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PathScan: a tool for discerning mutational significance in groups of putative cancer genes.

Wendl MC, Wallis JW, Lin L, Kandoth C, Mardis ER, Wilson RK, Ding L.

Bioinformatics. 2011 Jun 15;27(12):1595-602. doi: 10.1093/bioinformatics/btr193. Epub 2011 Apr 14.


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.


Finding co-mutated genes and candidate cancer genes in cancer genomes by stratified false discovery rate control.

Wang J, Zhang Y, Shen X, Zhu J, Zhang L, Zou J, Guo Z.

Mol Biosyst. 2011 Apr;7(4):1158-66. doi: 10.1039/c0mb00211a. Epub 2011 Jan 28.


Mutational analysis of EGFR and related signaling pathway genes in lung adenocarcinomas identifies a novel somatic kinase domain mutation in FGFR4.

Marks JL, McLellan MD, Zakowski MF, Lash AE, Kasai Y, Broderick S, Sarkaria IS, Pham D, Singh B, Miner TL, Fewell GA, Fulton LL, Mardis ER, Wilson RK, Kris MG, Rusch VW, Varmus H, Pao W.

PLoS One. 2007 May 9;2(5):e426.


Estimating the order of mutations during tumorigenesis from tumor genome sequencing data.

Youn A, Simon R.

Bioinformatics. 2012 Jun 15;28(12):1555-61. doi: 10.1093/bioinformatics/bts168. Epub 2012 Apr 6.


DrGaP: a powerful tool for identifying driver genes and pathways in cancer sequencing studies.

Hua X, Xu H, Yang Y, Zhu J, Liu P, Lu Y.

Am J Hum Genet. 2013 Sep 5;93(3):439-51. doi: 10.1016/j.ajhg.2013.07.003. Epub 2013 Aug 15.


Discovery of mutated subnetworks associated with clinical data in cancer.

Vandin F, Clay P, Upfal E, Raphael BJ.

Pac Symp Biocomput. 2012:55-66.


A robust tool for discriminative analysis and feature selection in paired samples impacts the identification of the genes essential for reprogramming lung tissue to adenocarcinoma.

Toh SH, Prathipati P, Motakis E, Kwoh CK, Yenamandra SP, Kuznetsov VA.

BMC Genomics. 2011 Nov 30;12 Suppl 3:S24. doi: 10.1186/1471-2164-12-S3-S24. Epub 2011 Nov 30.


Personalized pathway enrichment map of putative cancer genes from next generation sequencing data.

Jia P, Zhao Z.

PLoS One. 2012;7(5):e37595. doi: 10.1371/journal.pone.0037595. Epub 2012 May 18.


De novo discovery of mutated driver pathways in cancer.

Vandin F, Upfal E, Raphael BJ.

Genome Res. 2012 Feb;22(2):375-85. doi: 10.1101/gr.120477.111. Epub 2011 Jun 7.


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.


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.


TAGCNA: a method to identify significant consensus events of copy number alterations in cancer.

Yuan X, Zhang J, Yang L, Zhang S, Chen B, Geng Y, Wang Y.

PLoS One. 2012;7(7):e41082. doi: 10.1371/journal.pone.0041082. Epub 2012 Jul 18.


Design and analysis issues in genome-wide somatic mutation studies of cancer.

Parmigiani G, Boca S, Lin J, Kinzler KW, Velculescu V, Vogelstein B.

Genomics. 2009 Jan;93(1):17-21. doi: 10.1016/j.ygeno.2008.07.005. Epub 2008 Aug 23. Review.


Genomic and transcriptional alterations in lung adenocarcinoma in relation to EGFR and KRAS mutation status.

Planck M, Edlund K, Botling J, Micke P, Isaksson S, Staaf J.

PLoS One. 2013 Oct 24;8(10):e78614. doi: 10.1371/journal.pone.0078614. eCollection 2013.


MuSiC: identifying mutational significance in cancer genomes.

Dees ND, Zhang Q, Kandoth C, Wendl MC, Schierding W, Koboldt DC, Mooney TB, Callaway MB, Dooling D, Mardis ER, Wilson RK, Ding L.

Genome Res. 2012 Aug;22(8):1589-98. doi: 10.1101/gr.134635.111. Epub 2012 Jul 3.


Simultaneous identification of multiple driver pathways in cancer.

Leiserson MD, Blokh D, Sharan R, Raphael BJ.

PLoS Comput Biol. 2013;9(5):e1003054. doi: 10.1371/journal.pcbi.1003054. Epub 2013 May 23.


Genome-wide identification of significant aberrations in cancer genome.

Yuan X, Yu G, Hou X, Shih IeM, Clarke R, Zhang J, Hoffman EP, Wang RR, Zhang Z, Wang Y.

BMC Genomics. 2012 Jul 27;13:342. doi: 10.1186/1471-2164-13-342.


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.


Identification of rare cancer driver mutations by network reconstruction.

Torkamani A, Schork NJ.

Genome Res. 2009 Sep;19(9):1570-8. doi: 10.1101/gr.092833.109. Epub 2009 Jul 2.

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