Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0
Schellenberger, Jan, Que, Richard, Fleming, Ronan M T, Thiele, Ines, Orth, Jeffrey D, Feist, Adam M, Zielinski, Daniel C, Bordbar, Aarash +5 more·2011·Nature Protocols
Cited by (1,002)
Items 201–300 of 1,002
- Integration of single-cell RNA-seq data into population models to characterize cancer metabolismChiara Damiani, Davide Maspero, Marzia Di Filippo, Riccardo Colombo, Dario Pescini, Alex Graudenzi, Hans Victor Westerhoff, Lilia Alberghina, Marco Vanoni, Giancarlo Mauri · 2019 · PLoS Computational Biology
- Genome-scale modeling for metabolic engineeringEvangelos Simeonidis, Nathan D. Price · 2015 · Journal of Industrial Microbiology & Biotechnology
- A metabolic core model elucidates how enhanced utilization of glucose and glutamine, with enhanced glutamine-dependent lactate production, promotes cancer cell growth: The WarburQ effectChiara Damiani, Riccardo Colombo, Daniela Gaglio, Fabrizia Mastroianni, Dario Pescini, Hans Victor Westerhoff, Giancarlo Mauri, Marco Vanoni, Lilia Alberghina · 2017 · PLoS Computational Biology
- TIGER: Toolbox for integrating genome-scale metabolic models, expression data, and transcriptional regulatory networksPaul A. Jensen, Kyla Lutz, Jason A. Papin · 2011 · BMC Systems Biology
- iAB-RBC-283: A proteomically derived knowledge-base of erythrocyte metabolism that can be used to simulate its physiological and patho-physiological statesAarash Bordbar, Neema Jamshidi, Bernhard Ørn Palsson · 2011 · BMC Systems Biology
- Further developments towards a genome-scale metabolic model of yeastPaul D. Dobson, Kieran Smallbone A B, Daniel Jameson, Evangelos Simeonidis, Karin Lanthaler, Pınar Pir, Chuan Lü, Neil Swainston, Warwick B. Dunn, Paul Fisher et al. · 2010 · BMC Systems Biology
- Metabolic flux analysis and pharmaceutical productionBrett A. Boghigian, Gargi Seth, Robert Kiss, Blaine A. Pfeifer · 2009 · Metabolic Engineering
- A genome-scale metabolic model of Saccharomyces cerevisiae that integrates expression constraints and reaction thermodynamicsOftadeh, Omid, Salvy, Pierre, Masid, Maria, Curvat, Maxime, Miskovic, Ljubisa, Hatzimanikatis, Vassily · 2021 · Nature Communications
- Multiscale Modeling of Metabolism and Macromolecular Synthesis in E. coli and Its Application to the Evolution of Codon UsageInes Thiele, Ronan M. T. Fleming, Richard A. Que, Aarash Bordbar, Dinh H. Diep, Bernhard Ørn Palsson · 2012 · PLoS ONE
- An introduction to the maximum entropy approach and its application to inference problems in biologyAndrea De Martino, Daniele De Martino · 2018 · Heliyon
- Functional and Computational Genomics Reveal Unprecedented Flexibility in Stage-Specific Toxoplasma MetabolismAarti Krishnan, Joachim Kloehn, Matteo Lunghi, Anush Chiappino-Pepe, Benjamin S. Waldman, Damien Nicolas, Emmanuel Varesio, Adrian B. Hehl, Sebastian Lourido, Vassily Hatzimanikatis A et al. · 2020 · Cell Host & Microbe
- Metabolic network reconstruction and genome-scale model of butanol-producing strain Clostridium beijerinckii NCIMB 8052Caroline B. Milne, James A. Eddy, Ravali Raju, Soroush Ardekani, Pan‐Jun Kim, Ryan S. Senger, Yong‐Su Jin, Hans Peter Blaschek, Nathan D. Price · 2011 · BMC Systems Biology
