{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,9,25]],"date-time":"2025-09-25T14:00:56Z","timestamp":1758808856388},"reference-count":14,"publisher":"Oxford University Press (OUP)","issue":"4","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,2,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Although some histone modification chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) signals show abrupt peaks across narrow and specific genomic locations, others have diffuse distributions along chromosomes, and their large contiguous enrichment landscapes are better modeled as broad peaks. Here, we present BroadPeak, an algorithm for the identification of such broad peaks from diffuse ChIP-seq datasets. We show that BroadPeak is a linear time algorithm that requires only two parameters, and we validate its performance on real and simulated histone modification ChIP-seq datasets. BroadPeak calls peaks that are highly coincident with both the underlying ChIP-seq tag count distributions and relevant biological features, such as the gene bodies of actively transcribed genes, and it shows superior overall recall and precision of known broad peaks from simulated datasets.<\/jats:p>\n               <jats:p>Availability: The source code and documentations are available at http:\/\/jordan.biology.gatech.edu\/page\/software\/broadpeak\/.<\/jats:p>\n               <jats:p>Contact: \u00a0king.jordan@biology.gatech.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts722","type":"journal-article","created":{"date-parts":[[2013,1,9]],"date-time":"2013-01-09T19:44:45Z","timestamp":1357760685000},"page":"492-493","source":"Crossref","is-referenced-by-count":33,"title":["BroadPeak: a novel algorithm for identifying broad peaks in diffuse ChIP-seq datasets"],"prefix":"10.1093","volume":"29","author":[{"given":"Jianrong","family":"Wang","sequence":"first","affiliation":[{"name":"1 School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA, 2Buck Institute for Age Research, Novato, CA 94945, USA and 3PanAmerican Bioinformatics Institute, Santa Marta, Magdalena, Colombia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Victoria V.","family":"Lunyak","sequence":"additional","affiliation":[{"name":"1 School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA, 2Buck Institute for Age Research, Novato, CA 94945, USA and 3PanAmerican Bioinformatics Institute, Santa Marta, Magdalena, Colombia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"I. King","family":"Jordan","sequence":"additional","affiliation":[{"name":"1 School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA, 2Buck Institute for Age Research, Novato, CA 94945, USA and 3PanAmerican Bioinformatics Institute, Santa Marta, Magdalena, Colombia"},{"name":"1 School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA, 2Buck Institute for Age Research, Novato, CA 94945, USA and 3PanAmerican Bioinformatics Institute, Santa Marta, Magdalena, Colombia"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2013,1,7]]},"reference":[{"key":"2023012810251151000_bts722-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":"2023012810251151000_bts722-B2","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1101\/gr.082800.108","article-title":"Global analysis of the insulator binding protein CTCF in chromatin barrier regions reveals demarcation of active and repressive domains","volume":"19","author":"Cuddapah","year":"2009","journal-title":"Genome Res."},{"key":"2023012810251151000_bts722-B3","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1038\/nature09906","article-title":"Mapping and analysis of chromatin state dynamics in nine human cell types","volume":"473","author":"Ernst","year":"2011","journal-title":"Nature"},{"key":"2023012810251151000_bts722-B4","doi-asserted-by":"crossref","first-page":"2264","DOI":"10.1073\/pnas.87.6.2264","article-title":"Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes","volume":"87","author":"Karlin","year":"1990","journal-title":"Proc. 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