{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:42Z","timestamp":1772138082141,"version":"3.50.1"},"reference-count":24,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2016,12,20]],"date-time":"2016-12-20T00:00:00Z","timestamp":1482192000000},"content-version":"vor","delay-in-days":15,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"The Ohio State University and the Translational Data Analytics Initiative"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,3,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>Regulatory elements regulate gene transcription, and their location and accessibility is cell-type specific, particularly for enhancers. Mapping and comparing chromatin accessibility between different cell types may identify mechanisms involved in cellular development and disease progression. To streamline and simplify differential analysis of regulatory elements genome-wide using chromatin accessibility data, such as DNase-seq, ATAC-seq, we developed ALTRE (ALTered Regulatory Elements), an R package and associated R Shiny web app. ALTRE makes such analysis accessible to a wide range of users\u2014from novice to practiced computational biologists.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and Implementation<\/jats:title>\n                    <jats:p>https:\/\/github.com\/Mathelab\/ALTRE<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btw688","type":"journal-article","created":{"date-parts":[[2016,10,26]],"date-time":"2016-10-26T15:05:37Z","timestamp":1477494337000},"page":"740-742","source":"Crossref","is-referenced-by-count":2,"title":["ALTRE: workflow for defining ALTered Regulatory Elements using chromatin accessibility data"],"prefix":"10.1093","volume":"33","author":[{"given":"Elizabeth","family":"Baskin","sequence":"first","affiliation":[{"name":"Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH, USA"}]},{"given":"Rick","family":"Farouni","sequence":"additional","affiliation":[{"name":"Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH, USA"}]},{"given":"Ewy A","family":"Math\u00e9","sequence":"additional","affiliation":[{"name":"Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH, USA"}]}],"member":"286","published-online":{"date-parts":[[2016,12,5]]},"reference":[{"key":"2023020204502668300_btw688-B1","doi-asserted-by":"crossref","first-page":"433","DOI":"10.1007\/978-1-61779-477-3_26","article-title":"Quantitative analysis of genome-wide chromatin remodeling","volume":"833","author":"Baek","year":"2012","journal-title":"Methods Mol. 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