacterial metabolic pathways and reconstruction of accurate metabolic models
Zimmermann, Johannes; Kaleta, Christoph; Waschina, Silvio · 2021
Full title: gapseq: informed prediction of bacterial metabolic pathways and reconstruction of accurate metabolic models
Authors: Zimmermann, Johannes; Kaleta, Christoph; Waschina, Silvio
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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
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
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Metabolic characterization and viable delivery of Akkermansia muciniphila for its future application
Ark, Kees van der · 2018
Full title: Metabolic characterization and viable delivery of Akkermansia muciniphila for its future application
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Transcriptional landscapes of lipid producing microalgae
Carrères, Benoît M. · 2019
Full title: Transcriptional landscapes of lipid producing microalgae
Authors: Carrères, Benoît M.
Paper
Model-driven design of Mycoplasma as a vaccine chassis
Gaspari, Erika · 2021
Full title: Model-driven design of Mycoplasma as a vaccine chassis
Authors: Gaspari, Erika
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Microbiome.config : Deciphering microbial lifestyles for rational design of plant growth promoting communities
Poncheewin, Wasin · 2022
Full title: Microbiome.config : Deciphering microbial lifestyles for rational design of plant growth promoting communities
Authors: Poncheewin, Wasin
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Enzyme promiscuity approaches to predict metabolic pathways in the human gut microbiota.
Balzerani, Francesco · 2023
Full title: Enzyme promiscuity approaches to predict metabolic pathways in the human gut microbiota.
Authors: Balzerani, Francesco
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Metabolic modelling approaches for describing and engineering microbial communities
García-Jiménez, Beatriz; Torres‐Bacete, Jesús; Nogales, Juan · 2020
Full title: Metabolic modelling approaches for describing and engineering microbial communities
Authors: García-Jiménez, Beatriz; Torres‐Bacete, Jesús; Nogales, Juan
Paper
Microbiome Modeling: A Beginner’s Guide
Lange, Emanuel; Kranert, Lena; Krüger, Jacob et al. · 2024
Full title: Microbiome Modeling: A Beginner’s Guide
Authors: Lange, Emanuel; Kranert, Lena; Krüger, Jacob; Benndorf, Dirk; Heyer, Robert
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Experimental Definition and Validation of Protein Coding Transcripts in Chlamydomonas reinhardtii
Salehi‐Ashtiani, Kourosh; Papin, Jason A. · 2012
Full title: Experimental Definition and Validation of Protein Coding Transcripts in Chlamydomonas reinhardtii
Authors: Salehi‐Ashtiani, Kourosh; Papin, Jason A.
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Model-Based Hypothesis Testing in Biomedicine : How Systems Biology Can Drive the Growth of Scientific Knowledge
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Full title: Uncovering Novel Pathways for Enhancing Hyaluronan Synthesis in Recombinant Lactococcus lactis: Genome-Scale Metabolic Modeling and Experimental Validation
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Full title: Accelerating Biologics Manufacturing by Upstream Process Modelling
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Full title: True and Illusory Benefits of Modeling: Comment on “Genome-Scale Metabolic Network Reconstruction and In Silico Analysis of Hexanoic Acid Producing Megasphaera elsdenii. Microorganisms 2020, 8, 539”
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Full title: mergem : merging and comparing genome-scale metabolic models using universal identifiers
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Full title: The limitations of phenotype prediction in metabolism
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Full title: Debottlenecking and reformulating feed media for improved CHO cell growth and titer by data-driven and model-guided analyses
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Full title: Rational strain design with minimal phenotype perturbation
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Full title: A Bayesian model for genomic prediction using metabolic networks
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Full title: The necessity of considering enzymes as compartments in constraint-based genome-scale metabolic models
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Full title: Microbial community-scale metabolic modeling predicts personalized short chain fatty acid production profiles in the human gut
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Full title: Proteomics and constraint-based modelling reveal enzyme kinetic properties of <i>Chlamydomonas reinhardtii</i> on a genome scale
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Full title: Generative machine learning produces kinetic models that accurately characterize intracellular metabolic states
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Full title: Integrated Constraint-Based Modeling of E. coli Cell-Free Protein Synthesis
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Full title: Stochastic modeling of the dynamics of Salmonella infection of epithelial cells
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Full title: Improving genome-scale metabolic models of incomplete genomes with deep learning
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Full title: ModelSEED v2: High-throughput genome-scale metabolic model reconstruction with enhanced energy biosynthesis pathway prediction
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Full title: CFSA: Comparative Flux Sampling Analysis as a Guide for Strain Design
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Full title: BayFlux: A <i>Bay</i> esian method to quantify metabolic <i>Flux</i> es and their uncertainty at the genome scale
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Full title: Genome-scale metabolic models consistently predict <i>in vitro</i> characteristics of <i>Corynebacterium striatum</i>
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Full title: Unraveling principles of thermodynamics for genome-scale metabolic networks using graph neural networks
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Full title: lista -GEM: the genome-scale metabolic reconstruction of Lipomyces starkeyi
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Full title: First Genome-Scale Metabolic Modeling of <i>Brucella abortus</i> Predicts Pathogen Gene Essentiality and New Drug Target
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Full title: Systematic analysis of microorganisms’ metabolism for selective targeting
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Full title: Machine learning predicts system-wide metabolic flux control in cyanobacteria
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Full title: A new genome-scale metabolic model of oleaginous microalgae with refined lipid metabolism elucidates Microchloropsis gaditana mutant phenotypes.
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Full title: Multi-omic characterization of antibody-producing CHO cell lines elucidates metabolic reprogramming and nutrient uptake bottlenecks
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Full title: Quantitative differences in anaerobic growth and metabolism of three different <i>E. coli</i> strains using <sup>13</sup> C-Metabolic Flux Analysis
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Full title: Fast automated reconstruction of genome-scale metabolic models for microbial species and communities
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Full title: A constraint-based framework to reconstruct interaction networks in microbial communities
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Full title: BayesianSSA: a Bayesian statistical model based on structural sensitivity analysis for predicting responses to enzyme perturbations in metabolic networks
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Qiu, Sizhe; Zhao, Simiao; Yang, Aidong · 2023
Full title: DLTKcat: deep learning based prediction of temperature dependent enzyme turnover rates
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Full title: Entangled stoichiometric objectives shape microbial catabolism
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Full title: Experiments and simulations on short chain fatty acid production in a colonic bacterial community
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Full title: Emergent sub-population behavior uncovered with a community dynamic metabolic model of <i>Escherichia coli</i> diauxic growth
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Full title: SLIMEr: probing flexibility of lipid metabolism in yeast with an improved constraint-based modeling framework
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Badri, Abinaya; Raman, Karthik; Jayaraman, Guhan · 2018
Full title: Uncovering novel pathways for enhancing hyaluronan synthesis in recombinant <i>Lactococcus lactis</i> : Genome-scale metabolic modelling and experimental validation
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Full title: Cofactors revisited – Predicting the impact of flavoprotein-related diseases on a genome scale
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Full title: Bayesian inference of metabolic kinetics from genome-scale multiomics data
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Full title: A metabolic reconstruction of <i>Lactobacillus reuteri</i> JCM 1112 and analysis of its potential as a cell factory
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Full title: Modeling the Interplay between Photosynthesis, CO <sub>2</sub> Fixation, and the Quinone Pool in a Purple Non-Sulfur Bacterium
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Full title: MOMO - multi-objective metabolic mixed integer optimization: application to yeast strain engineering
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Full title: Laboratory evolution reveals a two-dimensional rate-yield tradeoff in microbial metabolism
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Full title: Revealing metabolic flexibility of <i>Candidatus</i> Accumulibacter phosphatis through redox cofactor analysis and metabolic network modeling
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Full title: Reconstruction of consensus tissue-specific metabolic models
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Full title: Modeling genome-wide evolution of catalytic turnover rates: Strong epistasis shaped modern enzyme kinetics
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Full title: A comprehensive genome-scale model for <i>Rhodosporidium toruloides</i> IFO0880 accounting for functional genomics and phenotypic data
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Full title: Genome-Scale reconstruction of <i>Paenarthrobacter aurescens</i> TC1 metabolic model towards the study of atrazine bioremediation
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Kuepfer, Lars; Sauer, Uwe; Blank, Lars M. · 2005
Full title: Metabolic functions of duplicate genes in Saccharomyces cerevisiae
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Full title: Predictive engineering and optimization of tryptophan metabolism in yeast through a combination of mechanistic and machine learning models
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Wendering, Philipp; Arend, Marius; Razaghi‐Moghadam, Zahra et al. · 2023
Full title: Data integration across conditions improves turnover number estimates and metabolic predictions
Authors: Wendering, Philipp; Arend, Marius; Razaghi‐Moghadam, Zahra; Nikoloski, Zoran
Paper
Proteome allocations change linearly with the specific growth rate of Saccharomyces cerevisiae under glucose limitation
Xia, Jianye; Sánchez, Benjamín J.; Chen, Yu et al. · 2022
Full title: Proteome allocations change linearly with the specific growth rate of Saccharomyces cerevisiae under glucose limitation
Authors: Xia, Jianye; Sánchez, Benjamín J.; Chen, Yu; Campbell, Kate; Kasvandik, Sergo; Nielsen, Jens
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
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.
