{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T11:52:30Z","timestamp":1674647550888},"reference-count":26,"publisher":"Springer Science and Business Media LLC","issue":"S11","license":[{"start":{"date-parts":[[2010,12,1]],"date-time":"2010-12-01T00:00:00Z","timestamp":1291161600000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2010,12]]},"DOI":"10.1186\/1471-2105-11-s11-s12","type":"journal-article","created":{"date-parts":[[2011,1,6]],"date-time":"2011-01-06T02:15:03Z","timestamp":1294280103000},"source":"Crossref","is-referenced-by-count":6,"title":["Detection and reconstruction of tandemly organized de novo copy number variations"],"prefix":"10.1186","volume":"11","author":[{"given":"Dan","family":"He","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nicholas","family":"Furlotte","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Eleazar","family":"Eskin","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2010,12,14]]},"reference":[{"issue":"9","key":"4300_CR1","doi-asserted-by":"publisher","first-page":"949","DOI":"10.1038\/ng1416","volume":"36","author":"A Iafrate","year":"2004","unstructured":"Iafrate A, Feuk L, Rivera M, Listewnik M, Donahoe P, Qi Y, Scherer S, Lee C: Detection of large-scale variation in the human genome. Nature genetics 2004, 36(9):949\u2013951. 10.1038\/ng1416","journal-title":"Nature genetics"},{"issue":"7","key":"4300_CR2","doi-asserted-by":"publisher","first-page":"727","DOI":"10.1038\/ng1562","volume":"37","author":"E Tuzun","year":"2005","unstructured":"Tuzun E, Sharp A, Bailey J, Kaul R, Morrison V, Pertz L, Haugen E, Hayden H, Albertson D, Pinkel D, et al.: Fine-scale structural variation of the human genome. Nature genetics 2005, 37(7):727\u2013732. 10.1038\/ng1562","journal-title":"Nature genetics"},{"key":"4300_CR3","doi-asserted-by":"publisher","first-page":"451","DOI":"10.1146\/annurev.genom.9.081307.164217","volume":"10","author":"F Zhang","year":"2009","unstructured":"Zhang F, Gu W, Hurles M, Lupski J: Copy Number Variation in Human Health, Disease, and Evolution. Annual Review of Genomics and Human Genetics 2009, 10: 451\u2013481. 10.1146\/annurev.genom.9.081307.164217","journal-title":"Annual Review of Genomics and Human Genetics"},{"key":"4300_CR4","doi-asserted-by":"publisher","first-page":"S37","DOI":"10.1038\/ng2080","volume":"29","author":"SA McCarroll","year":"2007","unstructured":"McCarroll SA, Alshuler D: Copy-number variation and association studies of human disease. Nature Supplement 2007, 29: S37-S42. 10.1038\/ng2080","journal-title":"Nature Supplement"},{"issue":"5813","key":"4300_CR5","doi-asserted-by":"publisher","first-page":"848","DOI":"10.1126\/science.1136678","volume":"315","author":"B Stranger","year":"2007","unstructured":"Stranger B, Forrest M, Dunning M, Ingle C, Beazley C, Thorne N, Redon R, Bird C, de Grassi A, Lee C, et al.: Relative impact of nucleotide and copy number variation on gene expression phenotypes. Science 2007, 315(5813):848. 10.1126\/science.1136678","journal-title":"Science"},{"issue":"7078","key":"4300_CR6","doi-asserted-by":"publisher","first-page":"851","DOI":"10.1038\/nature04489","volume":"439","author":"T Aitman","year":"2006","unstructured":"Aitman T, Dong R, Vyse T, Norsworthy P, Johnson M, Smith J, Mangion J, Roberton-Lowe C, Marshall A, Petretto E, et al.: Copy number polymorphism in Fcgr3 predisposes to glomerulonephritis in rats and humans. Nature 2006, 439(7078):851\u2013855. 10.1038\/nature04489","journal-title":"Nature"},{"issue":"5823","key":"4300_CR7","doi-asserted-by":"publisher","first-page":"445","DOI":"10.1126\/science.1138659","volume":"316","author":"J Sebat","year":"2007","unstructured":"Sebat J, Lakshmi B, Malhotra D, Troge J, Lese-Martin C, Walsh T, Yamrom B, Yoon S, Krasnitz A, Kendall J, et al.: Strong association of de novo copy number mutations with autism. Science 2007, 316(5823):445. 