{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2022,4,2]],"date-time":"2022-04-02T22:44:10Z","timestamp":1648939450131},"reference-count":31,"publisher":"Springer Science and Business Media LLC","issue":"S1","license":[{"start":{"date-parts":[[2015,1,21]],"date-time":"2015-01-21T00:00:00Z","timestamp":1421798400000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2015,12]]},"DOI":"10.1186\/1471-2105-16-s1-s4","type":"journal-article","created":{"date-parts":[[2019,12,11]],"date-time":"2019-12-11T02:00:51Z","timestamp":1576029651000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Estimating copy numbers of alleles from population-scale high-throughput sequencing data"],"prefix":"10.1186","volume":"16","author":[{"given":"Takahiro","family":"Mimori","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Naoki","family":"Nariai","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kaname","family":"Kojima","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yukuto","family":"Sato","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yosuke","family":"Kawai","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yumi","family":"Yamaguchi-Kabata","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Masao","family":"Nagasaki","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2015,1,21]]},"reference":[{"issue":"7063","key":"6793_CR1","doi-asserted-by":"publisher","first-page":"1299","DOI":"10.1038\/nature04226","volume":"437","author":"International HapMap Consortium","year":"2005","unstructured":"International HapMap Consortium, et al: A haplotype map of the human genome. Nature. 2005, 437 (7063): 1299-1320. 10.1038\/nature04226.","journal-title":"Nature"},{"issue":"7311","key":"6793_CR2","doi-asserted-by":"publisher","first-page":"52","DOI":"10.1038\/nature09298","volume":"467","author":"International HapMap 3 Consortium","year":"2010","unstructured":"International HapMap 3 Consortium, et al: Integrating common and rare genetic variation in diverse human populations. Nature. 2010, 467 (7311): 52-58. 10.1038\/nature09298.","journal-title":"Nature"},{"issue":"7319","key":"6793_CR3","doi-asserted-by":"publisher","first-page":"1061","DOI":"10.1038\/nature09534","volume":"467","author":"1000 Genomes Project Consortium","year":"2010","unstructured":"1000 Genomes Project Consortium, et al: A map of human genome variation from population-scale sequencing. Nature. 2010, 467 (7319): 1061-1073. 10.1038\/nature09534.","journal-title":"Nature"},{"key":"6793_CR4","doi-asserted-by":"publisher","first-page":"37","DOI":"10.1038\/ng2080","volume":"39","author":"SA McCarroll","year":"2007","unstructured":"McCarroll SA, Altshuler DM: Copy-number variation and association studies of human disease. Nature genetics. 2007, 39: 37-42. 10.1038\/ng2080.","journal-title":"Nature genetics"},{"issue":"5813","key":"6793_CR5","doi-asserted-by":"publisher","first-page":"848","DOI":"10.1126\/science.1136678","volume":"315","author":"BE Stranger","year":"2007","unstructured":"Stranger BE, Forrest MS, Dunning M, Ingle CE, Beazley C, Thorne N, Redon R, Bird CP, De Grassi A, Lee C, et al: Relative impact of nucleotide and copy number variation on gene expression phenotypes. Science. 2007, 315 (5813): 848-853. 10.1126\/science.1136678.","journal-title":"Science"},{"key":"6793_CR6","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 ME, Lupski JR: Copy number variation in human health, disease, and evolution. Annual review of genomics and human genetics. 2009, 10: 451-481. 10.1146\/annurev.genom.9.081307.164217.","journal-title":"Annual review of genomics and human genetics"},{"key":"6793_CR7","doi-asserted-by":"crossref","unstructured":"Conrad DF, Pinto D, Redon R, Feuk L, Gokcumen O, Zhang Y, Aerts J, Andrews TD, Barnes C, Campbell P, et al: Origins and functional impact of copy number variation in the human genome. Nature. 464 (7289): 704-712.","DOI":"10.1038\/nature08516"},{"issue":"1","key":"6793_CR8","doi-asserted-by":"publisher","first-page":"6","DOI":"10.1038\/jhg.2011.108","volume":"57","author":"SH Almal","year":"2011","unstructured":"Almal SH, Padh H: Implications of gene copy-number variation in health and diseases. Journal of human genetics. 2011, 57 (1): 6-13.","journal-title":"Journal of human genetics"},{"issue":"5","key":"6793_CR9","doi-asserted-by":"publisher","first-page":"353","DOI":"10.1093\/bfgp\/elp017","volume":"8","author":"L Winchester","year":"2009","unstructured":"Winchester L, Yau C, Ragoussis J: Comparing CNV detection methods for SNP arrays. Briefings in functional genomics & proteomics. 