{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,28]],"date-time":"2026-03-28T20:56:57Z","timestamp":1774731417605,"version":"3.50.1"},"reference-count":15,"publisher":"Oxford University Press (OUP)","issue":"17","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":772,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/3.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,9,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: The spatial conformation of the chromosome has a deep influence on gene regulation and expression. Hi-C technology allows the evaluation of the spatial proximity between any pair of loci along the genome. It results in a data matrix where blocks corresponding to (self-)interacting regions appear. The delimitation of such blocks is critical to better understand the spatial organization of the chromatin. From a computational point of view, it results in a 2D segmentation problem.<\/jats:p>\n               <jats:p>Results: We focus on the detection of cis-interacting regions, which appear to be prominent in observed data. We define a block-wise segmentation model for the detection of such regions. We prove that the maximization of the likelihood with respect to the block boundaries can be rephrased in terms of a 1D segmentation problem, for which the standard dynamic programming applies. The performance of the proposed methods is assessed by a simulation study on both synthetic and resampled data. A comparative study on public data shows good concordance with biologically confirmed regions.<\/jats:p>\n               <jats:p>Availability and implementation: The HiCseg R package is available from the Comprehensive R Archive Network and from the Web page of the corresponding author.<\/jats:p>\n               <jats:p>Contact: \u00a0celine.levy-leduc@agroparistech.fr<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu443","type":"journal-article","created":{"date-parts":[[2014,8,26]],"date-time":"2014-08-26T11:23:57Z","timestamp":1409052237000},"page":"i386-i392","source":"Crossref","is-referenced-by-count":147,"title":["Two-dimensional segmentation for analyzing Hi-C data"],"prefix":"10.1093","volume":"30","author":[{"given":"Celine","family":"L\u00e9vy-Leduc","sequence":"first","affiliation":[{"name":"1 AgroParisTech\/INRA MIA 518, 75005 Paris and 2UMR de G\u00e9n\u00e9tique V\u00e9g\u00e9tale, INRA\/Univ. Paris-Sud\/CNRS, 91190 Gif-sur-Yvette, France"}]},{"given":"M.","family":"Delattre","sequence":"additional","affiliation":[{"name":"1 AgroParisTech\/INRA MIA 518, 75005 Paris and 2UMR de G\u00e9n\u00e9tique V\u00e9g\u00e9tale, INRA\/Univ. Paris-Sud\/CNRS, 91190 Gif-sur-Yvette, France"}]},{"given":"T.","family":"Mary-Huard","sequence":"additional","affiliation":[{"name":"1 AgroParisTech\/INRA MIA 518, 75005 Paris and 2UMR de G\u00e9n\u00e9tique V\u00e9g\u00e9tale, INRA\/Univ. Paris-Sud\/CNRS, 91190 Gif-sur-Yvette, France"},{"name":"1 AgroParisTech\/INRA MIA 518, 75005 Paris and 2UMR de G\u00e9n\u00e9tique V\u00e9g\u00e9tale, INRA\/Univ. Paris-Sud\/CNRS, 91190 Gif-sur-Yvette, France"}]},{"given":"S.","family":"Robin","sequence":"additional","affiliation":[{"name":"1 AgroParisTech\/INRA MIA 518, 75005 Paris and 2UMR de G\u00e9n\u00e9tique V\u00e9g\u00e9tale, INRA\/Univ. 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