{"id":"https://openalex.org/W2963932607","doi":"https://doi.org/10.1371/journal.pcbi.1007185","title":"Assessing key decisions for transcriptomic data integration in biochemical networks","display_name":"Assessing key decisions for transcriptomic data integration in biochemical networks","publication_year":2019,"publication_date":"2019-07-19","ids":{"openalex":"https://openalex.org/W2963932607","doi":"https://doi.org/10.1371/journal.pcbi.1007185","mag":"2963932607","pmid":"https://pubmed.ncbi.nlm.nih.gov/31323017"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1007185","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1007185","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1007185&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.1007185&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5063466800","display_name":"Anne Richelle","orcid":"https://orcid.org/0000-0003-1491-114X"},"institutions":[{"id":"https://openalex.org/I2802640032","display_name":"Foundation Center","ror":"https://ror.org/0377f6951","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I2802640032"]},{"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"]},{"id":"https://openalex.org/I4210106615","display_name":"Novo Nordisk (United States)","ror":"https://ror.org/011y67d23","country_code":"US","type":"company","lineage":["https://openalex.org/I189090001","https://openalex.org/I2801134892","https://openalex.org/I4210106615","https://openalex.org/I4210159963"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Anne Richelle","raw_affiliation_strings":["Department of Pediatrics, University of California, San Diego, School of Medicine, La Jolla, California, United States of America","Novo Nordisk Foundation Center for Biosustainability at the University of California, San Diego, School of Medicine, La Jolla, California, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Pediatrics, University of California, San Diego, School of Medicine, La Jolla, California, United States of America","institution_ids":["https://openalex.org/I36258959"]},{"raw_affiliation_string":"Novo Nordisk Foundation Center for Biosustainability at the University of California, San Diego, School of Medicine, La Jolla, California, United States of America","institution_ids":["https://openalex.org/I36258959","https://openalex.org/I2802640032","https://openalex.org/I4210106615"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5055598565","display_name":"Chintan Joshi","orcid":"https://orcid.org/0000-0002-9339-2511"},"institutions":[{"id":"https://openalex.org/I2802640032","display_name":"Foundation Center","ror":"https://ror.org/0377f6951","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I2802640032"]},{"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"]},{"id":"https://openalex.org/I4210106615","display_name":"Novo Nordisk (United States)","ror":"https://ror.org/011y67d23","country_code":"US","type":"company","lineage":["https://openalex.org/I189090001","https://openalex.org/I2801134892","https://openalex.org/I4210106615","https://openalex.org/I4210159963"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Chintan Joshi","raw_affiliation_strings":["Department of Pediatrics, University of California, San Diego, School of Medicine, La Jolla, California, United States of America","Novo Nordisk Foundation Center for Biosustainability at the University of California, San Diego, School of Medicine, La Jolla, California, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Pediatrics, University of California, San Diego, School of Medicine, La Jolla, California, United States of America","institution_ids":["https://openalex.org/I36258959"]},{"raw_affiliation_string":"Novo Nordisk Foundation Center for Biosustainability at the University of California, San Diego, School of Medicine, La Jolla, California, United States of America","institution_ids":["https://openalex.org/I36258959","https://openalex.org/I2802640032","https://openalex.org/I4210106615"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5074538839","display_name":"Nathan E. Lewis","orcid":"https://orcid.org/0000-0001-7700-3654"},"institutions":[{"id":"https://openalex.org/I2802640032","display_name":"Foundation Center","ror":"https://ror.org/0377f6951","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I2802640032"]},{"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"]},{"id":"https://openalex.org/I4210106615","display_name":"Novo Nordisk (United States)","ror":"https://ror.org/011y67d23","country_code":"US","type":"company","lineage":["https://openalex.org/I189090001","https://openalex.org/I2801134892","https://openalex.org/I4210106615","https://openalex.org/I4210159963"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Nathan E. Lewis","raw_affiliation_strings":["Department of Bioengineering, University of California, San Diego, La Jolla, California, United States of America","Department of Pediatrics, University of California, San Diego, School of Medicine, La Jolla, California, United States of America","Novo Nordisk Foundation Center for Biosustainability at the University of California, San Diego, School of Medicine, 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"]},{"raw_affiliation_string":"Department of Pediatrics, University of California, San Diego, School of Medicine, La Jolla, California, United States of America","institution_ids":["https://openalex.org/I36258959"]},{"raw_affiliation_string":"Novo Nordisk Foundation Center for Biosustainability at the University of California, San Diego, School of Medicine, La Jolla, California, United States of America","institution_ids":["https://openalex.org/I36258959","https://openalex.org/I2802640032","https://openalex.org/I4210106615"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5074538839"],"corresponding_institution_ids":["https://openalex.org/I2802640032","https://openalex.org/I36258959","https://openalex.org/I4210106615"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":3.693,"has_fulltext":true,"cited_by_count":79,"citation_normalized_percentile":{"value":0.94166604,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"15","issue":"7","first_page":"e1007185","last_page":"e1007185"},"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":0.9988999962806702,"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":0.9965000152587891,"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/biological-network","display_name":"Biological