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GeneSrF and varSelRF: a web-based tool and R package for gene selection and classification using random forest.
Diaz-Uriarte R. Diaz-Uriarte R. BMC Bioinformatics. 2007 Sep 3;8:328. doi: 10.1186/1471-2105-8-328. BMC Bioinformatics. 2007. PMID: 17767709 Free PMC article.
Identifying restrictions in the order of accumulation of mutations during tumor progression: effects of passengers, evolutionary models, and sampling.
Diaz-Uriarte R. Diaz-Uriarte R. BMC Bioinformatics. 2015 Feb 12;16:41. doi: 10.1186/s12859-015-0466-7. BMC Bioinformatics. 2015. PMID: 25879190 Free PMC article.
OncoSimulR: genetic simulation with arbitrary epistasis and mutator genes in asexual populations.
Diaz-Uriarte R. Diaz-Uriarte R. Bioinformatics. 2017 Jun 15;33(12):1898-1899. doi: 10.1093/bioinformatics/btx077. Bioinformatics. 2017. PMID: 28186227 Free PMC article.
waviCGH: a web application for the analysis and visualization of genomic copy number alterations.
Carro A, Rico D, Rueda OM, Díaz-Uriarte R, Pisano DG. Carro A, et al. Nucleic Acids Res. 2010 Jul;38(Web Server issue):W182-7. doi: 10.1093/nar/gkq441. Epub 2010 May 27. Nucleic Acids Res. 2010. PMID: 20507915 Free PMC article.
ADaCGH2: parallelized analysis of (big) CNA data.
Diaz-Uriarte R. Diaz-Uriarte R. Bioinformatics. 2014 Jun 15;30(12):1759-61. doi: 10.1093/bioinformatics/btu099. Epub 2014 Feb 14. Bioinformatics. 2014. PMID: 24532724 Free article.
Discovering molecular functions significantly related to phenotypes by combining gene expression data and biological information.
Al-Shahrour F, Díaz-Uriarte R, Dopazo J. Al-Shahrour F, et al. Bioinformatics. 2005 Jul 1;21(13):2988-93. doi: 10.1093/bioinformatics/bti457. Epub 2005 Apr 19. Bioinformatics. 2005. PMID: 15840702
GEPAS, an experiment-oriented pipeline for the analysis of microarray gene expression data.
Vaquerizas JM, Conde L, Yankilevich P, Cabezón A, Minguez P, Díaz-Uriarte R, Al-Shahrour F, Herrero J, Dopazo J. Vaquerizas JM, et al. Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W616-20. doi: 10.1093/nar/gki500. Nucleic Acids Res. 2005. PMID: 15980548 Free PMC article.
A response to Yu et al. "A forward-backward fragment assembling algorithm for the identification of genomic amplification and deletion breakpoints using high-density single nucleotide polymorphism (SNP) array", BMC Bioinformatics 2007, 8: 145.
Rueda OM, Diaz-Uriarte R. Rueda OM, et al. BMC Bioinformatics. 2007 Oct 16;8:394. doi: 10.1186/1471-2105-8-394. BMC Bioinformatics. 2007. PMID: 17939873 Free PMC article.
SignS: a parallelized, open-source, freely available, web-based tool for gene selection and molecular signatures for survival and censored data.
Diaz-Uriarte R. Diaz-Uriarte R. BMC Bioinformatics. 2008 Jan 21;9:30. doi: 10.1186/1471-2105-9-30. BMC Bioinformatics. 2008. PMID: 18208605 Free PMC article.
Asterias: a parallelized web-based suite for the analysis of expression and aCGH data.
Alibés A, Morrissey ER, Cañada A, Rueda OM, Casado D, Yankilevich P, Díaz-Uriarte R. Alibés A, et al. Cancer Inform. 2007 Feb 3;3:1-9. Cancer Inform. 2007. PMID: 19455230 Free PMC article.
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