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cn.MOPS: mixture of Poissons for discovering copy number variations in next-generation sequencing data with a low false discovery rate.

Klambauer G, Schwarzbauer K, Mayr A, Clevert DA, Mitterecker A, Bodenhofer U, Hochreiter S.

Nucleic Acids Res. 2012 May;40(9):e69. doi: 10.1093/nar/gks003. Epub 2012 Feb 1.


Customisation of the exome data analysis pipeline using a combinatorial approach.

Pattnaik S, Vaidyanathan S, Pooja DG, Deepak S, Panda B.

PLoS One. 2012;7(1):e30080. doi: 10.1371/journal.pone.0030080. Epub 2012 Jan 6.


Exome sequencing-based copy-number variation and loss of heterozygosity detection: ExomeCNV.

Sathirapongsasuti JF, Lee H, Horst BA, Brunner G, Cochran AJ, Binder S, Quackenbush J, Nelson SF.

Bioinformatics. 2011 Oct 1;27(19):2648-54. doi: 10.1093/bioinformatics/btr462. Epub 2011 Aug 9.


CREST maps somatic structural variation in cancer genomes with base-pair resolution.

Wang J, Mullighan CG, Easton J, Roberts S, Heatley SL, Ma J, Rusch MC, Chen K, Harris CC, Ding L, Holmfeldt L, Payne-Turner D, Fan X, Wei L, Zhao D, Obenauer JC, Naeve C, Mardis ER, Wilson RK, Downing JR, Zhang J.

Nat Methods. 2011 Jun 12;8(8):652-4. doi: 10.1038/nmeth.1628.


CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing.

Abyzov A, Urban AE, Snyder M, Gerstein M.

Genome Res. 2011 Jun;21(6):974-84. doi: 10.1101/gr.114876.110. Epub 2011 Feb 7.


ReadDepth: a parallel R package for detecting copy number alterations from short sequencing reads.

Miller CA, Hampton O, Coarfa C, Milosavljevic A.

PLoS One. 2011 Jan 31;6(1):e16327. doi: 10.1371/journal.pone.0016327.


Mapping copy number variation by population-scale genome sequencing.

Mills RE, Walter K, Stewart C, Handsaker RE, Chen K, Alkan C, Abyzov A, Yoon SC, Ye K, Cheetham RK, Chinwalla A, Conrad DF, Fu Y, Grubert F, Hajirasouliha I, Hormozdiari F, Iakoucheva LM, Iqbal Z, Kang S, Kidd JM, Konkel MK, Korn J, Khurana E, Kural D, Lam HY, Leng J, Li R, Li Y, Lin CY, Luo R, Mu XJ, Nemesh J, Peckham HE, Rausch T, Scally A, Shi X, Stromberg MP, Stütz AM, Urban AE, Walker JA, Wu J, Zhang Y, Zhang ZD, Batzer MA, Ding L, Marth GT, McVean G, Sebat J, Snyder M, Wang J, Ye K, Eichler EE, Gerstein MB, Hurles ME, Lee C, McCarroll SA, Korbel JO; 1000 Genomes Project.

Nature. 2011 Feb 3;470(7332):59-65. doi: 10.1038/nature09708.


Control-free calling of copy number alterations in deep-sequencing data using GC-content normalization.

Boeva V, Zinovyev A, Bleakley K, Vert JP, Janoueix-Lerosey I, Delattre O, Barillot E.

Bioinformatics. 2011 Jan 15;27(2):268-9. doi: 10.1093/bioinformatics/btq635. Epub 2010 Nov 15.


Stampy: a statistical algorithm for sensitive and fast mapping of Illumina sequence reads.

Lunter G, Goodson M.

Genome Res. 2011 Jun;21(6):936-9. doi: 10.1101/gr.111120.110. Epub 2010 Oct 27.


CNAseg--a novel framework for identification of copy number changes in cancer from second-generation sequencing data.