network","score":0.6406834721565247},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.6112287640571594},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.5762427449226379},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5109023451805115},{"id":"https://openalex.org/keywords/metabolic-network","display_name":"Metabolic network","score":0.5105780363082886},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4766681492328644},{"id":"https://openalex.org/keywords/systems-biology","display_name":"Systems biology","score":0.47045814990997314},{"id":"https://openalex.org/keywords/key","display_name":"Key (lock)","score":0.41702359914779663},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3849424123764038},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.36450204253196716},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.34578776359558105},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.2981340289115906},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.19682952761650085}],"concepts":[{"id":"https://openalex.org/C28225019","wikidata":"https://www.wikidata.org/wiki/Q4915005","display_name":"Biological network","level":2,"score":0.6406834721565247},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.6112287640571594},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.5762427449226379},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5109023451805115},{"id":"https://openalex.org/C101810790","wikidata":"https://www.wikidata.org/wiki/Q2263094","display_name":"Metabolic network","level":2,"score":0.5105780363082886},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4766681492328644},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.47045814990997314},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.41702359914779663},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3849424123764038},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.36450204253196716},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.34578776359558105},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.2981340289115906},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.19682952761650085},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C38652104","wikidata":"https://www.wikidata.org/wiki/Q3510521","display_name":"Computer security","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D001669","descriptor_name":"Biochemical Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001669","descriptor_name":"Biochemical Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001669","descriptor_name":"Biochemical Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001669","descriptor_name":"Biochemical Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003627","descriptor_name":"Data Interpretation, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003627","descriptor_name":"Data Interpretation, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003627","descriptor_name":"Data Interpretation, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003627","descriptor_name":"Data Interpretation, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003661","descriptor_name":"Decision Support Techniques","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003661","descriptor_name":"Decision Support Techniques","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003661","descriptor_name":"Decision Support Techniques","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003661","descriptor_name":"Decision Support Techniques","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":"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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"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},{"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":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1371/journal.pcbi.1007185","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1007185","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1007185&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:31323017","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31323017","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:doaj.org/article:a997a824b3a44f66b521b23cbc82fd7d","is_oa":true,"landing_page_url":"https://doaj.org/article/a997a824b3a44f66b521b23cbc82fd7d","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 15, Iss 7, p e1007185 (2019)","raw_type":"article"},{"id":"pmh:oai:escholarship.org:ark:/13030/qt07w948k1","is_oa":true,"landing_page_url":"https://escholarship.org/uc/item/07w948k1","pdf_url":null,"source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"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 Computational Biology, vol 15, iss 7","raw_type":"article"},{"id":"pmh:oai:europepmc.org:5629185","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6668847","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:figshare.com:article/8966549","is_oa":true,"landing_page_url":"https://figshare.com/articles/dataset/Assessing_key_decisions_for_transcriptomic_data_integration_in_biochemical_networks/8966549","pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"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":"","raw_type":"Dataset"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1007185","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1007185","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1007185&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":[{"id":"https://metadata.un.org/sdg/16","score":0.6000000238418579,"display_name":"Peace, Justice and strong institutions"}],"awards":[{"id":"https://openalex.org/G1824364810","display_name":null,"funder_award_id":"Lilly Innovation Fellowship Award","funder_id":"https://openalex.org/F4320307758","funder_display_name":"Eli