Ramón Díaz-Uriarte

35 papers Journal 30Unranked 4
YearRankTypeTitle / Venue / Authors
2025 J jnl
A Picture Guide to Cancer Progression and Evolutionary Accumulation Models: Systematic Critique, Plausible Interpretations, and Alternative Uses.
IEEE Access
Ramón Díaz-Uriarte, Iain G. Johnston
2024 J jnl
HyperTraPS-CT: Inference and prediction for accumulation pathways with flexible data and model structures.
PLoS Comput. Biol.
Olav N. L. Aga, Morten Brun, Kazeem Adesina Dauda, Ramón Díaz-Uriarte, Konstantinos Giannakis, Iain G. Johnston
2022 J jnl
EvAM-Tools: tools for evolutionary accumulation and cancer progression models.
Bioinform.
Ramón Díaz-Uriarte, Pablo Herrera-Nieto
2022 J jnl
Ten quick tips for biomarker discovery and validation analyses using machine learning.
PLoS Comput. Biol.
Ramón Díaz-Uriarte, Elisa Gómez de Lope, Rosalba Giugno, Holger Fröhlich, Petr V. Nazarov, Isabel A. Nepomuceno-Chamorro, Armin Rauschenberger, Enrico Glaab
2021 J jnl
Conditional prediction of consecutive tumor evolution using cancer progression models: What genotype comes next?
PLoS Comput. Biol.
Juan Diaz-Colunga, Ramón Díaz-Uriarte
2019 J jnl
Estimating the predictability of cancer evolution.
Bioinform.
Sayed-Rzgar Hosseini, Ramón Díaz-Uriarte, Florian Markowetz, Niko Beerenwinkel
2019 J jnl
Every which way? On predicting tumor evolution using cancer progression models.
PLoS Comput. Biol.
Ramón Díaz-Uriarte, Claudia Vasallo
2018 J jnl
Cancer progression models and fitness landscapes: a many-to-many relationship.
Bioinform.
Ramón Díaz-Uriarte
2017 J jnl
OncoSimulR: genetic simulation with arbitrary epistasis and mutator genes in asexual populations.
Bioinform.
Ramón Díaz-Uriarte
2015 J jnl
Identifying restrictions in the order of accumulation of mutations during tumor progression: effects of passengers, evolutionary models, and sampling.
BMC Bioinform.
Ramón Díaz-Uriarte
2014 J jnl
ADaCGH2: parallelized analysis of (big) CNA data.
Bioinform.
Ramón Díaz-Uriarte
2010 J jnl
waviCGH: a web application for the analysis and visualization of genomic copy number alterations.
Nucleic Acids Res.
Angel Carro, Daniel Rico, Oscar M. Rueda, Ramón Díaz-Uriarte, David G. Pisano
2009 J jnl
Detection of recurrent copy number alterations in the genome: taking among-subject heterogeneity seriously.
BMC Bioinform.
Oscar M. Rueda, Ramón Díaz-Uriarte
2009 J jnl
Pomelo II: finding differentially expressed genes.
Nucleic Acids Res.
Edward R. Morrissey, Ramón Díaz-Uriarte
2009 J jnl
RJaCGH: Bayesian analysis of aCGH arrays for detecting copy number changes and recurrent regions.
Bioinform.
Oscar M. Rueda, Ramón Díaz-Uriarte
2008 J jnl
PaLS: filtering common literature, biological terms and pathway information.
Nucleic Acids Res.
Andreu Alibés, Andrés Cañada, Ramón Díaz-Uriarte
2008 J jnl
SignS: a parallelized, open-source, freely available, web-based tool for gene selection and molecular signatures for survival and censored data.
BMC Bioinform.
Ramón Díaz-Uriarte
2007 J jnl
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.
BMC Bioinform.
Oscar M. Rueda, Ramón Díaz-Uriarte
2007 J jnl
Asterias: integrated analysis of expression and aCGH data using an open-source, web-based, parallelized software suite.