- Recent Advances, Challenges, and Opportunities in Bioremediation of Hazardous MaterialsRobert Ramirez-Garcia, Nisarg Gohil, Vijai Singh · 2018 · Elsevier eBooks
- Emergence of microbial diversity due to cross-feeding interactions in a spatial model of gut microbial metabolismMilan J. A. Hoek, Roeland M. H. Merks · 2017 · BMC Systems Biology
- A retrosynthetic biology approach to metabolic pathway design for therapeutic productionPablo Carbonell, Anne‐Gaëlle Planson, Davide Fichera, Jean‐Loup Faulon · 2011 · BMC Systems Biology
- Spatially-resolved metabolic cooperativity within dense bacterial coloniesJohn A. Cole, Lars Kohler, Jamila Hedhli, Zaida Ann Luthey-Schulten · 2015 · BMC Systems Biology
- Applications of genome-scale metabolic network model in metabolic engineeringByoung‐Jin Kim, Won Jun Kim, Dong In Kim, Sang Yup Lee · 2014 · Journal of Industrial Microbiology & Biotechnology
- Systematic prediction of health-relevant human-microbial co-metabolism through a computational frameworkAlmut Heinken, Ines Thiele · 2015 · Gut Microbes
- A systems-level approach for metabolic engineering of yeast cell factoriesIl‐Kwon Kim, António Roldão, Verena Siewers, Jens Nielsen · 2011 · FEMS Yeast Research
- The ETFL formulation allows multi-omics integration in thermodynamics-compliant metabolism and expression modelsPierre Salvy, Vassily Hatzimanikatis A · 2020 · Nature Communications
- Analytics for Metabolic EngineeringChristopher J. Petzold, Leanne Jade G. Chan, Melissa Nhan, Paul D. Adams · 2015 · Frontiers in Bioengineering and Biotechnology
- Software applications for flux balance analysisMeiyappan Lakshmanan, Gerald Choon‐Huat Koh, Bevan Kai-Sheng Chung, Dong‐Yup Lee · 2012 · Briefings in Bioinformatics
- Metabolic modeling and analysis of the metabolic switch in Streptomyces coelicolorMohammad Tauqeer Alam, Maria Elena Merlo, David A. Hodgson, Elizabeth M. H. Wellington, Eriko Takano A, Rainer Breitling A · 2010 · BMC Genomics
- Mammalian Systems Biotechnology Reveals Global Cellular Adaptations in a Recombinant CHO Cell LineFaraaz N.K. Yusufi, Meiyappan Lakshmanan, Ying Swan Ho, Bernard Liat Wen Loo, Pramila Nuwantha Ariyaratne, Yuansheng Yang, Say Kong Ng, Tessa Rui Min Tan, Hock Chuan Yeo, Hsueh Lee Lim et al. · 2017 · Cell Systems
- A new genome-scale metabolic model of Corynebacterium glutamicum and its applicationYu Zhang, Jingyi Cai, Xiuling Shang, Bo Wang, Shuwen Liu, Xin Chai, Tianwei Tan, Yun Zhang, Tingyi Wen · 2017 · Biotechnology for Biofuels
- Systems assessment of transcriptional regulation on central carbon metabolism by Cra and CRPDonghyuk Kim, Sang Woo Seo, Ye Gao, Hojung Nam, Gabriela I. Guzmán, Byung‐Kwan Cho, Bernhard Ørn Palsson · 2018 · Nucleic Acids Research
- Membrane transporters in a human genome-scale metabolic knowledgebase and their implications for diseaseSwagatika Sahoo, Maike Kathrin Aurich, Jón J. Jónsson, Ines Thiele · 2014 · Frontiers in Physiology
- The Mycobacterium tuberculosis Drugome and Its Polypharmacological ImplicationsSarah Kinnings, Li Xie, Kingston H. Fung, Richard M. Jackson, Lei Xie, Philip E. Bourne · 2010 · PLoS Computational Biology