Paper
Turnover number predictions for kinetically uncharacterized enzymes using machine and deep learning
Kroll, Alexander; Rousset, Yvan; Hu, Xiao-Pan et al. · 2023
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.
Paper
Identification of gene function based on models capturing natural variability of Arabidopsis thaliana lipid metabolism
Córdoba, Sandra Correa; Tong, Hao; Burgos, Asdrúbal et al. · 2023
Full title: Identification of gene function based on models capturing natural variability of Arabidopsis thaliana lipid metabolism
Authors: Córdoba, Sandra Correa; Tong, Hao; Burgos, Asdrúbal; Zhu, Feng; Alseekh, Saleh; Fernie, Alisdair R.; Nikoloski, Zoran
Paper
Teasing out missing reactions in genome-scale metabolic networks through hypergraph learning
Chen, Can; Liao, Chen; Liu, Yang‐Yu · 2023
Full title: Teasing out missing reactions in genome-scale metabolic networks through hypergraph learning
Authors: Chen, Can; Liao, Chen; Liu, Yang‐Yu
Paper
Bayesian genome scale modelling identifies thermal determinants of yeast metabolism
Li, Gang; Hu, Yating; Zrimec, Jan et al. · 2021
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
Paper
Targeted and high-throughput gene knockdown in diverse bacteria using synthetic sRNAs
Cho, Jae Sung; Yang, Dongsoo; Prabowo, Cindy Pricilia Surya et al. · 2023
Full title: Targeted and high-throughput gene knockdown in diverse bacteria using synthetic sRNAs
Authors: Cho, Jae Sung; Yang, Dongsoo; Prabowo, Cindy Pricilia Surya; Ghiffary, Mohammad Rifqi; Han, Tae-Hee; Choi, Kyeong Rok; Moon, Cheon Woo; Zhou, Hengrui; Ryu, Jae Yong; Kim, Hyun Uk; Lee, Sang Yup
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
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
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
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
Paper
A neural-mechanistic hybrid approach improving the predictive power of genome-scale metabolic models
Faure, Léon; Mollet, Bastien; Liebermeister, Wolfram et al. · 2023
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
Paper
Predicting stress response and improved protein overproduction in Bacillus subtilis
Tibocha‐Bonilla, Juan D.; Zúñiga, Cristal; Lekbua, Asama et al. · 2022
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
Paper
Convergence of resistance and evolutionary responses in Escherichia coli and Salmonella enterica co-inhabiting chicken farms in China
Baker, Michelle; Zhang, Xibin; Maciel-Guerra, Alexandre et al. · 2024
Full title: Convergence of resistance and evolutionary responses in Escherichia coli and Salmonella enterica co-inhabiting chicken farms in China
Authors: Baker, Michelle; Zhang, Xibin; Maciel-Guerra, Alexandre; Babaarslan, Kubra; Dong, Yinping; Wang, Wei; Hu, Yujie; Renney, David; Liu, Longhai; Li, Hui; Hossain, Maqsud; Heeb, Stephan; Tong, Zhiqin; Pearcy, Nicole; Zhang, Meimei; Geng, Yingzhi; Zhao, Li; Hao, Zhihui; Senin, Nicola; Chen, Junshi; Peng, Zixin; Li, Fengqin; Dottorini, Tania
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
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
Paper
Proteomics and constraint-based modelling reveal enzyme kinetic properties of Chlamydomonas reinhardtii on a genome scale
Arend, Marius; Zimmer, David; Xu, Rudan et al. · 2023
Full title: Proteomics and constraint-based modelling reveal enzyme kinetic properties of Chlamydomonas reinhardtii on a genome scale
Authors: Arend, Marius; Zimmer, David; Xu, Rudan; Sommer, Frederik; Mühlhaus, Timo; Nikoloski, Zoran
Paper
Quantitative prediction of conditional vulnerabilities in regulatory and metabolic networks using PRIME
Immanuel, Selva Rupa Christinal; Arrieta‐Ortiz, Mario L.; Ruiz, Rene A. et al. · 2021
Full title: Quantitative prediction of conditional vulnerabilities in regulatory and metabolic networks using PRIME
Authors: Immanuel, Selva Rupa Christinal; Arrieta‐Ortiz, Mario L.; Ruiz, Rene A.; Pan, Min; Lomana, Adrián López García de; Peterson, Eliza J. R.; Baliga, Nitin S.
Paper
Rational strain design with minimal phenotype perturbation
Narayanan, Bharath; Weilandt, Daniel; Masid, María et al. · 2024
Full title: Rational strain design with minimal phenotype perturbation
Authors: Narayanan, Bharath; Weilandt, Daniel; Masid, María; Mišković, Ljubiša; Hatzimanikatis, Vassily
Paper
Modelling the pyrenoid-based CO2-concentrating mechanism provides insights into its operating principles and a roadmap for its engineering into crops
Fei, Chenyi; Wilson, Alexandra T.; Mangan, Niall M. et al. · 2022
Full title: Modelling the pyrenoid-based CO2-concentrating mechanism provides insights into its operating principles and a roadmap for its engineering into crops
Authors: Fei, Chenyi; Wilson, Alexandra T.; Mangan, Niall M.; Wingreen, Ned S.; Jonikas, Martin C.
Paper
Towards a widespread adoption of metabolic modeling tools in biopharmaceutical industry: a process systems biology engineering perspective
Richelle, Anne; David, Blandine; Demaegd, Didier et al. · 2020
Full title: Towards a widespread adoption of metabolic modeling tools in biopharmaceutical industry: a process systems biology engineering perspective
Authors: Richelle, Anne; David, Blandine; Demaegd, Didier; Dewerchin, Marianne; Kinet, Romain; Morreale, Angelo; Portela, Rui M. C.; Zune, Quentin; Stosch, Moritz von
Paper
13C-metabolic flux analysis of respiratory chain disrupted strain ΔndhF1 of Synechocystis sp. PCC 6803
Wada, Keisuke; Toya, Yoshihiro; Matsuda, Fumio et al. · 2025
Full title: 13C-metabolic flux analysis of respiratory chain disrupted strain ΔndhF1 of Synechocystis sp. PCC 6803
Authors: Wada, Keisuke; Toya, Yoshihiro; Matsuda, Fumio; Shimizu, Hiroshi
Paper
AGORA2: Large scale reconstruction of the microbiome highlights wide-spread drug-metabolising capacities
Heinken, Almut; Acharya, Geeta; Ravcheev, Dmitry A. et al. · 2020
Full title: AGORA2: Large scale reconstruction of the microbiome highlights wide-spread drug-metabolising capacities
Authors: Heinken, Almut; Acharya, Geeta; Ravcheev, Dmitry A.; Hertel, Johannes; Nyga, Malgorzata; Okpala, Onyedika Emmanuel; Hogan, Marcus; Magnúsdóttir, Stefanía; Boneschi, Filippo Martinelli; Preciat, German; Edirisinghe, Janaka N.; Henry, Christopher S.; Fleming, Ronan M. T.; Thiele, Ines
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
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
Paper
H2 drives metabolic rearrangements in gas-fermenting Clostridium autoethanogenum
Valgepea, Kaspar; Lemgruber, Renato de Souza Pinto; Abdalla, Tanus et al. · 2018
Full title: H2 drives metabolic rearrangements in gas-fermenting Clostridium autoethanogenum
Authors: Valgepea, Kaspar; Lemgruber, Renato de Souza Pinto; Abdalla, Tanus; Binos, Steve; Takemori, Nobuaki; Takemori, Ayako; Tanaka, Yuki; Tappel, Ryan; Köpke, Michael; Simpson, Séan D.; Nielsen, Lars K.; Marcellin, Esteban
Thesis
Metabolic modelling and analysis for the optimisation of Escherichia coli as a production host = Metabolische modellering en analyse voor de optimalisatie van Escherichia coli als productiestam
Lequeux, Gaspard · 2008
Full title: Metabolic modelling and analysis for the optimisation of Escherichia coli as a production host = Metabolische modellering en analyse voor de optimalisatie van Escherichia coli als productiestam
Authors: Lequeux, Gaspard
Thesis
Using Genome-Scale Metabolic Models to Compare Serovars of the Foodborne Pathogen Listeria monocytogenes
Metz, Zachary · 2016
Full title: Using Genome-Scale Metabolic Models to Compare Serovars of the Foodborne Pathogen Listeria monocytogenes
Authors: Metz, Zachary
Thesis
Improving cyanobacteria productivity: From theory to assay
Shabestary, Kiyan · 2020
Full title: Improving cyanobacteria productivity: From theory to assay
Authors: Shabestary, Kiyan
Thesis
Modeling and analysis of the rapid aerobic metabolism of Geobacillus sp. LC300
Ljungqvist, Emil E. · 2024
Full title: Modeling and analysis of the rapid aerobic metabolism of Geobacillus sp. LC300
Authors: Ljungqvist, Emil E.
