Joaquín Dopazo

120 papers C 3Misc 1Journal 100Unranked 12
YearRankTypeTitle / Venue / Authors
2023 — conf
Cell-Level Pathway Scoring Comparison with a Biologically Constrained Variational Autoencoder.
CMSB
Pelin Gundogdu, Miriam Payá-Milans, Inmaculada Alamo-Alvarez, Isabel A. Nepomuceno-Chamorro, Joaquín Dopazo, Carlos Loucera
2023 J jnl
Visualization of automatically combined disease maps and pathway diagrams for rare diseases.
Frontiers Bioinform.
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, Reinhard Schneider, Joaquín Dopazo, Laura I. Furlong, Marek Ostaszewski
2022 J jnl
Integrating pathway knowledge with deep neural networks to reduce the dimensionality in single-cell RNA-seq data.
BioData Min.
Pelin Gundogdu, Carlos Loucera, Inmaculada Alamo-Alvarez, Joaquín Dopazo, Isabel Nepomuceno
2021 J jnl
A comprehensive database for integrated analysis of omics data in autoimmune diseases.
BMC Bioinform.
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, Joaquín Dopazo, Julio Sáez-Rodríguez, Marta E. Alarcón-Riquelme, Pedro Carmona-Saez
2021 J jnl
A versatile workflow to integrate RNA-seq genomic and transcriptomic data into mechanistic models of signaling pathways.
PLoS Comput. Biol.
Martín Garrido-Rodriguez, Daniel López-López, Francisco M. Ortuño, María Peña-Chilet, Eduardo Muñoz, Marco A. Calzado, Joaquín Dopazo
2021 J jnl
CSVS, a crowdsourcing database of the Spanish population genetic variability.
Nucleic Acids Res.
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, Anna González-Neira, Guillermo Pita, Rocío Núñez-Torres, Javier Santoyo-Lopez, Carmen Ayuso, Pablo Minguez, Almudena Avila-Fernandez, Marta Corton, Miguel Ángel Moreno-Pelayo, Matías Morin, Alvaro Gallego-Martinez, Jose A. Lopez-Escamez, Salud Borrego, Guillermo Antiñolo, Jorge Amigo, Josefa Salgado-Garrido, Sara Pasalodos-Sanchez, Beatriz Morte, Fátima Al-Shahrour, Rafael Artuch, Javier Benitez, Luis Antonio Castaño, Ignacio Del Castillo, Aitor Delmiro, Carmina Espinos, Roser González, Daniel Grinberg, Encarnación Guillén, Pablo Lapunzina, Esther López, Ramon Martí, Montserrat Milá, Jose M. Millán, Virginia Nunes, Francesc Palau, Belen Perez, Luis A. Pérez-Jurado, Rosario Perona, Aurora Pujol, Feliciano Ramos, Antonia Ribes, Jordi Rosell, Eulalia Rovira, Jordi Surrallés, Isabel Tejada, Magdalena Ugarte, Ángel Carracedo, Ángel Alonso, Joaquín Dopazo
2021 J jnl
Mechanistic modeling of the SARS-CoV-2 disease map.
BioData Min.
Kinza Rian, Marina Esteban-Medina, Marta R. Hidalgo, Cankut Çubuk, Matias M. Falco, Carlos Loucera, Devrim Gunyel, Marek Ostaszewski, María Peña-Chilet, Joaquín Dopazo
2020 J jnl
The ELIXIR Human Copy Number Variations Community: building bioinformatics infrastructure for research.
F1000Research
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, Ivo Glynne Gut, Attila Gyenesei, Nina Habermann, John M. Hancock, Marc Hanauer, Eivind Hovig, Lennart F. Johansson, Thomas Keane, Jan Korbel, Katharina B. Lauer, Steve Laurie, Brane Leskosek, David Lloyd, Tomàs Marquès-Bonet, Hailiang Mei, Katalin Monostory, Janet Piñero, Krzysztof Poterlowicz, Ana Rath, Pubudu Samarakoon, Ferran Sanz, Gary Saunders, Daoud Sie, Morris A. Swertz, Kirill Tsukanov, Alfonso Valencia, Marko Vidak, Cristina Yenyxe González, Bauke Ylstra, Christophe Béroud
2019 J jnl
A comparison of mechanistic signaling pathway activity analysis methods.