- Metabolic engineering of Saccharomyces cerevisiae for itaconic acid productionJohn Blazeck, Jarrett Miller, Anny Pan, Jon Gengler, Clinton Holden, Mariam Jamoussi, Hal S. Alper · 2014 · Applied Microbiology and Biotechnology
- Version 6 of the consensus yeast metabolic network refines biochemical coverage and improves model performanceBen Heavner, Kieran Smallbone A B, Nathan D. Price, Larry P. Walker · 2013 · Database
- Low Concentrations of Vitamin C Reduce the Synthesis of Extracellular Polymers and Destabilize Bacterial BiofilmsSantosh Pandit, Vaishnavi Ravikumar, Alyaa M. Abdel‐Haleem, Abderahmane Derouiche, Venkata R. S. S. Mokkapati, Carina Sihlbom, Katsuhiko Mineta, Takashi Gojobori, Xin Gao, Fredrik Westerlund et al. · 2017 · Frontiers in Microbiology
- A Review of Dynamic Modeling Approaches and Their Application in Computational Strain Optimization for Metabolic EngineeringOsvaldo D. Kim, Miguel Rocha, Paulo Maia · 2018 · Frontiers in Microbiology
- Systems biology of host–microbe metabolomicsAlmut Heinken, Ines Thiele · 2015 · WIREs Systems Biology and Medicine
- BioMet Toolbox: genome-wide analysis of metabolismMarija Cvijović, Roberto Olivares‐Hernández, Rasmus Ågren, N. Dahr, Wanwipa Vongsangnak, Intawat Nookaew, Kiran Raosaheb Patil, Jens Nielsen · 2010 · Nucleic Acids Research
- Fine-tuning citrate synthase flux potentiates and refines metabolic innovation in the Lenski evolution experimentErik M. Quandt, Jimmy Gollihar, Zachary D. Blount, Andrew D. Ellington, George Georgiou, Jeffrey E. Barrick · 2015 · eLife
- Metabolic network analysis integrated with transcript verification for sequenced genomesAni W Manichaikul, Lila Ghamsari, Erik F. Y. Hom, Chenwei Lin, Ryan R. Murray, Roger L. Chang, S Balaji, Tong Hao, Yun Shen, Arvind K. Chavali et al. · 2009 · Nature Methods
- Computational tools for metabolic engineeringWilbert B. Copeland, Bryan Bartley, Deepak Chandran, Michal Galdzicki, Kyung H. Kim, Sean C. Sleight, Costas D. Maranas, Herbert M. Sauro · 2012 · Metabolic Engineering
- Genome-scale metabolic reconstructions of Bifidobacterium adolescentis L2-32 and Faecalibacterium prausnitzii A2-165 and their interactionIbrahim E. Elsemman, Fredrik H. Karlsson, Saeed Shoaie, Intawat Nookaew, Taysir Hassan A. Soliman, Jens Nielsen · 2014 · BMC Systems Biology
- Metabolic engineering for enhancing microbial biosynthesis of advanced biofuelsManali Das, Pradipta Patra, Amit Ghosh · 2019 · Renewable and Sustainable Energy Reviews
- Synthetic microbial communities of heterotrophs and phototrophs facilitate sustainable growthCristal Zúñiga, Tingting Li, Michael Thomas Guarnieri, Jackson P. Jenkins, Chien‐Ting Li, Kerem Bingol, Young‐Mo Kim, Michael J. Betenbaugh, Karsten Zengler · 2020 · Nature Communications
- Metage2Metabo, microbiota-scale metabolic complementarity for the identification of key speciesArnaud Belcour, Clémence Frioux, Méziane Aïte, Anthony Bretaudeau, Falk Hildebrand, Anne Siegel · 2020 · eLife
