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, Lewis, Nathan E, Rahmanian, Sorena, Kang, Joseph, Hyduke, Daniel R, Palsson, Bernhard Ø·2011·Nature Protocols

DOI 10.1038/nprot.2011.308

Cited by (1,002)

Items 501–600 of 1,002

i AK692: A genome-scale metabolic model of Spirulina platensis C1
Amornpan Klanchui, Chiraphan Khannapho, Atchara Phodee, Supapon Cheevadhanarak, Asawin Meechai · 2012 · BMC Systems Biology
Quantitative imaging for discovery and assembly of the metabo‐regulome
Sakiko Okumoto, Hitomi Takanaga, Wolf Bernd Frommer · 2008 · New Phytologist
Minimal metabolic pathway structure is consistent with associated biomolecular interactions
Aarash Bordbar, Harish Nagarajan, Nathan E. Lewis, Haythem Latif, Ali Ebrahim, Stephen Federowicz, Jan Schellenberger, Bernhard Ørn Palsson · 2014 · Molecular Systems Biology
Clarifying the regulation of NO/N2O production in Nitrosomonas europaea during anoxic–oxic transition via flux balance analysis of a metabolic network model
Octavio Perez‐Garcia, Silas Granato Villas-Bôas, Simon Swift, Kartik Chandran, Naresh Singhal · 2014 · Water Research
Metabolic flexibility of mitochondrial respiratory chain disorders predicted by computer modelling
Lukasz Piotr Zielinski, Anthony C. Smith, Alexander Smith, Alan J. Robinson · 2016 · Mitochondrion
Effects of microcompartmentation on flux distribution and metabolic pools in Chlamydomonas reinhardtii chloroplasts
Anika Küken, Frederik Sommer, Liliya Yaneva-Roder, Luke C. M. Mackinder, Melanie Höhne, Stefan Geimer, Martin C. Jonikas, Michael Schroda, Mark Stitt, Zoran Nikoloski et al. · 2018 · eLife
Systems biology based metabolic engineering for non-natural chemicals
Alessandra Biz, Scott Proulx, Zhi-Qing J. Xu, Kavya Siddartha, Alex Mulet Indrayanti, Radhakrishnan Mahadevan · 2019 · Biotechnology Advances
The Need for Integrated Approaches in Metabolic Engineering
Anna Lechner, Elizabeth Brunk, Jay D. Keasling · 2016 · Cold Spring Harbor Perspectives in Biology
Biotechnological potential of respiring Zymomonas mobilis: A stoichiometric analysis of its central metabolism
Agris Pentjuss, Ilona Odzina, Andrejs Kostromins, David A. Fell, Egils Stalidzāns, Uldis Kalnenieks · 2013 · Journal of Biotechnology
von Bertalanffy 1.0: a COBRA toolbox extension to thermodynamically constrain metabolic models
Ronan M. T. Fleming, Ines Thiele · 2010 · Bioinformatics
Fast thermodynamically constrained flux variability analysis
Arne C. Müller, Alexander Bockmayr · 2013 · Bioinformatics
Glycan Degradation (GlyDeR) Analysis Predicts Mammalian Gut Microbiota Abundance and Host Diet-Specific Adaptations
Omer Eilam, Raphy Zarecki, Matthew Oberhardt, Luke K. Ursell, Martin Kupiec, Rob D. Knight, Uri Gophna, Eytan Ruppin · 2014 · mBio
The Systems Biology Research Tool: evolvable open-source software
Jeremiah Wright, Andreas Wagner · 2008 · BMC Systems Biology
Multiscale Model of Mycobacterium tuberculosis Infection Maps Metabolite and Gene Perturbations to Granuloma Sterilization Predictions
Elsje Pienaar, William M. Matern, Jennifer J. Linderman, Joel S. Bader, Denise E. Kirschner · 2016 · Infection and Immunity
Genome-scale metabolic modeling underscores the potential of Cutaneotrichosporon oleaginosus ATCC 20509 as a cell factory for biofuel production
Nhung Pham, Maarten J. M. F. Reijnders, Maria Suarez Diez, Bart Nijsse, Jan Springer, Gerrit Eggink, Peter J. Schaap · 2021 · Biotechnology for Biofuels
What mRNA Abundances Can Tell us about Metabolism
Andreas Hoppe · 2012 · Metabolites
Systems biology of bacterial nitrogen fixation: High-throughput technology and its integrative description with constraint-based modeling
