{"id":"https://openalex.org/W2082948758","doi":"https://doi.org/10.1371/journal.pcbi.1000086","title":"Dynamic Analysis of Integrated Signaling, Metabolic, and Regulatory Networks","display_name":"Dynamic Analysis of Integrated Signaling, Metabolic, and Regulatory Networks","publication_year":2008,"publication_date":"2008-05-22","ids":{"openalex":"https://openalex.org/W2082948758","doi":"https://doi.org/10.1371/journal.pcbi.1000086","mag":"2082948758","pmid":"https://pubmed.ncbi.nlm.nih.gov/18483615"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1000086","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1000086","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1000086&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.1000086&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100382860","display_name":"Jong Min Lee","orcid":"https://orcid.org/0000-0001-5395-0067"},"institutions":[{"id":"https://openalex.org/I2799765794","display_name":"University of Virginia Health System","ror":"https://ror.org/00wn7d965","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2799765794"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jong Min Lee","raw_affiliation_strings":["Department of Biomedical Engineering, University of Virginia Health System, Charlottesville, Virginia, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Engineering, University of Virginia Health System, Charlottesville, Virginia, United States of America","institution_ids":["https://openalex.org/I2799765794"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5057658579","display_name":"Erwin P. Gianchandani","orcid":"https://orcid.org/0000-0003-4989-0246"},"institutions":[{"id":"https://openalex.org/I2799765794","display_name":"University of Virginia Health System","ror":"https://ror.org/00wn7d965","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2799765794"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Erwin P. Gianchandani","raw_affiliation_strings":["Department of Biomedical Engineering, University of Virginia Health System, Charlottesville, Virginia, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Engineering, University of Virginia Health System, Charlottesville, Virginia, United States of America","institution_ids":["https://openalex.org/I2799765794"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058971932","display_name":"James A. Eddy","orcid":"https://orcid.org/0000-0001-9758-0176"},"institutions":[{"id":"https://openalex.org/I2799765794","display_name":"University of Virginia Health System","ror":"https://ror.org/00wn7d965","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2799765794"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"James A. Eddy","raw_affiliation_strings":["Department of Biomedical Engineering, University of Virginia Health System, Charlottesville, Virginia, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Engineering, University of Virginia Health System, Charlottesville, Virginia, United States of America","institution_ids":["https://openalex.org/I2799765794"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5000119406","display_name":"Jason A. Papin","orcid":"https://orcid.org/0000-0002-2769-5805"},"institutions":[{"id":"https://openalex.org/I2799765794","display_name":"University of Virginia Health System","ror":"https://ror.org/00wn7d965","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2799765794"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Jason A. Papin","raw_affiliation_strings":["Department of Biomedical Engineering, University of Virginia Health System, Charlottesville, Virginia, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Engineering, University of Virginia Health System, Charlottesville, Virginia, United States of America","institution_ids":["https://openalex.org/I2799765794"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5000119406"],"corresponding_institution_ids":["https://openalex.org/I2799765794"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":9.162944,"has_fulltext":true,"cited_by_count":231,"citation_normalized_percentile":{"value":0.98474715,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":95,"max":100},"biblio":{"volume":"4","issue":"5","first_page":"e1000086","last_page":"e1000086"},"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9991999864578247,"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/T11663","display_name":"Viral Infectious Diseases and Gene