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)

Joint annotation of coding and non-coding single nucleotide polymorphisms and mutations in the SNPeffect and PupaSuite databases. - Joke Reumers; Lucía Conde; Ignacio Medina; Sebastian Maurer-Stroh; Joost J. J. van Durme; Joaquín Dopazo; Frederic Rousseau 001; Joost Schymkowitz (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)

Serial Expression Analysis: a web tool for the analysis of serial gene expression data. - María José Nueda; José Carbonell; Ignacio Medina; Joaquín Dopazo; Ana Conesa (Nucleic Acids Res., 2010)

Using Papers Citations for Selecting the Best Genomic Databases. - Daniel Lichtnow; Ronnie Alves; José Palazzo Moreira de Oliveira; Ana M. Levin; Oscar Pastor 001; Ignacio Medina Castello; Joaquín Dopazo (SCCC, 2011)

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)

Multicore and Cloud-Based Solutions for Genomic Variant Analysis. - Cristina Y. González; Marta Bleda; Francisco Salavert; Rubén Sánchez 002; Joaquín Dopazo; Ignacio Medina (Euro-Par Workshops, 2012)

Select Your SNPs (SYSNPs): a web tool for automatic and massive selection of SNPs. - Belén Lorente-Galdos; Ignacio Medina; Carlos Morcillo-Suarez; Txema Heredia; Angel Carreño-Torres; Ricardo Sangros; Josep Alegre; Guillermo Pita; Gemma Vellalta; Núria Malats; David G. Pisano; Joaquín Dopazo; et al. (Int. J. Data Min. Bioinform., 2012)

Inferring the regulatory network behind a gene expression experiment. - Marta Bleda; Ignacio Medina; Roberto Alonso; Alejandro de María; Francisco Salavert; Joaquín Dopazo (Nucleic Acids Res., 2012)

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)

VARIANT: Command Line, Web service and Web interface for fast and accurate functional characterization of variants found by Next-Generation Sequencing. - Ignacio Medina; Alejandro de María; Marta Bleda; Francisco Salavert; Roberto Alonso; Cristina Y. González; Joaquín Dopazo (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)

Genome Maps, a new generation genome browser. - Ignacio Medina; Francisco Salavert; Rubén Sánchez 002; Alejandro de María; Roberto Alonso; Pablo Escobar; Marta Bleda; Joaquín Dopazo (Nucleic Acids Res., 2013)

Inferring the functional effect of gene expression changes in signaling pathways. - Patricia Sebastián-León; José Carbonell; Francisco Salavert; Rubén Sánchez 002; Ignacio Medina; Joaquín Dopazo (Nucleic Acids Res., 2013)

Robust Error Correction for De Novo Assembly via Spectral Partitioning and Sequence Alignment. - Andrei Alic; Andrés Tomás; José Salavert Torres; Ignacio Medina; Ignacio Blanquer (IWBBIO, 2014)

Design of a Generic Architecture for executing Bioinformatics Workflows on Distributed Infrastructures. - Abel Carrión; Ignacio Blanquer; Miguel Caballer; Cristina Y. González; Ignacio Medina (IWBBIO, 2014)

Inexact Sequence Mapping Study Cases: Hybrid GPU Computing and Memory Demanding Indexes. - José Salavert Torres; Andrés Tomás; Ignacio Medina; Ignacio Blanquer (IWBBIO, 2014)

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)

A web tool for the design and management of panels of genes for targeted enrichment and massive sequencing for clinical applications. - Alejandro Alemán; Francisco García-García 002; Ignacio Medina; Joaquín Dopazo (Nucleic Acids Res., 2014)

A web-based interactive framework to assist in the prioritization of disease candidate genes in whole-exome sequencing studies. - Alejandro Alemán; Francisco García-García 002; Francisco Salavert; Ignacio Medina; Joaquín Dopazo (Nucleic Acids Res., 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)

Assessing the impact of mutations found in next generation sequencing data over human signaling pathways. - Rosa D. Hernansaiz-Ballesteros; Francisco Salavert; Patricia Sebastián-León; Alejandro Alemán; Ignacio Medina; Joaquín Dopazo (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)

Web-based network analysis and visualization using CellMaps. - Francisco Salavert; Luz Garcia-Alonso; Rubén Sánchez 002; Roberto Alonso; Marta Bleda; Ignacio Medina; Joaquín Dopazo (Bioinform., 2016)

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

MuffinEc: Error correction for de Novo assembly via greedy partitioning and sequence alignment. - Andy S. Alic; Andrés Tomás; Ignacio Medina; Ignacio Blanquer (Inf. Sci., 2016)

Actionable pathways: interactive discovery of therapeutic targets using signaling pathway models. - Francisco Salavert; Marta R. Hidalgo; Alicia Amadoz; Cankut Çubuk; Ignacio Medina; Daniel Crespo; José Carbonell-Caballero; Joaquín Dopazo (Nucleic Acids Res., 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)

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)

PyCellBase, an efficient python package for easy retrieval of biological data from heterogeneous sources. - Daniel Perez-Gil; Francisco J. Lopez; Joaquín Dopazo; Pablo Marín-García; Augusto Rendon; Ignacio Medina (BMC Bioinform., 2019)

Whole-genome sequencing of patients with rare diseases in a national health system. - Ernest Turro; William J. Astle; Karyn Megy; Stefan Gräf; Daniel Greene; Olga Shamardina; Hana Lango Allen; Alba Sanchis-Juan; Mattia Frontini; Chantal Thys; Jonathan Stephens; Rutendo Mapeta; et al. (Nat., 2020)