{"id":"https://openalex.org/W1984097115","doi":"https://doi.org/10.1371/journal.pcbi.1000935","title":"Thermodynamics-Based Models of Transcriptional Regulation by Enhancers: The Roles of Synergistic Activation, Cooperative Binding and Short-Range Repression","display_name":"Thermodynamics-Based Models of Transcriptional Regulation by Enhancers: The Roles of Synergistic Activation, Cooperative Binding and Short-Range Repression","publication_year":2010,"publication_date":"2010-09-16","ids":{"openalex":"https://openalex.org/W1984097115","doi":"https://doi.org/10.1371/journal.pcbi.1000935","mag":"1984097115","pmid":"https://pubmed.ncbi.nlm.nih.gov/20862354"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1000935","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1000935","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1000935&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1000935&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100749954","display_name":"Xin He","orcid":"https://orcid.org/0000-0002-8602-5166"},"institutions":[{"id":"https://openalex.org/I180670191","display_name":"University of California, San Francisco","ror":"https://ror.org/043mz5j54","country_code":"US","type":"education","lineage":["https://openalex.org/I180670191"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xin He","raw_affiliation_strings":["Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, California, United States of America","Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, California, United States of America","institution_ids":["https://openalex.org/I180670191"]},{"raw_affiliation_string":"Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, United States of America","institution_ids":["https://openalex.org/I180670191"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061946975","display_name":"Md. Abul Hassan Samee","orcid":"https://orcid.org/0000-0002-7472-1156"},"institutions":[{"id":"https://openalex.org/I157725225","display_name":"University of Illinois Urbana-Champaign","ror":"https://ror.org/047426m28","country_code":"US","type":"education","lineage":["https://openalex.org/I157725225"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Md. Abul Hassan Samee","raw_affiliation_strings":["Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America","Dept. of Computer Science, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America","institution_ids":["https://openalex.org/I157725225"]},{"raw_affiliation_string":"Dept. of Computer Science, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America","institution_ids":["https://openalex.org/I157725225"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065050523","display_name":"Charles Blatti","orcid":"https://orcid.org/0000-0002-4683-6271"},"institutions":[{"id":"https://openalex.org/I157725225","display_name":"University of Illinois Urbana-Champaign","ror":"https://ror.org/047426m28","country_code":"US","type":"education","lineage":["https://openalex.org/I157725225"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Charles Blatti","raw_affiliation_strings":["Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America","Dept. of Computer Science, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America","institution_ids":["https://openalex.org/I157725225"]},{"raw_affiliation_string":"Dept. of Computer Science, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America","institution_ids":["https://openalex.org/I157725225"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5101657008","display_name":"Saurabh Sinha","orcid":"https://orcid.org/0000-0001-6033-7746"},"institutions":[{"id":"https://openalex.org/I157725225","display_name":"University of Illinois Urbana-Champaign","ror":"https://ror.org/047426m28","country_code":"US","type":"education","lineage":["https://openalex.org/I157725225"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Saurabh Sinha","raw_affiliation_strings":["Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America","Dept. of Computer Science, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America","institution_ids":["https://openalex.org/I157725225"]},{"raw_affiliation_string":"Dept. of Computer Science, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America","institution_ids":["https://openalex.org/I157725225"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5101657008"],"corresponding_institution_ids":["https://openalex.org/I157725225"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":6.5325,"has_fulltext":true,"cited_by_count":190,"citation_normalized_percentile":{"value":0.97474611,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":100},"biblio":{"volume":"6","issue":"9","first_page":"e1000935","last_page":"e1000935"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9983999729156494,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9983999729156494,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9972000122070312,"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/T10540","display_name":"Advanced Fluorescence Microscopy Techniques","score":0.9901999831199646,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"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/enhancer","display_name":"Enhancer","score":0.7103801369667053},{"id":"https://openalex.org/keywords/cooperativity","display_name":"Cooperativity","score":0.6526987552642822},{"id":"https://openalex.org/keywords/psychological-repression","display_name":"Psychological repression","score":0.5660578608512878},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5319115519523621},{"id":"https://openalex.org/keywords/dna-binding-site","display_name":"DNA binding