{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,20]],"date-time":"2026-02-20T09:35:30Z","timestamp":1771580130741,"version":"3.50.1"},"reference-count":30,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2014,4,14]],"date-time":"2014-04-14T00:00:00Z","timestamp":1397433600000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2014,12]]},"DOI":"10.1186\/1471-2105-15-109","type":"journal-article","created":{"date-parts":[[2014,4,14]],"date-time":"2014-04-14T23:01:51Z","timestamp":1397516511000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":66,"title":["Copy number variation detection using next generation sequencing read counts"],"prefix":"10.1186","volume":"15","author":[{"given":"Heng","family":"Wang","sequence":"first","affiliation":[]},{"given":"Dan","family":"Nettleton","sequence":"additional","affiliation":[]},{"given":"Kai","family":"Ying","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2014,4,14]]},"reference":[{"key":"6359_CR1","first-page":"3","volume":"6","author":"S Banerjee","year":"2011","unstructured":"Banerjee S, Oldridge D, Poptsova M, Hussain WM, Chakravarty D, Demichelis F: A computational framework discovers new copy number variants with functional importance. PLoS ONE. 2011, 6: 3-","journal-title":"PLoS ONE"},{"key":"6359_CR2","doi-asserted-by":"publisher","first-page":"18","DOI":"10.1016\/j.ymeth.2009.06.001","volume":"49","author":"O Gokcumen","year":"2009","unstructured":"Gokcumen O, Lee C: Copy number variants (CNVs) in primate species using array-based comparative genomic hybridization. Methods. 2009, 49: 18-25. 10.1016\/j.ymeth.2009.06.001.","journal-title":"Methods"},{"key":"6359_CR3","doi-asserted-by":"publisher","first-page":"1112","DOI":"10.1126\/science.1178534","volume":"326","author":"PS Schnable","year":"2009","unstructured":"Schnable PS, Ware D, Fulton RS, Stein JC, Wei F, Pasternak S, Liang C, Zhang J, Fulton L, Graves T, Minx P, Reily A, Courtney L, Kruchowski S, Tomlinson C, Strong C, Delehaunty K, Fronick C, Courtney B, Rock S, Belter E, Du F, Kim K, Abbott R, Cotton M, Levy A, Marchetto P, Ochoa K, Jackson S, Gillam B, et al: The B73 maize genome: complexity, diversity, and dynamics. Science. 2009, 326: 1112-1115. 10.1126\/science.1178534.","journal-title":"Science"},{"key":"6359_CR4","doi-asserted-by":"publisher","first-page":"172","DOI":"10.1016\/j.pbi.2006.01.013","volume":"9","author":"ES Buckler","year":"2006","unstructured":"Buckler ES, Gaut BS, McMullen MD: Molecular and functional diversity of maize. Curr Opin Plant Biol. 2006, 9: 172-176. 10.1016\/j.pbi.2006.01.013.","journal-title":"Curr Opin Plant Biol"},{"key":"6359_CR5","doi-asserted-by":"publisher","first-page":"1689","DOI":"10.1101\/gr.109165.110","volume":"20","author":"RA Swanson-Wagner","year":"2010","unstructured":"Swanson-Wagner RA, Eichten SR, Kumari S, Tiffin P, Stein JC, Ware D, Nathan M, Springer NM: Pervasive gene content variation and copy number variation in maize and its undomesticated progenitor. Genome Res. 2010, 20: 1689-1699. 10.1101\/gr.109165.110.","journal-title":"Genome Res"},{"key":"6359_CR6","doi-asserted-by":"publisher","first-page":"355","DOI":"10.1007\/s00122-009-1128-9","volume":"120","author":"A Belo","year":"2010","unstructured":"Belo A, Beatty MK, Hondred D, Fengler KA, Li B, Rafalski A: Allelic Genome structural variation in maize detected by array comparative genome hybridization. Theor Appl Genet. 2010, 120: 355-367. 