{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,28]],"date-time":"2026-01-28T05:15:10Z","timestamp":1769577310218,"version":"3.49.0"},"reference-count":15,"publisher":"Oxford University Press (OUP)","issue":"20","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010,10,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: ChIP-Seq data are a new challenge for motif discovery. Such a data typically consists of thousands of DNA segments with base-specific coverage values. We present a new version of our DNA motif discovery software ChIPMunk adapted for ChIP-Seq data. ChIPMunk is an iterative algorithm that combines greedy optimization with bootstrapping and uses coverage profiles as motif positional preferences. ChIPMunk does not require truncation of long DNA segments and it is practical for processing up to tens of thousands of data sequences. Comparison with traditional (MEME) or ChIP-Seq-oriented (HMS) motif discovery tools shows that ChIPMunk identifies the correct motifs with the same or better quality but works dramatically faster.<\/jats:p>\n               <jats:p>Availability and implementation: ChIPMunk is freely available within the ru_genetika Java package: http:\/\/line.imb.ac.ru\/ChIPMunk. Web-based version is also available.<\/jats:p>\n               <jats:p>Contact: \u00a0ivan.kulakovskiy@gmail.com<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq488","type":"journal-article","created":{"date-parts":[[2010,8,25]],"date-time":"2010-08-25T01:53:25Z","timestamp":1282701205000},"page":"2622-2623","source":"Crossref","is-referenced-by-count":136,"title":["Deep and wide digging for binding motifs in ChIP-Seq data"],"prefix":"10.1093","volume":"26","author":[{"given":"I. V.","family":"Kulakovskiy","sequence":"first","affiliation":[{"name":"1 Research Institute for Genetics and Selection of Industrial Microorganisms, Moscow 117545, Russia, 2Institut Curie, 26 rue d'Ulm, 3INSERM, U900, 4INSERM, U830, Paris F\u221275248, 5Mines ParisTech, Fontainebleau F-77300, France, 6Johns Hopkins University, Baltimore, MD 21205, USA and 7Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia"},{"name":"1 Research Institute for Genetics and Selection of Industrial Microorganisms, Moscow 117545, Russia, 2Institut Curie, 26 rue d'Ulm, 3INSERM, U900, 4INSERM, U830, Paris F\u221275248, 5Mines ParisTech, Fontainebleau F-77300, France, 6Johns Hopkins University, Baltimore, MD 21205, USA and 7Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia"}]},{"given":"V. A.","family":"Boeva","sequence":"additional","affiliation":[{"name":"1 Research Institute for Genetics and Selection of Industrial Microorganisms, Moscow 117545, Russia, 2Institut Curie, 26 rue d'Ulm, 3INSERM, U900, 4INSERM, U830, Paris F\u221275248, 5Mines ParisTech, Fontainebleau F-77300, France, 6Johns Hopkins University, Baltimore, MD 21205, USA and 7Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia"},{"name":"1 Research Institute for Genetics and Selection of Industrial Microorganisms, Moscow 117545, Russia, 2Institut Curie, 26 rue d'Ulm, 3INSERM, U900, 4INSERM, U830, Paris F\u221275248, 5Mines ParisTech, Fontainebleau F-77300, France, 6Johns Hopkins University, Baltimore, MD 21205, USA and 7Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia"},{"name":"1 Research Institute for Genetics and Selection of Industrial Microorganisms, Moscow 117545, Russia, 2Institut Curie, 26 rue d'Ulm, 3INSERM, U900, 4INSERM, U830, Paris F\u221275248, 5Mines ParisTech, Fontainebleau F-77300, France, 6Johns Hopkins University, Baltimore, MD 21205, USA and 7Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia"},{"name":"1 Research Institute for Genetics and Selection of Industrial Microorganisms, Moscow 117545, Russia, 2Institut Curie, 26 rue d'Ulm, 3INSERM, U900, 4INSERM, U830, Paris F\u221275248, 5Mines ParisTech, Fontainebleau F-77300, France, 6Johns Hopkins University, Baltimore, MD 21205, USA and 7Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia"},{"name":"1 Research Institute for Genetics and Selection of Industrial Microorganisms, Moscow 117545, Russia, 2Institut Curie, 26 rue d'Ulm, 3INSERM, U900, 4INSERM, U830, Paris F\u221275248, 5Mines