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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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


A novel SNP analysis method to detect copy number alterations with an unbiased reference signal directly from tumor samples.

Lisovich A, Chandran UR, Lyons-Weiler MA, LaFramboise WA, Brown AR, Jakacki RI, Pollack IF, Sobol RW.

BMC Med Genomics. 2011 Jan 26;4:14. doi: 10.1186/1755-8794-4-14.


Software comparison for evaluating genomic copy number variation for Affymetrix 6.0 SNP array platform.

Eckel-Passow JE, Atkinson EJ, Maharjan S, Kardia SL, de Andrade M.

BMC Bioinformatics. 2011 May 31;12:220. doi: 10.1186/1471-2105-12-220.


CUSHAW3: sensitive and accurate base-space and color-space short-read alignment with hybrid seeding.

Liu Y, Popp B, Schmidt B.

PLoS One. 2014 Jan 22;9(1):e86869. doi: 10.1371/journal.pone.0086869.


Single nucleotide polymorphism microarray analysis of genetic alterations in cancer.

Mullighan CG.

Methods Mol Biol. 2011;730:235-58. doi: 10.1007/978-1-61779-074-4_17.


Statistical challenges associated with detecting copy number variations with next-generation sequencing.

Teo SM, Pawitan Y, Ku CS, Chia KS, Salim A.

Bioinformatics. 2012 Nov 1;28(21):2711-8. doi: 10.1093/bioinformatics/bts535. Review.

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