{"id":"https://openalex.org/W4401070509","doi":"https://doi.org/10.1371/journal.pcbi.1011858","title":"A rule-based multiscale model of hepatic stellate cell plasticity: Critical role of the inactivation loop in fibrosis progression","display_name":"A rule-based multiscale model of hepatic stellate cell plasticity: Critical role of the inactivation loop in fibrosis progression","publication_year":2024,"publication_date":"2024-07-29","ids":{"openalex":"https://openalex.org/W4401070509","doi":"https://doi.org/10.1371/journal.pcbi.1011858","pmid":"https://pubmed.ncbi.nlm.nih.gov/39074160"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1011858","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1011858","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","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1371/journal.pcbi.1011858","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5068922734","display_name":"Matthieu Bougu\u00e9on","orcid":null},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I154526488","display_name":"Inserm","ror":"https://ror.org/02vjkv261","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488"]},{"id":"https://openalex.org/I165283593","display_name":"\u00c9cole des Hautes \u00c9tudes en Sant\u00e9 Publique","ror":"https://ror.org/01sc83v92","country_code":"FR","type":"education","lineage":["https://openalex.org/I165283593"]},{"id":"https://openalex.org/I2802519937","display_name":"Institut de Recherche en Informatique et Syst\u00e8mes Al\u00e9atoires","ror":"https://ror.org/00myn0z94","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1326498283","https://openalex.org/I205703379","https://openalex.org/I2802204017","https://openalex.org/I2802519937","https://openalex.org/I28221208","https://openalex.org/I4210127572","https://openalex.org/I4210159245","https://openalex.org/I56067802"]},{"id":"https://openalex.org/I4210108239","display_name":"Institut de Recherche en Sant\u00e9, Environnement et Travail","ror":"https://ror.org/01p178v10","country_code":"FR","type":"facility","lineage":["https://openalex.org/I154526488","https://openalex.org/I165283593","https://openalex.org/I4210108239","https://openalex.org/I49451733","https://openalex.org/I56067802"]},{"id":"https://openalex.org/I4405260663","display_name":"DYLISS: Dynamics, Logics and Inference for biological Systems and Sequences","ror":"https://ror.org/043ja9593","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1326498283","https://openalex.org/I1326498283","https://openalex.org/I205703379","https://openalex.org/I2802204017","https://openalex.org/I2802519937","https://openalex.org/I28221208","https://openalex.org/I4210127572","https://openalex.org/I4210133778","https://openalex.org/I4210159245","https://openalex.org/I4405260663","https://openalex.org/I56067802"]},{"id":"https://openalex.org/I56067802","display_name":"Universit\u00e9 de Rennes","ror":"https://ror.org/015m7wh34","country_code":"FR","type":"education","lineage":["https://openalex.org/I56067802"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Matthieu Bougu\u00e9on","raw_affiliation_strings":["Univ Rennes, Inria, CNRS, IRISA, UMR 6074, Rennes, France","Univ Rennes, Inserm, EHESP, Irset, UMR S1085, Rennes, France","Dyliss - Dynamics, Logics and Inference for biological Systems and Sequences (Campus de Beaulieu 35042 Rennes cedex - France)","IRISA - Institut de Recherche en Informatique et Syst\u00e8mes Al\u00e9atoires (Avenue du g\u00e9n\u00e9ral Leclerc\r\nCampus de Beaulieu \r\n35042 RENNES CEDEX - France)","Irset - Institut de recherche en sant\u00e9, environnement et travail (263 avenue G\u00e9n\u00e9ral Leclerc 35042 Rennes Cedex - France)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Univ Rennes, Inria, CNRS, IRISA, UMR 6074, Rennes, France","institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I2802519937","https://openalex.org/I56067802"]},{"raw_affiliation_string":"Univ Rennes, Inserm, EHESP, Irset, UMR S1085, Rennes, France","institution_ids":["https://openalex.org/I154526488","https://openalex.org/I165283593","https://openalex.org/I4210108239","https://openalex.org/I56067802"]},{"raw_affiliation_string":"Dyliss - Dynamics, Logics and Inference for biological Systems and Sequences (Campus de Beaulieu 35042 Rennes cedex - France)","institution_ids":["https://openalex.org/I4405260663"]},{"raw_affiliation_string":"IRISA - Institut de Recherche en Informatique et Syst\u00e8mes Al\u00e9atoires (Avenue du g\u00e9n\u00e9ral Leclerc\r\nCampus de Beaulieu \r\n35042 RENNES CEDEX - France)","institution_ids":["https://openalex.org/I2802519937"]},{"raw_affiliation_string":"Irset - Institut de recherche en sant\u00e9, environnement et travail (263 avenue G\u00e9n\u00e9ral Leclerc 35042 Rennes Cedex - France)","institution_ids":["https://openalex.org/I4210108239"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046268343","display_name":"Vincent Legagneux","orcid":"https://orcid.org/0000-0002-1417-6678"},"institutions":[{"id":"https://openalex.org/I154526488","display_name":"Inserm","ror":"https://ror.org/02vjkv261","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488"]},{"id":"https://openalex.org/I165283593","display_name":"\u00c9cole des Hautes \u00c9tudes en Sant\u00e9 