{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,30]],"date-time":"2026-04-30T03:10:36Z","timestamp":1777518636315,"version":"3.51.4"},"reference-count":28,"publisher":"Springer Science and Business Media LLC","issue":"S3","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2017,3]]},"DOI":"10.1186\/s12859-017-1464-8","type":"journal-article","created":{"date-parts":[[2017,3,14]],"date-time":"2017-03-14T05:07:24Z","timestamp":1489468044000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":21,"title":["Pysim-sv: a package for simulating structural variation data with GC-biases"],"prefix":"10.1186","volume":"18","author":[{"given":"Yuchao","family":"Xia","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yun","family":"Liu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Minghua","family":"Deng","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ruibin","family":"Xi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2017,3,14]]},"reference":[{"issue":"7332","key":"1464_CR1","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1038\/nature09708","volume":"470","author":"RE Mills","year":"2011","unstructured":"Mills RE, Walter K, Stewart C, Handsaker RE, Chen K, Alkan C, Abyzov A, Yoon SC, Ye K, Cheetham RK, et al. Mapping copy number variation by population-scale genome sequencing. Nature. 2011; 470(7332):59\u201365.","journal-title":"Nature"},{"key":"1464_CR2","volume-title":"Genomic Elements in Health, Disease and Evolution","author":"C Sismani","year":"2015","unstructured":"Sismani C, Koufaris C, Voskarides K. Copy number variation in human health, disease and evolution. In: Genomic Elements in Health, Disease and Evolution. New York: Springer: 2015. p. 129\u201354."},{"issue":"R2","key":"1464_CR3","doi-asserted-by":"crossref","first-page":"188","DOI":"10.1093\/hmg\/ddq391","volume":"19","author":"L Ding","year":"2010","unstructured":"Ding L, Wendl MC, Koboldt DC, et al. Analysis of next generation genomic data in cancer: accomplishments and challenges. Hum Mol Genet. 2010; 19(R2):188\u201396.","journal-title":"Hum Mol Genet"},{"issue":"1","key":"1464_CR4","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1016\/j.cell.2010.11.055","volume":"144","author":"PJ Stephens","year":"2011","unstructured":"Stephens PJ, Greenman CD, Fu B, Yang F, Bignell GR, Mudie LJ, Pleasance ED, Lau KW, Beare D, Stebbings LA, et al. Massive genomic rearrangement acquired in a single catastrophic event during cancer development. Cell. 2011; 144(1):27\u201340.","journal-title":"Cell"},{"issue":"4","key":"1464_CR5","doi-asserted-by":"crossref","first-page":"919","DOI":"10.1016\/j.cell.2013.04.010","volume":"153","author":"L Yang","year":"2013","unstructured":"Yang L, Luquette LJ, Gehlenborg N, Xi R, Haseley PS, Hsieh CH, Zhang C, Ren X, Protopopov A, Chin L, et al. Diverse mechanisms of somatic structural variations in human cancer genomes. Cell. 2013; 153(4):919\u201329.","journal-title":"Cell"},{"issue":"9","key":"1464_CR6","doi-asserted-by":"crossref","first-page":"677","DOI":"10.1038\/nmeth.1363","volume":"6","author":"K Chen","year":"2009","unstructured":"Chen K, Wallis JW, McLellan MD, Larson DE, Kalicki JM, Pohl CS, McGrath SD, Wendl MC, Zhang Q, Locke DP, et al. BreakDancer: an algorithm for high-resolution mapping of genomic structural variation. Nat Methods. 2009; 6(9):677\u201381.","journal-title":"Nat Methods"},{"issue":"13","key":"1464_CR7","doi-asserted-by":"crossref","first-page":"1679","DOI":"10.1093\/bioinformatics\/btt198","volume":"29","author":"C Bartenhagen","year":"2013","unstructured":"Bartenhagen C, Dugas M. RSVSim: an R\/Bioconductor package for the simulation of structural variations. Bioinformatics. 2013; 29(13):1679\u201381.","journal-title":"Bioinformatics"},{"issue":"1","key":"1464_CR8","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s12859-014-0430-y","volume":"16","author":"M Qin","year":"2015","unstructured":"Qin M, Liu B, Conroy JM, et al. SCNVSim: somatic copy number variation and structure variation simulator. BMC Bioinforma. 