10.1126\/science.1138659","journal-title":"Science"},{"issue":"5714","key":"4300_CR8","doi-asserted-by":"publisher","first-page":"1434","DOI":"10.1126\/science.1101160","volume":"307","author":"E Gonzalez","year":"2005","unstructured":"Gonzalez E, Kulkarni H, Bolivar H, Mangano A, Sanchez R, Catano G, Nibbs R, Freedman B, Quinones M, Bamshad M, et al.: The influence of CCL3L1 gene-containing segmental duplications on HIV-1\/AIDS susceptibility. Science 2005, 307(5714):1434. 10.1126\/science.1101160","journal-title":"Science"},{"key":"4300_CR9","first-page":"218","volume-title":"Combinatorial Algorithms for Structural Variation Detection in High Throughput Sequenced Genomes","author":"S Sahinalp","year":"2009","unstructured":"Sahinalp S: Combinatorial Algorithms for Structural Variation Detection in High Throughput Sequenced Genomes. 2009, 218."},{"issue":"13","key":"4300_CR10","doi-asserted-by":"publisher","first-page":"7696","DOI":"10.1073\/pnas.1232418100","volume":"100","author":"S Volik","year":"2003","unstructured":"Volik S, Zhao S, Chin K, Brebner J, Herndon D, Tao Q, Kowbel D, Huang G, Lapuk A, Kuo W, et al.: End-sequence profiling: sequence-based analysis of aberrant genomes. Proceedings of the National Academy of Sciences 2003, 100(13):7696. 10.1073\/pnas.1232418100","journal-title":"Proceedings of the National Academy of Sciences"},{"issue":"5849","key":"4300_CR11","doi-asserted-by":"publisher","first-page":"420","DOI":"10.1126\/science.1149504","volume":"318","author":"J Korbel","year":"2007","unstructured":"Korbel J, Urban A, Affourtit J, Godwin B, Grubert F, Simons J, Kim P, Palejev D, Carriero N, Du L, et al.: Paired-end mapping reveals extensive structural variation in the human genome. Science 2007, 318(5849):420. 10.1126\/science.1149504","journal-title":"Science"},{"issue":"7191","key":"4300_CR12","doi-asserted-by":"publisher","first-page":"56","DOI":"10.1038\/nature06862","volume":"453","author":"J Kidd","year":"2008","unstructured":"Kidd J, Cooper G, Donahue W, Hayden H, Sampas N, Graves T, Hansen N, Teague B, Alkan C, Antonacci F, et al.: Mapping and sequencing of structural variation from eight human genomes. Nature 2008, 453(7191):56\u201364. 10.1038\/nature06862","journal-title":"Nature"},{"issue":"13","key":"4300_CR13","doi-asserted-by":"publisher","first-page":"i59","DOI":"10.1093\/bioinformatics\/btn176","volume":"24","author":"S Lee","year":"2008","unstructured":"Lee S, Cheran E, Brudno M: A robust framework for detecting structural variations in a genome. Bioinformatics 2008, 24(13):i59. 10.1093\/bioinformatics\/btn176","journal-title":"Bioinformatics"},{"issue":"10","key":"4300_CR14","doi-asserted-by":"publisher","first-page":"2291","DOI":"10.1101\/gr.1349003","volume":"13","author":"R Lucito","year":"2003","unstructured":"Lucito R, Healy J, Alexander J, Reiner A, Esposito D, Chi M, Rodgers L, Brady A, Sebat J, Troge J, et al.: Representational oligonucleotide microarray analysis: a high-resolution method to detect genome copy number variation. Genome Research 2003, 13(10):2291. 10.1101\/gr.1349003","journal-title":"Genome Research"},{"issue":"23","key":"4300_CR15","doi-asserted-by":"publisher","first-page":"2773","DOI":"10.1093\/bioinformatics\/btn517","volume":"24","author":"P Chen","year":"2008","unstructured":"Chen P, Liu H, Chao K: CNVDetector: locating copy number variations using array CGH data. Bioinformatics 2008, 24(23):2773. 10.1093\/bioinformatics\/btn517","journal-title":"Bioinformatics"},{"issue":"46","key":"4300_CR16","doi-asserted-by":"publisher","first-page":"16292","DOI":"10.1073\/pnas.0407247101","volume":"101","author":"R Daruwala","year":"2004","unstructured":"Daruwala R, Rudra A, Ostrer H, Lucito R, Wigler M, Mishra B: A versatile statistical analysis algorithm to detect genome copy number variation. Proceedings of the National Academy of Sciences of the United States of America 2004, 101(46):16292. 10.1073\/pnas.0407247101","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"issue":"19","key":"4300_CR17","doi-asserted-by":"publisher","first-page":"3763","DOI":"10.1093\/bioinformatics\/bti611","volume":"21","author":"W Lai","year":"2005","unstructured":"Lai W, Johnson M, Kucherlapati R, Park P: Comparative analysis of algorithms for identifying amplifications and deletions in array CGH data. Bioinformatics 2005, 21(19):3763. 