10.1007\/s00122-009-1128-9.","journal-title":"Theor Appl Genet"},{"key":"6359_CR7","doi-asserted-by":"publisher","first-page":"11","DOI":"10.1371\/journal.pgen.1000734","volume":"5","author":"NM Springer","year":"2009","unstructured":"Springer NM, Ying K, Fu Y, Ji T, Yeh CT, Jia Y, Wu W, Richmond T, Kitzman J, Rosenbaum H, Iniguez AL, Barbazuk WB, Jeddeloh JA, Nettleton D, Schnable PS: Maize inbreds exhibit high levels of copy number variation (CNV) and presence\/absence variation (PAV) in genome content. PLoS Genet. 2009, 5: 11-","journal-title":"PLoS Genet"},{"issue":"4","key":"6359_CR8","doi-asserted-by":"publisher","first-page":"399","DOI":"10.1002\/(SICI)1098-2264(199712)20:4<399::AID-GCC12>3.0.CO;2-I","volume":"20","author":"S Solinas-Toldo","year":"1997","unstructured":"Solinas-Toldo S, Lampel S, Stilgenbauer S, Nickolenko J, Benner A, Dohner H, Cremer T, Lichter P: Matrix-based comparative genomic hybridization: biochips to screen for genomic imbalances. Gene Chromosome Canc. 1997, 20 (4): 399-407. 10.1002\/(SICI)1098-2264(199712)20:4<399::AID-GCC12>3.0.CO;2-I.","journal-title":"Gene Chromosome Canc"},{"key":"6359_CR9","doi-asserted-by":"publisher","first-page":"85","DOI":"10.1038\/nrg1767","volume":"7","author":"L Feuk","year":"2006","unstructured":"Feuk L, Carson AR, Scherer SW: Structural variation in the human genome. Nat Rev Genet. 2006, 7: 85-97.","journal-title":"Nat Rev Genet"},{"key":"6359_CR10","doi-asserted-by":"publisher","first-page":"368","DOI":"10.1504\/IJCBDD.2008.022208","volume":"1","author":"NE Wineinger","year":"2008","unstructured":"Wineinger NE, Kennedy RE, Erickson SW, Wojczynski MK, Bruder CE, Tiwari HK: Statistical issues in the analysis of DNA copy number variations. Int J Comput Biol Drug Des. 2008, 1: 368-395. 10.1504\/IJCBDD.2008.022208.","journal-title":"Int J Comput Biol Drug Des"},{"key":"6359_CR11","doi-asserted-by":"publisher","first-page":"13","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. Nat Methods. 2009, 6: 13-20. 10.1038\/nmeth.1374.","journal-title":"Nat Methods"},{"issue":"3","key":"6359_CR12","doi-asserted-by":"publisher","first-page":"174","DOI":"10.1093\/bfgp\/elp013","volume":"8","author":"PJ Hurd","year":"2009","unstructured":"Hurd PJ, Nelson CJ: Advantages of next-generation sequencing versus the microarray in epigenetic research. Brief Funct Genomics. 2009, 8 (3): 174-183. 10.1093\/bfgp\/elp013.","journal-title":"Brief Funct Genomics"},{"issue":"9","key":"6359_CR13","doi-asserted-by":"publisher","first-page":"1486","DOI":"10.1021\/tx200103b","volume":"24","author":"Z Su","year":"2011","unstructured":"Su Z, Li Z, Chen T, Li QZ, Fang H, Ding D, Ge W, Ning B, Hong H, Perkins RG, Tong W, Shi L: Comparing next-generation sequencing and microarray technologies in a toxicological study of the effects of aristolochic acid on rat kidneys. Chem Res Toxicol. 2011, 24 (9): 1486-1493. 10.1021\/tx200103b.","journal-title":"Chem Res Toxicol"},{"key":"6359_CR14","doi-asserted-by":"publisher","first-page":"677","DOI":"10.1038\/nmeth.1276","volume":"6","author":"DY Chiang","year":"2009","unstructured":"Chiang DY, Getz G, Jaffe DB, O\u2019Kelly MJ, Zhao X, Carter SL, Russ C, Nusbaum C, Meyerson M, Lander ES: High-resolution mapping of copy-number alterations with massively parallel sequencing. Nat Methods. 2009, 6: 677-681. 