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)

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)

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)

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)

Ontologies and Functional Genomics. - Fátima Al-Shahrour; Joaquín Dopazo (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)

BABELOMICS: a suite of web tools for functional annotation and analysis of groups of genes in high-throughput experiments. - Fátima Al-Shahrour; Pablo Minguez; Juan M. Vaquerizas; Lucía Conde; Joaquín Dopazo (Nucleic Acids Res., 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)

BABELOMICS: a systems biology perspective in the functional annotation of genome-scale experiments. - Fátima Al-Shahrour; Pablo Minguez; Joaquín Tárraga; David Montaner; Eva Alloza; Juan M. Vaquerizas; Lucía Conde; Christian Blaschke; Javier Vera; Joaquín Dopazo (Nucleic Acids Res., 2006)

Next station in microarray data analysis: GEPAS. - David Montaner; Joaquín Tárraga; Jaime Huerta-Cepas; Jordi Burguet-Castell; Juan M. Vaquerizas; Lucía Conde; Pablo Minguez; Javier Vera; Sach Mukherjee; Joan Valls; Miguel A. G. Pujana; Eva Alloza; et al. (Nucleic Acids Res., 2006)

Functional profiling of microarray experiments using text-mining derived bioentities. - Pablo Minguez; Fátima Al-Shahrour; David Montaner; Joaquín Dopazo (Bioinform., 2007)

From genes to functional classes in the study of biological systems. - Fátima Al-Shahrour; Leonardo Arbiza; Hernán Dopazo; Jaime Huerta-Cepas; Pablo Minguez; David Montaner; Joaquín Dopazo (BMC Bioinform., 2007)

The AnnoLite and AnnoLyze programs for comparative annotation of protein structures. - Marc A. Martí-Renom; Andrea Rossi 005; Fátima Al-Shahrour; Fred P. Davis; Ursula Pieper 001; Joaquín Dopazo; Andrej Sali (BMC Bioinform., 2007)

FatiGO +: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments. - Fátima Al-Shahrour; Pablo Minguez; Joaquín Tárraga; Ignacio Medina; Eva Alloza; David Montaner; Joaquín Dopazo (Nucleic Acids Res., 2007)

ISACGH: a web-based environment for the analysis of Array CGH and gene expression which includes functional profiling. - Lucía Conde; David Montaner; Jordi Burguet-Castell; Joaquín Tárraga; Ignacio Medina; Fátima Al-Shahrour; Joaquín Dopazo (Nucleic Acids Res., 2007)

DBAli tools: mining the protein structure space. - Marc A. Martí-Renom; Ursula Pieper 001; Mallur S. Madhusudhan; Andrea Rossi 005; Narayanan Eswar; Fred P. Davis; Fátima Al-Shahrour; Joaquín Dopazo; Andrej Sali (Nucleic Acids Res., 2007)

Babelomics: advanced functional profiling of transcriptomics, proteomics and genomics experiments. - Fátima Al-Shahrour; José Carbonell; Pablo Minguez; Stefan Götz 003; Ana Conesa; Joaquín Tárraga; Ignacio Medina; Eva Alloza; David Montaner; Joaquín Dopazo (Nucleic Acids Res., 2008)

GEPAS, a web-based tool for microarray data analysis and interpretation. - Joaquín Tárraga; Ignacio Medina; José Carbonell; Jaime Huerta-Cepas; Pablo Minguez; Eva Alloza; Fátima Al-Shahrour; Susana Vegas-Azcárate; Stefan Götz 003; Pablo Escobar; Francisco García-García 002; Ana Conesa; et al. (Nucleic Acids Res., 2008)

Ultrasome: efficient aberration caller for copy number studies of ultra-high resolution. - Björn Nilsson; Mikael Johansson; Fátima Al-Shahrour; Anne E. Carpenter; Benjamin L. Ebert (Bioinform., 2009)

Gene set-based analysis of polymorphisms: finding pathways or biological processes associated to traits in genome-wide association studies. - Ignacio Medina; David Montaner; Nuria Bonifaci; Miguel Angel Pujana; José Carbonell; Joaquín Tárraga; Fátima Al-Shahrour; Joaquín Dopazo (Nucleic Acids Res., 2009)

SNOW, a web-based tool for the statistical analysis of protein-protein interaction networks. - Pablo Minguez; Stefan Götz 003; David Montaner; Fátima Al-Shahrour; Joaquín Dopazo (Nucleic Acids Res., 2009)

Selection upon Genome Architecture: Conservation of Functional Neighborhoods with Changing Genes. - Fátima Al-Shahrour; Pablo Minguez; Tomàs Marquès-Bonet; Elodie Gazave; Arcadi Navarro; Joaquín Dopazo (PLoS Comput. Biol., 2010)

Proposal of a New Bioinformatics Pipeline for Metataxonomics in Precision Medicine. - Osvaldo Graña-Castro; Hugo López-Fernández; Florentino Fdez-Riverola; Fátima Al-Shahrour; Daniel Glez-Peña (PACBB, 2019)

Precision medicine needs pioneering clinical bioinformaticians. - Gonzalo Gómez-López; Joaquín Dopazo; Juan C. Cigudosa; Alfonso Valencia; Fátima Al-Shahrour (Briefings Bioinform., 2019)

vulcanSpot: a tool to prioritize therapeutic vulnerabilities in cancer. - Javier Perales-Patón; Tomás Di Domenico; Coral Fustero Torre; Elena Piñeiro-Yáñez; Carlos Carretero-Puche; Héctor Tejero; Alfonso Valencia; Gonzalo Gómez-López; Fátima Al-Shahrour (Bioinform., 2019)

DREIMT: a drug repositioning database and prioritization tool for immunomodulation. - Kevin Troulé; Hugo López-Fernández; Santiago García-Martín; Miguel Reboiro-Jato; Carlos Carretero-Puche; Jordi Martorell-Marugan; Guillermo Martín-Serrano; Pedro Carmona-Saez; Daniel Glez-Peña; Fátima Al-Shahrour; Gonzalo Gómez-López (Bioinform., 2021)

A comprehensive database for integrated analysis of omics data in autoimmune diseases. - Jordi Martorell-Marugan; Raúl López-Domínguez; Adrián García-Moreno; Daniel Toro-Domínguez; Juan Antonio Villatoro-García; Guillermo Barturen; Adoración Martín-Gómez; Kevin Troulé; Gonzalo Gómez-López; Fátima Al-Shahrour; Víctor González-Rumayor; María Peña-Chilet; et al. (BMC Bioinform., 2021)

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)

bollito: a flexible pipeline for comprehensive single-cell RNA-seq analyses. - Luis García-Jimeno; Coral Fustero Torre; María José Jiménez-Santos; Gonzalo Gómez-López; Tomás Di Domenico; Fátima Al-Shahrour (Bioinform., 2022)

PanDrugs2: prioritizing cancer therapies using integrated individual multi-omics data. - María José Jiménez-Santos; Alba Nogueira-Rodríguez; Elena Piñeiro-Yáñez; Hugo López-Fernández; Santiago García-Martín; Paula Gómez-Plana; Miguel Reboiro-Jato; Gonzalo Gómez-López; Daniel Glez-Peña; Fátima Al-Shahrour (Nucleic Acids Res., 2023)