Osbaldo Reséndis-Antonio, Magdalena Hernández, Emmanuel Picasso Salazar, Sandra Contreras, Gabriel Martínez-Batallar, Yolanda Mora, Sergio Encarnación‐Guevara · 2011 · BMC Systems Biology
Metabolic reconstruction identifies strain‐specific regulation of virulence in Toxoplasma gondii
Carl Yulun Song, Melissa A. Chiasson, Nirvana Nursimulu, Stacy S. Hung, James D. Wasmuth, Michael E. Grigg, John Parkinson · 2013 · Molecular Systems Biology
Systems approach to investigating host-pathogen interactions in infections with the biothreat agent Francisella. Constraints-based model of Francisella tularensis
Anu Raghunathan, Sookil Shin, Simon Daefler · 2010 · BMC Systems Biology
EGFR Signal-Network Reconstruction Demonstrates Metabolic Crosstalk in EMT
Kumari Sonal Choudhary, Neha Rohatgi, Skarphéðinn Halldórsson, Eiríkur Briem, Þórarinn Guðjónsson, Steinn Guðmundsson, Óttar Rolfsson · 2016 · PLoS Computational Biology
Model-based dietary optimization for late-stage, levodopa-treated, Parkinson’s disease patients
Marouen Ben Guebila, Ines Thiele · 2016 · npj Systems Biology and Applications
Reconstruction and analysis of a genome-scale metabolic model of Nannochloropsis gaditana
Ab Rauf Shah, Ahmad Ahmad, Shireesh Srivastava, B. M. Jaffar Ali · 2017 · Algal Research
Reconstruction of genome-scale metabolic model of Yarrowia lipolytica and its application in overproduction of triacylglycerol
Songsong Wei, Xingxing Jian, Jun Chen, Cheng Zhang, Qiang Hua · 2017 · Bioresources and Bioprocessing
Metabolic Networks and Their Evolution
Andreas Wagner · 2012 · Advances in experimental medicine and biology
Metabolic Modeling of Microbial Community Interactions for Health, Environmental and Biotechnological Applications
Kok Siong Ang, Meiyappan Lakshmanan, Na‐Rae Lee, Dong‐Yup Lee · 2018 · Current Genomics
MoVE identifies metabolic valves to switch between phenotypic states
Naveen Venayak, Axel von Kamp, Steffen Klamt, Radhakrishnan Mahadevan · 2018 · Nature Communications
Modelling overflow metabolism in Escherichia coli with flux balance analysis incorporating differential proteomic efficiencies of energy pathways
Hong Zeng, Aidong Yang · 2019 · BMC Systems Biology
CHO cell productivity improvement by genome-scale modeling and pathway analysis: Application to feed supplements
Zhuangrong Huang, Jianlin Xu, Andrew Yongky, Caitlin S. Morris, Ashli Polanco, Michael D. Reily, Michael Borys, Zheng Jian Li, Seongkyu Yoon · 2020 · Biochemical Engineering Journal
Integrating molecular markers into metabolic models improves genomic selection for Arabidopsis growth
Hao Tong, Anika Küken, Zoran Nikoloski · 2020 · Nature Communications
A Multiphase Multiobjective Dynamic Genome-Scale Model Shows Different Redox Balancing among Yeast Species of the Saccharomyces Genus in Fermentation
David Henriques, Romain Minebois, Sebastián N. Mendoza, Laura G. Macías, Roberto Pérez‐Torrado, Eladio Barrio, Bas Teusink, Amparo Querol, Eva Balsa‐Canto · 2021 · mSystems
Multiscale Metabolic Modeling of C4 Plants: Connecting Nonlinear Genome-Scale Models to Leaf-Scale Metabolism in Developing Maize Leaves
Eli Bogart, Christopher R. Myers · 2016 · PLoS ONE
Transcriptome data modeling for targeted plant metabolic engineering
Keiko Yonekura‐Sakakibara, Atsushi Fukushima, Kazuki Saito · 2012 · Current Opinion in Biotechnology
Microalgal Metabolic Network Model Refinement through High-Throughput Functional Metabolic Profiling
Amphun Chaiboonchoe, Bushra Dohai, Hong Cai, David Roy Nelson, Kenan Jijakli, Kourosh Salehi‐Ashtiani · 2014 · Frontiers in Bioengineering and Biotechnology
Translational research in infectious disease: current paradigms and challenges ahead
Judith M. Fontana, Elizabeth L. Alexander, Mirella Salvatore · 2012 · Translational research
Understanding human metabolic physiology: a genome-to-systems approach