2015; 16(1):1\u20136.","journal-title":"BMC Bioinforma"},{"issue":"9","key":"1464_CR9","doi-asserted-by":"crossref","first-page":"1469","DOI":"10.1093\/bioinformatics\/btu828","volume":"31","author":"JC Mu","year":"2015","unstructured":"Mu JC, Mohiyuddin M, Li J, et al. VarSim: a high-fidelity simulation and validation framework for high-throughput genome sequencing with cancer applications. Bioinformatics. 2015; 31(9):1469\u201371.","journal-title":"Bioinformatics"},{"key":"1464_CR10","unstructured":"Yuan X, Zhang J, Yang L. IntSIM: An integrated simulator of next-generation sequencing data. IEEE Trans Biomed Eng. 2016;:1\u201311."},{"issue":"1","key":"1464_CR11","first-page":"1","volume":"15","author":"S Pattnaik","year":"2013","unstructured":"Pattnaik S, Gupta S, Rao AA, Panda B. SinC: an accurate and fast error-model based simulator for snps, indels and cnvs coupled with a read generator for short-read sequence data. Bmc Bioinformatic. 2013; 15(1):1\u20139.","journal-title":"Bmc Bioinformatic"},{"issue":"11","key":"1464_CR12","doi-asserted-by":"crossref","first-page":"1533","DOI":"10.1093\/bioinformatics\/bts187","volume":"28","author":"X Hu","year":"2012","unstructured":"Hu X, Yuan J, Shi Y, Lu J, Liu B, Li Z, Chen Y, Mu D, Zhang H, Li N. pIRS: Profile-based illumina pair-end reads simulator. Bioinformatics. 2012; 28(11):1533\u20135.","journal-title":"Bioinformatics"},{"issue":"13","key":"1464_CR13","doi-asserted-by":"crossref","first-page":"6274","DOI":"10.1093\/nar\/gkw491","volume":"44","author":"R Xi","year":"2016","unstructured":"Xi R, Lee S, Xia Y, et al. Copy number analysis of whole-genome data using BIC-Seq2 and its application to detection of cancer susceptibility variants. Nucleic Acids Res. 2016; 44(13):6274\u201386.","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"1464_CR14","doi-asserted-by":"crossref","first-page":"308","DOI":"10.1093\/nar\/29.1.308","volume":"29","author":"ST Sherry","year":"2001","unstructured":"Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K. dbSNP: the ncbi database of genetic variation. Nucleic Acids Res. 2001; 29(1):308\u201311.","journal-title":"Nucleic Acids Res"},{"issue":"2","key":"1464_CR15","doi-asserted-by":"crossref","first-page":"355","DOI":"10.1038\/sj.bjc.6601894","volume":"91","author":"S Bamford","year":"2004","unstructured":"Bamford S, Dawson E, Forbes S, Clements J, Pettett R, Dogan A, Flanagan A, Teague J, Futreal PA, Stratton M, et al. The COSMIC (catalogue of somatic mutations in cancer) database and website. Br J Cancer. 2004; 91(2):355\u20138.","journal-title":"Br J Cancer"},{"issue":"suppl_1","key":"1464_CR16","doi-asserted-by":"crossref","first-page":"D945","DOI":"10.1093\/nar\/gkq929","volume":"39","author":"SA Forbes","year":"2011","unstructured":"Forbes SA, Bindal N, Bamford S, et al. COSMIC: mining complete cancer genomes in the catalogue of somatic mutations in cancer. Nucleic Acids Res. 2011; 39(suppl_1):D945\u2013D950.","journal-title":"Nucleic Acids Res"},{"issue":"2","key":"1464_CR17","doi-asserted-by":"crossref","first-page":"81","DOI":"10.1007\/s40142-013-0012-8","volume":"1","author":"BB Currall","year":"2013","unstructured":"Currall BB, Chiangmai C, Talkowski ME, Morton CC. Mechanisms for structural variation in the human genome. Curr Genet Med Rep. 2013; 1(2):81\u201390.","journal-title":"Curr Genet Med Rep"},{"issue":"D1","key":"1464_CR18","doi-asserted-by":"crossref","first-page":"64","DOI":"10.1093\/nar\/gks1048","volume":"41","author":"LR Meyer","year":"2013","unstructured":"Meyer LR, Zweig AS, Hinrichs AS, Karolchik D, Kuhn RM, Wong M, Sloan CA, Rosenbloom KR, Roe G, Rhead B, et al. The UCSC genome browser database: extensions and updates 2013. Nucleic Acids Res. 2013; 41(D1):64\u20139.","journal-title":"Nucleic Acids Res"},{"issue":"3-4","key":"1464_CR19","doi-asserted-by":"crossref","first-page":"69","DOI":"10.1007\/s11568-009-9028-2","volume":"2","author":"D Kumar","year":"2008","unstructured":"Kumar D. Disorders of the genome architecture: a review. Genomic Med. 2008; 2(3-4):69\u201376.","journal-title":"Genomic Med"},{"issue":"4","key":"1464_CR20","doi-asserted-by":"crossref","first-page":"280","DOI":"10.1038\/35066065","volume":"2","author":"T Hassold","year":"2001","unstructured":"Hassold T, Hunt P. To err (meiotically) is human: the genesis of human aneuploidy. Nat Rev Genet. 