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 601–700 of 1,002

  1. Proteomics and Systems Biology: Current and Future Applications in the Nutritional Sciences
    J. Bernadette Moore, Mark E. Weeks · 2011 · Advances in Nutrition
  2. Genome sequencing and biodegradation characteristics of the n-butyl benzyl phthalate degrading bacterium-Rhodococcus sp. HS-D2
    Yunze Zhang, Huxing Chen, Jiamei Liu, Ge Geng, Deli Liu, Hui Geng, Xiong Li · 2016 · International Biodeterioration & Biodegradation
  3. Comprehensive reconstruction and in silico analysis of Aspergillus niger genome‐scale metabolic network model that accounts for 1210 ORFs
    Hongzhong Lu, Weiqiang Cao, Liming Ouyang, Jianye Xia, Mingzhi Huang, Ju Chu, Yingping Zhuang, Siliang Zhang, Henk J. Noorman · 2016 · Biotechnology and Bioengineering
  4. Integrated Regulatory and Metabolic Networks of the Marine Diatom Phaeodactylum tricornutum Predict the Response to Rising CO 2 Levels
    Jennifer Levering, Christopher L. Dupont, Andrew Ellis Allen, Bernhard Ørn Palsson, Karsten Zengler · 2017 · mSystems
  5. Metabolic systems analysis of LPS induced endothelial dysfunction applied to sepsis patient stratification
    Sarah McGarrity, Ósk Anuforo, Haraldur Halldórsson, Andreas Bergmann, Skarphéðinn Halldórsson, Sirus Palsson, H Henriksen, Pär I. Johansson, Óttar Rolfsson · 2018 · Scientific Reports
  6. Integration of large-scale data for extraction of integrated Arabidopsis root cell-type specific models
    Michael Scheunemann, Siobhán M. Brady, Zoran Nikoloski · 2018 · Scientific Reports
  7. A genome-scale metabolic model of potato late blight suggests a photosynthesis suppression mechanism
    Kelly Botero, Silvia Restrepo, Andrés Mauricio Pinzón · 2018 · BMC Genomics
  8. Plasma metabolome and cognitive skills in Down syndrome
    Francesca Antonaros, Veronica Ghini, Francesca Pulina, Giuseppe Ramacieri, Elena Cicchini, Elisa Mannini, Anna Martelli, Agnese Feliciello, Silvia Lanfranchi, Sara Onnivello et al. · 2020 · Scientific Reports
  9. Counting and Correcting Thermodynamically Infeasible Flux Cycles in Genome-Scale Metabolic Networks
    Daniele De Martino, Fabrizio Capuani, Matteo Mori, Andrea De Martino, Enzo Marinari · 2013
  10. Using Flux Balance Analysis to Guide Microbial Metabolic Engineering
    Kathleen A. Curran, Nathan Crook, Hal S. Alper · 2011 · Methods in molecular biology
  11. A Systems-Level Approach for Investigating Pseudomonas aeruginosa Biofilm Formation
    Zhaobin Xu, Xin De Fang, Thomas Keith Wood, Zuyi Jacky Huang · 2013 · PLoS ONE
  12. A genome‐scale metabolic reconstruction of soybean and Bradyrhizobium diazoefficiens reveals the cost–benefit of nitrogen fixation
    Bethany L Holland, Megan L. Matthews, Pedro Bota, Lee James Sweetlove, Stephen P. Long, George Colin diCenzo · 2023 · New Phytologist
  13. Probabilistic pathway construction
    Mona Yousofshahi, Kyongbum Lee, Soha Hassoun · 2011 · Metabolic Engineering
  14. Prediction of metabolic pathways from genome-scale metabolic networks
    Karoline Faust, Didier Croes, Jacques van Helden · 2011 · Biosystems
  15. Counting and Correcting Thermodynamically Infeasible Flux Cycles in Genome-Scale Metabolic Networks
    Daniele De Martino, Fabrizio Capuani, Matteo Mori, Andrea De Martino, Enzo Marinari · 2013 · Metabolites