2009, 8 (5): 353-366. 10.1093\/bfgp\/elp017.","journal-title":"Briefings in functional genomics & proteomics"},{"key":"6793_CR10","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-gene rati on sequencing. Nature methods. 2009, 6: 13-20. 10.1038\/nmeth.1374.","journal-title":"Nature methods"},{"issue":"6","key":"6793_CR11","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 research. 2011, 21 (6): 974-984. 10.1101\/gr.114876.110.","journal-title":"Genome research"},{"issue":"3","key":"6793_CR12","doi-asserted-by":"publisher","first-page":"408","DOI":"10.1016\/j.ajhg.2012.07.004","volume":"91","author":"M Zhu","year":"2012","unstructured":"Zhu M, Need AC, Han Y, Ge D, Maia JM, Zhu Q, Heinzen EL, Cirulli ET, Pelak K, He M, et al: Using ERDS to infer copy-number variants in high-coverage genomes. The American Journal of Human Genetics. 2012, 91 (3): 408-421. 10.1016\/j.ajhg.2012.07.004.","journal-title":"The American Journal of Human Genetics"},{"issue":"6","key":"6793_CR13","first-page":"1","volume":"7","author":"T Mimori","year":"2013","unstructured":"Mimori T, Nariai N, Kojima K, Takahashi M, Ono A, Sato Y, Yamaguchi-Kabata Y, Nagasaki M: iSVP: an integrated structural variant calling pipeline from high-throughput sequencing data. BMC systems biology. 2013, 7 (6): 1-8.","journal-title":"BMC systems biology"},{"issue":"2","key":"6793_CR14","doi-asserted-by":"publisher","first-page":"121","DOI":"10.1038\/nrg3642","volume":"15","author":"D Sims","year":"2014","unstructured":"Sims D, Sudbery I, Ilott NE, Heger A, Ponting CP: Sequencing depth and coverage: key considerations in genomic analyses. Nature Reviews Genetics. 2014, 15 (2): 121-132. 10.1038\/nrg3642.","journal-title":"Nature Reviews Genetics"},{"issue":"14","key":"6793_CR15","doi-asserted-by":"publisher","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-Wheeler transform. Bioinformatics. 2009, 25 (14): 1754-1760. 10.1093\/bioinformatics\/btp324.","journal-title":"Bioinformatics"},{"issue":"5","key":"6793_CR16","doi-asserted-by":"publisher","first-page":"1084","DOI":"10.1086\/521987","volume":"81","author":"SR Browning","year":"2007","unstructured":"Browning SR, Browning BL: Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering. The American Journal of Human Genetics. 2007, 81 (5): 1084-1097. 10.1086\/521987.","journal-title":"The American Journal of Human Genetics"},{"issue":"2","key":"6793_CR17","doi-asserted-by":"publisher","first-page":"179","DOI":"10.1038\/nmeth.1785","volume":"9","author":"O Delaneau","year":"2012","unstructured":"Delaneau O, Marchini J, Zagury J-F: A linear complexity phasing method for thousands of genomes. Nature methods. 2012, 9 (2): 179-181.","journal-title":"Nature methods"},{"issue":"1","key":"6793_CR18","doi-asserted-by":"publisher","first-page":"5","DOI":"10.1038\/nmeth.2307","volume":"10","author":"O Delaneau","year":"2013","unstructured":"Delaneau O, Zagury J-F, Marchini J: Improved whole-chromosome phasing for disease and population genetic studies. Nature methods. 2013, 10 (1): 5-6.","journal-title":"Nature methods"},{"issue":"5","key":"6793_CR19","doi-asserted-by":"publisher","first-page":"491","DOI":"10.1038\/ng.806","volume":"43","author":"MA DePristo","year":"2011","unstructured":"DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, Philippakis AA, del Angel G, Rivas MA, Hanna M, et al: A framework for variation discovery and genotyping using next-gene rat ion DNA sequencing data. Nature genetics. 2011, 43 (5): 491-498. 10.1038\/ng.806.","journal-title":"Nature genetics"},{"key":"6793_CR20","doi-asserted-by":"publisher","first-page":"107","DOI":"10.1007\/978-3-319-07953-0_9","volume":"8574","author":"K Kojima","year":"2014","unstructured":"Kojima K, Nariai N, Mimori T, Yamaguchi-Kabata Y, Sato Y, Kawai Y, Nagasaki M: HapMonster: A statistically unified approach for variant calling and haplotyping based on phase-informative reads. Lecture Notes in Computer Science. 2014, 8574: 107-118.","journal-title":"Lecture Notes in Computer Science"},{"issue":"7","key":"6793_CR21","doi-asserted-by":"publisher","first-page":"541","DOI":"10.1038\/nmeth.1466","volume":"7","author":"LJ Coin","year":"2010","unstructured":"Coin LJ, Asher JE, Walters RG, Moustafa JSE-S, de Smith AJ, Sladek R, Balding DJ, Froguel P, Blakemore AI: cnvHap: an integrative population and haplotype-based multiplatform model of SNPs and CNVs. Nature methods. 