Using gene ontology on genome-scale studies to find significant associations of biologically relevant terms to groups of genes. - Fátima Al-Shahrour; Javier Herrero; Álvaro Mateos; Javier Santoyo; Ramón Díaz-Uriarte; Joaquín Dopazo (NNSP, 2003)

Gene expression data preprocessing. - Javier Herrero; Ramón Díaz-Uriarte; Joaquín Dopazo (Bioinform., 2003)

GEPAS: a web-based resource for microarray gene expression data analysis. - Javier Herrero; Fátima Al-Shahrour; Ramón Díaz-Uriarte; Álvaro Mateos; Juan M. Vaquerizas; Javier Santoyo; Joaquín Dopazo (Nucleic Acids Res., 2003)

Variable Selection from Random Forests: Application to Gene Expression Data. - Ramón Díaz-Uriarte (Spanish Bioinformatics Conference, 2004)

Can we Find Molecular Signatures from Gene Expression Data? - Ramón Díaz-Uriarte; David Casado (Spanish Bioinformatics Conference, 2004)

FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes. - Fátima Al-Shahrour; Ramón Díaz-Uriarte; Joaquín Dopazo (Bioinform., 2004)

DNMAD: web-based diagnosis and normalization for microarray data. - Juan M. Vaquerizas; Joaquín Dopazo; Ramón Díaz-Uriarte (Bioinform., 2004)

New challenges in gene expression data analysis and the extended GEPAS. - Javier Herrero; Juan M. Vaquerizas; Fátima Al-Shahrour; Lucía Conde; Álvaro Mateos; Javier Santoyo; Ramón Díaz-Uriarte; Joaquín Dopazo (Nucleic Acids Res., 2004)

Supervised Methods with Genomic Data: a Review and Cautionary View. - Ramón Díaz-Uriarte (Data Analysis and Visualization in Genomics and Proteomics, 2005)

Discovering molecular functions significantly related to phenotypes by combining gene expression data and biological information. - Fátima Al-Shahrour; Ramón Díaz-Uriarte; Joaquín Dopazo (Bioinform., 2005)

GEPAS, an experiment-oriented pipeline for the analysis of microarray gene expression data. - Juan M. Vaquerizas; Lucía Conde; Patricio Yankilevich; Amaya Cabezón; Pablo Minguez; Ramón Díaz-Uriarte; Fátima Al-Shahrour; Javier Herrero; Joaquín Dopazo (Nucleic Acids Res., 2005)

Gene selection and classification of microarray data using random forest. - Ramón Díaz-Uriarte; Sara Alvarez de Andrés (BMC Bioinform., 2006)

IDconverter and IDClight: Conversion and annotation of gene and protein IDs. - Andreu Alibés; Patricio Yankilevich; Andrés Cañada; Ramón Díaz-Uriarte (BMC Bioinform., 2007)

GeneSrF and varSelRF: a web-based tool and R package for gene selection and classification using random forest. - Ramón Díaz-Uriarte (BMC Bioinform., 2007)

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. - Oscar M. Rueda; Ramón Díaz-Uriarte (BMC Bioinform., 2007)

Asterias: integrated analysis of expression and aCGH data using an open-source, web-based, parallelized software suite. - Ramón Díaz-Uriarte; Andreu Alibés; Edward R. Morrissey; Andrés Cañada; Oscar M. Rueda; Mariana L. Neves (Nucleic Acids Res., 2007)

Flexible and Accurate Detection of Genomic Copy-Number Changes from aCGH. - Oscar M. Rueda; Ramón Díaz-Uriarte (PLoS Comput. Biol., 2007)

SignS: a parallelized, open-source, freely available, web-based tool for gene selection and molecular signatures for survival and censored data. - Ramón Díaz-Uriarte (BMC Bioinform., 2008)

PaLS: filtering common literature, biological terms and pathway information. - Andreu Alibés; Andrés Cañada; Ramón Díaz-Uriarte (Nucleic Acids Res., 2008)

RJaCGH: Bayesian analysis of aCGH arrays for detecting copy number changes and recurrent regions. - Oscar M. Rueda; Ramón Díaz-Uriarte (Bioinform., 2009)

Detection of recurrent copy number alterations in the genome: taking among-subject heterogeneity seriously. - Oscar M. Rueda; Ramón Díaz-Uriarte (BMC Bioinform., 2009)

Pomelo II: finding differentially expressed genes. - Edward R. Morrissey; Ramón Díaz-Uriarte (Nucleic Acids Res., 2009)

waviCGH: a web application for the analysis and visualization of genomic copy number alterations. - Angel Carro; Daniel Rico; Oscar M. Rueda; Ramón Díaz-Uriarte; David G. Pisano (Nucleic Acids Res., 2010)

ADaCGH2: parallelized analysis of (big) CNA data. - Ramón Díaz-Uriarte (Bioinform., 2014)

Identifying restrictions in the order of accumulation of mutations during tumor progression: effects of passengers, evolutionary models, and sampling. - Ramón Díaz-Uriarte (BMC Bioinform., 2015)

OncoSimulR: genetic simulation with arbitrary epistasis and mutator genes in asexual populations. - Ramón Díaz-Uriarte (Bioinform., 2017)

Cancer progression models and fitness landscapes: a many-to-many relationship. - Ramón Díaz-Uriarte (Bioinform., 2018)

Estimating the predictability of cancer evolution. - Sayed-Rzgar Hosseini; Ramón Díaz-Uriarte; Florian Markowetz; Niko Beerenwinkel (Bioinform., 2019)

Every which way? On predicting tumor evolution using cancer progression models. - Ramón Díaz-Uriarte; Claudia Vasallo (PLoS Comput. Biol., 2019)

Conditional prediction of consecutive tumor evolution using cancer progression models: What genotype comes next? - Juan Diaz-Colunga; Ramón Díaz-Uriarte (PLoS Comput. Biol., 2021)

Ten quick tips for biomarker discovery and validation analyses using machine learning. - Ramón Díaz-Uriarte; Elisa Gómez de Lope; Rosalba Giugno; Holger Fröhlich; Petr V. Nazarov; Isabel A. Nepomuceno-Chamorro; Armin Rauschenberger; Enrico Glaab (PLoS Comput. Biol., 2022)

EvAM-Tools: tools for evolutionary accumulation and cancer progression models. - Ramón Díaz-Uriarte; Pablo Herrera-Nieto (Bioinform., 2022)

HyperTraPS-CT: Inference and prediction for accumulation pathways with flexible data and model structures. - Olav N. L. Aga; Morten Brun; Kazeem Adesina Dauda; Ramón Díaz-Uriarte; Konstantinos Giannakis; Iain G. Johnston (PLoS Comput. Biol., 2024)

A Picture Guide to Cancer Progression and Evolutionary Accumulation Models: Systematic Critique, Plausible Interpretations, and Alternative Uses. - Ramón Díaz-Uriarte; Iain G. Johnston (IEEE Access, 2025)