{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,11]],"date-time":"2025-12-11T07:35:06Z","timestamp":1765438506647,"version":"3.37.3"},"reference-count":12,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2017,11,23]],"date-time":"2017-11-23T00:00:00Z","timestamp":1511395200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["R15GM120650"],"award-info":[{"award-number":["R15GM120650"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,3,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>We build a software package scHiCNorm that uses zero-inflated and hurdle models to remove biases from single-cell Hi-C data. Our evaluations prove that our models can effectively eliminate systematic biases for single-cell Hi-C data, which better reveal cell-to-cell variances in terms of chromosomal structures.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>scHiCNorm is available at http:\/\/dna.cs.miami.edu\/scHiCNorm\/. Perl scripts are provided that can generate bias features. Pre-built bias features for human (hg19 and hg38) and mouse (mm9 and mm10) are available to download. R scripts can be downloaded to remove biases.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btx747","type":"journal-article","created":{"date-parts":[[2017,11,22]],"date-time":"2017-11-22T20:13:53Z","timestamp":1511381633000},"page":"1046-1047","source":"Crossref","is-referenced-by-count":20,"title":["scHiCNorm: a software package to eliminate systematic biases in single-cell Hi-C data"],"prefix":"10.1093","volume":"34","author":[{"given":"Tong","family":"Liu","sequence":"first","affiliation":[{"name":"Department of Computer Science, University of Miami, Coral Gables, FL, USA"}]},{"given":"Zheng","family":"Wang","sequence":"additional","affiliation":[{"name":"Department of Computer Science, University of Miami, Coral Gables, FL, USA"}]}],"member":"286","published-online":{"date-parts":[[2017,11,23]]},"reference":[{"key":"2023012712464699800_btx747-B1","doi-asserted-by":"crossref","first-page":"1306","DOI":"10.1126\/science.1067799","article-title":"Capturing chromosome conformation","volume":"295","author":"Dekker","year":"2002","journal-title":"Science"},{"key":"2023012712464699800_btx747-B2","doi-asserted-by":"crossref","first-page":"376","DOI":"10.1038\/nature11082","article-title":"Topological domains in mammalian genomes identified by analysis of chromatin interactions","volume":"485","author":"Dixon","year":"2012","journal-title":"Nature"},{"key":"2023012712464699800_btx747-B3","doi-asserted-by":"crossref","first-page":"e1002893","DOI":"10.1371\/journal.pcbi.1002893","article-title":"Bayesian inference of spatial organizations of chromosomes","volume":"9","author":"Hu","year":"2013","journal-title":"PLoS Comput. Biol"},{"key":"2023012712464699800_btx747-B4","doi-asserted-by":"crossref","first-page":"3131","DOI":"10.1093\/bioinformatics\/bts570","article-title":"HiCNorm: removing biases in Hi-C data via Poisson regression","volume":"28","author":"Hu","year":"2012","journal-title":"Bioinformatics"},{"key":"2023012712464699800_btx747-B5","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":"2023012712464699800_btx747-B6","doi-asserted-by":"crossref","first-page":"1029","DOI":"10.1093\/imanum\/drs019","article-title":"A fast algorithm for matrix balancing","volume":"33","author":"Knight","year":"2013","journal-title":"IMA J. Numer. Anal"},{"key":"2023012712464699800_btx747-B7","doi-asserted-by":"crossref","first-page":"1","DOI":"10.2307\/1269547","article-title":"Zero-inflated Poisson regression, with an application to defects in manufacturing","volume":"34","author":"Lambert","year":"1992","journal-title":"Technometrics"},{"key":"2023012712464699800_btx747-B8","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":"2023012712464699800_btx747-B9","doi-asserted-by":"crossref","first-page":"341","DOI":"10.1016\/0304-4076(86)90002-3","article-title":"Specification and testing of some modified count data models","volume":"33","author":"Mullahy","year":"1986","journal-title":"J. Econometrics"},{"key":"2023012712464699800_btx747-B10","doi-asserted-by":"crossref","first-page":"263","DOI":"10.1038\/nmeth.4155","article-title":"Massively multiplex single-cell Hi-C","volume":"14","author":"Ramani","year":"2017","journal-title":"Nat. Methods"},{"key":"2023012712464699800_btx747-B11","doi-asserted-by":"crossref","first-page":"1665","DOI":"10.1016\/j.cell.2014.11.021","article-title":"A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping","volume":"159","author":"Rao","year":"2014","journal-title":"Cell"},{"key":"2023012712464699800_btx747-B12","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"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/6\/1046\/48913565\/bioinformatics_34_6_1046.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/6\/1046\/48913565\/bioinformatics_34_6_1046.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,27]],"date-time":"2023-01-27T13:39:03Z","timestamp":1674826743000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/34\/6\/1046\/4653697"}},"subtitle":[],"editor":[{"given":"John","family":"Hancock","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2017,11,23]]},"references-count":12,"journal-issue":{"issue":"6","published-print":{"date-parts":[[2018,3,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btx747","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"type":"print","value":"1367-4803"},{"type":"electronic","value":"1367-4811"}],"subject":[],"published-other":{"date-parts":[[2018,3,15]]},"published":{"date-parts":[[2017,11,23]]}}}