{"id":"https://openalex.org/W2056486314","doi":"https://doi.org/10.1142/s0219720013300037","title":"FOUNDATIONS FOR MODELING THE DYNAMICS OF GENE REGULATORY NETWORKS: A MULTILEVEL-PERSPECTIVE REVIEW","display_name":"FOUNDATIONS FOR MODELING THE DYNAMICS OF GENE REGULATORY NETWORKS: A MULTILEVEL-PERSPECTIVE REVIEW","publication_year":2013,"publication_date":"2013-10-21","ids":{"openalex":"https://openalex.org/W2056486314","doi":"https://doi.org/10.1142/s0219720013300037","mag":"2056486314","pmid":"https://pubmed.ncbi.nlm.nih.gov/24467752"},"language":"en","primary_location":{"id":"doi:10.1142/s0219720013300037","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s0219720013300037","pdf_url":null,"source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","raw_type":"journal-article"},"type":"review","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5014491106","display_name":"Ismael S\u00e1nchez-Osorio","orcid":null},"institutions":[{"id":"https://openalex.org/I98461037","display_name":"Tecnol\u00f3gico de Monterrey","ror":"https://ror.org/03ayjn504","country_code":"MX","type":"education","lineage":["https://openalex.org/I98461037"]}],"countries":["MX"],"is_corresponding":true,"raw_author_name":"ISMAEL SANCHEZ-OSORIO","raw_affiliation_strings":["Department of Computer Science, Monterrey Institute of Technology and Higher Education Campus Cuernavaca, Autopista del Sol km 104, Xochitepec, Morelos 62790, Mexico"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Monterrey Institute of Technology and Higher Education Campus Cuernavaca, Autopista del Sol km 104, Xochitepec, Morelos 62790, Mexico","institution_ids":["https://openalex.org/I98461037"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002004675","display_name":"Fernando Ramos","orcid":"https://orcid.org/0000-0003-3405-6953"},"institutions":[{"id":"https://openalex.org/I98461037","display_name":"Tecnol\u00f3gico de Monterrey","ror":"https://ror.org/03ayjn504","country_code":"MX","type":"education","lineage":["https://openalex.org/I98461037"]}],"countries":["MX"],"is_corresponding":false,"raw_author_name":"FERNANDO RAMOS","raw_affiliation_strings":["Department of Computer Science, Monterrey Institute of Technology and Higher Education Campus Cuernavaca, Autopista del Sol km 104, Xochitepec, Morelos 62790, Mexico"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Monterrey Institute of Technology and Higher Education Campus Cuernavaca, Autopista del Sol km 104, Xochitepec, Morelos 62790, Mexico","institution_ids":["https://openalex.org/I98461037"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032492775","display_name":"Pedro Mayorga","orcid":"https://orcid.org/0000-0002-1889-6154"},"institutions":[{"id":"https://openalex.org/I98461037","display_name":"Tecnol\u00f3gico de Monterrey","ror":"https://ror.org/03ayjn504","country_code":"MX","type":"education","lineage":["https://openalex.org/I98461037"]}],"countries":["MX"],"is_corresponding":false,"raw_author_name":"PEDRO MAYORGA","raw_affiliation_strings":["Department of Computer Science, Monterrey Institute of Technology and Higher Education Campus Cuernavaca, Autopista del Sol km 104, Xochitepec, Morelos 62790, Mexico"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Monterrey Institute of Technology and Higher Education Campus Cuernavaca, Autopista del Sol km 104, Xochitepec, Morelos 62790, Mexico","institution_ids":["https://openalex.org/I98461037"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5001590616","display_name":"Edgar Dant\u00e1n","orcid":null},"institutions":[{"id":"https://openalex.org/I884181516","display_name":"Universidad Aut\u00f3noma del Estado de Morelos","ror":"https://ror.org/03rzb4f20","country_code":"MX","type":"education","lineage":["https://openalex.org/I884181516"]}],"countries":["MX"],"is_corresponding":false,"raw_author_name":"EDGAR DANTAN","raw_affiliation_strings":["Centro de Investigaci\u00f3n en Biotecnolog\u00eda, Universidad Aut\u00f3noma del Estado de Morelos, Avenida Universidad 1001, Cuernavaca, Morelos 62209, Mexico"],"affiliations":[{"raw_affiliation_string":"Centro de Investigaci\u00f3n en Biotecnolog\u00eda, Universidad Aut\u00f3noma del Estado de Morelos, Avenida Universidad 1001, Cuernavaca, Morelos 