Thesis
Tracing the fungal carbon metabolic roadmap
Pontes, María Victoria Aguilar · 2018
Full title: Tracing the fungal carbon metabolic roadmap
Authors: Pontes, María Victoria Aguilar
Thesis
Evaluating Microbial Community Interactions, using Ecology and Flux Balance Analysis
Seto, Charlie · 2019
Full title: Evaluating Microbial Community Interactions, using Ecology and Flux Balance Analysis
Authors: Seto, Charlie
Thesis
Unravelling the genetic complexity and redundancy of Aspergillus niger sugar metabolism
Chroumpi, Soultana · 2022
Full title: Unravelling the genetic complexity and redundancy of Aspergillus niger sugar metabolism
Authors: Chroumpi, Soultana
Thesis
Simulation, sensitivity analysis, and optimization of bioprocesses using dynamic flux balance analysis
Gomez, Jose Alberto, Ph. D. Massachusetts Institute of Technology · 2018
Full title: Simulation, sensitivity analysis, and optimization of bioprocesses using dynamic flux balance analysis
Authors: Gomez, Jose Alberto, Ph. D. Massachusetts Institute of Technology
Thesis
Selection and optimization of gene targets for the metabolic engineering of E. coli
Fischer, Curt R., Ph. D. Massachusetts Institute of Technology · 2010
Full title: Selection and optimization of gene targets for the metabolic engineering of E. coli
Authors: Fischer, Curt R., Ph. D. Massachusetts Institute of Technology
Thesis
From bacteria to cancer exploiting metabolic networks for industrial and therapeutic purposes
Tomi Andrino, Claudio · 2023
Full title: From bacteria to cancer exploiting metabolic networks for industrial and therapeutic purposes
Authors: Tomi Andrino, Claudio
Thesis
Computational modeling techniques for biological network productivity increases : optimization and rate-limiting reaction detection
Cui, Yuanyuan, Ph.D. Massachusetts Institute of Technology · 2013
Full title: Computational modeling techniques for biological network productivity increases : optimization and rate-limiting reaction detection
Authors: Cui, Yuanyuan, Ph.D. Massachusetts Institute of Technology
Thesis
Flux balance techniques for modelling metabolic networks and comparison with kinetic models
Coleman, Matthew · 2018
Full title: Flux balance techniques for modelling metabolic networks and comparison with kinetic models
Authors: Coleman, Matthew
Thesis
Expanding the Scope of Genome-scale Models of Metabolism and Gene Expression
Lloyd, Colton Joseph · 2019
Full title: Expanding the Scope of Genome-scale Models of Metabolism and Gene Expression
Authors: Lloyd, Colton Joseph
Thesis
Causation in biology : a biomolecular systems view
Lewis, Nathan Enoch · 2012
Full title: Causation in biology : a biomolecular systems view
Authors: Lewis, Nathan Enoch
Thesis
Comparative Systems Biology Analysis of Microbial Pathogens
Monk, Jonathan Mayock · 2015
Full title: Comparative Systems Biology Analysis of Microbial Pathogens
Authors: Monk, Jonathan Mayock
Thesis
Employing Systems Biology for Discovery and Engineering in Phototrophic Microorganisms
Broddrick, Jared Thomas · 2018
Full title: Employing Systems Biology for Discovery and Engineering in Phototrophic Microorganisms
Authors: Broddrick, Jared Thomas
Thesis
Model-driven discovery of adaptive mechanisms and underground metabolism in Escherichia coli
Guzman, Gabriela Ines · 2018
Full title: Model-driven discovery of adaptive mechanisms and underground metabolism in Escherichia coli
Authors: Guzman, Gabriela Ines
Thesis
Genome-scale metabolic modelling of Clostridium autoethanogenum
Norman, Rupert O.J. · 2019
Full title: Genome-scale metabolic modelling of Clostridium autoethanogenum
Authors: Norman, Rupert O.J.
Thesis
Development and Dissemination of Computational Methods for Genome-scale Modeling
Ebrahim, Ali · 2016
Full title: Development and Dissemination of Computational Methods for Genome-scale Modeling
Authors: Ebrahim, Ali
Thesis
Systems Biology of the Human Erythrocyte: Characterizing the Red Blood Cell Proteome Through Metabolic Modeling
Haiman, Zachary Brandon · 2024
Full title: Systems Biology of the Human Erythrocyte: Characterizing the Red Blood Cell Proteome Through Metabolic Modeling
Authors: Haiman, Zachary Brandon
Thesis
Utilizing genome-scale models to enhance high-throughput data analysis : : from pathways to dynamics
Bordbar, Aarash · 2014
Full title: Utilizing genome-scale models to enhance high-throughput data analysis : : from pathways to dynamics
Authors: Bordbar, Aarash
Thesis
A stoichiometric model of Escherichia coli &#x27;s macromolecular synthesis machinery and its integration with metabolism
Thiele, Ines · 2009
Full title: A stoichiometric model of Escherichia coli &#x27;s macromolecular synthesis machinery and its integration with metabolism
Authors: Thiele, Ines
Thesis
Chronicles of a pathogen’s lifestyle: from a single cell to a population
Seif, Yara · 2020
Full title: Chronicles of a pathogen’s lifestyle: from a single cell to a population
Authors: Seif, Yara
Thesis
The genetic basis for adaptation of Escherichia coli to growth in minimal media
Conrad, Thomas · 2010
Full title: The genetic basis for adaptation of Escherichia coli to growth in minimal media
Authors: Conrad, Thomas
Thesis
Systems biology analysis of Escherichia coli for discovery and metabolic engineering
Orth, Jeffrey David · 2012
Full title: Systems biology analysis of Escherichia coli for discovery and metabolic engineering
Authors: Orth, Jeffrey David
Thesis
The Impact of Saccharomyces cerevisiae Metabolism on Enological Fermentation Performance: A Systems Biology Approach
Scott, William · 2021
Full title: The Impact of Saccharomyces cerevisiae Metabolism on Enological Fermentation Performance: A Systems Biology Approach
Authors: Scott, William
Thesis
Monte Carlo simulation in systems biology
Schellenberger, Jan · 2010
Full title: Monte Carlo simulation in systems biology
Authors: Schellenberger, Jan
Thesis
Genome-Scale Reconstruction and Analysis of Eukaryotic Metabolic Networks
Hurlen, Natalie Christine · 2016
Full title: Genome-Scale Reconstruction and Analysis of Eukaryotic Metabolic Networks
Authors: Hurlen, Natalie Christine
Thesis
Systems analysis of energy metabolism elucidates the roles of mitochondria in human health and disease
Vo, Thuy D. · 2007
Full title: Systems analysis of energy metabolism elucidates the roles of mitochondria in human health and disease
Authors: Vo, Thuy D.
Thesis
Human platelet metabolic network reconstruction
Rahmaniyan, Sorena · 2012
Full title: Human platelet metabolic network reconstruction
Authors: Rahmaniyan, Sorena
Thesis
Model-driven metabolic engineering of Escherichia coli : a systems biology approach
Feist, Adam Michael · 2008
Full title: Model-driven metabolic engineering of Escherichia coli : a systems biology approach
Authors: Feist, Adam Michael
Thesis
Model driven analysis of Escherichia coli metabolism
Reed, Jennifer Leanne · 2005
Full title: Model driven analysis of Escherichia coli metabolism
Authors: Reed, Jennifer Leanne
Thesis
Biomass composition: the &quot;elephant in the room&quot; of metabolic modelling.
Dikicioglu, Duygu; Kırdar, Betul; Oliver, Stephen G · 2015
Full title: Biomass composition: the &quot;elephant in the room&quot; of metabolic modelling.