Publique","ror":"https://ror.org/01sc83v92","country_code":"FR","type":"education","lineage":["https://openalex.org/I165283593"]},{"id":"https://openalex.org/I4210108239","display_name":"Institut de Recherche en Sant\u00e9, Environnement et Travail","ror":"https://ror.org/01p178v10","country_code":"FR","type":"facility","lineage":["https://openalex.org/I154526488","https://openalex.org/I165283593","https://openalex.org/I4210108239","https://openalex.org/I49451733","https://openalex.org/I56067802"]},{"id":"https://openalex.org/I56067802","display_name":"Universit\u00e9 de Rennes","ror":"https://ror.org/015m7wh34","country_code":"FR","type":"education","lineage":["https://openalex.org/I56067802"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Vincent Legagneux","raw_affiliation_strings":["Univ Rennes, Inserm, EHESP, Irset, UMR S1085, Rennes, France","Irset - Institut de recherche en sant\u00e9, environnement et travail (263 avenue G\u00e9n\u00e9ral Leclerc 35042 Rennes Cedex - France)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Univ Rennes, Inserm, EHESP, Irset, UMR S1085, Rennes, France","institution_ids":["https://openalex.org/I154526488","https://openalex.org/I165283593","https://openalex.org/I4210108239","https://openalex.org/I56067802"]},{"raw_affiliation_string":"Irset - Institut de recherche en sant\u00e9, environnement et travail (263 avenue G\u00e9n\u00e9ral Leclerc 35042 Rennes Cedex - France)","institution_ids":["https://openalex.org/I4210108239"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5055698395","display_name":"Octave Hazard","orcid":null},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I142476485","display_name":"\u00c9cole Polytechnique","ror":"https://ror.org/05hy3tk52","country_code":"FR","type":"education","lineage":["https://openalex.org/I142476485","https://openalex.org/I4210145102"]},{"id":"https://openalex.org/I2746051580","display_name":"Universit\u00e9 Paris Sciences et Lettres","ror":"https://ror.org/013cjyk83","country_code":"FR","type":"education","lineage":["https://openalex.org/I2746051580"]},{"id":"https://openalex.org/I29607241","display_name":"\u00c9cole Normale Sup\u00e9rieure - PSL","ror":"https://ror.org/05a0dhs15","country_code":"FR","type":"other","lineage":["https://openalex.org/I2746051580","https://openalex.org/I29607241"]},{"id":"https://openalex.org/I4210139461","display_name":"Laboratoire d'Informatique de l'\u00c9cole Polytechnique","ror":"https://ror.org/04afed728","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1326498283","https://openalex.org/I142476485","https://openalex.org/I4210139461","https://openalex.org/I4210145102","https://openalex.org/I4210159245"]},{"id":"https://openalex.org/I4210161954","display_name":"D\u00e9partement d'Informatique","ror":"https://ror.org/05y6rqs46","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1326498283","https://openalex.org/I2746051580","https://openalex.org/I29607241","https://openalex.org/I4210159245","https://openalex.org/I4210161954"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Octave Hazard","raw_affiliation_strings":["DI-ENS (Inria, \u00c9NS, CNRS, PSL University), \u00c9cole normale sup\u00e9rieure, Paris, France","\u00c9cole Polytechnique, Palaiseau, France","DI-ENS - D\u00e9partement d'informatique - ENS Paris (\u00c9cole normale sup\u00e9rieure 45 rue d'Ulm F-75230 Paris Cedex 05 - France)","LIX - Laboratoire d'informatique de l'\u00c9cole polytechnique [Palaiseau] (1 Rue Honor\u00e9 d\u2019Estienne d\u2019Orves, B\u00e2timent Alain Turing, 91120 Palaiseau - France)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"DI-ENS (Inria, \u00c9NS, CNRS, PSL University), \u00c9cole normale sup\u00e9rieure, Paris, France","institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I2746051580","https://openalex.org/I29607241","https://openalex.org/I4210161954"]},{"raw_affiliation_string":"\u00c9cole Polytechnique, Palaiseau, France","institution_ids":["https://openalex.org/I142476485"]},{"raw_affiliation_string":"DI-ENS - D\u00e9partement d'informatique - ENS Paris (\u00c9cole normale sup\u00e9rieure 45 rue d'Ulm F-75230 Paris Cedex 05 - France)","institution_ids":["https://openalex.org/I29607241","https://openalex.org/I4210161954"]},{"raw_affiliation_string":"LIX - Laboratoire d'informatique de l'\u00c9cole polytechnique [Palaiseau] (1 Rue Honor\u00e9 d\u2019Estienne d\u2019Orves, B\u00e2timent Alain Turing, 91120 Palaiseau - France)","institution_ids":["https://openalex.org/I142476485","https://openalex.org/I4210139461"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5074640602","display_name":"J\u00e9r\u00e9my Bomo","orcid":"https://orcid.org/0000-0002-3065-449X"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I154526488","display_name":"Inserm","ror":"https://ror.org/02vjkv261","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488"]},{"id":"https://openalex.org/I165283593","display_name":"\u00c9cole des Hautes \u00c9tudes en Sant\u00e9 Publique","ror":"https://ror.org/01sc83v92","country_code":"FR","type":"education","lineage":["https://openalex.org/I165283593"]},{"id":"https://openalex.org/I2802519937","display_name":"Institut de Recherche en Informatique et Syst\u00e8mes