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Results: 1 to 20 of 97

Related Citations for PubMed (Select 23895164)

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.

2.

Quantifying tumor heterogeneity in whole-genome and whole-exome sequencing data.

Oesper L, Satas G, Raphael BJ.

Bioinformatics. 2014 Dec 15;30(24):3532-40. doi: 10.1093/bioinformatics/btu651. Epub 2014 Oct 8.

PMID:
25297070
3.

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.

4.

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.

5.

MixClone: a mixture model for inferring tumor subclonal populations.

Li Y, Xie X.

BMC Genomics. 2015;16 Suppl 2:S1. doi: 10.1186/1471-2164-16-S2-S1. Epub 2015 Jan 21.

6.

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.

7.

SomatiCA: identifying, characterizing and quantifying somatic copy number aberrations from cancer genome sequencing data.

Chen M, Gunel M, Zhao H.

PLoS One. 2013 Nov 12;8(11):e78143. doi: 10.1371/journal.pone.0078143. eCollection 2013.

8.

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.

9.

Leveraging reads that span multiple single nucleotide polymorphisms for haplotype inference from sequencing data.

Yang WY, Hormozdiari F, Wang Z, He D, Pasaniuc B, Eskin E.

Bioinformatics. 2013 Sep 15;29(18):2245-52. doi: 10.1093/bioinformatics/btt386. Epub 2013 Jul 3.

10.

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.

11.

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.

12.

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
13.

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.

14.

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.

15.
16.

PhyloWGS: Reconstructing subclonal composition and evolution from whole-genome sequencing of tumors.

Deshwar AG, Vembu S, Yung CK, Jang GH, Stein L, Morris Q.

Genome Biol. 2015 Feb 13;16(1):35. doi: 10.1186/s13059-015-0602-8.

17.

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

Zhang Q, Keleş S.

Bioinformatics. 2014 Oct 15;30(20):2860-7. doi: 10.1093/bioinformatics/btu402. Epub 2014 Jun 24.

PMID:
24966364
18.

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.

19.

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.

20.

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.

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