  16. Genome-scale reconstruction and in silico analysis of Aspergillus terreus metabolism
    Jie Liu, Qian Gao, Nan Xu, Li Liu · 2013 · Molecular BioSystems
  17. Logical transformation of genome-scale metabolic models for gene level applications and analysis
    Cheng Zhang, Boyang Ji, Adil Mardinoğlu, Jens Nielsen, Qiang Hua · 2015 · Bioinformatics
  18. A curated C. difficile strain 630 metabolic network: prediction of essential targets and inhibitors
    Mathieu Larocque, Thierry Chénard, Rafaël Najmanovich · 2014 · BMC Systems Biology
  19. Not just a colourful metaphor: modelling the landscape of cellular development using Hopfield networks
    Atefeh Taherian Fard, Sriganesh Srihari, Jessica C. Mar, Mark A. Ragan · 2016 · npj Systems Biology and Applications
  20. Enhancing fatty acid production in Escherichia coli by Vitreoscilla hemoglobin overexpression
    Di Liu, Ni Wan, Fuzhong Zhang, Yinjie Tang, Stephen Gang Wu · 2016 · Biotechnology and Bioengineering
  21. Reliable and efficient solution of genome-scale models of Metabolism and macromolecular Expression
    Ding Ma, Laurence Yang, Ronan M. T. Fleming, Ines Thiele, Bernhard Ørn Palsson, Michael A. Saunders · 2017 · Scientific Reports
  22. Kinetic modeling of the Calvin cycle identifies flux control and stable metabolomes in Synechocystis carbon fixation
    Markus Janasch, Johannes Asplund‐Samuelsson, Ralf Steuer, Elton Paul Hudson · 2018 · Journal of Experimental Botany
  23. Closing the gap between formats for storing layout information in systems biology
    D. Hoksza, P. Gawron, M. Ostaszewski, J. Hasenauer, Reinhard Schneider · 2019 · Briefings in Bioinformatics
  24. Metabolic Systems Analysis of Shock-Induced Endotheliopathy (SHINE) in Trauma
    H Henriksen, Sarah McGarrity, Rósa Sólveig Sigurðardóttir, Travis G. Nemkov, Angelo D’Alessandro, Bernhard Ørn Palsson, Jakob Stensballe, Charles E. Wade, Óttar Rolfsson, Pär I. Johansson · 2019 · Annals of Surgery
  25. Influence of the Crc global regulator on substrate uptake rates and the distribution of metabolic fluxes in Pseudomonas putida KT2440 growing in a complete medium
    Lázaro Molina, Ruggero La Rosa, Juan Nogales, Fernando Rojo · 2019 · Environmental Microbiology
  26. Improvement of Acetaldehyde Production in Zymomonas mobilis by Engineering of Its Aerobic Metabolism
    Uldis Kalnenieks, Elīna Balodīte, Steffi Strähler, Inese Strazdiņa, Julia Rex, Agris Pentjuss, Katsuya Fuchino, Per Bruheim, Reinis Rutkis, Katherine M. Pappas et al. · 2019 · Frontiers in Microbiology
  27. A comparison of Monte Carlo sampling methods for metabolic network models
    Shirin Fallahi, Hans Julius Skaug, Guttorm Alendal · 2020 · PLoS ONE
  28. MASSpy: Building, simulating, and visualizing dynamic biological models in Python using mass action kinetics
    Zachary B. Haiman, Daniel Craig Zielinski, Yuko Koike, James T. Yurkovich, Bernhard Ørn Palsson · 2021 · PLoS Computational Biology
  29. Engineering Bacteroides thetaiotaomicron to produce non-native butyrate based on a genome-scale metabolic model-guided design
    Kangsan Kim, Donghui Choe, Yoseb Song, Minjeong Kang, Seung‐Goo Lee, Dae‐Hee Lee, Byung‐Kwan Cho · 2021 · Metabolic Engineering
  30. Microbe-Plant Interactions Targeting Metal Stress: New Dimensions for Bioremediation Applications