Ivakhno S, Royce T, Cox AJ, Evers DJ, Cheetham RK, Tavaré S.

Bioinformatics. 2010 Dec 15;26(24):3051-8. doi: 10.1093/bioinformatics/btq587. Epub 2010 Oct 21.


Detecting copy number variation with mated short reads.

Medvedev P, Fiume M, Dzamba M, Smith T, Brudno M.

Genome Res. 2010 Nov;20(11):1613-22. doi: 10.1101/gr.106344.110. Epub 2010 Aug 30.


SVDetect: a tool to identify genomic structural variations from paired-end and mate-pair sequencing data.

Zeitouni B, Boeva V, Janoueix-Lerosey I, Loeillet S, Legoix-né P, Nicolas A, Delattre O, Barillot E.

Bioinformatics. 2010 Aug 1;26(15):1895-6. doi: 10.1093/bioinformatics/btq293.


Discovery of common Asian copy number variants using integrated high-resolution array CGH and massively parallel DNA sequencing.

Park H, Kim JI, Ju YS, Gokcumen O, Mills RE, Kim S, Lee S, Suh D, Hong D, Kang HP, Yoo YJ, Shin JY, Kim HJ, Yavartanoo M, Chang YW, Ha JS, Chong W, Hwang GR, Darvishi K, Kim H, Yang SJ, Yang KS, Kim H, Hurles ME, Scherer SW, Carter NP, Tyler-Smith C, Lee C, Seo JS.

Nat Genet. 2010 May;42(5):400-5. doi: 10.1038/ng.555. Epub 2010 Apr 4.


BFAST: an alignment tool for large scale genome resequencing.

Homer N, Merriman B, Nelson SF.

PLoS One. 2009 Nov 11;4(11):e7767. doi: 10.1371/journal.pone.0007767.


Origins and functional impact of copy number variation in the human genome.

Conrad DF, Pinto D, Redon R, Feuk L, Gokcumen O, Zhang Y, Aerts J, Andrews TD, Barnes C, Campbell P, Fitzgerald T, Hu M, Ihm CH, Kristiansson K, Macarthur DG, Macdonald JR, Onyiah I, Pang AW, Robson S, Stirrups K, Valsesia A, Walter K, Wei J; Wellcome Trust Case Control Consortium, Tyler-Smith C, Carter NP, Lee C, Scherer SW, Hurles ME.

Nature. 2010 Apr 1;464(7289):704-12. doi: 10.1038/nature08516. Epub 2009 Oct 7.


Personalized copy number and segmental duplication maps using next-generation sequencing.

Alkan C, Kidd JM, Marques-Bonet T, Aksay G, Antonacci F, Hormozdiari F, Kitzman JO, Baker C, Malig M, Mutlu O, Sahinalp SC, Gibbs RA, Eichler EE.

Nat Genet. 2009 Oct;41(10):1061-7. doi: 10.1038/ng.437. Epub 2009 Aug 30.


Sensitive and accurate detection of copy number variants using read depth of coverage.

Yoon S, Xuan Z, Makarov V, Ye K, Sebat J.

Genome Res. 2009 Sep;19(9):1586-92. doi: 10.1101/gr.092981.109. Epub 2009 Aug 5.


Fast and accurate short read alignment with Burrows-Wheeler transform.

Li H, Durbin R.

Bioinformatics. 2009 Jul 15;25(14):1754-60. doi: 10.1093/bioinformatics/btp324. Epub 2009 May 18.


The cancer genome.

Stratton MR, Campbell PJ, Futreal PA.

Nature. 2009 Apr 9;458(7239):719-24. doi: 10.1038/nature07943. Review.


CNV-seq, a new method to detect copy number variation using high-throughput sequencing.

Xie C, Tammi MT.

BMC Bioinformatics. 2009 Mar 6;10:80. doi: 10.1186/1471-2105-10-80.

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