Reducing the effect of the data order in algorithms for constructing phylogenetic trees. - Joaquín Dopazo (Comput. Appl. Biosci., 1988)

Design of primers for PCR amplification of highly variable genomes. - Joaquín Dopazo; A. Rodriguez; J. C. Saiz; Francisco Sobrino (Comput. Appl. Biosci., 1993)

Quantitative characterization of antigens using monoclonal antibody reactivities. - Joaquín Dopazo; Ana Taberner; Andrés Moya (Comput. Appl. Biosci., 1993)

Estimation of the intrinsic rate of natural increase and its error by both algebraic and resampling approaches. - Ana Taberner; Pedro Castanera; Enrique Silvestre; Joaquín Dopazo (Comput. Appl. Biosci., 1993)

An image-processing approach to dotplots: an X-Window-based program for interactive analysis of dotplots derived from sequence and structural data. - Oswaldo Trelles-Salazar; Emilio L. Zapata; Joaquín Dopazo; A. F. Coulson; José María Carazo (Comput. Appl. Biosci., 1995)

A New Type of Unsupervised Growing Neural Network for Biological Sequence Classification That Adopts the Topology of a Phylogenetic Tree. - Joaquín Dopazo; Huaichun Wang; José María Carazo (IWANN, 1997)

A new index to find regions showing an unexpected variability or conservation in sequence alignments. - Joaquín Dopazo (Comput. Appl. Biosci., 1997)

New phylogenetic venues opened by a novel implementation of the DNAml algorithm. - Oswaldo Trelles; C. Ceron; Huaichun Wang; Joaquín Dopazo; José María Carazo (Bioinform., 1998)

Self-organizing tree growing network for classifying amino acids. - Huaichun Wang; Joaquín Dopazo; José María Carazo (Bioinform., 1998)

Parallel Implementation of DNAml Program on Message-Passing Architectures. - C. Ceron; Joaquín Dopazo; Emilio L. Zapata; José María Carazo; Oswaldo Trelles (Parallel Comput., 1998)

A hierarchical unsupervised growing neural network for clustering gene expression patterns. - Javier Herrero; Alfonso Valencia; Joaquín Dopazo (Bioinform., 2001)

Using Perceptrons for Supervised Classification of DNA Microarray Samples: Obtaining the Optimal Level of Information and Finding Differentially Expressed Genes. - Álvaro Mateos; Javier Herrero; Joaquín Dopazo (ICANN, 2002)

Unsupervised reduction of the dimensionality followed by supervised learning with a perceptron improves the classification of conditions in DNA microarray gene expression data. - Lucía Conde; Álvaro Mateos; Javier Herrero; Joaquín Dopazo (NNSP, 2002)

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)

Using a Genetic Algorithm and a Perceptron for Feature Selection and Supervised Class Learning in DNA Microarray Data. - Michal Karzynski; Álvaro Mateos; Javier Herrero; Joaquín Dopazo (Artif. Intell. Rev., 2003)

Gene expression data preprocessing. - Javier Herrero; Ramón Díaz-Uriarte; Joaquín Dopazo (Bioinform., 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)

Improved Class Prediction in DNA Microarray Gene Expression Data by Unsupervised Reduction of the Dimensionality followed by Supervised Learning with a Perceptron. - Lucía Conde; Álvaro Mateos; Javier Herrero; Joaquín Dopazo (J. VLSI Signal Process., 2003)

Gene expression correlation and gene ontology-based similarity: an assessment of quantitative relationships. - Haiying Wang 001; Francisco Azuaje; Olivier Bodenreider; Joaquín Dopazo (CIBCB, 2004)

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)

Infering Non-Neutral Evolution within the Context of a Growing Genomic Framework: Preliminary Results using Human-Chimp Proteomes. - Leonardo Arbiza; Joaquín Dopazo; Hernán Dopazo (Spanish Bioinformatics Conference, 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)

An Approach to the Modular Structure of Cancer. - Álvaro Mateos; 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)

DNMAD: web-based diagnosis and normalization for microarray data. - Juan M. Vaquerizas; Joaquín Dopazo; Ramón Díaz-Uriarte (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)

Integrative Data Analysis and Visualization: Introduction to Critical Problems, Goals and Challenges. - Francisco Azuaje; Joaquín Dopazo (Data Analysis and Visualization in Genomics and Proteomics, 2005)

Data and Predictive Model Integration: An Overview of Key Concepts, Problems and Solutions. - Francisco Azuaje; Joaquín Dopazo; Haiying Wang 001 (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)

Highly specific and accurate selection of siRNAs for high-throughput functional assays. - Javier Santoyo; Juan M. Vaquerizas; 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)

