{"id":"https://openalex.org/W1515749105","doi":"https://doi.org/10.1371/journal.pcbi.1004418","title":"Contribution of Sequence Motif, Chromatin State, and DNA Structure Features to Predictive Models of Transcription Factor Binding in Yeast","display_name":"Contribution of Sequence Motif, Chromatin State, and DNA Structure Features to Predictive Models of Transcription Factor Binding in Yeast","publication_year":2015,"publication_date":"2015-08-20","ids":{"openalex":"https://openalex.org/W1515749105","doi":"https://doi.org/10.1371/journal.pcbi.1004418","mag":"1515749105","pmid":"https://pubmed.ncbi.nlm.nih.gov/26291518"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1004418","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1004418","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1004418&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.1004418&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5039196692","display_name":"Zing Tsung\u2010Yeh Tsai","orcid":"https://orcid.org/0000-0002-4006-1559"},"institutions":[{"id":"https://openalex.org/I4210098366","display_name":"Institute of Information Science, Academia Sinica","ror":"https://ror.org/00z83z196","country_code":"TW","type":"facility","lineage":["https://openalex.org/I4210098366","https://openalex.org/I84653119"]},{"id":"https://openalex.org/I4210111179","display_name":"Michigan United","ror":"https://ror.org/0291ys696","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210111179"]},{"id":"https://openalex.org/I87216513","display_name":"Michigan State University","ror":"https://ror.org/05hs6h993","country_code":"US","type":"education","lineage":["https://openalex.org/I87216513"]}],"countries":["TW","US"],"is_corresponding":false,"raw_author_name":"Zing Tsung-Yeh Tsai","raw_affiliation_strings":["Institute of Information Science, Academia Sinica, Taipei, Taiwan; Department of Plant Biology, Michigan State University, East Lansing, Michigan, United States of America","Department of Plant Biology, Michigan State University, East Lansing, Michigan, United States of America","Institute of Information Science, Academia Sinica, Taipei, Taiwan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Information Science, Academia Sinica, Taipei, Taiwan; Department of Plant Biology, Michigan State University, East Lansing, Michigan, United States of America","institution_ids":["https://openalex.org/I4210098366","https://openalex.org/I87216513"]},{"raw_affiliation_string":"Department of Plant Biology, Michigan State University, East Lansing, Michigan, United States of America","institution_ids":["https://openalex.org/I4210111179","https://openalex.org/I87216513"]},{"raw_affiliation_string":"Institute of Information Science, Academia Sinica, Taipei, Taiwan","institution_ids":["https://openalex.org/I4210098366"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5059271655","display_name":"Shin\u2010Han Shiu","orcid":"https://orcid.org/0000-0001-6470-235X"},"institutions":[{"id":"https://openalex.org/I4210111179","display_name":"Michigan United","ror":"https://ror.org/0291ys696","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210111179"]},{"id":"https://openalex.org/I87216513","display_name":"Michigan State University","ror":"https://ror.org/05hs6h993","country_code":"US","type":"education","lineage":["https://openalex.org/I87216513"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Shin-Han Shiu","raw_affiliation_strings":["Department of Plant Biology, Michigan State University, East Lansing, Michigan, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Plant Biology, Michigan State University, East Lansing, Michigan, United States of America","institution_ids":["https://openalex.org/I4210111179","https://openalex.org/I87216513"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5000235008","display_name":"Huai\u2010Kuang Tsai","orcid":"https://orcid.org/0000-0002-4200-8137"},"institutions":[{"id":"https://openalex.org/I4210098366","display_name":"Institute of Information Science, Academia Sinica","ror":"https://ror.org/00z83z196","country_code":"TW","type":"facility","lineage":["https://openalex.org/I4210098366","https://openalex.org/I84653119"]}],"countries":["TW"],"is_corresponding":true,"raw_author_name":"Huai-Kuang Tsai","raw_affiliation_strings":["Institute of Information Science, Academia Sinica, Taipei, Taiwan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Information Science, Academia Sinica, Taipei, Taiwan","institution_ids":["https://openalex.org/I4210098366"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5000235008","https://openalex.org/A5059271655"],"corresponding_institution_ids":["https://openalex.org/I4210098366","https://openalex.org/I4210111179","https://openalex.org/I87216513"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":1.6536,"has_fulltext":true,"cited_by_count":31,"citation_normalized_percentile":{"value":0.83043161,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"11","issue":"8","first_page":"e1004418","last_page":"e1004418"},"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9991999864578247,"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":0.9919000267982483,"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/chromatin","display_name":"Chromatin","score":0.5975551605224609},{"id":"https://openalex.org/keywords/transcription-factor","display_name":"Transcription