{"id":"https://openalex.org/W2534730685","doi":"https://doi.org/10.1186/s12918-017-0394-4","title":"Markov State Models of gene regulatory networks","display_name":"Markov State Models of gene regulatory networks","publication_year":2017,"publication_date":"2017-02-06","ids":{"openalex":"https://openalex.org/W2534730685","doi":"https://doi.org/10.1186/s12918-017-0394-4","mag":"2534730685","pmid":"https://pubmed.ncbi.nlm.nih.gov/28166778"},"language":"en","primary_location":{"id":"doi:10.1186/s12918-017-0394-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12918-017-0394-4","pdf_url":"https://bmcsystbiol.biomedcentral.com/track/pdf/10.1186/s12918-017-0394-4","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Systems Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"diamond","oa_url":"https://bmcsystbiol.biomedcentral.com/track/pdf/10.1186/s12918-017-0394-4","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5010752873","display_name":"Brian Chu","orcid":"https://orcid.org/0000-0002-0803-5529"},"institutions":[{"id":"https://openalex.org/I204250578","display_name":"University of California, Irvine","ror":"https://ror.org/04gyf1771","country_code":"US","type":"education","lineage":["https://openalex.org/I204250578"]},{"id":"https://openalex.org/I4210140791","display_name":"Irvine University","ror":"https://ror.org/04ysmca02","country_code":"US","type":"education","lineage":["https://openalex.org/I4210140791"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Brian K. Chu","raw_affiliation_strings":["Department of Chemical Engineering and Materials Science, University of California Irvine, Irvine, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemical Engineering and Materials Science, University of California Irvine, Irvine, CA, USA","institution_ids":["https://openalex.org/I4210140791","https://openalex.org/I204250578"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077479510","display_name":"Margaret J. Tse","orcid":null},"institutions":[{"id":"https://openalex.org/I204250578","display_name":"University of California, Irvine","ror":"https://ror.org/04gyf1771","country_code":"US","type":"education","lineage":["https://openalex.org/I204250578"]},{"id":"https://openalex.org/I4210140791","display_name":"Irvine University","ror":"https://ror.org/04ysmca02","country_code":"US","type":"education","lineage":["https://openalex.org/I4210140791"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Margaret J. Tse","raw_affiliation_strings":["Department of Chemical Engineering and Materials Science, University of California Irvine, Irvine, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemical Engineering and Materials Science, University of California Irvine, Irvine, CA, USA","institution_ids":["https://openalex.org/I4210140791","https://openalex.org/I204250578"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019210082","display_name":"Royce R. Sato","orcid":null},"institutions":[{"id":"https://openalex.org/I204250578","display_name":"University of California, Irvine","ror":"https://ror.org/04gyf1771","country_code":"US","type":"education","lineage":["https://openalex.org/I204250578"]},{"id":"https://openalex.org/I4210140791","display_name":"Irvine University","ror":"https://ror.org/04ysmca02","country_code":"US","type":"education","lineage":["https://openalex.org/I4210140791"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Royce R. Sato","raw_affiliation_strings":["Department of Chemical Engineering and Materials Science, University of California Irvine, Irvine, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemical Engineering and Materials Science, University of California Irvine, Irvine, CA, USA","institution_ids":["https://openalex.org/I4210140791","https://openalex.org/I204250578"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5046882565","display_name":"Elizabeth L. Read","orcid":"https://orcid.org/0000-0002-9186-284X"},"institutions":[{"id":"https://openalex.org/I4210140791","display_name":"Irvine University","ror":"https://ror.org/04ysmca02","country_code":"US","type":"education","lineage":["https://openalex.org/I4210140791"]},{"id":"https://openalex.org/I204250578","display_name":"University of California, Irvine","ror":"https://ror.org/04gyf1771","country_code":"US","type":"education","lineage":["https://openalex.org/I204250578"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Elizabeth L. Read","raw_affiliation_strings":["Department of Chemical Engineering and Materials Science, University of California Irvine, Irvine, CA, USA. elread@uci.edu","Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, CA, USA. elread@uci.edu","Department