Al\u00e9atoires","ror":"https://ror.org/00myn0z94","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1326498283","https://openalex.org/I205703379","https://openalex.org/I2802204017","https://openalex.org/I2802519937","https://openalex.org/I28221208","https://openalex.org/I4210127572","https://openalex.org/I4210159245","https://openalex.org/I56067802"]},{"id":"https://openalex.org/I4210108239","display_name":"Institut de Recherche en Sant\u00e9, Environnement et Travail","ror":"https://ror.org/01p178v10","country_code":"FR","type":"facility","lineage":["https://openalex.org/I154526488","https://openalex.org/I165283593","https://openalex.org/I4210108239","https://openalex.org/I49451733","https://openalex.org/I56067802"]},{"id":"https://openalex.org/I56067802","display_name":"Universit\u00e9 de Rennes","ror":"https://ror.org/015m7wh34","country_code":"FR","type":"education","lineage":["https://openalex.org/I56067802"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"J\u00e9r\u00e9my Bomo","raw_affiliation_strings":["Univ Rennes, Inria, CNRS, IRISA, UMR 6074, Rennes, France","Univ Rennes, Inserm, EHESP, Irset, UMR S1085, Rennes, France","IRISA - Institut de Recherche en Informatique et Syst\u00e8mes Al\u00e9atoires (Avenue du g\u00e9n\u00e9ral Leclerc\r\nCampus de Beaulieu \r\n35042 RENNES CEDEX - France)","Irset - Institut de recherche en sant\u00e9, environnement et travail (263 avenue G\u00e9n\u00e9ral Leclerc 35042 Rennes Cedex - France)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Univ Rennes, Inria, CNRS, IRISA, UMR 6074, Rennes, France","institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I2802519937","https://openalex.org/I56067802"]},{"raw_affiliation_string":"Univ Rennes, Inserm, EHESP, Irset, UMR S1085, Rennes, France","institution_ids":["https://openalex.org/I154526488","https://openalex.org/I165283593","https://openalex.org/I4210108239","https://openalex.org/I56067802"]},{"raw_affiliation_string":"IRISA - Institut de Recherche en Informatique et Syst\u00e8mes Al\u00e9atoires (Avenue du g\u00e9n\u00e9ral Leclerc\r\nCampus de Beaulieu \r\n35042 RENNES CEDEX - France)","institution_ids":["https://openalex.org/I2802519937"]},{"raw_affiliation_string":"Irset - Institut de recherche en sant\u00e9, environnement et travail (263 avenue G\u00e9n\u00e9ral Leclerc 35042 Rennes Cedex - France)","institution_ids":["https://openalex.org/I4210108239"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063755415","display_name":"Anne Siegel","orcid":"https://orcid.org/0000-0001-6542-1568"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I2802519937","display_name":"Institut de Recherche en Informatique et Syst\u00e8mes Al\u00e9atoires","ror":"https://ror.org/00myn0z94","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1326498283","https://openalex.org/I205703379","https://openalex.org/I2802204017","https://openalex.org/I2802519937","https://openalex.org/I28221208","https://openalex.org/I4210127572","https://openalex.org/I4210159245","https://openalex.org/I56067802"]},{"id":"https://openalex.org/I4405260663","display_name":"DYLISS: Dynamics, Logics and Inference for biological Systems and Sequences","ror":"https://ror.org/043ja9593","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1326498283","https://openalex.org/I1326498283","https://openalex.org/I205703379","https://openalex.org/I2802204017","https://openalex.org/I2802519937","https://openalex.org/I28221208","https://openalex.org/I4210127572","https://openalex.org/I4210133778","https://openalex.org/I4210159245","https://openalex.org/I4405260663","https://openalex.org/I56067802"]},{"id":"https://openalex.org/I56067802","display_name":"Universit\u00e9 de Rennes","ror":"https://ror.org/015m7wh34","country_code":"FR","type":"education","lineage":["https://openalex.org/I56067802"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Anne Siegel","raw_affiliation_strings":["Univ Rennes, Inria, CNRS, IRISA, UMR 6074, Rennes, France","Dyliss - Dynamics, Logics and Inference for biological Systems and Sequences (Campus de Beaulieu 35042 Rennes cedex - France)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Univ Rennes, Inria, CNRS, IRISA, UMR 6074, Rennes, France","institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I2802519937","https://openalex.org/I56067802"]},{"raw_affiliation_string":"Dyliss - Dynamics, Logics and Inference for biological Systems and Sequences (Campus de Beaulieu 35042 Rennes cedex - France)","institution_ids":["https://openalex.org/I4405260663"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085031854","display_name":"J\u00e9r\u00f4me Fer\u00eat","orcid":"https://orcid.org/0000-0002-2601-2785"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I142476485","display_name":"\u00c9cole Polytechnique","ror":"https://ror.org/05hy3tk52","country_code":"FR","type":"education","lineage":["https://openalex.org/I142476485","https://openalex.org/I4210145102"]},{"id":"https://openalex.org/I2746051580","display_name":"Universit\u00e9 Paris Sciences et Lettres","ror":"https://ror.org/013cjyk83","country_code":"FR","type":"education","lineage":["https://openalex.org/I2746051580"]},{"id":"https://openalex.org/I29607241","display_name":"\u00c9cole Normale Sup\u00e9rieure - PSL","ror":"https://ror.org/05a0dhs15","country_code":"FR","type":"other","lineage":["https://openalex.org/I2746051580","https://openalex.org/I29607241"]},{"id":"https://openalex.org/I4210139461","display_name":"Laboratoire d'Informatique de l'\u00c9cole