{"id":"https://openalex.org/W2132241624","doi":"https://doi.org/10.1093/bioinformatics/btr539","title":"Pybedtools: a flexible Python library for manipulating genomic datasets and annotations","display_name":"Pybedtools: a flexible Python library for manipulating genomic datasets and annotations","publication_year":2011,"publication_date":"2011-09-23","ids":{"openalex":"https://openalex.org/W2132241624","doi":"https://doi.org/10.1093/bioinformatics/btr539","mag":"2132241624","pmid":"https://pubmed.ncbi.nlm.nih.gov/21949271"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btr539","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btr539","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/27/24/3423/48862135/bioinformatics_27_24_3423.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","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":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/27/24/3423/48862135/bioinformatics_27_24_3423.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5046206826","display_name":"Ryan Dale","orcid":"https://orcid.org/0000-0003-2664-3744"},"institutions":[{"id":"https://openalex.org/I4210090567","display_name":"National Institute of Diabetes and Digestive and Kidney Diseases","ror":"https://ror.org/00adh9b73","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210090567"]},{"id":"https://openalex.org/I1299303238","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238"]},{"id":"https://openalex.org/I51556381","display_name":"University of Virginia","ror":"https://ror.org/0153tk833","country_code":"US","type":"education","lineage":["https://openalex.org/I51556381"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Ryan K. Dale","raw_affiliation_strings":["1 Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, 2Department of Medicine, University of Colorado, Denver, Anschutz Medical Campus, Aurora, CO 80045 and 3Department of Public Health Sciences, Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA"],"affiliations":[{"raw_affiliation_string":"1 Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, 2Department of Medicine, University of Colorado, Denver, Anschutz Medical Campus, Aurora, CO 80045 and 3Department of Public Health Sciences, Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA","institution_ids":["https://openalex.org/I4210090567","https://openalex.org/I51556381","https://openalex.org/I1299303238"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005439778","display_name":"Brent S. Pedersen","orcid":"https://orcid.org/0000-0003-1786-2216"},"institutions":[{"id":"https://openalex.org/I51556381","display_name":"University of Virginia","ror":"https://ror.org/0153tk833","country_code":"US","type":"education","lineage":["https://openalex.org/I51556381"]},{"id":"https://openalex.org/I1299303238","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238"]},{"id":"https://openalex.org/I4210090567","display_name":"National Institute of Diabetes and Digestive and Kidney Diseases","ror":"https://ror.org/00adh9b73","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210090567"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Brent S. Pedersen","raw_affiliation_strings":["1 Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, 2Department of Medicine, University of Colorado, Denver, Anschutz Medical Campus, Aurora, CO 80045 and 3Department of Public Health Sciences, Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA"],"affiliations":[{"raw_affiliation_string":"1 Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, 2Department of Medicine, University of Colorado, Denver, Anschutz Medical Campus, Aurora, CO 80045 and 3Department of Public Health Sciences, Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA","institution_ids":["https://openalex.org/I4210090567","https://openalex.org/I51556381","https://openalex.org/I1299303238"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5079803961","display_name":"Aaron R. Quinlan","orcid":"https://orcid.org/0000-0003-1756-0859"},"institutions":[{"id":"https://openalex.org/I51556381","display_name":"University of Virginia","ror":"https://ror.org/0153tk833","country_code":"US","type":"education","lineage":["https://openalex.org/I51556381"]},{"id":"https://openalex.org/I4210090567","display_name":"National Institute of Diabetes and Digestive and Kidney Diseases","ror":"https://ror.org/00adh9b73","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210090567"]},{"id":"https://openalex.org/I1299303238","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Aaron R. Quinlan","raw_affiliation_strings":["1 Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, 2Department of Medicine, University of Colorado, Denver, Anschutz Medical Campus, Aurora, CO 80045 and 3Department of Public Health Sciences, Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA"],"affiliations":[{"raw_affiliation_string":"1 Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, 2Department of Medicine, University of Colorado, Denver, Anschutz Medical Campus, Aurora, CO 80045 and 3Department of Public Health Sciences, Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA","institution_ids":["https://openalex.org/I4210090567","https://openalex.org/I51556381","https://openalex.org/I1299303238"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5046206826"],"corresponding_institution_ids":["https://openalex.org/I1299303238","https://openalex.org/I4210090567","https://openalex.org/I51556381"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":3.8689,"has_fulltext":true,"cited_by_count":590,"citation_normalized_percentile":{"value":0.94452095,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"27","issue":"24","first_page":"3423","last_page":"3424"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9991000294685364,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9991000294685364,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9977999925613403,"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":0.9940000176429749,"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/python","display_name":"Python (programming language)","score":0.9728580713272095},{"id":"https://openalex.org/keywords/mit-license","display_name":"MIT License","score":0.8446654677391052},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7993420362472534},{"id":"https://openalex.org/keywords/scripting-language","display_name":"Scripting language","score":0.7546012997627258},{"id":"https://openalex.org/keywords/documentation","display_name":"Documentation","score":0.6333019733428955},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.6052675843238831},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.45824098587036133},{"id":"https://openalex.org/keywords/license","display_name":"License","score":0.4226452112197876},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.35753118991851807},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.20384261012077332}],"concepts":[{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.9728580713272095},{"id":"https://openalex.org/C174183944","wikidata":"https://www.wikidata.org/wiki/Q334661","display_name":"MIT License","level":3,"score":0.8446654677391052},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7993420362472534},{"id":"https://openalex.org/C61423126","wikidata":"https://www.wikidata.org/wiki/Q187432","display_name":"Scripting language","level":2,"score":0.7546012997627258},{"id":"https://openalex.org/C56666940","wikidata":"https://www.wikidata.org/wiki/Q788790","display_name":"Documentation","level":2,"score":0.6333019733428955},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.6052675843238831},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.45824098587036133},{"id":"https://openalex.org/C2780560020","wikidata":"https://www.wikidata.org/wiki/Q79719","display_name":"License","level":2,"score":0.4226452112197876},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.35753118991851807},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.20384261012077332}],"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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1093/bioinformatics/btr539","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btr539","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/27/24/3423/48862135/bioinformatics_27_24_3423.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:21949271","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/21949271","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:pubmedcentral.nih.gov:3232365","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3232365","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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.817.7294","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.817.7294","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"https://bioinformatics.oxfordjournals.org/content/early/2011/09/23/bioinformatics.btr539.full.pdf","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.818.4833","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.818.4833","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"https://bioinformatics.oxfordjournals.org/content/27/24/3423.full.pdf","raw_type":"text"},{"id":"pmh:oai:open-archive.highwire.org:bioinfo:27/24/3423","is_oa":false,"landing_page_url":"http://bioinformatics.oxfordjournals.org/cgi/content/short/27/24/3423","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"TEXT"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btr539","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btr539","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/27/24/3423/48862135/bioinformatics_27_24_3423.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320337357","display_name":"National Institute of Diabetes and Digestive and Kidney Diseases","ror":"https://ror.org/00adh9b73"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2132241624.pdf","grobid_xml":"https://content.openalex.org/works/W2132241624.grobid-xml"},"referenced_works_count":9,"referenced_works":["https://openalex.org/W1544691147","https://openalex.org/W2065783627","https://openalex.org/W2102619694","https://openalex.org/W2108234281","https://openalex.org/W2128016314","https://openalex.org/W2149992227","https://openalex.org/W2161645441","https://openalex.org/W2171777347","https://openalex.org/W2885727518"],"related_works":["https://openalex.org/W3023169329","https://openalex.org/W2782165897","https://openalex.org/W4300438041","https://openalex.org/W2054104202","https://openalex.org/W2139703748","https://openalex.org/W2761254753","https://openalex.org/W2188981919","https://openalex.org/W3084909426","https://openalex.org/W3108811894","https://openalex.org/W9028451"],"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":21},{"year":2025,"cited_by_count":70},{"year":2024,"cited_by_count":82},{"year":2023,"cited_by_count":79},{"year":2022,"cited_by_count":63},{"year":2021,"cited_by_count":59},{"year":2020,"cited_by_count":39},{"year":2019,"cited_by_count":48},{"year":2018,"cited_by_count":35},{"year":2017,"cited_by_count":31},{"year":2016,"cited_by_count":14},{"year":2015,"cited_by_count":18},{"year":2014,"cited_by_count":15},{"year":2013,"cited_by_count":13},{"year":2012,"cited_by_count":1}],"updated_date":"2026-04-18T07:56:08.524223","created_date":"2025-10-10T00:00:00"}