ParisTech, Fontainebleau F-77300, France, 6Johns Hopkins University, Baltimore, MD 21205, USA and 7Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia"}]},{"given":"A. V.","family":"Favorov","sequence":"additional","affiliation":[{"name":"1 Research Institute for Genetics and Selection of Industrial Microorganisms, Moscow 117545, Russia, 2Institut Curie, 26 rue d'Ulm, 3INSERM, U900, 4INSERM, U830, Paris F\u221275248, 5Mines ParisTech, Fontainebleau F-77300, France, 6Johns Hopkins University, Baltimore, MD 21205, USA and 7Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia"},{"name":"1 Research Institute for Genetics and Selection of Industrial Microorganisms, Moscow 117545, Russia, 2Institut Curie, 26 rue d'Ulm, 3INSERM, U900, 4INSERM, U830, Paris F\u221275248, 5Mines ParisTech, Fontainebleau F-77300, France, 6Johns Hopkins University, Baltimore, MD 21205, USA and 7Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia"}]},{"given":"V. J.","family":"Makeev","sequence":"additional","affiliation":[{"name":"1 Research Institute for Genetics and Selection of Industrial Microorganisms, Moscow 117545, Russia, 2Institut Curie, 26 rue d'Ulm, 3INSERM, U900, 4INSERM, U830, Paris F\u221275248, 5Mines ParisTech, Fontainebleau F-77300, France, 6Johns Hopkins University, Baltimore, MD 21205, USA and 7Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia"},{"name":"1 Research Institute for Genetics and Selection of Industrial Microorganisms, Moscow 117545, Russia, 2Institut Curie, 26 rue d'Ulm, 3INSERM, U900, 4INSERM, U830, Paris F\u221275248, 5Mines ParisTech, Fontainebleau F-77300, France, 6Johns Hopkins University, Baltimore, MD 21205, USA and 7Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia"}]}],"member":"286","published-online":{"date-parts":[[2010,10,20]]},"reference":[{"key":"2023012507554316900_B1","doi-asserted-by":"crossref","first-page":"W202","DOI":"10.1093\/nar\/gkp335","article-title":"MEME SUITE: tools for motif discovery and searching","volume":"37","author":"Bailey","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"2023012507554316900_B2","doi-asserted-by":"crossref","first-page":"1106","DOI":"10.1016\/j.cell.2008.04.043","article-title":"Integration of external signaling pathways with the core transcriptional network in embryonic stem cells","volume":"133","author":"Chen","year":"2008","journal-title":"Cell"},{"key":"2023012507554316900_B3","doi-asserted-by":"crossref","first-page":"2240","DOI":"10.1093\/bioinformatics\/bti336","article-title":"A Gibbs sampler for identification of symmetrically structured, spaced DNA motifs with improved estimation of the signal length","volume":"21","author":"Favorov","year":"2005","journal-title":"Bioinformatics"},{"key":"2023012507554316900_B4","doi-asserted-by":"crossref","first-page":"1729","DOI":"10.1093\/bioinformatics\/btn305","article-title":"FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology","volume":"24","author":"Fejes","year":"2008","journal-title":"Bioinformatics"},{"key":"2023012507554316900_B5","doi-asserted-by":"crossref","first-page":"R19","DOI":"10.1186\/gb-2010-11-2-r19","article-title":"Evidence-ranked motif identification","volume":"11","author":"Georgiev","year":"2010","journal-title":"Genome Biol."},{"key":"2023012507554316900_B6","doi-asserted-by":"crossref","first-page":"e4932","DOI":"10.1371\/journal.pone.0004932","article-title":"The oncogenic EWS-FLI1 protein binds in vivo GGAA microsatellite sequences with potential transcriptional activation function","volume":"4","author":"Guillon","year":"2009","journal-title":"PLoS ONE"},{"key":"2023012507554316900_B7","doi-asserted-by":"crossref","first-page":"2154","DOI":"10.1093\/nar\/gkp1180","article-title":"On the detection and refinement of transcription factor binding sites using ChIP-Seq data","volume":"38","author":"Hu","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"2023012507554316900_B8","doi-asserted-by":"crossref","first-page":"1293","DOI":"10.1038\/nbt.1505","article-title":"An integrated software system for analyzing ChIP-chip and ChIP-seq data","volume":"26","author":"Ji","year":"2008","journal-title":"Nat. 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