Ramón Díaz-Uriarte

According to our database, Ramón Díaz-Uriarte authored at least 33 papers between 2003 and 2024.

Collaborative distances:

• Dijkstra number of five.
• Erdős number of four.

2024

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

2022

EvAM-Tools: tools for evolutionary accumulation and cancer progression models.

Ramón Díaz-Uriarte, Pablo Herrera-Nieto

Bioinform., December, 2022

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

2021

Conditional prediction of consecutive tumor evolution using cancer progression models: What genotype comes next?

Juan Diaz-Colunga, Ramón Díaz-Uriarte

PLoS Comput. Biol., 2021

2019

Every which way? On predicting tumor evolution using cancer progression models.

Ramón Díaz-Uriarte, Claudia Vasallo

PLoS Comput. Biol., 2019

Estimating the predictability of cancer evolution.

Sayed-Rzgar Hosseini, Ramón Díaz-Uriarte, Florian Markowetz, Niko Beerenwinkel

Bioinform., 2019

2018

Cancer progression models and fitness landscapes: a many-to-many relationship.

Ramón Díaz-Uriarte

Bioinform., 2018

2017

OncoSimulR: genetic simulation with arbitrary epistasis and mutator genes in asexual populations.

Ramón Díaz-Uriarte

Bioinform., 2017

2015

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

2014

ADaCGH2: parallelized analysis of (big) CNA data.

Ramón Díaz-Uriarte

Bioinform., 2014

2010

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

2009

Pomelo II: finding differentially expressed genes.

Edward R. Morrissey, Ramón Díaz-Uriarte

Nucleic Acids Res., 2009

Detection of recurrent copy number alterations in the genome: taking among-subject heterogeneity seriously.

Oscar M. Rueda, Ramón Díaz-Uriarte

BMC Bioinform., 2009

RJaCGH: Bayesian analysis of aCGH arrays for detecting copy number changes and recurrent regions.

Oscar M. Rueda, Ramón Díaz-Uriarte

Bioinform., 2009

2008

PaLS: filtering common literature, biological terms and pathway information.

Andreu Alibés, Andrés Cañada, Ramón Díaz-Uriarte

Nucleic Acids Res., 2008

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

2007

Flexible and Accurate Detection of Genomic Copy-Number Changes from aCGH.

Oscar M. Rueda, Ramón Díaz-Uriarte

PLoS Comput. Biol., 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

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

GeneSrF and varSelRF: a web-based tool and R package for gene selection and classification using random forest.

Ramón Díaz-Uriarte

BMC Bioinform., 2007

IDconverter and IDClight: Conversion and annotation of gene and protein IDs.

Andreu Alibés, Patricio Yankilevich, Andrés Cañada, Ramón Díaz-Uriarte

BMC Bioinform., 2007

2006

Gene selection and classification of microarray data using random forest.

Ramón Díaz-Uriarte, Sara Alvarez de Andrés

BMC Bioinform., 2006

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

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

Supervised Methods with Genomic Data: a Review and Cautionary View.

Ramón Díaz-Uriarte

Proceedings of the Data Analysis and Visualization in Genomics and Proteomics, 2005

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

DNMAD: web-based diagnosis and normalization for microarray data.

Juan M. Vaquerizas, Joaquín Dopazo, Ramón Díaz-Uriarte

Bioinform., 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

Can we Find Molecular Signatures from Gene Expression Data?

Ramón Díaz-Uriarte, David Casado

Proceedings of the 5th Annual Spanish Bioinformatics Conference, Barcelona, Catalonia, 2004

Variable Selection from Random Forests: Application to Gene Expression Data.

Ramón Díaz-Uriarte

Proceedings of the 5th Annual Spanish Bioinformatics Conference, Barcelona, Catalonia, 2004

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

Gene expression data preprocessing.

Javier Herrero, Ramón Díaz-Uriarte, Joaquín Dopazo

Bioinform., 2003

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

Proceedings of the NNSP 2003, 2003