{"id":"https://openalex.org/W2000887105","doi":"https://doi.org/10.1186/1752-0509-5-147","title":"TIGER: Toolbox for integrating genome-scale metabolic models, expression data, and transcriptional regulatory networks","display_name":"TIGER: Toolbox for integrating genome-scale metabolic models, expression data, and transcriptional regulatory networks","publication_year":2011,"publication_date":"2011-09-23","ids":{"openalex":"https://openalex.org/W2000887105","doi":"https://doi.org/10.1186/1752-0509-5-147","mag":"2000887105","pmid":"https://pubmed.ncbi.nlm.nih.gov/21943338","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/3224351"},"language":"en","primary_location":{"id":"doi:10.1186/1752-0509-5-147","doi":"https://doi.org/10.1186/1752-0509-5-147","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1752-0509-5-147","pdf_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-5-147","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","jufo-1","poland-70","vabb-shw"],"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Systems Biology","raw_type":"journal-article"},"volume":null,"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-5-147","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5085807421","display_name":"Paul A. Jensen","orcid":"https://orcid.org/0000-0002-1257-9836","observed_orcids":["https://orcid.org/0000-0002-1257-9836"]},"institutions":[{"id":"https://openalex.org/I51556381","display_name":"University of Virginia","ror":"https://ror.org/0153tk833","country_code":"US","type":"education","lineage":["https://openalex.org/I51556381"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Paul A Jensen","raw_affiliation_strings":["Department of Biomedical Engineering, University of Virginia, Charlottesville, VA 22908, USA","Dept. of Biomedical Engineering, University of Virginia, Charlottesville, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomedical Engineering, University of Virginia, Charlottesville, VA 22908, USA","institution_ids":["https://openalex.org/I51556381"]},{"raw_affiliation_string":"Dept. of Biomedical Engineering, University of Virginia, Charlottesville, USA","institution_ids":["https://openalex.org/I51556381"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5104090873","display_name":"Kyla Lutz","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I51556381","display_name":"University of Virginia","ror":"https://ror.org/0153tk833","country_code":"US","type":"education","lineage":["https://openalex.org/I51556381"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kyla A Lutz","raw_affiliation_strings":["Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, 22908, USA","Dept. of Biomedical Engineering, University of Virginia, Charlottesville, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, 22908, USA","institution_ids":["https://openalex.org/I51556381"]},{"raw_affiliation_string":"Dept. of Biomedical Engineering, University of Virginia, Charlottesville, USA","institution_ids":["https://openalex.org/I51556381"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5000119406","display_name":"Jason A. Papin","orcid":"https://orcid.org/0000-0002-2769-5805","observed_orcids":["https://orcid.org/0000-0002-2769-5805"]},"institutions":[{"id":"https://openalex.org/I51556381","display_name":"University of Virginia","ror":"https://ror.org/0153tk833","country_code":"US","type":"education","lineage":["https://openalex.org/I51556381"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Jason A Papin","raw_affiliation_strings":["Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, 22908, USA","Dept. of Biomedical Engineering, University of Virginia, Charlottesville, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, 22908, USA","institution_ids":["https://openalex.org/I51556381"]},{"raw_affiliation_string":"Dept. of Biomedical Engineering, University of Virginia, Charlottesville, USA","institution_ids":["https://openalex.org/I51556381"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5000119406"],"corresponding_institution_ids":["https://openalex.org/I51556381"],"apc_list":{"value":2290,"currency":"USD","value_usd":2290},"apc_paid":{"value":2290,"currency":"USD","value_usd":2290},"fwci":2.8027,"has_fulltext":true,"cited_by_count":108,"citation_normalized_percentile":{"value":0.91447082,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":92,"max":99},"biblio":{"volume":"5","issue":"1","first_page":"147","last_page":"147"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9746000170707703,"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":0.9746000170707703,"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":0.024399999529123306,"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":0.0005000000237487257,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/genome-scale-metabolic-models","display_name":"genome-scale