Polytechnique","ror":"https://ror.org/04afed728","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1326498283","https://openalex.org/I142476485","https://openalex.org/I4210139461","https://openalex.org/I4210145102","https://openalex.org/I4210159245"]},{"id":"https://openalex.org/I4210161954","display_name":"D\u00e9partement d'Informatique","ror":"https://ror.org/05y6rqs46","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1326498283","https://openalex.org/I2746051580","https://openalex.org/I29607241","https://openalex.org/I4210159245","https://openalex.org/I4210161954"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"J\u00e9r\u00f4me Feret","raw_affiliation_strings":["DI-ENS (Inria, \u00c9NS, CNRS, PSL University), \u00c9cole normale sup\u00e9rieure, Paris, France","Team Antique, Inria, Paris, France","DI-ENS - D\u00e9partement d'informatique - ENS Paris (\u00c9cole normale sup\u00e9rieure 45 rue d'Ulm F-75230 Paris Cedex 05 - France)","LIX - Laboratoire d'informatique de l'\u00c9cole polytechnique [Palaiseau] (1 Rue Honor\u00e9 d\u2019Estienne d\u2019Orves, B\u00e2timent Alain Turing, 91120 Palaiseau - France)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"DI-ENS (Inria, \u00c9NS, CNRS, PSL University), \u00c9cole normale sup\u00e9rieure, Paris, France","institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I2746051580","https://openalex.org/I29607241","https://openalex.org/I4210161954"]},{"raw_affiliation_string":"Team Antique, Inria, Paris, France","institution_ids":[]},{"raw_affiliation_string":"DI-ENS - D\u00e9partement d'informatique - ENS Paris (\u00c9cole normale sup\u00e9rieure 45 rue d'Ulm F-75230 Paris Cedex 05 - France)","institution_ids":["https://openalex.org/I29607241","https://openalex.org/I4210161954"]},{"raw_affiliation_string":"LIX - Laboratoire d'informatique de l'\u00c9cole polytechnique [Palaiseau] (1 Rue Honor\u00e9 d\u2019Estienne d\u2019Orves, B\u00e2timent Alain Turing, 91120 Palaiseau - France)","institution_ids":["https://openalex.org/I142476485","https://openalex.org/I4210139461"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5046388663","display_name":"Nathalie Th\u00e9ret","orcid":"https://orcid.org/0000-0002-5857-7828"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I154526488","display_name":"Inserm","ror":"https://ror.org/02vjkv261","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488"]},{"id":"https://openalex.org/I165283593","display_name":"\u00c9cole des Hautes \u00c9tudes en Sant\u00e9 Publique","ror":"https://ror.org/01sc83v92","country_code":"FR","type":"education","lineage":["https://openalex.org/I165283593"]},{"id":"https://openalex.org/I2802519937","display_name":"Institut de Recherche en Informatique et Syst\u00e8mes Al\u00e9atoires","ror":"https://ror.org/00myn0z94","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1326498283","https://openalex.org/I205703379","https://openalex.org/I2802204017","https://openalex.org/I2802519937","https://openalex.org/I28221208","https://openalex.org/I4210127572","https://openalex.org/I4210159245","https://openalex.org/I56067802"]},{"id":"https://openalex.org/I4210108239","display_name":"Institut de Recherche en Sant\u00e9, Environnement et Travail","ror":"https://ror.org/01p178v10","country_code":"FR","type":"facility","lineage":["https://openalex.org/I154526488","https://openalex.org/I165283593","https://openalex.org/I4210108239","https://openalex.org/I49451733","https://openalex.org/I56067802"]},{"id":"https://openalex.org/I4405260663","display_name":"DYLISS: Dynamics, Logics and Inference for biological Systems and Sequences","ror":"https://ror.org/043ja9593","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1326498283","https://openalex.org/I1326498283","https://openalex.org/I205703379","https://openalex.org/I2802204017","https://openalex.org/I2802519937","https://openalex.org/I28221208","https://openalex.org/I4210127572","https://openalex.org/I4210133778","https://openalex.org/I4210159245","https://openalex.org/I4405260663","https://openalex.org/I56067802"]},{"id":"https://openalex.org/I56067802","display_name":"Universit\u00e9 de Rennes","ror":"https://ror.org/015m7wh34","country_code":"FR","type":"education","lineage":["https://openalex.org/I56067802"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Nathalie Th\u00e9ret","raw_affiliation_strings":["Univ Rennes, Inria, CNRS, IRISA, UMR 6074, Rennes, France","Univ Rennes, Inserm, EHESP, Irset, UMR S1085, Rennes, France","Dyliss - Dynamics, Logics and Inference for biological Systems and Sequences (Campus de Beaulieu 35042 Rennes cedex - France)","IRISA - Institut de Recherche en Informatique et Syst\u00e8mes Al\u00e9atoires (Avenue du g\u00e9n\u00e9ral Leclerc\r\nCampus de Beaulieu \r\n35042 RENNES CEDEX - France)","Irset - Institut de recherche en sant\u00e9, environnement et travail (263 avenue G\u00e9n\u00e9ral Leclerc 35042 Rennes Cedex - France)"],"raw_orcid":"https://orcid.org/0000-0002-5857-7828","affiliations":[{"raw_affiliation_string":"Univ Rennes, Inria, CNRS, IRISA, UMR 6074, Rennes, France","institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I2802519937","https://openalex.org/I56067802"]},{"raw_affiliation_string":"Univ Rennes, Inserm, EHESP, Irset, UMR S1085, Rennes, France","institution_ids":["https://openalex.org/I154526488","https://openalex.org/I165283593","https://openalex.org/I4210108239","https://openalex.org/I56067802"]},{"raw_affiliation_string":"Dyliss - Dynamics, Logics and Inference for biological Systems and Sequences (Campus de Beaulieu 35042 Rennes cedex - France)","institution_ids":["https://openalex.org/I4405260663"]},{"raw_affiliation_string":"IRISA - Institut de Recherche en Informatique et Syst\u00e8mes Al\u00e9atoires (Avenue du g\u00e9n\u00e9ral Leclerc\r\nCampus de Beaulieu \r\n35042 RENNES CEDEX - France)","institution_ids":["https://openalex.org/I2802519937"]},{"raw_affiliation_string":"Irset - Institut de recherche en sant\u00e9, environnement et travail (263 avenue G\u00e9n\u00e9ral Leclerc 35042 Rennes Cedex - France)","institution_ids":["https://openalex.org/I4210108239"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":12,"corresponding_author_ids":["https://openalex.org/A5046388663","https://openalex.org/A5085031854"],"corresponding_institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I142476485","https://openalex.org/I154526488","https://openalex.org/I165283593","https://openalex.org/I2746051580","https://openalex.org/I2802519937","https://openalex.org/I29607241","https://openalex.org/I4210108239","https://openalex.org/I4210139461","https://openalex.org/I4210161954","https://openalex.org/I4405260663","https://openalex.org/I56067802"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":2.6184,"has_fulltext":true,"cited_by_count":11,"citation_normalized_percentile":{"value":0.90960663,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"20","issue":"7","first_page":"e1011858","last_page":"e1011858"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10966","display_name":"Liver physiology and pathology","score":0.9997000098228455,"subfield":{"id":"https://openalex.org/subfields/2721","display_name":"Hepatology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},"topics":[{"id":"https://openalex.org/T10966","display_name":"Liver physiology and pathology","score":0.9997000098228455,"subfield":{"id":"https://openalex.org/subfields/2721","display_name":"Hepatology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T10351","display_name":"Liver Disease Diagnosis and Treatment","score":0.9951000213623047,"subfield":{"id":"https://openalex.org/subfields/2713","display_name":"Epidemiology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T11834","display_name":"Liver Diseases and Immunity","score":0.9879000186920166,"subfield":{"id":"https://openalex.org/subfields/2721","display_name":"Hepatology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/hepatic-stellate-cell","display_name":"Hepatic stellate cell","score":0.8347660303115845},{"id":"https://openalex.org/keywords/reversion","display_name":"Reversion","score":0.6699199080467224},{"id":"https://openalex.org/keywords/fibrosis","display_name":"Fibrosis","score":0.6637259721755981},{"id":"https://openalex.org/keywords/extracellular-matrix","display_name":"Extracellular matrix","score":0.6064833998680115},{"id":"https://openalex.org/keywords/hepatic-fibrosis","display_name":"Hepatic fibrosis","score":0.5828298330307007},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5675607323646545},{"id":"https://openalex.org/keywords/chronic-liver-disease","display_name":"Chronic liver disease","score":0.44037431478500366},{"id":"https://openalex.org/keywords/cancer-research","display_name":"Cancer research","score":0.3930905759334564},{"id":"https://openalex.org/keywords/cell-biology","display_name":"Cell biology","score":0.3716941475868225},{"id":"https://openalex.org/keywords/phenotype","display_name":"Phenotype","score":0.3254305422306061},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3203296661376953},{"id":"https://openalex.org/keywords/cirrhosis","display_name":"Cirrhosis","score":0.30374976992607117},{"id":"https://openalex.org/keywords/pathology","display_name":"Pathology","score":0.2233390212059021},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.19681790471076965},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.18877092003822327},{"id":"https://openalex.org/keywords/internal-medicine","display_name":"Internal medicine","score":0.12458977103233337},{"id":"https://openalex.org/keywords/endocrinology","display_name":"Endocrinology","score":0.10795339941978455},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.10196542739868164}],"concepts":[{"id":"https://openalex.org/C176891718","wikidata":"https://www.wikidata.org/wiki/Q1997459","display_name":"Hepatic stellate cell","level":2,"score":0.8347660303115845},{"id":"https://openalex.org/C70883133","wikidata":"https://www.wikidata.org/wiki/Q7318316","display_name":"Reversion","level":4,"score":0.6699199080467224},{"id":"https://openalex.org/C2780559512","wikidata":"https://www.wikidata.org/wiki/Q605709","display_name":"Fibrosis","level":2,"score":0.6637259721755981},{"id":"https://openalex.org/C189165786","wikidata":"https://www.wikidata.org/wiki/Q193825","display_name":"Extracellular matrix","level":2,"score":0.6064833998680115},{"id":"https://openalex.org/C2993667909","wikidata":"https://www.wikidata.org/wiki/Q147778","display_name":"Hepatic fibrosis","level":3,"score":0.5828298330307007},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5675607323646545},{"id":"https://openalex.org/C2779102576","wikidata":"https://www.wikidata.org/wiki/Q5113984","display_name":"Chronic