{"id":"https://openalex.org/W2030816054","doi":"https://doi.org/10.1371/journal.pcbi.0030099","title":"Frequent Gain and Loss of Functional Transcription Factor Binding Sites","display_name":"Frequent Gain and Loss of Functional Transcription Factor Binding Sites","publication_year":2007,"publication_date":"2007-05-23","ids":{"openalex":"https://openalex.org/W2030816054","doi":"https://doi.org/10.1371/journal.pcbi.0030099","mag":"2030816054","pmid":"https://pubmed.ncbi.nlm.nih.gov/17530920"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.0030099","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.0030099","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.0030099&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.0030099&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5023045060","display_name":"Scott W Doniger","orcid":null},"institutions":[{"id":"https://openalex.org/I204465549","display_name":"Washington University in St. Louis","ror":"https://ror.org/01yc7t268","country_code":"US","type":"education","lineage":["https://openalex.org/I204465549"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Scott W Doniger","raw_affiliation_strings":["Computational Biology Program, Washington University School of Medicine, St. Louis, Missouri, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computational Biology Program, Washington University School of Medicine, St. Louis, Missouri, United States of America","institution_ids":["https://openalex.org/I204465549"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5014443770","display_name":"Justin C. Fay","orcid":"https://orcid.org/0000-0003-1893-877X"},"institutions":[{"id":"https://openalex.org/I204465549","display_name":"Washington University in St. Louis","ror":"https://ror.org/01yc7t268","country_code":"US","type":"education","lineage":["https://openalex.org/I204465549"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Justin C Fay","raw_affiliation_strings":["","Computational Biology Program, Washington University School of Medicine, St. Louis, Missouri, United States of America","Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"","institution_ids":[]},{"raw_affiliation_string":"Computational Biology Program, Washington University School of Medicine, St. Louis, Missouri, United States of America","institution_ids":["https://openalex.org/I204465549"]},{"raw_affiliation_string":"Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America","institution_ids":["https://openalex.org/I204465549"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5014443770"],"corresponding_institution_ids":["https://openalex.org/I204465549"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":6.4164,"has_fulltext":true,"cited_by_count":161,"citation_normalized_percentile":{"value":0.97597516,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"3","issue":"5","first_page":"e99","last_page":"e99"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10497","display_name":"Fungal and yeast genetics research","score":0.9997000098228455,"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/T10497","display_name":"Fungal and yeast genetics research","score":0.9997000098228455,"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":0.9990000128746033,"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":0.995199978351593,"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/dna-binding-site","display_name":"DNA binding site","score":0.7373487949371338},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.727505087852478},{"id":"https://openalex.org/keywords/binding-site","display_name":"Binding site","score":0.6859829425811768},{"id":"https://openalex.org/keywords/transcription-factor","display_name":"Transcription factor","score":0.6818734407424927},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.6115462183952332},{"id":"https://openalex.org/keywords/regulatory-sequence","display_name":"Regulatory sequence","score":0.6062057018280029},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.5922325253486633},{"id":"https://openalex.org/keywords/functional-divergence","display_name":"Functional divergence","score":0.5405626893043518},{"id":"https://openalex.org/keywords/regulation-of-gene-expression","display_name":"Regulation of gene expression","score":0.5199769139289856},{"id":"https://openalex.org/keywords/lineage","display_name":"Lineage (genetic)","score":0.458196222782135},{"id":"https://openalex.org/keywords/conserved-sequence","display_name":"Conserved sequence","score":0.4422281086444855},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.4023907482624054},{"id":"https://openalex.org/keywords/evolutionary-biology","display_name":"Evolutionary biology","score":0.3411408066749573},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3302891254425049},{"id":"https://openalex.org/keywords/promoter","display_name":"Promoter","score":0.2979443073272705},{"id":"https://openalex.org/keywords/gene-family","display_name":"Gene family","score":0.2642686367034912},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.15066257119178772}],"concepts":[{"id":"https://openalex.org/C3662595","wikidata":"https://www.wikidata.org/wiki/Q5205743","display_name":"DNA binding site","level":5,"score":0.7373487949371338},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.727505087852478},{"id":"https://openalex.org/C107824862","wikidata":"https://www.wikidata.org/wiki/Q616005","display_name":"Binding