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Items: 1 to 20 of 129

1.

COPS: a sensitive and accurate tool for detecting somatic Copy Number Alterations using short-read sequence data from paired samples.

Krishnan NM, Gaur P, Chaudhary R, Rao AA, Panda B.

PLoS One. 2012;7(10):e47812. doi: 10.1371/journal.pone.0047812. Epub 2012 Oct 22.

2.

VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing.

Koboldt DC, Zhang Q, Larson DE, Shen D, McLellan MD, Lin L, Miller CA, Mardis ER, Ding L, Wilson RK.

Genome Res. 2012 Mar;22(3):568-76. doi: 10.1101/gr.129684.111. Epub 2012 Feb 2.

3.

Comparative analysis of methods for identifying somatic copy number alterations from deep sequencing data.

Alkodsi A, Louhimo R, Hautaniemi S.

Brief Bioinform. 2015 Mar;16(2):242-54. doi: 10.1093/bib/bbu004. Epub 2014 Mar 5.

PMID:
24599115
4.
5.

DNA replication timing and long-range DNA interactions predict mutational landscapes of cancer genomes.

De S, Michor F.

Nat Biotechnol. 2011 Nov 20;29(12):1103-8. doi: 10.1038/nbt.2030.

6.

Correcting for cancer genome size and tumour cell content enables better estimation of copy number alterations from next-generation sequence data.

Gusnanto A, Wood HM, Pawitan Y, Rabbitts P, Berri S.

Bioinformatics. 2012 Jan 1;28(1):40-7. doi: 10.1093/bioinformatics/btr593. Epub 2011 Oct 28.

7.

Comparison of methods to detect copy number alterations in cancer using simulated and real genotyping data.

Mosén-Ansorena D, Aransay AM, Rodríguez-Ezpeleta N.

BMC Bioinformatics. 2012 Aug 7;13:192. doi: 10.1186/1471-2105-13-192.

8.

Genome-wide identification of significant aberrations in cancer genome.

Yuan X, Yu G, Hou X, Shih IeM, Clarke R, Zhang J, Hoffman EP, Wang RR, Zhang Z, Wang Y.

BMC Genomics. 2012 Jul 27;13:342. doi: 10.1186/1471-2164-13-342.

9.

rSW-seq: algorithm for detection of copy number alterations in deep sequencing data.

Kim TM, Luquette LJ, Xi R, Park PJ.

BMC Bioinformatics. 2010 Aug 18;11:432. doi: 10.1186/1471-2105-11-432.

10.

Estimation of copy number alterations from exome sequencing data.

Valdés-Mas R, Bea S, Puente DA, López-Otín C, Puente XS.

PLoS One. 2012;7(12):e51422. doi: 10.1371/journal.pone.0051422. Epub 2012 Dec 19.

11.

CONSERTING: integrating copy-number analysis with structural-variation detection.

Chen X, Gupta P, Wang J, Nakitandwe J, Roberts K, Dalton JD, Parker M, Patel S, Holmfeldt L, Payne D, Easton J, Ma J, Rusch M, Wu G, Patel A, Baker SJ, Dyer MA, Shurtleff S, Espy S, Pounds S, Downing JR, Ellison DW, Mullighan CG, Zhang J.

Nat Methods. 2015 Jun;12(6):527-30. doi: 10.1038/nmeth.3394. Epub 2015 May 4.

12.

SomatiCA: identifying, characterizing and quantifying somatic copy number aberrations from cancer genome sequencing data.

Chen M, Gunel M, Zhao H.

PLoS One. 2013 Nov 12;8(11):e78143. doi: 10.1371/journal.pone.0078143. eCollection 2013.

13.

Comparative analysis of somatic copy-number alterations across different human cancer types reveals two distinct classes of breakpoint hotspots.

Li Y, Zhang L, Ball RL, Liang X, Li J, Lin Z, Liang H.

Hum Mol Genet. 2012 Nov 15;21(22):4957-65. doi: 10.1093/hmg/dds340. Epub 2012 Aug 16.

14.

BACOM: in silico detection of genomic deletion types and correction of normal cell contamination in copy number data.

Yu G, Zhang B, Bova GS, Xu J, Shih IeM, Wang Y.

Bioinformatics. 2011 Jun 1;27(11):1473-80. doi: 10.1093/bioinformatics/btr183. Epub 2011 Apr 15.

15.

WaveCNV: allele-specific copy number alterations in primary tumors and xenograft models from next-generation sequencing.

Holt C, Losic B, Pai D, Zhao Z, Trinh Q, Syam S, Arshadi N, Jang GH, Ali J, Beck T, McPherson J, Muthuswamy LB.

Bioinformatics. 2014 Mar 15;30(6):768-74. doi: 10.1093/bioinformatics/btt611. Epub 2013 Nov 4.

16.

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.

17.

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.

18.

ClipCrop: a tool for detecting structural variations with single-base resolution using soft-clipping information.

Suzuki S, Yasuda T, Shiraishi Y, Miyano S, Nagasaki M.

BMC Bioinformatics. 2011 Dec 14;12 Suppl 14:S7. doi: 10.1186/1471-2105-12-S14-S7.

19.

seqCNA: an R package for DNA copy number analysis in cancer using high-throughput sequencing.

Mosen-Ansorena D, Telleria N, Veganzones S, De la Orden V, Maestro ML, Aransay AM.

BMC Genomics. 2014 Mar 5;15:178. doi: 10.1186/1471-2164-15-178.

20.

No evidence of somatic DNA copy number alterations in eutopic and ectopic endometrial tissue in endometriosis.

Saare M, Sõritsa D, Vaidla K, Palta P, Remm M, Laan M, Karro H, Sõritsa A, Salumets A, D'Hooghe T, Peters M.

Hum Reprod. 2012 Jun;27(6):1857-64. doi: 10.1093/humrep/des125. Epub 2012 Apr 3.

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