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)

Prophet, a web-based tool for class prediction using microarray data. - Ignacio Medina; David Montaner; Joaquín Tárraga; Joaquín Dopazo (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)

Phylemon: a suite of web tools for molecular evolution, phylogenetics and phylogenomics. - Joaquín Tárraga; Ignacio Medina; Leonardo Arbiza; Jaime Huerta-Cepas; Toni Gabaldón; Joaquín Dopazo; Hernán Dopazo (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)

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)

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)

Phylemon 2.0: a suite of web-tools for molecular evolution, phylogenetics, phylogenomics and hypotheses testing. - Rubén Sánchez 002; François Serra; Joaquín Tárraga; Ignacio Medina; José Carbonell; Luis Pulido; Alejandro de María; Salvador Capella-Gutiérrez; Jaime Huerta-Cepas; Toni Gabaldón; Joaquín Dopazo; Hernán Dopazo (Nucleic Acids Res., 2011)

CellBase, a comprehensive collection of RESTful web services for retrieving relevant biological information from heterogeneous sources. - Marta Bleda; Joaquín Tárraga; Alejandro de María; Francisco Salavert; Luz Garcia-Alonso; Matilde Celma; Ainoha Martín; Joaquín Dopazo; Ignacio Medina (Nucleic Acids Res., 2012)

Using GPUs for the Exact Alignment of Short-Read Genetic Sequences by Means of the Burrows-Wheeler Transform. - José Salavert Torres; Ignacio Blanquer Espert; Andrés Tomás Dominguez; Vicente Hernández; Ignacio Medina; Joaquín Tárraga; Joaquín Dopazo (IEEE ACM Trans. Comput. Biol. Bioinform., 2012)

A dynamic pipeline for RNA sequencing on multicore processors. - Héctor Martínez 002; Joaquín Tárraga; Ignacio Medina; Sergio Barrachina 001; Maribel Castillo; Joaquín Dopazo; Enrique S. Quintana-Ortí (EuroMPI, 2013)

Concurrent and Accurate RNA Sequencing on Multicore Platforms - Héctor Martínez 002; Joaquín Tárraga; Ignacio Medina; Sergio Barrachina 001; Maribel Castillo; Joaquín Dopazo; Enrique S. Quintana-Ortí (CoRR, 2013)

Acceleration of short and long DNA read mapping without loss of accuracy using suffix array. - Joaquín Tárraga; Vicente Arnau; Héctor Martínez 002; Raul Moreno; Diego Cazorla; José Salavert Torres; Ignacio Blanquer Espert; Joaquín Dopazo; Ignacio Medina (Bioinform., 2014)

Scalable RNA Sequencing on Clusters of Multicore Processors. - Héctor Martínez 002; Sergio Barrachina 001; Maribel Castillo; Joaquín Tárraga; Ignacio Medina; Joaquín Dopazo; Enrique S. Quintana-Ortí (TrustCom/BigDataSE/ISPA (3), 2015)

A parallel and sensitive software tool for methylation analysis on multicore platforms. - Joaquín Tárraga; Mariano Pérez; Juan M. Orduña; José Duato; Ignacio Medina; Joaquín Dopazo (Bioinform., 2015)

Babelomics 5.0: functional interpretation for new generations of genomic data. - Roberto Alonso; Francisco Salavert; Francisco García-García 002; José Carbonell-Caballero; Marta Bleda; Luz Garcia-Alonso; Alba Sanchis-Juan; Daniel Perez-Gil; Pablo Marín-García; Rubén Sánchez 002; Cankut Çubuk; Marta R. Hidalgo; et al. (Nucleic Acids Res., 2015)

Concurrent and Accurate Short Read Mapping on Multicore Processors. - Héctor Martínez 002; Joaquín Tárraga; Ignacio Medina; Sergio Barrachina 001; Maribel Castillo; Joaquín Dopazo; Enrique S. Quintana-Ortí (IEEE ACM Trans. Comput. Biol. Bioinform., 2015)

HPG pore: an efficient and scalable framework for nanopore sequencing data. - Joaquín Tárraga; Asunción Gallego; Vicente Arnau; Ignacio Medina; Joaquín Dopazo (BMC Bioinform., 2016)

VISMapper: ultra-fast exhaustive cartography of viral insertion sites for gene therapy. - José M. Juanes; Asunción Gallego; Joaquín Tárraga; Felipe J. Chaves; Pablo Marín-García; Ignacio Medina; Vicente Arnau; Joaquín Dopazo (BMC Bioinform., 2017)

A new parallel pipeline for DNA methylation analysis of long reads datasets. - Ricardo Olanda; Mariano Pérez; Juan M. Orduña; Joaquín Tárraga; Joaquín Dopazo (BMC Bioinform., 2017)

HGVA: the Human Genome Variation Archive. - Javier López; Jacobo Coll; Matthias Haimel; Swaathi Kandasamy; Joaquín Tárraga; Pedro Furió-Tarí; Wasim Bari; Marta Bleda; Antonio Rueda; Stefan Gräf; Augusto Rendon; Joaquín Dopazo; et al. (Nucleic Acids Res., 2017)

A framework for genomic sequencing on clusters of multicore and manycore processors. - Héctor Martínez 002; Sergio Barrachina 001; Maribel Castillo; Joaquín Tárraga; Ignacio Medina; Joaquín Dopazo; Enrique S. Quintana-Ortí (Int. J. High Perform. Comput. Appl., 2018)