- Laboratory Evolution to Alternating Substrate Environments Yields Distinct Phenotypic and Genetic Adaptive StrategiesTroy E. Sandberg, Colton J. Lloyd, Bernhard Ørn Palsson, Adam M. Feist · 2017 · Applied and Environmental Microbiology
- Identification of a critical determinant that enables efficient fatty acid synthesis in oleaginous fungiHaiqin Chen, Guangfei Hao, Lei Wang, Hongchao Wang, Zhennan Gu, Li Liu, Hao Zhang, Wei Chen, Yong Q. Chen · 2015 · Scientific Reports
- Improved Triacylglycerol Production in Acinetobacter baylyi ADP1 by Metabolic EngineeringSuvi Santala, Elena Efimova, Virpi Kivinen, Antti Larjo, Tommi Aho, Matti Tapani Karp, Ville P. Santala · 2011 · Microbial Cell Factories
- Computational systems biology and in silico modeling of the human microbiomeElhanan Borenstein · 2012 · Briefings in Bioinformatics
- Construction and completion of flux balance models from pathway databasesMario Latendresse, Markus Krummenacker, Miles Trupp, Peter D. Karp · 2012 · Bioinformatics
- Identified metabolic signature for assessing red blood cell unit quality is associated with endothelial damage markers and clinical outcomesAarash Bordbar, Pär I. Johansson, Giuseppe Paglia, Scott James Harrison, Kristine Wichuk, Manuela Magnúsdóttir, Sóley Valgeirsdóttir, Mikkel Gybel‐Brask, Sisse Rye Ostrowski, Sirus Palsson et al. · 2016 · Transfusion
- Metabolic model of Synechococcus sp. PCC 7002: Prediction of flux distribution and network modification for enhanced biofuel productionJohn I. Hendry, Charulata B. Prasannan, Aditi A. Joshi, Santanu Dasgupta, Pramod P. Wangikar · 2016 · Bioresource Technology
- Standardizing biomass reactions and ensuring complete mass balance in genome-scale metabolic modelsSiu Hung Joshua Chan, Jingyi Cai, Lin Wang, Margaret Simons, Costas D. Maranas · 2017 · Bioinformatics
- Genome-scale metabolic reconstruction of the symbiosis between a leguminous plant and a nitrogen-fixing bacteriumGeorge Colin diCenzo, Michelangelo Tesi, Thomas Pfau, Alessio Mengoni, Marco Fondi · 2020 · Nature Communications
- Computational modeling of metabolism in microbial communities on a genome-scaleAnaleigha V. Colarusso, Isabella M. Goodchild-Michelman, Maya Rayle, Ali R. Zomorrodi · 2021 · Current Opinion in Systems Biology
- pyTFA and matTFA: a Python package and a Matlab toolbox for Thermodynamics-based Flux AnalysisPierre Salvy, Georgios Fengos, Meriç Ataman, Thomas Pathier, Keng Cher Soh, Vassily Hatzimanikatis A · 2018 · Bioinformatics
- Dynamic flux balance analysis for synthetic microbial communitiesMichael A. Henson, Timothy J. Hanly · 2014 · IET Systems Biology
- High Production of 3-Hydroxypropionic Acid in Klebsiella pneumoniae by Systematic Optimization of Glycerol MetabolismYing Li, Xi Wang, Xizhen Ge, Pingfang Tian · 2016 · Scientific Reports
- Multidisciplinary approaches for studying rhizobium–legume symbiosesGeorge Colin diCenzo, Maryam Zamani, Alice Checcucci, Marco Fondi, Joel S. Griffitts, Turlough M. Finan, Alessio Mengoni · 2018 · Canadian Journal of Microbiology
- Co-Regulation of Metabolic Genes Is Better Explained by Flux Coupling Than by Network DistanceRichard A. Notebaart, Bas Teusink, Roland J. Siezen, Balázs Papp · 2008 · PLoS Computational Biology