metabolic models","score":0.9959999918937683},{"id":"https://openalex.org/keywords/transcriptional-regulatory-networks","display_name":"transcriptional regulatory networks","score":0.9309999942779541},{"id":"https://openalex.org/keywords/mixed-integer-programming","display_name":"mixed integer programming","score":0.8880000114440918},{"id":"https://openalex.org/keywords/flux-balance-analysis","display_name":"flux balance analysis","score":0.6850000023841858},{"id":"https://openalex.org/keywords/saccharomyces-cerevisiae","display_name":"Saccharomyces cerevisiae","score":0.8320000171661377}],"concepts":[{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.6752867102622986},{"id":"https://openalex.org/C66746571","wikidata":"https://www.wikidata.org/wiki/Q1134833","display_name":"ENCODE","level":3,"score":0.664432942867279},{"id":"https://openalex.org/C167091322","wikidata":"https://www.wikidata.org/wiki/Q5463029","display_name":"Flux balance analysis","level":2,"score":0.6453229188919067},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5836803317070007},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.5537511110305786},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5310020446777344},{"id":"https://openalex.org/C2777655017","wikidata":"https://www.wikidata.org/wiki/Q1501161","display_name":"Toolbox","level":2,"score":0.4466889500617981},{"id":"https://openalex.org/C27153228","wikidata":"https://www.wikidata.org/wiki/Q3787274","display_name":"Transcriptional regulation","level":4,"score":0.426962673664093},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.36857789754867554},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2794431447982788},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.16903918981552124},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.138344407081604},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D055432","descriptor_name":"Metabolomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1186/1752-0509-5-147","doi":"https://doi.org/10.1186/1752-0509-5-147","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1752-0509-5-147","pdf_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-5-147","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","jufo-1","poland-70","vabb-shw"],"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Systems Biology","raw_type":"journal-article"},{"id":"pmh:oai:pubmedcentral.nih.gov:3224351","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3224351","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,"listed_in":[],"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":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Syst Biol","raw_type":"Text"},{"id":"pmid:21943338","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/21943338","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,"listed_in":[],"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":"BMC systems biology","raw_type":"Journal Article"}],"best_oa_location":{"id":"doi:10.1186/1752-0509-5-147","doi":"https://doi.org/10.1186/1752-0509-5-147","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1752-0509-5-147","pdf_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-5-147","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","jufo-1","poland-70","vabb-shw"],"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Systems Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G6385745987","display_name":"Network Analysis of Pathogenicity in Pseudomonas aeruginosa","funder_award_id":"R01GM088244","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G6671297155","display_name":null,"funder_award_id":"CAREER","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G7356386875","display_name":"CAREER: Interrogating the pathogen-host relationship with genome-scale network