{"id":"https://openalex.org/W3213751857","doi":"https://doi.org/10.1371/journal.pcbi.1009589","title":"\u0394FBA\u2014Predicting metabolic flux alterations using genome-scale metabolic models and differential transcriptomic data","display_name":"\u0394FBA\u2014Predicting metabolic flux alterations using genome-scale metabolic models and differential transcriptomic data","publication_year":2021,"publication_date":"2021-11-10","ids":{"openalex":"https://openalex.org/W3213751857","doi":"https://doi.org/10.1371/journal.pcbi.1009589","mag":"3213751857","pmid":"https://pubmed.ncbi.nlm.nih.gov/34758020"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1009589","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1009589","pdf_url":null,"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","datacite","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1371/journal.pcbi.1009589","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5058075551","display_name":"Sudharshan Ravi","orcid":"https://orcid.org/0000-0001-6059-5403"},"institutions":[{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]},{"id":"https://openalex.org/I4210090941","display_name":"Institute for Biomedical Engineering","ror":"https://ror.org/00baskk38","country_code":"CH","type":"facility","lineage":["https://openalex.org/I202697423","https://openalex.org/I2799323385","https://openalex.org/I35440088","https://openalex.org/I4210090941"]},{"id":"https://openalex.org/I4210092485","display_name":"Bioengineering (Switzerland)","ror":"https://ror.org/00m2xfz17","country_code":"CH","type":"company","lineage":["https://openalex.org/I4210092485"]},{"id":"https://openalex.org/I63190737","display_name":"University at Buffalo, State University of New York","ror":"https://ror.org/01y64my43","country_code":"US","type":"education","lineage":["https://openalex.org/I63190737"]}],"countries":["CH","US"],"is_corresponding":false,"raw_author_name":"Sudharshan Ravi","raw_affiliation_strings":["Department of Chemical and Biological Engineering, University at Buffalo-SUNY, Buffalo, New York, United States of America","Institute for Chemical and Bioengineering, ETH Zurich, Zurich, Switzerland"],"raw_orcid":"https://orcid.org/0000-0001-6059-5403","affiliations":[{"raw_affiliation_string":"Department of Chemical and Biological Engineering, University at Buffalo-SUNY, Buffalo, New York, United States of America","institution_ids":["https://openalex.org/I63190737"]},{"raw_affiliation_string":"Institute for Chemical and Bioengineering, ETH Zurich, Zurich, Switzerland","institution_ids":["https://openalex.org/I4210090941","https://openalex.org/I4210092485","https://openalex.org/I35440088"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5054672110","display_name":"Rudiyanto Gunawan","orcid":"https://orcid.org/0000-0002-6480-7976"},"institutions":[{"id":"https://openalex.org/I63190737","display_name":"University at Buffalo, State University of New York","ror":"https://ror.org/01y64my43","country_code":"US","type":"education","lineage":["https://openalex.org/I63190737"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Rudiyanto Gunawan","raw_affiliation_strings":["Department of Chemical and Biological Engineering, University at Buffalo-SUNY, Buffalo, New York, United States of America"],"raw_orcid":"https://orcid.org/0000-0002-6480-7976","affiliations":[{"raw_affiliation_string":"Department of Chemical and Biological Engineering, University at Buffalo-SUNY, Buffalo, New York, United States of America","institution_ids":["https://openalex.org/I63190737"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5054672110"],"corresponding_institution_ids":["https://openalex.org/I63190737"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2306,"currency":"EUR","value_usd":2487},"fwci":2.8548,"has_fulltext":false,"cited_by_count":38,"citation_normalized_percentile":{"value":0.92195704,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":97,"max":99},"biblio":{"volume":"17","issue":"11","first_page":"e1009589","last_page":"e1009589"},"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/T10171","display_name":"Biofuel production and bioconversion","score":0.992900013923645,"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"}},{"id":"https://openalex.org/T10404","display_name":"Enzyme Catalysis and Immobilization","score":0.9908000230789185,"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":0.8636679649353027},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.6895032525062561},{"id":"https://openalex.org/keywords/flux","display_name":"Flux (metallurgy)","score":0.6175000071525574},{"id":"https://openalex.org/keywords/metabolic-flux-analysis","display_name":"Metabolic flux analysis","score":0.567108690738678},{"id":"https://openalex.org/keywords/metabolic-network","display_name":"Metabolic network","score":0.5237167477607727},{"id":"https://openalex.org/keywords/consistency","display_name":"Consistency (knowledge bases)","score":0.520719587802887},{"id":"https://openalex.org/keywords/constraint","display_name":"Constraint (computer-aided