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Items: 1 to 20 of 93


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.


CNAmet: an R package for integrating copy number, methylation and expression data.

Louhimo R, Hautaniemi S.

Bioinformatics. 2011 Mar 15;27(6):887-8. doi: 10.1093/bioinformatics/btr019. Epub 2011 Jan 12.


PLRS: a flexible tool for the joint analysis of DNA copy number and mRNA expression data.

Leday GG, van de Wiel MA.

Bioinformatics. 2013 Apr 15;29(8):1081-2. doi: 10.1093/bioinformatics/btt082. Epub 2013 Feb 17.


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.


Clinical omics analysis of colorectal cancer incorporating copy number aberrations and gene expression data.

Yoshida T, Kobayashi T, Itoda M, Muto T, Miyaguchi K, Mogushi K, Shoji S, Shimokawa K, Iida S, Uetake H, Ishikawa T, Sugihara K, Mizushima H, Tanaka H.

Cancer Inform. 2010 Jul 29;9:147-61.


Identification of genes involved in squamous cell carcinoma of the lung using synchronized data from DNA copy number and transcript expression profiling analysis.

Lo KC, Stein LC, Panzarella JA, Cowell JK, Hawthorn L.

Lung Cancer. 2008 Mar;59(3):315-31. Epub 2007 Oct 29.


Parent-specific copy number in paired tumor-normal studies using circular binary segmentation.

Olshen AB, Bengtsson H, Neuvial P, Spellman PT, Olshen RA, Seshan VE.

Bioinformatics. 2011 Aug 1;27(15):2038-46. doi: 10.1093/bioinformatics/btr329. Epub 2011 Jun 11.


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.


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.


Gene copy-number alterations: a cost-benefit analysis.

Tang YC, Amon A.

Cell. 2013 Jan 31;152(3):394-405. doi: 10.1016/j.cell.2012.11.043. Review.


Identification of osteosarcoma driver genes by integrative analysis of copy number and gene expression data.

Kuijjer ML, Rydbeck H, Kresse SH, Buddingh EP, Lid AB, Roelofs H, Bürger H, Myklebost O, Hogendoorn PC, Meza-Zepeda LA, Cleton-Jansen AM.

Genes Chromosomes Cancer. 2012 Jul;51(7):696-706. doi: 10.1002/gcc.21956. Epub 2012 Mar 27.


Integrative genome-wide analysis reveals a robust genomic glioblastoma signature associated with copy number driving changes in gene expression.

de Tayrac M, Etcheverry A, Aubry M, Saïkali S, Hamlat A, Quillien V, Le Treut A, Galibert MD, Mosser J.

Genes Chromosomes Cancer. 2009 Jan;48(1):55-68. doi: 10.1002/gcc.20618.


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.


Array CGH identifies distinct DNA copy number profiles of oncogenes and tumor suppressor genes in chromosomal- and microsatellite-unstable sporadic colorectal carcinomas.

Lassmann S, Weis R, Makowiec F, Roth J, Danciu M, Hopt U, Werner M.

J Mol Med (Berl). 2007 Mar;85(3):293-304. Epub 2006 Dec 2.


Cancer gene prioritization by integrative analysis of mRNA expression and DNA copy number data: a comparative review.

Lahti L, Schäfer M, Klein HU, Bicciato S, Dugas M.

Brief Bioinform. 2013 Jan;14(1):27-35. doi: 10.1093/bib/bbs005. Epub 2012 Mar 22. Review.


DNA copy number data analysis using the CGHAnalyzer software suite.

Greshock J.

Methods Mol Biol. 2007;396:255-66.


Integrated analysis of copy number alterations and gene expression: a bivariate assessment of equally directed abnormalities.

Schäfer M, Schwender H, Merk S, Haferlach C, Ickstadt K, Dugas M.

Bioinformatics. 2009 Dec 15;25(24):3228-35. doi: 10.1093/bioinformatics/btp592. Epub 2009 Oct 14.


Identifying multi-layer gene regulatory modules from multi-dimensional genomic data.

Li W, Zhang S, Liu CC, Zhou XJ.

Bioinformatics. 2012 Oct 1;28(19):2458-66. Epub 2012 Aug 3.


A sparse regulatory network of copy-number driven gene expression reveals putative breast cancer oncogenes.

Yuan Y, Curtis C, Caldas C, Markowetz F.

IEEE/ACM Trans Comput Biol Bioinform. 2012 Jul-Aug;9(4):947-54. doi: 10.1109/TCBB.2011.105.


Genome-wide analysis of DNA copy-number changes using cDNA microarrays.

Pollack JR, Perou CM, Alizadeh AA, Eisen MB, Pergamenschikov A, Williams CF, Jeffrey SS, Botstein D, Brown PO.

Nat Genet. 1999 Sep;23(1):41-6.

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