Expression in Insects","score":0.9957000017166138,"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/flux-balance-analysis","display_name":"Flux balance analysis","score":0.7350950837135315},{"id":"https://openalex.org/keywords/metabolic-network","display_name":"Metabolic network","score":0.6554059982299805},{"id":"https://openalex.org/keywords/systems-biology","display_name":"Systems biology","score":0.6085940599441528},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.5468846559524536},{"id":"https://openalex.org/keywords/saccharomyces-cerevisiae","display_name":"Saccharomyces cerevisiae","score":0.5324745178222656},{"id":"https://openalex.org/keywords/cellular-metabolism","display_name":"Cellular metabolism","score":0.5236801505088806},{"id":"https://openalex.org/keywords/extracellular","display_name":"Extracellular","score":0.502110481262207},{"id":"https://openalex.org/keywords/phenotype","display_name":"Phenotype","score":0.49511948227882385},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4781990051269531},{"id":"https://openalex.org/keywords/organism","display_name":"Organism","score":0.4713149666786194},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4625069499015808},{"id":"https://openalex.org/keywords/metabolic-pathway","display_name":"Metabolic pathway","score":0.43327999114990234},{"id":"https://openalex.org/keywords/intracellular","display_name":"Intracellular","score":0.4141734838485718},{"id":"https://openalex.org/keywords/robustness","display_name":"Robustness (evolution)","score":0.41198089718818665},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.37559330463409424},{"id":"https://openalex.org/keywords/cell-biology","display_name":"Cell biology","score":0.24957653880119324},{"id":"https://openalex.org/keywords/metabolism","display_name":"Metabolism","score":0.23654690384864807},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.21679827570915222},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.18422266840934753},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.17267602682113647},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.11925908923149109}],"concepts":[{"id":"https://openalex.org/C167091322","wikidata":"https://www.wikidata.org/wiki/Q5463029","display_name":"Flux balance analysis","level":2,"score":0.7350950837135315},{"id":"https://openalex.org/C101810790","wikidata":"https://www.wikidata.org/wiki/Q2263094","display_name":"Metabolic network","level":2,"score":0.6554059982299805},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.6085940599441528},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.5468846559524536},{"id":"https://openalex.org/C2777576037","wikidata":"https://www.wikidata.org/wiki/Q719725","display_name":"Saccharomyces cerevisiae","level":3,"score":0.5324745178222656},{"id":"https://openalex.org/C2994212657","wikidata":"https://www.wikidata.org/wiki/Q1057","display_name":"Cellular metabolism","level":3,"score":0.5236801505088806},{"id":"https://openalex.org/C28406088","wikidata":"https://www.wikidata.org/wiki/Q5571762","display_name":"Extracellular","level":2,"score":0.502110481262207},{"id":"https://openalex.org/C127716648","wikidata":"https://www.wikidata.org/wiki/Q104053","display_name":"Phenotype","level":3,"score":0.49511948227882385},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4781990051269531},{"id":"https://openalex.org/C137858568","wikidata":"https://www.wikidata.org/wiki/Q7239","display_name":"Organism","level":2,"score":0.4713149666786194},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4625069499015808},{"id":"https://openalex.org/C192989942","wikidata":"https://www.wikidata.org/wiki/Q68685","display_name":"Metabolic pathway","level":3,"score":0.43327999114990234},{"id":"https://openalex.org/C79879829","wikidata":"https://www.wikidata.org/wiki/Q5571762","display_name":"Intracellular","level":2,"score":0.4141734838485718},{"id":"https://openalex.org/C63479239","wikidata":"https://www.wikidata.org/wiki/Q7353546","display_name":"Robustness (evolution)","level":3,"score":0.41198089718818665},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.37559330463409424},{"id":"https://openalex.org/C95444343","wikidata":"https://www.wikidata.org/wiki/Q7141","display_name":"Cell