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Results: 1 to 20 of 95

1.

THetA: inferring intra-tumor heterogeneity from high-throughput DNA sequencing data.

Oesper L, Mahmoody A, Raphael BJ.

Genome Biol. 2013 Jul 29;14(7):R80. doi: 10.1186/gb-2013-14-7-r80.

PMID:
23895164
[PubMed - in process]
Free PMC Article
2.

A combinatorial approach for analyzing intra-tumor heterogeneity from high-throughput sequencing data.

Hajirasouliha I, Mahmoody A, Raphael BJ.

Bioinformatics. 2014 Jun 15;30(12):i78-86. doi: 10.1093/bioinformatics/btu284.

PMID:
24932008
[PubMed - in process]
Free PMC Article
3.

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
4.

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.

PMID:
24845652
[PubMed - in process]
Free PMC Article
5.

Reconstructing cancer genomes from paired-end sequencing data.

Oesper L, Ritz A, Aerni SJ, Drebin R, Raphael BJ.

BMC Bioinformatics. 2012 Apr 19;13 Suppl 6:S10. doi: 10.1186/1471-2105-13-S6-S10.

PMID:
22537039
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Detecting independent and recurrent copy number aberrations using interval graphs.

Wu HT, Hajirasouliha I, Raphael BJ.

Bioinformatics. 2014 Jun 15;30(12):i195-203. doi: 10.1093/bioinformatics/btu276.

PMID:
24931984
[PubMed - in process]
Free PMC Article
7.

Inferring clonal evolution of tumors from single nucleotide somatic mutations.

Jiao W, Vembu S, Deshwar AG, Stein L, Morris Q.

BMC Bioinformatics. 2014 Feb 1;15:35. doi: 10.1186/1471-2105-15-35.

PMID:
24484323
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Inferring viral quasispecies spectra from 454 pyrosequencing reads.

Astrovskaya I, Tork B, Mangul S, Westbrooks K, Măndoiu I, Balfe P, Zelikovsky A.

BMC Bioinformatics. 2011;12 Suppl 6:S1. doi: 10.1186/1471-2105-12-S6-S1. Epub 2011 Jul 28.

PMID:
21989211
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

AbsCN-seq: a statistical method to estimate tumor purity, ploidy and absolute copy numbers from next-generation sequencing data.

Bao L, Pu M, Messer K.

Bioinformatics. 2014 Jan 13. [Epub ahead of print]

PMID:
24389661
[PubMed - as supplied by publisher]
10.

CNV-guided multi-read allocation for ChIP-seq.

Zhang Q, Keleş S.

Bioinformatics. 2014 Jun 24. pii: btu402. [Epub ahead of print]

PMID:
24966364
[PubMed - as supplied by publisher]
11.

Savant: genome browser for high-throughput sequencing data.

Fiume M, Williams V, Brook A, Brudno M.

Bioinformatics. 2010 Aug 15;26(16):1938-44. doi: 10.1093/bioinformatics/btq332. Epub 2010 Jun 20.

PMID:
20562449
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

High-definition reconstruction of clonal composition in cancer.

Fischer A, Vázquez-García I, Illingworth CJ, Mustonen V.

Cell Rep. 2014 Jun 12;7(5):1740-52. doi: 10.1016/j.celrep.2014.04.055. Epub 2014 May 29.

PMID:
24882004
[PubMed - in process]
Free PMC Article
13.

Deconvolving tumor purity and ploidy by integrating copy number alterations and loss of heterozygosity.

Li Y, Xie X.

Bioinformatics. 2014 Aug 1;30(15):2121-9. doi: 10.1093/bioinformatics/btu174. Epub 2014 Apr 2.

PMID:
24695406
[PubMed - in process]
14.

CNAseg--a novel framework for identification of copy number changes in cancer from second-generation sequencing data.

Ivakhno S, Royce T, Cox AJ, Evers DJ, Cheetham RK, Tavaré S.

Bioinformatics. 2010 Dec 15;26(24):3051-8. doi: 10.1093/bioinformatics/btq587. Epub 2010 Oct 21.

PMID:
20966003
[PubMed - indexed for MEDLINE]
Free Article
15.

BACOM: in silico detection of genomic deletion types and correction of normal cell contamination in copy number data.

Yu G, Zhang B, Bova GS, Xu J, Shih IeM, Wang Y.

Bioinformatics. 2011 Jun 1;27(11):1473-80. doi: 10.1093/bioinformatics/btr183. Epub 2011 Apr 15.

PMID:
21498400
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

WaveCNV: allele-specific copy number alterations in primary tumors and xenograft models from next-generation sequencing.

Holt C, Losic B, Pai D, Zhao Z, Trinh Q, Syam S, Arshadi N, Jang GH, Ali J, Beck T, McPherson J, Muthuswamy LB.

Bioinformatics. 2014 Mar 15;30(6):768-74. doi: 10.1093/bioinformatics/btt611. Epub 2013 Nov 4.

PMID:
24192544
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

GenHtr: a tool for comparative assessment of genetic heterogeneity in microbial genomes generated by massive short-read sequencing.

Yu G.

BMC Bioinformatics. 2010 Oct 12;11:508. doi: 10.1186/1471-2105-11-508.

PMID:
20939910
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Fast and accurate read alignment for resequencing.

Mu JC, Jiang H, Kiani A, Mohiyuddin M, Bani Asadi N, Wong WH.

Bioinformatics. 2012 Sep 15;28(18):2366-73. doi: 10.1093/bioinformatics/bts450. Epub 2012 Jul 18.

PMID:
22811546
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

SHEAR: sample heterogeneity estimation and assembly by reference.

Landman SR, Hwang TH, Silverstein KA, Li Y, Dehm SM, Steinbach M, Kumar V.

BMC Genomics. 2014 Jan 29;15:84. doi: 10.1186/1471-2164-15-84.

PMID:
24476358
[PubMed - in process]
Free PMC Article
20.

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.

PMID:
21305028
[PubMed - indexed for MEDLINE]
Free PMC Article

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