PupasView: a visual tool for selecting suitable SNPs, with putative pathological effect in genes, for genotyping purposes. - Lucía Conde; Juan M. Vaquerizas; Carles Ferrer-Costa; Xavier de la Cruz; Modesto Orozco; Joaquín Dopazo (Nucleic Acids Res., 2005)

HCAD, closing the gap between breakpoints and genes. - Robert Hoffmann; Joaquín Dopazo; Juan C. Cigudosa; Alfonso Valencia (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)

PupaSuite: finding functional single nucleotide polymorphisms for large-scale genotyping purposes. - Lucía Conde; Juan M. Vaquerizas; Hernán Dopazo; Leonardo Arbiza; Joke Reumers; Frederic Rousseau 001; Joost Schymkowitz; 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)

Positive Selection, Relaxation, and Acceleration in the Evolution of the Human and Chimp Genome. - Leonardo Arbiza; Joaquín Dopazo; Hernán Dopazo (PLoS Comput. Biol., 2006)

Prophet, a web-based tool for class prediction using microarray data. - Ignacio Medina; David Montaner; Joaquín Tárraga; Joaquín Dopazo (Bioinform., 2007)

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)

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)

CLEAR-test: Combining inference for differential expression and variability in microarray data analysis. - Joan Valls; Mònica Grau; Xavier Solé; Pilar Hernández; David Montaner; Joaquín Dopazo; Miguel A. Peinado; Gabriel Capellá; Víctor Moreno; Miguel Angel Pujana (J. Biomed. Informatics, 2008)

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)

PhylomeDB: a database for genome-wide collections of gene phylogenies. - Jaime Huerta-Cepas; Anibal Bueno; Joaquín Dopazo; Toni Gabaldón (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)

Formulating and testing hypotheses in functional genomics. - Joaquín Dopazo (Artif. Intell. Medicine, 2009)

Papers on normalization, variable selection, classification or clustering of microarray data. - David M. Rocke; Trey Ideker; Olga G. Troyanskaya; John Quackenbush; Joaquín Dopazo (Bioinform., 2009)

Functional assessment of time course microarray data. - María José Nueda; Patricia Sebastián; Sonia Tarazona; Francisco García-García 002; Joaquín Dopazo; Alberto Ferrer 001; Ana Conesa (BMC 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)

ETE: a python Environment for Tree Exploration. - Jaime Huerta-Cepas; Joaquín Dopazo; Toni Gabaldón (BMC Bioinform., 2010)

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)

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)

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)

Evidence for short-time divergence and long-time conservation of tissue-specific expression after gene duplication. - Jaime Huerta-Cepas; Joaquín Dopazo; Martijn A. Huynen; Toni Gabaldón (Briefings Bioinform., 2011)

Paintomics: a web based tool for the joint visualization of transcriptomics and metabolomics data. - Fernando García-Alcalde; Federico García-López; Joaquín Dopazo; Ana Conesa (Bioinform., 2011)

B2G-FAR, a species-centered GO annotation repository. - Stefan Götz 003; Roland Arnold; Patricia Sebastián-León; Samuel Martín-Rodríguez; Patrick Tischler; Marc-André Jehl; Joaquín Dopazo; Thomas Rattei; Ana Conesa (Bioinform., 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)

An Evolutionary Trade-Off between Protein Turnover Rate and Protein Aggregation Favors a Higher Aggregation Propensity in Fast Degrading Proteins. - Greet De Baets; Joke Reumers; Javier Delgado Blanco; Joaquín Dopazo; Joost Schymkowitz; Frederic Rousseau 001 (PLoS Comput. Biol., 2011)

Natural Selection on Functional Modules, a Genome-Wide Analysis. - François Serra; Leonardo Arbiza; Joaquín Dopazo; Hernán Dopazo (PLoS Comput. Biol., 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)

Qualimap: evaluating next-generation sequencing alignment data. - Fernando García-Alcalde; Konstantin Okonechnikov; José Carbonell; Luis M. Cruz; Stefan Götz 003; Sonia Tarazona; Joaquín Dopazo; Thomas F. Meyer; Ana Conesa (Bioinform., 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)

Protein Interactions for Functional Genomics. - Pablo Minguez; Joaquín Dopazo (Int. J. Knowl. Discov. Bioinform., 2012)

SNPeffect 4.0: on-line prediction of molecular and structural effects of protein-coding variants. - Greet De Baets; Joost J. J. van Durme; Joke Reumers; Sebastian Maurer-Stroh; Peter Vanhee; Joaquín Dopazo; Joost Schymkowitz; Frederic Rousseau 001 (Nucleic Acids Res., 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)

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)

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)