- A Markov chain model for N-linked protein glycosylation – towards a low-parameter tool for model-driven glycoengineeringPhilipp N. Spahn, Anders Holmgaard Hansen, Henning Gram Hansen, Johnny Arnsdorf, Helene Faustrup Kildegaard, Nathan E. Lewis · 2015 · Metabolic Engineering
- Personalized Whole-Cell Kinetic Models of Metabolism for Discovery in Genomics and PharmacodynamicsAarash Bordbar, Douglas McCloskey, Daniel Craig Zielinski, Nikolaus Sonnenschein, Neema Jamshidi, Bernhard Ørn Palsson · 2015 · Cell Systems
- A workflow for generating multi-strain genome-scale metabolic models of prokaryotesCharles J. Norsigian, Xin De Fang, Yara Seif, Jonathan M. Monk, Bernhard Ørn Palsson · 2019 · Nature Protocols
- Networks and Graphs Discovery in Metabolomics Data Analysis and InterpretationAdam Amara, Clément Frainay, Fabien Jourdan, Thomas Naake, Steffen Neumann, Elva María Novoa‐del‐Toro, Reza M. Salek, Liesa Salzer, Sarah Scharfenberg, Michael A. Witting · 2022 · Frontiers in Molecular Biosciences
- Unpredictability of metabolism—the key role of metabolomics science in combination with next-generation genome sequencingWolfram Weckwerth · 2011 · Analytical and Bioanalytical Chemistry
- CHRR: coordinate hit-and-run with rounding for uniform sampling of constraint-based modelsHulda S. Haraldsdóttir, Ben Cousins, Ines Thiele, Ronan M. T. Fleming, Santosh Vempala · 2017 · Bioinformatics
- Heterogeneity in protein expression induces metabolic variability in a modeled
<i>Escherichia coli</i>
populationLabhsetwar, Piyush, Cole, John Andrew, Roberts, Elijah, Price, Nathan D., Luthey-Schulten, Zaida A. · 2013 · Proceedings of the National Academy of Sciences
- Diversity, Function, and Application of Clostridium in Chinese Strong Flavor Baijiu Ecosystem: A ReviewWei Zou, Guangbin Ye, Kaizheng Zhang · 2018 · Journal of Food Science
- Generalized framework for context-specific metabolic model extraction methodsSemidán Robaina‐Estévez, Zoran Nikoloski · 2014 · Frontiers in Plant Science
- Systems biology of yeast: enabling technology for development of cell factories for production of advanced biofuelsBouke Wim de Jong, Verena Siewers, Jens Nielsen · 2011 · Current Opinion in Biotechnology
- Shrinking the Metabolic Solution Space Using Experimental DatasetsJennifer L. Reed · 2012 · PLoS Computational Biology
- Use of CellNetAnalyzer in biotechnology and metabolic engineeringAxel von Kamp, Sven Thiele, Oliver Hädicke, Steffen Klamt · 2017 · Journal of Biotechnology
- Metabolic systems biologyBernhard Ørn Palsson · 2009 · FEBS Letters
- Dissecting the energy metabolism in Mycoplasma pneumoniae through genome-scale metabolic modelingWodke, Judith A H, Puchałka, Jacek, Lluch‐Senar, Maria, Marcos, Josep, Yus, Eva, Godinho, Miguel, Gutiérrez‐Gallego, Ricardo, dos Santos, Vitor A P Martins, Serrano, Luis, Klipp, Edda et al. · 2013 · Molecular Systems Biology
- Fine‐tuning the P. pastoris iMT1026 genome‐scale metabolic model for improved prediction of growth on methanol or glycerol as sole carbon sourcesMàrius Tomàs‐Gamisans, Pau Ferrer, Joan Albiol · 2017 · Microbial Biotechnology