Authors: Dikicioglu, Duygu; Kırdar, Betul; Oliver, Stephen G
Thesis
Making life difficult for Clostridium difficile: augmenting the pathogen&#x27;s metabolic model with transcriptomic and codon usage data for better therapeutic target characterization.
Kashaf, SS; Angione, C; Lió, P · 2017
Full title: Making life difficult for Clostridium difficile: augmenting the pathogen&#x27;s metabolic model with transcriptomic and codon usage data for better therapeutic target characterization.
Authors: Kashaf, SS; Angione, C; Lió, P
Thesis
Predictive analytics of environmental adaptability in multi-omic network models.
Angione, Claudio; Lió, Pietro · 2018
Full title: Predictive analytics of environmental adaptability in multi-omic network models.
Authors: Angione, Claudio; Lió, Pietro
Thesis
Integrating Petri Nets and Flux Balance Methods in Computational Biology Models: a Methodological and Computational Practice
Simone, Pernice; Laura, Follia; Gianfranco, Balbo et al. · 2020
Full title: Integrating Petri Nets and Flux Balance Methods in Computational Biology Models: a Methodological and Computational Practice
Authors: Simone, Pernice; Laura, Follia; Gianfranco, Balbo; Luciano, Milanesi; Giulia, Sartini; Niccoló, Totis; Pietro, Lió; Ivan, Merelli; Francesca, Cordero; Marco, Beccuti
Thesis
Evolutionary programming as a platform for in silico metabolic engineering.
Patil, Kiran Raosaheb; Rocha, Isabel; Förster, Jochen et al. · 2020
Full title: Evolutionary programming as a platform for in silico metabolic engineering.
Authors: Patil, Kiran Raosaheb; Rocha, Isabel; Förster, Jochen; Nielsen, Jens
Thesis
Multi-Omics and Genome-Scale Modeling Reveal a Metabolic Shift During C. elegans Aging.
Hastings, Janna; Mains, Abraham; Virk, Bhupinder et al. · 2019
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
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
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
Thesis
metaGEM: reconstruction of genome scale metabolic models directly from metagenomes.
Zorrilla, Francisco; Buric, Filip; Patil, Kiran R et al. · 2025
Full title: metaGEM: reconstruction of genome scale metabolic models directly from metagenomes.
Authors: Zorrilla, Francisco; Buric, Filip; Patil, Kiran R; Zelezniak, Aleksej
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
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
Thesis
Predictive evolution of metabolic phenotypes using model-designed environments.
Jouhten, Paula; Konstantinidis, Dimitrios; Pereira, Filipa et al. · 2022
Full title: Predictive evolution of metabolic phenotypes using model-designed environments.
Authors: Jouhten, Paula; Konstantinidis, Dimitrios; Pereira, Filipa; Andrejev, Sergej; Grkovska, Kristina; Castillo, Sandra; Ghiachi, Payam; Beltran, Gemma; Almaas, Eivind; Mas, Albert; Warringer, Jonas; Gonzalez, Ramon; Morales, Pilar; Patil, Kiran R
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
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
Thesis
Quantitative evaluation of anaerobic microbial metabolism via comparative genomics and metabolic modeling
Tang, Wentao · 2022
Full title: Quantitative evaluation of anaerobic microbial metabolism via comparative genomics and metabolic modeling
Authors: Tang, Wentao
Thesis
Design principles for engineering bacteria to maximise chemical production from batch cultures
Mannan, Ahmad; Darlington, Alexander; Tanaka, Reiko et al. · 2024
Full title: Design principles for engineering bacteria to maximise chemical production from batch cultures
Authors: Mannan, Ahmad; Darlington, Alexander; Tanaka, Reiko; Bates, Declan
Thesis
An exact arithmetic toolbox for a consistent and reproducible structural analysis of metabolic network models
Chindelevitch, Leonid; Trigg, Jason; Regev, Aviv et al. · 2020
Full title: An exact arithmetic toolbox for a consistent and reproducible structural analysis of metabolic network models
Authors: Chindelevitch, Leonid; Trigg, Jason; Regev, Aviv; Berger, Bonnie
Thesis
Flux-dependent graphs for metabolic networks
Beguerisse, Mariano; Bosque, Gabriel; Oyarzun, DA et al. · 2018
Full title: Flux-dependent graphs for metabolic networks
Authors: Beguerisse, Mariano; Bosque, Gabriel; Oyarzun, DA; Pico, Jesus; Barahona, Mauricio
Thesis
Opportunities at the interface of network science and metabolic modelling
Dusad, Varshit; Thiel, Denise; Barahona, Mauricio et al. · 2021
Full title: Opportunities at the interface of network science and metabolic modelling
Authors: Dusad, Varshit; Thiel, Denise; Barahona, Mauricio; Keun, Hector; Oyarzun, Diego
Thesis
Modular dynamic biomolecular modelling with bond graphs: The unification of stoichiometry, thermodynamics, kinetics and data
Gawthrop, PJ; Pan, M; Crampin, EJ · 2021
Full title: Modular dynamic biomolecular modelling with bond graphs: The unification of stoichiometry, thermodynamics, kinetics and data
Authors: Gawthrop, PJ; Pan, M; Crampin, EJ
Thesis
Genome-scale metabolic modeling reveals metabolic alterations of multidrug-resistant acinetobacter Baumannii in a murine bloodstream infection model
Zhao, J; Zhu, Y; Han, J et al. · 2020
Full title: Genome-scale metabolic modeling reveals metabolic alterations of multidrug-resistant acinetobacter Baumannii in a murine bloodstream infection model
Authors: Zhao, J; Zhu, Y; Han, J; Lin, YW; Aichem, M; Wang, J; Chen, K; Velkov, T; Schreiber, F; Li, J
Thesis
NIBBS-search for fast and accurate prediction of phenotype-biased metabolic systems
Schmidt, MC; Rocha, AM; Padmanabhan, K et al. · 2022
Full title: NIBBS-search for fast and accurate prediction of phenotype-biased metabolic systems
Authors: Schmidt, MC; Rocha, AM; Padmanabhan, K; Shpanskaya, Y; Banfield, J; Scott, K; Mihelcic, JR; Samatova, NF
Thesis
Strategies for extending metabolomics studies with stable isotope labelling and fluxomics
Srivastava, A; Kowalski, GM; Callahan, DL et al. · 2021
Full title: Strategies for extending metabolomics studies with stable isotope labelling and fluxomics
Authors: Srivastava, A; Kowalski, GM; Callahan, DL; Meikle, PJ; Creek, DJ
Thesis
Metabolic Responses to Polymyxin Treatment in Acinetobacter baumannii ATCC 19606: Integrating Transcriptomics and Metabolomics with Genome-Scale Metabolic Modeling
Zhu, Y; Zhao, J; Maifiah, MHM et al. · 2019
Full title: Metabolic Responses to Polymyxin Treatment in Acinetobacter baumannii ATCC 19606: Integrating Transcriptomics and Metabolomics with Genome-Scale Metabolic Modeling
Authors: Zhu, Y; Zhao, J; Maifiah, MHM; Velkov, T; Schreiber, F; Li, J
Thesis
Comparative analysis of metabolic models of microbial communities reconstructed from automated tools and consensus approaches
Hsieh, YE; Tandon, K; Verbruggen, H et al. · 2024
Full title: Comparative analysis of metabolic models of microbial communities reconstructed from automated tools and consensus approaches
Authors: Hsieh, YE; Tandon, K; Verbruggen, H; Nikoloski, Z
Thesis
Genome-scale metabolic modeling of responses to polymyxins in Pseudomonas aeruginosa
Zhu, Y; Czauderna, T; Zhao, J et al. · 2019
Full title: Genome-scale metabolic modeling of responses to polymyxins in Pseudomonas aeruginosa
Authors: Zhu, Y; Czauderna, T; Zhao, J; Klapperstueck, M; Maifiah, MHM; Han, ML; Lu, J; Sommer, B; Velkov, T; Lithgow, T; Song, J; Schreiber, F; Li, J
Thesis
Comparison of Optimization-Modelling Methods for Metabolites Production in Escherichia coli
Lee, MK; Mohamad, MS; Choon, YW et al. · 2020
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
Thesis
A curated collection of Klebsiella metabolic models reveals variable substrate usage and gene essentiality
Hawkey, J; Vezina, B; Monk, JM et al. · 2022
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
Thesis
Modelling of the metabolism of Escherichia coli for the bio-based production of 1,4-BDO
Velez Jimenez, Guillermo · 2025
Full title: Modelling of the metabolism of Escherichia coli for the bio-based production of 1,4-BDO
