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Items: 1 to 20 of 108

1.

OncodriveCLUST: exploiting the positional clustering of somatic mutations to identify cancer genes.

Tamborero D, Gonzalez-Perez A, Lopez-Bigas N.

Bioinformatics. 2013 Sep 15;29(18):2238-44. doi: 10.1093/bioinformatics/btt395. Epub 2013 Jul 24.

PMID:
23884480
2.

Identifying cancer driver genes in tumor genome sequencing studies.

Youn A, Simon R.

Bioinformatics. 2011 Jan 15;27(2):175-81. doi: 10.1093/bioinformatics/btq630. Epub 2010 Dec 17.

3.

Functional impact bias reveals cancer drivers.

Gonzalez-Perez A, Lopez-Bigas N.

Nucleic Acids Res. 2012 Nov;40(21):e169. doi: 10.1093/nar/gks743. Epub 2012 Aug 16.

4.

e-Driver: a novel method to identify protein regions driving cancer.

Porta-Pardo E, Godzik A.

Bioinformatics. 2014 Nov 1;30(21):3109-14. doi: 10.1093/bioinformatics/btu499. Epub 2014 Jul 26.

5.

LowMACA: exploiting protein family analysis for the identification of rare driver mutations in cancer.

Melloni GE, de Pretis S, Riva L, Pelizzola M, Céol A, Costanza J, Müller H, Zammataro L.

BMC Bioinformatics. 2016 Feb 9;17:80. doi: 10.1186/s12859-016-0935-7.

6.

Utilizing protein structure to identify non-random somatic mutations.

Ryslik GA, Cheng Y, Cheung KH, Modis Y, Zhao H.

BMC Bioinformatics. 2013 Jun 13;14:190. doi: 10.1186/1471-2105-14-190.

7.

Statistical method on nonrandom clustering with application to somatic mutations in cancer.

Ye J, Pavlicek A, Lunney EA, Rejto PA, Teng CH.

BMC Bioinformatics. 2010 Jan 7;11:11. doi: 10.1186/1471-2105-11-11.

8.

Distinguishing between driver and passenger mutations in individual cancer genomes by network enrichment analysis.

Merid SK, Goranskaya D, Alexeyenko A.

BMC Bioinformatics. 2014 Sep 19;15:308. doi: 10.1186/1471-2105-15-308.

9.

Identifying novel constrained elements by exploiting biased substitution patterns.

Garber M, Guttman M, Clamp M, Zody MC, Friedman N, Xie X.

Bioinformatics. 2009 Jun 15;25(12):i54-62. doi: 10.1093/bioinformatics/btp190.

10.

Feature-based classifiers for somatic mutation detection in tumour-normal paired sequencing data.

Ding J, Bashashati A, Roth A, Oloumi A, Tse K, Zeng T, Haffari G, Hirst M, Marra MA, Condon A, Aparicio S, Shah SP.

Bioinformatics. 2012 Jan 15;28(2):167-75. doi: 10.1093/bioinformatics/btr629. Epub 2011 Nov 13.

11.

OncodriveROLE classifies cancer driver genes in loss of function and activating mode of action.

Schroeder MP, Rubio-Perez C, Tamborero D, Gonzalez-Perez A, Lopez-Bigas N.

Bioinformatics. 2014 Sep 1;30(17):i549-55. doi: 10.1093/bioinformatics/btu467.

12.

Domain landscapes of somatic mutations in cancer.

Nehrt NL, Peterson TA, Park D, Kann MG.

BMC Genomics. 2012 Jun 18;13 Suppl 4:S9. doi: 10.1186/1471-2164-13-S4-S9.

13.

Efficient methods for identifying mutated driver pathways in cancer.

Zhao J, Zhang S, Wu LY, Zhang XS.

Bioinformatics. 2012 Nov 15;28(22):2940-7. doi: 10.1093/bioinformatics/bts564. Epub 2012 Sep 14.

PMID:
22982574
14.

A graph theoretic approach to utilizing protein structure to identify non-random somatic mutations.

Ryslik GA, Cheng Y, Cheung KH, Modis Y, Zhao H.

BMC Bioinformatics. 2014 Mar 26;15:86. doi: 10.1186/1471-2105-15-86.

15.

Cancer driver gene discovery through an integrative genomics approach in a non-parametric Bayesian framework.

Yang H, Wei Q, Zhong X, Yang H, Li B.

Bioinformatics. 2017 Feb 15;33(4):483-490. doi: 10.1093/bioinformatics/btw662.

PMID:
27797769
16.

High accuracy mutation detection in leukemia on a selected panel of cancer genes.

Kalender Atak Z, De Keersmaecker K, Gianfelici V, Geerdens E, Vandepoel R, Pauwels D, Porcu M, Lahortiga I, Brys V, Dirks WG, Quentmeier H, Cloos J, Cuppens H, Uyttebroeck A, Vandenberghe P, Cools J, Aerts S.

PLoS One. 2012;7(6):e38463. doi: 10.1371/journal.pone.0038463. Epub 2012 Jun 4.

17.

A comprehensive analysis of cancer-driving mutations and genes in kidney cancer.

Long C, Jian J, Li X, Wang G, Wang J.

Oncol Lett. 2017 Apr;13(4):2151-2160. doi: 10.3892/ol.2017.5689. Epub 2017 Feb 7.

18.

ContrastRank: a new method for ranking putative cancer driver genes and classification of tumor samples.

Tian R, Basu MK, Capriotti E.

Bioinformatics. 2014 Sep 1;30(17):i572-8. doi: 10.1093/bioinformatics/btu466.

19.

Important role of indels in somatic mutations of human cancer genes.

Yang H, Zhong Y, Peng C, Chen JQ, Tian D.

BMC Med Genet. 2010 Sep 1;11:128. doi: 10.1186/1471-2350-11-128.

20.

Patterns of somatic mutation in human cancer genomes.

Greenman C, Stephens P, Smith R, Dalgliesh GL, Hunter C, Bignell G, Davies H, Teague J, Butler A, Stevens C, Edkins S, O'Meara S, Vastrik I, Schmidt EE, Avis T, Barthorpe S, Bhamra G, Buck G, Choudhury B, Clements J, Cole J, Dicks E, Forbes S, Gray K, Halliday K, Harrison R, Hills K, Hinton J, Jenkinson A, Jones D, Menzies A, Mironenko T, Perry J, Raine K, Richardson D, Shepherd R, Small A, Tofts C, Varian J, Webb T, West S, Widaa S, Yates A, Cahill DP, Louis DN, Goldstraw P, Nicholson AG, Brasseur F, Looijenga L, Weber BL, Chiew YE, DeFazio A, Greaves MF, Green AR, Campbell P, Birney E, Easton DF, Chenevix-Trench G, Tan MH, Khoo SK, Teh BT, Yuen ST, Leung SY, Wooster R, Futreal PA, Stratton MR.

Nature. 2007 Mar 8;446(7132):153-8.

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