62209, Mexico","institution_ids":["https://openalex.org/I884181516"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5014491106"],"corresponding_institution_ids":["https://openalex.org/I98461037"],"apc_list":null,"apc_paid":null,"fwci":0.4386,"has_fulltext":false,"cited_by_count":16,"citation_normalized_percentile":{"value":0.64898131,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"12","issue":"01","first_page":"1330003","last_page":"1330003"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11764","display_name":"Evolution and Genetic Dynamics","score":0.9962999820709229,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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":0.9950000047683716,"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":0.6000178456306458},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5946712493896484},{"id":"https://openalex.org/keywords/hierarchy","display_name":"Hierarchy","score":0.5377151966094971},{"id":"https://openalex.org/keywords/abstraction","display_name":"Abstraction","score":0.5336224436759949},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.5046111345291138},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.5018079280853271},{"id":"https://openalex.org/keywords/perspective","display_name":"Perspective (graphical)","score":0.47410517930984497},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.28700241446495056},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.16679900884628296},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.16575077176094055},{"id":"https://openalex.org/keywords/epistemology","display_name":"Epistemology","score":0.10569828748703003},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.08794137835502625}],"concepts":[{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.6000178456306458},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5946712493896484},{"id":"https://openalex.org/C31170391","wikidata":"https://www.wikidata.org/wiki/Q188619","display_name":"Hierarchy","level":2,"score":0.5377151966094971},{"id":"https://openalex.org/C124304363","wikidata":"https://www.wikidata.org/wiki/Q673661","display_name":"Abstraction","level":2,"score":0.5336224436759949},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.5046111345291138},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.5018079280853271},{"id":"https://openalex.org/C12713177","wikidata":"https://www.wikidata.org/wiki/Q1900281","display_name":"Perspective (graphical)","level":2,"score":0.47410517930984497},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.28700241446495056},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.16679900884628296},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.16575077176094055},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.10569828748703003},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.08794137835502625},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C34447519","wikidata":"https://www.wikidata.org/wiki/Q179522","display_name":"Market economy","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/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005828","descriptor_name":"Genetics, Population","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005828","descriptor_name":"Genetics, Population","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005828","descriptor_name":"Genetics, Population","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"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":2,"locations":[{"id":"doi:10.1142/s0219720013300037","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s0219720013300037","pdf_url":null,"source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","raw_type":"journal-article"},{"id":"pmid:24467752","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24467752","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":"Journal of bioinformatics and computational