factor","score":0.592313826084137},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5830985307693481},{"id":"https://openalex.org/keywords/binding-site","display_name":"Binding site","score":0.5747332572937012},{"id":"https://openalex.org/keywords/dna-binding-site","display_name":"DNA binding site","score":0.5692284107208252},{"id":"https://openalex.org/keywords/in-silico","display_name":"In silico","score":0.554751992225647},{"id":"https://openalex.org/keywords/nucleosome","display_name":"Nucleosome","score":0.5546481013298035},{"id":"https://openalex.org/keywords/dna-binding-domain","display_name":"DNA-binding domain","score":0.539618730545044},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.5298746824264526},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4996376037597656},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.4486154615879059},{"id":"https://openalex.org/keywords/binding-energy","display_name":"Binding energy","score":0.4335900545120239},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.3071798086166382},{"id":"https://openalex.org/keywords/promoter","display_name":"Promoter","score":0.2113928198814392},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.2090146243572235},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.17378687858581543}],"concepts":[{"id":"https://openalex.org/C83640560","wikidata":"https://www.wikidata.org/wiki/Q180951","display_name":"Chromatin","level":3,"score":0.5975551605224609},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.592313826084137},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5830985307693481},{"id":"https://openalex.org/C107824862","wikidata":"https://www.wikidata.org/wiki/Q616005","display_name":"Binding site","level":2,"score":0.5747332572937012},{"id":"https://openalex.org/C3662595","wikidata":"https://www.wikidata.org/wiki/Q5205743","display_name":"DNA binding site","level":5,"score":0.5692284107208252},{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.554751992225647},{"id":"https://openalex.org/C84772758","wikidata":"https://www.wikidata.org/wiki/Q271794","display_name":"Nucleosome","level":4,"score":0.5546481013298035},{"id":"https://openalex.org/C33987129","wikidata":"https://www.wikidata.org/wiki/Q13479514","display_name":"DNA-binding domain","level":4,"score":0.539618730545044},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.5298746824264526},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4996376037597656},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.4486154615879059},{"id":"https://openalex.org/C93282013","wikidata":"https://www.wikidata.org/wiki/Q420754","display_name":"Binding energy","level":2,"score":0.4335900545120239},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3071798086166382},{"id":"https://openalex.org/C101762097","wikidata":"https://www.wikidata.org/wiki/Q224093","display_name":"Promoter","level":4,"score":0.2113928198814392},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.2090146243572235},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.17378687858581543},{"id":"https://openalex.org/C185544564","wikidata":"https://www.wikidata.org/wiki/Q81197","display_name":"Nuclear physics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004271","descriptor_name":"DNA, Fungal","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004271","descriptor_name":"DNA, Fungal","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004271","descriptor_name":"DNA, Fungal","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004271","descriptor_name":"DNA, Fungal","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004271","descriptor_name":"DNA, Fungal","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004271","descriptor_name":"DNA, Fungal","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004271","descriptor_name":"DNA, Fungal","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004271","descriptor_name":"DNA, Fungal","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004271","descriptor_name":"DNA, Fungal","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D005656","descriptor_name":"Fungal Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D005656","descriptor_name":"Fungal Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D005656","descriptor_name":"Fungal Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D005656","descriptor_name":"Fungal Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D005656","descriptor_name":"Fungal Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D005656","descriptor_name":"Fungal Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D005656","descriptor_name":"Fungal Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D005656","descriptor_name":"Fungal Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D005656","descriptor_name":"Fungal Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":"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":"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":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":"D059372","descriptor_name":"Nucleotide