{"id":"https://openalex.org/W2892572630","doi":"https://doi.org/10.1093/bioinformatics/bty703","title":"Characterizing protein\u2013DNA binding event subtypes in ChIP-exo data","display_name":"Characterizing protein\u2013DNA binding event subtypes in ChIP-exo data","publication_year":2018,"publication_date":"2018-08-23","ids":{"openalex":"https://openalex.org/W2892572630","doi":"https://doi.org/10.1093/bioinformatics/bty703","mag":"2892572630","pmid":"https://pubmed.ncbi.nlm.nih.gov/30165373"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bty703","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty703","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/6/903/28079345/bty703.pdf","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":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/35/6/903/28079345/bty703.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5057263363","display_name":"Naomi Yamada","orcid":"https://orcid.org/0000-0003-2524-1153"},"institutions":[{"id":"https://openalex.org/I130769515","display_name":"Pennsylvania State University","ror":"https://ror.org/04p491231","country_code":"US","type":"education","lineage":["https://openalex.org/I130769515"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Naomi Yamada","raw_affiliation_strings":["Department of Biochemistry & Molecular Biology and Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biochemistry & Molecular Biology and Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA, USA","institution_ids":["https://openalex.org/I130769515"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000405432","display_name":"William Lai","orcid":"https://orcid.org/0000-0003-4351-7037"},"institutions":[{"id":"https://openalex.org/I130769515","display_name":"Pennsylvania State University","ror":"https://ror.org/04p491231","country_code":"US","type":"education","lineage":["https://openalex.org/I130769515"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"William K M Lai","raw_affiliation_strings":["Department of Biochemistry & Molecular Biology and Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biochemistry & Molecular Biology and Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA, USA","institution_ids":["https://openalex.org/I130769515"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5112472711","display_name":"Nina Farrell","orcid":"https://orcid.org/0000-0002-5452-2344"},"institutions":[{"id":"https://openalex.org/I130769515","display_name":"Pennsylvania State University","ror":"https://ror.org/04p491231","country_code":"US","type":"education","lineage":["https://openalex.org/I130769515"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Nina Farrell","raw_affiliation_strings":["Department of Biochemistry & Molecular Biology and Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biochemistry & Molecular Biology and Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA, USA","institution_ids":["https://openalex.org/I130769515"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046527896","display_name":"B. Franklin Pugh","orcid":"https://orcid.org/0000-0001-8341-4476"},"institutions":[{"id":"https://openalex.org/I130769515","display_name":"Pennsylvania State University","ror":"https://ror.org/04p491231","country_code":"US","type":"education","lineage":["https://openalex.org/I130769515"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"B Franklin Pugh","raw_affiliation_strings":["Department of Biochemistry & Molecular Biology and Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biochemistry & Molecular Biology and Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA, USA","institution_ids":["https://openalex.org/I130769515"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5077269033","display_name":"Shaun Mahony","orcid":"https://orcid.org/0000-0002-2641-1807"},"institutions":[{"id":"https://openalex.org/I130769515","display_name":"Pennsylvania State University","ror":"https://ror.org/04p491231","country_code":"US","type":"education","lineage":["https://openalex.org/I130769515"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Shaun Mahony","raw_affiliation_strings":["Department of Biochemistry & Molecular Biology and Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biochemistry & Molecular Biology and Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA, USA","institution_ids":["https://openalex.org/I130769515"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5077269033"],"corresponding_institution_ids":["https://openalex.org/I130769515"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":2.9671,"has_fulltext":false,"cited_by_count":43,"citation_normalized_percentile":{"value":0.92261629,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"35","issue":"6","first_page":"903","last_page":"913"},"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/T10604","display_name":"RNA Research and Splicing","score":0.9980999827384949,"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":0.9976999759674072,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.5693321824073792},{"id":"https://openalex.org/keywords/chip","display_name":"Chip","score":0.5470007061958313},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5290614366531372},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5007665157318115},{"id":"https://openalex.org/keywords/event","display_name":"Event (particle