Authors: Velez Jimenez, Guillermo
Thesis
Near-optimal experimental design for model selection in systems biology
Busetto, AG; Hauser, A; Krummenacher, G et al. · 2021
Full title: Near-optimal experimental design for model selection in systems biology
Authors: Busetto, AG; Hauser, A; Krummenacher, G; Sunnåker, M; Dimopoulos, S; Ong, CS; Stelling, J; Buhmann, JM
Thesis
FBA-PRCC. Partial Rank Correlation Coefficient (PRCC) Global Sensitivity Analysis (GSA) in Application to Constraint-Based Models
Sorokin, Anatoly; Goryanin, Igor · 2023
Full title: FBA-PRCC. Partial Rank Correlation Coefficient (PRCC) Global Sensitivity Analysis (GSA) in Application to Constraint-Based Models
Authors: Sorokin, Anatoly; Goryanin, Igor
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
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
Thesis
Genomic study of Photobacterium marinum strain J15 and development of genome scale metabolic model for cellular metabolism identification
Roslan, Noordiyanah Nadhirah · 2017
Full title: Genomic study of Photobacterium marinum strain J15 and development of genome scale metabolic model for cellular metabolism identification
Authors: Roslan, Noordiyanah Nadhirah
Thesis
Genome-wide characterization of Phytophthora infestans metabolism: a systems biology approach
Rodenburg, Sander Y A; Seidl, Michael F; de Ridder, Dick et al. · 2018
Full title: Genome-wide characterization of Phytophthora infestans metabolism: a systems biology approach
Authors: Rodenburg, Sander Y A; Seidl, Michael F; de Ridder, Dick; Govers, Francine
Thesis
Generalized metabolic flux analysis framework provides mechanism-based predictions of ophthalmic complications in type 2 diabetes patients
Batagov, Arsen; Dalan, Rinkoo; Wu, Andrew et al. · 2023
Full title: Generalized metabolic flux analysis framework provides mechanism-based predictions of ophthalmic complications in type 2 diabetes patients
Authors: Batagov, Arsen; Dalan, Rinkoo; Wu, Andrew; Lai, Wenbin; Tan, Colin S.; Eisenhaber, Frank
Thesis
Lipid Metabolic Versatility in Malassezia spp. Yeasts Studied through Metabolic Modeling
Triana, Sergio; de Cock, Hans; Ohm, Robin A et al. · 2017
Full title: Lipid Metabolic Versatility in Malassezia spp. Yeasts Studied through Metabolic Modeling
Authors: Triana, Sergio; de Cock, Hans; Ohm, Robin A; Danies, Giovanna; Wösten, Han A B; Restrepo, Silvia; González Barrios, Andrés F; Celis Ramirez, Adriana
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
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
Thesis
Predictive biology: modelling, understanding and harnessing microbial complexity
Lopatkin, Allison J.; Collins, James J. · 2021
Full title: Predictive biology: modelling, understanding and harnessing microbial complexity
Authors: Lopatkin, Allison J.; Collins, James J.
Thesis
Spatiotemporal modeling of microbial metabolism
Chen, Jin; Phalak, Poonam; Gomez, Jose A. et al. · 2016
Full title: Spatiotemporal modeling of microbial metabolism
Authors: Chen, Jin; Phalak, Poonam; Gomez, Jose A.; Barton, Paul I.; Henson, Michael A.; Hoeffner, Kai
Thesis
Towards a whole-cell modeling approach for synthetic biology
Purcell, Oliver; Jain, Bonny; Karr, Jonathan R. et al. · 2016
Full title: Towards a whole-cell modeling approach for synthetic biology
Authors: Purcell, Oliver; Jain, Bonny; Karr, Jonathan R.; Covert, Markus W.; Lu, Timothy K.
Thesis
Exploring the gap between dynamic and constraint-based models of metabolism
Machado, Daniel; Costa, Rafael S.; Rocha, Isabel et al. · 2016
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.
Thesis
Design of robust metabolic pathways
Umeton, Renato; Stracquadanio, Giovanni; Sorathiya, Anilkumar et al. · 2016
Full title: Design of robust metabolic pathways
Authors: Umeton, Renato; Stracquadanio, Giovanni; Sorathiya, Anilkumar; Papini, Alessio; Nicosia, Giuseppe; Lio, Pietro
Thesis
Efficient solution of ordinary differential equations with a parametric lexicographic linear program embedded
Höffner, Kai; Barton, Paul I.; Harwood, Stuart Maxwell et al. · 2016
Full title: Efficient solution of ordinary differential equations with a parametric lexicographic linear program embedded
Authors: Höffner, Kai; Barton, Paul I.; Harwood, Stuart Maxwell; Hoeffner, Kai
Thesis
Nutrition or nature: using elementary flux modes to disentangle the complex forces shaping prokaryote pan-genomes
Garza, Daniel R; von Meijenfeldt, F A Bastiaan; van Dijk, Bram et al. · 2022
Full title: Nutrition or nature: using elementary flux modes to disentangle the complex forces shaping prokaryote pan-genomes
Authors: Garza, Daniel R; von Meijenfeldt, F A Bastiaan; van Dijk, Bram; Boleij, Annemarie; Huynen, Martijn A; Dutilh, Bas E
Thesis
Metabolic requirements for cancer cell proliferation
Iliopoulos, Othon; Keibler, Mark Andrew; Wasylenko, Thomas Michael et al. · 2018
Full title: Metabolic requirements for cancer cell proliferation
Authors: Iliopoulos, Othon; Keibler, Mark Andrew; Wasylenko, Thomas Michael; Vander Heiden, Matthew G.; Stephanopoulos, Gregory; Kelleher, Joanne Keene
Thesis
Genome-scale metabolic reconstruction of 7,302 human microorganisms for personalized medicine
Heinken, Almut; Hertel, Johannes; Acharya, Geeta et al. · 2023
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
Thesis
Ensemble Kinetic Modeling of Metabolic Networks from Dynamic Metabolic Profiles
Jia, Gengjie; Stephanopoulos, Gregory; Gunawan, Rudiyanto · 2018
Full title: Ensemble Kinetic Modeling of Metabolic Networks from Dynamic Metabolic Profiles
Authors: Jia, Gengjie; Stephanopoulos, Gregory; Gunawan, Rudiyanto
Thesis
Reply to &quot;Do genome-scale models need exact solvers or clearer standards?&quot;
Chindelevitch, Leonid; Regev, Aviv; Berger Leighton, Bonnie et al. · 2016
Full title: Reply to &quot;Do genome-scale models need exact solvers or clearer standards?&quot;
Authors: Chindelevitch, Leonid; Regev, Aviv; Berger Leighton, Bonnie; Trigg, Jason
Thesis
Large-scale identification of genetic design strategies using local search
Lun, Desmond S.; Rockwell, Graham; Guido, Nicholas J. et al. · 2011
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.
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
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
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
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
Thesis
Integrating Genome-Scale and Superstructure Optimization Models in Techno-Economic Studies of Biorefineries
Akbari, Amir; Barton, Paul I · 2021
Full title: Integrating Genome-Scale and Superstructure Optimization Models in Techno-Economic Studies of Biorefineries
Authors: Akbari, Amir; Barton, Paul I
Thesis
Recon 2.2: from reconstruction to model of human metabolism
Swainston, Neil; Smallbone, Kieran; Hefzi, Hooman et al. · 2017
Full title: Recon 2.2: from reconstruction to model of human metabolism
Authors: Swainston, Neil; Smallbone, Kieran; Hefzi, Hooman; Hanscho, Michael; Kyriakopoulos, Sarantos; Lakshmanan, Meiyappan; Li, Shangzhong; Quek, Lake-Ee; Thomas, Alex; Zanghellini, Juergen; Borth, Nicole; Lee, Dong-Yup; Mendes, Pedro; Dobson, Paul D.; Zielinski, Daniel C.; Ang, Kok Siong; Gardiner, Natalie J.; Gutierrez, Jahir M.; Liu, Joanne K.; Martínez, Veronica S.; Orellana, Camila A.; Nielsen, Lars K.; Kell, Douglas B.; Lewis, Nathan E.; Brewer, Judith A
Thesis
An Improved Multi-parametric Programming Algorithm for Flux Balance Analysis of Metabolic Networks
Akbari, Amir; Barton, Paul I · 2021
Full title: An Improved Multi-parametric Programming Algorithm for Flux Balance Analysis of Metabolic Networks
Authors: Akbari, Amir; Barton, Paul I
Thesis
Metabolic modeling of synthesis gas fermentation in bubble column reactors
Chen, Jin; Henson, Michael A; Gomez, Jose Alberto et al. · 2015
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.
