{"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":true,"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","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"]},{"raw_affiliation_string":"Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America","institution_ids":["https://openalex.org/I204465549"]},{"raw_affiliation_string":"Computational Biology Program, 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":2,"corresponding_author_ids":["https://openalex.org/A5014443770","https://openalex.org/A5023045060"],"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":6.8625,"has_fulltext":true,"cited_by_count":160,"citation_normalized_percentile":{"value":0.97763919,"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":[{"display_name":"Life in Land","score":0.6899999976158142,"id":"https://metadata.un.org/sdg/15"}],"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"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"}],"has_content":{"grobid_xml":true,"pdf":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":"2026-05-06T08:25:59.206177","created_date":"2025-10-10T00:00:00"}