{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,9]],"date-time":"2026-01-09T12:34:23Z","timestamp":1767962063080,"version":"3.49.0"},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"9","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,5,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: With the introduction of the Hi-C method new and fundamental properties of the nuclear architecture are emerging. The ability to interpret data generated by this method, which aims to capture the physical proximity between and within chromosomes, is crucial for uncovering the three dimensional structure of the nucleus. Providing researchers with tools for interactive visualization of Hi-C data can help in gaining new and important insights. Specifically, visual comparison can pinpoint changes in spatial organization between Hi-C datasets, originating from different cell lines or different species, or normalized by different methods. Here, we present CytoHiC, a Cytsocape plugin, which allow users to view and compare spatial maps of genomic landmarks, based on normalized Hi-C datasets. CytoHiC was developed to support intuitive visual comparison of Hi-C data and integration of additional genomic annotations.<\/jats:p>\n               <jats:p>Availability: The CytoHiC plugin, source code, user manual, example files and documentation are available at: http:\/\/apps.cytoscape.org\/apps\/cytohicplugin<\/jats:p>\n               <jats:p>Contact: \u00a0yolisha@gmail.com or ys388@cam.ac.uk<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt120","type":"journal-article","created":{"date-parts":[[2013,3,19]],"date-time":"2013-03-19T00:40:12Z","timestamp":1363653612000},"page":"1206-1207","source":"Crossref","is-referenced-by-count":18,"title":["CytoHiC: a cytoscape plugin for visual comparison of Hi-C networks"],"prefix":"10.1093","volume":"29","author":[{"given":"Yoli","family":"Shavit","sequence":"first","affiliation":[{"name":"Computer Laboratory, University of Cambridge, Cambridge CB3 0FD, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pietro","family":"Lio'","sequence":"additional","affiliation":[{"name":"Computer Laboratory, University of Cambridge, Cambridge CB3 0FD, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2013,3,18]]},"reference":[{"key":"2023012810370019700_btt120-B1","doi-asserted-by":"crossref","first-page":"426","DOI":"10.1038\/msb.2010.79","article-title":"Intra- and inter-chromosomal interactions correlate with CTCF binding genome wide","volume":"6","author":"Botta","year":"2010","journal-title":"Mol. Syst. Biol."},{"key":"2023012810370019700_btt120-B2","doi-asserted-by":"crossref","first-page":"704","DOI":"10.1186\/1471-2164-11-704","article-title":"Human transcriptional interactome of chromatin contribute to gene co-expression","volume":"11","author":"Dong","year":"2010","journal-title":"BMC Genomics"},{"key":"2023012810370019700_btt120-B3","doi-asserted-by":"crossref","first-page":"e44196","DOI":"10.1371\/journal.pone.0044196","article-title":"Three-dimensional genome architecture influences partner selection for chromosomal translocations in human disease","volume":"7","author":"Engreitz","year":"2012","journal-title":"PLoS One"},{"key":"2023012810370019700_btt120-B4","doi-asserted-by":"crossref","first-page":"R37","DOI":"10.1186\/gb-2009-10-4-r37","article-title":"Chromatin conformation signatures of cellular differentiation","volume":"10","author":"Fraser","year":"2009","journal-title":"Genome Biol."},{"key":"2023012810370019700_btt120-B5","first-page":"3","article-title":"HiCNorm: removing biases in Hi-C data via Poisson regression","author":"Hu","year":"2012","journal-title":"Bioinformatics"},{"key":"2023012810370019700_btt120-B6","doi-asserted-by":"crossref","first-page":"999","DOI":"10.1038\/nmeth.2148","article-title":"Iterative correction of Hi-C data reveals hallmarks of chromosome organization","volume":"9","author":"Imakaev","year":"2012","journal-title":"Nat. Methods"},{"key":"2023012810370019700_btt120-B7","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1126\/science.1181369","article-title":"Comprehensive mapping of long-range interactions reveals folding principles of the human genome","volume":"326","author":"Lieberman-Aiden","year":"2009","journal-title":"Science"},{"key":"2023012810370019700_btt120-B8","doi-asserted-by":"crossref","first-page":"2498","DOI":"10.1101\/gr.1239303","article-title":"Cytoscape: a software environment for integrated models of biomolecular interaction networks","volume":"13","author":"Shannon","year":"2003","journal-title":"Genome Res."},{"key":"2023012810370019700_btt120-B9","doi-asserted-by":"crossref","first-page":"1059","DOI":"10.1038\/ng.947","article-title":"Probabilistic modeling of Hi-C contact maps eliminates systematic biases to characterize global chromosomal architecture","volume":"43","author":"Yaffe","year":"2011","journal-title":"Nat. Genet."},{"key":"2023012810370019700_btt120-B10","doi-asserted-by":"crossref","first-page":"908","DOI":"10.1016\/j.cell.2012.02.002","article-title":"Spatial organization of the mouse genome and its role in recurrent chromosomal translocations","volume":"148","author":"Zhang","year":"2012","journal-title":"Cell"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/29\/9\/1206\/48895700\/bioinformatics_29_9_1206.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/29\/9\/1206\/48895700\/bioinformatics_29_9_1206.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,28]],"date-time":"2023-01-28T12:21:47Z","timestamp":1674908507000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/29\/9\/1206\/221293"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2013,3,18]]},"references-count":10,"journal-issue":{"issue":"9","published-print":{"date-parts":[[2013,5,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btt120","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2013,5,1]]},"published":{"date-parts":[[2013,3,18]]}}}