{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,8]],"date-time":"2026-04-08T16:12:46Z","timestamp":1775664766810,"version":"3.50.1"},"reference-count":14,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2023,4,17]],"date-time":"2023-04-17T00:00:00Z","timestamp":1681689600000},"content-version":"vor","delay-in-days":16,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"George and Lavinia Blick Research Scholarship"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,4,3]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Exclusion regions are sections of reference genomes with abnormal pileups of short sequencing reads. Removing reads overlapping them improves biological signal, and these benefits are most pronounced in differential analysis settings. Several labs created exclusion region sets, available primarily through ENCODE and Github. However, the variety of exclusion sets creates uncertainty which sets to use. Furthermore, gap regions (e.g. centromeres, telomeres, short arms) create additional considerations in generating exclusion sets. We generated exclusion sets for the latest human T2T-CHM13 and mouse GRCm39 genomes and systematically assembled and annotated these and other sets in the excluderanges R\/Bioconductor data package, also accessible via the BEDbase.org API. The package provides unified access to 82 GenomicRanges objects covering six organisms, multiple genome assemblies, and types of exclusion regions. For human hg38 genome assembly, we recommend hg38.Kundaje.GRCh38_unified_blacklist as the most well-curated and annotated, and sets generated by the Blacklist tool for other organisms.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>https:\/\/bioconductor.org\/packages\/excluderanges\/. Package website: https:\/\/dozmorovlab.github.io\/excluderanges\/.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btad198","type":"journal-article","created":{"date-parts":[[2023,4,17]],"date-time":"2023-04-17T14:25:58Z","timestamp":1681741558000},"source":"Crossref","is-referenced-by-count":21,"title":["excluderanges: exclusion sets for T2T-CHM13, GRCm39, and other genome assemblies"],"prefix":"10.1093","volume":"39","author":[{"given":"Jonathan D","family":"Ogata","sequence":"first","affiliation":[{"name":"Department of Biostatistics, Virginia Commonwealth University , Richmond, VA 23298, United States"}]},{"given":"Wancen","family":"Mu","sequence":"additional","affiliation":[{"name":"Department of Biostatistics, University of North Carolina-Chapel Hill , Chapel Hill, NC 27514, United States"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4051-3217","authenticated-orcid":false,"given":"Eric S","family":"Davis","sequence":"additional","affiliation":[{"name":"Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill , Chapel Hill, NC 27599, United States"}]},{"given":"Bingjie","family":"Xue","sequence":"additional","affiliation":[{"name":"Center for Public Health Genomics, University of Virginia , Charlottesville, VA 22908, United States"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3541-8418","authenticated-orcid":false,"given":"J Chuck","family":"Harrell","sequence":"additional","affiliation":[{"name":"Department of Pathology, Virginia Commonwealth University , Richmond, VA 23284, United States"},{"name":"Massey Cancer Center, Virginia Commonwealth University , Richmond, VA 23220, United States"}]},{"given":"Nathan C","family":"Sheffield","sequence":"additional","affiliation":[{"name":"Center for Public Health Genomics, University of Virginia , Charlottesville, VA 22908, United States"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2123-0051","authenticated-orcid":false,"given":"Douglas H","family":"Phanstiel","sequence":"additional","affiliation":[{"name":"Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill , Chapel Hill, NC 27599, United States"},{"name":"Thurston Arthritis Research Center, University of North Carolina at Chapel Hill , Chapel Hill, NC 27599, United States"},{"name":"Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill , Chapel Hill, NC 27599, United States"},{"name":"Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill , Chapel Hill, NC 27599, United States"},{"name":"Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill , Chapel Hill, NC 27599, United States"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8401-0545","authenticated-orcid":false,"given":"Michael 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