2010, 7 (7): 541-546. 10.1038\/nmeth.1466.","journal-title":"Nature methods"},{"issue":"1","key":"6793_CR22","doi-asserted-by":"publisher","first-page":"35","DOI":"10.1534\/g3.111.000174","volume":"1","author":"M Kato","year":"2011","unstructured":"Kato M, Yoon S, Hosono N, Leotta A, Sebat J, Tsunoda T, Zhang MQ: Inferring haplotypes of copy number variations from high-throughput data with uncertainty. G3 (Bethesda). 2011, 1 (1): 35-42. 2011.","journal-title":"G3 (Bethesda)"},{"issue":"11","key":"6793_CR23","doi-asserted-by":"publisher","first-page":"1437","DOI":"10.1093\/bioinformatics\/btq157","volume":"26","author":"S-Y Su","year":"2010","unstructured":"Su S-Y, Asher JE, Jarvelin M-R, Froguel P, Blakemore AI, Balding DJ, Coin LJ: Inferring combined CNV\/SNP haplotypes from genotype data. Bioinformatics. 2010, 26 (11): 1437-1445. 10.1093\/bioinformatics\/btq157.","journal-title":"Bioinformatics"},{"key":"6793_CR24","first-page":"993","volume-title":"Latent dirichlet allocation, the Journal of machine Learning research","author":"DM Blei","year":"2003","unstructured":"Blei DM, Ng AY, Jordan MI: Latent dirichlet allocation, the Journal of machine Learning research. 2003, 3: 993-1022."},{"key":"6793_CR25","first-page":"1353","volume-title":"Advances in Neural Information Processing Systems","author":"YW Teh","year":"2006","unstructured":"Teh YW, Newman D, Welling M: A collapsed variational Bayesian inference algorithm for latent Dirichlet allocation. Advances in Neural Information Processing Systems. 2006, 1353-1360."},{"issue":"18","key":"6793_CR26","doi-asserted-by":"publisher","first-page":"2292","DOI":"10.1093\/bioinformatics\/btt381","volume":"29","author":"N Nariai","year":"2013","unstructured":"Nariai N, Hirose O, Kojima K, Nagasaki M: TIGAR: transcript isoform abundance estimation method with gapped alignment of RNA-Seq data by variational Bayesian inference. Bioinformatics. 2013, 29 (18): 2292-2299. 10.1093\/bioinformatics\/btt381.","journal-title":"Bioinformatics"},{"key":"6793_CR27","volume-title":"Platinum genomes project","author":"Corporation Illumina","year":"2013","unstructured":"Illumina Corporation: Platinum genomes project. 2013, [http:\/\/www.platinumgenomes.org]"},{"issue":"10","key":"6793_CR28","doi-asserted-by":"publisher","first-page":"1256","DOI":"10.1038\/ng2123","volume":"39","author":"GH Perry","year":"2007","unstructured":"Perry GH, Dominy NJ, Claw KG, Lee AS, Fiegler H, Redon R, Werner J, Villanea FA, Mountain JL, Misra R, et al: Diet and the evolution of human amylase gene copy number variation. Nature genetics. 2007, 39 (10): 1256-1260. 10.1038\/ng2123.","journal-title":"Nature genetics"},{"issue":"2","key":"6793_CR29","doi-asserted-by":"crossref","first-page":"97","DOI":"10.1038\/nrg2689","volume":"11","author":"H Innan","year":"2010","unstructured":"Innan H, Kondrashov F: The evolution of gene duplications: classifying and distinguishing between models. Nature Reviews Genetics. 2010, 11 (2): 97-108.","journal-title":"Nature Reviews Genetics"},{"issue":"3","key":"6793_CR30","doi-asserted-by":"publisher","first-page":"1077","DOI":"10.1534\/genetics.111.135343","volume":"190","author":"KM Teshima","year":"2012","unstructured":"Teshima KM, Innan H: The coalescent with selection on copy number variants. Genetics. 2012, 190 (3): 1077-1086. 10.1534\/genetics.111.135343.","journal-title":"Genetics"},{"issue":"5","key":"6793_CR31","first-page":"1121","volume":"35","author":"J Zeng","year":"2013","unstructured":"Zeng J, Cheung WK, Liu J: Learning topic models by belief propagation. Pattern Analysis and Machine Intelligence. IEEE Transactions. 2013, 35 (5): 1121-1134.","journal-title":"IEEE Transactions"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-16-S1-S4.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/1471-2105-16-S1-S4\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-16-S1-S4.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,2]],"date-time":"2021-09-02T19:26:44Z","timestamp":1630610804000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-16-S1-S4"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2015,1,21]]},"references-count":31,"journal-issue":{"issue":"S1","published-print":{"date-parts":[[2015,12]]}},"alternative-id":["6793"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-16-s1-s4","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2015,1,21]]},"assertion":[{"value":"21 January 2015","order":1,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"S4"}}