2001; 2(4):280\u201391.","journal-title":"Nat Rev Genet"},{"issue":"5","key":"1464_CR21","doi-asserted-by":"crossref","first-page":"822","DOI":"10.1016\/j.cell.2009.08.017","volume":"138","author":"M Shackleton","year":"2009","unstructured":"Shackleton M, Quintana E, Fearon ER, Morrison SJ. Heterogeneity in cancer: cancer stem cells versus clonal evolution. Cell. 2009; 138(5):822\u20139.","journal-title":"Cell"},{"issue":"4","key":"1464_CR22","doi-asserted-by":"crossref","first-page":"593","DOI":"10.1093\/bioinformatics\/btr708","volume":"28","author":"W Huang","year":"2012","unstructured":"Huang W, Li L, Myers JR, Marth GT. ART: a next-generation sequencing read simulator. Bioinformatics. 2012; 28(4):593\u20134.","journal-title":"Bioinformatics"},{"issue":"9","key":"1464_CR23","doi-asserted-by":"crossref","first-page":"1297","DOI":"10.1101\/gr.107524.110","volume":"20","author":"A McKenna","year":"2010","unstructured":"McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, et al. The genome analysis toolkit: a mapreduce framework for analyzing next-generation dna sequencing data. Genome Res. 2010; 20(9):1297\u2013303.","journal-title":"Genome Res"},{"issue":"17","key":"1464_CR24","doi-asserted-by":"crossref","first-page":"2283","DOI":"10.1093\/bioinformatics\/btp373","volume":"25","author":"DC Koboldt","year":"2009","unstructured":"Koboldt DC, Chen K, Wylie T, Larson DE, McLellan MD, Mardis ER, Weinstock GM, Wilson RK, Ding L. VarScan: variant detection in massively parallel sequencing of individual and pooled samples. Bioinformatics. 2009; 25(17):2283\u2013285.","journal-title":"Bioinformatics"},{"issue":"18","key":"1464_CR25","doi-asserted-by":"crossref","first-page":"333","DOI":"10.1093\/bioinformatics\/bts378","volume":"28","author":"T Rausch","year":"2012","unstructured":"Rausch T, Zichner T, Schlattl A, St\u00fctz AM, Benes V, Korbel JO. Delly: structural variant discovery by integrated paired-end and split-read analysis. Bioinformatics. 2012; 28(18):333\u20139.","journal-title":"Bioinformatics"},{"issue":"3","key":"1464_CR26","doi-asserted-by":"crossref","first-page":"22","DOI":"10.1186\/gb-2012-13-3-r22","volume":"13","author":"SS Sindi","year":"2012","unstructured":"Sindi SS, Onal S, Peng LC, Wu HT, Raphael BJ. An integrative probabilistic model for identification of structural variation in sequencing data. Genome Biol. 2012; 13(3):22.","journal-title":"Genome Biol"},{"issue":"46","key":"1464_CR27","doi-asserted-by":"crossref","first-page":"1128","DOI":"10.1073\/pnas.1110574108","volume":"108","author":"R Xi","year":"2011","unstructured":"Xi R, Hadjipanayis AG, Luquette LJ, Kim TM, Lee E, Zhang J, Johnson MD, Muzny DM, Wheeler DA, Gibbs RA, et al. Copy number variation detection in whole-genome sequencing data using the bayesian information criterion. Proc Natl Acad Sci. 2011; 108(46):1128\u201336.","journal-title":"Proc Natl Acad Sci"},{"issue":"14","key":"1464_CR28","doi-asserted-by":"crossref","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","volume":"25","author":"H Li","year":"2009","unstructured":"Li H, Durbin R. Fast and accurate short read alignment with burrows\u2013wheeler transform. Bioinformatics. 2009; 25(14):1754\u201360.","journal-title":"Bioinformatics"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-017-1464-8.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,9,19]],"date-time":"2019-09-19T14:02:36Z","timestamp":1568901756000},"score":1,"resource":{"primary":{"URL":"http:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-017-1464-8"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017,3]]},"references-count":28,"journal-issue":{"issue":"S3","published-print":{"date-parts":[[2017,3]]}},"alternative-id":["1464"],"URL":"https:\/\/doi.org\/10.1186\/s12859-017-1464-8","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2017,3]]},"article-number":"53"}}