    Baljeet Singh Saharan, Twinkle Chaudhary, Balwan Singh Mandal, Dharmender Kumar, Ravinder Kumar, Pardeep Kumar Sadh, Joginder Singh Duhan · 2023 · Journal of Xenobiotics
  31. Flux balance analysis-based metabolic modeling of microbial secondary metabolism: Current status and outlook
    Sizhe Qiu, Aidong Yang, Hong Zeng · 2023 · PLoS Computational Biology
  32. In silico analysis and experimental improvement of taxadiene heterologous biosynthesis in Escherichia coli
    Hailin Meng, Yong Wang, Qiang Hua, Siliang Zhang, Xiao‐Ning Wang · 2011 · Biotechnology and Bioprocess Engineering
  33. Systems biotechnology of animal cells: the road to prediction
    Nuno Carinhas, Rui Oliveira, Paula M. Alves, Manuel J.T. Carrondo, Ana P. Teixeira · 2012 · Trends in biotechnology
  34. Construction of robust dynamic genome-scale metabolic model structures of Saccharomyces cerevisiae through iterative re-parameterization
    Benjamín J. Sánchez, José Ricardo Pérez‐Correa, Eduardo E. Agosin · 2014 · Metabolic Engineering
  35. Reconstruction and analysis of a genome-scale metabolic model of the vitamin C producing industrial strain Ketogulonicigenium vulgare WSH-001
    Wei Zou, Li Liu, Jing Zhang, Haoru Yang, Maoda Zhou, Qiang Hua, Jian Chen · 2012 · Journal of Biotechnology
  36. Genome‐wide characterization of Phytophthora infestans metabolism: a systems biology approach
    Sander Y.A. Rodenburg, Michael F. Seidl, Dick de Ridder, Francine Govers · 2017 · Molecular Plant Pathology
  37. Integration of genome-scale metabolic networks into whole-body PBPK models shows phenotype-specific cases of drug-induced metabolic perturbation
    Henrik Cordes, Christoph Thiel, Vanessa Baier, Lars M. Blank, Lars Kuepfer · 2018 · npj Systems Biology and Applications
  38. Modular systems metabolic engineering enables balancing of relevant pathways for l-histidine production with Corynebacterium glutamicum
    Andreas Schwentner, André Feith, Eugenia Münch, Judith Stiefelmaier, Ira Lauer, Lorenzo Favilli, Christoph Massner, Johannes Öhrlein, B. Grund, Andrea T. Hüser et al. · 2019 · Biotechnology for Biofuels
  39. Kinetic models of metabolism that consider alternative steady-state solutions of intracellular fluxes and concentrations
    Hameri Tuure, Georgios Fengos, Meriç Ataman, Ljubiša Mišković, Vassily Hatzimanikatis A · 2018 · Metabolic Engineering
  40. Novel Plasmodium falciparum metabolic network reconstruction identifies shifts associated with clinical antimalarial resistance
    Maureen A. Carey, Jason A. Papin, Jennifer L. Güler · 2017 · BMC Genomics
  41. Utilizing genome-scale models to optimize nutrient supply for sustained algal growth and lipid productivity
    Chien‐Ting Li, Jacob Stephan Yelsky, Yiqun Chen, Cristal Zúñiga, Richard Eng, Liqun Jiang, Alison J. Shapiro, Kai-Wen Huang, Karsten Zengler, Michael J. Betenbaugh · 2019 · npj Systems Biology and Applications
  42. Dynamic co‐culture metabolic models reveal the fermentation dynamics, metabolic capacities and interplays of cheese starter cultures
    Emrah Özcan, Merve Seven, Burcu Şirin, Tunahan Çakır, Emrah Nıkerel, Bas Teusink, Ebru Toksoy Öner · 2020 · Biotechnology and Bioengineering
  43. Biotechnological and industrial applications of Streptomyces metabolites
