{"id":"https://openalex.org/W2097311877","doi":"https://doi.org/10.1371/journal.pcbi.0020130","title":"Large-Scale Turnover of Functional Transcription Factor Binding Sites in Drosophila","display_name":"Large-Scale Turnover of Functional Transcription Factor Binding Sites in Drosophila","publication_year":2006,"publication_date":"2006-10-09","ids":{"openalex":"https://openalex.org/W2097311877","doi":"https://doi.org/10.1371/journal.pcbi.0020130","mag":"2097311877","pmid":"https://pubmed.ncbi.nlm.nih.gov/17040121"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.0020130","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.0020130","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.0020130&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.0020130&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5086545231","display_name":"Alan M Moses","orcid":"https://orcid.org/0000-0003-3118-3121"},"institutions":[{"id":"https://openalex.org/I95457486","display_name":"University of California, Berkeley","ror":"https://ror.org/01an7q238","country_code":"US","type":"education","lineage":["https://openalex.org/I95457486"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Alan M Moses","raw_affiliation_strings":["Graduate Group in Biophysics, University of California Berkeley, Berkeley, California, United States of America"],"affiliations":[{"raw_affiliation_string":"Graduate Group in Biophysics, University of California Berkeley, Berkeley, California, United States of America","institution_ids":["https://openalex.org/I95457486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103260743","display_name":"Daniel A Pollard","orcid":"https://orcid.org/0000-0002-3275-7185"},"institutions":[{"id":"https://openalex.org/I95457486","display_name":"University of California, Berkeley","ror":"https://ror.org/01an7q238","country_code":"US","type":"education","lineage":["https://openalex.org/I95457486"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Daniel A Pollard","raw_affiliation_strings":["Graduate Group in Biophysics, University of California Berkeley, Berkeley, California, United States of America"],"affiliations":[{"raw_affiliation_string":"Graduate Group in Biophysics, University of California Berkeley, Berkeley, California, United States of America","institution_ids":["https://openalex.org/I95457486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5050013277","display_name":"David A. Nix","orcid":"https://orcid.org/0009-0002-3383-8582"},"institutions":[{"id":"https://openalex.org/I148283060","display_name":"Lawrence Berkeley National Laboratory","ror":"https://ror.org/02jbv0t02","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I148283060","https://openalex.org/I39565521"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"David A Nix","raw_affiliation_strings":["Department of Genome Sciences, Genomics Division, Ernest Orlando Lawrence Berkeley National Lab, Berkeley, California, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Genome Sciences, Genomics Division, Ernest Orlando Lawrence Berkeley National Lab, Berkeley, California, United States of America","institution_ids":["https://openalex.org/I148283060"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047544648","display_name":"Venky N. Iyer","orcid":null},"institutions":[{"id":"https://openalex.org/I95457486","display_name":"University of California, Berkeley","ror":"https://ror.org/01an7q238","country_code":"US","type":"education","lineage":["https://openalex.org/I95457486"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Venky N Iyer","raw_affiliation_strings":["Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, California, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, California, United States of America","institution_ids":["https://openalex.org/I95457486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100673960","display_name":"Xiaoyong Li","orcid":"https://orcid.org/0009-0008-3199-6441"},"institutions":[{"id":"https://openalex.org/I148283060","display_name":"Lawrence Berkeley National Laboratory","ror":"https://ror.org/02jbv0t02","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I148283060","https://openalex.org/I39565521"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xiao-Yong Li","raw_affiliation_strings":["Department of Genome Sciences, Genomics Division, Ernest Orlando Lawrence Berkeley National Lab, Berkeley, California, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Genome Sciences, Genomics Division, Ernest Orlando Lawrence Berkeley National Lab, Berkeley, California, United States of America","institution_ids":["https://openalex.org/I148283060"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5106079538","display_name":"Mark D. Biggin","orcid":"https://orcid.org/0000-0002-7661-8013"},"institutions":[{"id":"https://openalex.org/I148283060","display_name":"Lawrence Berkeley National Laboratory","ror":"https://ror.org/02jbv0t02","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I148283060","https://openalex.org/I39565521"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mark D Biggin","raw_affiliation_strings":["Department