site","level":2,"score":0.6859829425811768},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.6818734407424927},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.6115462183952332},{"id":"https://openalex.org/C21592294","wikidata":"https://www.wikidata.org/wiki/Q3238407","display_name":"Regulatory sequence","level":4,"score":0.6062057018280029},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.5922325253486633},{"id":"https://openalex.org/C103077935","wikidata":"https://www.wikidata.org/wiki/Q5508811","display_name":"Functional divergence","level":5,"score":0.5405626893043518},{"id":"https://openalex.org/C165864922","wikidata":"https://www.wikidata.org/wiki/Q411391","display_name":"Regulation of gene expression","level":3,"score":0.5199769139289856},{"id":"https://openalex.org/C2776817793","wikidata":"https://www.wikidata.org/wiki/Q6553369","display_name":"Lineage (genetic)","level":3,"score":0.458196222782135},{"id":"https://openalex.org/C199216141","wikidata":"https://www.wikidata.org/wiki/Q4995178","display_name":"Conserved sequence","level":4,"score":0.4422281086444855},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.4023907482624054},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.3411408066749573},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3302891254425049},{"id":"https://openalex.org/C101762097","wikidata":"https://www.wikidata.org/wiki/Q224093","display_name":"Promoter","level":4,"score":0.2979443073272705},{"id":"https://openalex.org/C5911399","wikidata":"https://www.wikidata.org/wiki/Q2278983","display_name":"Gene family","level":4,"score":0.2642686367034912},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.15066257119178772}],"mesh":[{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005787","descriptor_name":"Gene Frequency","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005787","descriptor_name":"Gene Frequency","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005787","descriptor_name":"Gene Frequency","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012045","descriptor_name":"Regulatory Sequences, Nucleic Acid","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012045","descriptor_name":"Regulatory Sequences, Nucleic Acid","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012045","descriptor_name":"Regulatory Sequences, Nucleic Acid","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","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":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014644","descriptor_name":"Genetic Variation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014644","descriptor_name":"Genetic Variation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014644","descriptor_name":"Genetic Variation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D029701","descriptor_name":"Saccharomyces cerevisiae Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D029701","descriptor_name":"Saccharomyces cerevisiae Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D029701","descriptor_name":"Saccharomyces cerevisiae Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":7,"locations":[{"id":"doi:10.1371/journal.pcbi.0030099","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.0030099","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.0030099&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:17530920","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/17530920","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:digitalcommons.wustl.edu:open_access_pubs-1458","is_oa":true,"landing_page_url":"https://digitalcommons.wustl.edu/open_access_pubs/459","pdf_url":"https://digitalcommons.wustl.edu/open_access_pubs/459","source":{"id":"https://openalex.org/S4306400764","display_name":"Digital Commons@Becker (Washington University School of Medicine)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I204465549","host_organization_name":"Washington University in St. Louis","host_organization_lineage":["https://openalex.org/I204465549"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Open Access Publications","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.279.9834","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.279.9834","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/de/07/PLoS_Comput_Biol_2007_May_25_3(5)_e99.tar.gz","raw_type":"text"},{"id":"pmh:oai:doaj.org/article:a379c382f65140adabb6397a4e90e556","is_oa":true,"landing_page_url":"https://doaj.org/article/a379c382f65140adabb6397a4e90e556","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 3, Iss 5, p e99 (2007)","raw_type":"article"},{"id":"pmh:oai:figshare.com:article/152068","is_oa":true,"landing_page_url":"https://figshare.com/articles/dataset/Frequent_Gain_and_Loss_of_Functional_Transcription_Factor_Binding_Sites/152068","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:1876492","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/1876492","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.0030099","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.0030099","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.0030099&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":[{"score":0.6899999976158142,"id":"https://metadata.un.org/sdg/15","display_name":"Life in Land"}],"awards":[{"id":"https://openalex.org/G1615454986","display_name":"Graduate Research Fellowship","funder_award_id":"0202737","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G2239319422","display_name":null,"funder_award_id":"R01 