{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,8,6]],"date-time":"2024-08-06T03:19:26Z","timestamp":1722914366922},"reference-count":22,"publisher":"Oxford University Press (OUP)","issue":"17","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,9,1]]},"abstract":"<jats:p>Motivation: We have witnessed an enormous increase in ChIP-Seq data for histone modifications in the past few years. Discovering significant patterns in these data is an important problem for understanding biological mechanisms.<\/jats:p>\n               <jats:p>Results: We propose probabilistic partitioning methods to discover significant patterns in ChIP-Seq data. Our methods take into account signal magnitude, shape, strand orientation and shifts. We compare our methods with some current methods and demonstrate significant improvements, especially with sparse data. Besides pattern discovery and classification, probabilistic partitioning can serve other purposes in ChIP-Seq data analysis. Specifically, we exemplify its merits in the context of peak finding and partitioning of nucleosome positioning patterns in human promoters.<\/jats:p>\n               <jats:p>Availability and implementation: The software and code are available in the supplementary material.<\/jats:p>\n               <jats:p>Contact: \u00a0Philipp.Bucher@isb-sib.ch<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary Data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu318","type":"journal-article","created":{"date-parts":[[2014,5,9]],"date-time":"2014-05-09T04:37:58Z","timestamp":1399610278000},"page":"2406-2413","source":"Crossref","is-referenced-by-count":13,"title":["Probabilistic partitioning methods to find significant patterns in ChIP-Seq data"],"prefix":"10.1093","volume":"30","author":[{"given":"Nishanth Ulhas","family":"Nair","sequence":"first","affiliation":[{"name":"1 \u00a01Laboratory for Computational Biology and Bioinformatics, School of Computer and Communication Sciences, 2Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, \u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne (EPFL), 1015 Lausanne and 3Swiss Institute for Bioinformatics, 1015 Lausanne, Switzerland"}]},{"given":"Sunil","family":"Kumar","sequence":"additional","affiliation":[{"name":"1 \u00a01Laboratory for Computational Biology and Bioinformatics, School of Computer and Communication Sciences, 2Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, \u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne (EPFL), 1015 Lausanne and 3Swiss Institute for Bioinformatics, 1015 Lausanne, Switzerland"}]},{"given":"Bernard M.E.","family":"Moret","sequence":"additional","affiliation":[{"name":"1 \u00a01Laboratory for Computational Biology and Bioinformatics, School of Computer and Communication Sciences, 2Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, \u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne (EPFL), 1015 Lausanne and 3Swiss Institute for Bioinformatics, 1015 Lausanne, Switzerland"}]},{"given":"Philipp","family":"Bucher","sequence":"additional","affiliation":[{"name":"1 \u00a01Laboratory for Computational Biology and Bioinformatics, School of Computer and Communication Sciences, 2Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, \u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne (EPFL), 1015 Lausanne and 3Swiss Institute for Bioinformatics, 1015 Lausanne, Switzerland"}]}],"member":"286","published-online":{"date-parts":[[2014,5,7]]},"reference":[{"key":"2023012711524890100_btu318-B1","doi-asserted-by":"crossref","first-page":"D991","DOI":"10.1093\/nar\/gks1193","article-title":"Ncbi geo: archive for functional genomics data sets-update","volume":"41","author":"Barrett","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"2023012711524890100_btu318-B2","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":"2023012711524890100_btu318-B3","doi-asserted-by":"crossref","first-page":"21931","DOI":"10.1073\/pnas.1016071107","article-title":"Histone H3K27ac separates active from poised enhancers and predicts developmental state","volume":"107","author":"Creyghton","year":"2010","journal-title":"Proc. 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