{"id":"https://openalex.org/W2998424375","doi":"https://doi.org/10.1093/bioinformatics/btz975","title":"Application of topic models to a compendium of ChIP-Seq datasets uncovers recurrent transcriptional regulatory modules","display_name":"Application of topic models to a compendium of ChIP-Seq datasets uncovers recurrent transcriptional regulatory modules","publication_year":2019,"publication_date":"2019-12-30","ids":{"openalex":"https://openalex.org/W2998424375","doi":"https://doi.org/10.1093/bioinformatics/btz975","mag":"2998424375","pmid":"https://pubmed.ncbi.nlm.nih.gov/31899481"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btz975","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz975","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5021506562","display_name":"Guodong Yang","orcid":"https://orcid.org/0000-0002-6307-2963"},"institutions":[{"id":"https://openalex.org/I150468666","display_name":"Emory University","ror":"https://ror.org/03czfpz43","country_code":"US","type":"education","lineage":["https://openalex.org/I150468666"]},{"id":"https://openalex.org/I4210121771","display_name":"First Affiliated Hospital of Xi'an Jiaotong University","ror":"https://ror.org/02tbvhh96","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210121771"]}],"countries":["CN","US"],"is_corresponding":false,"raw_author_name":"Guodong Yang","raw_affiliation_strings":["Department of Biostatistics and Bioinformatics, Rollins School of Public Health , Emory University, Atlanta, GA 30322, USA","Department of Cardiovascular Medicine, First Affiliated Hospital of Xi\u2019an Jiaotong University , Xi'an, Shaanxi, 710061, P. R. China"],"affiliations":[{"raw_affiliation_string":"Department of Biostatistics and Bioinformatics, Rollins School of Public Health , Emory University, Atlanta, GA 30322, USA","institution_ids":["https://openalex.org/I150468666"]},{"raw_affiliation_string":"Department of Cardiovascular Medicine, First Affiliated Hospital of Xi\u2019an Jiaotong University , Xi'an, Shaanxi, 710061, P. R. China","institution_ids":["https://openalex.org/I4210121771"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084147857","display_name":"Aiqun Ma","orcid":null},"institutions":[{"id":"https://openalex.org/I4210121771","display_name":"First Affiliated Hospital of Xi'an Jiaotong University","ror":"https://ror.org/02tbvhh96","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210121771"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Aiqun Ma","raw_affiliation_strings":["Department of Cardiovascular Medicine, First Affiliated Hospital of Xi\u2019an Jiaotong University , Xi'an, Shaanxi, 710061, P. R. China"],"affiliations":[{"raw_affiliation_string":"Department of Cardiovascular Medicine, First Affiliated Hospital of Xi\u2019an Jiaotong University , Xi'an, Shaanxi, 710061, P. R. China","institution_ids":["https://openalex.org/I4210121771"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042399779","display_name":"Zhaohui Qin","orcid":"https://orcid.org/0000-0002-1583-146X"},"institutions":[{"id":"https://openalex.org/I150468666","display_name":"Emory University","ror":"https://ror.org/03czfpz43","country_code":"US","type":"education","lineage":["https://openalex.org/I150468666"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Zhaohui S Qin","raw_affiliation_strings":["Department of Biostatistics and Bioinformatics, Rollins School of Public Health , Emory University, Atlanta, GA 30322, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biostatistics and Bioinformatics, Rollins School of Public Health , Emory University, Atlanta, GA 30322, USA","institution_ids":["https://openalex.org/I150468666"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100379195","display_name":"Li Chen","orcid":"https://orcid.org/0000-0001-9372-5606"},"institutions":[{"id":"https://openalex.org/I4394709130","display_name":"Indiana University School of Medicine","ror":"https://ror.org/02ets8c94","country_code":null,"type":"education","lineage":["https://openalex.org/I4394709130","https://openalex.org/I592451"]},{"id":"https://openalex.org/I55769427","display_name":"Indiana University \u2013 Purdue University Indianapolis","ror":"https://ror.org/05gxnyn08","country_code":"US","type":"education","lineage":["https://openalex.org/I55769427","https://openalex.org/I592451"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Li Chen","raw_affiliation_strings":["Center for Computational Biology and Bioinformatics , Indiana University School of Medicine, Indianapolis, IN 46202, USA","Department of Medicine, Indiana University School of Medicine , Indianapolis, IN 46202, USA"],"affiliations":[{"raw_affiliation_string":"Center for Computational Biology and Bioinformatics , Indiana University School of Medicine, Indianapolis, IN 46202, USA","institution_ids":["https://openalex.org/I55769427","https://openalex.org/I4394709130"]},{"raw_affiliation_string":"Department of Medicine, Indiana University School of Medicine , Indianapolis, IN 46202, USA","institution_ids":["https://openalex.org/I55769427","https://openalex.org/I4394709130"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5042399779","https://openalex.org/A5100379195"],"corresponding_institution_ids":["https://openalex.org/I150468666","https://openalex.org/I4394709130","https://openalex.org/I55769427"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.257,"has_fulltext":false,"cited_by_count":4,"citation_normalized_percentile":{"value":0.5766209,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":97},"biblio":{"volume":"36","issue":"8","first_page":"2352","last_page":"2358"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9890999794006348,"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/T10604","display_name":"RNA Research and Splicing","score":0.9857000112533569,"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/decipher","display_name":"DECIPHER","score":0.8643282651901245},{"id":"https://openalex.org/keywords/compendium","display_name":"Compendium","score":0.8598381280899048},{"id":"https://openalex.org/keywords/chromatin-immunoprecipitation","display_name":"Chromatin