liver disease","level":3,"score":0.44037431478500366},{"id":"https://openalex.org/C502942594","wikidata":"https://www.wikidata.org/wiki/Q3421914","display_name":"Cancer research","level":1,"score":0.3930905759334564},{"id":"https://openalex.org/C95444343","wikidata":"https://www.wikidata.org/wiki/Q7141","display_name":"Cell biology","level":1,"score":0.3716941475868225},{"id":"https://openalex.org/C127716648","wikidata":"https://www.wikidata.org/wiki/Q104053","display_name":"Phenotype","level":3,"score":0.3254305422306061},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3203296661376953},{"id":"https://openalex.org/C2777214474","wikidata":"https://www.wikidata.org/wiki/Q147778","display_name":"Cirrhosis","level":2,"score":0.30374976992607117},{"id":"https://openalex.org/C142724271","wikidata":"https://www.wikidata.org/wiki/Q7208","display_name":"Pathology","level":1,"score":0.2233390212059021},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.19681790471076965},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.18877092003822327},{"id":"https://openalex.org/C126322002","wikidata":"https://www.wikidata.org/wiki/Q11180","display_name":"Internal medicine","level":1,"score":0.12458977103233337},{"id":"https://openalex.org/C134018914","wikidata":"https://www.wikidata.org/wiki/Q162606","display_name":"Endocrinology","level":1,"score":0.10795339941978455},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.10196542739868164}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","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":"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":"D005109","descriptor_name":"Extracellular Matrix","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D005109","descriptor_name":"Extracellular Matrix","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D005109","descriptor_name":"Extracellular Matrix","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D005109","descriptor_name":"Extracellular Matrix","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D005109","descriptor_name":"Extracellular Matrix","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008099","descriptor_name":"Liver","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D008099","descriptor_name":"Liver","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D008099","descriptor_name":"Liver","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D008099","descriptor_name":"Liver","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D008099","descriptor_name":"Liver","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D008099","descriptor_name":"Liver","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":false},{"descriptor_ui":"D008099","descriptor_name":"Liver","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":false},{"descriptor_ui":"D008099","descriptor_name":"Liver","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":false},{"descriptor_ui":"D008099","descriptor_name":"Liver","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":false},{"descriptor_ui":"D008099","descriptor_name":"Liver","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":false},{"descriptor_ui":"D008103","descriptor_name":"Liver Cirrhosis","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D008103","descriptor_name":"Liver Cirrhosis","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D008103","descriptor_name":"Liver Cirrhosis","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D008103","descriptor_name":"Liver Cirrhosis","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D008103","descriptor_name":"Liver Cirrhosis","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D008103","descriptor_name":"Liver Cirrhosis","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":true},{"descriptor_ui":"D008103","descriptor_name":"Liver Cirrhosis","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":true},{"descriptor_ui":"D008103","descriptor_name":"Liver Cirrhosis","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":true},{"descriptor_ui":"D008103","descriptor_name":"Liver Cirrhosis","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":true},{"descriptor_ui":"D008103","descriptor_name":"Liver Cirrhosis","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","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":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","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":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018450","descriptor_name":"Disease Progression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018450","descriptor_name":"Disease Progression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018450","descriptor_name":"Disease Progression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018450","descriptor_name":"Disease Progression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018450","descriptor_name":"Disease Progression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D024042","descriptor_name":"Collagen Type I","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D024042","descriptor_name":"Collagen Type I","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D024042","descriptor_name":"Collagen Type I","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D024042","descriptor_name":"Collagen