Monica L. Mo, Bernhard Ørn Palsson · 2008 · Trends in biotechnology
Pharmacogenomic and clinical data link non-pharmacokinetic metabolic dysregulation to drug side effect pathogenesis
Daniel Craig Zielinski, Fabian V. Filipp, Aarash Bordbar, Kasper Jensen, Jeffrey W. Smith, Markus J. Herrgård, Monica L. Mo, Bernhard Ørn Palsson · 2015 · Nature Communications
Assessing methanotrophy and carbon fixation for biofuel production by Methanosarcina acetivorans
Hadi Nazem‐Bokaee, Saratram Gopalakrishnan, James Gregory Ferry, Thomas Keith Wood, Costas D. Maranas · 2016 · Microbial Cell Factories
The post‐transcriptional regulatory system CSR controls the balance of metabolic pools in upper glycolysis of Escherichia coli
Manon Morin, Delphine Ropers, Fabien Létisse, Sandrine Laguerre, Jean‐Charles Portais, Muriel Cocaign‐Bousquet, Brice Enjalbert · 2016 · Molecular Microbiology
A Comprehensively Curated Genome-Scale Two-Cell Model for the Heterocystous Cyanobacterium Anabaena sp. PCC 7120
Dávid Malatinszky, Ralf Steuer, Patrik Raymond Jones · 2016 · PLANT PHYSIOLOGY
Pathway-Consensus Approach to Metabolic Network Reconstruction for Pseudomonas putida KT2440 by Systematic Comparison of Published Models
Qianqian Yuan, Teng Huang, Peishun Li, Tong Hao, Feiran Li, Hongwu Ma, Zhiwen Wang, Xueming Zhao, Tao Chen, Igor Goryanin · 2017 · PLoS ONE
Functional genomics for the oleaginous yeast Yarrowia lipolytica
Kurt Patterson, James Yu, Jenny Landberg, Ivan Chang, Farbod Shavarebi, Virginia Bilanchone, Suzanne B. Sandmeyer · 2018 · Metabolic Engineering
Combining inferred regulatory and reconstructed metabolic networks enhances phenotype prediction in yeast
Zhuo Wang, Samuel A. Danziger, Ben Heavner, Shuyi Ma, Jennifer J. Smith, Li Song, Thurston Herricks, Evangelos Simeonidis, Nitin S. Baliga, John D. Aitchison et al. · 2017 · PLoS Computational Biology
novoPathFinder: a webserver of designing novel-pathway with integrating GEM-model
Shaozhen Ding, Yu Ting Tian, Pengli Cai, Dachuan Zhang, Xingxiang Cheng, Dandan Sun, Le Yuan, Junni Chen, Weizhong Tu, Dong‐Qing Wei et al. · 2020 · Nucleic Acids Research
Has nature already identified all useful antibacterial targets?
Dirk Bumann · 2008 · Current Opinion in Microbiology
A Computational Analysis of Stoichiometric Constraints and Trade-Offs in Cyanobacterial Biofuel Production
Henning Knoop, Ralf Steuer · 2015 · Frontiers in Bioengineering and Biotechnology
Genomically and biochemically accurate metabolic reconstruction of Methanosarcina barkeri Fusaro, iMG746
Matthew C. Gonnerman, Matthew N. Benedict, Adam M. Feist, William W. Metcalf, Nathan D. Price · 2013 · Biotechnology Journal
Metabolic stasis in an ancient symbiosis: genome-scale metabolic networks from two Blattabacterium cuenoti strains, primary endosymbionts of cockroaches
Carmen María González-Domenech, Eugeni Belda, Rafael Patiño‐Navarrete, Andrés Moyá, Juli G. Peretó, Amparo Latorre · 2012 · BMC Microbiology
Metabolic Cancer Biology: Structural-based analysis of cancer as a metabolic disease, new sights and opportunities for disease treatment
Ali Masoudi‐Nejad, Yazdan Asgari · 2014 · Seminars in Cancer Biology
Transcriptomics‐based strain optimization tool for designing secondary metabolite overproducing strains of Streptomyces coelicolor
Minsuk Kim, Jeong Sang Yi, Meiyappan Lakshmanan, Dong‐Yup Lee, Byung‐Gee Kim · 2015 · Biotechnology and Bioengineering
A computational exploration of bacterial metabolic diversity identifying metabolic interactions and growth-efficient strain communities
Eleftheria Tzamali, Panayiota Poirazi, Ioannis G. Tollis, Martin Reczko · 2011 · BMC Systems Biology
Improving the flux distributions simulated with genome-scale metabolic models of Saccharomyces cerevisiae