Briefings Bioinform.
Alicia Amadoz, Marta R. Hidalgo, Cankut Çubuk, José Carbonell-Caballero, Joaquín Dopazo
2019 J jnl
Exploring the druggable space around the Fanconi anemia pathway using machine learning and mechanistic models.
BMC Bioinform.
Marina Esteban-Medina, María Peña-Chilet, Carlos Loucera, Joaquín Dopazo
2019 J jnl
Precision medicine needs pioneering clinical bioinformaticians.
Briefings Bioinform.
Gonzalo Gómez-López, Joaquín Dopazo, Juan C. Cigudosa, Alfonso Valencia, Fátima Al-Shahrour
2019 J jnl
PyCellBase, an efficient python package for easy retrieval of biological data from heterogeneous sources.
BMC Bioinform.
Daniel Perez-Gil, Francisco J. Lopez, Joaquín Dopazo, Pablo Marín-García, Augusto Rendon, Ignacio Medina
2018 J jnl
A framework for genomic sequencing on clusters of multicore and manycore processors.
Int. J. High Perform. Comput. Appl.
Héctor Martínez, Sergio Barrachina, Maribel Castillo, Joaquín Tárraga, Ignacio Medina, Joaquín Dopazo, Enrique S. Quintana-Ortí
2017 J jnl
A new parallel pipeline for DNA methylation analysis of long reads datasets.
BMC Bioinform.
Ricardo Olanda, Mariano Pérez, Juan M. Orduña, Joaquín Tárraga, Joaquín Dopazo
2017 J jnl
ATGC transcriptomics: a web-based application to integrate, explore and analyze de novo transcriptomic data.
BMC Bioinform.
Sergio Gonzalez, Bernardo J. Clavijo, Máximo Rivarola, Patricio Moreno, Paula Fernandez, Joaquín Dopazo, Norma Paniego
2017 J jnl
HGVA: the Human Genome Variation Archive.
Nucleic Acids Res.
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, Ignacio Medina
2017 J jnl
Reference genome assessment from a population scale perspective: an accurate profile of variability and noise.
Bioinform.
José Carbonell-Caballero, Alicia Amadoz, Roberto Alonso, Marta R. Hidalgo, Cankut Çubuk, David V. Conesa, Antonio López-Quílez, Joaquín Dopazo
2017 J jnl
VISMapper: ultra-fast exhaustive cartography of viral insertion sites for gene therapy.
BMC Bioinform.
José M. Juanes, Asunción Gallego, Joaquín Tárraga, Felipe Javier Chaves, Pablo Marín-García, Ignacio Medina, Vicente Arnau, Joaquín Dopazo
2016 J jnl
Actionable pathways: interactive discovery of therapeutic targets using signaling pathway models.
Nucleic Acids Res.
Francisco Salavert, Marta R. Hidalgo, Alicia Amadoz, Cankut Çubuk, Ignacio Medina, Daniel Crespo, José Carbonell-Caballero, Joaquín Dopazo
2016 J jnl
HPG pore: an efficient and scalable framework for nanopore sequencing data.
BMC Bioinform.
Joaquín Tárraga, Asunción Gallego, Vicente Arnau, Ignacio Medina, Joaquín Dopazo
2016 J jnl
Integrated gene set analysis for microRNA studies.
Bioinform.
Francisco García-García, Joaquin Panadero, Joaquín Dopazo, David Montaner
2016 J jnl
Web-based network analysis and visualization using CellMaps.
Bioinform.
Francisco Salavert, Luz Garcia-Alonso, Rubén Sánchez, Roberto Alonso, Marta Bleda, Ignacio Medina, Joaquín Dopazo
2015 J jnl
A Pan-Cancer Catalogue of Cancer Driver Protein Interaction Interfaces.
PLoS Comput. Biol.
Eduard Porta-Pardo, Luz Garcia-Alonso, Thomas Hrabe, Joaquín Dopazo, Adam Godzik
2015 J jnl
A parallel and sensitive software tool for methylation analysis on multicore platforms.
Bioinform.
Joaquín Tárraga, Mariano Pérez, Juan M. Orduña, José Duato, Ignacio Medina, Joaquín Dopazo
2015 J jnl
Assessing the impact of mutations found in next generation sequencing data over human signaling pathways.
Nucleic Acids Res.
