{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,10]],"date-time":"2026-06-10T21:41:05Z","timestamp":1781127665676,"version":"3.54.1"},"reference-count":51,"publisher":"Oxford University Press (OUP)","issue":"1","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Motivation: Although peak finding in next-generation sequencing (NGS) datasets has been addressed extensively, there is no consensus on how to analyze and process biological replicates. Furthermore, most peak finders do not focus on accurate determination of enrichment site widths and are not widely applicable to different types of datasets.<\/jats:p><jats:p>Results: We developed JAMM ( J oint A nalysis of NGS replicates via M ixture M odel clustering): a peak finder that can integrate information from biological replicates, determine enrichment site widths accurately and resolve neighboring narrow peaks. JAMM is a universal peak finder that is applicable to different types of datasets. We show that JAMM is among the best performing peak finders in terms of site detection accuracy and in terms of accurate determination of enrichment sites widths. In addition, JAMM\u2019s replicate integration improves peak spatial resolution, sorting and peak finding accuracy.<\/jats:p><jats:p>Availability and implementation: JAMM is available for free and can run on Linux machines through the command line: http:\/\/code.google.com\/p\/jamm-peak-finder<\/jats:p><jats:p>Contact : mahmoud.ibrahim@mdc-berlin.de or uwe.ohler@mdc-berlin.de .<\/jats:p><jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu568","type":"journal-article","created":{"date-parts":[[2014,9,16]],"date-time":"2014-09-16T00:23:19Z","timestamp":1410826999000},"page":"48-55","source":"Crossref","is-referenced-by-count":66,"title":["JAMM: a peak finder for joint analysis of NGS replicates"],"prefix":"10.1093","volume":"31","author":[{"given":"Mahmoud M.","family":"Ibrahim","sequence":"first","affiliation":[{"name":"1 Department of Biology, Humboldt University, Invalidenstrasse 43, D-10115 Berlin, Germany and 2 The Berlin Institute for Medical Systems Biology, Max Delbr\u00fcck Center for Molecular Medicine Berlin-Buch, Robert R\u00f6ssle Str. 10, Berlin 13125, Germany"},{"name":"1 Department of Biology, Humboldt University, Invalidenstrasse 43, D-10115 Berlin, Germany and 2 The Berlin Institute for Medical Systems Biology, Max Delbr\u00fcck Center for Molecular Medicine Berlin-Buch, Robert R\u00f6ssle Str. 10, Berlin 13125, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Scott A.","family":"Lacadie","sequence":"additional","affiliation":[{"name":"1 Department of Biology, Humboldt University, Invalidenstrasse 43, D-10115 Berlin, Germany and 2 The Berlin Institute for Medical Systems Biology, Max Delbr\u00fcck Center for Molecular Medicine Berlin-Buch, Robert R\u00f6ssle Str. 10, Berlin 13125, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Uwe","family":"Ohler","sequence":"additional","affiliation":[{"name":"1 Department of Biology, Humboldt University, Invalidenstrasse 43, D-10115 Berlin, Germany and 2 The Berlin Institute for Medical Systems Biology, Max Delbr\u00fcck Center for Molecular Medicine Berlin-Buch, Robert R\u00f6ssle Str. 10, Berlin 13125, Germany"},{"name":"1 Department of Biology, Humboldt University, Invalidenstrasse 43, D-10115 Berlin, Germany and 2 The Berlin Institute for Medical Systems Biology, Max Delbr\u00fcck Center for Molecular Medicine Berlin-Buch, Robert R\u00f6ssle Str. 10, Berlin 13125, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2014,9,15]]},"reference":[{"key":"2023020116154628000_btu568-B1","doi-asserted-by":"crossref","first-page":"2979","DOI":"10.1093\/bioinformatics\/btt524","article-title":"HMCan: a method for detecting chromatin modifications in cancer samples using ChIP-seq data","volume":"29","author":"Ashoor","year":"2013","journal-title":"Bioinformatics"},{"key":"2023020116154628000_btu568-B2","first-page":"803","article-title":"Model-based gaussian and non-gaussian clustering","volume":"49","author":"Banfield","year":"1993","journal-title":"Bio-metrics"},{"key":"2023020116154628000_btu568-B3","doi-asserted-by":"crossref","first-page":"2705","DOI":"10.1093\/bioinformatics\/btt470","article-title":"Identification of transcription factor binding sites from ChIP-seq data at high resolution","volume":"29","author":"Bardet","year":"2013","journal-title":"Bioinformatics"},{"key":"2023020116154628000_btu568-B4","doi-asserted-by":"crossref","first-page":"283","DOI":"10.1111\/j.2517-6161.1995.tb02031.x","article-title":"Controlling the false discovery rate: A practical and powerful approach to multiple testing","volume":"57","author":"Benjamini","year":"1995","journal-title":"J. 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