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Items: 1 to 20 of 98

1.

Reconstructing DNA copy number by joint segmentation of multiple sequences.

Zhang Z, Lange K, Sabatti C.

BMC Bioinformatics. 2012 Aug 16;13:205. doi: 10.1186/1471-2105-13-205.

2.

Simple binary segmentation frameworks for identifying variation in DNA copy number.

Yang TY.

BMC Bioinformatics. 2012 Oct 30;13:277. doi: 10.1186/1471-2105-13-277.

3.

Personalized copy number and segmental duplication maps using next-generation sequencing.

Alkan C, Kidd JM, Marques-Bonet T, Aksay G, Antonacci F, Hormozdiari F, Kitzman JO, Baker C, Malig M, Mutlu O, Sahinalp SC, Gibbs RA, Eichler EE.

Nat Genet. 2009 Oct;41(10):1061-7. doi: 10.1038/ng.437. Epub 2009 Aug 30.

4.

Copynumber: Efficient algorithms for single- and multi-track copy number segmentation.

Nilsen G, Liestøl K, Van Loo P, Moen Vollan HK, Eide MB, Rueda OM, Chin SF, Russell R, Baumbusch LO, Caldas C, Børresen-Dale AL, Lingjaerde OC.

BMC Genomics. 2012 Nov 4;13:591. doi: 10.1186/1471-2164-13-591.

5.

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. Epub 2009 Mar 10.

6.

Detection of DNA copy number alterations using penalized least squares regression.

Huang T, Wu B, Lizardi P, Zhao H.

Bioinformatics. 2005 Oct 15;21(20):3811-7. Epub 2005 Aug 30.

PMID:
16131523
7.

Copy number variation of individual cattle genomes using next-generation sequencing.

Bickhart DM, Hou Y, Schroeder SG, Alkan C, Cardone MF, Matukumalli LK, Song J, Schnabel RD, Ventura M, Taylor JF, Garcia JF, Van Tassell CP, Sonstegard TS, Eichler EE, Liu GE.

Genome Res. 2012 Apr;22(4):778-90. doi: 10.1101/gr.133967.111. Epub 2012 Feb 2.

8.

Common copy number variation detection from multiple sequenced samples.

Duan J, Deng HW, Wang YP.

IEEE Trans Biomed Eng. 2014 Mar;61(3):928-37. doi: 10.1109/TBME.2013.2292588.

9.

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. Epub 2010 Jul 12.

10.

Sensitive and accurate detection of copy number variants using read depth of coverage.

Yoon S, Xuan Z, Makarov V, Ye K, Sebat J.

Genome Res. 2009 Sep;19(9):1586-92. doi: 10.1101/gr.092981.109. Epub 2009 Aug 5.

11.

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.

12.

CNV-seq, a new method to detect copy number variation using high-throughput sequencing.

Xie C, Tammi MT.

BMC Bioinformatics. 2009 Mar 6;10:80. doi: 10.1186/1471-2105-10-80.

13.

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.

14.

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.

PMID:
10471496
15.

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

Alkodsi A, Louhimo R, Hautaniemi S.

Brief Bioinform. 2015 Mar;16(2):242-54. doi: 10.1093/bib/bbu004. Epub 2014 Mar 5.

PMID:
24599115
16.

SLMSuite: a suite of algorithms for segmenting genomic profiles.

Orlandini V, Provenzano A, Giglio S, Magi A.

BMC Bioinformatics. 2017 Jun 28;18(1):321. doi: 10.1186/s12859-017-1734-5.

17.

Estimation of correlations between copy-number variants in non-coding DNA.

Stamoulis C.

Conf Proc IEEE Eng Med Biol Soc. 2011;2011:5563-6. doi: 10.1109/IEMBS.2011.6091345.

18.

A fast and flexible method for the segmentation of aCGH data.

Ben-Yaacov E, Eldar YC.

Bioinformatics. 2008 Aug 15;24(16):i139-45. doi: 10.1093/bioinformatics/btn272.

PMID:
18689815
19.

A sensitive method for detecting variation in copy numbers of duplicated genes.

Pielberg G, Day AE, Plastow GS, Andersson L.

Genome Res. 2003 Sep;13(9):2171-7.

20.

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.

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