Rosa D. Hernansaiz-Ballesteros, Francisco Salavert, Patricia Sebastián-León, Alejandro Alemán, Ignacio Medina, Joaquín Dopazo
2015 J jnl
Babelomics 5.0: functional interpretation for new generations of genomic data.
Nucleic Acids Res.
Roberto Alonso, Francisco Salavert, Francisco García-García, José Carbonell-Caballero, Marta Bleda, Luz Garcia-Alonso, Alba Sanchis-Juan, Daniel Perez-Gil, Pablo Marín-García, Rubén Sánchez, Cankut Çubuk, Marta R. Hidalgo, Alicia Amadoz, Rosa D. Hernansaiz-Ballesteros, Alejandro Alemán, Joaquín Tárraga, David Montaner, Ignacio Medina, Joaquín Dopazo
2015 J jnl
Concurrent and Accurate Short Read Mapping on Multicore Processors.
IEEE ACM Trans. Comput. Biol. Bioinform.
Héctor Martínez, Joaquín Tárraga, Ignacio Medina, Sergio Barrachina, Maribel Castillo, Joaquín Dopazo, Enrique S. Quintana-Ortí
2015 J jnl
PTMcode v2: a resource for functional associations of post-translational modifications within and between proteins.
Nucleic Acids Res.
Pablo Minguez, Ivica Letunic, Luca Parca, Luz Garcia-Alonso, Joaquín Dopazo, Jaime Huerta-Cepas, Peer Bork
2015 — conf
Scalable RNA Sequencing on Clusters of Multicore Processors.
TrustCom/BigDataSE/ISPA (3)
Héctor Martínez, Sergio Barrachina, Maribel Castillo, Joaquín Tárraga, Ignacio Medina, Joaquín Dopazo, Enrique S. Quintana-Ortí
2014 J jnl
A web tool for the design and management of panels of genes for targeted enrichment and massive sequencing for clinical applications.
Nucleic Acids Res.
Alejandro Alemán, Francisco García-García, Ignacio Medina, Joaquín Dopazo
2014 J jnl
A web-based interactive framework to assist in the prioritization of disease candidate genes in whole-exome sequencing studies.
Nucleic Acids Res.
Alejandro Alemán, Francisco García-García, Francisco Salavert, Ignacio Medina, Joaquín Dopazo
2014 J jnl
Acceleration of short and long DNA read mapping without loss of accuracy using suffix array.
Bioinform.
Joaquín Tárraga, Vicente Arnau, Héctor Martínez, Raul Moreno, Diego Cazorla, José Salavert Torres, Ignacio Blanquer Espert, Joaquín Dopazo, Ignacio Medina
2014 J jnl
Pathway network inference from gene expression data.
BMC Syst. Biol.
Ignacio Ponzoni, María José Nueda, Sonia Tarazona, Stefan Götz, David Montaner, Julieta Sol Dussaut, Joaquín Dopazo, Ana Conesa
2014 J jnl
Understanding disease mechanisms with models of signaling pathway activities.
BMC Syst. Biol.
Patricia Sebastián-León, Enrique Vidal, Pablo Minguez, Ana Conesa, Sonia Tarazona, Alicia Amadoz, Carmen Armero, Francisco Salavert, Antonio Vidal-Puig, David Montaner, Joaquín Dopazo
2014 J jnl
ngsCAT: a tool to assess the efficiency of targeted enrichment sequencing.
Bioinform.
Francisco J. López-Domingo, Javier Perez-Florido, Antonio Rueda, Joaquín Dopazo, Javier Santoyo-Lopez
2013 C conf
A dynamic pipeline for RNA sequencing on multicore processors.
EuroMPI
Héctor Martínez, Joaquín Tárraga, Ignacio Medina, Sergio Barrachina, Maribel Castillo, Joaquín Dopazo, Enrique S. Quintana-Ortí
2013 J jnl
Concurrent and Accurate RNA Sequencing on Multicore Platforms
CoRR
Héctor Martínez, Joaquín Tárraga, Ignacio Medina, Sergio Barrachina, Maribel Castillo, Joaquín Dopazo, Enrique S. Quintana-Ortí
2013 J jnl
Genome Maps, a new generation genome browser.
Nucleic Acids Res.