GM080669","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2030816054.pdf","grobid_xml":"https://content.openalex.org/works/W2030816054.grobid-xml"},"referenced_works_count":66,"referenced_works":["https://openalex.org/W791550880","https://openalex.org/W1498410508","https://openalex.org/W1644724366","https://openalex.org/W1930635754","https://openalex.org/W1970921900","https://openalex.org/W1976183531","https://openalex.org/W1985237887","https://openalex.org/W1987229243","https://openalex.org/W1989293350","https://openalex.org/W1990987722","https://openalex.org/W1994190548","https://openalex.org/W2001706442","https://openalex.org/W2002635370","https://openalex.org/W2003967338","https://openalex.org/W2008395467","https://openalex.org/W2009596137","https://openalex.org/W2012354488","https://openalex.org/W2013449615","https://openalex.org/W2014279841","https://openalex.org/W2026398852","https://openalex.org/W2030978639","https://openalex.org/W2034817839","https://openalex.org/W2037652809","https://openalex.org/W2038605451","https://openalex.org/W2054624670","https://openalex.org/W2055753427","https://openalex.org/W2060181803","https://openalex.org/W2071924033","https://openalex.org/W2074703985","https://openalex.org/W2080498142","https://openalex.org/W2085454778","https://openalex.org/W2086514583","https://openalex.org/W2093749169","https://openalex.org/W2094248448","https://openalex.org/W2095925603","https://openalex.org/W2097311877","https://openalex.org/W2102424972","https://openalex.org/W2109314645","https://openalex.org/W2113391242","https://openalex.org/W2118308505","https://openalex.org/W2119169205","https://openalex.org/W2119632499","https://openalex.org/W2120248467","https://openalex.org/W2125126554","https://openalex.org/W2125985596","https://openalex.org/W2130317490","https://openalex.org/W2133027051","https://openalex.org/W2133147430","https://openalex.org/W2135951244","https://openalex.org/W2137502130","https://openalex.org/W2140538490","https://openalex.org/W2142437744","https://openalex.org/W2144102935","https://openalex.org/W2144857133","https://openalex.org/W2151907070","https://openalex.org/W2153530880","https://openalex.org/W2155237411","https://openalex.org/W2157749235","https://openalex.org/W2157848631","https://openalex.org/W2160659074","https://openalex.org/W2161387979","https://openalex.org/W2162984838","https://openalex.org/W2165378709","https://openalex.org/W2167120442","https://openalex.org/W2409000123","https://openalex.org/W2593075177"],"related_works":["https://openalex.org/W1970337814","https://openalex.org/W1619964209","https://openalex.org/W2133027051","https://openalex.org/W2072226307","https://openalex.org/W2972782405","https://openalex.org/W2162630564","https://openalex.org/W2163667623","https://openalex.org/W4367173723","https://openalex.org/W2130150170","https://openalex.org/W1502510273"],"abstract_inverted_index":{"Cis-regulatory":[0],"sequences":[1,11,38,196],"are":[2,181,197],"not":[3,182],"always":[4],"conserved":[5,183],"across":[6,184],"species.":[7,98,185],"Divergence":[8],"within":[9],"cis-regulatory":[10,29,37,195],"may":[12,205],"result":[13],"from":[14],"the":[15,24,28,45,64,109,138,201],"evolution":[16,51],"of":[17,20,27,33,47,66,81,114,126,166,174,191,203,210],"species-specific":[18,208],"patterns":[19,209],"gene":[21,48,119,152,211],"expression":[22,153],"or":[23],"flexible":[25],"nature":[26],"code.":[30],"The":[31,186],"identification":[32],"functional":[34],"divergence":[35],"in":[36,50,89,154,200],"is":[39,162],"therefore":[40],"important":[41],"for":[42],"both":[43],"understanding":[44],"role":[46],"regulation":[49],"and":[52,112,189],"annotating":[53],"regulatory":[54],"elements.":[55],"We":[56,75,121,157],"have":[57,86],"developed":[58],"an":[59],"evolutionary":[60],"model":[61],"to":[62,142,207],"detect":[63],"loss":[65,101,113,128,145,190],"constraint":[67],"on":[68],"individual":[69],"transcription":[70],"factor":[71],"binding":[72,84,116,134,143,167,179],"sites":[73,85,180],"(TFBSs).":[74],"find":[76],"that":[77,123,140,147,160,194],"a":[78,90,115,163],"significant":[79],"fraction":[80],"functionally":[82],"constrained":[83],"been":[87,104],"lost":[88],"lineage-specific":[91],"manner":[92],"among":[93],"three":[94],"closely":[95],"related":[96],"yeast":[97],"Binding":[99],"site":[100,117,135,144,168],"has":[102],"previously":[103],"explained":[105,132],"by":[106,133],"turnover,":[107,204],"where":[108],"concurrent":[110],"gain":[111,188],"maintains":[118],"regulation.":[120],"estimate":[122,159],"nearly":[124],"half":[125,173],"all":[127],"events":[129],"cannot":[130],"be":[131],"turnover.":[136],"Recreating":[137],"mutations":[139],"led":[141],"confirms":[146],"these":[148],"sequence":[149],"changes":[150],"affect":[151],"some":[155],"cases.":[156],"also":[158],"there":[161],"high":[164],"rate":[165],"gain,":[169],"as":[170],"more":[171],"than":[172],"experimentally":[175],"identified":[176],"S.":[177],"cerevisiae":[178],"frequent":[187],"TFBSs":[192],"implies":[193],"labile":[198],"and,":[199],"absence":[202],"contribute":[206],"expression.":[212]},"counts_by_year":[{"year":2025,"cited_by_count":6},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":6},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":5},{"year":2016,"cited_by_count":12},{"year":2015,"cited_by_count":8},{"year":2014,"cited_by_count":15},{"year":2013,"cited_by_count":9},{"year":2012,"cited_by_count":13}],"updated_date":"2026-07-30T17:31:21.811387","created_date":"2025-10-10T00:00:00"}