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Results: 1 to 20 of 93

1.

Virmid: accurate detection of somatic mutations with sample impurity inference.

Kim S, Jeong K, Bhutani K, Lee J, Patel A, Scott E, Nam H, Lee H, Gleeson JG, Bafna V.

Genome Biol. 2013 Aug 29;14(8):R90. doi: 10.1186/gb-2013-14-8-r90.

PMID:
23987214
[PubMed - in process]
Free PMC Article
2.

Strelka: accurate somatic small-variant calling from sequenced tumor-normal sample pairs.

Saunders CT, Wong WS, Swamy S, Becq J, Murray LJ, Cheetham RK.

Bioinformatics. 2012 Jul 15;28(14):1811-7. doi: 10.1093/bioinformatics/bts271. Epub 2012 May 10.

PMID:
22581179
[PubMed - indexed for MEDLINE]
Free Article
3.

HapMuC: somatic mutation calling using heterozygous germ line variants near candidate mutations.

Usuyama N, Shiraishi Y, Sato Y, Kume H, Homma Y, Ogawa S, Miyano S, Imoto S.

Bioinformatics. 2014 Aug 14. pii: btu537. [Epub ahead of print]

PMID:
25123903
[PubMed - as supplied by publisher]
Free Article
4.

Mutascope: sensitive detection of somatic mutations from deep amplicon sequencing.

Yost SE, Alakus H, Matsui H, Schwab RB, Jepsen K, Frazer KA, Harismendy O.

Bioinformatics. 2013 Aug 1;29(15):1908-9. doi: 10.1093/bioinformatics/btt305. Epub 2013 May 27.

PMID:
23712659
[PubMed - indexed for MEDLINE]
Free PMC Article
5.
6.

An empirical Bayesian framework for somatic mutation detection from cancer genome sequencing data.

Shiraishi Y, Sato Y, Chiba K, Okuno Y, Nagata Y, Yoshida K, Shiba N, Hayashi Y, Kume H, Homma Y, Sanada M, Ogawa S, Miyano S.

Nucleic Acids Res. 2013 Apr;41(7):e89. doi: 10.1093/nar/gkt126. Epub 2013 Mar 6.

PMID:
23471004
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data.

Li H.

Bioinformatics. 2011 Nov 1;27(21):2987-93. doi: 10.1093/bioinformatics/btr509. Epub 2011 Sep 8.

PMID:
21903627
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Short read sequence typing (SRST): multi-locus sequence types from short reads.

Inouye M, Conway TC, Zobel J, Holt KE.

BMC Genomics. 2012 Jul 24;13:338.

PMID:
22827703
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

JointSNVMix: a probabilistic model for accurate detection of somatic mutations in normal/tumour paired next-generation sequencing data.

Roth A, Ding J, Morin R, Crisan A, Ha G, Giuliany R, Bashashati A, Hirst M, Turashvili G, Oloumi A, Marra MA, Aparicio S, Shah SP.

Bioinformatics. 2012 Apr 1;28(7):907-13. doi: 10.1093/bioinformatics/bts053. Epub 2012 Jan 27.

PMID:
22285562
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Power for genetic association studies with random allele frequencies and genotype distributions.

Ambrosius WT, Lange EM, Langefeld CD.

Am J Hum Genet. 2004 Apr;74(4):683-93. Epub 2004 Mar 12.

PMID:
15024689
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

FaSD-somatic: a fast and accurate somatic SNV detection algorithm for cancer genome sequencing data.

Wang W, Wang P, Xu F, Luo R, Wong MP, Lam TW, Wang J.

Bioinformatics. 2014 Sep 1;30(17):2498-500. doi: 10.1093/bioinformatics/btu338. Epub 2014 May 14.

PMID:
24833803
[PubMed - in process]
12.

Mitochondrial DNA mutations in pancreatic cancer.

Kassauei K, Habbe N, Mullendore ME, Karikari CA, Maitra A, Feldmann G.

Int J Gastrointest Cancer. 2006;37(2-3):57-64.

PMID:
17827523
[PubMed - indexed for MEDLINE]
13.

Identification of somatic mutations in cancer through Bayesian-based analysis of sequenced genome pairs.

Christoforides A, Carpten JD, Weiss GJ, Demeure MJ, Von Hoff DD, Craig DW.

BMC Genomics. 2013 May 4;14:302. doi: 10.1186/1471-2164-14-302.

PMID:
23642077
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

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
15.

qpure: A tool to estimate tumor cellularity from genome-wide single-nucleotide polymorphism profiles.

Song S, Nones K, Miller D, Harliwong I, Kassahn KS, Pinese M, Pajic M, Gill AJ, Johns AL, Anderson M, Holmes O, Leonard C, Taylor D, Wood S, Xu Q, Newell F, Cowley MJ, Wu J, Wilson P, Fink L, Biankin AV, Waddell N, Grimmond SM, Pearson JV.

PLoS One. 2012;7(9):e45835. doi: 10.1371/journal.pone.0045835. Epub 2012 Sep 25.

PMID:
23049875
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Detection of rare genomic variants from pooled sequencing using SPLINTER.

Vallania F, Ramos E, Cresci S, Mitra RD, Druley TE.

J Vis Exp. 2012 Jun 23;(64). pii: 3943. doi: 10.3791/3943.

PMID:
22760212
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

[Screening for K-ras mutations in colorectal and lung cancers by using a novel real-time PCR with ADx-K-ras kit and Sanger DNA sequencing].

Zhang HP, Fu L, Chen PQ, Ye YB, Ji TH, Zheng LM.

Zhonghua Bing Li Xue Za Zhi. 2010 Nov;39(11):757-61. Chinese.

PMID:
21215167
[PubMed - indexed for MEDLINE]
18.

MTML-msBayes: approximate Bayesian comparative phylogeographic inference from multiple taxa and multiple loci with rate heterogeneity.

Huang W, Takebayashi N, Qi Y, Hickerson MJ.

BMC Bioinformatics. 2011 Jan 3;12:1. doi: 10.1186/1471-2105-12-1.

PMID:
21199577
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Real-time bidirectional pyrophosphorolysis-activated polymerization for quantitative detection of somatic mutations.

Song N, Zhong X, Li Q.

PLoS One. 2014 Apr 25;9(4):e96420. doi: 10.1371/journal.pone.0096420. eCollection 2014.

PMID:
24769870
[PubMed - in process]
Free PMC Article
20.

Further steps in TANGO: improved taxonomic assignment in metagenomics.

Alonso-Alemany D, Barré A, Beretta S, Bonizzoni P, Nikolski M, Valiente G.

Bioinformatics. 2014 Jan 1;30(1):17-23. doi: 10.1093/bioinformatics/btt256. Epub 2013 May 3.

PMID:
23645816
[PubMed - indexed for MEDLINE]

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