Ignacio Medina, Francisco Salavert, Rubén Sánchez, Alejandro de María, Roberto Alonso, Pablo Escobar, Marta Bleda, Joaquín Dopazo
2013 J jnl
Inferring the functional effect of gene expression changes in signaling pathways.
Nucleic Acids Res.
Patricia Sebastián-León, José Carbonell, Francisco Salavert, Rubén Sánchez, Ignacio Medina, Joaquín Dopazo
2012 J jnl
CellBase, a comprehensive collection of RESTful web services for retrieving relevant biological information from heterogeneous sources.
Nucleic Acids Res.
Marta Bleda, Joaquín Tárraga, Alejandro de María, Francisco Salavert, Luz Garcia-Alonso, Matilde Celma, Ainoha Martín, Joaquín Dopazo, Ignacio Medina
2012 J jnl
Inferring the regulatory network behind a gene expression experiment.
Nucleic Acids Res.
Marta Bleda, Ignacio Medina, Roberto Alonso, Alejandro de María, Francisco Salavert, Joaquín Dopazo
2012 — conf
Multicore and Cloud-Based Solutions for Genomic Variant Analysis.
Euro-Par Workshops
Cristina Y. González, Marta Bleda, Francisco Salavert, Rubén Sánchez, Joaquín Dopazo, Ignacio Medina
2012 J jnl
Protein Interactions for Functional Genomics.
Int. J. Knowl. Discov. Bioinform.
Pablo Minguez, Joaquín Dopazo
2012 J jnl
Qualimap: evaluating next-generation sequencing alignment data.
Bioinform.
Fernando García-Alcalde, Konstantin Okonechnikov, José Carbonell, Luis M. Cruz, Stefan Götz, Sonia Tarazona, Joaquín Dopazo, Thomas F. Meyer, Ana Conesa
2012 J jnl
SNPeffect 4.0: on-line prediction of molecular and structural effects of protein-coding variants.
Nucleic Acids Res.
Greet De Baets, Joost J. J. van Durme, Joke Reumers, Sebastian Maurer-Stroh, Peter Vanhee, Joaquín Dopazo, Joost Schymkowitz, Frederic Rousseau
2012 J jnl
Select Your SNPs (SYSNPs): a web tool for automatic and massive selection of SNPs.
Int. J. Data Min. Bioinform.
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, Arcadi Navarro
2012 J jnl
Using GPUs for the Exact Alignment of Short-Read Genetic Sequences by Means of the Burrows-Wheeler Transform.
IEEE ACM Trans. Comput. Biol. Bioinform.
José Salavert Torres, Ignacio Blanquer Espert, Andrés Tomás Dominguez, Vicente Hernández, Ignacio Medina, Joaquín Tárraga, Joaquín Dopazo
2012 J jnl
VARIANT: Command Line, Web service and Web interface for fast and accurate functional characterization of variants found by Next-Generation Sequencing.
Nucleic Acids Res.
Ignacio Medina, Alejandro de María, Marta Bleda, Francisco Salavert, Roberto Alonso, Cristina Y. González, Joaquín Dopazo
2011 J jnl
An Evolutionary Trade-Off between Protein Turnover Rate and Protein Aggregation Favors a Higher Aggregation Propensity in Fast Degrading Proteins.
PLoS Comput. Biol.
Greet De Baets, Joke Reumers, Javier Delgado Blanco, Joaquín Dopazo, Joost Schymkowitz, Frederic Rousseau
2011 J jnl
B2G-FAR, a species-centered GO annotation repository.
Bioinform.
Stefan Götz, Roland Arnold, Patricia Sebastián-León, Samuel Martín-Rodríguez, Patrick Tischler, Marc-André Jehl, Joaquín Dopazo, Thomas Rattei, Ana Conesa
2011 J jnl
Evidence for short-time divergence and long-time conservation of tissue-specific expression after gene duplication.
Briefings Bioinform.
Jaime Huerta-Cepas, Joaquín Dopazo, Martijn A. Huynen, Toni Gabaldón
2011 J jnl
Natural Selection on Functional Modules, a Genome-Wide Analysis.
PLoS Comput. Biol.
François Serra, Leonardo Arbiza, Joaquín Dopazo, Hernán Dopazo
2011 J jnl
Paintomics: a web based tool for the joint visualization of transcriptomics and metabolomics data.
Bioinform.
