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Functional impact bias reveals cancer drivers.
Gonzalez-Perez A, Lopez-Bigas N. Gonzalez-Perez A, et al. Nucleic Acids Res. 2012 Nov;40(21):e169. doi: 10.1093/nar/gks743. Epub 2012 Aug 16. Nucleic Acids Res. 2012. PMID: 22904074 Free PMC article.
Improving the assessment of the outcome of nonsynonymous SNVs with a consensus deleteriousness score, Condel.
González-Pérez A, López-Bigas N. González-Pérez A, et al. Am J Hum Genet. 2011 Apr 8;88(4):440-9. doi: 10.1016/j.ajhg.2011.03.004. Epub 2011 Mar 31. Am J Hum Genet. 2011. PMID: 21457909 Free PMC article.
PARADIGM-SHIFT predicts the function of mutations in multiple cancers using pathway impact analysis.
Ng S, Collisson EA, Sokolov A, Goldstein T, Gonzalez-Perez A, Lopez-Bigas N, Benz C, Haussler D, Stuart JM. Ng S, et al. Bioinformatics. 2012 Sep 15;28(18):i640-i646. doi: 10.1093/bioinformatics/bts402. Bioinformatics. 2012. PMID: 22962493 Free PMC article.
Improving the prediction of the functional impact of cancer mutations by baseline tolerance transformation.
Gonzalez-Perez A, Deu-Pons J, Lopez-Bigas N. Gonzalez-Perez A, et al. Genome Med. 2012 Nov 26;4(11):89. doi: 10.1186/gm390. eCollection 2012. Genome Med. 2012. PMID: 23181723 Free PMC article.
Visualizing multidimensional cancer genomics data.
Schroeder MP, Gonzalez-Perez A, Lopez-Bigas N. Schroeder MP, et al. Genome Med. 2013 Jan 31;5(1):9. doi: 10.1186/gm413. eCollection 2013. Genome Med. 2013. PMID: 23363777 Free PMC article. Review.
Oncodrive-CIS: a method to reveal likely driver genes based on the impact of their copy number changes on expression.
Tamborero D, Lopez-Bigas N, Gonzalez-Perez A. Tamborero D, et al. PLoS One. 2013;8(2):e55489. doi: 10.1371/journal.pone.0055489. Epub 2013 Feb 8. PLoS One. 2013. PMID: 23408991 Free PMC article.
OncodriveCLUST: exploiting the positional clustering of somatic mutations to identify cancer genes.
Tamborero D, Gonzalez-Perez A, Lopez-Bigas N. Tamborero D, et al. Bioinformatics. 2013 Sep 15;29(18):2238-44. doi: 10.1093/bioinformatics/btt395. Epub 2013 Jul 24. Bioinformatics. 2013. PMID: 23884480
Computational approaches to identify functional genetic variants in cancer genomes.
Gonzalez-Perez A, Mustonen V, Reva B, Ritchie GR, Creixell P, Karchin R, Vazquez M, Fink JL, Kassahn KS, Pearson JV, Bader GD, Boutros PC, Muthuswamy L, Ouellette BF, Reimand J, Linding R, Shibata T, Valencia A, Butler A, Dronov S, Flicek P, Shannon NB, Carter H, Ding L, Sander C, Stuart JM, Stein LD, Lopez-Bigas N; International Cancer Genome Consortium Mutation Pathways and Consequences Subgroup of the Bioinformatics Analyses Working Group. Gonzalez-Perez A, et al. Nat Methods. 2013 Aug;10(8):723-9. doi: 10.1038/nmeth.2562. Nat Methods. 2013. PMID: 23900255 Free PMC article.
IntOGen-mutations identifies cancer drivers across tumor types.
Gonzalez-Perez A, Perez-Llamas C, Deu-Pons J, Tamborero D, Schroeder MP, Jene-Sanz A, Santos A, Lopez-Bigas N. Gonzalez-Perez A, et al. Nat Methods. 2013 Nov;10(11):1081-2. doi: 10.1038/nmeth.2642. Epub 2013 Sep 15. Nat Methods. 2013. PMID: 24037244 Free PMC article.
Comprehensive identification of mutational cancer driver genes across 12 tumor types.
Tamborero D, Gonzalez-Perez A, Perez-Llamas C, Deu-Pons J, Kandoth C, Reimand J, Lawrence MS, Getz G, Bader GD, Ding L, Lopez-Bigas N. Tamborero D, et al. Sci Rep. 2013 Oct 2;3:2650. doi: 10.1038/srep02650. Sci Rep. 2013. PMID: 24084849 Free PMC article.
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