Nucleic Acids Res.
Ramón Díaz-Uriarte, Andreu Alibés, Edward R. Morrissey, Andrés Cañada, Oscar M. Rueda, Mariana L. Neves
2007 J jnl
Flexible and Accurate Detection of Genomic Copy-Number Changes from aCGH.
PLoS Comput. Biol.
Oscar M. Rueda, Ramón Díaz-Uriarte
2007 J jnl
GeneSrF and varSelRF: a web-based tool and R package for gene selection and classification using random forest.
BMC Bioinform.
Ramón Díaz-Uriarte
2007 J jnl
IDconverter and IDClight: Conversion and annotation of gene and protein IDs.
BMC Bioinform.
Andreu Alibés, Patricio Yankilevich, Andrés Cañada, Ramón Díaz-Uriarte
2006 J jnl
Gene selection and classification of microarray data using random forest.
BMC Bioinform.
Ramón Díaz-Uriarte, Sara Alvarez de Andrés
2005 J jnl
Discovering molecular functions significantly related to phenotypes by combining gene expression data and biological information.
Bioinform.
Fátima Al-Shahrour, Ramón Díaz-Uriarte, Joaquín Dopazo
2005 J jnl
GEPAS, an experiment-oriented pipeline for the analysis of microarray gene expression data.
Nucleic Acids Res.
Juan M. Vaquerizas, Lucía Conde, Patricio Yankilevich, Amaya Cabezón, Pablo Minguez, Ramón Díaz-Uriarte, Fátima Al-Shahrour, Javier Herrero, Joaquín Dopazo
2005 — ch.
Supervised Methods with Genomic Data: a Review and Cautionary View.
Data Analysis and Visualization in Genomics and Proteomics
Ramón Díaz-Uriarte
2004 — conf
Can we Find Molecular Signatures from Gene Expression Data?
Spanish Bioinformatics Conference
Ramón Díaz-Uriarte, David Casado
2004 J jnl
DNMAD: web-based diagnosis and normalization for microarray data.
Bioinform.
Juan M. Vaquerizas, Joaquín Dopazo, Ramón Díaz-Uriarte
2004 J jnl
FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes.
Bioinform.
Fátima Al-Shahrour, Ramón Díaz-Uriarte, Joaquín Dopazo
2004 — conf
New Challenges in Gene Expression Data Analysis and the Extended GEPAS.
Spanish Bioinformatics Conference
Javier Herrero, Juan M. Vaquerizas, Fátima Al-Shahrour, Lucía Conde, Álvaro Mateos, Javier Santoyo, Ramón Díaz-Uriarte, Joaquín Dopazo
2004 J jnl
New challenges in gene expression data analysis and the extended GEPAS.
Nucleic Acids Res.
Javier Herrero, Juan M. Vaquerizas, Fátima Al-Shahrour, Lucía Conde, Álvaro Mateos, Javier Santoyo, Ramón Díaz-Uriarte, Joaquín Dopazo
2004 — conf
Variable Selection from Random Forests: Application to Gene Expression Data.
Spanish Bioinformatics Conference
Ramón Díaz-Uriarte
2003 J jnl
GEPAS: a web-based resource for microarray gene expression data analysis.
Nucleic Acids Res.
Javier Herrero, Fátima Al-Shahrour, Ramón Díaz-Uriarte, Álvaro Mateos, Juan M. Vaquerizas, Javier Santoyo, Joaquín Dopazo
2003 J jnl
Gene expression data preprocessing.
Bioinform.
Javier Herrero, Ramón Díaz-Uriarte, Joaquín Dopazo
2003 — conf
Using gene ontology on genome-scale studies to find significant associations of biologically relevant terms to groups of genes.
NNSP
Fátima Al-Shahrour, Javier Herrero, Álvaro Mateos, Javier Santoyo, Ramón Díaz-Uriarte, Joaquín Dopazo