Fernando García-Alcalde, Federico García-López, Joaquín Dopazo, Ana Conesa
2011 J jnl
Phylemon 2.0: a suite of web-tools for molecular evolution, phylogenetics, phylogenomics and hypotheses testing.
Nucleic Acids Res.
Rubén Sánchez, 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
2011 — conf
Using Papers Citations for Selecting the Best Genomic Databases.
SCCC
Daniel Lichtnow, Ronnie Alves, José Palazzo Moreira de Oliveira, Ana M. Levin, Oscar Pastor, Ignacio Medina Castello, Joaquín Dopazo
2010 J jnl
Babelomics: an integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling.
Nucleic Acids Res.
Ignacio Medina, José Carbonell, Luis Pulido, Sara C. Madeira, Stefan Götz, Ana Conesa, Joaquín Tárraga, Alberto D. Pascual-Montano, Rubén Nogales-Cadenas, Javier Santoyo, Francisco García-García, Martina Marbà, David Montaner, Joaquín Dopazo
2010 J jnl
ETE: a python Environment for Tree Exploration.
BMC Bioinform.
Jaime Huerta-Cepas, Joaquín Dopazo, Toni Gabaldón
2010 J jnl
Selection upon Genome Architecture: Conservation of Functional Neighborhoods with Changing Genes.
PLoS Comput. Biol.
Fátima Al-Shahrour, Pablo Minguez, Tomàs Marquès-Bonet, Elodie Gazave, Arcadi Navarro, Joaquín Dopazo
2010 J jnl
Serial Expression Analysis: a web tool for the analysis of serial gene expression data.
Nucleic Acids Res.
María José Nueda, José Carbonell, Ignacio Medina, Joaquín Dopazo, Ana Conesa
2009 J jnl
Formulating and testing hypotheses in functional genomics.
Artif. Intell. Medicine
Joaquín Dopazo
2009 J jnl
Functional assessment of time course microarray data.
BMC Bioinform.
María José Nueda, Patricia Sebastián, Sonia Tarazona, Francisco García-García, Joaquín Dopazo, Alberto Ferrer, Ana Conesa
2009 J jnl
Gene set-based analysis of polymorphisms: finding pathways or biological processes associated to traits in genome-wide association studies.
Nucleic Acids Res.
Ignacio Medina, David Montaner, Nuria Bonifaci, Miguel Angel Pujana, José Carbonell, Joaquín Tárraga, Fátima Al-Shahrour, Joaquín Dopazo
2009 J jnl
Papers on normalization, variable selection, classification or clustering of microarray data.
Bioinform.
David M. Rocke, Trey Ideker, Olga G. Troyanskaya, John Quackenbush, Joaquín Dopazo
2009 J jnl
SNOW, a web-based tool for the statistical analysis of protein-protein interaction networks.
Nucleic Acids Res.
Pablo Minguez, Stefan Götz, David Montaner, Fátima Al-Shahrour, Joaquín Dopazo
2008 J jnl
Babelomics: advanced functional profiling of transcriptomics, proteomics and genomics experiments.
Nucleic Acids Res.
Fátima Al-Shahrour, José Carbonell, Pablo Minguez, Stefan Götz, Ana Conesa, Joaquín Tárraga, Ignacio Medina, Eva Alloza, David Montaner, Joaquín Dopazo
2008 J jnl
CLEAR-test: Combining inference for differential expression and variability in microarray data analysis.
J. Biomed. Informatics
Joan Valls, Mònica Grau, Xavier Solé, Pilar Hernández, David Montaner, Joaquín Dopazo, Miguel A. Peinado, Gabriel Capellá, Víctor Moreno, Miguel Angel Pujana
2008 J jnl
GEPAS, a web-based tool for microarray data analysis and interpretation.
Nucleic Acids Res.
Joaquín Tárraga, Ignacio Medina, José Carbonell, Jaime Huerta-Cepas, Pablo Minguez, Eva Alloza, Fátima Al-Shahrour, Susana Vegas-Azcárate, Stefan Götz, Pablo Escobar, Francisco García-García, Ana Conesa, David Montaner, Joaquín Dopazo
2008 J jnl
Joint annotation of coding and non-coding single nucleotide polymorphisms and mutations in the SNPeffect and PupaSuite databases.
Nucleic Acids Res.