Thesis
Using Topology of the Metabolic Network to Predict Viability of Mutant Strains
Mirny, Leonid A.; Wunderlich, Zeba · 2010
Full title: Using Topology of the Metabolic Network to Predict Viability of Mutant Strains
Authors: Mirny, Leonid A.; Wunderlich, Zeba
Thesis
Statistics-based model for prediction of chemical biosynthesis yield from Saccharomyces cerevisiae
Xiao, Yi; Leonard, Effendi; Varman, Arul M. et al. · 2011
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.
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
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
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
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
Thesis
DFBAlab: a fast and reliable MATLAB code for dynamic flux balance analysis
Gomez, Jose Alberto; Hoeffner, Kai; Barton, Paul I. · 2015
Full title: DFBAlab: a fast and reliable MATLAB code for dynamic flux balance analysis
Authors: Gomez, Jose Alberto; Hoeffner, Kai; Barton, Paul I.
Thesis
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.
Thesis
Incremental parameter estimation of kinetic metabolic network models
Jia, Gengjie; Stephanopoulos, Gregory; Gunawan, Rudiyanto · 2013
Full title: Incremental parameter estimation of kinetic metabolic network models
Authors: Jia, Gengjie; Stephanopoulos, Gregory; Gunawan, Rudiyanto
Thesis
Employing metabolic models of Salmonella Typhimurium to predict synthetically lethal gene pairs to guide antibiotic discovery
Fong, Nicole Liu · 2012
Full title: Employing metabolic models of Salmonella Typhimurium to predict synthetically lethal gene pairs to guide antibiotic discovery
Authors: Fong, Nicole Liu
Thesis
Statistical Modeling of Sensors and Dials in Metabolic Networks
Hoysala, Swathi Vishwanath · 2018
Full title: Statistical Modeling of Sensors and Dials in Metabolic Networks
Authors: Hoysala, Swathi Vishwanath
Thesis
The Study of Overflow Metabolism and kinetics in a model of metabolism and gene expression of Escherichia coli
Cheng, Chuankai · 2017
Full title: The Study of Overflow Metabolism and kinetics in a model of metabolism and gene expression of Escherichia coli
Authors: Cheng, Chuankai
Thesis
Genome-Scale Reconstruction of the Chlorella vulgaris UTEX 395 Metabolic Network
Huelsman, Tyler Paul · 2015
Full title: Genome-Scale Reconstruction of the Chlorella vulgaris UTEX 395 Metabolic Network
Authors: Huelsman, Tyler Paul
Thesis
The establishment of endosymbiosis: An experimental and computational investigation using the artificial symbiont Synechocystis
Sørensen, Megan · 2015
Full title: The establishment of endosymbiosis: An experimental and computational investigation using the artificial symbiont Synechocystis
Authors: Sørensen, Megan
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
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
Thesis
Identification of growth-coupled and kinetically robust production in strain designs using genome-scale models
Dinh, Hoang Viet · 2017
Full title: Identification of growth-coupled and kinetically robust production in strain designs using genome-scale models
Authors: Dinh, Hoang Viet
Thesis
Genome-scale models of metabolism and expression predict the metabolic burden of recombinant protein expression
Oftadeh, Omid; Hatzimanikatis, Vassily · 2025
Full title: Genome-scale models of metabolism and expression predict the metabolic burden of recombinant protein expression
Authors: Oftadeh, Omid; Hatzimanikatis, Vassily
Thesis
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
Thesis
Essential metabolic pathways in Trypanosoma cruzi
Souza Shiratsubaki, Isabel · 2019
Full title: Essential metabolic pathways in Trypanosoma cruzi
Authors: Souza Shiratsubaki, Isabel
Thesis
Rationally reduced libraries for combinatorial pathway optimization minimizing experimental effort
Jeschek, Markus; Gerngross, Daniel; Panke, Sven · 2025
Full title: Rationally reduced libraries for combinatorial pathway optimization minimizing experimental effort
Authors: Jeschek, Markus; Gerngross, Daniel; Panke, Sven
Thesis
Uncertainty reduction in biochemical kinetic models: Enforcing desired model properties
Miskovic, Ljubisa; Béal, Jonas; Moret, Michael et al. · 2019
Full title: Uncertainty reduction in biochemical kinetic models: Enforcing desired model properties
Authors: Miskovic, Ljubisa; Béal, Jonas; Moret, Michael; Hatzimanikatis, Vassily
Thesis
Kinetic models of metabolism that consider alternative steady-state solutions of intracellular fluxes and concentrations
Hameri, Tuure Eelis; Fengos, Georgios; Ataman, Meriç et al. · 2018
Full title: Kinetic models of metabolism that consider alternative steady-state solutions of intracellular fluxes and concentrations
Authors: Hameri, Tuure Eelis; Fengos, Georgios; Ataman, Meriç; Miskovic, Ljubisa; Hatzimanikatis, Vassily
Thesis
Computational Inference of Metabolic Programs: A Case Study Analyzing the Effect of BRCA1 Loss
Masid, Maria; Rota, Ioanna A.; Barras, David et al. · 2025
Full title: Computational Inference of Metabolic Programs: A Case Study Analyzing the Effect of BRCA1 Loss
Authors: Masid, Maria; Rota, Ioanna A.; Barras, David; De Carlo, Flavia; Ginefra, Pierpaolo; Desbuisson, Matthieu; Ortiz-Miranda, Yaquelin; Zamarin, Dmitriy; Shah, Sohrab P; Vannini, Nicola; Coukos, George; Laniti, Denarda Dangaj; Hatzimanikatis, Vassily
Thesis
Constraint-based metabolic control analysis for rational strain engineering
Tsouka, Sofia; Ataman, Meriç; Hameri, Tuure Eelis et al. · 2021
Full title: Constraint-based metabolic control analysis for rational strain engineering
Authors: Tsouka, Sofia; Ataman, Meriç; Hameri, Tuure Eelis; Miskovic, Ljubisa; Hatzimanikatis, Vassily
Thesis
Extending a dynamic mathematical model of metabolism in Trypanosoma brucei
Kerkhoven, Eduard Johannes · 2012
Full title: Extending a dynamic mathematical model of metabolism in Trypanosoma brucei
Authors: Kerkhoven, Eduard Johannes
Thesis
The ETFL formulation allows multi-omics integration in thermodynamics-compliant metabolism and expression models
Salvy, Pierre; Hatzimanikatis, Vassily · 2020
Full title: The ETFL formulation allows multi-omics integration in thermodynamics-compliant metabolism and expression models
Authors: Salvy, Pierre; Hatzimanikatis, Vassily
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
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
Thesis
Large-scale kinetic metabolic models of Pseudomonas putida KT2440 for consistent design of metabolic engineering strategies
Tokic, Milenko; Hatzimanikatis, Vassily; Miskovic, Ljubisa · 2020
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
Thesis
Analysis of human metabolism by reducing the complexity of the genome-scale models using redHUMAN
Masid, Maria; Ataman, Meric; Hatzimanikatis, Vassily · 2020
Full title: Analysis of human metabolism by reducing the complexity of the genome-scale models using redHUMAN
Authors: Masid, Maria; Ataman, Meric; Hatzimanikatis, Vassily
Thesis
Quantitative modeling of human metabolism: A call for a community effort
Masid Barcon, Maria; Hatzimanikatis, Vassily · 2021
Full title: Quantitative modeling of human metabolism: A call for a community effort
Authors: Masid Barcon, Maria; Hatzimanikatis, Vassily
Thesis
Mechanistic insights into bacterial metabolic reprogramming from omics-integrated genome-scale models
Hadadi, Noushin; Pandey, Vikash; Chiappino-Pepe, Anush et al. · 2020
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.
