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Results: 1 to 20 of 104

1.

Allele-specific copy number analysis of tumor samples with aneuploidy and tumor heterogeneity.

Rasmussen M, Sundström M, Göransson Kultima H, Botling J, Micke P, Birgisson H, Glimelius B, Isaksson A.

Genome Biol. 2011 Oct 24;12(10):R108. doi: 10.1186/gb-2011-12-10-r108.

PMID:
22023820
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

ACNE: a summarization method to estimate allele-specific copy numbers for Affymetrix SNP arrays.

Ortiz-Estevez M, Bengtsson H, Rubio A.

Bioinformatics. 2010 Aug 1;26(15):1827-33. doi: 10.1093/bioinformatics/btq300. Epub 2010 Jun 6.

PMID:
20529889
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

A Hidden Markov Model to estimate population mixture and allelic copy-numbers in cancers using Affymetrix SNP arrays.

Lamy P, Andersen CL, Dyrskjot L, Torring N, Wiuf C.

BMC Bioinformatics. 2007 Nov 9;8:434.

PMID:
17996079
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Analyzing cancer samples with SNP arrays.

Van Loo P, Nilsen G, Nordgard SH, Vollan HK, Børresen-Dale AL, Kristensen VN, Lingjærde OC.

Methods Mol Biol. 2012;802:57-72. doi: 10.1007/978-1-61779-400-1_4.

PMID:
22130873
[PubMed - indexed for MEDLINE]
5.

SiDCoN: a tool to aid scoring of DNA copy number changes in SNP chip data.

Nancarrow DJ, Handoko HY, Stark MS, Whiteman DC, Hayward NK.

PLoS One. 2007 Oct 31;2(10):e1093.

PMID:
17971856
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Major copy proportion analysis of tumor samples using SNP arrays.

Li C, Beroukhim R, Weir BA, Winckler W, Garraway LA, Sellers WR, Meyerson M.

BMC Bioinformatics. 2008 Apr 21;9:204. doi: 10.1186/1471-2105-9-204.

PMID:
18426588
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Precise inference of copy number alterations in tumor samples from SNP arrays.

Chen GK, Chang X, Curtis C, Wang K.

Bioinformatics. 2013 Dec 1;29(23):2964-70. doi: 10.1093/bioinformatics/btt521. Epub 2013 Sep 9.

PMID:
24021380
[PubMed - indexed for MEDLINE]
8.

Computational method for estimating DNA copy numbers in normal samples, cancer cell lines, and solid tumors using array comparative genomic hybridization.

Abkevich V, Iliev D, Timms KM, Tran T, Skolnick M, Lanchbury JS, Gutin A.

J Biomed Biotechnol. 2010;2010. pii: 386870. doi: 10.1155/2010/386870. Epub 2010 Jul 8.

PMID:
20706610
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

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
10.

High-resolution array copy number analyses for detection of deletion, gain, amplification and copy-neutral LOH in primary neuroblastoma tumors: four cases of homozygous deletions of the CDKN2A gene.

Carén H, Erichsen J, Olsson L, Enerbäck C, Sjöberg RM, Abrahamsson J, Kogner P, Martinsson T.

BMC Genomics. 2008 Jul 29;9:353. doi: 10.1186/1471-2164-9-353.

PMID:
18664255
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

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
12.

GPHMM: an integrated hidden Markov model for identification of copy number alteration and loss of heterozygosity in complex tumor samples using whole genome SNP arrays.

Li A, Liu Z, Lezon-Geyda K, Sarkar S, Lannin D, Schulz V, Krop I, Winer E, Harris L, Tuck D.

Nucleic Acids Res. 2011 Jul;39(12):4928-41. doi: 10.1093/nar/gkr014. Epub 2011 Mar 11.

PMID:
21398628
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

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. Epub 2004 Jul 29.

PMID:
15284100
[PubMed - indexed for MEDLINE]
Free Article
14.

Aneuploidy prediction and tumor classification with heterogeneous hidden conditional random fields.

Barutcuoglu Z, Airoldi EM, Dumeaux V, Schapire RE, Troyanskaya OG.

Bioinformatics. 2009 May 15;25(10):1307-13. doi: 10.1093/bioinformatics/btn585. Epub 2008 Dec 3.

PMID:
19052061
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Improvements in the analysis strategy make single nucleotide polymorphism analysis a powerful tool in the detection and characterization of amplified chromosomal regions in human tumors.

Korsching E, Agelopolous K, Schmidt H, Buchroth I, Gosheger G, Wülfing P, Boecker W, Brandt B, Buerger H.

Pathobiology. 2006;73(1):18-25.

PMID:
16785764
[PubMed - indexed for MEDLINE]
16.

Ploidy status and copy number aberrations in primary glioblastomas defined by integrated analysis of allelic ratios, signal ratios and loss of heterozygosity using 500K SNP Mapping Arrays.

Gardina PJ, Lo KC, Lee W, Cowell JK, Turpaz Y.

BMC Genomics. 2008 Oct 17;9:489. doi: 10.1186/1471-2164-9-489.

PMID:
18928532
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

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
18.

PICNIC: an algorithm to predict absolute allelic copy number variation with microarray cancer data.

Greenman CD, Bignell G, Butler A, Edkins S, Hinton J, Beare D, Swamy S, Santarius T, Chen L, Widaa S, Futreal PA, Stratton MR.

Biostatistics. 2010 Jan;11(1):164-75. doi: 10.1093/biostatistics/kxp045. Epub 2009 Oct 15.

PMID:
19837654
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

MOCSphaser: a haplotype inference tool from a mixture of copy number variation and single nucleotide polymorphism data.

Kato M, Nakamura Y, Tsunoda T.

Bioinformatics. 2008 Jul 15;24(14):1645-6. doi: 10.1093/bioinformatics/btn242. Epub 2008 May 20.

PMID:
18492685
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

MixHMM: inferring copy number variation and allelic imbalance using SNP arrays and tumor samples mixed with stromal cells.

Liu Z, Li A, Schulz V, Chen M, Tuck D.

PLoS One. 2010 Jun 1;5(6):e10909. doi: 10.1371/journal.pone.0010909.

PMID:
20532221
[PubMed - indexed for MEDLINE]
Free PMC Article

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