{"id":"https://openalex.org/W2162666840","doi":"https://doi.org/10.1371/journal.pcbi.1000082","title":"Context-Specific Metabolic Networks Are Consistent with Experiments","display_name":"Context-Specific Metabolic Networks Are Consistent with Experiments","publication_year":2008,"publication_date":"2008-05-15","ids":{"openalex":"https://openalex.org/W2162666840","doi":"https://doi.org/10.1371/journal.pcbi.1000082","mag":"2162666840","pmid":"https://pubmed.ncbi.nlm.nih.gov/18483554"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1000082","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1000082","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1000082&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1000082&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5037382955","display_name":"Scott A. Becker","orcid":"https://orcid.org/0000-0003-0194-4874"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Scott A. Becker","raw_affiliation_strings":["Department of Bioengineering, University of California San Diego, La Jolla, California, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of California San Diego, La Jolla, California, United States of America","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5051097609","display_name":"Bernhard \u00d8. Palsson","orcid":"https://orcid.org/0000-0003-2357-6785"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Bernhard O. Palsson","raw_affiliation_strings":["Department of Bioengineering, University of California San Diego, La Jolla, California, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of California San Diego, La Jolla, California, United States of America","institution_ids":["https://openalex.org/I36258959"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5051097609"],"corresponding_institution_ids":["https://openalex.org/I36258959"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":5.3954,"has_fulltext":true,"cited_by_count":629,"citation_normalized_percentile":{"value":0.96561252,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"4","issue":"5","first_page":"e1000082","last_page":"e1000082"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9916999936103821,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10171","display_name":"Biofuel production and bioconversion","score":0.9861999750137329,"subfield":{"id":"https://openalex.org/subfields/2204","display_name":"Biomedical Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/in-silico","display_name":"In silico","score":0.6483362913131714},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6440489292144775},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.5952062606811523},{"id":"https://openalex.org/keywords/metabolic-network","display_name":"Metabolic network","score":0.5223796963691711},{"id":"https://openalex.org/keywords/systems-biology","display_name":"Systems biology","score":0.47958317399024963},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.47771477699279785},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.47529375553131104},{"id":"https://openalex.org/keywords/gene-expression-profiling","display_name":"Gene expression profiling","score":0.46871891617774963},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4365261197090149},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.32370197772979736},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.2881639897823334},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.22076526284217834}],"concepts":[{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.6483362913131714},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6440489292144775},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5952062606811523},{"id":"https://openalex.org/C101810790","wikidata":"https://www.wikidata.org/wiki/Q2263094","display_name":"Metabolic network","level":2,"score":0.5223796963691711},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.47958317399024963},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.47771477699279785},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.47529375553131104},{"id":"https://openalex.org/C18431079","wikidata":"https://www.wikidata.org/wiki/Q1502169","display_name":"Gene expression profiling","level":4,"score":0.46871891617774963},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4365261197090149},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.32370197772979736},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.2881639897823334},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.22076526284217834},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012107","descriptor_name":"Research Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012107","descriptor_name":"Research Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012107","descriptor_name":"Research Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1371/journal.pcbi.1000082","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1000082","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1000082&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},{"id":"pmid:18483554","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/18483554","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.275.6060","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.275.6060","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/ec/9c/PLoS_Comput_Biol_2008_May_16_4(5)_e1000082.tar.gz","raw_type":"text"},{"id":"pmh:oai:RePEc:plo:pcbi00:1000082","is_oa":false,"landing_page_url":"https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1000082","pdf_url":null,"source":{"id":"https://openalex.org/S4306401271","display_name":"RePEc: