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)

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)

Phylogenomics and the number of characters required for obtaining an accurate phylogeny of eukaryote model species. - Hernán Dopazo; Javier Santoyo; Joaquín Dopazo (ISMB/ECCB (Supplement of Bioinformatics), 2004)

Finding SNPs with Putative Phenotypic Effect at Transcriptional Level. - Lucía Conde; Juan M. Vaquerizas; Javier Santoyo; Fátima Al-Shahrour; Joaquín Dopazo (Spanish Bioinformatics Conference, 2004)

PupaSNP Finder: a web tool for finding SNPs with putative effect at transcriptional level. - Lucía Conde; Juan M. Vaquerizas; Javier Santoyo; Fátima Al-Shahrour; Sergio Ruiz-Llorente; Mercedes Robledo; Joaquín Dopazo (Nucleic Acids Res., 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)

Highly specific and accurate selection of siRNAs for high-throughput functional assays. - Javier Santoyo; Juan M. Vaquerizas; Joaquín Dopazo (Bioinform., 2005)

Babelomics: an integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling. - Ignacio Medina; José Carbonell; Luis Pulido; Sara C. Madeira; Stefan Götz 003; Ana Conesa; Joaquín Tárraga; Alberto D. Pascual-Montano; Rubén Nogales-Cadenas; Javier Santoyo; Francisco García-García 002; Martina Marbà; et al. (Nucleic Acids Res., 2010)

Whole exome sequencing analysis pipeline for the discovery of mutations causative of human rare diseases. - Francisco Javier Lopez Domingo; Antonio Rueda Martin; Javier Perez-Florido; Alicia Vela Boza; Pablo Arce Garcia; Luis Miguel Cruz Renedo; Javier Escalante; Ana Isabel Lopez Perez; Federica Trombetta; Guillermo Antiñolo; Javier Santoyo-Lopez (IWBBIO, 2013)

ngsCAT: a tool to assess the efficiency of targeted enrichment sequencing. - Francisco J. López-Domingo; Javier Perez-Florido; Antonio Rueda; Joaquín Dopazo; Javier Santoyo-Lopez (Bioinform., 2014)

poRe: an R package for the visualization and analysis of nanopore sequencing data. - Mick Watson; Marian Thomson; Judith E. Risse; Richard Talbot; Javier Santoyo-Lopez; Karim Gharbi; Mark L. Blaxter (Bioinform., 2015)

CSVS, a crowdsourcing database of the Spanish population genetic variability. - María Peña-Chilet; Gema Roldán; Javier Perez-Florido; Francisco M. Ortuño; Rosario Carmona; Virginia Aquino; Daniel López-López; Carlos Loucera; Jose Luis Fernandez-Rueda; Asunción Gallego; Francisco García-García 002; Anna González-Neira; et al. (Nucleic Acids Res., 2021)