- Metabolic engineering of Saccharomyces cerevisiae for the production of triacetic acid lactoneJavier Cárdenas, Nancy A. Da Silva · 2014 · Metabolic Engineering
- Reconstruction and In Silico Analysis of Metabolic Network for an Oleaginous Yeast, Yarrowia lipolyticaPengcheng Pan, Qiang Hua · 2012 · PLoS ONE
- Uncoupling of mucosal gene regulation, mRNA splicing and adherent microbiota signatures in inflammatory bowel diseaseRobert Häsler, Raheleh Sheibani‐Tezerji, Anupam N. Sinha, Matthias Barann, Ateequr Rehman, Daniela Esser, Konrad Aden, Carolin Knecht, Berenice Brandt, Susanna Nikolaus et al. · 2016 · Gut
- FAME, the Flux Analysis and Modeling EnvironmentJoost Boele, Brett G. Olivier, Bas Teusink · 2012 · BMC Systems Biology
- Metabolic Network Analysis of Pseudomonas aeruginosa during Chronic Cystic Fibrosis Lung InfectionMatthew Oberhardt, Joanna B. Goldberg, Michael Hogardt, Jason A. Papin · 2010 · Journal of Bacteriology
- Computational metabolic engineering strategies for growth-coupled biofuel production by SynechocystisKiyan Shabestary, Elton Paul Hudson · 2016 · Metabolic Engineering Communications
- Algal Cell Factories: Approaches, Applications, and PotentialsWeiqi Fu, Amphun Chaiboonchoe, Basel Khraiwesh, David Roy Nelson, Dina Al-Khairy, Alexandra Mystikou, Amnah Salem Alzahmi, Kourosh Salehi‐Ashtiani · 2016 · Marine Drugs
- Reconstruction and Validation of a Genome-Scale Metabolic Model for the Filamentous Fungus Neurospora crassa Using FARMJonathan M. Dreyfuss, Jeremy Zucker, Heather M. Hood, Linda R. Ocasio, Matthew S. Sachs, James E. Galagan · 2013 · PLoS Computational Biology
- RELATCH: relative optimality in metabolic networks explains robust metabolic and regulatory responses to perturbationsJoonhoon Kim, Jennifer L. Reed · 2012 · Genome biology
- Targeted Repression of Essential Genes To Arrest Growth and Increase Carbon Partitioning and Biofuel Titers in CyanobacteriaKiyan Shabestary, Josefine Anfelt, Emil Ljungqvist, Michael Jahn, Lun Yao, Elton Paul Hudson · 2018 · ACS Synthetic Biology
- Use of genome‐scale metabolic models for understanding microbial physiologyLi Liu, Rasmus Ågren, Sergio Bordel, Jens Nielsen · 2010 · FEBS Letters
- Gut bacteria responding to dietary change encode sialidases that exhibit preference for red meat-associated carbohydratesLivia Soares Zaramela, Cameron Martino, Frederico Alisson‐Silva, Steven D. Rees, Sandra L. Diaz, Léa Chuzel, Mehul B. Ganatra, Christopher H. Taron, Patrick Secrest, Cristal Zúñiga et al. · 2019 · Nature Microbiology
- Environmental stimuli drive a transition from cooperation to competition in synthetic phototrophic communitiesCristal Zúñiga, Chien‐Ting Li, Geng Yu, Mahmoud M. Al‐Bassam, Tingting Li, Liqun Jiang, Livia Soares Zaramela, Michael Thomas Guarnieri, Michael J. Betenbaugh, Karsten Zengler · 2019 · Nature Microbiology
- Long-term phenotypic evolution of bacteriaGermán Plata, Christopher S. Henry, Dennis Vitkup · 2014 · Nature
- Reconstruction and analysis of a genome-scale metabolic model of the oleaginous fungus Mortierella alpinaChao Ye, Nan Xu, Haiqin Chen, Yong Q. Chen, Wei Chen, Li Liu · 2015 · BMC Systems Biology