physics)","score":0.49259430170059204},{"id":"https://openalex.org/keywords/event-data","display_name":"Event data","score":0.4429132044315338},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.3412868082523346},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.2994215786457062},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2787556052207947},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.2459074854850769},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.10918211936950684}],"concepts":[{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.5693321824073792},{"id":"https://openalex.org/C165005293","wikidata":"https://www.wikidata.org/wiki/Q1074500","display_name":"Chip","level":2,"score":0.5470007061958313},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5290614366531372},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5007665157318115},{"id":"https://openalex.org/C2779662365","wikidata":"https://www.wikidata.org/wiki/Q5416694","display_name":"Event (particle physics)","level":2,"score":0.49259430170059204},{"id":"https://openalex.org/C2987896495","wikidata":"https://www.wikidata.org/wiki/Q5416716","display_name":"Event data","level":3,"score":0.4429132044315338},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.3412868082523346},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.2994215786457062},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2787556052207947},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.2459074854850769},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.10918211936950684},{"id":"https://openalex.org/C76155785","wikidata":"https://www.wikidata.org/wiki/Q418","display_name":"Telecommunications","level":1,"score":0.0},{"id":"https://openalex.org/C79158427","wikidata":"https://www.wikidata.org/wiki/Q485396","display_name":"Analytics","level":2,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","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":"D004247","descriptor_name":"DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"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":"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},{"descriptor_ui":"D059372","descriptor_name":"Nucleotide Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059372","descriptor_name":"Nucleotide Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059372","descriptor_name":"Nucleotide Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/bty703","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty703","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/6/903/28079345/bty703.pdf","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:30165373","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30165373","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},{"id":"pmh:oai:europepmc.org:6006079","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6419906","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bty703","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty703","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/6/903/28079345/bty703.pdf","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"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2855855348","display_name":null,"funder_award_id":"GM059055","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2892572630.pdf","grobid_xml":"https://content.openalex.org/works/W2892572630.grobid-xml"},"referenced_works_count":38,"referenced_works":["https://openalex.org/W1592870802","https://openalex.org/W1746680969","https://openalex.org/W1768880427","https://openalex.org/W1873501834","https://openalex.org/W1989419347","https://openalex.org/W2002262418","https://openalex.org/W2008051478","https://openalex.org/W2015245929","https://openalex.org/W2015416439","https://openalex.org/W2033169664","https://openalex.org/W2049684926","https://openalex.org/W2068379897","https://openalex.org/W2078236750","https://openalex.org/W2091244202","https://openalex.org/W2100286927","https://openalex.org/W2103441770","https://openalex.org/W2108234281","https://openalex.org/W2109897790","https://openalex.org/W2118608526","https://openalex.org/W2123436615","https://openalex.org/W2124080033","https://openalex.org/W2124985265","https://openalex.org/W2125248983","https://openalex.org/W2129795133","https://openalex.org/W2132215769","https://openalex.org/W2142136518","https://openalex.org/W2148507330","https://openalex.org/W2158734721","https://openalex.org/W2162415896","https://openalex.org/W2165232124","https://openalex.org/W2171808845","https://openalex.org/W2331147307","https://openalex.org/W2476248562","https://openalex.org/W2509628464","https://openalex.org/W2520313731","https://openalex.org/W2546760250","https://openalex.org/W2567948266","https://openalex.org/W2951699110"],"related_works":["https://openalex.org/W2025614457","https://openalex.org/W4385573527","https://openalex.org/W4308672222","https://openalex.org/W4319877673","https://openalex.org/W4309044578","https://openalex.org/W3111366672","https://openalex.org/W2185070550","https://openalex.org/W4206497353","https://openalex.org/W2109809809","https://openalex.org/W148577365"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":13},{"year":2020,"cited_by_count":10},{"year":2019,"cited_by_count":8},{"year":2018,"cited_by_count":1}],"updated_date":"2026-03-08T08:50:53.379069","created_date":"2025-10-10T00:00:00"}