{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,6]],"date-time":"2026-05-06T08:57:13Z","timestamp":1778057833157,"version":"3.51.4"},"reference-count":15,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":690,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,3,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Genome-wide proximity ligation assays, e.g. Hi-C and its variant TCC, have recently become important tools to study spatial genome organization. Removing biases from chromatin contact matrices generated by such techniques is a critical preprocessing step of subsequent analyses. The continuing decline of sequencing costs has led to an ever-improving resolution of the Hi-C data, resulting in very large matrices of chromatin contacts. Such large-size matrices, however, pose a great challenge on the memory usage and speed of its normalization. Therefore, there is an urgent need for fast and memory-efficient methods for normalization of Hi-C data. We developed Hi-Corrector, an easy-to-use, open source implementation of the Hi-C data normalization algorithm. Its salient features are (i) scalability\u2014the software is capable of normalizing Hi-C data of any size in reasonable times; (ii) memory efficiency\u2014the sequential version can run on any single computer with very limited memory, no matter how little; (iii) fast speed\u2014the parallel version can run very fast on multiple computing nodes with limited local memory.<\/jats:p>\n               <jats:p>Availability and implementation: The sequential version is implemented in ANSI C and can be easily compiled on any system; the parallel version is implemented in ANSI C with the MPI library (a standardized and portable parallel environment designed for solving large-scale scientific problems). The package is freely available at http:\/\/zhoulab.usc.edu\/Hi-Corrector\/.<\/jats:p>\n               <jats:p>Contact: \u00a0alber@usc.edu or xjzhou@usc.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu747","type":"journal-article","created":{"date-parts":[[2014,11,13]],"date-time":"2014-11-13T05:02:10Z","timestamp":1415854930000},"page":"960-962","source":"Crossref","is-referenced-by-count":67,"title":["Hi-Corrector: a fast, scalable and memory-efficient package for normalizing large-scale Hi-C data"],"prefix":"10.1093","volume":"31","author":[{"given":"Wenyuan","family":"Li","sequence":"first","affiliation":[{"name":"Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ke","family":"Gong","sequence":"additional","affiliation":[{"name":"Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Qingjiao","family":"Li","sequence":"additional","affiliation":[{"name":"Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Frank","family":"Alber","sequence":"additional","affiliation":[{"name":"Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xianghong Jasmine","family":"Zhou","sequence":"additional","affiliation":[{"name":"Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2014,11,12]]},"reference":[{"key":"2023020116174628900_btu747-B1","first-page":"301","article-title":"A parallel matrix scaling algorithm","volume-title":"High Performance Computing for Computational Science","author":"Amestoy","year":"2008"},{"key":"2023020116174628900_btu747-B2","doi-asserted-by":"crossref","first-page":"974","DOI":"10.1101\/gr.169417.113","article-title":"Three-dimensional modeling of the P. falciparum genome during the erythrocytic cycle reveals a strong connection between genome architecture and gene expression","volume":"24","author":"Ay","year":"2014","journal-title":"Genome Res."},{"key":"2023020116174628900_btu747-B3","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":"2023020116174628900_btu747-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":"2023020116174628900_btu747-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":"2023020116174628900_btu747-B6","doi-asserted-by":"crossref","first-page":"290","DOI":"10.1038\/nature12644","article-title":"A high-resolution map of the three-dimensional chromatin interactome in human cells","volume":"503","author":"Jin","year":"2013","journal-title":"Nature"},{"key":"2023020116174628900_btu747-B7","doi-asserted-by":"crossref","first-page":"90","DOI":"10.1038\/nbt.2057","article-title":"Genome architectures revealed by tethered chromosome conformation capture and population-based modeling","volume":"30","author":"Kalhor","year":"2012","journal-title":"Nat. Biotechnol."},{"key":"2023020116174628900_btu747-B8","doi-asserted-by":"crossref","first-page":"261","DOI":"10.1137\/060659624","article-title":"The Sinkhorn\u2013Knopp algorithm: convergence and applications","volume":"30","author":"Knight","year":"2008","journal-title":"SIAM J. Matrix Anal. Appl."},{"key":"2023020116174628900_btu747-B9","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":"2012","journal-title":"IMA J. Numer. Anal."},{"key":"2023020116174628900_btu747-B10","doi-asserted-by":"crossref","first-page":"731","DOI":"10.1126\/science.1242059","article-title":"High-resolution mapping of the spatial organization of a bacterial chromosome","volume":"342","author":"Le","year":"2013","journal-title":"Science"},{"key":"2023020116174628900_btu747-B11","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":"2023020116174628900_btu747-B12","doi-asserted-by":"crossref","first-page":"948","DOI":"10.1126\/science.1236083","article-title":"Organization of the mitotic chromosome","volume":"342","author":"Naumova","year":"2013","journal-title":"Science"},{"key":"2023020116174628900_btu747-B13","doi-asserted-by":"crossref","first-page":"i26","DOI":"10.1093\/bioinformatics\/btu268","article-title":"A statistical approach for inferring the 3D structure of the genome","volume":"30","author":"Varoquaux","year":"2014","journal-title":"Bioinformatics"},{"key":"2023020116174628900_btu747-B14","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":"2023020116174628900_btu747-B15","doi-asserted-by":"crossref","first-page":"161","DOI":"10.1007\/BF02023052","article-title":"Vector and parallel computing for matrix balancing","volume":"22","author":"Zenios","year":"1990","journal-title":"Ann. Oper. Res."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/31\/6\/960\/49011380\/bioinformatics_31_6_960.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/31\/6\/960\/49011380\/bioinformatics_31_6_960.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,2]],"date-time":"2023-02-02T00:30:42Z","timestamp":1675297842000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/31\/6\/960\/215261"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014,11,12]]},"references-count":15,"journal-issue":{"issue":"6","published-print":{"date-parts":[[2015,3,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btu747","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2015,3,15]]},"published":{"date-parts":[[2014,11,12]]}}}