{"id":"https://openalex.org/W2118053673","doi":"https://doi.org/10.1093/bioinformatics/btr681","title":"Construction and completion of flux balance models from pathway databases","display_name":"Construction and completion of flux balance models from pathway databases","publication_year":2012,"publication_date":"2012-01-18","ids":{"openalex":"https://openalex.org/W2118053673","doi":"https://doi.org/10.1093/bioinformatics/btr681","mag":"2118053673","pmid":"https://pubmed.ncbi.nlm.nih.gov/22262672"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btr681","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btr681","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/3/388/48872840/bioinformatics_28_3_388.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/28/3/388/48872840/bioinformatics_28_3_388.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5053894822","display_name":"Mario Latendresse","orcid":"https://orcid.org/0000-0002-6292-0158"},"institutions":[{"id":"https://openalex.org/I1298353152","display_name":"SRI International","ror":"https://ror.org/05s570m15","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1298353152"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Mario Latendresse","raw_affiliation_strings":["Bioinformatics Research Group/Artificial Intelligence Center, SRI International, Menlo Park, CA 94025, USA","Bioinformatics Research Group, Artificial Intelligence Center, SRI International Menlo Park, CA 94025, USA"],"affiliations":[{"raw_affiliation_string":"Bioinformatics Research Group/Artificial Intelligence Center, SRI International, Menlo Park, CA 94025, USA","institution_ids":["https://openalex.org/I1298353152"]},{"raw_affiliation_string":"Bioinformatics Research Group, Artificial Intelligence Center, SRI International Menlo Park, CA 94025, USA","institution_ids":["https://openalex.org/I1298353152"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007704760","display_name":"Markus Krummenacker","orcid":"https://orcid.org/0000-0002-2546-3007"},"institutions":[{"id":"https://openalex.org/I1298353152","display_name":"SRI International","ror":"https://ror.org/05s570m15","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1298353152"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Markus Krummenacker","raw_affiliation_strings":["Bioinformatics Research Group/Artificial Intelligence Center, SRI International, Menlo Park, CA 94025, USA","Bioinformatics Research Group, Artificial Intelligence Center, SRI International Menlo Park, CA 94025, USA"],"affiliations":[{"raw_affiliation_string":"Bioinformatics Research Group/Artificial Intelligence Center, SRI International, Menlo Park, CA 94025, USA","institution_ids":["https://openalex.org/I1298353152"]},{"raw_affiliation_string":"Bioinformatics Research Group, Artificial Intelligence Center, SRI International Menlo Park, CA 94025, USA","institution_ids":["https://openalex.org/I1298353152"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027498563","display_name":"Miles Trupp","orcid":"https://orcid.org/0000-0001-8095-053X"},"institutions":[{"id":"https://openalex.org/I1298353152","display_name":"SRI International","ror":"https://ror.org/05s570m15","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1298353152"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Miles Trupp","raw_affiliation_strings":["Bioinformatics Research Group/Artificial Intelligence Center, SRI International, Menlo Park, CA 94025, USA","Bioinformatics Research Group, Artificial Intelligence Center, SRI International Menlo Park, CA 94025, USA"],"affiliations":[{"raw_affiliation_string":"Bioinformatics Research Group/Artificial Intelligence Center, SRI International, Menlo Park, CA 94025, USA","institution_ids":["https://openalex.org/I1298353152"]},{"raw_affiliation_string":"Bioinformatics Research Group, Artificial Intelligence Center, SRI International Menlo Park, CA 94025, USA","institution_ids":["https://openalex.org/I1298353152"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5082071104","display_name":"Peter D. Karp","orcid":"https://orcid.org/0000-0002-5876-6418"},"institutions":[{"id":"https://openalex.org/I1298353152","display_name":"SRI International","ror":"https://ror.org/05s570m15","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1298353152"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Peter D. Karp","raw_affiliation_strings":["Bioinformatics Research Group/Artificial Intelligence Center, SRI International, Menlo Park, CA 94025, USA","Bioinformatics Research Group, Artificial Intelligence Center, SRI International Menlo Park, CA 94025, USA"],"affiliations":[{"raw_affiliation_string":"Bioinformatics Research Group/Artificial Intelligence Center, SRI International, Menlo Park, CA 94025, USA","institution_ids":["https://openalex.org/I1298353152"]},{"raw_affiliation_string":"Bioinformatics Research Group, Artificial Intelligence Center, SRI International Menlo Park, CA 