    Khushboo, Punit Kumar, Kashyap Kumar Dubey, Zeba Usmani, Minaxi Sharma, Vijai Kumar Gupta · 2021 · Biofuels Bioproducts and Biorefining
  44. Computer-aided design for metabolic engineering
    Alfred Fernández‐Castané, Tamás Fehér, Pablo Carbonell, Cyrille Pauthenier, Jean‐Loup Faulon · 2014 · Journal of Biotechnology
  45. Data-driven synthetic microbes for sustainable future
    Iqra Mariam, Ulrika Rova, Paul Christakopoulos, Λεωνίδας Μάτσακας, Alok Patel · 2025 · npj Systems Biology and Applications
  46. Microarray data can predict diurnal changes of starch content in the picoalga Ostreococcus
    Oksana Sorokina, Florence Corellou, David Dauvillée, Anatoly Sorokin, Igor Goryanin, Steven G. Ball, François‐Yves Bouget, Andrew John Millar · 2011 · BMC Systems Biology
  47. Reconstruction and analysis of the genome-scale metabolic model of Lactobacillus casei LC2W
    Nan Xu, Jie Liu, Lianzhong Ai, Li Liu · 2014 · Gene
  48. Development and analysis of an in vivo-compatible metabolic network of Mycobacterium tuberculosis
    Xin De Fang, Anders Wallqvist, Jaques Reifman A · 2010 · BMC Systems Biology
  49. MetDraw: automated visualization of genome-scale metabolic network reconstructions and high-throughput data
    Paul A. Jensen, Jason A. Papin · 2014 · Bioinformatics
  50. Comparative evaluation of atom mapping algorithms for balanced metabolic reactions: application to Recon 3D
    German Preciat, Lemmer R. P. El Assal, Alberto Noronha, Ines Thiele, Hulda S. Haraldsdóttir, Ronan M. T. Fleming · 2017 · Journal of Cheminformatics
  51. CO2 to succinic acid – Estimating the potential of biocatalytic routes
    Ulf W. Liebal, Lars M. Blank, Birgitta E. Ebert · 2018 · Metabolic Engineering Communications
  52. A simplified metabolic network reconstruction to promote understanding and development of flux balance analysis tools
    Kristopher D. Rawls, Bonnie V. Dougherty, Edik Matthew Blais, Ethan Stancliffe, Glynis L. Kolling, Kalyan C. Vinnakota, Venkat Reddy Pannala, Anders Wallqvist, Jason A. Papin · 2018 · Computers in Biology and Medicine
  53. Improving the accuracy of flux balance analysis through the implementation of carbon availability constraints for intracellular reactions
    Maximilian Lularevic, Andrew J. Racher, Colin M. Jaques, Alexandros Kiparissides · 2019 · Biotechnology and Bioengineering
  54. Core Metabolism Shifts during Growth on Methanol versus Methane in the Methanotroph Methylomicrobium buryatense 5GB1
    Yanfen Fu, Lian He, Jennifer Reeve, David A. C. Beck, Mary E. Lidstrom · 2019 · mBio
  55. Computational Methods for Modification of Metabolic Networks
    Takeyuki Tamura, Wei Lu, Tatsuya Akutsu · 2015 · Computational and Structural Biotechnology Journal
  56. Systems-level modeling of mycobacterial metabolism for the identification of new (multi-)drug targets
    Rienk A. Rienksma, Maria Suarez Diez, Lucie Spina, Peter J. Schaap, Vítor A. P. Martins dos Santos · 2014 · Seminars in Immunology
  57. Bridging the Gap between Fluxomics and Industrial Biotechnology
    Xueyang Feng, Lawrence Page, Jacob R. Rubens, Lauren M. Chircus, Peter F. Colletti, Himadri B. Pakrasi, Yinjie Tang · 2010 · BioMed Research International
  58. Comparative genome-scale metabolic modeling of actinomycetes: The topology of essential core metabolism