of Genome Sciences, Genomics Division, Ernest Orlando Lawrence Berkeley National Lab, Berkeley, California, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Genome Sciences, Genomics Division, Ernest Orlando Lawrence Berkeley National Lab, Berkeley, California, United States of America","institution_ids":["https://openalex.org/I148283060"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5068063822","display_name":"Michael B. Eisen","orcid":"https://orcid.org/0000-0002-7528-738X"},"institutions":[{"id":"https://openalex.org/I148283060","display_name":"Lawrence Berkeley National Laboratory","ror":"https://ror.org/02jbv0t02","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I148283060","https://openalex.org/I39565521"]},{"id":"https://openalex.org/I4210109258","display_name":"Innovative Genomics Institute","ror":"https://ror.org/01r4tcq81","country_code":"US","type":"education","lineage":["https://openalex.org/I180670191","https://openalex.org/I4210109258","https://openalex.org/I95457486"]},{"id":"https://openalex.org/I95457486","display_name":"University of California, Berkeley","ror":"https://ror.org/01an7q238","country_code":"US","type":"education","lineage":["https://openalex.org/I95457486"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Michael B Eisen","raw_affiliation_strings":["Center for Integrative Genomics, University of California Berkeley, Berkeley, California, United States of America","Department of Genome Sciences, Genomics Division, Ernest Orlando Lawrence Berkeley National Lab, Berkeley, California, United States of America","Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, California, United States of America","Graduate Group in Biophysics, University of California Berkeley, Berkeley, California, United States of America"],"affiliations":[{"raw_affiliation_string":"Center for Integrative Genomics, University of California Berkeley, Berkeley, California, United States of America","institution_ids":["https://openalex.org/I4210109258","https://openalex.org/I95457486"]},{"raw_affiliation_string":"Department of Genome Sciences, Genomics Division, Ernest Orlando Lawrence Berkeley National Lab, Berkeley, California, United States of America","institution_ids":["https://openalex.org/I148283060"]},{"raw_affiliation_string":"Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, California, United States of America","institution_ids":["https://openalex.org/I95457486"]},{"raw_affiliation_string":"Graduate Group in Biophysics, University of California Berkeley, Berkeley, California, United States of America","institution_ids":["https://openalex.org/I95457486"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5068063822"],"corresponding_institution_ids":["https://openalex.org/I148283060","https://openalex.org/I4210109258","https://openalex.org/I95457486"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":14.0306,"has_fulltext":true,"cited_by_count":258,"citation_normalized_percentile":{"value":0.99476985,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":100},"biblio":{"volume":"2","issue":"10","first_page":"e130","last_page":"e130"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9995999932289124,"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":0.9995999932289124,"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":0.9987000226974487,"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/T10434","display_name":"Chromosomal and Genetic Variations","score":0.9973999857902527,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/drosophila-melanogaster","display_name":"Drosophila melanogaster","score":0.8707298040390015},{"id":"https://openalex.org/keywords/melanogaster","display_name":"Melanogaster","score":0.7412081956863403},{"id":"https://openalex.org/keywords/dna-binding-site","display_name":"DNA binding site","score":0.734713077545166},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.6997970342636108},{"id":"https://openalex.org/keywords/transcription-factor","display_name":"Transcription factor","score":0.6468678712844849},{"id":"https://openalex.org/keywords/lineage","display_name":"Lineage (genetic)","score":0.6266593337059021},{"id":"https://openalex.org/keywords/binding-site","display_name":"Binding site","score":0.6151553392410278},{"id":"https://openalex.org/keywords/evolutionary-biology","display_name":"Evolutionary biology","score":0.5851256847381592},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.5544025897979736},{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.5121243000030518},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.47914618253707886},{"id":"https://openalex.org/keywords/evolutionary-dynamics","display_name":"Evolutionary dynamics","score":0.43072929978370667},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3608675003051758},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.33720290660858154},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.15611138939857483},{"id":"https://openalex.org/keywords/population","display_name":"Population","score":0.10411995649337769},{"id":"https://openalex.org/keywords/promoter","display_name":"Promoter","score":0.07975438237190247}],"concepts":[{"id":"https://openalex.org/C2780104201","wikidata":"https://www.wikidata.org/wiki/Q130888","display_name":"Drosophila