Thesis
MEMOTE for standardized genome-scale metabolic model testing
Lieven, Christian; Beber, Moritz E.; Olivier, Brett G. et al. · 2020
Full title: MEMOTE for standardized genome-scale metabolic model testing
Authors: Lieven, Christian; Beber, Moritz E.; Olivier, Brett G.; Bergmann, Frank T.; Ataman, Meric; Babaei, Parizad; Bartell, Jennifer A.; Blank, Lars M.; Chauhan, Siddharth; Correia, Kevin; Diener, Christian; Draeger, Andreas; Ebert, Birgitta E.; Edirisinghe, Janaka N.; Faria, Jose P.; Feist, Adam M.; Fengos, Georgios; Fleming, Ronan M. T.; Garcia-Jimenez, Beatriz; Hatzimanikatis, Vassily; van Helvoirt, Wout; Henry, Christopher S.; Hermjakob, Henning; Herrgard, Markus J.; Kaafarani, Ali; Kim, Hyun Uk; King, Zachary; Klamt, Steffen; Klipp, Edda; Koehorst, Jasper J.; Koenig, Matthias; Lakshmanan, Meiyappan; Lee, Dong-Yup; Lee, Sang Yup; Lee, Sunjae; Lewis, Nathan E.; Liu, Filipe; Ma, Hongwu; Machado, Daniel; Mahadevan, Radhakrishnan; Maia, Paulo; Mardinoglu, Adil; Medlock, Gregory L.; Monk, Jonathan M.; Nielsen, Jens; Nielsen, Lars Keld; Nogales, Juan; Nookaew, Intawat; Palsson, Bernhard O.; Papin, Jason A.; Patil, Kiran R.; Poolman, Mark; Price, Nathan D.; Resendis-Antonio, Osbaldo; Richelle, Anne; Rocha, Isabel; Sanchez, Benjamin J.; Schaap, Peter J.; Malik Sheriff, Rahuman S.; Shoaie, Saeed; Sonnenschein, Nikolaus; Teusink, Bas; Vilaca, Paulo; Vik, Jon Olav; Wodke, Judith A. H.; Xavier, Joana C.; Yuan, Qianqian; Zakhartsev, Maksim; Zhang, Cheng
Thesis
Generative machine learning produces kinetic models that accurately characterize intracellular metabolic states
Choudhury, Subham; Narayanan, Bharath; Moret, Michael et al. · 2023
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
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
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
Thesis
Production of biofuels and biochemicals: in need of an ORACLE
Miskovic, Ljubisa; Hatzimanikatis, Vassily · 2010
Full title: Production of biofuels and biochemicals: in need of an ORACLE
Authors: Miskovic, Ljubisa; Hatzimanikatis, Vassily
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
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
Thesis
Analysis and Design of Biological Circuits and Systems
Koeppl, H.; Setti, G. · 2009
Full title: Analysis and Design of Biological Circuits and Systems
Authors: Koeppl, H.; Setti, G.
Thesis
Data, Parameters &amp; Nonlinearities: Development and Applications of Large-scale Dynamic Models of Metabolism
Chakrabarti, Anirikh; Miskovic, Ljubisa; Soh, Keng Cher et al. · 2013
Full title: Data, Parameters &amp; Nonlinearities: Development and Applications of Large-scale Dynamic Models of Metabolism
Authors: Chakrabarti, Anirikh; Miskovic, Ljubisa; Soh, Keng Cher; Hatzimanikatis, Vassily
Thesis
Rational strain design with minimal phenotype perturbation
Narayanan, Bharath; Weilandt, Daniel R.; Masid, Maria et al. · 2024
Full title: Rational strain design with minimal phenotype perturbation
Authors: Narayanan, Bharath; Weilandt, Daniel R.; Masid, Maria; Miskovic, Ljubisa; Hatzimanikatis, Vassily
Thesis
Reconstructing Kinetic Models for Dynamical Studies of Metabolism using Generative Adversarial Networks
Choudhury, Subham; Moret, Michael; Salvy, Pierre et al. · 2022
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
Thesis
Identification of Feasible Metabolic Fluxes and Metabolite Concentrations using Large-scale Kinetic Models
Chakrabarti, Anirikh; Miskovic, Ljubisa; Soh, Keng Cher et al. · 2013
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
Thesis
Rites of passage: requirements and standards for building kinetic models of metabolic phenotypes
Miskovic, Ljubisa; Tokic, Milenko; Fengos, Georgios et al. · 2015
Full title: Rites of passage: requirements and standards for building kinetic models of metabolic phenotypes
Authors: Miskovic, Ljubisa; Tokic, Milenko; Fengos, Georgios; Hatzimanikatis, Vassily
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
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
Thesis
Metabolic Needs and Capabilities of Toxoplasma gondii through Combined Computational and Experimental Analysis
Tymoshenko, Stepan; Oppenheim, Rebecca D.; Agren, Rasmus et al. · 2015
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
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
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
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
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
Thesis
lumpGEM: Systematic generation of subnetworks and elementally balanced lumped reactions for the biosynthesis of target metabolites
Ataman, Meric; Hatzimanikatis, Vassily · 2017
Full title: lumpGEM: Systematic generation of subnetworks and elementally balanced lumped reactions for the biosynthesis of target metabolites
Authors: Ataman, Meric; Hatzimanikatis, Vassily
Thesis
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
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
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
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
Thesis
Optimization of microbial cell factories with systems biology
King, Zachary Andrew · 2016
Full title: Optimization of microbial cell factories with systems biology
Authors: King, Zachary Andrew
Thesis
Multi-scale modeling to elucidate biological network structure and properties
Du, Bin · 2019
Full title: Multi-scale modeling to elucidate biological network structure and properties
Authors: Du, Bin
Thesis
Pan-Genome Enriched Analytics: Systems Biology Examination of the Diversity of Microbial Pathogens
Norsigian, Charles Joseph · 2021
Full title: Pan-Genome Enriched Analytics: Systems Biology Examination of the Diversity of Microbial Pathogens
Authors: Norsigian, Charles Joseph
Thesis
Understanding genetic variation in the proteome: a multi-scale structural systems biology toolkit
Mih, Nathan Da-Wei · 2018
Full title: Understanding genetic variation in the proteome: a multi-scale structural systems biology toolkit
Authors: Mih, Nathan Da-Wei
Thesis
Biologically-interpretable machine learning for microbial genomics
Kavvas, Erol · 2020
Full title: Biologically-interpretable machine learning for microbial genomics
Authors: Kavvas, Erol
Thesis
Genome-scale Models of Metabolism and Gene Expression : : Construction and Use for Growth Phenotype Prediction
Lerman, Joshua Adam · 2014
Full title: Genome-scale Models of Metabolism and Gene Expression : : Construction and Use for Growth Phenotype Prediction
Authors: Lerman, Joshua Adam
Thesis
On the systems characterization of metabolic networks
Jamshidi, Neema · 2009
Full title: On the systems characterization of metabolic networks
Authors: Jamshidi, Neema
Thesis
Systems biology of the cardiac hypoxia response in Drosophila
Feala, Jacob Daniel · 2008
Full title: Systems biology of the cardiac hypoxia response in Drosophila
Authors: Feala, Jacob Daniel
Thesis
Metabolic systems biology of the malaria parasite
Forth, Thomas · 2012
Full title: Metabolic systems biology of the malaria parasite
Authors: Forth, Thomas
Thesis
Using metabolic network reconstructions to analyze complex data sets
Zielinski, Daniel Craig · 2015
Full title: Using metabolic network reconstructions to analyze complex data sets
Authors: Zielinski, Daniel Craig
Thesis
Genome-Scale Metabolic Network Reconstruction of Thermotoga sp.Strain RQ7
Gautam, Jyotshana · 2020
Full title: Genome-Scale Metabolic Network Reconstruction of Thermotoga sp.Strain RQ7
Authors: Gautam, Jyotshana
Thesis
Predicting growth optimization strategies with metabolic/expression models
Liu, Joanne · 2017
Full title: Predicting growth optimization strategies with metabolic/expression models
Authors: Liu, Joanne
Thesis
A novel approach to dynamic flux balance analysis that accounts for the dynamic transfer of information by internal metabolites
Iizuka, Kazuki · 2016
Full title: A novel approach to dynamic flux balance analysis that accounts for the dynamic transfer of information by internal metabolites
Authors: Iizuka, Kazuki
Thesis
Improved computational model of the malaria metabolic network and flux analysis for drug target prediction
Totanes, Francis Isidore Garcia · 2017
Full title: Improved computational model of the malaria metabolic network and flux analysis for drug target prediction
Authors: Totanes, Francis Isidore Garcia
Thesis
Validation of drug targets in malaria parasites predicted by metabolic modelling using CRISPR-Cas9
Taweechai, Supannee · 2018
Full title: Validation of drug targets in malaria parasites predicted by metabolic modelling using CRISPR-Cas9
Authors: Taweechai, Supannee
Thesis
Development of Machine Learning methods for the kinetic modelling of metabolic networks for biotechnological and biomedical applications
Choudhury, Subham · 2024
Full title: Development of Machine Learning methods for the kinetic modelling of metabolic networks for biotechnological and biomedical applications
Authors: Choudhury, Subham
Thesis
Multi-omics-driven kinetic modeling reveals metabolic vulnerabilities and differential drug-response dynamics in ovarian cancer
Toumpe, Ilias; Masid, Maria; Hatzimanikatis, Vassily et al. · 2025
Full title: Multi-omics-driven kinetic modeling reveals metabolic vulnerabilities and differential drug-response dynamics in ovarian cancer
Authors: Toumpe, Ilias; Masid, Maria; Hatzimanikatis, Vassily; Miskovic, Ljubisa
Thesis
Analysis of cellular and drug action mechanisms in the malaria parasites using systems biology approaches
Chiappino-Pepe, Anush · 2018
Full title: Analysis of cellular and drug action mechanisms in the malaria parasites using systems biology approaches
Authors: Chiappino-Pepe, Anush
Thesis
Computational studies of industrial hosts for improved production of the 2nd generation of biofuels
Tokic, Milenko · 2019
Full title: Computational studies of industrial hosts for improved production of the 2nd generation of biofuels
Authors: Tokic, Milenko
Thesis
Towards comprehensive and consistent kinetic models of metabolism under uncertainty
Hameri, Tuure Eelis · 2019
Full title: Towards comprehensive and consistent kinetic models of metabolism under uncertainty
Authors: Hameri, Tuure Eelis
Thesis
Genome-Scale Identification of Essential Metabolic Processes for Targeting the Plasmodium Liver Stage
Stanway, Rebecca R.; Bushell, Ellen; Chiappino-Pepe, Anush et al. · 2019
Full title: Genome-Scale Identification of Essential Metabolic Processes for Targeting the Plasmodium Liver Stage
Authors: Stanway, Rebecca R.; Bushell, Ellen; Chiappino-Pepe, Anush; Roques, Magali; Sanderson, Theo; Franke-Fayard, Blandine; Caldelari, Reto; Golomingi, Murielle; Nyonda, Mary; Pandey, Vikash; Schwach, Frank; Chevalley, Severine; Ramesar, Jai; Metcalf, Tom; Herd, Colin; Burda, Paul-Christian; Rayner, Julian C.; Soldati-Favre, Dominique; Janse, Chris J.; Hatzimanikatis, Vassily; Billker, Oliver; Heussler, Volker T.