biology","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":412,"referenced_works":["https://openalex.org/W1046806","https://openalex.org/W11463020","https://openalex.org/W66994666","https://openalex.org/W74971858","https://openalex.org/W212854950","https://openalex.org/W408793434","https://openalex.org/W567310294","https://openalex.org/W591494124","https://openalex.org/W595997847","https://openalex.org/W614012683","https://openalex.org/W631551263","https://openalex.org/W1482678044","https://openalex.org/W1484033701","https://openalex.org/W1495469487","https://openalex.org/W1502406759","https://openalex.org/W1510479004","https://openalex.org/W1511368807","https://openalex.org/W1519577127","https://openalex.org/W1527441981","https://openalex.org/W1528643580","https://openalex.org/W1544259807","https://openalex.org/W1555224914","https://openalex.org/W1557060163","https://openalex.org/W1563463966","https://openalex.org/W1566694705","https://openalex.org/W1584397582","https://openalex.org/W1599969036","https://openalex.org/W1603293791","https://openalex.org/W1603900493","https://openalex.org/W1642251103","https://openalex.org/W1644749979","https://openalex.org/W1685940597","https://openalex.org/W1748503351","https://openalex.org/W1883779479","https://openalex.org/W1913409399","https://openalex.org/W1917347435","https://openalex.org/W1926807800","https://openalex.org/W1963522244","https://openalex.org/W1964107188","https://openalex.org/W1965278175","https://openalex.org/W1966722314","https://openalex.org/W1966757367","https://openalex.org/W1968233513","https://openalex.org/W1970995078","https://openalex.org/W1971224531","https://openalex.org/W1973109523","https://openalex.org/W1973483476","https://openalex.org/W1973526956","https://openalex.org/W1973685599","https://openalex.org/W1973890190","https://openalex.org/W1974184286","https://openalex.org/W1975586684","https://openalex.org/W1976205989","https://openalex.org/W1976484445","https://openalex.org/W1976488701","https://openalex.org/W1976535231","https://openalex.org/W1976962685","https://openalex.org/W1978159078","https://openalex.org/W1978408051","https://openalex.org/W1978486653","https://openalex.org/W1979038838","https://openalex.org/W1979302584","https://openalex.org/W1979847955","https://openalex.org/W1980253661","https://openalex.org/W1980944685","https://openalex.org/W1981272174","https://openalex.org/W1981333260","https://openalex.org/W1981747417","https://openalex.org/W1982233439","https://openalex.org/W1983874017","https://openalex.org/W1984097115","https://openalex.org/W1984543814","https://openalex.org/W1984618686","https://openalex.org/W1985032743","https://openalex.org/W1985313286","https://openalex.org/W1986163307","https://openalex.org/W1986436385","https://openalex.org/W1986772002","https://openalex.org/W1986789040","https://openalex.org/W1988370350","https://openalex.org/W1988402499","https://openalex.org/W1988410238","https://openalex.org/W1989925383","https://openalex.org/W1990507623","https://openalex.org/W1990728218","https://openalex.org/W1991799786","https://openalex.org/W1991985606","https://openalex.org/W1992643930","https://openalex.org/W1993051221","https://openalex.org/W1993546274","https://openalex.org/W1994141319","https://openalex.org/W1994660545","https://openalex.org/W1994706449","https://openalex.org/W1995012220","https://openalex.org/W1995791498","https://openalex.org/W1996391065","https://openalex.org/W1997051196","https://openalex.org/W1997057704","https://openalex.org/W1998904894","https://openalex.org/W1999118347","https://openalex.org/W1999777663","https://openalex.org/W2000523053","https://openalex.org/W2001394772","https://openalex.org/W2002227368","https://openalex.org/W2003573017","https://openalex.org/W2003713758","https://openalex.org/W2005202913","https://openalex.org/W2005773703","https://openalex.org/W2007286218","https://openalex.org/W2007592424","https://openalex.org/W2008057778","https://openalex.org/W2008206597","https://openalex.org/W2009563180","https://openalex.org/W2010173857","https://openalex.org/W2011302286","https://openalex.org/W2011894114","https://openalex.org/W2012639206","https://openalex.org/W2014761472","https://openalex.org/W2015764015","https://openalex.org/W2015790024","https://openalex.org/W2016830368","https://openalex.org/W2016912251","https://openalex.org/W2018435536","https://openalex.org/W2018670096","https://openalex.org/W2018711905","https://openalex.org/W2019149882","https://openalex.org/W2019472515","https://openalex.org/W2020767071","https://openalex.org/W2021716683","https://openalex.org/W2022178479","https://openalex.org/W2022891974","https://openalex.org/W2023013684","https://openalex.org/W2023525048","https://openalex.org/W2026422850","https://openalex.org/W2027576577","https://openalex.org/W2027723603","https://openalex.org/W2028601571","https://openalex.org/W2028670901","https://openalex.org/W2028747292","https://openalex.org/W2028783611","https://openalex.org/W2030125944","https://openalex.org/W2030669427","https://openalex.org/W2031220210","https://openalex.org/W2031369606","https://openalex.org/W2031822229","https://openalex.org/W2032799661","https://openalex.org/W2034252449","https://openalex.org/W2034665579","https://openalex.org/W2034876354","https://openalex.org/W2036122730","https://openalex.org/W2037685552","https://openalex.org/W2038896022","https://openalex.org/W2039305326","https://openalex.org/W2039841218","https://openalex.org/W2040645185","https://openalex.org/W2040699033","https://openalex.org/W2042321087","https://openalex.org/W2043785977","https://openalex.org/W2044692345","https://openalex.org/W2044859335","https://openalex.org/W2045696953","https://openalex.org/W2046355391","https://openalex.org/W2046451925","https://openalex.org/W2046538693","https://openalex.org/W2047278530","https://openalex.org/W2047723546","https://openalex.org/W2048634371","https://openalex.org/W2049403730","https://openalex.org/W2049883071","https://openalex.org/W2051419265","https://openalex.org/W2051813288","https://openalex.org/W2052094781","https://openalex.org/W2052195371","https://openalex.org/W2053291786","https://openalex.org/W2053460598","https://openalex.org/W2054655080","https://openalex.org/W2055579049","https://openalex.org/W2056270264","https://openalex.org/W2056313562","https://openalex.org/W2056393594","https://openalex.org/W2057349693","https://openalex.org/W2057993765","https://openalex.org/W2058135815","https://openalex.org/W2058942402","https://openalex.org/W2059223531","https://openalex.org/W2059603481","https://openalex.org/W2059786834","https://openalex.org/W2060457543","https://openalex.org/W2060690745","https://openalex.org/W2061267510","https://openalex.org/W2061425021","https://openalex.org/W2061851611","https://openalex.org/W2062029454","https://openalex.org/W2063346607","https://openalex.org/W2064483836","https://openalex.org/W2066594542","https://openalex.org/W2067630518","https://openalex.org/W2067797420","https://openalex.org/W2068359975","https://openalex.org/W2068447646","https://openalex.org/W2069364984","https://openalex.org/W2069471533","https://openalex.org/W2071747231","https://openalex.org/W2072077152","https://openalex.org/W2072973641","https://openalex.org/W2073276244","https://openalex.org/W2074142433","https://openalex.org/W2075251971","https://openalex.org/W2075460992","https://openalex.org/W2077046573","https://openalex.org/W2077346271","https://openalex.org/W2078119846","https://openalex.org/W2078664343","https://openalex.org/W2078734278","https://openalex.org/W2079022706","https://openalex.org/W2080131977","https://openalex.org/W2081434722","https://openalex.org/W2081655333","https://openalex.org/W2082027302","https://openalex.org/W2082221311","https://openalex.org/W2082946409","https://openalex.org/W2083456183","https://openalex.org/W2083561084","https://openalex.org/W2083561802","https://openalex.org/W2084559690","https://openalex.org/W2084774345","https://openalex.org/W2084924279","https://openalex.org/W2085033875","https://openalex.org/W2085061065","https://openalex.org/W2085116222","https://openalex.org/W2086128646","https://openalex.org/W2086411786","https://openalex.org/W2086634897","https://openalex.org/W2086885045","https://openalex.org/W2087234479","https://openalex.org/W2088259098","https://openalex.org/W2089102241","https://openalex.org/W2090248212","https://openalex.org/W2090629368","https://openalex.org/W2090806625","https://openalex.org/W2091198609","https://openalex.org/W2091266182","https://openalex.org/W2091424423","https://openalex.org/W2091491561","https://openalex.org/W2093179886","https://openalex.org/W2093221728","https://openalex.org/W2093470850","https://openalex.org/W2095416319","https://openalex.org/W2095481462","https://openalex.org/W2096