melanogaster","level":3,"score":0.8707298040390015},{"id":"https://openalex.org/C2776998849","wikidata":"https://www.wikidata.org/wiki/Q3766082","display_name":"Melanogaster","level":4,"score":0.7412081956863403},{"id":"https://openalex.org/C3662595","wikidata":"https://www.wikidata.org/wiki/Q5205743","display_name":"DNA binding site","level":5,"score":0.734713077545166},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6997970342636108},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.6468678712844849},{"id":"https://openalex.org/C2776817793","wikidata":"https://www.wikidata.org/wiki/Q6553369","display_name":"Lineage (genetic)","level":3,"score":0.6266593337059021},{"id":"https://openalex.org/C107824862","wikidata":"https://www.wikidata.org/wiki/Q616005","display_name":"Binding site","level":2,"score":0.6151553392410278},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.5851256847381592},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.5544025897979736},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.5121243000030518},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.47914618253707886},{"id":"https://openalex.org/C171578705","wikidata":"https://www.wikidata.org/wiki/Q5418700","display_name":"Evolutionary dynamics","level":3,"score":0.43072929978370667},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3608675003051758},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.33720290660858154},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.15611138939857483},{"id":"https://openalex.org/C2908647359","wikidata":"https://www.wikidata.org/wiki/Q2625603","display_name":"Population","level":2,"score":0.10411995649337769},{"id":"https://openalex.org/C101762097","wikidata":"https://www.wikidata.org/wiki/Q224093","display_name":"Promoter","level":4,"score":0.07975438237190247},{"id":"https://openalex.org/C144024400","wikidata":"https://www.wikidata.org/wiki/Q21201","display_name":"Sociology","level":0,"score":0.0},{"id":"https://openalex.org/C149923435","wikidata":"https://www.wikidata.org/wiki/Q37732","display_name":"Demography","level":1,"score":0.0}],"mesh":[{"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":"D000818","descriptor_name":"Animals","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":"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":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004268","descriptor_name":"DNA-Binding Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004268","descriptor_name":"DNA-Binding Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004268","descriptor_name":"DNA-Binding Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004268","descriptor_name":"DNA-Binding Proteins","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":"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":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004331","descriptor_name":"Drosophila melanogaster","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004331","descriptor_name":"Drosophila melanogaster","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004331","descriptor_name":"Drosophila melanogaster","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","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":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","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":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":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011401","descriptor_name":"Promoter Regions, Genetic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011401","descriptor_name":"Promoter Regions, Genetic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011401","descriptor_name":"Promoter Regions, Genetic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011401","descriptor_name":"Promoter Regions, Genetic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012641","descriptor_name":"Selection, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012641","descriptor_name":"Selection, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012641","descriptor_name":"Selection, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012641","descriptor_name":"Selection, Genetic","qualifier_ui":null,"qualifier_name":null,"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":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017124","descriptor_name":"Conserved Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017124","descriptor_name":"Conserved Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017124","descriptor_name":"Conserved Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017124","descriptor_name":"Conserved Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020218","descriptor_name":"Response Elements","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020218","descriptor_name":"Response Elements","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020218","descriptor_name":"Response