    Mohammad Tauqeer Alam, Marnix H. Medema, Eriko Takano A, Rainer Breitling A · 2011 · FEBS Letters
  59. Computational Modeling of Human Metabolism and Its Application to Systems Biomedicine
    Maike Kathrin Aurich, Ines Thiele · 2015 · Methods in molecular biology
  60. Benchmarking Procedures for High-Throughput Context Specific Reconstruction Algorithms
    Maria Pires Pacheco, Thomas Pfau, Thomas Sauter · 2016 · Frontiers in Physiology
  61. Engineering Escherichia coli for poly-(3-hydroxybutyrate) production guided by genome-scale metabolic network analysis
    Yangyang Zheng, Qianqian Yuan, Xiaoyan Yang, Hongwu Ma · 2017 · Enzyme and Microbial Technology
  62. Genome-scale metabolic networks in time and space
    Ove Øyås, Jörg Stelling · 2017 · Current Opinion in Systems Biology
  63. Biochemical Characterization of Human Gluconokinase and the Proposed Metabolic Impact of Gluconic Acid as Determined by Constraint Based Metabolic Network Analysis
    Neha Rohatgi, Tine Kragh Nielsen, Sara Petersen Bjørn, Ivar T Axelsson, Giuseppe Paglia, Bjørn Gunnar Rude Voldborg, Bernhard Ørn Palsson, Óttar Rolfsson · 2014 · PLoS ONE
  64. MultiMetEval: Comparative and Multi-Objective Analysis of Genome-Scale Metabolic Models
    Piotr Zakrzewski, Marnix H. Medema, Albert Gevorgyan, Andrzej M. Kierzek, Rainer Breitling, Eriko Takano · 2012 · PLoS ONE
  65. Pantograph: A template-based method for genome-scale metabolic model reconstruction
    Nicolás Loira, Anna Zhukova, David James Sherman · 2014 · Journal of Bioinformatics and Computational Biology
  66. A systems biology framework for modeling metabolic enzyme inhibition of Mycobacterium tuberculosis
    Xin De Fang, Anders Wallqvist, Jaques Reifman A · 2009 · BMC Systems Biology
  67. DeepMetabolism: A Deep Learning System to Predict Phenotype from Genome Sequencing
    Weihua Guo, You (Eric) Xu, Xueyang Feng · 2017 · bioRxiv (Cold Spring Harbor Laboratory)
  68. Bio-upcycling of polyethylene terephthalate
    Till Tiso, Tanja Narančić, Ren Wei, Éric Pollet, Niall Beagan, Katja Schröder, Annett Honak, Mengying Jiang, Shane T. Kenny, Nick J. P. Wierckx et al. · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
  69. Engineering the synthetic β-alanine pathway in Komagataella phaffii for conversion of methanol into 3-hydroxypropionic acid
    Sílvia Àvila-Cabré, Míriam Pérez‐Trujillo, Joan Albiol, Pau Ferrer · 2023 · Microbial Cell Factories
  70. GENOME-BASED MODELING AND DESIGN OF METABOLIC INTERACTIONS IN MICROBIAL COMMUNITIES
    Radhakrishnan Mahadevan, Michael A. Henson · 2012 · Computational and Structural Biotechnology Journal
  71. TrypanoCyc: a community-led biochemical pathways database for Trypanosoma brucei
    Sanu Shameer, Flora Logan-Klumpler, Florence Vinson, Ludovic Cottret, Benjamin Merlet, Fiona Achcar, Michael Boshart, Matthew Berriman, Rainer Breitling A, Frédéric Bringaud et al. · 2014 · Nucleic Acids Research
  72. A novel synthetic medium and expression system for subzero growth and recombinant protein production in Pseudoalteromonas haloplanktis TAC125
    Filomena Sannino, M. Giuliani, U. Salvatore, Gennaro Antonio Apuzzo, Donatella de Pascale, Renato Fani, Marco Fondi, Gennaro Marino, Maria Luisa Tutino, Ermenegilda Parrilli · 2016 · Applied Microbiology and Biotechnology