immunoprecipitation","score":0.7359553575515747},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6263937950134277},{"id":"https://openalex.org/keywords/transcription-factor","display_name":"Transcription factor","score":0.5686984062194824},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5573279857635498},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.42116862535476685},{"id":"https://openalex.org/keywords/chromatin","display_name":"Chromatin","score":0.41789817810058594},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.41266536712646484},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.30842334032058716},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.22811484336853027},{"id":"https://openalex.org/keywords/promoter","display_name":"Promoter","score":0.15043985843658447},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.14368706941604614},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.1416930854320526},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.0936174988746643}],"concepts":[{"id":"https://openalex.org/C164614171","wikidata":"https://www.wikidata.org/wiki/Q5204775","display_name":"DECIPHER","level":2,"score":0.8643282651901245},{"id":"https://openalex.org/C2778473407","wikidata":"https://www.wikidata.org/wiki/Q1459574","display_name":"Compendium","level":2,"score":0.8598381280899048},{"id":"https://openalex.org/C134320426","wikidata":"https://www.wikidata.org/wiki/Q901026","display_name":"Chromatin immunoprecipitation","level":5,"score":0.7359553575515747},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6263937950134277},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.5686984062194824},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5573279857635498},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.42116862535476685},{"id":"https://openalex.org/C83640560","wikidata":"https://www.wikidata.org/wiki/Q180951","display_name":"Chromatin","level":3,"score":0.41789817810058594},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.41266536712646484},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.30842334032058716},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.22811484336853027},{"id":"https://openalex.org/C101762097","wikidata":"https://www.wikidata.org/wiki/Q224093","display_name":"Promoter","level":4,"score":0.15043985843658447},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.14368706941604614},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1416930854320526},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0936174988746643},{"id":"https://openalex.org/C95457728","wikidata":"https://www.wikidata.org/wiki/Q309","display_name":"History","level":0,"score":0.0},{"id":"https://openalex.org/C166957645","wikidata":"https://www.wikidata.org/wiki/Q23498","display_name":"Archaeology","level":1,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000081204","descriptor_name":"Chromatin Immunoprecipitation Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000081204","descriptor_name":"Chromatin Immunoprecipitation Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000081204","descriptor_name":"Chromatin Immunoprecipitation Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D047369","descriptor_name":"Chromatin Immunoprecipitation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D047369","descriptor_name":"Chromatin Immunoprecipitation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D047369","descriptor_name":"Chromatin Immunoprecipitation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btz975","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz975","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:31899481","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31899481","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":"Bioinformatics (Oxford, England)","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/17","score":0.550000011920929,"display_name":"Partnerships for the goals"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":44,"referenced_works":["https://openalex.org/W1519958729","https://openalex.org/W1900337607","https://openalex.org/W1953731166","https://openalex.org/W1967735816","https://openalex.org/W1977412717","https://openalex.org/W1988393300","https://openalex.org/W1992621257","https://openalex.org/W1994600118","https://openalex.org/W2001082470","https://openalex.org/W2012814330","https://openalex.org/W2014677321","https://openalex.org/W2016202595","https://openalex.org/W2040230246","https://openalex.org/W2044193890","https://openalex.org/W2047207093","https://openalex.org/W2051104517","https://openalex.org/W2051875167","https://openalex.org/W2073145822","https://openalex.org/W2076154138","https://openalex.org/W2079591709","https://openalex.org/W2081754347","https://openalex.org/W2085669858","https://openalex.org/W2098811581","https://openalex.org/W2121171791","https://openalex.org/W2135030836","https://openalex.org/W2139617657","https://openalex.org/W2142570576","https://openalex.org/W2143701918","https://openalex.org/W2148995578","https://openalex.org/W2151373442","https://openalex.org/W2153496521","https://openalex.org/W2156143491","https://openalex.org/W2158266063","https://openalex.org/W2159849240","https://openalex.org/W2160649479","https://openalex.org/W2171808845","https://openalex.org/W2215072981","https://openalex.org/W2259938310","https://openalex.org/W2917858269","https://openalex.org/W2934716754","https://openalex.org/W4231510805","https://openalex.org/W4236512674","https://openalex.org/W6639619044","https://openalex.org/W6663076490"],"related_works":["https://openalex.org/W2384167225","https://openalex.org/W2113182373","https://openalex.org/W2119005669","https://openalex.org/W2088998312","https://openalex.org/W4255195499","https://openalex.org/W4250965783","https://openalex.org/W2481793228","https://openalex.org/W2403214044","https://openalex.org/W2379604225","https://openalex.org/W4205600000"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2021,"cited_by_count":3}],"updated_date":"2026-03-27T05:58:40.876381","created_date":"2025-10-10T00:00:00"}