10.1038\/nmeth.1363.","journal-title":"Nat Methods"},{"key":"6359_CR15","doi-asserted-by":"publisher","first-page":"1586","DOI":"10.1101\/gr.092981.109","volume":"19","author":"S Yoon","year":"2007","unstructured":"Yoon S, Xuan Z, Makarov V, Ye K, Sebat J: Sensitive and accurate detection of copy number variants using read depth of coverage. Genome Res. 2007, 19: 1586-1592.","journal-title":"Genome Res"},{"key":"6359_CR16","doi-asserted-by":"publisher","first-page":"432","DOI":"10.1186\/1471-2105-11-432","volume":"11","author":"TM Kim","year":"2010","unstructured":"Kim TM, Luquette LJ, Xi R, Park PJ: rSW-seq: algorithm for detection of copy number alterations in deep sequencing data. BMC Bioinformatics. 2010, 11: 432-10.1186\/1471-2105-11-432.","journal-title":"BMC Bioinformatics"},{"key":"6359_CR17","doi-asserted-by":"publisher","first-page":"e65","DOI":"10.1093\/nar\/gkr068","volume":"39","author":"A Magi","year":"2011","unstructured":"Magi A, Benelli M, Yoon S, Roviello F, Torricelli F: Detecting common copy number variants in high-throughput sequencing data by using JointSLM algorithm. Nucleic Acids Res. 2011, 39: e65-10.1093\/nar\/gkr068.","journal-title":"Nucleic Acids Res"},{"key":"6359_CR18","doi-asserted-by":"publisher","first-page":"3051","DOI":"10.1093\/bioinformatics\/btq587","volume":"26","author":"S Ivakhno","year":"2010","unstructured":"Ivakhno S, Royce T, Cox AJ, Evers DJ, Cheetham RK, Tavare S: CNAseg - a novel framework for identification of copy number changes in cancer from second-generation sequencing data. Bioinformatics. 2010, 26: 3051-3058. 10.1093\/bioinformatics\/btq587.","journal-title":"Bioinformatics"},{"key":"6359_CR19","doi-asserted-by":"publisher","first-page":"80","DOI":"10.1186\/1471-2105-10-80","volume":"10","author":"C Xie","year":"2009","unstructured":"Xie C, Tammi MT: CNV-seq, a new method to detect copy number variation using high-throughtput sequencing. BMC Bioinformatics. 2009, 10: 80-10.1186\/1471-2105-10-80.","journal-title":"BMC Bioinformatics"},{"issue":"6","key":"6359_CR20","doi-asserted-by":"publisher","first-page":"1554","DOI":"10.1214\/aoms\/1177699147","volume":"37","author":"LE Baum","year":"1966","unstructured":"Baum LE, Petrie T: Statistical inference for proba-bilistic functions of finite state Markov chains. Ann Math Stat. 1966, 37 (6): 1554-1563. 10.1214\/aoms\/1177699147.","journal-title":"Ann Math Stat"},{"issue":"3","key":"6359_CR21","doi-asserted-by":"publisher","first-page":"360","DOI":"10.1090\/S0002-9904-1967-11751-8","volume":"73","author":"LE Baum","year":"1967","unstructured":"Baum LE, Eagon JA: An inequality with applications to statistical estimation for probabilistic functions of a Markov process and to a model for ecology. Bull Am Math Soc. 1967, 73 (3): 360-363. 10.1090\/S0002-9904-1967-11751-8.","journal-title":"Bull Am Math Soc"},{"issue":"1","key":"6359_CR22","doi-asserted-by":"publisher","first-page":"164","DOI":"10.1214\/aoms\/1177697196","volume":"41","author":"LE Baum","year":"1970","unstructured":"Baum LE, Petrie T, Soules G, Weiss N: A maximization technique occurring in the statistical analysis of probabilistic functions of Markov chains. Ann Math Stat. 1970, 41 (1): 164-171. 10.1214\/aoms\/1177697196.","journal-title":"Ann Math Stat"},{"key":"6359_CR23","first-page":"1","volume-title":"Inequalities III: Proceedings of the Third Symposium on Inequalities","author":"LE Baum","year":"1972","unstructured":"Baum LE: An inequality and associated maximization technique in statistical estimation for probabilistic functions of Markov processes. Inequalities III: Proceedings of the Third Symposium on Inequalities. Edited by: Shisha O. 1972, New York: Academic Press, 1-8."