  73. In silico engineering of Pseudomonas metabolism reveals new biomarkers for increased biosurfactant production
    Annalisa Occhipinti, Filmon Eyassu, Thahira Rahman, Pattanathu K. S. M. Rahman, Claudio Angione · 2018 · PeerJ
  74. Cellular Plasticity in Response to Suppression of Storage Proteins in the Brassica napus Embryo
    Hardy Rolletschek, Jörg Schwender, Christina König, Kent Dean Chapman, Trevor B. Romsdahl, Christin Lorenz, Hans‐Peter Braun, Peter Denolf, Katrien Van Audenhove, Eberhard Munz et al. · 2020 · The Plant Cell
  75. Thermodynamics and H2 Transfer in a Methanogenic, Syntrophic Community
    Joshua J. Hamilton, Montserrat Calixto Contreras, Jennifer L. Reed · 2015 · PLoS Computational Biology
  76. Link between Phosphate Starvation and Glycogen Metabolism in Corynebacterium glutamicum , Revealed by Metabolomics
    Han Min Woo, Stephan Noack, Gerd Michael Seibold, Sabine Willbold, Bernhard J. Eikmanns, Michael H. Bott · 2010 · Applied and Environmental Microbiology
  77. Moving from genome-scale to community-scale metabolic models for the human gut microbiome
    Nick Quinn-Bohmann, Alex V. Carr, Christian Diener, Sean M. Gibbons · 2025 · Nature Microbiology
  78. Reconstruction and analysis of a genome-scale metabolic network of Corynebacterium glutamicum S9114
    Jie Mei, Nan Xu, Chao Ye, Li Liu, Jianrong Wu · 2015 · Gene
  79. Metabolic Constraint-Based Refinement of Transcriptional Regulatory Networks
    Sriram Chandrasekaran, Nathan D. Price · 2013 · PLoS Computational Biology
  80. In silico assessment of the metabolic capabilities of an engineered functional reversal of the β-oxidation cycle for the synthesis of longer-chain (C≥4) products
    Ángela Cintolesi, James M. Clomburg, Ramón González · 2014 · Metabolic Engineering
  81. Metabolic systems analysis to advance algal biotechnology
    Brian James Schmidt, Xiefan Lin‐Schmidt, Austin Chamberlin, Kourosh Salehi‐Ashtiani, Jason A. Papin · 2010 · Biotechnology Journal
  82. Connecting genotype to phenotype in the era of high-throughput sequencing
    Christopher S. Henry, Ross Overbeek, Fangfang Xia, Aaron A. Best, Elizabeth M. Glass, Jack A. Gilbert, Peter Larsen, Robert Alan Edwards, Terry L. Disz, Folker Meyer et al. · 2011 · Biochimica et Biophysica Acta (BBA) - General Subjects
  83. Impact of Stoichiometry Representation on Simulation of Genotype-Phenotype Relationships in Metabolic Networks
    Ana Rita Brochado, Sergej Andrejev, Costas D. Maranas, Kiran Raosaheb Patil · 2012 · PLoS Computational Biology
  84. Modeling of Zymomonas mobilis central metabolism for novel metabolic engineering strategies
    Uldis Kalnenieks, Agris Pentjuss, Reinis Rutkis, Egils Stalidzāns, David A. Fell · 2014 · Frontiers in Microbiology
  85. Modeling the effects of commonly used drugs on human metabolism
    Swagatika Sahoo, Hulda S. Haraldsdóttir, Ronan M. T. Fleming, Ines Thiele · 2014 · FEBS Journal
  86. Interrogation of global mutagenesis data with a genome scale model of Neisseria meningitidis to assess gene fitness in vitro and in sera
    Tom A. Mendum, Jane Newcombe, Ahmad A. Mannan, Andrzej M. Kierzek, Johnjoe McFadden · 2011 · Genome biology
  87. A constraint-based model of Scheffersomyces stipitis for improved ethanol production
    Ting Liu, Wei Zou, Li Liu, Jian Chen · 2012 · Biotechnology for Biofuels
