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Items: 1 to 20 of 153

1.

Joint estimation of copy number variation and reference intensities on multiple DNA arrays using GADA.

Pique-Regi R, Ortega A, Asgharzadeh S.

Bioinformatics. 2009 May 15;25(10):1223-30. doi: 10.1093/bioinformatics/btp119.

2.

Sparse representation and Bayesian detection of genome copy number alterations from microarray data.

Pique-Regi R, Monso-Varona J, Ortega A, Seeger RC, Triche TJ, Asgharzadeh S.

Bioinformatics. 2008 Feb 1;24(3):309-18. doi: 10.1093/bioinformatics/btm601.

3.

Segmentation and estimation for SNP microarrays: a Bayesian multiple change-point approach.

Tai YC, Kvale MN, Witte JS.

Biometrics. 2010 Sep;66(3):675-83. doi: 10.1111/j.1541-0420.2009.01328.x.

4.

Normalization of Illumina Infinium whole-genome SNP data improves copy number estimates and allelic intensity ratios.

Staaf J, Vallon-Christersson J, Lindgren D, Juliusson G, Rosenquist R, Höglund M, Borg A, Ringnér M.

BMC Bioinformatics. 2008 Oct 2;9:409. doi: 10.1186/1471-2105-9-409.

5.

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.

6.

Accurate detection of aneuploidies in array CGH and gene expression microarray data.

Myers CL, Dunham MJ, Kung SY, Troyanskaya OG.

Bioinformatics. 2004 Dec 12;20(18):3533-43.

7.

Estimation and assessment of raw copy numbers at the single locus level.

Bengtsson H, Irizarry R, Carvalho B, Speed TP.

Bioinformatics. 2008 Mar 15;24(6):759-67. doi: 10.1093/bioinformatics/btn016.

8.

Joint estimation of DNA copy number from multiple platforms.

Zhang NR, Senbabaoglu Y, Li JZ.

Bioinformatics. 2010 Jan 15;26(2):153-60. doi: 10.1093/bioinformatics/btp653.

9.

Assessment of algorithms for high throughput detection of genomic copy number variation in oligonucleotide microarray data.

Baross A, Delaney AD, Li HI, Nayar T, Flibotte S, Qian H, Chan SY, Asano J, Ally A, Cao M, Birch P, Brown-John M, Fernandes N, Go A, Kennedy G, Langlois S, Eydoux P, Friedman JM, Marra MA.

BMC Bioinformatics. 2007 Oct 2;8:368.

10.

Detection of copy number variation from array intensity and sequencing read depth using a stepwise Bayesian model.

Zhang ZD, Gerstein MB.

BMC Bioinformatics. 2010 Oct 31;11:539. doi: 10.1186/1471-2105-11-539.

11.

R-Gada: a fast and flexible pipeline for copy number analysis in association studies.

Pique-Regi R, Cáceres A, González JR.

BMC Bioinformatics. 2010 Jul 16;11:380. doi: 10.1186/1471-2105-11-380.

12.

ITALICS: an algorithm for normalization and DNA copy number calling for Affymetrix SNP arrays.

Rigaill G, Hupé P, Almeida A, La Rosa P, Meyniel JP, Decraene C, Barillot E.

Bioinformatics. 2008 Mar 15;24(6):768-74. doi: 10.1093/bioinformatics/btn048.

13.

Modified screening and ranking algorithm for copy number variation detection.

Xiao F, Min X, Zhang H.

Bioinformatics. 2015 May 1;31(9):1341-8. doi: 10.1093/bioinformatics/btu850.

14.

Estimating genome-wide copy number using allele-specific mixture models.

Wang W, Carvalho B, Miller ND, Pevsner J, Chakravarti A, Irizarry RA.

J Comput Biol. 2008 Sep;15(7):857-66. doi: 10.1089/cmb.2007.0148.

15.

Gene expression and isoform variation analysis using Affymetrix Exon Arrays.

Bemmo A, Benovoy D, Kwan T, Gaffney DJ, Jensen RV, Majewski J.

BMC Genomics. 2008 Nov 7;9:529. doi: 10.1186/1471-2164-9-529. Erratum in: BMC Genomics. 2009 Mar 23;10. doi: 10.1186/1471-2164-10-121.

16.

A Bayesian segmentation approach to ascertain copy number variations at the population level.

Wu LY, Chipman HA, Bull SB, Briollais L, Wang K.

Bioinformatics. 2009 Jul 1;25(13):1669-79. doi: 10.1093/bioinformatics/btp270.

17.

Hybridization modeling of oligonucleotide SNP arrays for accurate DNA copy number estimation.

Wan L, Sun K, Ding Q, Cui Y, Li M, Wen Y, Elston RC, Qian M, Fu WJ.

Nucleic Acids Res. 2009 Sep;37(17):e117. doi: 10.1093/nar/gkp559.

18.

Normalization of array-CGH data: influence of copy number imbalances.

Staaf J, Jönsson G, Ringnér M, Vallon-Christersson J.

BMC Genomics. 2007 Oct 22;8:382.

19.

Integrated high-resolution genome-wide analysis of gene dosage and gene expression in human brain tumors.

Juric D, Bredel C, Sikic BI, Bredel M.

Methods Mol Biol. 2007;377:187-202. Review.

PMID:
17634618
20.

A multilevel model to address batch effects in copy number estimation using SNP arrays.

Scharpf RB, Ruczinski I, Carvalho B, Doan B, Chakravarti A, Irizarry RA.

Biostatistics. 2011 Jan;12(1):33-50. doi: 10.1093/biostatistics/kxq043.

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