{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,3]],"date-time":"2026-04-03T06:13:09Z","timestamp":1775196789061,"version":"3.50.1"},"reference-count":8,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":2055,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.0\/uk\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,3,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Post-translational modifications to histones have several well known associations with regulation of gene expression. While some modifications appear concentrated narrowly, covering promoters or enhancers, others are dispersed as epigenomic domains. These domains mark contiguous regions sharing an epigenomic property, such as actively transcribed or poised genes, or heterochromatically silenced regions. While high-throughput methods like ChIP-Seq have led to a flood of high-quality data about these epigenomic domains, there remain important analysis problems that are not adequately solved by current analysis tools.<\/jats:p>\n               <jats:p>Results: We present the RSEG method for identifying epigenomic domains from ChIP-Seq data for histone modifications. In contrast with other methods emphasizing the locations of \u2018peaks\u2019 in read density profiles, our method identifies the boundaries of domains. RSEG is also able to incorporate a control sample and find genomic regions with differential histone modifications between two samples.<\/jats:p>\n               <jats:p>Availability: RSEG, including source code and documentation, is freely available at http:\/\/smithlab.cmb.usc.edu\/histone\/rseg\/.<\/jats:p>\n               <jats:p>Contact: \u00a0andrewds@usc.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr030","type":"journal-article","created":{"date-parts":[[2011,2,17]],"date-time":"2011-02-17T01:15:09Z","timestamp":1297905309000},"page":"870-871","source":"Crossref","is-referenced-by-count":158,"title":["Identifying dispersed epigenomic domains from ChIP-Seq data"],"prefix":"10.1093","volume":"27","author":[{"given":"Qiang","family":"Song","sequence":"first","affiliation":[{"name":"Molecular and Computational Biology, University of Southern California, Los Angeles, California 90089"}]},{"given":"Andrew D.","family":"Smith","sequence":"additional","affiliation":[{"name":"Molecular and Computational Biology, University of Southern California, Los Angeles, California 90089"}]}],"member":"286","published-online":{"date-parts":[[2011,2,16]]},"reference":[{"key":"2023012511543333000_B1","doi-asserted-by":"crossref","first-page":"823","DOI":"10.1016\/j.cell.2007.05.009","article-title":"High-resolution profiling of histone methylations in the human genome","volume":"129","author":"Barski","year":"2007","journal-title":"Cell"},{"key":"2023012511543333000_B2","doi-asserted-by":"crossref","first-page":"693","DOI":"10.1016\/j.cell.2007.02.005","article-title":"Chromatin modifications and their function","volume":"128","author":"Kouzarides","year":"2007","journal-title":"Cell"},{"key":"2023012511543333000_B3","doi-asserted-by":"crossref","first-page":"553","DOI":"10.1038\/nature06008","article-title":"Genome-wide maps of chromatin state in pluripotent and lineage-committed cells","volume":"448","author":"Mikkelsen","year":"2007","journal-title":"Nature"},{"key":"2023012511543333000_B4","doi-asserted-by":"crossref","first-page":"S22","DOI":"10.1038\/nmeth.1371","article-title":"Computation for ChIP-seq and RNA-seq studies","volume":"6","author":"Pepke","year":"2009","journal-title":"Nat. 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