{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,31]],"date-time":"2025-10-31T14:16:23Z","timestamp":1761920183372,"version":"3.37.3"},"reference-count":34,"publisher":"Oxford University Press (OUP)","issue":"24","funder":[{"DOI":"10.13039\/100000054","name":"National Cancer Institute","doi-asserted-by":"publisher","award":["NIH U54CA193461"],"award-info":[{"award-number":["NIH U54CA193461"]}],"id":[{"id":"10.13039\/100000054","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,12,15]]},"abstract":"<jats:p>Motivation: The Hi-C technology was designed to decode the three-dimensional conformation of the genome. Despite progress towards more and more accurate contact maps, several systematic biases have been demonstrated to affect the resulting data matrix. Here we report a new source of bias that can arise in tumor Hi-C data, which is related to the copy number of genomic DNA. To address this bias, we designed a chromosome-adjusted iterative correction method called caICB. Our caICB correction method leads to significant improvements when compared with the original iterative correction in terms of eliminating copy number bias.<\/jats:p>\n               <jats:p>Availability and Implementation: The method is available at https:\/\/bitbucket.org\/mthjwu\/hicapp.<\/jats:p>\n               <jats:p>Contact: \u00a0michor@jimmy.harvard.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btw540","type":"journal-article","created":{"date-parts":[[2016,8,17]],"date-time":"2016-08-17T02:39:40Z","timestamp":1471401580000},"page":"3695-3701","source":"Crossref","is-referenced-by-count":37,"title":["A computational strategy to adjust for copy number in tumor Hi-C data"],"prefix":"10.1093","volume":"32","author":[{"given":"Hua-Jun","family":"Wu","sequence":"first","affiliation":[{"name":"Department of Computational Biology and Biostatistics, Dana-Farber Cancer Institute, and Department of Biostatistics, Harvard School of Public Health, Boston, MA 02215, USA"}]},{"given":"Franziska","family":"Michor","sequence":"additional","affiliation":[{"name":"Department of Computational Biology and Biostatistics, Dana-Farber Cancer Institute, and Department of Biostatistics, Harvard School of Public Health, Boston, MA 02215, USA"}]}],"member":"286","published-online":{"date-parts":[[2016,8,16]]},"reference":[{"key":"2023020114083759800_btw540-B1","doi-asserted-by":"crossref","first-page":"999","DOI":"10.1101\/gr.160374.113","article-title":"Statistical confidence estimation for Hi-C data reveals regulatory chromatin contacts","volume":"24","author":"Ay","year":"2014","journal-title":"Genome Res"},{"key":"2023020114083759800_btw540-B2","doi-asserted-by":"crossref","first-page":"183.","DOI":"10.1186\/s13059-015-0745-7","article-title":"Analysis methods for studying the 3D architecture of the genome","volume":"16","author":"Ay","year":"2015","journal-title":"Genome Biol"},{"key":"2023020114083759800_btw540-B3","doi-asserted-by":"crossref","first-page":"603","DOI":"10.1038\/nature11003","article-title":"The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity","volume":"483","author":"Barretina","year":"2012","journal-title":"Nature"},{"key":"2023020114083759800_btw540-B4","doi-asserted-by":"crossref","first-page":"214","DOI":"10.1186\/s13059-015-0768-0","article-title":"Chromatin interaction analysis reveals changes in small chromosome and telomere clustering between epithelial and breast cancer cells","volume":"16","author":"Barutcu","year":"2015","journal-title":"Genome Biol"},{"key":"2023020114083759800_btw540-B5","doi-asserted-by":"crossref","first-page":"1103","DOI":"10.1038\/nbt.2030","article-title":"DNA replication timing and long-range DNA interactions predict mutational landscapes of cancer genomes","volume":"29","author":"De","year":"2011","journal-title":"Nat. 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