- Critical assessment of genome-scale metabolic networks: the need for a unified standardRavikrishnan, A., Raman, K. · 2015 · Briefings in Bioinformatics
- The metabolic background is a global player in Saccharomyces gene expression epistasisMohammad Tauqeer Alam, Aleksej Zelezniak, Michael Mülleder, Pavel V. Shliaha, Roland F. Schwarz, Floriana Capuano, Jakob Vowinckel, Elahe Radmaneshfar, Antje Krüger, Enrica Calvani et al. · 2016 · Nature Microbiology
- Human Systems Biology and Metabolic Modelling: A Review—From Disease Metabolism to Precision MedicineClaudio Angione · 2019 · BioMed Research International
- History and Future Perspectives on the Discipline of Quantitative Systems Pharmacology Modeling and Its ApplicationsKarim Azer, Chanchala D. Kaddi, Jeffrey S. Barrett, Jane P. F. Bai, Sean T. McQuade, Nathaniel J. Merrill, Benedetto Piccoli, Susana R. Neves, Luca Marchetti, Rosario Lombardo et al. · 2021 · Frontiers in Physiology
- Network analysis identifies Rv0324 and Rv0880 as regulators of bedaquiline tolerance in Mycobacterium tuberculosisEliza J. R. Peterson, Shuyi Ma, David R. Sherman, Nitin S. Baliga · 2016 · Nature Microbiology
- Metabolic Modeling of Human Gut Microbiota on a Genome Scale: An OverviewPartho Sen, Matej Orešič · 2019 · Metabolites
- Plasma and urinary metabolomic profiles of Down syndrome correlate with alteration of mitochondrial metabolismCaracausi, Maria, Ghini, Veronica, Locatelli, Chiara, Mericio, Martina, Piovesan, Allison, Antonaros, Francesca, Pelleri, Maria Chiara, Vitale, Lorenza, Vacca, Rosa Anna, Bedetti, Federica et al. · 2018 · Scientific Reports
- Metabolic modelling reveals the specialization of secondary replicons for niche adaptation in Sinorhizobium melilotiGeorge Colin diCenzo, Alice Checcucci, Marco Bazzicalupo, Alessio Mengoni, Carlo Viti, Łukasz Dziewit, Turlough M. Finan, Marco Galardini, Marco Fondi · 2016 · Nature Communications
- Metabolism of the fast-growing bacterium Vibrio natriegens elucidated by 13C metabolic flux analysisChristopher P. Long, Jacqueline E. Gonzalez, Robert M. Cipolla, Maciek R. Antoniewicz · 2017 · Metabolic Engineering
- Understanding the Representative Gut Microbiota Dysbiosis in Metformin-Treated Type 2 Diabetes Patients Using Genome-Scale Metabolic ModelingDorinês Rosário, Rui Benfeitas, Gholamreza Bidkhori, Cheng Zhang, Mathias Uhlén, Saeed Shoaie, Adil Mardinoğlu · 2018 · Frontiers in Physiology
- Reconstructing Kinetic Models for Dynamical Studies of Metabolism using Generative Adversarial NetworksSubham Choudhury, Michael Moret, Pierre Salvy, Daniel R. Weilandt, V. Hatzimanikatis, L. Miskovic · 2022 · Nature Machine Intelligence
- Why Is the Correlation between Gene Importance and Gene Evolutionary Rate So Weak?Zhi Wang, Jianzhi Zhang · 2009 · PLoS Genetics
- Novel Multiscale Modeling Tool Applied to Pseudomonas aeruginosa Biofilm FormationMatthew B. Biggs, Jason A. Papin · 2013 · PLoS ONE
- Likelihood-Based Gene Annotations for Gap Filling and Quality Assessment in Genome-Scale Metabolic ModelsMatthew N. Benedict, Michael B. Mundy, Christopher S. Henry, Nicholas Chia, Nathan D. Price · 2014 · PLoS Computational Biology