Joke Reumers, Lucía Conde, Ignacio Medina, Sebastian Maurer-Stroh, Joost J. J. van Durme, Joaquín Dopazo, Frederic Rousseau, Joost Schymkowitz
2008 J jnl
PhylomeDB: a database for genome-wide collections of gene phylogenies.
Nucleic Acids Res.
Jaime Huerta-Cepas, Anibal Bueno, Joaquín Dopazo, Toni Gabaldón
2007 J jnl
DBAli tools: mining the protein structure space.
Nucleic Acids Res.
Marc A. Martí-Renom, Ursula Pieper, Mallur S. Madhusudhan, Andrea Rossi, Narayanan Eswar, Fred P. Davis, Fátima Al-Shahrour, Joaquín Dopazo, Andrej Sali
2007 J jnl
FatiGO +: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments.
Nucleic Acids Res.
Fátima Al-Shahrour, Pablo Minguez, Joaquín Tárraga, Ignacio Medina, Eva Alloza, David Montaner, Joaquín Dopazo
2007 J jnl
From genes to functional classes in the study of biological systems.
BMC Bioinform.
Fátima Al-Shahrour, Leonardo Arbiza, Hernán Dopazo, Jaime Huerta-Cepas, Pablo Minguez, David Montaner, Joaquín Dopazo
2007 J jnl
Functional profiling of microarray experiments using text-mining derived bioentities.
Bioinform.
Pablo Minguez, Fátima Al-Shahrour, David Montaner, Joaquín Dopazo
2007 J jnl
ISACGH: a web-based environment for the analysis of Array CGH and gene expression which includes functional profiling.
Nucleic Acids Res.
Lucía Conde, David Montaner, Jordi Burguet-Castell, Joaquín Tárraga, Ignacio Medina, Fátima Al-Shahrour, Joaquín Dopazo
2007 J jnl
Phylemon: a suite of web tools for molecular evolution, phylogenetics and phylogenomics.
Nucleic Acids Res.
Joaquín Tárraga, Ignacio Medina, Leonardo Arbiza, Jaime Huerta-Cepas, Toni Gabaldón, Joaquín Dopazo, Hernán Dopazo
2007 J jnl
Prophet, a web-based tool for class prediction using microarray data.
Bioinform.
Ignacio Medina, David Montaner, Joaquín Tárraga, Joaquín Dopazo
2007 J jnl
The AnnoLite and AnnoLyze programs for comparative annotation of protein structures.
BMC Bioinform.
Marc A. Martí-Renom, Andrea Rossi, Fátima Al-Shahrour, Fred P. Davis, Ursula Pieper, Joaquín Dopazo, Andrej Sali
2006 J jnl
BABELOMICS: a systems biology perspective in the functional annotation of genome-scale experiments.
Nucleic Acids Res.
Fátima Al-Shahrour, Pablo Minguez, Joaquín Tárraga, David Montaner, Eva Alloza, Juan M. Vaquerizas, Lucía Conde, Christian Blaschke, Javier Vera, Joaquín Dopazo
2006 J jnl
Next station in microarray data analysis: GEPAS.
Nucleic Acids Res.
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, Javier Herrero, Fátima Al-Shahrour, Joaquín Dopazo
2006 J jnl
Positive Selection, Relaxation, and Acceleration in the Evolution of the Human and Chimp Genome.
PLoS Comput. Biol.
Leonardo Arbiza, Joaquín Dopazo, Hernán Dopazo
2006 J jnl
PupaSuite: finding functional single nucleotide polymorphisms for large-scale genotyping purposes.
Nucleic Acids Res.
Lucía Conde, Juan M. Vaquerizas, Hernán Dopazo, Leonardo Arbiza, Joke Reumers, Frederic Rousseau, Joost Schymkowitz, Joaquín Dopazo
2005 J jnl
BABELOMICS: a suite of web tools for functional annotation and analysis of groups of genes in high-throughput experiments.
Nucleic Acids Res.
Fátima Al-Shahrour, Pablo Minguez, Juan M. Vaquerizas, Lucía Conde, Joaquín Dopazo
2005 — book
Data Analysis and Visualization in Genomics and Proteomics
Francisco Azuaje, Joaquín Dopazo
2005 — ch.
Data and Predictive Model Integration: An Overview of Key Concepts, Problems and Solutions.