Rui Pereira, Jens Nielsen, Isabel Rocha · 2016 · Metabolic Engineering Communications
Model-based biotechnological potential analysis of Kluyveromyces marxianus central metabolism
Agris Pentjuss, Egils Stalidzāns, Jānis Liepiņš, Agnese Kokina, Jekaterina Martynova, Pēteris Zikmanis, Ivars Mozga, Rita Scherbaka, Hassan B. Hartman, Mark G. Poolman et al. · 2017 · Journal of Industrial Microbiology & Biotechnology
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
Yasutaka Hirokawa, Shingo Matsuo, Hiroyuki Hamada, Fumio Matsuda, Taizo Hanai · 2017 · Microbial Cell Factories
Integrated Experimental and Computational Analyses Reveal Differential Metabolic Functionality in Antibiotic-Resistant Pseudomonas aeruginosa
Laura J. Dunphy, Phillip Yen, Jason A. Papin · 2019 · Cell Systems
Advances in the integration of transcriptional regulatory information into genome-scale metabolic models
R.P. Vivek-Ananth, Areejit Samal · 2016 · Biosystems
Integration of comprehensive data and biotechnological tools for industrial applications of Kluyveromyces marxianus
Mochamad Nurcholis, Noppon Lertwattanasakul, Nadchanok Rodrussamee, Tomoyuki Kosaka, Masayuki Murata, Mamoru Carlos Yamada · 2019 · Applied Microbiology and Biotechnology
Identifying the essential nutritional requirements of the probiotic bacteria Bifidobacterium animalis and Bifidobacterium longum through genome-scale modeling
Marie Schöpping, Paula Gaspar, Ana Rute Neves, Carl Johan Franzén, Ahmad A. Zeidan · 2021 · npj Systems Biology and Applications
Machine learning based analyses on metabolic networks supports high-throughput knockout screens
Kitiporn Plaimas, Jan‐Philipp Mallm, Marcus Oswald, Fabian Svara, Victor Sourjik, Roland Eils, Rainer König · 2008 · BMC Systems Biology
Genome-scale metabolic models of Microbacterium species isolated from a high altitude desert environment
Dinka Mandaković, Ángela Cintolesi, Jonathan E. Maldonado, Sebastián N. Mendoza, Méziane Aïte, Alexis Gaete, Francisco Saitua, Miguel L. Allende, Verónica Cambiazo, Anne Siegel et al. · 2020 · Scientific Reports
Current and Emerging Options for Taxol Production
Yi Li, Guojian Zhang, Blaine A. Pfeifer · 2014 · Advances in biochemical engineering, biotechnology
Constraint-Based Modeling of Carbon Fixation and the Energetics of Electron Transfer in Geobacter metallireducens
Adam M. Feist, Harish Nagarajan, Amelia‐Elena Rotaru, Pier‐Luc Tremblay, Tian Zhang, Kelly P. Nevin, Derek R. Lovley, Karsten Zengler · 2014 · PLoS Computational Biology
Optimal cofactor swapping can increase the theoretical yield for chemical production in Escherichia coli and Saccharomyces cerevisiae
Zachary A. King, Adam M. Feist · 2014 · Metabolic Engineering
Phenotypic differentiation of gastrointestinal microbes is reflected in their encoded metabolic repertoires
Eugen Bauer, Cedric Christian Laczny, Stefanía Magnúsdóttir, Paul Wilmes, Ines Thiele · 2015 · Microbiome
Genome-scale modeling and transcriptome analysis of Leuconostoc mesenteroides unravel the redox governed metabolic states in obligate heterofermentative lactic acid bacteria
Lokanand Koduru, Yu‐Jin Kim, Jeongsu Bang, Meiyappan Lakshmanan, Nam Soo Han, Dong‐Yup Lee · 2017 · Scientific Reports
Metabolic network percolation quantifies biosynthetic capabilities across the human oral microbiome
David B. Bernstein, Floyd E. Dewhirst, Daniel Segrè · 2019 · eLife
GEMSiRV: a software platform for GEnome-scale metabolic model simulation, reconstruction and visualization
Yu-Chieh Liao, Ming-Hsin Tsai, Feng‐Chi Chen, Chao Agnes Hsiung · 2012 · Bioinformatics
Applications of genome-scale metabolic models to investigate microbial metabolic adaptations in response to genetic or environmental perturbations
