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Results: 1 to 20 of 97

1.

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.

PMID:
23531354
[PubMed - in process]
Free PMC Article
2.

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.

PMID:
24845652
[PubMed - in process]
Free PMC Article
3.

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.

PMID:
22039209
[PubMed - indexed for MEDLINE]
Free Article
4.

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.

PMID:
24265680
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

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.

PMID:
21305028
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

AbsCN-seq: a statistical method to estimate tumor purity, ploidy and absolute copy numbers from next-generation sequencing data.

Bao L, Pu M, Messer K.

Bioinformatics. 2014 Jan 13. [Epub ahead of print]

PMID:
24389661
[PubMed - as supplied by publisher]
7.

Performance evaluation of DNA copy number segmentation methods.

Pierre-Jean M, Rigaill G, Neuvial P.

Brief Bioinform. 2014 Sep 8. pii: bbu026. [Epub ahead of print]

PMID:
25202135
[PubMed - as supplied by publisher]
8.

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.

PMID:
21272361
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

DR-Integrator: a new analytic tool for integrating DNA copy number and gene expression data.

Salari K, Tibshirani R, Pollack JR.

Bioinformatics. 2010 Feb 1;26(3):414-6. doi: 10.1093/bioinformatics/btp702. Epub 2009 Dec 22.

PMID:
20031972
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Allele-specific copy number analysis of tumors.

Van Loo P, Nordgard SH, Lingjærde OC, Russnes HG, Rye IH, Sun W, Weigman VJ, Marynen P, Zetterberg A, Naume B, Perou CM, Børresen-Dale AL, Kristensen VN.

Proc Natl Acad Sci U S A. 2010 Sep 28;107(39):16910-5. doi: 10.1073/pnas.1009843107. Epub 2010 Sep 13.

PMID:
20837533
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

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.

PMID:
23577066
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

POLYSAT: an R package for polyploid microsatellite analysis.

Clark LV, Jasieniuk M.

Mol Ecol Resour. 2011 May;11(3):562-6. doi: 10.1111/j.1755-0998.2011.02985.x. Epub 2011 Feb 6.

PMID:
21481215
[PubMed - indexed for MEDLINE]
13.

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.

PMID:
25167919
[PubMed - in process]
Free Article
14.

Determination of genomic copy number alteration emphasizing a restriction site-based strategy of genome re-sequencing.

Zheng C, Miao X, Li Y, Huang Y, Ruan J, Ma X, Wang L, Wu CI, Cai J.

Bioinformatics. 2013 Nov 15;29(22):2813-21. doi: 10.1093/bioinformatics/btt481. Epub 2013 Aug 20.

PMID:
23962614
[PubMed - indexed for MEDLINE]
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.

PMID:
24192544
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

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.

PMID:
24597965
[PubMed - in process]
Free PMC Article
17.

bammds: a tool for assessing the ancestry of low-depth whole-genome data using multidimensional scaling (MDS).

Malaspinas AS, Tange O, Moreno-Mayar JV, Rasmussen M, DeGiorgio M, Wang Y, Valdiosera CE, Politis G, Willerslev E, Nielsen R.

Bioinformatics. 2014 Jun 28. pii: btu410. [Epub ahead of print]

PMID:
24974206
[PubMed - as supplied by publisher]
Free Article
18.

Tumor-associated copy number changes in the circulation of patients with prostate cancer identified through whole-genome sequencing.

Heitzer E, Ulz P, Belic J, Gutschi S, Quehenberger F, Fischereder K, Benezeder T, Auer M, Pischler C, Mannweiler S, Pichler M, Eisner F, Haeusler M, Riethdorf S, Pantel K, Samonigg H, Hoefler G, Augustin H, Geigl JB, Speicher MR.

Genome Med. 2013 Apr 5;5(4):30. doi: 10.1186/gm434. eCollection 2013.

PMID:
23561577
[PubMed]
Free PMC Article
19.

A patchwork interspersed sequence is present in a high copy number in the sheep genome.

D'Aiuto L, Barsanti P, Cserpan I, Minardi G, Ciccarese S.

Gene. 2003 Jan 16;303:69-76.

PMID:
12559568
[PubMed - indexed for MEDLINE]
20.

Allele-specific amplification in cancer revealed by SNP array analysis.

LaFramboise T, Weir BA, Zhao X, Beroukhim R, Li C, Harrington D, Sellers WR, Meyerson M.

PLoS Comput Biol. 2005 Nov;1(6):e65. Epub 2005 Nov 25.

PMID:
16322765
[PubMed - indexed for MEDLINE]
Free PMC Article

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