of Chemical Engineering and Materials Science, University of California Irvine, Irvine, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemical Engineering and Materials Science, University of California Irvine, Irvine, CA, USA. elread@uci.edu","institution_ids":[]},{"raw_affiliation_string":"Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, CA, USA. elread@uci.edu","institution_ids":[]},{"raw_affiliation_string":"Department of Chemical Engineering and Materials Science, University of California Irvine, Irvine, CA, USA","institution_ids":["https://openalex.org/I4210140791","https://openalex.org/I204250578"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5010752873"],"corresponding_institution_ids":["https://openalex.org/I204250578","https://openalex.org/I4210140791"],"apc_list":null,"apc_paid":null,"fwci":1.6796,"has_fulltext":true,"cited_by_count":35,"citation_normalized_percentile":{"value":0.83659857,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"11","issue":"1","first_page":"14","last_page":"14"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9952999949455261,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9952999949455261,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.0006000000284984708,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.0005000000237487257,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.8544510006904602},{"id":"https://openalex.org/keywords/multistability","display_name":"Multistability","score":0.7753180265426636},{"id":"https://openalex.org/keywords/systems-biology","display_name":"Systems biology","score":0.6548173427581787},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5905391573905945},{"id":"https://openalex.org/keywords/markov-chain","display_name":"Markov chain","score":0.5733979940414429},{"id":"https://openalex.org/keywords/network-dynamics","display_name":"Network dynamics","score":0.558332622051239},{"id":"https://openalex.org/keywords/biological-network","display_name":"Biological network","score":0.5408076047897339},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.4579834043979645},{"id":"https://openalex.org/keywords/markov-model","display_name":"Markov model","score":0.4571495056152344},{"id":"https://openalex.org/keywords/complex-network","display_name":"Complex network","score":0.44846755266189575},{"id":"https://openalex.org/keywords/stochastic-modelling","display_name":"Stochastic modelling","score":0.42111632227897644},{"id":"https://openalex.org/keywords/markov-process","display_name":"Markov process","score":0.4207727611064911},{"id":"https://openalex.org/keywords/reprogramming","display_name":"Reprogramming","score":0.4187923073768616},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.38883262872695923},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.274888813495636},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.21861448884010315},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.20356789231300354},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.15330934524536133},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.13197433948516846},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.12148064374923706},{"id":"https://openalex.org/keywords/nonlinear-system","display_name":"Nonlinear system","score":0.10876789689064026},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.09056732058525085}],"concepts":[{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.8544510006904602},{"id":"https://openalex.org/C2776966350","wikidata":"https://www.wikidata.org/wiki/Q6935096","display_name":"Multistability","level":3,"score":0.7753180265426636},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.6548173427581787},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5905391573905945},{"id":"https://openalex.org/C98763669","wikidata":"https://www.wikidata.org/wiki/Q176645","display_name":"Markov chain","level":2,"score":0.5733979940414429},{"id":"https://openalex.org/C123757187","wikidata":"https://www.wikidata.org/wiki/Q9195957","display_name":"Network dynamics","level":2,"score":0.558332622051239},{"id":"https://openalex.org/C28225019","wikidata":"https://www.wikidata.org/wiki/Q4915005","display_name":"Biological network","level":2,"score":0.5408076047897339},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.4579834043979645},{"id":"https://openalex.org/C163836022","wikidata":"https://www.wikidata.org/wiki/Q6771326","display_name":"Markov model","level":3,"score":0.4571495056152344},{"id":"https://openalex.org/C34947359","wikidata":"https://www.wikidata.org/wiki/Q665189","display_name":"Complex