Motifs","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D059372","descriptor_name":"Nucleotide Motifs","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D059372","descriptor_name":"Nucleotide Motifs","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1371/journal.pcbi.1004418","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1004418","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1004418&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:26291518","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26291518","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:RePEc:plo:pcbi00:1004418","is_oa":false,"landing_page_url":"https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004418","pdf_url":null,"source":{"id":"https://openalex.org/S4306401271","display_name":"RePEc: Research Papers in Economics","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I77793887","host_organization_name":"Federal Reserve Bank of St. Louis","host_organization_lineage":["https://openalex.org/I77793887"],"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":"article"},{"id":"pmh:oai:doaj.org/article:895b6ac8776540f682eff83b597f87e9","is_oa":true,"landing_page_url":"https://doaj.org/article/895b6ac8776540f682eff83b597f87e9","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 11, Iss 8, p e1004418 (2015)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:3521218","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4546298","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:figshare.com:article/1515348","is_oa":true,"landing_page_url":"https://figshare.com/articles/dataset/_Contribution_of_Sequence_Motif_Chromatin_State_and_DNA_Structure_Features_to_Predictive_Models_of_Transcription_Factor_Binding_in_Yeast_/1515348","pdf_url":null,"source":{"id":"https://openalex.org/S4306402621","display_name":"INDIGO (University of Illinois at Chicago)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I39422238","host_organization_name":"University of Illinois Chicago","host_organization_lineage":["https://openalex.org/I39422238"],"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"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1004418","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1004418","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1004418&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":[{"id":"https://metadata.un.org/sdg/7","display_name":"Affordable and clean energy","score":0.5799999833106995}],"awards":[{"id":"https://openalex.org/G6889813529","display_name":"Computational and Experimental Studies of Plastid Functional Networks","funder_award_id":"1119778","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":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1515749105.pdf","grobid_xml":"https://content.openalex.org/works/W1515749105.grobid-xml"},"referenced_works_count":74,"referenced_works":["https://openalex.org/W273955616","https://openalex.org/W1592075643","https://openalex.org/W1964963969","https://openalex.org/W1986723677","https://openalex.org/W1989338936","https://openalex.org/W1989419347","https://openalex.org/W1990558912","https://openalex.org/W1993702002","https://openalex.org/W2008226163","https://openalex.org/W2012661761","https://openalex.org/W2022181671","https://openalex.org/W2022736304","https://openalex.org/W2026690931","https://openalex.org/W2027458139","https://openalex.org/W2029873987","https://openalex.org/W2031750380","https://openalex.org/W2034340491","https://openalex.org/W2034511309","https://openalex.org/W2043016308","https://openalex.org/W2046374070","https://openalex.org/W2058517672","https://openalex.org/W2063679723","https://openalex.org/W2063909589","https://openalex.org/W2067899297","https://openalex.org/W2067958295","https://openalex.org/W2077026063","https://openalex.org/W2078034709","https://openalex.org/W2080498142","https://openalex.org/W2082500271","https://openalex.org/W2086893629","https://openalex.org/W2087058596","https://openalex.org/W2088990426","https://openalex.org/W2091112786","https://openalex.org/W2093897670","https://openalex.org/W2095791120","https://openalex.org/W2098599292","https://openalex.org/W2099922553","https://openalex.org/W2103302926","https://openalex.org/W2103453943","https://openalex.org/W2105623411","https://openalex.org/W2106217652","