Pathway network inference from gene expression data. - Ignacio Ponzoni; María José Nueda; Sonia Tarazona; Stefan Götz 003; David Montaner; Julieta Sol Dussaut; Joaquín Dopazo; Ana Conesa (BMC Syst. Biol., 2014)

Understanding disease mechanisms with models of signaling pathway activities. - Patricia Sebastián-León; Enrique Vidal 002; Pablo Minguez; Ana Conesa; Sonia Tarazona; Alicia Amadoz; Carmen Armero; Francisco Salavert; Antonio Vidal-Puig; David Montaner; Joaquín Dopazo (BMC Syst. Biol., 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)

PTMcode v2: a resource for functional associations of post-translational modifications within and between proteins. - Pablo Minguez; Ivica Letunic; Luca Parca; Luz Garcia-Alonso; Joaquín Dopazo; Jaime Huerta-Cepas; Peer Bork (Nucleic Acids Res., 2015)

A Pan-Cancer Catalogue of Cancer Driver Protein Interaction Interfaces. - Eduard Porta-Pardo; Luz Garcia-Alonso; Thomas Hrabe; Joaquín Dopazo; Adam Godzik (PLoS Comput. Biol., 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)

Integrated gene set analysis for microRNA studies. - Francisco García-García 002; Joaquin Panadero; Joaquín Dopazo; David Montaner (Bioinform., 2016)

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)

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)

Reference genome assessment from a population scale perspective: an accurate profile of variability and noise. - José Carbonell-Caballero; Alicia Amadoz; Roberto Alonso; Marta R. Hidalgo; Cankut Çubuk; David V. Conesa; Antonio López-Quílez; Joaquín Dopazo (Bioinform., 2017)

ATGC transcriptomics: a web-based application to integrate, explore and analyze de novo transcriptomic data. - Sergio Gonzalez; Bernardo J. Clavijo; Máximo Rivarola; Patricio Moreno; Paula Fernandez; Joaquín Dopazo; Norma Paniego (BMC Bioinform., 2017)

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)

A comparison of mechanistic signaling pathway activity analysis methods. - Alicia Amadoz; Marta R. Hidalgo; Cankut Çubuk; José Carbonell-Caballero; Joaquín Dopazo (Briefings Bioinform., 2019)

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

Exploring the druggable space around the Fanconi anemia pathway using machine learning and mechanistic models. - Marina Esteban-Medina; María Peña-Chilet; Carlos Loucera; Joaquín Dopazo (BMC Bioinform., 2019)

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)

The ELIXIR Human Copy Number Variations Community: building bioinformatics infrastructure for research. - David Salgado; Irina M. Armean; Michael Baudis; Sergi Beltran; Salvador Capella-Gutiérrez; Denise Carvalho-Silva; Victoria Dominguez Del Angel; Joaquín Dopazo; Laura I. Furlong; Bo Gao; Leyla Jael García Castro; Dietlind Gerloff; et al. (F1000Research, 2020)

Mechanistic modeling of the SARS-CoV-2 disease map. - Kinza Rian; Marina Esteban-Medina; Marta R. Hidalgo; Cankut Çubuk; Matias M. Falco; Carlos Loucera; Devrim Gunyel; Marek Ostaszewski; María Peña-Chilet; Joaquín Dopazo (BioData Min., 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)

A versatile workflow to integrate RNA-seq genomic and transcriptomic data into mechanistic models of signaling pathways. - Martín Garrido-Rodriguez; Daniel López-López; Francisco M. Ortuño; María Peña-Chilet; Eduardo Muñoz; Marco A. Calzado; Joaquín Dopazo (PLoS Comput. Biol., 2021)

Integrating pathway knowledge with deep neural networks to reduce the dimensionality in single-cell RNA-seq data. - Pelin Gundogdu; Carlos Loucera; Inmaculada Alamo-Alvarez; Joaquín Dopazo; Isabel Nepomuceno (BioData Min., 2022)

Cell-Level Pathway Scoring Comparison with a Biologically Constrained Variational Autoencoder. - Pelin Gundogdu; Miriam Payá-Milans; Inmaculada Alamo-Alvarez; Isabel A. Nepomuceno-Chamorro; Joaquín Dopazo; Carlos Loucera (CMSB, 2023)

Visualization of automatically combined disease maps and pathway diagrams for rare diseases. - Piotr Gawron; David Hoksza; Janet Piñero; María Peña-Chilet; Marina Esteban-Medina; Jose Luis Fernandez-Rueda; Vincenza Colonna; Ewa Smula; Laurent Heirendt; François Ancien; Valentin Grouès; Venkata P. Satagopam; et al. (Frontiers Bioinform., 2023)