{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,23]],"date-time":"2026-04-23T06:01:39Z","timestamp":1776924099374,"version":"3.51.2"},"reference-count":28,"publisher":"Public Library of Science (PLoS)","issue":"5","license":[{"start":{"date-parts":[[2008,5,16]],"date-time":"2008-05-16T00:00:00Z","timestamp":1210896000000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1000082","type":"journal-article","created":{"date-parts":[[2008,5,15]],"date-time":"2008-05-15T17:50:16Z","timestamp":1210873816000},"page":"e1000082","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":574,"title":["Context-Specific Metabolic Networks Are Consistent with Experiments"],"prefix":"10.1371","volume":"4","author":[{"given":"Scott A.","family":"Becker","sequence":"first","affiliation":[]},{"given":"Bernhard O.","family":"Palsson","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2008,5,16]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"130","DOI":"10.1038\/nrg1769","article-title":"Towards multidimensional genome annotation.","volume":"7","author":"JL Reed","year":"2006","journal-title":"Nat Rev Genet"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"511","DOI":"10.1016\/j.mib.2006.08.007","article-title":"Transcriptional regulatory networks in bacteria: From input signals to output responses.","volume":"9","author":"AS Seshasayee","year":"2006","journal-title":"Curr Opin Microbiol"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"95","DOI":"10.1007\/978-1-59745-390-5_5","article-title":"Predictive models of gene regulation: Application of regression methods to microarray data.","volume":"377","author":"D Das","year":"2007","journal-title":"Methods Mol Biol"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"19103","DOI":"10.1073\/pnas.0505231102","article-title":"The global transcriptional regulatory network for metabolism in <italic>Escherichia coli<\/italic> exhibits few dominant functional states.","volume":"102","author":"CL Barrett","year":"2005","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"28058","DOI":"10.1074\/jbc.M201691200","article-title":"Transcriptional regulation in constraints-based metabolic models of <italic>Escherichia coli<\/italic>.","volume":"277","author":"MW Covert","year":"2002","journal-title":"J Biol Chem"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"92","DOI":"10.1038\/nature02456","article-title":"Integrating high-throughput and computational data elucidates bacterial networks.","volume":"429","author":"MW Covert","year":"2004","journal-title":"Nature"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1038\/msb4100162","article-title":"Systematic evaluation of objective functions for predicting intracellular fluxes in <italic>Escherichia coli<\/italic>.","volume":"3","author":"R Schuetz","year":"2007","journal-title":"Mol Syst Biol"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"1797","DOI":"10.1101\/gr.2546004","article-title":"Genome-scale in silico models of <italic>E. coli<\/italic> have multiple equivalent phenotypic states: Assessment of correlated reaction subsets that comprise network states.","volume":"14","author":"JL Reed","year":"2004","journal-title":"Genome Res"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"R108","DOI":"10.1186\/gb-2006-7-11-r108","article-title":"Metabolic network driven analysis of genome-wide transcription data from <italic>Aspergillus nidulans<\/italic>.","volume":"7","author":"H David","year":"2006","journal-title":"Genome Biol"},{"key":"ref10","first-page":"98","article-title":"Global functional profiling of gene expression.","volume":"81","author":"S Draghici","year":"2003","journal-title":"Genomics"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"285","DOI":"10.1016\/j.ymben.2003.12.002","article-title":"Integration of gene expression data into genome-scale metabolic models.","volume":"6","author":"M Akesson","year":"2004","journal-title":"Metab Eng"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"R123","DOI":"10.1186\/gb-2007-8-6-r123","article-title":"Observing metabolic functions at the genome scale.","volume":"8","author":"JM Schwartz","year":"2007","journal-title":"Genome Biol"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1186\/1471-2105-7-23","article-title":"Evaluation of methods for oligonucleotide array data via quantitative real-time PCR.","volume":"7","author":"LX Qin","year":"2006","journal-title":"BMC Bioinformatics"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"789","DOI":"10.1093\/bioinformatics\/btk046","article-title":"Comparison of affymetrix GeneChip expression measures.","volume":"22","author":"RA