},{"key":"6359_CR24","doi-asserted-by":"publisher","first-page":"1144","DOI":"10.1093\/bioinformatics\/btl089","volume":"22","author":"JC Marioni","year":"2006","unstructured":"Marioni JC, Thorne NP, Tavare S: BioHMM: A heterogeneous Hidden Markov model for segmenting array CGH data. Bioinformatics. 2006, 22: 1144-1146. 10.1093\/bioinformatics\/btl089.","journal-title":"Bioinformatics"},{"issue":"6","key":"6359_CR25","doi-asserted-by":"publisher","first-page":"974","DOI":"10.1101\/gr.114876.110","volume":"21","author":"A Abyzov","year":"2011","unstructured":"Abyzov A, Urban AE, Snyder M, Gerstein M: CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing. Genome Res. 2011, 21 (6): 974-984. 10.1101\/gr.114876.110.","journal-title":"Genome Res"},{"issue":"5956","key":"6359_CR26","doi-asserted-by":"publisher","first-page":"1115","DOI":"10.1126\/science.1177837","volume":"326","author":"MA Gore","year":"2009","unstructured":"Gore MA, Chia JM, Elshire RJ, Sun Q, Ersoz ES, Hurwitz BL, Peiffer JA, McMullen MD, Grills GS, Ross-Ibarra J, Ware DH, Buckler ES: A first-generation haplotype map of maize. Science. 2009, 326 (5956): 1115-1117. 10.1126\/science.1177837.","journal-title":"Science"},{"key":"6359_CR27","doi-asserted-by":"publisher","first-page":"121","DOI":"10.1038\/nrg3642","volume":"15","author":"D Sims","year":"2014","unstructured":"Sims D, Sudbery I, Ilott N, Heger A, Ponting C: Sequencing depth and coverage: key considerations in genomic analyses. Nat Rev Genet. 2014, 15: 121-132. 10.1038\/nrg3642.","journal-title":"Nat Rev Genet"},{"issue":"Suppl 6","key":"6359_CR28","doi-asserted-by":"publisher","first-page":"S16","DOI":"10.1186\/1471-2164-13-S6-S16","volume":"13","author":"A Janevski","year":"2012","unstructured":"Janevski A, Varadan V, Kamalakaran S, Banerjee N, Dimitrova N: Effective normalization for copy number variation detection from whole genome sequencing. BMC Genomics. 2012, 13 (Suppl 6): S16-10.1186\/1471-2164-13-S6-S16.","journal-title":"BMC Genomics"},{"key":"6359_CR29","doi-asserted-by":"publisher","first-page":"480","DOI":"10.1186\/1471-2105-12-480","volume":"12","author":"D Risso","year":"2011","unstructured":"Risso D, Schwartz K, Sherlock G, Dudoit S: GC-content normalization for RNA-seq data. BMC Bioinformatics. 2011, 12: 480-10.1186\/1471-2105-12-480.","journal-title":"BMC Bioinformatics"},{"issue":"1","key":"6359_CR30","doi-asserted-by":"publisher","first-page":"4","DOI":"10.1109\/MASSP.1986.1165342","volume":"3","author":"LR Rabiner","year":"1986","unstructured":"Rabiner LR, Juang BH: An introduction to Hidden Markov Models. IEEE ASSP Mag. 1986, 3 (1): 4-16.","journal-title":"IEEE ASSP Mag"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-15-109.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/1471-2105-15-109\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-15-109.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,1,23]],"date-time":"2019-01-23T00:46:48Z","timestamp":1548204408000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-15-109"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014,4,14]]},"references-count":30,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2014,12]]}},"alternative-id":["6359"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-15-109","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2014,4,14]]},"assertion":[{"value":"15 August 2013","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"2 April 2014","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"14 April 2014","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"109"}}