Research Papers in Economics","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I77793887","host_organization_name":"Federal Reserve Bank of St. Louis","host_organization_lineage":["https://openalex.org/I77793887"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article"},{"id":"pmh:oai:doaj.org/article:11ece9b2364e48acb2a9008dac481f22","is_oa":true,"landing_page_url":"https://doaj.org/article/11ece9b2364e48acb2a9008dac481f22","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 4, Iss 5, p e1000082 (2008)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:2366062","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2366062","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Comput Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1000082","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1000082","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1000082&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2162666840.pdf","grobid_xml":"https://content.openalex.org/works/W2162666840.grobid-xml"},"referenced_works_count":29,"referenced_works":["https://openalex.org/W1535641839","https://openalex.org/W1840387029","https://openalex.org/W1982309495","https://openalex.org/W1993170943","https://openalex.org/W1996529795","https://openalex.org/W2003489966","https://openalex.org/W2004964623","https://openalex.org/W2009940763","https://openalex.org/W2009990638","https://openalex.org/W2012991302","https://openalex.org/W2025663053","https://openalex.org/W2031681107","https://openalex.org/W2046254395","https://openalex.org/W2047649079","https://openalex.org/W2056218698","https://openalex.org/W2104108767","https://openalex.org/W2111421616","https://openalex.org/W2119015994","https://openalex.org/W2120865735","https://openalex.org/W2130301347","https://openalex.org/W2130364940","https://openalex.org/W2147472054","https://openalex.org/W2154362705","https://openalex.org/W2158951820","https://openalex.org/W2160697532","https://openalex.org/W2161309440","https://openalex.org/W2170427655","https://openalex.org/W2615601957","https://openalex.org/W4238101851"],"related_works":["https://openalex.org/W1504020891","https://openalex.org/W2133150343","https://openalex.org/W2072067873","https://openalex.org/W2047632644","https://openalex.org/W2031492751","https://openalex.org/W3033588432","https://openalex.org/W2147102947","https://openalex.org/W2075919068","https://openalex.org/W1989168955","https://openalex.org/W235738631"],"abstract_inverted_index":{"Reconstructions":[0],"of":[1,10,44,142,168,172,189],"cellular":[2],"metabolism":[3,190],"are":[4,21,192],"publicly":[5],"available":[6,127],"for":[7,80,165],"a":[8,48,60,81,86,133,140,148],"variety":[9],"different":[11],"microorganisms":[12],"and":[13,23,94,109,163,176],"some":[14],"mammalian":[15],"genomes.":[16],"To":[17],"date,":[18],"these":[19,67],"reconstructions":[20,70],"\"genome-scale\"":[22],"strive":[24],"to":[25,65,97,116,194],"include":[26],"all":[27],"reactions":[28,46],"implied":[29],"by":[30,92],"the":[31,45,118,126,130,195,198],"genome":[32],"annotation,":[33],"as":[34,36],"well":[35],"those":[37],"with":[38,125,147,160],"direct":[39],"experimental":[40],"evidence.":[41],"Clearly,":[42],"many":[43],"in":[47,59,77],"genome-scale":[49,69],"reconstruction":[50,120],"will":[51,74],"not":[52],"be":[53],"active":[54],"under":[55],"particular":[56,61,82,149],"conditions":[57,196],"or":[58,111],"cell":[62],"type.":[63],"Methods":[64],"tailor":[66],"comprehensive":[68],"into":[71],"context-specific":[72,119],"networks":[73],"aid":[75],"predictive":[76],"silico":[78],"modeling":[79],"situation.":[83],"We":[84,152],"present":[85],"method":[87],"called":[88],"Gene":[89],"Inactivity":[90],"Moderated":[91],"Metabolism":[93],"Expression":[95],"(GIMME)":[96],"achieve":[98],"this":[99,155],"goal.":[100],"The":[101],"GIMME":[102],"algorithm":[103,131,156],"uses":[104],"quantitative":[105,134],"gene":[106,143],"expression":[107,144,199],"data":[108,145,201],"one":[110],"more":[112],"presupposed":[113],"metabolic":[114,150,173],"objectives":[115],"produce":[117],"that":[121,154,191],"is":[122,146,202],"most":[123],"consistent":[124,139,159],"data.":[128],"Furthermore,":[129],"provides":[132],"inconsistency":[135],"score":[136],"indicating":[137],"how":[138],"set":[141],"objective.":[151],"show":[153],"produces":[157],"results":[158],"biological":[161],"experiments":[162],"intuition":[164],"adaptive":[166],"evolution":[167],"bacteria,":[169],"rational":[170],"design":[171],"engineering":[174],"strains,":[175],"human":[177],"skeletal":[178],"muscle":[179],"cells.":[180],"This":[181],"work":[182],"represents":[183],"progress":[184],"towards":[185],"producing":[186],"constraint-based":[187],"models":[188],"specific":[193],"where":[197],"profiling":[200],"available.":[203]},"counts_by_year":[{"year":2026,"cited_by_count":18},{"year":2025,"cited_by_count":42},{"year":2024,"cited_by_count":45},{"year":2023,"cited_by_count":56},{"year":2022,"cited_by_count":42},{"year":2021,"cited_by_count":39},{"year":2020,"cited_by_count":48},{"year":2019,"cited_by_count":45},{"year":2018,"cited_by_count":31},{"year":2017,"cited_by_count":42},{"year":2016,"cited_by_count":38},{"year":2015,"cited_by_count":46},{"year":2014,"cited_by_count":40},{"year":2013,"cited_by_count":22},{"year":2012,"cited_by_count":37}],"updated_date":"2026-04-23T09:07:50.710637","created_date":"2025-10-10T00:00:00"}