network","level":2,"score":0.44846755266189575},{"id":"https://openalex.org/C127491075","wikidata":"https://www.wikidata.org/wiki/Q7617825","display_name":"Stochastic modelling","level":2,"score":0.42111632227897644},{"id":"https://openalex.org/C159886148","wikidata":"https://www.wikidata.org/wiki/Q176645","display_name":"Markov process","level":2,"score":0.4207727611064911},{"id":"https://openalex.org/C77255625","wikidata":"https://www.wikidata.org/wiki/Q402093","display_name":"Reprogramming","level":3,"score":0.4187923073768616},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.38883262872695923},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.274888813495636},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.21861448884010315},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.20356789231300354},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.15330934524536133},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.13197433948516846},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.12148064374923706},{"id":"https://openalex.org/C158622935","wikidata":"https://www.wikidata.org/wiki/Q660848","display_name":"Nonlinear system","level":2,"score":0.10876789689064026},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.09056732058525085},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.0},{"id":"https://openalex.org/C118615104","wikidata":"https://www.wikidata.org/wiki/Q121416","display_name":"Discrete mathematics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D007700","descriptor_name":"Kinetics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007700","descriptor_name":"Kinetics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007700","descriptor_name":"Kinetics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1186/s12918-017-0394-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12918-017-0394-4","pdf_url":"https://bmcsystbiol.biomedcentral.com/track/pdf/10.1186/s12918-017-0394-4","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Systems Biology","raw_type":"journal-article"},{"id":"pmid:28166778","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/28166778","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":"BMC systems biology","raw_type":null},{"id":"pmh:oai:escholarship.org:ark:/13030/qt8665m7rf","is_oa":false,"landing_page_url":"https://escholarship.org/uc/item/8665m7rf","pdf_url":null,"source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Systems Biology, vol 11, iss 1","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:5294885","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5294885","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":"BMC Syst Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12918-017-0394-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12918-017-0394-4","pdf_url":"https://bmcsystbiol.biomedcentral.com/track/pdf/10.1186/s12918-017-0394-4","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Systems Biology","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/17","score":0.4000000059604645,"display_name":"Partnerships for the goals"}],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2534730685.pdf","grobid_xml":"https://content.openalex.org/works/W2534730685.grobid-xml"},"referenced_works_count":94,"referenced_works":["https://openalex.org/W11463020","https://openalex.org/W565175910","https://openalex.org/W1137540706","https://openalex.org/W1525349614","https://openalex.org/W1799986736","https://openalex.org/W1946177469","https://openalex.org/W1966758700","https://openalex.org/W1969674103","https://openalex.org/W1970779075","https://openalex.org/W1973875954","https://openalex.org/W1977969550","https://openalex.org/W1979070806","https://openalex.org/W1980944685","https://openalex.org/W1989192823","https://openalex.org/W1997108831","https://openalex.org/W1999777663","https://openalex.org/W2006901939","https://openalex.org/W2008206597","https://openalex.org/W2011276078","https://openalex.org/W2012029966","https://openalex.org/W2014392153","https://openalex.org/W2016180314","https://openalex.org/W2017896410","https://openalex.org/W2025899185","https://openalex.org/W2027703497","https://openalex.org/W2029991507","https://openalex.org/W2031843459","https://openalex.org/W2032570525","https://openalex.org/W2033738243","https://openalex.org/W2040889971","https://openalex.org/W2043782614","https://openalex.org/W2047365291","https://openalex.org/W2048438929","https://openalex.org/W2053348581","https://openalex.org/W2054443920","https://openalex.org/W2055484248","https