050955","https://openalex.org/W2096705138","https://openalex.org/W2097842145","https://openalex.org/W2097851712","https://openalex.org/W2098289043","https://openalex.org/W2098296039","https://openalex.org/W2098941494","https://openalex.org/W2099015579","https://openalex.org/W2100237973","https://openalex.org/W2101744167","https://openalex.org/W2101765772","https://openalex.org/W2101955906","https://openalex.org/W2101966172","https://openalex.org/W2103240113","https://openalex.org/W2103331163","https://openalex.org/W2103448550","https://openalex.org/W2103811483","https://openalex.org/W2104763072","https://openalex.org/W2105057212","https://openalex.org/W2105466636","https://openalex.org/W2106362845","https://openalex.org/W2106442734","https://openalex.org/W2106689809","https://openalex.org/W2107208446","https://openalex.org/W2107342968","https://openalex.org/W2108020239","https://openalex.org/W2108208689","https://openalex.org/W2108648156","https://openalex.org/W2108914215","https://openalex.org/W2110071847","https://openalex.org/W2110460556","https://openalex.org/W2110804923","https://openalex.org/W2110823478","https://openalex.org/W2110872379","https://openalex.org/W2111167674","https://openalex.org/W2111419541","https://openalex.org/W2111724365","https://openalex.org/W2112959255","https://openalex.org/W2113053834","https://openalex.org/W2114849571","https://openalex.org/W2114870653","https://openalex.org/W2115150990","https://openalex.org/W2115286109","https://openalex.org/W2116696234","https://openalex.org/W2116698317","https://openalex.org/W2117238525","https://openalex.org/W2117915703","https://openalex.org/W2118274513","https://openalex.org/W2118839548","https://openalex.org/W2119780058","https://openalex.org/W2119781194","https://openalex.org/W2119861659","https://openalex.org/W2120526231","https://openalex.org/W2121061408","https://openalex.org/W2121400889","https://openalex.org/W2121806138","https://openalex.org/W2122121413","https://openalex.org/W2122404311","https://openalex.org/W2124735489","https://openalex.org/W2124977728","https://openalex.org/W2125340100","https://openalex.org/W2125465188","https://openalex.org/W2126147862","https://openalex.org/W2126592495","https://openalex.org/W2126733261","https://openalex.org/W2127249846","https://openalex.org/W2127535453","https://openalex.org/W2128014106","https://openalex.org/W2128116330","https://openalex.org/W2130021498","https://openalex.org/W2130341284","https://openalex.org/W2130912501","https://openalex.org/W2131187223","https://openalex.org/W2132940078","https://openalex.org/W2133122037","https://openalex.org/W2134759932","https://openalex.org/W2135249635","https://openalex.org/W2136716105","https://openalex.org/W2137012440","https://openalex.org/W2137088684","https://openalex.org/W2138505529","https://openalex.org/W2139009181","https://openalex.org/W2140664742","https://openalex.org/W2141362320","https://openalex.org/W2141594707","https://openalex.org/W2141688036","https://openalex.org/W2142321063","https://openalex.org/W2142400903","https://openalex.org/W2142501768","https://openalex.org/W2142688660","https://openalex.org/W2142691347","https://openalex.org/W2143784594","https://openalex.org/W2143842076","https://openalex.org/W2143920302","https://openalex.org/W2146007026","https://openalex.org/W2146496997","https://openalex.org/W2149778176","https://openalex.org/W2150519862","https://openalex.org/W2150766477","https://openalex.org/W2151364744","https://openalex.org/W2152223517","https://openalex.org/W2153326344","https://openalex.org/W2153901189","https://openalex.org/W2154192340","https://openalex.org/W2155408323","https://openalex.org/W2155418451","https://openalex.org/W2155617496","https://openalex.org/W2156302599","https://openalex.org/W2156311466","https://openalex.org/W2157886837","https://openalex.org/W2158417515","https://openalex.org/W2158469604","https://openalex.org/W2159307080","https://openalex.org/W2159844490","https://openalex.org/W2160269647","https://openalex.org/W2160317546","https://openalex.org/W2160533336","https://openalex.org/W2160838409","https://openalex.org/W2163126094","https://openalex.org/W2163706779","https://openalex.org/W2165187344","https://openalex.org/W2165591265","https