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Patchwork: allele-specific copy number analysis of whole-genome sequenced tumor tissue.

Mayrhofer M, DiLorenzo S, Isaksson A.

Genome Biol. 2013 Mar 25;14(3):R24. doi: 10.1186/gb-2013-14-3-r24.


Sequenza: allele-specific copy number and mutation profiles from tumor sequencing data.

Favero F, Joshi T, Marquard AM, Birkbak NJ, Krzystanek M, Li Q, Szallasi Z, Eklund AC.

Ann Oncol. 2015 Jan;26(1):64-70. doi: 10.1093/annonc/mdu479. Epub 2014 Oct 15.


CLImAT: accurate detection of copy number alteration and loss of heterozygosity in impure and aneuploid tumor samples using whole-genome sequencing data.

Yu Z, Liu Y, Shen Y, Wang M, Li A.

Bioinformatics. 2014 Sep 15;30(18):2576-83. doi: 10.1093/bioinformatics/btu346. Epub 2014 May 19.


DNA copy number analysis of fresh and formalin-fixed specimens by shallow whole-genome sequencing with identification and exclusion of problematic regions in the genome assembly.

Scheinin I, Sie D, Bengtsson H, van de Wiel MA, Olshen AB, van Thuijl HF, van Essen HF, Eijk PP, Rustenburg F, Meijer GA, Reijneveld JC, Wesseling P, Pinkel D, Albertson DG, Ylstra B.

Genome Res. 2014 Dec;24(12):2022-32. doi: 10.1101/gr.175141.114. Epub 2014 Sep 18.


High resolution copy number variation data in the NCI-60 cancer cell lines from whole genome microarrays accessible through CellMiner.

Varma S, Pommier Y, Sunshine M, Weinstein JN, Reinhold WC.

PLoS One. 2014 Mar 26;9(3):e92047. doi: 10.1371/journal.pone.0092047. eCollection 2014.


Deconvolving tumor purity and ploidy by integrating copy number alterations and loss of heterozygosity.

Li Y, Xie X.

Bioinformatics. 2014 Aug 1;30(15):2121-9. doi: 10.1093/bioinformatics/btu174. Epub 2014 Apr 2. Erratum in: Bioinformatics. 2015 Feb 15;31(4):618.


MixClone: a mixture model for inferring tumor subclonal populations.

Li Y, Xie X.

BMC Genomics. 2015;16 Suppl 2:S1. doi: 10.1186/1471-2164-16-S2-S1. Epub 2015 Jan 21.


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.


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.


Inferring copy number and genotype in tumour exome data.

Amarasinghe KC, Li J, Hunter SM, Ryland GL, Cowin PA, Campbell IG, Halgamuge SK.

BMC Genomics. 2014 Aug 28;15:732. doi: 10.1186/1471-2164-15-732.


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.


Detecting copy number status and uncovering subclonal markers in heterogeneous tumor biopsies.

Parisi F, Ariyan S, Narayan D, Bacchiocchi A, Hoyt K, Cheng E, Xu F, Li P, Halaban R, Kluger Y.

BMC Genomics. 2011 May 11;12:230. doi: 10.1186/1471-2164-12-230.


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.


VegaMC: a R/bioconductor package for fast downstream analysis of large array comparative genomic hybridization datasets.

Morganella S, Ceccarelli M.

Bioinformatics. 2012 Oct 1;28(19):2512-4. Epub 2012 Jul 18.


The use of ultra-dense array CGH analysis for the discovery of micro-copy number alterations and gene fusions in the cancer genome.

Przybytkowski E, Ferrario C, Basik M.

BMC Med Genomics. 2011 Jan 27;4:16. doi: 10.1186/1755-8794-4-16.


Whole genome sequencing reveals potential targets for therapy in patients with refractory KRAS mutated metastatic colorectal cancer.

Shanmugam V, Ramanathan RK, Lavender NA, Sinari S, Chadha M, Liang WS, Kurdoglu A, Izatt T, Christoforides A, Benson H, Phillips L, Baker A, Murray C, Hostetter G, Von Hoff DD, Craig DW, Carpten JD.

BMC Med Genomics. 2014 Jun 18;7:36. doi: 10.1186/1755-8794-7-36.


Comprehensive characterization of human genome variation by high coverage whole-genome sequencing of forty four Caucasians.

Shen H, Li J, Zhang J, Xu C, Jiang Y, Wu Z, Zhao F, Liao L, Chen J, Lin Y, Tian Q, Papasian CJ, Deng HW.

PLoS One. 2013;8(4):e59494. doi: 10.1371/journal.pone.0059494. Epub 2013 Apr 5.


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.


Advances in understanding cancer genomes through second-generation sequencing.

Meyerson M, Gabriel S, Getz G.

Nat Rev Genet. 2010 Oct;11(10):685-96. doi: 10.1038/nrg2841. Review.

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