site","score":0.5037104487419128},{"id":"https://openalex.org/keywords/transcription-factor","display_name":"Transcription factor","score":0.4850699007511139},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.46086156368255615},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.45675262808799744},{"id":"https://openalex.org/keywords/regulation-of-gene-expression","display_name":"Regulation of gene expression","score":0.45144057273864746},{"id":"https://openalex.org/keywords/repressor","display_name":"Repressor","score":0.44765955209732056},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.36664819717407227},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.33537912368774414},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.31852781772613525},{"id":"https://openalex.org/keywords/promoter","display_name":"Promoter","score":0.20649310946464539}],"concepts":[{"id":"https://openalex.org/C111936080","wikidata":"https://www.wikidata.org/wiki/Q913367","display_name":"Enhancer","level":4,"score":0.7103801369667053},{"id":"https://openalex.org/C166014724","wikidata":"https://www.wikidata.org/wiki/Q337217","display_name":"Cooperativity","level":2,"score":0.6526987552642822},{"id":"https://openalex.org/C186310378","wikidata":"https://www.wikidata.org/wiki/Q941796","display_name":"Psychological repression","level":4,"score":0.5660578608512878},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5319115519523621},{"id":"https://openalex.org/C3662595","wikidata":"https://www.wikidata.org/wiki/Q5205743","display_name":"DNA binding site","level":5,"score":0.5037104487419128},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.4850699007511139},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.46086156368255615},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.45675262808799744},{"id":"https://openalex.org/C165864922","wikidata":"https://www.wikidata.org/wiki/Q411391","display_name":"Regulation of gene expression","level":3,"score":0.45144057273864746},{"id":"https://openalex.org/C158448853","wikidata":"https://www.wikidata.org/wiki/Q425218","display_name":"Repressor","level":4,"score":0.44765955209732056},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.36664819717407227},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.33537912368774414},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.31852781772613525},{"id":"https://openalex.org/C101762097","wikidata":"https://www.wikidata.org/wiki/Q224093","display_name":"Promoter","level":4,"score":0.20649310946464539},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004331","descriptor_name":"Drosophila melanogaster","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004331","descriptor_name":"Drosophila melanogaster","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004331","descriptor_name":"Drosophila melanogaster","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004742","descriptor_name":"Enhancer Elements, Genetic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004742","descriptor_name":"Enhancer Elements, Genetic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004742","descriptor_name":"Enhancer Elements, Genetic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D005075","descriptor_name":"Biological Evolution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005075","descriptor_name":"Biological Evolution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005075","descriptor_name":"Biological Evolution","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":true},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1371/journal.pcbi.1000935","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1000935","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1000935&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},{"id":"pmid:20862354","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/20862354","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:doaj.org/article:356c7dacb5ed4458a1f4696f847ae04f","is_oa":true,"landing_page_url":"https://doaj.org/article/356c7dacb5ed4458a1f4696f847ae04f","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 6, Iss 9 (2010)","raw_type":"article"},{"id":"pmh:oai:figshare.com:article/141765","is_oa":true,"landing_page_url":"https://figshare.com/articles/Thermodynamics_Based_Models_of_Transcriptional_Regulation_by_Enhancers_The_Roles_of_Synergistic_Activation_Cooperative_Binding_and_Short_Range_Repression/141765","pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Dataset"},{"id":"pmh:oai:pubmedcentral.nih.gov:2940721","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2940721","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Comput Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1000935","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1000935","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1000935&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G5030985158","display_name":"CAREER:  Probabilistic Frameworks for Studying Gene Regulatory Sequences and their