Type I","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D024042","descriptor_name":"Collagen Type I","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D024042","descriptor_name":"Collagen Type I","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D024042","descriptor_name":"Collagen Type I","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D024042","descriptor_name":"Collagen Type I","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D024042","descriptor_name":"Collagen Type I","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D024042","descriptor_name":"Collagen Type I","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053773","descriptor_name":"Transforming Growth Factor beta1","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D053773","descriptor_name":"Transforming Growth Factor beta1","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D053773","descriptor_name":"Transforming Growth Factor beta1","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D053773","descriptor_name":"Transforming Growth Factor beta1","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D053773","descriptor_name":"Transforming Growth Factor beta1","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D055166","descriptor_name":"Hepatic Stellate Cells","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D055166","descriptor_name":"Hepatic Stellate Cells","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D055166","descriptor_name":"Hepatic Stellate Cells","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D055166","descriptor_name":"Hepatic Stellate Cells","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D055166","descriptor_name":"Hepatic Stellate Cells","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1371/journal.pcbi.1011858","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1011858","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:39074160","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39074160","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":"Journal Article"},{"id":"pmh:oai:HAL:hal-04689199v1","is_oa":true,"landing_page_url":"https://hal.science/hal-04689199","pdf_url":"https://hal.science/hal-04689199v1/file/journal.pcbi.1011858.pdf","source":{"id":"https://openalex.org/S4306402512","display_name":"HAL (Le Centre pour la Communication Scientifique Directe)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1294671590","host_organization_name":"Centre National de la Recherche Scientifique","host_organization_lineage":["https://openalex.org/I1294671590"],"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, 2024, 20 (7), pp.e1011858. &#x27E8;10.1371/journal.pcbi.1011858&#x27E9;","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:pubmedcentral.nih.gov:11309422","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11309422","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11309422/pdf/pcbi.1011858.pdf","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:doaj.org/article:4e8d8be507604fb5b0fd775570547d7c","is_oa":true,"landing_page_url":"https://doaj.org/article/4e8d8be507604fb5b0fd775570547d7c","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 20, Iss 7, p e1011858 (2024)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1011858","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1011858","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":[],"funders":[{"id":"https://openalex.org/F4320313934","display_name":"Institut national de recherche en informatique et en automatique (INRIA)","ror":"https://ror.org/02kvxyf05"},{"id":"https://openalex.org/F4320320893","display_name":"Institut National de la Sant\u00e9 et de la Recherche M\u00e9dicale","ror":"https://ror.org/02vjkv261"},{"id":"https://openalex.org/F4320322892","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":84,"referenced_works":["https://openalex.org/W28771307","https://openalex.org/W126680197","https://openalex.org/W1511537290","https://openalex.org/W1513962738","https://openalex.org/W1563071114","https://openalex.org/W1584748694","https://openalex.org/W1593160355","https://openalex.org/W1808406820","https://openalex.org/W1844303090","https://openalex.org/W1960272757","https://openalex.org/W1974955986","https://openalex.org/W1976377883","https://openalex.org/W1982147469","https://openalex.org/W1983350265","https://openalex.org/W1984883254","https://openalex.org/W1986649132","https://openalex.org/W2010180179","https://openalex.org/W2020573317","https://openalex.org/W2028130113","https://openalex.org/W2038313328","https://openalex.org/W2039426167","https://openalex.org/W2046983857","https://openalex.org/W2055562316","https://openalex.org/W2063495563","https://openalex.org/W2075290880","https://openalex.org/W2099040076","https://openalex.org/W2103863906","https://openalex.org/W2111199541","https://openalex.org/W2123106337","https://openalex.org/W2127030655","https://openalex.org/W2130410032","https://openalex.org/W2132224453","https://openalex.org/W2136002823","https://openalex.org/W2154497431","https://openalex.org/W2155418451","https://openalex.org/W2163036793","https://openalex.org/W2163386417","https://openalex.org/W2165527951","https://openalex.org/W2169193349","https://openalex.org/W2179438025","https://openalex.org/W2184606859","https://openalex.org/W2303100661","https://openalex.org/W2