Elements","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020218","descriptor_name":"Response Elements","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D021901","descriptor_name":"DNA, Intergenic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D021901","descriptor_name":"DNA, Intergenic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D021901","descriptor_name":"DNA, Intergenic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D021901","descriptor_name":"DNA, Intergenic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D029721","descriptor_name":"Drosophila Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D029721","descriptor_name":"Drosophila Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D029721","descriptor_name":"Drosophila Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D029721","descriptor_name":"Drosophila Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":13,"locations":[{"id":"doi:10.1371/journal.pcbi.0020130","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.0020130","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.0020130&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:17040121","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/17040121","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:info:ark/67531/metadc885228","is_oa":false,"landing_page_url":"https://digital.library.unt.edu/ark:/67531/metadc885228/","pdf_url":null,"source":{"id":"https://openalex.org/S4306400792","display_name":"University of North Texas Digital Library (University of North Texas)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I123534392","host_organization_name":"University of North Texas","host_organization_lineage":["https://openalex.org/I123534392"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal Name: PLoS Computational Biology; Journal Volume: 2; Journal Issue: 10; Related Information: Journal Publication Date: 2006","raw_type":"Article"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.324.4477","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.324.4477","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://labs.csb.utoronto.ca/moses/Moses_Eisen_PLoS_Comp_Biol_2006.pdf","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.333.250","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.333.250","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://rana.lbl.gov/CisEvolver/pdfs/moses_ploscompbio_2006.pdf","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.74.7659","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.74.7659","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://rana.lbl.gov/papers/Moses_PLOSCB_2006.pdf","raw_type":"text"},{"id":"pmh:oai:doaj.org/article:e507c3247223428d92c4d27065ada7a7","is_oa":true,"landing_page_url":"https://doaj.org/article/e507c3247223428d92c4d27065ada7a7","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"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 2, Iss 10, p e130 (2006)","raw_type":"article"},{"id":"pmh:oai:escholarship.org/ark:/13030/qt5b956733","is_oa":false,"landing_page_url":"https://escholarship.org/uc/item/5b956733","pdf_url":null,"source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"article"},{"id":"pmh:oai:europepmc.org:2622138","is_oa":true,"landing_page_url":"http://europepmc.org/articles/PMC1599766","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:figshare.com:article/152765","is_oa":true,"landing_page_url":"https://figshare.com/articles/Large_Scale_Turnover_of_Functional_Transcription_Factor_Binding_Sites_in_Drosophila_/152765","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:osti.gov:913276","is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/913276","pdf_url":null,"source":{"id":"https://openalex.org/S4306402487","display_name":"OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I139351228","host_organization_name":"Office of Scientific and Technical Information","host_organization_lineage":["https://openalex.org/I139351228"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:1599766","is_oa":true,"landing_page_url":"http://doi.org/10.1371/journal.pcbi.0020130","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Comput Biol","raw_type":"Text"},{"id":"pmh:qt5b956733","is_oa":false,"landing_page_url":"http://www.escholarship.org/uc/item/5b956733","pdf_url":null,"source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Moses, Alan M.; Pollard, Daniel A.; Nix, David A.; Iyer, Venky N.; Li, Xiao-Yong; Biggin, Mark D.; \u00c2\u00a0et al.