Genome-scale metabolic network reconstruction.

[1]  Zeeshan Ahmed,et al.  Software applications toward quantitative metabolic flux analysis and modeling , 2014, Briefings Bioinform..

[2]  D. Sarkar,et al.  Dynamic flux balance analysis of batch fermentation: effect of genetic manipulations on ethanol production , 2014, Bioprocess and Biosystems Engineering.

[3]  Bas Teusink,et al.  Basic concepts and principles of stoichiometric modeling of metabolic networks , 2013, Biotechnology journal.

[4]  Peter D. Karp,et al.  A systematic comparison of the MetaCyc and KEGG pathway databases , 2013, BMC Bioinformatics.

[5]  Intawat Nookaew,et al.  The RAVEN Toolbox and Its Use for Generating a Genome-scale Metabolic Model for Penicillium chrysogenum , 2013, PLoS Comput. Biol..

[6]  Linda Broadbelt,et al.  Computational tools for guided discovery and engineering of metabolic pathways. , 2013, Methods in molecular biology.

[7]  Joshua A. Lerman,et al.  COBRApy: COnstraints-Based Reconstruction and Analysis for Python , 2013, BMC Systems Biology.

[8]  Liming Liu,et al.  Reconstruction and analysis of a genome-scale metabolic model of the vitamin C producing industrial strain Ketogulonicigenium vulgare WSH-001. , 2012, Journal of biotechnology.

[9]  Jaques Reifman,et al.  Modeling Phenotypic Metabolic Adaptations of Mycobacterium tuberculosis H37Rv under Hypoxia , 2012, PLoS Comput. Biol..

[10]  Yixin Chen,et al.  MicrobesFlux: a web platform for drafting metabolic models from the KEGG database , 2012, BMC Systems Biology.

[11]  Feng-Chi Chen,et al.  GEMSiRV: a software platform for GEnome-scale metabolic model simulation, reconstruction and visualization , 2012, Bioinform..

[12]  Arnau Montagud,et al.  Automation on the Generation of Genome-Scale Metabolic Models , 2012, J. Comput. Biol..

[13]  Deepak Chandran,et al.  Computational tools for metabolic engineering. , 2012, Metabolic engineering.

[14]  Joost Boele,et al.  FAME, the Flux Analysis and Modeling Environment , 2012, BMC Systems Biology.

[15]  Norman W. Paton,et al.  The SuBliMinaL Toolbox: automating steps in the reconstruction of metabolic networks , 2011, J. Integr. Bioinform..

[16]  Jason A. Papin,et al.  Reconciliation of Genome-Scale Metabolic Reconstructions for Comparative Systems Analysis , 2011, PLoS Comput. Biol..

[17]  Ronan M. T. Fleming,et al.  Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0 , 2007, Nature Protocols.

[18]  Peter D. Karp,et al.  Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology , 2015, Briefings Bioinform..

[19]  Suhua Chang,et al.  Exploring the metabolic network of the epidemic pathogen Burkholderia cenocepacia J2315 via genome-scale reconstruction , 2011, BMC Systems Biology.

[20]  Rick L. Stevens,et al.  High-throughput generation, optimization and analysis of genome-scale metabolic models , 2010, Nature Biotechnology.

[21]  A. Goesmann,et al.  CARMEN - Comparative Analysis and in silico Reconstruction of organism-specific MEtabolic Networks. , 2010, Genetics and molecular research : GMR.

[22]  Ines Thiele,et al.  Reconstruction annotation jamborees: a community approach to systems biology , 2010, Molecular systems biology.

[23]  Jeffrey D Orth,et al.  What is flux balance analysis? , 2010, Nature Biotechnology.

[24]  B. Palsson,et al.  A protocol for generating a high-quality genome-scale metabolic reconstruction , 2010 .

[25]  Jason A. Papin,et al.  Applications of genome-scale metabolic reconstructions , 2009, Molecular systems biology.

[26]  Jong Myoung Park,et al.  Constraints-based genome-scale metabolic simulation for systems metabolic engineering. , 2009, Biotechnology advances.

[27]  V. Schachter,et al.  Genome-scale models of bacterial metabolism: reconstruction and applications , 2008, FEMS microbiology reviews.

[28]  Jason A Papin,et al.  Flux balance analysis: interrogating genome-scale metabolic networks. , 2009, Methods in molecular biology.

[29]  M. Ferrer,et al.  Recent trends in industrial microbiology. , 2008, Current opinion in microbiology.

[30]  Michael Hucka,et al.  LibSBML: an API Library for SBML , 2008, Bioinform..

[31]  Jason A. Papin,et al.  * Corresponding authors , 2006 .

[32]  Rick L. Stevens,et al.  The RAST Server: Rapid Annotations using Subsystems Technology , 2008, BMC Genomics.

[33]  Adam M. Feist,et al.  A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information , 2007, Molecular systems biology.

[34]  John W. Pinney,et al.  metaSHARK: a WWW platform for interactive exploration of metabolic networks , 2006, Nucleic Acids Res..

[35]  Milton H. Saier,et al.  TCDB: the Transporter Classification Database for membrane transport protein analyses and information , 2005, Nucleic Acids Res..

[36]  S. Lee,et al.  Metabolic Engineering of Escherichia coli for Enhanced Production of Succinic Acid, Based on Genome Comparison and In Silico Gene Knockout Simulation , 2005, Applied and Environmental Microbiology.

[37]  Naryttza N. Diaz,et al.  The Subsystems Approach to Genome Annotation and its Use in the Project to Annotate 1000 Genomes , 2005, Nucleic acids research.

[38]  J. Pinney,et al.  metaSHARK: software for automated metabolic network prediction from DNA sequence and its application to the genomes of Plasmodium falciparum and Eimeria tenella , 2005, Nucleic acids research.

[39]  Hiroaki Kitano,et al.  The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models , 2003, Bioinform..

[40]  D. Downs Genomics and bacterial metabolism. , 2003, Current issues in molecular biology.

[41]  F. Doyle,et al.  Dynamic flux balance analysis of diauxic growth in Escherichia coli. , 2002, Biophysical journal.

[42]  Peter D. Karp,et al.  The Pathway Tools software , 2002, ISMB.

[43]  Minoru Kanehisa,et al.  The KEGG database. , 2002, Novartis Foundation symposium.

[44]  Peter D. Karp,et al.  The MetaCyc Database , 2002, Nucleic Acids Res..

[45]  J. Casas,et al.  Xanthan gum: production, recovery, and properties. , 2000, Biotechnology Advances.

[46]  Peter D. Karp,et al.  The EcoCyc and MetaCyc databases , 2000, Nucleic Acids Res..

[47]  C. M. Sperberg-McQueen,et al.  Extensible Markup Language (XML) , 1997, World Wide Web J..

[48]  Peter D. Karp,et al.  Integrated Access to Metabolic and Genomic Data , 1996, J. Comput. Biol..

[49]  B. Palsson,et al.  Stoichiometric flux balance models quantitatively predict growth and metabolic by-product secretion in wild-type Escherichia coli W3110 , 1994, Applied and environmental microbiology.

[50]  W. Moore,et al.  Acetone, Isopropanol, and Butanol Production by Clostridium beijerinckii (syn. Clostridium butylicum) and Clostridium aurantibutyricum , 1983, Applied and environmental microbiology.