design)","score":0.47770360112190247},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.467781662940979},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4481930136680603},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.42116886377334595},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.3421485424041748},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.1928236186504364},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.17986342310905457},{"id":"https://openalex.org/keywords/metabolism","display_name":"Metabolism","score":0.09717705845832825},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.09077873826026917}],"concepts":[{"id":"https://openalex.org/C167091322","wikidata":"https://www.wikidata.org/wiki/Q5463029","display_name":"Flux balance analysis","level":2,"score":0.8636679649353027},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.6895032525062561},{"id":"https://openalex.org/C68709404","wikidata":"https://www.wikidata.org/wiki/Q1134475","display_name":"Flux (metallurgy)","level":2,"score":0.6175000071525574},{"id":"https://openalex.org/C160941953","wikidata":"https://www.wikidata.org/wiki/Q6822342","display_name":"Metabolic flux analysis","level":3,"score":0.567108690738678},{"id":"https://openalex.org/C101810790","wikidata":"https://www.wikidata.org/wiki/Q2263094","display_name":"Metabolic network","level":2,"score":0.5237167477607727},{"id":"https://openalex.org/C2776436953","wikidata":"https://www.wikidata.org/wiki/Q5163215","display_name":"Consistency (knowledge bases)","level":2,"score":0.520719587802887},{"id":"https://openalex.org/C2776036281","wikidata":"https://www.wikidata.org/wiki/Q48769818","display_name":"Constraint (computer-aided design)","level":2,"score":0.47770360112190247},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.467781662940979},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4481930136680603},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.42116886377334595},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.3421485424041748},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.1928236186504364},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.17986342310905457},{"id":"https://openalex.org/C62231903","wikidata":"https://www.wikidata.org/wiki/Q1057","display_name":"Metabolism","level":2,"score":0.09717705845832825},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.09077873826026917},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"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/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C134018914","wikidata":"https://www.wikidata.org/wiki/Q162606","display_name":"Endocrinology","level":1,"score":0.0}],"mesh":[{"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":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064688","descriptor_name":"Metabolic Flux Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D064688","descriptor_name":"Metabolic Flux Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D064688","descriptor_name":"Metabolic Flux Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1371/journal.pcbi.1009589","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1009589","pdf_url":null,"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:34758020","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34758020","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:ae273aeebba34f3db087b274601b0e01","is_oa":true,"landing_page_url":"https://doaj.org/article/ae273aeebba34f3db087b274601b0e01","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"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 17, Iss 11, p e1009589 (2021)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:8608322","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8608322","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Comput Biol","raw_type":"Text"},{"id":"pmh:oai:www.research-collection.ethz.ch:20.500.11850/517069","is_oa":true,"landing_page_url":"http://hdl.handle.net/20.500.11850/517069","pdf_url":null,"source":{"id":"https://openalex.org/S4306402302","display_name":"Repository for Publications and Research Data (ETH Zurich)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I35440088","host_organization_name":"ETH Zurich","host_organization_lineage":["https://openalex.org/I35440088"],"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, 17 (11)","raw_type":"info:eu-repo/semantics/article"},{"id":"doi:10.3929/ethz-b-000517069","is_oa":true,"landing_page_url":"https://doi.org/10.3929/ethz-b-000517069","pdf_url":null,"source":{"id":"https://openalex.org/S7407051236","display_name":"ETH Z\u00fcrich Research Collection","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article-journal"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1009589","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1009589","pdf_url":null,"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":[{"id":"https://openalex.org/G4530913083","display_name":"Single cell transcriptomics on genealogically identified differentiating cells","funder_award_id":"ANR-17-CE12-0031","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"},{"id":"https://openalex.org/G5040728590","display_name":"MetAge: Metabolic network analysis for understanding the biology of ageing","funder_award_id":"163390","funder_id":"https://openalex.org/F4320320924","funder_display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung"},{"id":"https://openalex.org/G8933597632","display_name":"Single