Elena Lucy Carter, Chrystala Constantinidou, Mohammad Tauqeer Alam · 2023 · Briefings in Bioinformatics
Whole-Genome Metabolic Network Reconstruction and Constraint-Based Modeling⋆
Charles R. Haggart, Jennifer A. Bartell, Jeffrey J. Saucerman, Jason A. Papin · 2011 · Methods in enzymology on CD-ROM/Methods in enzymology
Identification of Novel Knockout Targets for Improving Terpenoids Biosynthesis in Saccharomyces cerevisiae
Zhiqiang Sun, Hailin Meng, Jing Li, Jianfeng Wang, Qian Li, Yong Wang, Yansheng Zhang · 2014 · PLoS ONE
Integration of a constraint-based metabolic model of Brassica napus developing seeds with 13C-metabolic flux analysis
Jordan O. Hay, Hai Shi, Nicolas Heinzel, Inga Hebbelmann, Hardy Rolletschek, Jörg Schwender · 2014 · Frontiers in Plant Science
Using Gene Essentiality and Synthetic Lethality Information to Correct Yeast and CHO Cell Genome-Scale Models
Ratul Chowdhury, Anupam Chowdhury, Costas D. Maranas · 2015 · Metabolites
Insights into metabolic efficiency from flux analysis
Xuewen Chen, Yair Shachar‐Hill · 2012 · Journal of Experimental Botany
Diversity of flux distribution in central carbon metabolism of S. cerevisiae strains from diverse environments
Thibault Nidelet, Pascale Brial, Carole Camarasa, Sylvie Dequin · 2016 · Microbial Cell Factories
Insights on the virulence of swine respiratory tract mycoplasmas through genome-scale metabolic modeling
Mariana Galvão Ferrarini, Franciele Maboni Siqueira, Scheila Gabriele Mucha, Tony Palama, Élodie Jobard, Bénédicte Elena‐Herrmann, Ana Tereza Ribeiro de Vasconcelos, Florence Tardy, Irene Silveira Schrank, Arnaldo Zaha et al. · 2016 · BMC Genomics
In silico metabolic engineering of Clostridium ljungdahlii for synthesis gas fermentation
Jin Chen, Michael A. Henson · 2016 · Metabolic Engineering
A sperm-specific proteome-scale metabolic network model identifies non-glycolytic genes for energy deficiency in asthenozoospermia
Arvand Asghari, Sayed‐Amir Marashi, Naser Ansari‐Pour · 2017 · Systems Biology in Reproductive Medicine
Constraint-based modeling identifies new putative targets to fight colistin-resistant A. baumannii infections
Luana Presta, Emanuele Bosi, Leila Mansouri, Lenie Dijkshoorn, Renato Fani, Marco Fondi · 2017 · Scientific Reports
An insight to flux-balance analysis for biochemical networks
Shreya Anand, Koel Mukherjee, Padmini Padmanabhan · 2020 · Biotechnology and Genetic Engineering Reviews
The LASER database: Formalizing design rules for metabolic engineering
James D. Winkler, Andrea L. Halweg‐Edwards, Ryan T. Gill · 2015 · Metabolic Engineering Communications
Information theory, evolutionary innovations and evolvability
Andreas Wagner · 2017 · Philosophical Transactions of the Royal Society B Biological Sciences
From genotype to phenotype: computational approaches for inferring microbial traits relevant to the food industry
Signe Tang Karlsen, Martin Holm Rau, Benjamín J. Sánchez, Kristian Lund Jensen, Ahmad A. Zeidan · 2023 · FEMS Microbiology Reviews
Genome-scale metabolic flux analysis of Streptomyces lividans growing on a complex medium
Pieter-Jan D’Huys, Ivan Lule, Dominique Vercammen, Jozef Anné, Jan Frans M. van Impe, Kristel Bernaerts · 2012 · Journal of Biotechnology
Flux Balance Analysis Inspired Bioprocess Upgrading for Lycopene Production by a Metabolically Engineered Strain of Yarrowia lipolytica
Komi Nambou, Xingxing Jian, Xin-Kai Zhang, Liujing Wei, Jiajia Lou, Catherine Madzak, Qiang Hua · 2015 · Metabolites
A method for analysis and design of metabolism using metabolomics data and kinetic models: Application on lipidomics using a novel kinetic model of sphingolipid metabolism
Georgios Savoglidis, Aline Xavier da Silveira dos Santos, Isabelle Riezman, Paolo Angelino, Howard Riezman, Vassily Hatzimanikatis A · 2016 · Metabolic Engineering
