{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,1]],"date-time":"2026-02-01T04:29:30Z","timestamp":1769920170198,"version":"3.49.0"},"reference-count":8,"publisher":"Oxford University Press (OUP)","issue":"15","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":3013,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.0\/uk\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2008,8,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Next-generation sequencing can provide insight into protein\u2013DNA association events on a genome-wide scale, and is being applied in an increasing number of applications in genomics and meta-genomics research. However, few software applications are available for interpreting these experiments. We present here an efficient application for use with chromatin-immunoprecipitation (ChIP-Seq) experimental data that includes novel functionality for identifying areas of gene enrichment and transcription factor binding site locations, as well as for estimating DNA fragment size distributions in enriched areas. The FindPeaks application can generate UCSC compatible custom \u2018WIG\u2019 track files from aligned-read files for short-read sequencing technology. The software application can be executed on any platform capable of running a Java Runtime Environment. Memory requirements are proportional to the number of sequencing reads analyzed; typically 4 GB permits processing of up to 40 million reads.<\/jats:p>\n               <jats:p>Availability: The FindPeaks 3.1 package and manual, containing algorithm descriptions, usage instructions and examples, are available at http:\/\/www.bcgsc.ca\/platform\/bioinfo\/software\/findpeaks Source files for FindPeaks 3.1 are available for academic use.<\/jats:p>\n               <jats:p>Contact: \u00a0afejes@bcgsc.ca<\/jats:p>","DOI":"10.1093\/bioinformatics\/btn305","type":"journal-article","created":{"date-parts":[[2008,7,4]],"date-time":"2008-07-04T00:26:14Z","timestamp":1215131174000},"page":"1729-1730","source":"Crossref","is-referenced-by-count":226,"title":["FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology"],"prefix":"10.1093","volume":"24","author":[{"given":"Anthony P.","family":"Fejes","sequence":"first","affiliation":[{"name":"1 Genome Sciences Centre, BC Cancer Agency, Suite 100 570 West 7th Avenue, Vancouver, British Columbia, Canada V5Z 4S6 and 2College of Medicine, Houston, Texas, One Baylor Plaza, MS: BCM215, Houston, TX 77030, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gordon","family":"Robertson","sequence":"additional","affiliation":[{"name":"1 Genome Sciences Centre, BC Cancer Agency, Suite 100 570 West 7th Avenue, Vancouver, British Columbia, Canada V5Z 4S6 and 2College of Medicine, Houston, Texas, One Baylor Plaza, MS: BCM215, Houston, TX 77030, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mikhail","family":"Bilenky","sequence":"additional","affiliation":[{"name":"1 Genome Sciences Centre, BC Cancer Agency, Suite 100 570 West 7th Avenue, Vancouver, British Columbia, Canada V5Z 4S6 and 2College of Medicine, Houston, Texas, One Baylor Plaza, MS: BCM215, Houston, TX 77030, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Richard","family":"Varhol","sequence":"additional","affiliation":[{"name":"1 Genome Sciences Centre, BC Cancer Agency, Suite 100 570 West 7th Avenue, Vancouver, British Columbia, Canada V5Z 4S6 and 2College of Medicine, Houston, Texas, One Baylor Plaza, MS: BCM215, Houston, TX 77030, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Matthew","family":"Bainbridge","sequence":"additional","affiliation":[{"name":"1 Genome Sciences Centre, BC Cancer Agency, Suite 100 570 West 7th Avenue, Vancouver, British Columbia, Canada V5Z 4S6 and 2College of Medicine, Houston, Texas, One Baylor Plaza, MS: BCM215, Houston, TX 77030, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Steven J. M.","family":"Jones","sequence":"additional","affiliation":[{"name":"1 Genome Sciences Centre, BC Cancer Agency, Suite 100 570 West 7th Avenue, Vancouver, British Columbia, Canada V5Z 4S6 and 2College of Medicine, Houston, Texas, One Baylor Plaza, MS: BCM215, Houston, TX 77030, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2008,7,3]]},"reference":[{"key":"2023020210481162100_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":"2023020210481162100_B2","doi-asserted-by":"crossref","first-page":"1497","DOI":"10.1126\/science.1141319","article-title":"Genome-wide mapping of in vivo protein-DNA interactions","volume":"316","author":"Johnson","year":"2007","journal-title":"Science"},{"key":"2023020210481162100_B3","doi-asserted-by":"crossref","first-page":"231","DOI":"10.1016\/0888-7543(88)90007-9","article-title":"Genomic mapping by fingerprinting random clones: a mathematical analysis","volume":"2","author":"Lander","year":"1988","journal-title":"Genomics"},{"key":"2023020210481162100_B4","doi-asserted-by":"crossref","first-page":"610","DOI":"10.1101\/gr.7179508","article-title":"Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells","volume":"18","author":"Morin","year":"2008","journal-title":"Genome Res"},{"key":"2023020210481162100_B5","doi-asserted-by":"crossref","first-page":"651","DOI":"10.1038\/nmeth1068","article-title":"Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing","volume":"4","author":"Robertson","year":"2007","journal-title":"Nat. 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