334094525","https://openalex.org/W2395803168","https://openalex.org/W2531076154","https://openalex.org/W2563505417","https://openalex.org/W2588964480","https://openalex.org/W2611943439","https://openalex.org/W2613180696","https://openalex.org/W2782460017","https://openalex.org/W2807744179","https://openalex.org/W2902518326","https://openalex.org/W2945705065","https://openalex.org/W2951799803","https://openalex.org/W2980820618","https://openalex.org/W2986691533","https://openalex.org/W3002179283","https://openalex.org/W3003175993","https://openalex.org/W3009052374","https://openalex.org/W3025115700","https://openalex.org/W3095484986","https://openalex.org/W3100717035","https://openalex.org/W3109708108","https://openalex.org/W3110189951","https://openalex.org/W3128309898","https://openalex.org/W3136060713","https://openalex.org/W3161450531","https://openalex.org/W3163583874","https://openalex.org/W3165286527","https://openalex.org/W3169361071","https://openalex.org/W3177468946","https://openalex.org/W3186843381","https://openalex.org/W3195482803","https://openalex.org/W3214975922","https://openalex.org/W4205272242","https://openalex.org/W4206163377","https://openalex.org/W4206997168","https://openalex.org/W4225339204","https://openalex.org/W4250007760","https://openalex.org/W4251538155","https://openalex.org/W4287504679","https://openalex.org/W4298280860","https://openalex.org/W4307843054","https://openalex.org/W4360618851"],"related_works":["https://openalex.org/W2985074236","https://openalex.org/W2954470577","https://openalex.org/W1995261957","https://openalex.org/W3028957131","https://openalex.org/W2356869055","https://openalex.org/W2321214792","https://openalex.org/W3038928394","https://openalex.org/W4245493393","https://openalex.org/W2802633545","https://openalex.org/W2318211403"],"abstract_inverted_index":{"Hepatic":[0],"stellate":[1],"cells":[2],"(HSC)":[3],"are":[4,98,163],"the":[5,27,53,81,119,125,129,134,138,171,194,212,220,259,275],"source":[6],"of":[7,29,42,50,55,121,128,137,151,159,183,189,206,222,252,262,278],"extracellular":[8],"matrix":[9],"(ECM)":[10],"whose":[11],"overproduction":[12],"leads":[13],"to":[14,35,70,93,165,174,180,273,290],"fibrosis,":[15,209,242],"a":[16,181,203],"condition":[17],"that":[18,102,109,269],"impairs":[19],"liver":[20,24,208,226,241,267,281],"functions":[21],"in":[22,265,280,296],"chronic":[23,225,266],"diseases.":[25],"Understanding":[26],"dynamics":[28,73,264],"HSCs":[30,97,153,161],"will":[31],"provide":[32],"insights":[33],"needed":[34],"develop":[36],"new":[37,199],"therapeutic":[38],"approaches.":[39],"Few":[40],"models":[41,69],"hepatic":[43],"fibrosis":[44,75,143,253,295],"have":[45],"been":[46],"proposed,":[47],"and":[48,77,91,108,118,145,294],"none":[49],"them":[51],"include":[52],"heterogeneity":[54],"HSC":[56,72,116,139,263],"phenotypes":[57],"recently":[58],"highlighted":[59],"by":[60],"single-cell":[61],"RNA":[62,230],"sequencing":[63,231],"analyses.":[64],"Here,":[65],"we":[66,88,169,210,243],"developed":[67],"rule-based":[68],"study":[71,257],"during":[74,142,154,224,292],"progression":[76,144],"reversion.":[78,146],"We":[79],"used":[80,89,272],"Kappa":[82],"graph":[83],"rewriting":[84],"language,":[85],"for":[86,186],"which":[87,114,187],"tokens":[90],"counters":[92],"overcome":[94],"temporal":[95],"explosion.":[96],"modeled":[99],"as":[100,249],"agents":[101],"present":[103],"seven":[104],"physiological":[105],"cellular":[106],"states":[107],"interact":[110],"with":[111,193,235,240],"(TGF\u03b21)":[112,175,190],"molecules":[113],"regulate":[115],"activation":[117],"secretion":[120],"type":[122],"I":[123],"collagen,":[124],"main":[126],"component":[127],"ECM.":[130],"Simulation":[131],"studies":[132],"revealed":[133],"critical":[135],"role":[136,277],"inactivation":[140,148],"process":[141],"While":[147],"allows":[149],"elimination":[150],"activated":[152],"reversion":[155],"steps,":[156],"reactivation":[157],"loops":[158],"inactivated":[160],"(iHSCs)":[162],"required":[164],"sustain":[166],"fibrosis.":[167],"Furthermore,":[168],"demonstrated":[170],"model's":[172],"sensitivity":[173],"parameters,":[176],"suggesting":[177],"its":[178],"adaptability":[179],"variety":[182],"pathophysiological":[184],"conditions":[185],"levels":[188],"production":[191],"associated":[192,239],"inflammatory":[195],"response":[196],"differ.":[197],"Using":[198],"experimental":[200],"data":[201,232],"from":[202,233],"mouse":[204],"model":[205,217,261,285],"CCl4-induced":[207],"validated":[211],"predicted":[213],"ECM":[214],"dynamics.":[215],"Our":[216],"also":[218,287],"predicts":[219],"accumulation":[221],"iHSCs":[223,248,279],"disease.":[227],"By":[228],"analyzing":[229],"patients":[234],"non-alcoholic":[236],"steatohepatitis":[237],"(NASH)":[238],"confirmed":[244],"this":[245],"accumulation,":[246],"identifying":[247],"novel":[250],"markers":[251],"progression.":[254],"Overall,":[255],"our":[256,284],"provides":[258],"first":[260],"disease":[268],"can":[270,286],"be":[271,288],"explore":[274],"regulatory":[276],"homeostasis.":[282],"Moreover,":[283],"generalized":[289],"fibroblasts":[291],"repair":[293],"other":[297],"tissues.":[298]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":6},{"year":2024,"cited_by_count":2}],"updated_date":"2026-08-19T15:00:24.278416","created_date":"2025-10-10T00:00:00"}
