{"id":"https://openalex.org/W4366083654","doi":"https://doi.org/10.1093/bioinformatics/btad198","title":"excluderanges: exclusion sets for T2T-CHM13, GRCm39, and other genome assemblies","display_name":"excluderanges: exclusion sets for T2T-CHM13, GRCm39, and other genome assemblies","publication_year":2023,"publication_date":"2023-04-01","ids":{"openalex":"https://openalex.org/W4366083654","doi":"https://doi.org/10.1093/bioinformatics/btad198","pmid":"https://pubmed.ncbi.nlm.nih.gov/37067481"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btad198","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad198","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad198/49989340/btad198.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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","license_id":"https://openalex.org/licenses/cc-by","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":"gold","oa_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad198/49989340/btad198.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5016013375","display_name":"Jonathan Ogata","orcid":"https://orcid.org/0000-0002-8082-7395"},"institutions":[{"id":"https://openalex.org/I184840846","display_name":"Virginia Commonwealth University","ror":"https://ror.org/02nkdxk79","country_code":"US","type":"education","lineage":["https://openalex.org/I184840846"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jonathan D Ogata","raw_affiliation_strings":["Department of Biostatistics, Virginia Commonwealth University , Richmond, VA 23298, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biostatistics, Virginia Commonwealth University , Richmond, VA 23298, United States","institution_ids":["https://openalex.org/I184840846"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5014212936","display_name":"Wancen Mu","orcid":"https://orcid.org/0000-0002-5061-7581"},"institutions":[{"id":"https://openalex.org/I114027177","display_name":"University of North Carolina at Chapel Hill","ror":"https://ror.org/0130frc33","country_code":"US","type":"education","lineage":["https://openalex.org/I114027177"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Wancen Mu","raw_affiliation_strings":["Department of Biostatistics, University of North Carolina-Chapel Hill , Chapel Hill, NC 27514, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biostatistics, University of North Carolina-Chapel Hill , Chapel Hill, NC 27514, United States","institution_ids":["https://openalex.org/I114027177"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5010223887","display_name":"Eric S. Davis","orcid":"https://orcid.org/0000-0003-4051-3217"},"institutions":[{"id":"https://openalex.org/I114027177","display_name":"University of North Carolina at Chapel Hill","ror":"https://ror.org/0130frc33","country_code":"US","type":"education","lineage":["https://openalex.org/I114027177"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Eric S Davis","raw_affiliation_strings":["Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill , Chapel Hill, NC 27599, United States"],"raw_orcid":"https://orcid.org/0000-0003-4051-3217","affiliations":[{"raw_affiliation_string":"Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill , Chapel Hill, NC 27599, United States","institution_ids":["https://openalex.org/I114027177"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5089189215","display_name":"Bingjie Xue","orcid":"https://orcid.org/0000-0002-9947-6484"},"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"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Bingjie Xue","raw_affiliation_strings":["Center for Public Health Genomics, University of Virginia , Charlottesville, VA 22908, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Public Health Genomics, University of Virginia , Charlottesville, VA 22908, United States","institution_ids":["https://openalex.org/I51556381"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5057868655","display_name":"J. Chuck Harrell","orcid":"https://orcid.org/0000-0003-3541-8418"},"institutions":[{"id":"https://openalex.org/I184840846","display_name":"Virginia Commonwealth University","ror":"https://ror.org/02nkdxk79","country_code":"US","type":"education","lineage":["https://openalex.org/I184840846"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"J Chuck Harrell","raw_affiliation_strings":["Department of Pathology, Virginia Commonwealth University , Richmond, VA 23284, United States","Massey Cancer Center, Virginia Commonwealth University , Richmond, VA 23220, United States"],"raw_orcid":"https://orcid.org/0000-0003-3541-8418","affiliations":[{"raw_affiliation_string":"Department of Pathology, Virginia Commonwealth University , Richmond, VA 23284, United States","institution_ids":["https://openalex.org/I184840846"]},{"raw_affiliation_string":"Massey Cancer Center, Virginia Commonwealth University , Richmond, VA 23220, United States","institution_ids":["https://openalex.org/I184840846"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5055872618","display_name":"Nathan C. Sheffield","orcid":"https://orcid.org/0000-0001-5643-4068"},"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"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Nathan C Sheffield","raw_affiliation_strings":["Center for Public Health Genomics, University of Virginia , Charlottesville, VA 22908, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Public Health Genomics, University of Virginia , Charlottesville, VA 22908, United States","institution_ids":["https://openalex.org/I51556381"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005038887","display_name":"Douglas H. Phanstiel","orcid":"https://orcid.org/0000-0003-2123-0051"},"institutions":[{"id":"https://openalex.org/I114027177","display_name":"University