Irizarry","year":"2006","journal-title":"Bioinformatics"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"886","DOI":"10.1038\/nrmicro1023","article-title":"Genome-scale models of microbial cells: Evaluating the consequences of constraints.","volume":"2","author":"ND Price","year":"2004","journal-title":"Nat Rev Microbiol"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"186","DOI":"10.1038\/nature01149","article-title":"<italic>Escherichia coli<\/italic> K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth.","volume":"420","author":"RU Ibarra","year":"2002","journal-title":"Nature"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"1056","DOI":"10.1038\/ng1432","article-title":"Metabolic gene-deletion strains of <italic>Escherichia coli<\/italic> evolve to computationally predicted growth phenotypes.","volume":"36","author":"SS Fong","year":"2004","journal-title":"Nat Genet"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"121","DOI":"10.1038\/msb4100155","article-title":"A genome-scale metabolic reconstruction for <italic>Escherichia coli<\/italic> K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information.","volume":"3","author":"AM Feist","year":"2007","journal-title":"Mol Syst Biol"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"1365","DOI":"10.1101\/gr.3832305","article-title":"Parallel adaptive evolution cultures of <italic>Escherichia coli<\/italic> lead to convergent growth phenotypes with different gene expression states.","volume":"15","author":"SS Fong","year":"2005","journal-title":"Genome Res"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"647","DOI":"10.1002\/bit.10803","article-title":"Optknock: A bilevel programming framework for identifying gene knockout strategies for microbial strain optimization.","volume":"84","author":"AP Burgard","year":"2003","journal-title":"Biotechnol Bioeng"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"643","DOI":"10.1002\/bit.20542","article-title":"In silico design and adaptive evolution of <italic>Escherichia coli<\/italic> for production of lactic acid.","volume":"91","author":"SS Fong","year":"2005","journal-title":"Biotechnol Bioeng"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"1777","DOI":"10.1073\/pnas.0610772104","article-title":"Global reconstruction of the human metabolic network based on genomic and bibliomic data.","volume":"104","author":"NC Duarte","year":"2007","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"727","DOI":"10.1038\/nprot.2007.99","article-title":"Quantitative prediction of cellular metabolism with constraint-based models: The COBRA toolbox.","volume":"2","author":"SA Becker","year":"2007","journal-title":"Nat Protoc"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"D760","DOI":"10.1093\/nar\/gkl887","article-title":"NCBI GEO: Mining tens of millions of expression profiles\u2013database and tools update.","author":"T Barrett","year":"2007","journal-title":"Nucleic Acids Res"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"R80","DOI":"10.1186\/gb-2004-5-10-r80","article-title":"Bioconductor: Open software development for computational biology and bioinformatics.","volume":"5","author":"RC Gentleman","year":"2004","journal-title":"Genome Biol"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"185","DOI":"10.1093\/bioinformatics\/19.2.185","article-title":"A comparison of normalization methods for high density oligonucleotide array data based on variance and bias.","volume":"19","author":"BM Bolstad","year":"2003","journal-title":"Bioinformatics"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"114","DOI":"10.1152\/physiolgenomics.00045.2006","article-title":"GRB14, GPD1, and GDF8 as potential network collaborators in weight loss-induced improvements in insulin action in human skeletal muscle.","volume":"27","author":"JJ Park","year":"2006","journal-title":"Physiol Genomics"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"e158","DOI":"10.1371\/journal.pmed.0040158","article-title":"TXNIP regulates peripheral glucose metabolism in humans.","volume":"4","author":"H Parikh","year":"2007","journal-title":"PLoS Med"}],"container-title":["PLoS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1000082","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2018,10,19]],"date-time":"2018-10-19T14:44:32Z","timestamp":1539960272000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1000082"}},"subtitle":[],"editor":[{"given":"Herbert M.","family":"Sauro","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2008,5,16]]},"references-count":28,"journal-issue":{"issue":"5","published-online":{"date-parts":[[2008,5,16]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1000082","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2008,5,16]]}}}