://openalex.org/W2057311914","https://openalex.org/W2060457543","https://openalex.org/W2062029454","https://openalex.org/W2062856462","https://openalex.org/W2063021109","https://openalex.org/W2065281489","https://openalex.org/W2066594542","https://openalex.org/W2074401358","https://openalex.org/W2075243501","https://openalex.org/W2078097311","https://openalex.org/W2081076340","https://openalex.org/W2081645999","https://openalex.org/W2081848717","https://openalex.org/W2083886791","https://openalex.org/W2084218480","https://openalex.org/W2085213650","https://openalex.org/W2089340422","https://openalex.org/W2091707670","https://openalex.org/W2093922799","https://openalex.org/W2096705138","https://openalex.org/W2102787760","https://openalex.org/W2106391833","https://openalex.org/W2110507597","https://openalex.org/W2110688728","https://openalex.org/W2111167674","https://openalex.org/W2115351194","https://openalex.org/W2117559095","https://openalex.org/W2117589890","https://openalex.org/W2122864540","https://openalex.org/W2127740987","https://openalex.org/W2134759932","https://openalex.org/W2140855217","https://openalex.org/W2142806844","https://openalex.org/W2143592395","https://openalex.org/W2147848673","https://openalex.org/W2148323109","https://openalex.org/W2153453980","https://openalex.org/W2155418451","https://openalex.org/W2159875969","https://openalex.org/W2160341881","https://openalex.org/W2167244112","https://openalex.org/W2168221215","https://openalex.org/W2171280873","https://openalex.org/W2183803433","https://openalex.org/W2226825552","https://openalex.org/W2266613162","https://openalex.org/W2284830105","https://openalex.org/W2313914485","https://openalex.org/W2318561339","https://openalex.org/W2331030820","https://openalex.org/W2403698174","https://openalex.org/W2468559033","https://openalex.org/W2788301533","https://openalex.org/W3100237731","https://openalex.org/W3100810942","https://openalex.org/W3101205262","https://openalex.org/W3105015898","https://openalex.org/W3125096507"],"related_works":["https://openalex.org/W1551306373","https://openalex.org/W2386065843","https://openalex.org/W4319917430","https://openalex.org/W2158714033","https://openalex.org/W78967844","https://openalex.org/W3213185671","https://openalex.org/W4386628104","https://openalex.org/W4206945140","https://openalex.org/W2130939068","https://openalex.org/W3163717165"],"abstract_inverted_index":{"BACKGROUND:":[0],"Gene":[1],"regulatory":[2,81],"networks":[3],"with":[4],"dynamics":[5,30,59,97],"characterized":[6],"by":[7,42],"multiple":[8],"stable":[9],"states":[10,74],"underlie":[11],"cell":[12],"fate-decisions.":[13],"Quantitative":[14],"models":[15],"that":[16,119,142],"can":[17],"link":[18],"molecular-level":[19],"knowledge":[20],"of":[21,28,53,56,72,78,85,101,148],"gene":[22,80,137],"regulation":[23],"to":[24,34,89],"a":[25,76,99,125,153],"global":[26,58,96],"understanding":[27],"network":[29,82,162],"have":[31],"the":[32,43,57,67,90,120,146,161],"potential":[33],"guide":[35],"cell-reprogramming":[36],"strategies.":[37],"Networks":[38],"are":[39,60],"often":[40],"modeled":[41],"stochastic":[44,110,132],"Chemical":[45],"Master":[46],"Equation,":[47],"but":[48],"methods":[49],"for":[50,75,109,128,156],"systematic":[51],"identification":[52],"key":[54],"properties":[55],"currently":[61],"lacking.":[62],"RESULTS:":[63],"The":[64],"method":[65],"identifies":[66],"number,":[68],"phenotypes,":[69],"and":[70,105,130,134],"lifetimes":[71],"long-lived":[73],"set":[77,100],"common":[79],"models.":[83],"Application":[84],"transition":[86,103],"path":[87],"theory":[88],"constructed":[91],"Markov":[92,121],"State":[93,122],"Model":[94,123],"decomposes":[95],"into":[98],"dominant":[102],"paths":[104],"associated":[106],"relative":[107],"probabilities":[108],"state-switching.":[111],"CONCLUSIONS:":[112],"In":[113],"this":[114,143],"proof-of-concept":[115],"study,":[116],"we":[117],"found":[118],"provides":[124],"general":[126],"framework":[127],"analyzing":[129],"visualizing":[131],"multistability":[133],"state-transitions":[135],"in":[136],"networks.":[138],"Our":[139],"results":[140],"suggest":[141],"framework-adopted":[144],"from":[145],"field":[147],"atomistic":[149],"Molecular":[150],"Dynamics-can":[151],"be":[152],"useful":[154],"tool":[155],"quantitative":[157],"Systems":[158],"Biology":[159],"at":[160],"scale.":[163]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":5},{"year":2020,"cited_by_count":7},{"year":2019,"cited_by_count":4},{"year":2018,"cited_by_count":4}],"updated_date":"2026-04-29T09:16:38.111599","created_date":"2025-10-10T00:00:00"}