of North Carolina at Chapel Hill","ror":"https://ror.org/0130frc33","country_code":"US","type":"education","lineage":["https://openalex.org/I114027177"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Douglas H Phanstiel","raw_affiliation_strings":["Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill , Chapel Hill, NC 27599, United States","Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill , Chapel Hill, NC 27599, United States","Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill , Chapel Hill, NC 27599, United States","Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill , Chapel Hill, NC 27599, United States","Thurston Arthritis Research Center, University of North Carolina at Chapel Hill , Chapel Hill, NC 27599, United States"],"raw_orcid":"https://orcid.org/0000-0003-2123-0051","affiliations":[{"raw_affiliation_string":"Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill , Chapel Hill, NC 27599, United States","institution_ids":["https://openalex.org/I114027177"]},{"raw_affiliation_string":"Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill , Chapel Hill, NC 27599, United States","institution_ids":["https://openalex.org/I114027177"]},{"raw_affiliation_string":"Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill , Chapel Hill, NC 27599, United States","institution_ids":["https://openalex.org/I114027177"]},{"raw_affiliation_string":"Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill , Chapel Hill, NC 27599, United States","institution_ids":["https://openalex.org/I114027177"]},{"raw_affiliation_string":"Thurston Arthritis Research Center, University of North Carolina at Chapel Hill , Chapel Hill, NC 27599, United States","institution_ids":["https://openalex.org/I114027177"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049770701","display_name":"Michael I. Love","orcid":"https://orcid.org/0000-0001-8401-0545"},"institutions":[{"id":"https://openalex.org/I114027177","display_name":"University of North Carolina at Chapel Hill","ror":"https://ror.org/0130frc33","country_code":"US","type":"education","lineage":["https://openalex.org/I114027177"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Michael I Love","raw_affiliation_strings":["Department of Biostatistics, University of North Carolina-Chapel Hill , Chapel Hill, NC 27514, United States","Department of Genetics, University of North Carolina-Chapel Hill , Chapel Hill, NC 27514, United States"],"raw_orcid":"https://orcid.org/0000-0001-8401-0545","affiliations":[{"raw_affiliation_string":"Department of Biostatistics, University of North Carolina-Chapel Hill , Chapel Hill, NC 27514, United States","institution_ids":["https://openalex.org/I114027177"]},{"raw_affiliation_string":"Department of Genetics, University of North Carolina-Chapel Hill , Chapel Hill, NC 27514, United States","institution_ids":["https://openalex.org/I114027177"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5056470952","display_name":"Mikhail G. Dozmorov","orcid":"https://orcid.org/0000-0002-0086-8358"},"institutions":[{"id":"https://openalex.org/I184840846","display_name":"Virginia Commonwealth University","ror":"https://ror.org/02nkdxk79","country_code":"US","type":"education","lineage":["https://openalex.org/I184840846"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Mikhail G Dozmorov","raw_affiliation_strings":["Department of Biostatistics, Virginia Commonwealth University , Richmond, VA 23298, United States","Department of Pathology, Virginia Commonwealth University , Richmond, VA 23284, United States"],"raw_orcid":"https://orcid.org/0000-0002-0086-8358","affiliations":[{"raw_affiliation_string":"Department of Biostatistics, Virginia Commonwealth University , Richmond, VA 23298, United States","institution_ids":["https://openalex.org/I184840846"]},{"raw_affiliation_string":"Department of Pathology, Virginia Commonwealth University , Richmond, VA 23284, United States","institution_ids":["https://openalex.org/I184840846"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":9,"corresponding_author_ids":["https://openalex.org/A5056470952"],"corresponding_institution_ids":["https://openalex.org/I184840846"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":3.5232,"has_fulltext":true,"cited_by_count":25,"citation_normalized_percentile":{"value":0.93047149,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":100},"biblio":{"volume":"39","issue":"4","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.35519999265670776,"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":0.35519999265670776,"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":0.26330000162124634,"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"}},{"id":"https://openalex.org/T13664","display_name":"Genome Rearrangement Algorithms","score":0.16099999845027924,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/bioconductor","display_name":"Bioconductor","score":0.7947361469268799},{"id":"https://openalex.org/keywords/blacklist","display_name":"Blacklist","score":0.7218031287193298},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.7112058997154236},{"id":"https://openalex.org/keywords/encode","display_name":"ENCODE","score":0.6251688599586487},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5725500583648682},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5017733573913574},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.41010576486587524},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3030273914337158},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.1308818757534027},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.12003830075263977}],"concepts":[{"id":"https://openalex.org/C2779694