Lilly and Company"},{"id":"https://openalex.org/G3106793215","display_name":null,"funder_award_id":"GM119850","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G4592421031","display_name":null,"funder_award_id":"analysis","funder_id":"https://openalex.org/F4320322436","funder_display_name":"Novo Nordisk"},{"id":"https://openalex.org/G4907446228","display_name":null,"funder_award_id":"R35 GM119850","funder_id":"https://openalex.org/F4320323153","funder_display_name":"Danmarks Tekniske Universitet"},{"id":"https://openalex.org/G5127131829","display_name":null,"funder_award_id":"NNF16CC0021858","funder_id":"https://openalex.org/F4320325957","funder_display_name":"Novo Nordisk Fonden"},{"id":"https://openalex.org/G575492909","display_name":null,"funder_award_id":"R35 GM119850","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G7304640901","display_name":null,"funder_award_id":"Keck Funding","funder_id":"https://openalex.org/F4320306159","funder_display_name":"W. M. Keck Foundation"}],"funders":[{"id":"https://openalex.org/F4320306159","display_name":"W. M. Keck Foundation","ror":"https://ror.org/000dswa46"},{"id":"https://openalex.org/F4320307758","display_name":"Eli Lilly and Company","ror":"https://ror.org/01qat3289"},{"id":"https://openalex.org/F4320322436","display_name":"Novo Nordisk","ror":"https://ror.org/0435rc536"},{"id":"https://openalex.org/F4320323153","display_name":"Danmarks Tekniske Universitet","ror":"https://ror.org/04qtj9h94"},{"id":"https://openalex.org/F4320325957","display_name":"Novo Nordisk Fonden","ror":"https://ror.org/04txyc737"},{"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/W2963932607.pdf","grobid_xml":"https://content.openalex.org/works/W2963932607.grobid-xml"},"referenced_works_count":37,"referenced_works":["https://openalex.org/W1982309495","https://openalex.org/W2000887105","https://openalex.org/W2003495172","https://openalex.org/W2009282793","https://openalex.org/W2012034410","https://openalex.org/W2012991302","https://openalex.org/W2045921664","https://openalex.org/W2062581381","https://openalex.org/W2067094344","https://openalex.org/W2068855150","https://openalex.org/W2106894342","https://openalex.org/W2113365252","https://openalex.org/W2119781196","https://openalex.org/W2121404287","https://openalex.org/W2124653577","https://openalex.org/W2128312954","https://openalex.org/W2128776645","https://openalex.org/W2129918713","https://openalex.org/W2144589197","https://openalex.org/W2152186196","https://openalex.org/W2162666840","https://openalex.org/W2171214502","https://openalex.org/W2172129062","https://openalex.org/W2247374442","https://openalex.org/W2254469873","https://openalex.org/W2264489059","https://openalex.org/W2264568396","https://openalex.org/W2291465340","https://openalex.org/W2397999424","https://openalex.org/W2418056440","https://openalex.org/W2587946751","https://openalex.org/W2590457070","https://openalex.org/W2592821669","https://openalex.org/W2762019694","https://openalex.org/W2949189298","https://openalex.org/W3100644055","https://openalex.org/W6666145905"],"related_works":["https://openalex.org/W2158714033","https://openalex.org/W2072067873","https://openalex.org/W78967844","https://openalex.org/W2949927938","https://openalex.org/W2047632644","https://openalex.org/W2031492751","https://openalex.org/W3213185671","https://openalex.org/W4210989272","https://openalex.org/W4206945140","https://openalex.org/W4386628104"],"abstract_inverted_index":{"To":[0,156],"gain":[1],"insights":[2],"into":[3],"complex":[4],"biological":[5],"processes,":[6],"genome-scale":[7,137],"data":[8,49,80,187],"(e.g.,":[9],"RNA-Seq)":[10],"are":[11,96],"often":[12],"overlaid":[13],"on":[14,45,78],"biochemical":[15,190],"networks.":[16,51],"However,":[17,98],"many":[18],"networks":[19,191],"do":[20],"not":[21,105],"have":[22],"a":[23,115,141],"one-to-one":[24],"relationship":[25],"between":[26],"genes":[27],"and":[28,37,88,121,192],"network":[29,139],"edges,":[30],"due":[31],"to":[32,47,62,81,185],"the":[33,71,83,90,99,136,147,158,168,194],"existence":[34],"of":[35,76,101,125,135,170,196],"isozymes":[36],"protein":[38],"complexes.":[39],"Therefore,":[40],"decisions":[41,58,103,166],"must":[42],"be":[43,129],"made":[44],"how":[46,61,164],"overlay":[48],"onto":[50],"For":[52],"example,":[53],"for":[54,74],"metabolic":[55,138,198],"networks,":[56],"these":[57,94,102,165],"include":[59],"(1)":[60],"integrate":[63],"gene":[64,85],"expression":[65,79,143],"levels":[66],"using":[67,114],"gene-protein-reaction":[68],"rules,":[69],"(2)":[70],"approach":[72,154],"used":[73],"selection":[75],"thresholds":[77],"consider":[82],"associated":[84],"as":[86,131],"\"active\",":[87],"(3)":[89],"order":[91],"in":[92],"which":[93,126],"steps":[95],"imposed.":[97],"influence":[100],"has":[104],"been":[106],"systematically":[107],"tested.":[108],"We":[109],"compared":[110],"20":[111],"decision":[112],"combinations":[113],"transcriptomic":[116],"dataset":[117],"across":[118],"32":[119],"tissues":[120],"showed":[122],"that":[123,175],"definition":[124],"reaction":[127,173],"may":[128],"considered":[130],"active":[132,172],"(i.e.,":[133],"reactions":[134],"with":[140,189],"non-zero":[142],"level":[144],"after":[145],"overlaying":[146],"data)":[148],"is":[149],"mainly":[150],"influenced":[151],"by":[152],"thresholding":[153],"used.":[155],"determine":[157],"most":[159],"appropriate":[160],"decisions,":[161],"we":[162],"evaluated":[163],"impact":[167],"acquisition":[169],"tissue-specific":[171],"lists":[174],"recapitulate":[176],"organ-system":[177],"tissue":[178],"groups.":[179],"These":[180],"results":[181],"will":[182],"provide":[183],"guidelines":[184],"improve":[186],"analyses":[188],"facilitate":[193],"construction":[195],"context-specific":[197],"models.":[199]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":9},{"year":2024,"cited_by_count":9},{"year":2023,"cited_by_count":15},{"year":2022,"cited_by_count":12},{"year":2021,"cited_by_count":14},{"year":2020,"cited_by_count":12},{"year":2019,"cited_by_count":5},{"year":2018,"cited_by_count":1}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}