Data Analysis and Visualization in Genomics and Proteomics
Francisco Azuaje, Joaquín Dopazo, Haiying Wang
2005 J jnl
Discovering molecular functions significantly related to phenotypes by combining gene expression data and biological information.
Bioinform.
Fátima Al-Shahrour, Ramón Díaz-Uriarte, Joaquín Dopazo
2005 J jnl
GEPAS, an experiment-oriented pipeline for the analysis of microarray gene expression data.
Nucleic Acids Res.
Juan M. Vaquerizas, Lucía Conde, Patricio Yankilevich, Amaya Cabezón, Pablo Minguez, Ramón Díaz-Uriarte, Fátima Al-Shahrour, Javier Herrero, Joaquín Dopazo
2005 J jnl
HCAD, closing the gap between breakpoints and genes.
Nucleic Acids Res.
Robert Hoffmann, Joaquín Dopazo, Juan C. Cigudosa, Alfonso Valencia
2005 J jnl
Highly specific and accurate selection of siRNAs for high-throughput functional assays.
Bioinform.
Javier Santoyo, Juan M. Vaquerizas, Joaquín Dopazo
2005 — ch.
Integrative Data Analysis and Visualization: Introduction to Critical Problems, Goals and Challenges.
Data Analysis and Visualization in Genomics and Proteomics
Francisco Azuaje, Joaquín Dopazo
2005 — ch.
Ontologies and Functional Genomics.
Data Analysis and Visualization in Genomics and Proteomics
Fátima Al-Shahrour, Joaquín Dopazo
2005 J jnl
PupasView: a visual tool for selecting suitable SNPs, with putative pathological effect in genes, for genotyping purposes.
Nucleic Acids Res.
Lucía Conde, Juan M. Vaquerizas, Carles Ferrer-Costa, Xavier de la Cruz, Modesto Orozco, Joaquín Dopazo
2004 — conf
An Approach to the Modular Structure of Cancer.
Spanish Bioinformatics Conference
Álvaro Mateos, Joaquín Dopazo
2004 J jnl
DNMAD: web-based diagnosis and normalization for microarray data.
Bioinform.
Juan M. Vaquerizas, Joaquín Dopazo, Ramón Díaz-Uriarte
2004 J jnl
FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes.
Bioinform.
Fátima Al-Shahrour, Ramón Díaz-Uriarte, Joaquín Dopazo
2004 — conf
Finding SNPs with Putative Phenotypic Effect at Transcriptional Level.
Spanish Bioinformatics Conference
Lucía Conde, Juan M. Vaquerizas, Javier Santoyo, Fátima Al-Shahrour, Joaquín Dopazo
2004 C conf
Gene expression correlation and gene ontology-based similarity: an assessment of quantitative relationships.
CIBCB
Haiying Wang, Francisco Azuaje, Olivier Bodenreider, Joaquín Dopazo
2004 — conf
Highly Specific and Accurate Selection of siRNAs for High-Throughput Functional Assays.
Spanish Bioinformatics Conference
Javier Santoyo, Juan M. Vaquerizas, Joaquín Dopazo
2004 — conf
Infering Non-Neutral Evolution within the Context of a Growing Genomic Framework: Preliminary Results using Human-Chimp Proteomes.
Spanish Bioinformatics Conference
Leonardo Arbiza, Joaquín Dopazo, Hernán Dopazo
2004 — conf
New Challenges in Gene Expression Data Analysis and the Extended GEPAS.
Spanish Bioinformatics Conference
Javier Herrero, Juan M. Vaquerizas, Fátima Al-Shahrour, Lucía Conde, Álvaro Mateos, Javier Santoyo, Ramón Díaz-Uriarte, Joaquín Dopazo
2004 J jnl
New challenges in gene expression data analysis and the extended GEPAS.
Nucleic Acids Res.
Javier Herrero, Juan M. Vaquerizas, Fátima Al-Shahrour, Lucía Conde, Álvaro Mateos, Javier Santoyo, Ramón Díaz-Uriarte, Joaquín Dopazo
2004 — conf
Phylogenomics and the number of characters required for obtaining an accurate phylogeny of eukaryote model species.
ISMB/ECCB (Supplement of Bioinformatics)
Hernán Dopazo, Javier Santoyo, Joaquín Dopazo
2004 J jnl
PupaSNP Finder: a web tool for finding SNPs with putative effect at transcriptional level.
Nucleic Acids Res.