10.1093\/bioinformatics\/bti611","journal-title":"Bioinformatics"},{"key":"4300_CR18","volume-title":"New Genomics Technology: Copy Number Variation Analysis Methods","author":"A Mah","year":"2008","unstructured":"Mah A, Brutlag D: New Genomics Technology: Copy Number Variation Analysis Methods. 2008."},{"key":"4300_CR19","doi-asserted-by":"publisher","first-page":"99","DOI":"10.1038\/nmeth.1276","volume":"6","author":"D Chiang","year":"2009","unstructured":"Chiang D, Getz G, Jaffe D, O\u2019Kelly M, Zhao X, Carter S, Russ C, Nusbaum C, Meyerson M, Lander E: High-resolution mapping of copy-number alterations with massively parallel sequencing. Nature methods 2009, 6: 99. 10.1038\/nmeth.1276","journal-title":"Nature methods"},{"issue":"14","key":"4300_CR20","doi-asserted-by":"publisher","first-page":"6071","DOI":"10.1158\/0008-5472.CAN-05-0465","volume":"65","author":"Y Nannya","year":"2005","unstructured":"Nannya Y, Sanada M, Nakazaki K, Hosoya N, Wang L, Hangaishi A, Kurokawa M, Chiba S, Bailey D, Kennedy G, et al.: A robust algorithm for copy number detection using high-density oligonucleotide single nucleotide polymorphism genotyping arrays. Cancer research 2005, 65(14):6071. 10.1158\/0008-5472.CAN-05-0465","journal-title":"Cancer research"},{"issue":"11","key":"4300_CR21","doi-asserted-by":"publisher","first-page":"1665","DOI":"10.1101\/gr.6861907","volume":"17","author":"K Wang","year":"2007","unstructured":"Wang K, Li M, Hadley D, Liu R, Glessner J, Grant S, Hakonarson H, Bucan M: PennCNV: an integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data. Genome Research 2007, 17(11):1665. 10.1101\/gr.6861907","journal-title":"Genome Research"},{"issue":"4","key":"4300_CR22","doi-asserted-by":"publisher","first-page":"565","DOI":"10.1093\/bioinformatics\/btp693","volume":"26","author":"J Simpson","year":"2010","unstructured":"Simpson J, McIntyre R, Adams D, Durbin R: Copy number variant detection in inbred strains from short read sequence data. Bioinformatics 2010, 26(4):565\u2013567. 10.1093\/bioinformatics\/btp693","journal-title":"Bioinformatics"},{"key":"4300_CR23","doi-asserted-by":"publisher","first-page":"S13","DOI":"10.1038\/nmeth.1374","volume":"6","author":"P Medvedev","year":"2009","unstructured":"Medvedev P, Stanciu M, Brudno M: Computational methods for discovering structural variation with next-generation sequencing. Nature Methods 2009, 6: S13-S20. 10.1038\/nmeth.1374","journal-title":"Nature Methods"},{"key":"4300_CR24","volume-title":"Genome Research","author":"P Medvedev","year":"2010","unstructured":"Medvedev P, Fiume M, Dzamba M, Smith T, Brudno M: Detecting Copy Number Variation with Mated Short Reads. Genome Research 2010."},{"issue":"7","key":"4300_CR25","doi-asserted-by":"publisher","first-page":"909","DOI":"10.1038\/ng.172","volume":"40","author":"X She","year":"2008","unstructured":"She X, Cheng Z, Z\u201dollner S, Church D, Eichler E: Mouse Segmental Duplication and Copy-Number Variation. Nature genetics 2008, 40(7):909. 10.1038\/ng.172","journal-title":"Nature genetics"},{"issue":"11","key":"4300_CR26","doi-asserted-by":"publisher","first-page":"1851","DOI":"10.1101\/gr.078212.108","volume":"18","author":"H Li","year":"2008","unstructured":"Li H, Ruan J, Durbin R: Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome research 2008, 18(11):1851. 10.1101\/gr.078212.108","journal-title":"Genome research"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-11-S11-S12.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/1471-2105-11-S11-S12\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-11-S11-S12.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,1,22]],"date-time":"2019-01-22T09:07:51Z","timestamp":1548148071000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-11-S11-S12"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2010,12]]},"references-count":26,"journal-issue":{"issue":"S11","published-print":{"date-parts":[[2010,12]]}},"alternative-id":["4300"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-11-s11-s12","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2010,12]]},"article-number":"S12"}}