biology","level":1,"score":0.24957653880119324},{"id":"https://openalex.org/C62231903","wikidata":"https://www.wikidata.org/wiki/Q1057","display_name":"Metabolism","level":2,"score":0.23654690384864807},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.21679827570915222},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.18422266840934753},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.17267602682113647},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.11925908923149109}],"mesh":[{"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":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":"Q000502","qualifier_name":"physiology","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":"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":"D018511","descriptor_name":"Systems Integration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018511","descriptor_name":"Systems Integration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018511","descriptor_name":"Systems Integration","qualifier_ui":null,"qualifier_name":null,"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}],"locations_count":5,"locations":[{"id":"doi:10.1371/journal.pcbi.1000086","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1000086","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1000086&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:18483615","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/18483615","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:a4306b199f87410db40f69492af99cc8","is_oa":true,"landing_page_url":"https://doaj.org/article/a4306b199f87410db40f69492af99cc8","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 e1000086 (2008)","raw_type":"article"},{"id":"pmh:oai:figshare.com:article/150511","is_oa":true,"landing_page_url":"https://figshare.com/articles/Dynamic_Analysis_of_Integrated_Signaling_Metabolic_and_Regulatory_Networks/150511","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"},{"id":"pmh:oai:pubmedcentral.nih.gov:2377155","is_oa":true,"landing_page_url":"http://doi.org/10.1371/journal.pcbi.1000086","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"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.1000086","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1000086","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1000086&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":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2082948758.pdf","grobid_xml":"https://content.openalex.org/works/W2082948758.grobid-xml"},"referenced_works_count":70,"referenced_works":["https://openalex.org/W79654898","https://openalex.org/W1491758006","https://openalex.org/W1504774114","https://openalex.org/W1550716269","https://openalex.org/W1574498833","https://openalex.org/W1600765471","https://openalex.org/W1641228030","https://openalex.org/W1869042642","https://openalex.org/W1873506857","https://openalex.org/W1970970926","https://openalex.org/W1975351609","https://openalex.org/W1977985274","https://openalex.org/W1979955019","https://openalex.org/W1982195171","https://openalex.org/W1983673069","https://openalex.org/W1994134392","https://openalex.org/W1996529795","https://openalex.org/W1997774242","https://openalex.org/W2001072557","https://openalex.org/W2002880495","https://openalex.org/W2007728693","https://openalex.org/W2009163705","https://openalex.org/W2012133308","https://openalex.org/W2021123893","https://openalex.org/W2021674783","https://openalex.org/W2026089579","https://openalex.org/W2029640436","https://openalex.org/W2046254395","https://openalex.org/W2048596643","https://openalex.org/W2064251066","https://openalex.org/W2065669781","https://openalex.org/W2066580949","https://openalex.org/W2072159031","https://openalex.org/W2074190281","https://openalex.org/W2075161553","https://openalex.org/W2077046573","https://openalex.org/W2079588007","https://openalex.org/W2085236271","https://openalex.org/W2086568203","https://openalex.org/W2094831175","https://openalex.org/W2101155309","https://openalex.org/W2102164505","https://openalex.org/W2103838923","https://openalex.org/W2105587783","https://openalex.org/W2106576546","https://openalex.org/W2107333582","https://openalex.org/W2113101487","https://openalex.org/W2118893325","https://openalex.org/W2122553662","https://openalex.org/W2126602684","https://openalex.org/W2128572161","https://openalex.org/W2131740293","https://openalex.org/W2134981469","https://openalex.org/W2138992053","https://openalex.org/W2143861551","https://openalex.org/W2143883853","https://openalex.org/W2144568050","https://openalex.org/W2144856591","https://openalex.org/W2153373497","https://