94025, USA","institution_ids":["https://openalex.org/I1298353152"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5053894822"],"corresponding_institution_ids":["https://openalex.org/I1298353152"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":6.0504,"has_fulltext":false,"cited_by_count":97,"citation_normalized_percentile":{"value":0.97312253,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"28","issue":"3","first_page":"388","last_page":"396"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":1.0,"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":1.0,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9959999918937683,"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":0.994700014591217,"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/database","display_name":"Database","score":0.5884471535682678},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5654796361923218},{"id":"https://openalex.org/keywords/balance","display_name":"Balance (ability)","score":0.5467461943626404},{"id":"https://openalex.org/keywords/flux","display_name":"Flux (metallurgy)","score":0.5161348581314087},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.1364094316959381}],"concepts":[{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.5884471535682678},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5654796361923218},{"id":"https://openalex.org/C168031717","wikidata":"https://www.wikidata.org/wiki/Q1530280","display_name":"Balance (ability)","level":2,"score":0.5467461943626404},{"id":"https://openalex.org/C68709404","wikidata":"https://www.wikidata.org/wiki/Q1134475","display_name":"Flux (metallurgy)","level":2,"score":0.5161348581314087},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.1364094316959381},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.0},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.0},{"id":"https://openalex.org/C99508421","wikidata":"https://www.wikidata.org/wiki/Q2678675","display_name":"Physical medicine and rehabilitation","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btr681","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btr681","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/3/388/48872840/bioinformatics_28_3_388.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:22262672","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22262672","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.870.3597","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.870.3597","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://bioinformatics.oxfordjournals.org/content/28/3/388.full.pdf","raw_type":"text"},{"id":"pmh:oai:europepmc.org:2273118","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3268246","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btr681","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btr681","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/3/388/48872840/bioinformatics_28_3_388.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2118053673.pdf","grobid_xml":"https://content.openalex.org/works/W2118053673.grobid-xml"},"referenced_works_count":38,"referenced_works":["https://openalex.org/W75855990","https://openalex.org/W1543408256","https://openalex.org/W1965264154","https://openalex.org/W1986656046","https://openalex.org/W1989277878","https://openalex.org/W2041115195","https://openalex.org/W2049059275","https://openalex.org/W2056281205","https://openalex.org/W2058501095","https://openalex.org/W2073837631","https://openalex.org/W2078355959","https://openalex.org/W2084782365","https://openalex.org/W2085993965","https://openalex.org/W2098983518","https://openalex.org/W2100084634","https://openalex.org/W2102944388","https://openalex.org/W2106193566","https://openalex.org/W2107459209","https://openalex.org/W2115107663","https://openalex.org/W2127872845","https://openalex.org/W2128601422","https://openalex.org/W2131684839","https://openalex.org/W2134394193","https://openalex.org/W2139915240","https://openalex.org/W2147472054","https://openalex.org/W2149829228","https://openalex.org/W2165554064","https://openalex.org/W2166262739","https://openalex.org/W2167919951","https://openalex.org/W2168465568","https://openalex.org/W2170427655","https://openalex.org/W2170940180","https://openalex.org/W2171092495","https://openalex.org/W2314807489","https://openalex.org/W4233060585","https://openalex.org/W4238101851","https://openalex.org/W4285719527","https://openalex.org/W6664772463"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W2382290278","https://openalex.org/W2350741829","https://openalex.org/W2530322880","https://openalex.org/W1596801655","https://openalex.org/W2359140296"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":6},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":8},{"year":2018,"cited_by_count":9},{"year":2017,"cited_by_count":12},{"year":2016,"cited_by_count":6},{"year":2015,"cited_by_count":10},{"year":2014,"cited_by_count":16},{"year":2013,"cited_by_count":12},{"year":2012,"cited_by_count":7}],"updated_date":"2026-04-04T16:13:02.066488","created_date":"2025-10-10T00:00:00"}