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Results: 1 to 20 of 84

1.

GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers.

Mermel CH, Schumacher SE, Hill B, Meyerson ML, Beroukhim R, Getz G.

Genome Biol. 2011;12(4):R41. doi: 10.1186/gb-2011-12-4-r41. Epub 2011 Apr 28.

PMID:
21527027
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

The landscape of somatic copy-number alteration across human cancers.

Beroukhim R, Mermel CH, Porter D, Wei G, Raychaudhuri S, Donovan J, Barretina J, Boehm JS, Dobson J, Urashima M, Mc Henry KT, Pinchback RM, Ligon AH, Cho YJ, Haery L, Greulich H, Reich M, Winckler W, Lawrence MS, Weir BA, Tanaka KE, Chiang DY, Bass AJ, Loo A, Hoffman C, Prensner J, Liefeld T, Gao Q, Yecies D, Signoretti S, Maher E, Kaye FJ, Sasaki H, Tepper JE, Fletcher JA, Tabernero J, Baselga J, Tsao MS, Demichelis F, Rubin MA, Janne PA, Daly MJ, Nucera C, Levine RL, Ebert BL, Gabriel S, Rustgi AK, Antonescu CR, Ladanyi M, Letai A, Garraway LA, Loda M, Beer DG, True LD, Okamoto A, Pomeroy SL, Singer S, Golub TR, Lander ES, Getz G, Sellers WR, Meyerson M.

Nature. 2010 Feb 18;463(7283):899-905. doi: 10.1038/nature08822.

PMID:
20164920
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

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.

PMID:
23110103
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Pan-cancer patterns of somatic copy number alteration.

Zack TI, Schumacher SE, Carter SL, Cherniack AD, Saksena G, Tabak B, Lawrence MS, Zhang CZ, Wala J, Mermel CH, Sougnez C, Gabriel SB, Hernandez B, Shen H, Laird PW, Getz G, Meyerson M, Beroukhim R.

Nat Genet. 2013 Sep 26;45(10):1134-1140. doi: 10.1038/ng.2760. [Epub ahead of print]

PMID:
24071852
[PubMed - as supplied by publisher]
5.

Comparative analysis of algorithms for integration of copy number and expression data.

Louhimo R, Lepikhova T, Monni O, Hautaniemi S.

Nat Methods. 2012 Feb 12;9(4):351-5. doi: 10.1038/nmeth.1893.

PMID:
22327835
[PubMed - indexed for MEDLINE]
6.

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.

PMID:
22839576
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

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

Alkodsi A, Louhimo R, Hautaniemi S.

Brief Bioinform. 2014 Mar 5. [Epub ahead of print]

PMID:
24599115
[PubMed - as supplied by publisher]
8.

A double-layered mixture model for the joint analysis of DNA copy number and gene expression data.

Choi H, Qin ZS, Ghosh D.

J Comput Biol. 2010 Feb;17(2):121-37. doi: 10.1089/cmb.2009.0019.

PMID:
20170400
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

TAGCNA: a method to identify significant consensus events of copy number alterations in cancer.

Yuan X, Zhang J, Yang L, Zhang S, Chen B, Geng Y, Wang Y.

PLoS One. 2012;7(7):e41082. doi: 10.1371/journal.pone.0041082. Epub 2012 Jul 18.

PMID:
22815924
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

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.

PMID:
22300766
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Estimation of tumor heterogeneity using CGH array data.

Wang K, Li J, Li S, Bolund L, Wiuf C.

BMC Bioinformatics. 2009 Jan 9;10:12. doi: 10.1186/1471-2105-10-12.

PMID:
19134174
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Towards precise classification of cancers based on robust gene functional expression profiles.

Guo Z, Zhang T, Li X, Wang Q, Xu J, Yu H, Zhu J, Wang H, Wang C, Topol EJ, Wang Q, Rao S.

BMC Bioinformatics. 2005 Mar 17;6:58.

PMID:
15774002
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Statistical tools for transgene copy number estimation based on real-time PCR.

Yuan JS, Burris J, Stewart NR, Mentewab A, Stewart CN Jr.

BMC Bioinformatics. 2007 Nov 1;8 Suppl 7:S6.

PMID:
18047729
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

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.

PMID:
21569352
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Distinguishing somatic and germline copy number events in cancer patient DNA hybridized to whole-genome SNP genotyping arrays.

Ha G, Shah S.

Methods Mol Biol. 2013;973:355-72. doi: 10.1007/978-1-62703-281-0_22.

PMID:
23412801
[PubMed - indexed for MEDLINE]
16.

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.

PMID:
22101487
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

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.

PMID:
22899649
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Copy number alterations and expression profiles of candidate genes in a pulmonary inflammatory myofibroblastic tumor.

Jung SH, Yim SH, Hu HJ, Jung CK, Lee SH, Kim DH, Chung YJ.

Lung Cancer. 2010 Nov;70(2):152-7. doi: 10.1016/j.lungcan.2010.01.019. Epub 2010 Feb 24. Review.

PMID:
20185201
[PubMed - indexed for MEDLINE]
19.

CNAnova: a new approach for finding recurrent copy number abnormalities in cancer SNP microarray data.

Ivakhno S, Tavaré S.

Bioinformatics. 2010 Jun 1;26(11):1395-402. doi: 10.1093/bioinformatics/btq145. Epub 2010 Apr 18.

PMID:
20403815
[PubMed - indexed for MEDLINE]
Free Article
20.

CARAT: a novel method for allelic detection of DNA copy number changes using high density oligonucleotide arrays.

Huang J, Wei W, Chen J, Zhang J, Liu G, Di X, Mei R, Ishikawa S, Aburatani H, Jones KW, Shapero MH.

BMC Bioinformatics. 2006 Feb 21;7:83.

PMID:
16504045
[PubMed - indexed for MEDLINE]
Free PMC Article

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