An experimentally-supported genome-scale metabolic network reconstruction for Yersinia pestis CO92
Pep Charusanti, Sadhana Chauhan, Kathleen McAteer, Joshua A. Lerman, Daniel R. Hyduke, Мотин Владимир Леонидович, Charles K. Ansong, Joshua Adkins, Bernhard Ørn Palsson · 2011 · BMC Systems Biology
ll-ACHRB: a scalable algorithm for sampling the feasible solution space of metabolic networks
Pedro A. Saa, Lars Keld Nielsen · 2016 · Bioinformatics
Investigating Moorella thermoacetica metabolism with a genome-scale constraint-based metabolic model
Islam, M. Ahsanul, Zengler, Karsten, Edwards, Elizabeth A., Mahadevan, Radhakrishnan, Stephanopoulos, Gregory · 2015 · Integrative Biology
Decomposing flux distributions into elementary flux modes in genome-scale metabolic networks
Siu Hung Joshua Chan, Ping Ji · 2011 · Bioinformatics
CAVE: a cloud-based platform for analysis and visualization of metabolic pathways
Zhitao Mao, Qianqian Yuan, Haoran Li, Yue Zhang, Yuanyuan Huang, Chunhe Yang, Ruoyu Wang, Yongfu Yang, Yalun Wu, Shihui Yang et al. · 2023 · Nucleic Acids Research
Targeting cancer stem cell OXPHOS with tailored ruthenium complexes as a new anti-cancer strategy
Sonia Alcalá, Lara Villarino, Laura Ruíz-Cañas, José R. Couceiro, Miguel Martínez‐Calvo, Adrián Palencia‐Campos, Diego Navarro, Pablo Cabezas‐Sainz, Iker Rodríguez-Arabaolaza, Alfonso Cordero Barreal et al. · 2024 · Journal of Experimental & Clinical Cancer Research
Structure of deviations from optimality in biological systems
Alfonso Pérez‐Escudero, Marta Rivera-Alba, Gonzalo G. de Polavieja · 2009 · Proceedings of the National Academy of Sciences
Metabolic model reconstruction and analysis of an artificial microbial ecosystem for vitamin C production
Chao Ye, Wei Zou, Nan Xu, Li Liu · 2014 · Journal of Biotechnology
Genotypic and phenotypic analyses of a Pseudomonas aeruginosa chronic bronchiectasis isolate reveal differences from cystic fibrosis and laboratory strains
John J. Varga, Mariette Barbier, Xavier Mulet, Piotr Bielecki, Jennifer A. Bartell, Joshua P. Owings, Inmaculada Martínez-Ramos, Lauren E. Hittle, Michael R. Davis, Fredrick Heath Damron et al. · 2015 · BMC Genomics
A quantitative evaluation of ethylene production in the recombinant cyanobacterium Synechocystis sp. PCC 6803 harboring the ethylene-forming enzyme by membrane inlet mass spectrometry
Tomáš Zavřel, Henning Knoop, Ralf Steuer, Patrik Raymond Jones, Jan Červený, Martin Trtílek · 2015 · Bioresource Technology
Comprehensive analysis of a metabolic model for lipid production in Rhodosporidium toruloides
María Teresita Castañeda, Sebastián Núñez, Fabricio Garelli, Claudio E. Voget, Hernán De Battista · 2018 · Journal of Biotechnology
MitoCore: a curated constraint-based model for simulating human central metabolism
Anthony C. Smith, Filmon Eyassu, Jean‐Pierre Mazat, Alan J. Robinson · 2017 · BMC Systems Biology
Paint4Net: COBRA Toolbox extension for visualization of stoichiometric models of metabolism
Andrejs Kostromins, Egils Stalidzāns · 2012 · Biosystems
MEMOSys: Bioinformatics platform for genome-scale metabolic models
Stephan Pabinger, Robert Rader, Rasmus Ågren, Jens Nielsen, Zlatko Trajanoski · 2011 · BMC Systems Biology
A variational principle for computing nonequilibrium fluxes and potentials in genome-scale biochemical networks
Ronan M. T. Fleming, Christopher M. Maes, Michael A. Saunders, Yinyu Ye Y, Bernhard Ørn Palsson · 2011 · Journal of Theoretical Biology
Toward metabolic engineering in the context of system biology and synthetic biology: advances and prospects
Yanfeng Liu, Hyun‐Dong Shin, Jianghua Li, Long Liu · 2014 · Applied Microbiology and Biotechnology