Thesis
Optimization methods and objective functions for analysis of metabolic network models
Hosseini, Zhaleh · 2020
Full title: Optimization methods and objective functions for analysis of metabolic network models
Authors: Hosseini, Zhaleh
Thesis
Mapping and Analysis of the Complexity of Lipid Metabolism for Applications in Health and Sustainability
Tsouka, Sofia · 2020
Full title: Mapping and Analysis of the Complexity of Lipid Metabolism for Applications in Health and Sustainability
Authors: Tsouka, Sofia
Thesis
Modeling, analysis, and design of complex biological networks
Oftadeh, Mohammad Omid · 2023
Full title: Modeling, analysis, and design of complex biological networks
Authors: Oftadeh, Mohammad Omid
Thesis
Reconstruction and analysis of genome-scale metabolic networks in single organisms and microbial communities
Vagena, Evangelia · 2024
Full title: Reconstruction and analysis of genome-scale metabolic networks in single organisms and microbial communities
Authors: Vagena, Evangelia
Thesis
New and improved methods for integrated models of metabolism and gene expression
Salvy, Pierre Guy Rémy · 2021
Full title: New and improved methods for integrated models of metabolism and gene expression
Authors: Salvy, Pierre Guy Rémy
Thesis
Modelling the Intracellular Environment under Uncertainty, from Post-translational Modification to Metabolic Networks
Denhardt-Eriksson, Robin Alexander · 2021
Full title: Modelling the Intracellular Environment under Uncertainty, from Post-translational Modification to Metabolic Networks
Authors: Denhardt-Eriksson, Robin Alexander
Thesis
Reconstruction and systems analysis of metabolism in apicomplexan parasites Toxoplasma gondii and Plasmodium falciparum
Tymoshenko, Stepan · 2015
Full title: Reconstruction and systems analysis of metabolism in apicomplexan parasites Toxoplasma gondii and Plasmodium falciparum
Authors: Tymoshenko, Stepan
Thesis
Computational Studies on Cellular Metabolism : From Biochemical Pathways to Complex Metabolic Networks
Hadadi, Noushin · 2015
Full title: Computational Studies on Cellular Metabolism : From Biochemical Pathways to Complex Metabolic Networks
Authors: Hadadi, Noushin
Thesis
Navigating and Managing the Complexity of Genome Scale Metabolic Networks for Studies in Cellular Physiology and Industrial Biotechnology
Ataman, Meriç · 2016
Full title: Navigating and Managing the Complexity of Genome Scale Metabolic Networks for Studies in Cellular Physiology and Industrial Biotechnology
Authors: Ataman, Meriç
Thesis
Computational methods and modeling of cellular function for the optimization of protein production and the study of cellular disease states
Pinto Vieira, Joana Raquel · 2017
Full title: Computational methods and modeling of cellular function for the optimization of protein production and the study of cellular disease states
Authors: Pinto Vieira, Joana Raquel
Thesis
Development of a Theoretical Workflow for Metabolic Engineering and its Application to Terpenoid Production in Escherichia coli
Valderrama Gomez, Miguel Angel · 2018
Full title: Development of a Theoretical Workflow for Metabolic Engineering and its Application to Terpenoid Production in Escherichia coli
Authors: Valderrama Gomez, Miguel Angel
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
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
Thesis
Constraint-based analysis of substructures of metabolic networks
Marashi, Sayed-Amir · 2011
Full title: Constraint-based analysis of substructures of metabolic networks
Authors: Marashi, Sayed-Amir
Thesis
Mathematical Modeling of Metabolic-Genetic Networks
Ali Salem Eshtewy, Neveen · 2020
Full title: Mathematical Modeling of Metabolic-Genetic Networks
Authors: Ali Salem Eshtewy, Neveen
Thesis
New concepts and tools in constraint-based analysis of metabolic networks
Larhlimi, Abdelhalim · 2009
Full title: New concepts and tools in constraint-based analysis of metabolic networks
Authors: Larhlimi, Abdelhalim
Thesis
Unifying metabolic networks, regulatory constraints, and resource allocation
Liu, Lin · 2020
Full title: Unifying metabolic networks, regulatory constraints, and resource allocation
Authors: Liu, Lin
Thesis
Algorithms for the constraint-based analysis of metabolic networks
Dávid, László · 2015
Full title: Algorithms for the constraint-based analysis of metabolic networks
Authors: Dávid, László
Thesis
Fundamentals and application of metabolic engineering
Wong, Kelvin Wai Wah · 2006
Full title: Fundamentals and application of metabolic engineering
Authors: Wong, Kelvin Wai Wah
Thesis
Bioinformatics tools for cell modeling and metabolomics using Lactococcus lactis as a model organism
Aggio, Raphael · 2013
Full title: Bioinformatics tools for cell modeling and metabolomics using Lactococcus lactis as a model organism
Authors: Aggio, Raphael
Thesis
Reconstruction of linlog kinetics combining constraint-based and bayesian methodologies
Gotama, Michael · 2017
Full title: Reconstruction of linlog kinetics combining constraint-based and bayesian methodologies
Authors: Gotama, Michael
Thesis
Model-guided Analysis of Plant Metabolism and Design of Metabolic Engineering Strategies
Yen, Jiun Yang · 2018
Full title: Model-guided Analysis of Plant Metabolism and Design of Metabolic Engineering Strategies
Authors: Yen, Jiun Yang
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
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
Thesis
Computational Modeling of Planktonic and Biofilm Metabolism
Guo, Weihua · 2017
Full title: Computational Modeling of Planktonic and Biofilm Metabolism
Authors: Guo, Weihua
Thesis
Systems Biology in an Imperfect World: Modeling Biological Systems with Incomplete Information
Pokrzywa, Revonda Maria · 2014
Full title: Systems Biology in an Imperfect World: Modeling Biological Systems with Incomplete Information
Authors: Pokrzywa, Revonda Maria
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
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
Thesis
Computational methods for multi-omic models of cell metabolism and their importance for theoretical computer science
Angione, Claudio · 2015
Full title: Computational methods for multi-omic models of cell metabolism and their importance for theoretical computer science
Authors: Angione, Claudio
Thesis
Systems metabolic engineering of Arabidopsis for increased cellulose production
Yen, Jiun Yang · 2015
Full title: Systems metabolic engineering of Arabidopsis for increased cellulose production
Authors: Yen, Jiun Yang
Thesis
Systems metabolic engineering through application of genome-scale metabolic flux modeling
Nazem Bokaee, Hadi · 2015
Full title: Systems metabolic engineering through application of genome-scale metabolic flux modeling
Authors: Nazem Bokaee, Hadi
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