Lucía Conde, Juan M. Vaquerizas, Javier Santoyo, Fátima Al-Shahrour, Sergio Ruiz-Llorente, Mercedes Robledo, Joaquín Dopazo
2003 J jnl
GEPAS: a web-based resource for microarray gene expression data analysis.
Nucleic Acids Res.
Javier Herrero, Fátima Al-Shahrour, Ramón Díaz-Uriarte, Álvaro Mateos, Juan M. Vaquerizas, Javier Santoyo, Joaquín Dopazo
2003 J jnl
Gene expression data preprocessing.
Bioinform.
Javier Herrero, Ramón Díaz-Uriarte, Joaquín Dopazo
2003 J jnl
Improved Class Prediction in DNA Microarray Gene Expression Data by Unsupervised Reduction of the Dimensionality followed by Supervised Learning with a Perceptron.
J. VLSI Signal Process.
Lucía Conde, Álvaro Mateos, Javier Herrero, Joaquín Dopazo
2003 J jnl
Using a Genetic Algorithm and a Perceptron for Feature Selection and Supervised Class Learning in DNA Microarray Data.
Artif. Intell. Rev.
Michal Karzynski, Álvaro Mateos, Javier Herrero, Joaquín Dopazo
2003 — conf
Using gene ontology on genome-scale studies to find significant associations of biologically relevant terms to groups of genes.
NNSP
Fátima Al-Shahrour, Javier Herrero, Álvaro Mateos, Javier Santoyo, Ramón Díaz-Uriarte, Joaquín Dopazo
2002 — conf
Unsupervised reduction of the dimensionality followed by supervised learning with a perceptron improves the classification of conditions in DNA microarray gene expression data.
NNSP
Lucía Conde, Álvaro Mateos, Javier Herrero, Joaquín Dopazo
2002 C conf
Using Perceptrons for Supervised Classification of DNA Microarray Samples: Obtaining the Optimal Level of Information and Finding Differentially Expressed Genes.
ICANN
Álvaro Mateos, Javier Herrero, Joaquín Dopazo
2001 J jnl
A hierarchical unsupervised growing neural network for clustering gene expression patterns.
Bioinform.
Javier Herrero, Alfonso Valencia, Joaquín Dopazo
1998 J jnl
New phylogenetic venues opened by a novel implementation of the DNAml algorithm.
Bioinform.
Oswaldo Trelles, C. Ceron, Huaichun Wang, Joaquín Dopazo, José María Carazo
1998 J jnl
Parallel Implementation of DNAml Program on Message-Passing Architectures.
Parallel Comput.
C. Ceron, Joaquín Dopazo, Emilio L. Zapata, José María Carazo, Oswaldo Trelles
1998 J jnl
Self-organizing tree growing network for classifying amino acids.
Bioinform.
Huaichun Wang, Joaquín Dopazo, José María Carazo
1997 Misc conf
A New Type of Unsupervised Growing Neural Network for Biological Sequence Classification That Adopts the Topology of a Phylogenetic Tree.
IWANN
Joaquín Dopazo, Huaichun Wang, José María Carazo
1997 J jnl
A new index to find regions showing an unexpected variability or conservation in sequence alignments.
Comput. Appl. Biosci.
Joaquín Dopazo
1995 J jnl
An image-processing approach to dotplots: an X-Window-based program for interactive analysis of dotplots derived from sequence and structural data.
Comput. Appl. Biosci.
Oswaldo Trelles-Salazar, Emilio L. Zapata, Joaquín Dopazo, A. F. Coulson, José María Carazo
1993 J jnl
Design of primers for PCR amplification of highly variable genomes.
Comput. Appl. Biosci.
Joaquín Dopazo, A. Rodriguez, J. C. Saiz, Francisco Sobrino
1993 J jnl
Estimation of the intrinsic rate of natural increase and its error by both algebraic and resampling approaches.
Comput. Appl. Biosci.
Ana Taberner, Pedro Castanera, Enrique Silvestre, Joaquín Dopazo
1993 J jnl
Quantitative characterization of antigens using monoclonal antibody reactivities.
Comput. Appl. Biosci.
Joaquín Dopazo, Ana Taberner, Andrés Moya
1988 J jnl
Reducing the effect of the data order in algorithms for constructing phylogenetic trees.
Comput. Appl. Biosci.
Joaquín Dopazo