297","wikidata":"https://www.wikidata.org/wiki/Q2888953","display_name":"Bioconductor","level":3,"score":0.7947361469268799},{"id":"https://openalex.org/C2781345505","wikidata":"https://www.wikidata.org/wiki/Q2535979","display_name":"Blacklist","level":2,"score":0.7218031287193298},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.7112058997154236},{"id":"https://openalex.org/C66746571","wikidata":"https://www.wikidata.org/wiki/Q1134833","display_name":"ENCODE","level":3,"score":0.6251688599586487},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5725500583648682},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5017733573913574},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.41010576486587524},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3030273914337158},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1308818757534027},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.12003830075263977}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D035501","descriptor_name":"Uncertainty","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D035501","descriptor_name":"Uncertainty","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D035501","descriptor_name":"Uncertainty","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D035501","descriptor_name":"Uncertainty","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btad198","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad198","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad198/49989340/btad198.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:37067481","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37067481","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:10126321","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10126321","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10126321/pdf/btad198.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btad198","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad198","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad198/49989340/btad198.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.800000011920929,"id":"https://metadata.un.org/sdg/10","display_name":"Reduced inequalities"}],"awards":[{"id":"https://openalex.org/G4164419861","display_name":null,"funder_award_id":"R35 GM128645","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G821642606","display_name":null,"funder_award_id":"R35-GM128645","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4366083654.pdf"},"referenced_works_count":15,"referenced_works":["https://openalex.org/W1645912598","https://openalex.org/W1978537438","https://openalex.org/W1996203485","https://openalex.org/W2016200633","https://openalex.org/W2064802634","https://openalex.org/W2102904139","https://openalex.org/W2161313889","https://openalex.org/W2162391642","https://openalex.org/W2945678788","https://openalex.org/W2949074346","https://openalex.org/W2953622121","https://openalex.org/W4220999759","https://openalex.org/W4296782027","https://openalex.org/W4385720261","https://openalex.org/W6636878359"],"related_works":["https://openalex.org/W3172840274","https://openalex.org/W50122730","https://openalex.org/W2245533262","https://openalex.org/W3129811130","https://openalex.org/W3185731761","https://openalex.org/W2265547225","https://openalex.org/W4379616178","https://openalex.org/W4292158217","https://openalex.org/W2181543702","https://openalex.org/W2953622121"],"abstract_inverted_index":{"SUMMARY:":[0],"Exclusion":[1],"regions":[2,58],"are":[3,25],"sections":[4],"of":[5,11,47,122],"reference":[6],"genomes":[7,83],"with":[8],"abnormal":[9],"pileups":[10],"short":[12,62],"sequencing":[13],"reads.":[14],"Removing":[15],"reads":[16],"overlapping":[17],"them":[18],"improves":[19],"biological":[20],"signal,":[21],"and":[22,42,80,84,87,90,120,137,139],"these":[23,89],"benefits":[24],"most":[26,135],"pronounced":[27],"in":[28,67,93],"differential":[29],"analysis":[30],"settings.":[31],"Several":[32],"labs":[33],"created":[34],"exclusion":[35,48,69,73,123],"region":[36],"sets,":[37],"available":[38],"primarily":[39],"through":[40],"ENCODE":[41],"Github.":[43],"However,":[44],"the":[45,76,94,102,134,143],"variety":[46],"sets":[49,53,74,92,140],"creates":[50],"uncertainty":[51],"which":[52],"to":[54,110],"use.":[55],"Furthermore,":[56],"gap":[57],"(e.g.":[59],"centromeres,":[60],"telomeres,":[61],"arms)":[63],"create":[64],"additional":[65],"considerations":[66],"generating":[68],"sets.":[70],"We":[71],"generated":[72,141],"for":[75,146],"latest":[77],"human":[78,126],"T2T-CHM13":[79],"mouse":[81],"GRCm39":[82],"systematically":[85],"assembled":[86],"annotated":[88],"other":[91,147],"excluderanges":[95],"R/Bioconductor":[96],"data":[97],"package,":[98],"also":[99],"accessible":[100],"via":[101],"BEDbase.org":[103],"API.":[104],"The":[105],"package":[106],"provides":[107],"unified":[108],"access":[109],"82":[111],"GenomicRanges":[112],"objects":[113],"covering":[114],"six":[115],"organisms,":[116],"multiple":[117],"genome":[118,128],"assemblies,":[119],"types":[121],"regions.":[124],"For":[125],"hg38":[127],"assembly,":[129],"we":[130],"recommend":[131],"hg38.Kundaje.GRCh38_unified_blacklist":[132],"as":[133],"well-curated":[136],"annotated,":[138],"by":[142],"Blacklist":[144],"tool":[145],"organisms.":[148],"AVAILABILITY":[149],"AND":[150],"IMPLEMENTATION:":[151],"https://bioconductor.org/packages/excluderanges/.":[152],"Package":[153],"website:":[154],"https://dozmorovlab.github.io/excluderanges/.":[155]},"counts_by_year":[{"year":2026,"cited_by_count":6},{"year":2025,"cited_by_count":10},{"year":2024,"cited_by_count":7},{"year":2023,"cited_by_count":2}],"updated_date":"2026-06-24T13:16:06.693445","created_date":"2025-10-10T00:00:00"}