(2006). Large-scale turnover of functional transcription factor binding sites in Drosophila. Lawrence Berkeley National Laboratory. Lawrence Berkeley National Laboratory: Lawrence Berkeley National Laboratory. Retrieved from: http://www.escholarship.org/uc/item/5b956733","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.0020130","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.0020130","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.0020130&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":[],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2097311877.pdf","grobid_xml":"https://content.openalex.org/works/W2097311877.grobid-xml"},"referenced_works_count":67,"referenced_works":["https://openalex.org/W118114067","https://openalex.org/W791550880","https://openalex.org/W1811470210","https://openalex.org/W1863643864","https://openalex.org/W1933795817","https://openalex.org/W1967184294","https://openalex.org/W1979858621","https://openalex.org/W1985237887","https://openalex.org/W1987229243","https://openalex.org/W1994190548","https://openalex.org/W2001706442","https://openalex.org/W2006378142","https://openalex.org/W2008900336","https://openalex.org/W2009570821","https://openalex.org/W2009596137","https://openalex.org/W2014832270","https://openalex.org/W2017051353","https://openalex.org/W2017641297","https://openalex.org/W2025665146","https://openalex.org/W2026398852","https://openalex.org/W2026882865","https://openalex.org/W2033785622","https://openalex.org/W2035564383","https://openalex.org/W2037142940","https://openalex.org/W2041877620","https://openalex.org/W2046233233","https://openalex.org/W2050332532","https://openalex.org/W2055208125","https://openalex.org/W2055533988","https://openalex.org/W2057000344","https://openalex.org/W2059288327","https://openalex.org/W2062150244","https://openalex.org/W2062402656","https://openalex.org/W2066908868","https://openalex.org/W2085380563","https://openalex.org/W2085912910","https://openalex.org/W2086453622","https://openalex.org/W2086597509","https://openalex.org/W2092006839","https://openalex.org/W2095178364","https://openalex.org/W2097343392","https://openalex.org/W2102159699","https://openalex.org/W2102424972","https://openalex.org/W2106931934","https://openalex.org/W2109314645","https://openalex.org/W2111811789","https://openalex.org/W2115435518","https://openalex.org/W2118487996","https://openalex.org/W2118628540","https://openalex.org/W2119632499","https://openalex.org/W2120248467","https://openalex.org/W2121331980","https://openalex.org/W2125126554","https://openalex.org/W2128937741","https://openalex.org/W2137075650","https://openalex.org/W2137428312","https://openalex.org/W2140538490","https://openalex.org/W2144857133","https://openalex.org/W2149769193","https://openalex.org/W2155237411","https://openalex.org/W2155940790","https://openalex.org/W2158714788","https://openalex.org/W2160348650","https://openalex.org/W2160659074","https://openalex.org/W2168786813","https://openalex.org/W2170628952","https://openalex.org/W4248318091"],"related_works":["https://openalex.org/W3217674162","https://openalex.org/W1972794703","https://openalex.org/W2086842568","https://openalex.org/W2075087776","https://openalex.org/W2013474102","https://openalex.org/W2429278941","https://openalex.org/W4230768823","https://openalex.org/W2014093629","https://openalex.org/W2503941435","https://openalex.org/W1866195437"],"abstract_inverted_index":{"The":[0],"gain":[1,53,158],"and":[2,23,50,54,93,104,152,169,183],"loss":[3,55,151,184],"of":[4,17,70,73,97,117,136,149,156,185],"functional":[5,89,118],"transcription":[6,77],"factor":[7,78],"binding":[8,48,71,85,91,120],"sites":[9,72,121],"has":[10],"been":[11],"proposed":[12],"as":[13],"a":[14,58,146],"major":[15],"source":[16],"evolutionary":[18,30,44,68],"change":[19],"in":[20,82,122],"cis-regulatory":[21],"DNA":[22],"gene":[24],"expression.":[25],"We":[26,61,111,140],"have":[27,145],"developed":[28],"an":[29,153],"model":[31,64],"to":[32,41,51,65,87,107,160,176],"study":[33,66,108],"binding-site":[34,150,157,167],"turnover":[35],"that":[36,113,142,166],"uses":[37],"multiple":[38],"sequence":[39],"alignments":[40],"assess":[42],"the":[43,67,74,94,128,137],"constraint":[45],"on":[46],"individual":[47],"sites,":[49,92],"map":[52],"events":[56],"along":[57,127,134],"phylogenetic":[59],"tree.":[60],"apply":[62],"this":[63],"dynamics":[69],"Drosophila":[75],"melanogaster":[76,124,130],"Zeste,":[79],"using":[80],"genome-wide":[81],"vivo":[83],"(ChIP-chip)":[84],"data":[86],"identify":[88],"Zeste":[90,119],"genome":[95],"sequences":[96],"D.":[98,100,102,105,123,129,177],"melanogaster,":[99,178],"simulans,":[101],"erecta,":[103],"yakuba":[106],"their":[109],"evolution.":[110],"estimate":[112],"more":[114],"than":[115],"5%":[116],"were":[125],"gained":[126],"lineage":[131],"or":[132],"lost":[133],"one":[135],"other":[138],"lineages.":[139],"find":[141],"Zeste-bound":[143],"regions":[144],"reduced":[147],"rate":[148,155],"increased":[154],"relative":[159],"flanking":[161],"sequences.":[162],"Finally,":[163],"we":[164],"show":[165],"gains":[168],"losses":[170],"are":[171],"asymmetrically":[172],"distributed":[173],"with":[174,180],"respect":[175],"consistent":[179],"lineage-specific":[181],"acquisition":[182],"Zeste-responsive":[186],"regulatory":[187],"elements.":[188]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":6},{"year":2022,"cited_by_count":5},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":5},{"year":2018,"cited_by_count":12},{"year":2017,"cited_by_count":5},{"year":2016,"cited_by_count":5},{"year":2015,"cited_by_count":16},{"year":2014,"cited_by_count":15},{"year":2013,"cited_by_count":12},{"year":2012,"cited_by_count":15}],"updated_date":"2026-04-05T17:49:38.594831","created_date":"2025-10-10T00:00:00"}