Evolution","funder_award_id":"0746303","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G6671297155","display_name":null,"funder_award_id":"CAREER","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1984097115.pdf","grobid_xml":"https://content.openalex.org/works/W1984097115.grobid-xml"},"referenced_works_count":65,"referenced_works":["https://openalex.org/W614012683","https://openalex.org/W1498410508","https://openalex.org/W1593308984","https://openalex.org/W1634746048","https://openalex.org/W1753000577","https://openalex.org/W1884509322","https://openalex.org/W1905113765","https://openalex.org/W1970486372","https://openalex.org/W1977620504","https://openalex.org/W1979259341","https://openalex.org/W1980253661","https://openalex.org/W1990342419","https://openalex.org/W1992031919","https://openalex.org/W1992927069","https://openalex.org/W1993129179","https://openalex.org/W1994190548","https://openalex.org/W1995156097","https://openalex.org/W2001167864","https://openalex.org/W2001212353","https://openalex.org/W2013449615","https://openalex.org/W2018345118","https://openalex.org/W2018913767","https://openalex.org/W2019297217","https://openalex.org/W2020749481","https://openalex.org/W2023635398","https://openalex.org/W2024280474","https://openalex.org/W2031830181","https://openalex.org/W2032548898","https://openalex.org/W2037602867","https://openalex.org/W2038282326","https://openalex.org/W2041966847","https://openalex.org/W2043789254","https://openalex.org/W2046355391","https://openalex.org/W2046374070","https://openalex.org/W2058552632","https://openalex.org/W2069605909","https://openalex.org/W2073727170","https://openalex.org/W2075861065","https://openalex.org/W2077941487","https://openalex.org/W2086634897","https://openalex.org/W2088286107","https://openalex.org/W2094507479","https://openalex.org/W2095809934","https://openalex.org/W2096118921","https://openalex.org/W2096720319","https://openalex.org/W2097311877","https://openalex.org/W2099351601","https://openalex.org/W2102304447","https://openalex.org/W2110988653","https://openalex.org/W2117858386","https://openalex.org/W2119022656","https://openalex.org/W2124954570","https://openalex.org/W2125840362","https://openalex.org/W2130174998","https://openalex.org/W2135816732","https://openalex.org/W2143855992","https://openalex.org/W2150687466","https://openalex.org/W2151240250","https://openalex.org/W2162979438","https://openalex.org/W2166269027","https://openalex.org/W2166277117","https://openalex.org/W2167684670","https://openalex.org/W2170628952","https://openalex.org/W3026157297","https://openalex.org/W4233751197"],"related_works":["https://openalex.org/W2121322585","https://openalex.org/W2888828946","https://openalex.org/W2022959303","https://openalex.org/W2017534687","https://openalex.org/W1893155809","https://openalex.org/W3208125806","https://openalex.org/W2082929826","https://openalex.org/W1837413175","https://openalex.org/W1967829049","https://openalex.org/W4302763046"],"abstract_inverted_index":{"Quantitative":[0],"models":[1,19],"of":[2,13,36,59,82,101,120,126,147,170,206,213,230,234],"cis-regulatory":[3],"activity":[4],"have":[5,22,42],"the":[6,17,29,37,80,92,118,124,152,168,180,188,214,219,227],"potential":[7],"to":[8,47,72,115,144,192],"improve":[9],"our":[10],"mechanistic":[11,95],"understanding":[12],"transcriptional":[14,141,182],"regulation.":[15],"However,":[16],"few":[18],"available":[20,127,222],"today":[21],"been":[23],"based":[24],"on":[25,87,133],"simplistic":[26],"assumptions":[27],"about":[28],"sequences":[30],"being":[31],"modeled,":[32],"or":[33],"heuristic":[34],"approximations":[35],"underlying":[38],"regulatory":[39,228],"mechanisms.":[40],"We":[41,163,184],"developed":[43],"a":[44,57,203,231],"thermodynamics-based":[45],"model":[46,73,93,132],"predict":[48],"gene":[49,88],"expression":[50,128],"driven":[51],"by":[52,159],"any":[53],"DNA":[54],"sequence,":[55],"as":[56,98],"function":[58,195],"transcription":[60,110],"factor":[61],"concentrations":[62],"and":[63,85,107,202],"their":[64],"DNA-binding":[65,161],"specificities.":[66],"It":[67],"uses":[68],"statistical":[69],"thermodynamics":[70],"theory":[71],"not":[74,176,197],"only":[75],"protein-DNA":[76],"interaction,":[77],"but":[78],"also":[79,185],"effect":[81,100],"DNA-bound":[83],"activators":[84,149],"repressors":[86,174],"expression.":[89],"In":[90],"addition,":[91],"incorporates":[94],"features":[96,122],"such":[97],"synergistic":[99],"multiple":[102,148],"activators,":[103],"short":[104],"range":[105],"repression,":[106,172],"cooperativity":[108],"in":[109,123,136],"factor-DNA":[111],"binding,":[112],"allowing":[113],"us":[114],"systematically":[116],"evaluate":[117],"significance":[119],"these":[121,207],"context":[125],"data.":[129],"Using":[130],"this":[131],"segmentation-related":[134],"enhancers":[135],"Drosophila,":[137],"we":[138],"find":[139,164,186],"that":[140,187],"synergy":[142],"due":[143],"simultaneous":[145],"action":[146],"helps":[150],"explain":[151],"data":[153],"beyond":[154],"what":[155],"can":[156],"be":[157,198],"explained":[158],"cooperative":[160],"alone.":[162],"clear":[165],"support":[166],"for":[167,224],"phenomenon":[169],"short-range":[171],"where":[173],"do":[175],"directly":[177],"interact":[178],"with":[179],"basal":[181],"machinery.":[183],"binding":[189],"sites":[190],"contributing":[191],"an":[193],"enhancer's":[194],"may":[196],"conserved":[199],"during":[200],"evolution,":[201],"noticeable":[204],"fraction":[205],"undergo":[208],"lineage-specific":[209],"changes.":[210],"Our":[211],"implementation":[212],"model,":[215],"called":[216],"GEMSTAT,":[217],"is":[218],"first":[220],"publicly":[221],"program":[223],"simultaneously":[225],"modeling":[226],"activities":[229],"given":[232],"set":[233],"sequences.":[235]},"counts_by_year":[{"year":2025,"cited_by_count":8},{"year":2024,"cited_by_count":9},{"year":2023,"cited_by_count":6},{"year":2022,"cited_by_count":9},{"year":2021,"cited_by_count":10},{"year":2020,"cited_by_count":9},{"year":2019,"cited_by_count":13},{"year":2018,"cited_by_count":10},{"year":2017,"cited_by_count":9},{"year":2016,"cited_by_count":14},{"year":2015,"cited_by_count":25},{"year":2014,"cited_by_count":18},{"year":2013,"cited_by_count":25},{"year":2012,"cited_by_count":15}],"updated_date":"2026-05-06T08:25:59.206177","created_date":"2025-10-10T00:00:00"}