openalex.org/W2155049977","https://openalex.org/W2159100436","https://openalex.org/W2165603655","https://openalex.org/W2167391679","https://openalex.org/W2169104686","https://openalex.org/W2399357114","https://openalex.org/W2611560603","https://openalex.org/W4239403073","https://openalex.org/W4285719527","https://openalex.org/W6630220215","https://openalex.org/W6817966389"],"related_works":["https://openalex.org/W3033588432","https://openalex.org/W2020641517","https://openalex.org/W2075919068","https://openalex.org/W2216418212","https://openalex.org/W2137898013","https://openalex.org/W2025172803","https://openalex.org/W1544925715","https://openalex.org/W2540651481","https://openalex.org/W2573984017","https://openalex.org/W1975098623"],"abstract_inverted_index":{"Extracellular":[0],"cues":[1,207],"affect":[2],"signaling,":[3,14,54,96,133,252],"metabolic,":[4,15,55,97,134,253],"and":[5,16,56,98,108,135,145,170,211,230,254],"regulatory":[6,17,57,99,136,172,255],"processes":[7,29,137,256],"to":[8,72,160,185,246],"elicit":[9],"cellular":[10,81,209],"responses.":[11],"Although":[12],"intracellular":[13,248],"networks":[18],"are":[19],"highly":[20],"integrated,":[21],"previous":[22],"analyses":[23],"have":[24],"largely":[25],"focused":[26],"on":[27,150,208],"independent":[28],"(e.g.,":[30],"metabolism)":[31],"without":[32],"considering":[33],"the":[34,113,122,161,178,190,258,263],"interplay":[35],"that":[36,44,78,250],"exists":[37],"among":[38],"them.":[39],"However,":[40],"there":[41],"is":[42],"evidence":[43],"many":[45],"diseases":[46],"arise":[47],"from":[48,84],"multifunctional":[49],"components":[50],"with":[51,138,218],"roles":[52],"throughout":[53],"networks.":[58,86],"Therefore,":[59],"in":[60,116,155,181],"this":[61],"study,":[62],"we":[63,126,176],"propose":[64],"a":[65,117,128,182,186,226],"flux":[66],"balance":[67],"analysis":[68,201],"(FBA)-based":[69],"strategy,":[70],"referred":[71],"as":[73,262],"integrated":[74,85,92,130,247],"dynamic":[75,200],"FBA":[76],"(idFBA),":[77],"dynamically":[79],"simulates":[80],"phenotypes":[82,210],"arising":[83],"The":[87],"idFBA":[88,157,179,197,224],"framework":[89,180],"requires":[90],"an":[91,219,234],"stoichiometric":[93,114],"reconstruction":[94],"of":[95,124,142,189,202,205,237],"processes.":[100],"It":[101],"assumes":[102],"quasi-steady-state":[103],"conditions":[104],"for":[105,167],"\"fast\"":[106],"reactions":[107,111],"incorporates":[109],"\"slow\"":[110],"into":[112],"formalism":[115],"time-delayed":[118],"manner.":[119],"To":[120],"assess":[121],"efficacy":[123],"idFBA,":[125],"developed":[127],"prototypic":[129,162],"system":[131,266],"comprising":[132],"network":[139],"features":[140],"characteristic":[141],"actual":[143],"systems":[144,249],"incorporated":[146],"kinetic":[147,221,239],"parameters":[148],"based":[149],"typical":[151],"time":[152],"scales":[153],"observed":[154],"literature.":[156],"was":[158,165],"applied":[159,177],"system,":[163],"which":[164],"evaluated":[166],"different":[168],"environments":[169],"gene":[171],"rules.":[173],"In":[174],"addition,":[175],"similar":[183],"manner":[184],"representative":[187],"module":[188],"single-cell":[191],"eukaryotic":[192],"organism":[193],"Saccharomyces":[194],"cerevisiae.":[195],"Ultimately,":[196],"facilitated":[198],"quantitative,":[199],"systemic":[203],"effects":[204],"extracellular":[206],"generated":[212],"comparable":[213],"time-course":[214],"predictions":[215],"when":[216],"contrasted":[217],"equivalent":[220],"model.":[222],"Since":[223],"solves":[225],"linear":[227],"programming":[228],"problem":[229],"does":[231],"not":[232],"require":[233],"exhaustive":[235],"list":[236],"detailed":[238],"parameters,":[240],"it":[241],"may":[242],"be":[243],"efficiently":[244],"scaled":[245],"incorporate":[251],"at":[257],"genome":[259],"scale,":[260],"such":[261],"S.":[264],"cerevisiae":[265],"presented":[267],"here.":[268]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":9},{"year":2023,"cited_by_count":6},{"year":2022,"cited_by_count":8},{"year":2021,"cited_by_count":10},{"year":2020,"cited_by_count":11},{"year":2019,"cited_by_count":9},{"year":2018,"cited_by_count":8},{"year":2017,"cited_by_count":12},{"year":2016,"cited_by_count":7},{"year":2015,"cited_by_count":16},{"year":2014,"cited_by_count":14},{"year":2013,"cited_by_count":19},{"year":2012,"cited_by_count":34}],"updated_date":"2026-02-12T00:53:03.260389","created_date":"2016-06-24T00:00:00"}
