{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,10]],"date-time":"2026-01-10T02:24:15Z","timestamp":1768011855983,"version":"3.49.0"},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"15","license":[{"start":{"date-parts":[[2017,4,27]],"date-time":"2017-04-27T00:00:00Z","timestamp":1493251200000},"content-version":"vor","delay-in-days":5,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"funder":[{"DOI":"10.13039\/100000026","name":"National Institute on Drug Abuse","doi-asserted-by":"publisher","award":["R01DA016750"],"award-info":[{"award-number":["R01DA016750"]}],"id":[{"id":"10.13039\/100000026","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["DMS-1309507"],"award-info":[{"award-number":["DMS-1309507"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100008899","name":"University of South Carolina","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100008899","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,8,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Chromosomal copy number variation (CNV) refers to a polymorphism that a DNA segment presents deletion or duplication in the population. The computational algorithms developed to identify this type of variation are usually of high computational complexity. Here we present a user-friendly R package, modSaRa, designed to perform copy number variants identification. The package is developed based on a change-point based method with optimal computational complexity and desirable accuracy. The current version of modSaRa package is a comprehensive tool with integration of preprocessing steps and main CNV calling steps.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and Implementation<\/jats:title>\n                  <jats:p>modSaRa is an R package written in R, C\u2009++\u2009and Rcpp and is now freely available for download at http:\/\/c2s2.yale.edu\/software\/modSaRa.<\/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\/btx212","type":"journal-article","created":{"date-parts":[[2017,4,25]],"date-time":"2017-04-25T19:11:59Z","timestamp":1493147519000},"page":"2384-2385","source":"Crossref","is-referenced-by-count":11,"title":["modSaRa: a computationally efficient R package for CNV identification"],"prefix":"10.1093","volume":"33","author":[{"given":"Feifei","family":"Xiao","sequence":"first","affiliation":[{"name":"Department of Epidemiology and Biostatistics, University of South Carolina, Columbia, SC, USA"}]},{"given":"Yue","family":"Niu","sequence":"additional","affiliation":[{"name":"Department of Mathematics, University of Arizona, Tucson, AZ, USA"}]},{"given":"Ning","family":"Hao","sequence":"additional","affiliation":[{"name":"Department of Mathematics, University of Arizona, Tucson, AZ, USA"}]},{"given":"Yanxun","family":"Xu","sequence":"additional","affiliation":[{"name":"Department of Applied Mathematics & Statistics, Johns Hopkins University, Baltimore, MD, USA"}]},{"given":"Zhilin","family":"Jin","sequence":"additional","affiliation":[{"name":"Department of Applied Mathematics & Statistics, Johns Hopkins University, Baltimore, MD, USA"}]},{"given":"Heping","family":"Zhang","sequence":"additional","affiliation":[{"name":"Department of Biostatistics, Yale School of Public Health, New Haven, CT, USA"}]}],"member":"286","published-online":{"date-parts":[[2017,4,22]]},"reference":[{"key":"2023070101190097100_btx212-B1","doi-asserted-by":"crossref","first-page":"5012","DOI":"10.1093\/hmg\/ddr415","article-title":"Genome-wide association study identifies novel loci predisposing to cutaneous melanoma","volume":"20","author":"Amos","year":"2011","journal-title":"Hum. Mol. Genet"},{"key":"2023070101190097100_btx212-B2","doi-asserted-by":"crossref","first-page":"301","DOI":"10.1093\/biomet\/87.2.301","article-title":"Multiple changepoint fitting via quasilikelihood, with application to DNA sequence segmentation","volume":"87","author":"Braun","year":"2000","journal-title":"Biometrika"},{"key":"2023070101190097100_btx212-B3","doi-asserted-by":"crossref","first-page":"306","DOI":"10.1159\/000354737","article-title":"Analysis of germline gene copy number variants of patients with sporadic pancreatic adenocarcinoma reveals specific variations","volume":"85","author":"Fanale","year":"2013","journal-title":"Oncology"},{"key":"2023070101190097100_btx212-B5","doi-asserted-by":"crossref","first-page":"1306","DOI":"10.1214\/12-AOAS539","article-title":"The screening and ranking algorithm to detect dna copy number variations","volume":"6","author":"Niu","year":"2012","journal-title":"Ann. Appl. Stat"},{"key":"2023070101190097100_btx212-B6","doi-asserted-by":"crossref","first-page":"557","DOI":"10.1093\/biostatistics\/kxh008","article-title":"Circular binary segmentation for the analysis of array-based DNA copy number data","volume":"5","author":"Olshen","year":"2004","journal-title":"Biostatistics"},{"key":"2023070101190097100_btx212-B7","doi-asserted-by":"crossref","first-page":"607","DOI":"10.1016\/j.ajhg.2013.09.001","article-title":"Identification of small exonic CNV from whole-exome sequence data and application to autism spectrum disorder","volume":"93","author":"Poultney","year":"2013","journal-title":"Am. J. Hum. Genet"},{"key":"2023070101190097100_btx212-B8","first-page":"270","article-title":"Detection of the disorder in multidimensional random-processes","volume":"259","author":"Vostrikova","year":"1981","journal-title":"Dokl Akad Nauk Sssr+"},{"key":"2023070101190097100_btx212-B9","doi-asserted-by":"crossref","first-page":"1341","DOI":"10.1093\/bioinformatics\/btu850","article-title":"Modified screening and ranking algorithm for copy number variation detection","volume":"31","author":"Xiao","year":"2015","journal-title":"Bioinformatics"},{"key":"2023070101190097100_btx212-B10","first-page":"370","article-title":"Least-squares estimation of a step function","volume":"51","author":"Yao","year":"1989","journal-title":"Sankhya A"},{"key":"2023070101190097100_btx212-B11","doi-asserted-by":"crossref","first-page":"e1003365.","DOI":"10.1371\/journal.pgen.1003365","article-title":"Rare copy number variants are a common cause of short stature","volume":"9","author":"Zahnleiter","year":"2013","journal-title":"PLoS Genet"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/33\/15\/2384\/50756535\/bioinformatics_33_15_2384.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/33\/15\/2384\/50756535\/bioinformatics_33_15_2384.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,7,1]],"date-time":"2023-07-01T01:19:15Z","timestamp":1688174355000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/33\/15\/2384\/3768591"}},"subtitle":[],"editor":[{"given":"John","family":"Hancock","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2017,4,22]]},"references-count":10,"journal-issue":{"issue":"15","published-print":{"date-parts":[[2017,8,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btx212","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2017,8,1]]},"published":{"date-parts":[[2017,4,22]]}}}