://openalex.org/W2166301566","https://openalex.org/W2167105834","https://openalex.org/W2167154952","https://openalex.org/W2167244112","https://openalex.org/W2167437179","https://openalex.org/W2167746224","https://openalex.org/W2168208027","https://openalex.org/W2169242133","https://openalex.org/W2169509065","https://openalex.org/W2169756968","https://openalex.org/W2170862894","https://openalex.org/W2171280873","https://openalex.org/W2171327609","https://openalex.org/W2171539493","https://openalex.org/W2171582839","https://openalex.org/W2171648521","https://openalex.org/W2171893485","https://openalex.org/W2210900609","https://openalex.org/W2227339975","https://openalex.org/W2242726375","https://openalex.org/W2279626446","https://openalex.org/W2323178299","https://openalex.org/W2327963705","https://openalex.org/W2394638567","https://openalex.org/W2413320931","https://openalex.org/W2484972490","https://openalex.org/W2486082615","https://openalex.org/W2605543710","https://openalex.org/W2751862591","https://openalex.org/W3010525046","https://openalex.org/W3021966610","https://openalex.org/W3098223981","https://openalex.org/W3099222462","https://openalex.org/W3103877777","https://openalex.org/W3104859924","https://openalex.org/W3105606003","https://openalex.org/W3106262409","https://openalex.org/W3106434303","https://openalex.org/W3125980488","https://openalex.org/W3145242807","https://openalex.org/W4231937919"],"related_works":["https://openalex.org/W3216885170","https://openalex.org/W2141327274","https://openalex.org/W50425026","https://openalex.org/W2108135022","https://openalex.org/W2363283490","https://openalex.org/W2115735252","https://openalex.org/W2964223703","https://openalex.org/W80490337","https://openalex.org/W2257275784","https://openalex.org/W2065575849"],"abstract_inverted_index":{"A":[0],"promising":[1],"alternative":[2],"for":[3,157],"unraveling":[4],"the":[5,9,30,37,67,71,85,98,106,122,125,147,161,185,191,197],"principles":[6],"under":[7,49],"which":[8],"dynamic":[10,134],"interactions":[11,35],"among":[12,43],"genes":[13],"lead":[14],"to":[15,36,57,78,160],"cellular":[16],"phenotypes":[17],"relies":[18],"on":[19],"mathematical":[20,142],"and":[21,105,121,141,163,184],"computational":[22],"models":[23,80,135,172],"at":[24,66,84,152],"different":[25,181],"levels":[26,183],"of":[27,33,40,55,74,111,124,131,173],"abstraction,":[28],"from":[29,63,136],"molecular":[31],"level":[32,39,69],"protein-DNA":[34],"system":[38],"functional":[41],"relationships":[42],"genes.":[44],"This":[45,149],"review":[46],"article":[47,150],"presents,":[48],"a":[50,53,117],"bottom-up":[51],"perspective,":[52],"hierarchy":[54],"approaches":[56,91],"modeling":[58,90,192],"gene":[59,132,174],"regulatory":[60],"network":[61,133],"dynamics,":[62],"microscopic":[64],"descriptions":[65,83],"single-molecule":[68],"in":[70,190],"spatial":[72],"context":[73,120],"an":[75,154],"individual":[76],"cell":[77],"macroscopic":[79],"providing":[81,153],"phenomenological":[82],"population-average":[86],"level.":[87],"The":[88,129,176],"reviewed":[89],"include":[92],"Molecular":[93],"Dynamics,":[94,97],"Particle-Based":[95],"Brownian":[96],"Master":[99],"Equation":[100],"approach,":[101],"Ordinary":[102],"Differential":[103],"Equations,":[104],"Boolean":[107],"logic":[108],"abstraction.":[109],"Each":[110],"these":[112],"frameworks":[113,138],"is":[114],"motivated":[115],"by":[116,146],"particular":[118],"biological":[119],"nature":[123],"insight":[126],"being":[127],"pursued.":[128],"setting":[130],"such":[137],"involves":[139],"assumptions":[140],"artifacts":[143],"often":[144],"ignored":[145],"non-specialist.":[148],"aims":[151],"entry":[155],"point":[156],"biologists":[158],"new":[159],"field":[162],"computer":[164],"scientists":[165],"not":[166],"acquainted":[167],"with":[168],"some":[169],"recent":[170],"biophysically-inspired":[171],"regulation.":[175],"connections":[177],"promoting":[178],"intuition":[179],"between":[180],"abstraction":[182],"role":[186],"that":[187],"approximations":[188],"play":[189],"process":[193],"are":[194],"highlighted":[195],"throughout":[196],"paper.":[198]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":3},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