  88. Genome-scale metabolic modeling of Mucor circinelloides and comparative analysis with other oleaginous species
    Wanwipa Vongsangnak, Amornpan Klanchui, Iyarest Tawornsamretkit, Witthawin Tatiyaborwornchai, Kobkul Laoteng, Asawin Meechai · 2016 · Gene
  89. Reconstructed Metabolic Network Models Predict Flux-Level Metabolic Reprogramming in Glioblastoma
    Emrah Özcan, Tunahan Çakır · 2016 · Frontiers in Neuroscience
  90. Modulation of Nitrous Oxide (N 2 O) Accumulation by Primary Metabolites in Denitrifying Cultures Adapting to Changes in Environmental C and N
    Octavio Perez‐Garcia, Cody Mankelow, Kartik Chandran, Silas Granato Villas-Bôas, Naresh Singhal · 2017 · Environmental Science & Technology
  91. Functional interrogation of Plasmodium genus metabolism identifies species- and stage-specific differences in nutrient essentiality and drug targeting
    Alyaa M. Abdel‐Haleem, Hooman Hefzi, Katsuhiko Mineta, Xin Gao, Takashi Gojobori, Bernhard Ørn Palsson, Nathan E. Lewis, Neema Jamshidi · 2018 · PLoS Computational Biology
  92. Simulation and optimization of dynamic flux balance analysis models using an interior point method reformulation
    Felipe Scott, Pamela Wilson, Raúl Conejeros, Vassilios S. Vassiliadis · 2018 · Computers & Chemical Engineering
  93. Fed‐batch production of l ‐tryptophan from glycerol using recombinant Escherichia coli
    Julia Tröndle, Natalia Viktorovna Trachtmann, Georg A. Sprenger, Dirk Weuster‐Botz · 2018 · Biotechnology and Bioengineering
  94. Kinetic ensemble model of gas fermenting Clostridium autoethanogenum for improved ethanol production
    Jennifer L. Greene, James Daniell, Michael Köpke, Linda J. Broadbelt, Keith E. J. Tyo · 2019 · Biochemical Engineering Journal
  95. Linking metabolic phenotypes to pathogenic traits among “Candidatus Liberibacter asiaticus” and its hosts
    Cristal Zúñiga, Beth B. Peacock, Bo Liang, Greg McCollum, Sonia C. Irigoyen, Diego Tec-Campos, Clarisse A. Marotz, Nien-Chen Weng, Alejandro Zepeda, Georgios Vidalakis et al. · 2020 · npj Systems Biology and Applications
  96. Channelling carbon flux through the meta ‐cleavage route for improved poly(3‐hydroxyalkanoate) production from benzoate and lignin‐based aromatics in Pseudomonas putida H
    José Manuel Borrero‐de Acuña, Izabook Gutiérrez‐Urrutia, Cristian Hidalgo-Dumont, Carla Aravena-Carrasco, Matias Orellana‐Saez, Nestor Palominos-Gonzalez, Jozef B. J. H. van Duuren, Viktoria Wagner, Lars Gläser, Judith Becker et al. · 2020 · Microbial Biotechnology
  97. Systematic evaluation of parameters for genome-scale metabolic models of cultured mammalian cells
    Song‐Min Schinn, Carly Morrison, Wei Wei, Lin Zhang, Nathan E. Lewis · 2021 · Metabolic Engineering
  98. Dynamic flux balance analysis of the metabolism of Saccharomyces cerevisiae during the shift from fully respirative or respirofermentative metabolic states to anaerobiosis
    Paula Jouhten, Marilyn G. Wiebe, Merja E. Penttilä · 2012 · FEBS Journal
  99. What Can Causal Networks Tell Us about Metabolic Pathways?
    Rachael Hageman Blair, Daniel J. Kliebenstein, Gary A. Churchill · 2012 · PLoS Computational Biology
  100. An analytic approximation of the feasible space of metabolic networks
    Alfredo Braunstein, Anna Paola Muntoni, Andrea Pagnani · 2017 · Nature Communications