cell transcriptomics on genealogically identified differentiating cells","funder_award_id":"176279","funder_id":"https://openalex.org/F4320320924","funder_display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320320883","display_name":"Agence Nationale de la Recherche","ror":"https://ror.org/00rbzpz17"},{"id":"https://openalex.org/F4320320924","display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung","ror":"https://ror.org/00yjd3n13"},{"id":"https://openalex.org/F4320332641","display_name":"University at Buffalo","ror":"https://ror.org/01y64my43"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":58,"referenced_works":["https://openalex.org/W592715486","https://openalex.org/W1586184005","https://openalex.org/W1754578874","https://openalex.org/W1862094217","https://openalex.org/W1979787145","https://openalex.org/W1987840126","https://openalex.org/W1990994166","https://openalex.org/W2022039337","https://openalex.org/W2031367929","https://openalex.org/W2043748764","https://openalex.org/W2044935306","https://openalex.org/W2045921664","https://openalex.org/W2062581381","https://openalex.org/W2066089342","https://openalex.org/W2078355959","https://openalex.org/W2082382448","https://openalex.org/W2084769889","https://openalex.org/W2098450614","https://openalex.org/W2098824895","https://openalex.org/W2102164505","https://openalex.org/W2102957972","https://openalex.org/W2113365252","https://openalex.org/W2119781196","https://openalex.org/W2121020192","https://openalex.org/W2122860350","https://openalex.org/W2124653577","https://openalex.org/W2129346318","https://openalex.org/W2130330935","https://openalex.org/W2135476401","https://openalex.org/W2141360045","https://openalex.org/W2141776893","https://openalex.org/W2144102835","https://openalex.org/W2146512944","https://openalex.org/W2148044817","https://openalex.org/W2160541874","https://openalex.org/W2162666840","https://openalex.org/W2171932269","https://openalex.org/W2172129062","https://openalex.org/W2223326830","https://openalex.org/W2497610175","https://openalex.org/W2546694518","https://openalex.org/W2584561009","https://openalex.org/W2587946751","https://openalex.org/W2743063996","https://openalex.org/W2759571522","https://openalex.org/W2762019694","https://openalex.org/W2782463766","https://openalex.org/W2900182750","https://openalex.org/W2937845779","https://openalex.org/W2950093550","https://openalex.org/W2951171318","https://openalex.org/W2952015518","https://openalex.org/W2963932607","https://openalex.org/W2969638481","https://openalex.org/W3000663720","https://openalex.org/W4229885360","https://openalex.org/W6679074824","https://openalex.org/W7074213355"],"related_works":["https://openalex.org/W1999460937","https://openalex.org/W2113329733","https://openalex.org/W2341681417","https://openalex.org/W1984242440","https://openalex.org/W1983989854","https://openalex.org/W2070388085","https://openalex.org/W2909696795","https://openalex.org/W2613838074","https://openalex.org/W2350881169","https://openalex.org/W2047334633"],"abstract_inverted_index":{"Genome-scale":[0],"metabolic":[1,34,38,46,66,89,137],"models":[2],"(GEMs)":[3],"provide":[4],"a":[5,17,20,53,74,164],"powerful":[6],"framework":[7],"for":[8,36,52],"simulating":[9],"the":[10,43,63,101,109,115,125,134],"entire":[11],"set":[12],"of":[13,65,127,136,168],"biochemical":[14],"reactions":[15],"in":[16,145,153,157],"cell":[18],"using":[19,40],"constraint-based":[21],"modeling":[22],"strategy":[23],"called":[24,77],"flux":[25,67,90,117,169],"balance":[26],"analysis":[27],"(FBA).":[28],"FBA":[29],"relies":[30],"on":[31],"an":[32],"assumed":[33],"objective":[35,47],"generating":[37],"fluxes":[39],"GEMs.":[41],"But,":[42],"most":[44],"appropriate":[45],"is":[48,57],"not":[49,98],"always":[50],"obvious":[51],"given":[54],"condition":[55],"and":[56,111,119,142,148],"likely":[58],"context-specific,":[59],"which":[60],"often":[61],"complicate":[62],"estimation":[64],"alterations":[68,138],"between":[69,92,114],"conditions.":[70,94],"Here,":[71],"we":[72],"propose":[73],"new":[75],"method,":[76],"\u0394FBA":[78,96,105,128,162],"(deltaFBA),":[79],"that":[80],"integrates":[81],"differential":[82,120],"gene":[83,121],"expression":[84],"data":[85],"to":[86,107,159],"evaluate":[87],"directly":[88],"differences":[91,118],"two":[93],"Notably,":[95],"does":[97],"require":[99],"specifying":[100],"cellular":[102],"objective.":[103],"Rather,":[104],"seeks":[106],"maximize":[108],"consistency":[110],"minimize":[112],"inconsistency":[113],"predicted":[116],"expression.":[122],"We":[123],"showcased":[124],"performance":[126],"through":[129],"several":[130],"case":[131],"studies":[132],"involving":[133],"prediction":[135,167],"caused":[139,149],"by":[140,150],"genetic":[141],"environmental":[143],"perturbations":[144],"Escherichia":[146],"coli":[147],"Type-2":[151],"diabetes":[152],"human":[154],"muscle.":[155],"Importantly,":[156],"comparison":[158],"existing":[160],"methods,":[161],"gives":[163],"more":[165],"accurate":[166],"differences.":[170]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":8},{"year":2024,"cited_by_count":7},{"year":2023,"cited_by_count":14},{"year":2022,"cited_by_count":7}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}