analysis","funder_award_id":"0643548","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"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":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2000887105.pdf","grobid_xml":"https://content.openalex.org/works/W2000887105.grobid-xml"},"referenced_works_count":28,"referenced_works":["https://openalex.org/W1507194301","https://openalex.org/W1978408474","https://openalex.org/W1982309495","https://openalex.org/W1997872521","https://openalex.org/W2022616740","https://openalex.org/W2029403511","https://openalex.org/W2031010225","https://openalex.org/W2036748232","https://openalex.org/W2048214825","https://openalex.org/W2076262841","https://openalex.org/W2078355959","https://openalex.org/W2098450614","https://openalex.org/W2098824895","https://openalex.org/W2098983518","https://openalex.org/W2107333582","https://openalex.org/W2109880272","https://openalex.org/W2112933558","https://openalex.org/W2127020923","https://openalex.org/W2128776645","https://openalex.org/W2130364940","https://openalex.org/W2144568050","https://openalex.org/W2147472054","https://openalex.org/W2154061034","https://openalex.org/W2162666840","https://openalex.org/W2168244801","https://openalex.org/W2795674018","https://openalex.org/W4238101851","https://openalex.org/W7100096270"],"related_works":["https://openalex.org/W2568731166","https://openalex.org/W7097530854","https://openalex.org/W2955844457","https://openalex.org/W3208634423","https://openalex.org/W3202091418","https://openalex.org/W2139896722","https://openalex.org/W2781174748","https://openalex.org/W1975783914","https://openalex.org/W2259525313","https://openalex.org/W2949144734"],"abstract_inverted_index":{"BACKGROUND:":[0],"Several":[1],"methods":[2],"have":[3],"been":[4,47],"developed":[5],"for":[6,72,89,159,204],"analyzing":[7],"genome-scale":[8,127,143,210],"models":[9,128,150,181,212],"of":[10,16,65,76,100,109,118,129,141,151,182,193],"metabolism":[11,130],"and":[12,33,38,68,94,131,149,162,178,207,216],"transcriptional":[13,132,152,183,190],"regulation.":[14,133],"Many":[15],"these":[17,51,61],"methods,":[18],"such":[19],"as":[20,156],"Flux":[21],"Balance":[22],"Analysis,":[23],"use":[24],"constrained":[25],"optimization":[26,58],"to":[27,49,78,121,175],"predict":[28],"relationships":[29,54],"between":[30],"metabolic":[31,144,164,211],"flux":[32],"the":[34,74,139,188],"genes":[35],"that":[36],"encode":[37,50],"regulate":[39],"enzyme":[40],"activity.":[41],"Recently,":[42],"mixed":[43,110],"integer":[44,111],"programming":[45],"has":[46],"used":[48,174],"gene-protein-reaction":[52],"(GPR)":[53],"into":[55,106],"a":[56,70,79,87,98,107,142,157,201],"single":[57],"problem,":[59],"but":[60],"techniques":[62],"are":[63],"often":[64],"limited":[66],"generality":[67],"lack":[69],"tool":[71],"automating":[73],"conversion":[75],"rules":[77,105],"coupled":[80],"regulatory/metabolic":[81],"model.":[82],"RESULTS:":[83],"We":[84,134],"present":[85],"TIGER,":[86],"Toolbox":[88],"Integrating":[90],"Genome-scale":[91],"Metabolism,":[92],"Expression,":[93],"Regulation.":[95],"TIGER":[96,137,198],"converts":[97],"series":[99],"generalized,":[101],"Boolean":[102],"or":[103],"multilevel":[104],"set":[108],"inequalities.":[112],"The":[113,197],"package":[114,199],"also":[115],"includes":[116],"implementations":[117],"existing":[119,180,209],"algorithms":[120,171],"integrate":[122],"high-throughput":[123,217],"expression":[124],"data":[125],"with":[126,146,185,213],"demonstrate":[135,168],"how":[136,169],"automates":[138],"coupling":[140],"model":[145],"GPR":[147],"logic":[148],"regulation,":[153],"thereby":[154],"serving":[155],"platform":[158,203],"algorithm":[160,205],"development":[161,206],"large-scale":[163],"analysis.":[165],"Additionally,":[166],"we":[167],"TIGER's":[170],"can":[172],"be":[173],"identify":[176],"inconsistencies":[177],"improve":[179],"regulation":[184],"examples":[186],"from":[187],"reconstructed":[189],"regulatory":[191,214],"network":[192],"Saccharomyces":[194],"cerevisiae.":[195],"CONCLUSION:":[196],"provides":[200],"consistent":[202],"extending":[208],"networks":[215],"data.":[218]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":6},{"year":2023,"cited_by_count":10},{"year":2022,"cited_by_count":5},{"year":2021,"cited_by_count":9},{"year":2020,"cited_by_count":10},{"year":2019,"cited_by_count":10},{"year":2018,"cited_by_count":10},{"year":2017,"cited_by_count":5},{"year":2016,"cited_by_count":8},{"year":2015,"cited_by_count":8},{"year":2014,"cited_by_count":9},{"year":2013,"cited_by_count":4},{"year":2012,"cited_by_count":9}],"updated_date":"2026-11-04T10:54:05.112534","created_date":"2016-06-24T00:00:00"}