https://openalex.org/W2107733618","https://openalex.org/W2111729969","https://openalex.org/W2112293785","https://openalex.org/W2112741367","https://openalex.org/W2113423333","https://openalex.org/W2114803986","https://openalex.org/W2118608526","https://openalex.org/W2127081697","https://openalex.org/W2129795133","https://openalex.org/W2132688829","https://openalex.org/W2133376865","https://openalex.org/W2134957137","https://openalex.org/W2135951244","https://openalex.org/W2137683543","https://openalex.org/W2140754446","https://openalex.org/W2141408320","https://openalex.org/W2142305821","https://openalex.org/W2142317566","https://openalex.org/W2142410561","https://openalex.org/W2144688273","https://openalex.org/W2145126338","https://openalex.org/W2148056478","https://openalex.org/W2152296813","https://openalex.org/W2155718935","https://openalex.org/W2155926374","https://openalex.org/W2157766348","https://openalex.org/W2159324718","https://openalex.org/W2162066191","https://openalex.org/W2162836426","https://openalex.org/W2167895347","https://openalex.org/W2911964244","https://openalex.org/W4245023496","https://openalex.org/W6610017368"],"related_works":["https://openalex.org/W2027133237","https://openalex.org/W2586219588","https://openalex.org/W1891403707","https://openalex.org/W2041718959","https://openalex.org/W4240870951","https://openalex.org/W324520939","https://openalex.org/W2139954320","https://openalex.org/W1776902257","https://openalex.org/W2110652556","https://openalex.org/W1965921489"],"abstract_inverted_index":{"Transcription":[0],"factor":[1],"(TF)":[2],"binding":[3,43,62,65,93,112,132,147,197,216,222,241,255],"is":[4,20,248,265],"determined":[5],"by":[6,22],"the":[7,18,107,110,115,185,234],"presence":[8],"of":[9,67,109,119,125,196,240,257],"specific":[10],"sequence":[11],"motifs":[12],"(SM)":[13],"and":[14,27,35,52,103,128,142,169,251],"chromatin":[15,24],"accessibility,":[16],"where":[17],"latter":[19],"influenced":[21],"both":[23],"state":[25],"(CS)":[26],"DNA":[28,158],"structure":[29],"(DS)":[30],"properties.":[31,122],"Although":[32],"SM,":[33,126],"CS,":[34,127],"DS":[36,53,85,104,129],"have":[37,225],"been":[38,56],"used":[39],"to":[40,58,95,131,267],"predict":[41,59],"TF":[42,111,146,221,249,270],"sites,":[44],"a":[45,151,226,269],"predictive":[46,153],"model":[47,154,186,193,237,272],"that":[48,76,173,183,224,263],"jointly":[49],"considers":[50],"CS":[51,83,102],"has":[54,181],"not":[55,199],"developed":[57],"either":[60,82],"TF-specific":[61,92,140],"or":[63,84],"general":[64,254],"properties":[66],"TFs.":[68,258],"Using":[69],"budding":[70],"yeast":[71],"as":[72],"model,":[73],"we":[74],"found":[75],"machine":[77],"learning":[78],"classifiers":[79],"trained":[80],"with":[81,209],"features":[86,130],"alone":[87,180],"perform":[88],"better":[89],"in":[90,278],"predicting":[91],"compared":[94],"SM-based":[96],"classifiers.":[97],"In":[98,149],"addition,":[99,150],"simultaneously":[100],"considering":[101],"further":[105],"improves":[106],"accuracy":[108],"predictions,":[113],"indicating":[114],"highly":[116],"complementary":[117],"nature":[118],"these":[120,214],"two":[121],"The":[123],"contributions":[124],"site":[133],"predictions":[134,141],"differ":[135],"greatly":[136],"between":[137],"TFs,":[138,202],"allowing":[139],"potentially":[143,279],"reflecting":[144],"different":[145],"mechanisms.":[148],"\"TF-agnostic\"":[152],"based":[155],"on":[156,229],"three":[157],"\"intrinsic":[159],"properties\"":[160],"(in":[161],"silico":[162],"predicted":[163,215],"nucleosome":[164],"occupancy,":[165],"major":[166],"groove":[167],"geometry,":[168],"dinucleotide":[170],"free":[171],"energy)":[172],"can":[174,218],"be":[175],"calculated":[176],"from":[177],"genomic":[178],"sequences":[179],"performance":[182],"rivals":[184],"incorporating":[187],"experiment-derived":[188],"data.":[189],"This":[190],"intrinsic":[191,235],"property":[192,236],"allows":[194,238],"prediction":[195,239],"regions":[198,217,242,277],"only":[200],"across":[201,205,243],"but":[203],"also":[204],"DNA-binding":[206,244],"domain":[207,245],"families":[208],"distinct":[210],"structural":[211],"folds.":[212],"Furthermore,":[213],"help":[219],"identify":[220],"sites":[223],"significant":[227],"impact":[228],"target":[230],"gene":[231],"expression.":[232],"Because":[233],"families,":[246],"it":[247,264],"agnostic":[250,271],"likely":[252],"describes":[253],"potential":[256],"Thus,":[259],"our":[260],"findings":[261],"suggest":[262],"feasible":[266],"establish":[268],"for":[273],"identifying":[274],"functional":[275],"regulatory":[276],"any":[280],"sequenced":[281],"genome.":[282]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":7},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":5},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":5},{"year":2016,"cited_by_count":3}],"updated_date":"2026-08-06T08:24:18.245995","created_date":"2025-10-10T00:00:00"}
