{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,6]],"date-time":"2026-02-06T21:57:06Z","timestamp":1770415026002,"version":"3.49.0"},"reference-count":6,"publisher":"Oxford University Press (OUP)","issue":"23","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":429,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,12,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: ChIA-PET is rapidly emerging as an important experimental approach to detect chromatin long-range interactions at high resolution. Here, we present Model based Interaction Calling from ChIA-PET data (MICC), an easy-to-use R package to detect chromatin interactions from ChIA-PET sequencing data. By applying a Bayesian mixture model to systematically remove random ligation and random collision noise, MICC could identify chromatin interactions with a significantly higher sensitivity than existing methods at the same false discovery rate.<\/jats:p>\n               <jats:p>Availability and implementation: \u00a0http:\/\/bioinfo.au.tsinghua.edu.cn\/member\/xwwang\/MICCusage<\/jats:p>\n               <jats:p>Contact: \u00a0michael.zhang@utdallas.edu or xwwang@tsinghua.edu.cn<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btv445","type":"journal-article","created":{"date-parts":[[2015,8,1]],"date-time":"2015-08-01T00:40:08Z","timestamp":1438389608000},"page":"3832-3834","source":"Crossref","is-referenced-by-count":33,"title":["MICC: an R package for identifying chromatin interactions from ChIA-PET data"],"prefix":"10.1093","volume":"31","author":[{"given":"Chao","family":"He","sequence":"first","affiliation":[{"name":"1 MOE Key Laboratory of Bioinformatics and Bioinformatics Division, Center for Synthetic and System Biology, TNLIST\/Department of Automation, Tsinghua University, Beijing 100084, China and"}]},{"given":"Michael Q.","family":"Zhang","sequence":"additional","affiliation":[{"name":"2 Department of Molecular and Cell Biology, Center for Systems Biology, The University of Texas, Richardson, TX 75080-3021, USA"},{"name":"1 MOE Key Laboratory of Bioinformatics and Bioinformatics Division, Center for Synthetic and System Biology, TNLIST\/Department of Automation, Tsinghua University, Beijing 100084, China and"}]},{"given":"Xiaowo","family":"Wang","sequence":"additional","affiliation":[{"name":"1 MOE Key Laboratory of Bioinformatics and Bioinformatics Division, Center for Synthetic and System Biology, TNLIST\/Department of Automation, Tsinghua University, Beijing 100084, China and"}]}],"member":"286","published-online":{"date-parts":[[2015,7,31]]},"reference":[{"key":"2023020202423930000_btv445-B1","doi-asserted-by":"crossref","first-page":"109","DOI":"10.1038\/nature11279","article-title":"The long-range interaction landscape of gene promoters","volume":"489","author":"Amartya","year":"2012","journal-title":"Nature"},{"key":"2023020202423930000_btv445-B2","doi-asserted-by":"crossref","first-page":"58","DOI":"10.1038\/nature08497","article-title":"An oestrogen-receptor-\u03b1-bound human chromatin interactome","volume":"462","author":"Fullwood","year":"2009","journal-title":"Nature"},{"key":"2023020202423930000_btv445-B3","doi-asserted-by":"crossref","first-page":"48","DOI":"10.1090\/S0002-9947-1935-1501802-5","article-title":"Distribution functions and the Riemann zeta function","volume":"38","author":"Jessen","year":"1935","journal-title":"Trans. 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Soc."},{"key":"2023020202423930000_btv445-B4","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/gb-2010-11-2-r22","article-title":"ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing","volume":"11","author":"Li","year":"2010","journal-title":"Genome Biol."},{"key":"2023020202423930000_btv445-B5","doi-asserted-by":"crossref","first-page":"84","DOI":"10.1016\/j.cell.2011.12.014","article-title":"Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation","volume":"148","author":"Li","year":"2012","journal-title":"Cell"},{"key":"2023020202423930000_btv445-B6","doi-asserted-by":"crossref","first-page":"e143","DOI":"10.1093\/nar\/gku738","article-title":"A statistical model of ChIA-PET data for accurate detection of chromatin 3D interactions","volume":"42","author":"Paulsen","year":"2015","journal-title":"Nucleic Acids Res."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/31\/23\/3832\/49036233\/bioinformatics_31_23_3832.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/31\/23\/3832\/49036233\/bioinformatics_31_23_3832.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,2]],"date-time":"2023-02-02T03:51:04Z","timestamp":1675309864000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/31\/23\/3832\/208584"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2015,7,31]]},"references-count":6,"journal-issue":{"issue":"23","published-print":{"date-parts":[[2015,12,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btv445","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2015,12,1]]},"published":{"date-parts":[[2015,7,31]]}}}