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2020 – today
- 2023
[j98]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:
Visualization of automatically combined disease maps and pathway diagrams for rare diseases. Frontiers Bioinform. 3 (2023)- [c16]Pelin Gundogdu
, Miriam Payá-Milans, Inmaculada Alamo-Alvarez, Isabel A. Nepomuceno-Chamorro, Joaquín Dopazo, Carlos Loucera:
Cell-Level Pathway Scoring Comparison with a Biologically Constrained Variational Autoencoder. CMSB 2023: 62-77 - 2022
- [j97]Pelin Gundogdu, Carlos Loucera, Inmaculada Alamo-Alvarez, Joaquín Dopazo, Isabel Nepomuceno:
Integrating pathway knowledge with deep neural networks to reduce the dimensionality in single-cell RNA-seq data. BioData Min. 15(1) (2022) - 2021
- [j96]Kinza Rian, Marina Esteban-Medina, Marta R. Hidalgo, Cankut Çubuk, Matias M. Falco, Carlos Loucera, Devrim Gunyel, Marek Ostaszewski, María Peña-Chilet, Joaquín Dopazo:
Mechanistic modeling of the SARS-CoV-2 disease map. BioData Min. 14(1): 5 (2021) - [j95]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:
A comprehensive database for integrated analysis of omics data in autoimmune diseases. BMC Bioinform. 22(1): 343 (2021) - [j94]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:
CSVS, a crowdsourcing database of the Spanish population genetic variability. Nucleic Acids Res. 49(Database-Issue): D1130-D1137 (2021) - [j93]Martín Garrido-Rodriguez, Daniel López-López, Francisco M. Ortuño, María Peña-Chilet, Eduardo Muñoz, Marco A. Calzado, Joaquín Dopazo:
A versatile workflow to integrate RNA-seq genomic and transcriptomic data into mechanistic models of signaling pathways. PLoS Comput. Biol. 17(2) (2021) - 2020
- [i2]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 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:
The ELIXIR Human Copy Number Variations Community: building bioinformatics infrastructure for research. F1000Research 9: 1229 (2020)
2010 – 2019
- 2019
- [j92]Gonzalo Gómez-López, Joaquín Dopazo, Juan C. Cigudosa, Alfonso Valencia, Fátima Al-Shahrour:
Precision medicine needs pioneering clinical bioinformaticians. Briefings Bioinform. 20(3): 752-766 (2019) - [j91]Alicia Amadoz, Marta R. Hidalgo, Cankut Çubuk, José Carbonell-Caballero, Joaquín Dopazo:
A comparison of mechanistic signaling pathway activity analysis methods. Briefings Bioinform. 20(5): 1655-1668 (2019) - [j90]Daniel Perez-Gil, Francisco J. Lopez, Joaquín Dopazo, Pablo Marín-García, Augusto Rendon, Ignacio Medina:
PyCellBase, an efficient python package for easy retrieval of biological data from heterogeneous sources. BMC Bioinform. 20(1): 159:1-159:5 (2019) - [j89]Marina Esteban-Medina, María Peña-Chilet, Carlos Loucera, Joaquín Dopazo:
Exploring the druggable space around the Fanconi anemia pathway using machine learning and mechanistic models. BMC Bioinform. 20(1): 370:1-370:15 (2019) - 2018
- [j88]Héctor Martínez, Sergio Barrachina, Maribel Castillo, Joaquín Tárraga, Ignacio Medina, Joaquín Dopazo, Enrique S. Quintana-Ortí:
A framework for genomic sequencing on clusters of multicore and manycore processors. Int. J. High Perform. Comput. Appl. 32(3): 393-406 (2018) - 2017
- [j87]José Carbonell-Caballero, Alicia Amadoz, Roberto Alonso, Marta R. Hidalgo, Cankut Çubuk, David V. Conesa, Antonio López-Quílez, Joaquín Dopazo:
Reference genome assessment from a population scale perspective: an accurate profile of variability and noise. Bioinform. 33(22): 3511-3517 (2017) - [j86]Sergio Gonzalez, Bernardo J. Clavijo, Máximo Rivarola, Patricio Moreno, Paula Fernandez, Joaquín Dopazo, Norma Paniego:
ATGC transcriptomics: a web-based application to integrate, explore and analyze de novo transcriptomic data. BMC Bioinform. 18(1): 121:1-121:9 (2017) - [j85]Ricardo Olanda, Mariano Pérez, Juan M. Orduña, Joaquín Tárraga, Joaquín Dopazo:
A new parallel pipeline for DNA methylation analysis of long reads datasets. BMC Bioinform. 18(1): 161:1-161:6 (2017) - [j84]José M. Juanes, Asunción Gallego, Joaquín Tárraga, Felipe J. Chaves, Pablo Marín-García, Ignacio Medina, Vicente Arnau, Joaquín Dopazo:
VISMapper: ultra-fast exhaustive cartography of viral insertion sites for gene therapy. BMC Bioinform. 18(1): 421:1-421:5 (2017) - [j83]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:
HGVA: the Human Genome Variation Archive. Nucleic Acids Res. 45(Webserver-Issue): W189-W194 (2017) - 2016
- [j82]Francisco García-García, Joaquin Panadero, Joaquín Dopazo, David Montaner:
Integrated gene set analysis for microRNA studies. Bioinform. 32(18): 2809-2816 (2016) - [j81]Francisco Salavert, Luz Garcia-Alonso, Rubén Sánchez, Roberto Alonso, Marta Bleda, Ignacio Medina, Joaquín Dopazo:
Web-based network analysis and visualization using CellMaps. Bioinform. 32(19): 3041-3043 (2016) - [j80]Joaquín Tárraga, Asunción Gallego, Vicente Arnau, Ignacio Medina, Joaquín Dopazo:
HPG pore: an efficient and scalable framework for nanopore sequencing data. BMC Bioinform. 17: 107 (2016) - [j79]Francisco Salavert, Marta R. Hidalgo, Alicia Amadoz, Cankut Çubuk, Ignacio Medina, Daniel Crespo, José Carbonell-Caballero, Joaquín Dopazo:
Actionable pathways: interactive discovery of therapeutic targets using signaling pathway models. Nucleic Acids Res. 44(Webserver-Issue): W212-W216 (2016) - 2015
- [j78]Joaquín Tárraga, Mariano Pérez, Juan M. Orduña, José Duato, Ignacio Medina, Joaquín Dopazo:
A parallel and sensitive software tool for methylation analysis on multicore platforms. Bioinform. 31(19): 3130-3138 (2015) - [j77]Pablo Minguez, Ivica Letunic, Luca Parca, Luz Garcia-Alonso, Joaquín Dopazo, Jaime Huerta-Cepas, Peer Bork:
PTMcode v2: a resource for functional associations of post-translational modifications within and between proteins. Nucleic Acids Res. 43(Database-Issue): 494-502 (2015) - [j76]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:
Babelomics 5.0: functional interpretation for new generations of genomic data. Nucleic Acids Res. 43(Webserver-Issue): W117-W121 (2015) - [j75]Rosa D. Hernansaiz-Ballesteros, Francisco Salavert, Patricia Sebastián-León, Alejandro Alemán, Ignacio Medina, Joaquín Dopazo:
Assessing the impact of mutations found in next generation sequencing data over human signaling pathways. Nucleic Acids Res. 43(Webserver-Issue): W270-W275 (2015) - [j74]Eduard Porta-Pardo, Luz Garcia-Alonso, Thomas Hrabe, Joaquín Dopazo, Adam Godzik:
A Pan-Cancer Catalogue of Cancer Driver Protein Interaction Interfaces. PLoS Comput. Biol. 11(10) (2015) - [j73]Héctor Martínez, Joaquín Tárraga, Ignacio Medina, Sergio Barrachina, Maribel Castillo, Joaquín Dopazo, Enrique S. Quintana-Ortí:
Concurrent and Accurate Short Read Mapping on Multicore Processors. IEEE ACM Trans. Comput. Biol. Bioinform. 12(5): 995-1007 (2015) - [c15]Héctor Martínez, Sergio Barrachina, Maribel Castillo, Joaquín Tárraga, Ignacio Medina, Joaquín Dopazo, Enrique S. Quintana-Ortí:
Scalable RNA Sequencing on Clusters of Multicore Processors. TrustCom/BigDataSE/ISPA (3) 2015: 190-195 - 2014
- [j72]Francisco J. López-Domingo, Javier Perez-Florido, Antonio Rueda, Joaquín Dopazo, Javier Santoyo-Lopez:
ngsCAT: a tool to assess the efficiency of targeted enrichment sequencing. Bioinform. 30(12): 1767-1768 (2014) - [j71]Joaquín Tárraga, Vicente Arnau, Héctor Martínez, Raul Moreno, Diego Cazorla, José Salavert Torres, Ignacio Blanquer Espert, Joaquín Dopazo, Ignacio Medina:
Acceleration of short and long DNA read mapping without loss of accuracy using suffix array. Bioinform. 30(23): 3396-3398 (2014) - [j70]Patricia Sebastián-León, Enrique Vidal, Pablo Minguez, Ana Conesa, Sonia Tarazona, Alicia Amadoz, Carmen Armero, Francisco Salavert, Antonio Vidal-Puig, David Montaner, Joaquín Dopazo:
Understanding disease mechanisms with models of signaling pathway activities. BMC Syst. Biol. 8: 121 (2014) - [j69]Ignacio Ponzoni, María José Nueda, Sonia Tarazona, Stefan Götz, David Montaner, Julieta Sol Dussaut, Joaquín Dopazo, Ana Conesa:
Pathway network inference from gene expression data. BMC Syst. Biol. 8(S-2): S7 (2014) - [j68]Alejandro Alemán, Francisco García-García, Ignacio Medina, Joaquín Dopazo:
A web tool for the design and management of panels of genes for targeted enrichment and massive sequencing for clinical applications. Nucleic Acids Res. 42(Webserver-Issue): 83-87 (2014) - [j67]Alejandro Alemán, Francisco García-García, Francisco Salavert, Ignacio Medina, Joaquín Dopazo:
A web-based interactive framework to assist in the prioritization of disease candidate genes in whole-exome sequencing studies. Nucleic Acids Res. 42(Webserver-Issue): 88-93 (2014) - 2013
- [j66]Ignacio Medina, Francisco Salavert, Rubén Sánchez, Alejandro de María, Roberto Alonso, Pablo Escobar, Marta Bleda, Joaquín Dopazo:
Genome Maps, a new generation genome browser. Nucleic Acids Res. 41(Webserver-Issue): 41-46 (2013) - [j65]Patricia Sebastián-León, José Carbonell, Francisco Salavert, Rubén Sánchez, Ignacio Medina, Joaquín Dopazo:
Inferring the functional effect of gene expression changes in signaling pathways. Nucleic Acids Res. 41(Webserver-Issue): 213-217 (2013) - [c14]Héctor Martínez, Joaquín Tárraga, Ignacio Medina, Sergio Barrachina, Maribel Castillo, Joaquín Dopazo, Enrique S. Quintana-Ortí:
A dynamic pipeline for RNA sequencing on multicore processors. EuroMPI 2013: 235-240 - [i1]Héctor Martínez, Joaquín Tárraga, Ignacio Medina, Sergio Barrachina, Maribel Castillo, Joaquín Dopazo, Enrique S. Quintana-Ortí:
Concurrent and Accurate RNA Sequencing on Multicore Platforms. CoRR abs/1304.0681 (2013) - 2012
- [j64]Fernando García-Alcalde, Konstantin Okonechnikov, José Carbonell, Luis M. Cruz, Stefan Götz, Sonia Tarazona, Joaquín Dopazo, Thomas F. Meyer, Ana Conesa:
Qualimap: evaluating next-generation sequencing alignment data. Bioinform. 28(20): 2678-2679 (2012) - [j63]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:
Select Your SNPs (SYSNPs): a web tool for automatic and massive selection of SNPs. Int. J. Data Min. Bioinform. 6(3): 324-334 (2012) - [j62]Pablo Minguez, Joaquín Dopazo:
Protein Interactions for Functional Genomics. Int. J. Knowl. Discov. Bioinform. 3(4): 15-30 (2012) - [j61]Greet De Baets, Joost J. J. van Durme, Joke Reumers, Sebastian Maurer-Stroh, Peter Vanhee, Joaquín Dopazo, Joost Schymkowitz, Frederic Rousseau:
SNPeffect 4.0: on-line prediction of molecular and structural effects of protein-coding variants. Nucleic Acids Res. 40(Database-Issue): 935-939 (2012) - [j60]Ignacio Medina, Alejandro de María, Marta Bleda, Francisco Salavert, Roberto Alonso, Cristina Y. González, Joaquín Dopazo:
VARIANT: Command Line, Web service and Web interface for fast and accurate functional characterization of variants found by Next-Generation Sequencing. Nucleic Acids Res. 40(Web-Server-Issue): 54-58 (2012) - [j59]Marta Bleda, Ignacio Medina, Roberto Alonso, Alejandro de María, Francisco Salavert, Joaquín Dopazo:
Inferring the regulatory network behind a gene expression experiment. Nucleic Acids Res. 40(Web-Server-Issue): 168-172 (2012) - [j58]Marta Bleda, Joaquín Tárraga, Alejandro de María, Francisco Salavert, Luz Garcia-Alonso, Matilde Celma, Ainoha Martín, Joaquín Dopazo, Ignacio Medina:
CellBase, a comprehensive collection of RESTful web services for retrieving relevant biological information from heterogeneous sources. Nucleic Acids Res. 40(Web-Server-Issue): 609-614 (2012) - [j57]José Salavert Torres, Ignacio Blanquer Espert, Andrés Tomás Dominguez, Vicente Hernández, Ignacio Medina, Joaquín Tárraga, Joaquín Dopazo:
Using GPUs for the Exact Alignment of Short-Read Genetic Sequences by Means of the Burrows-Wheeler Transform. IEEE ACM Trans. Comput. Biol. Bioinform. 9(4): 1245-1256 (2012) - [c13]Cristina Y. González, Marta Bleda, Francisco Salavert, Rubén Sánchez, Joaquín Dopazo, Ignacio Medina:
Multicore and Cloud-Based Solutions for Genomic Variant Analysis. Euro-Par Workshops 2012: 273-284 - 2011
- [j56]Jaime Huerta-Cepas, Joaquín Dopazo, Martijn A. Huynen, Toni Gabaldón:
Evidence for short-time divergence and long-time conservation of tissue-specific expression after gene duplication. Briefings Bioinform. 12(5): 442-448 (2011) - [j55]Fernando García-Alcalde, Federico García-López, Joaquín Dopazo, Ana Conesa:
Paintomics: a web based tool for the joint visualization of transcriptomics and metabolomics data. Bioinform. 27(1): 137-139 (2011) - [j54]Stefan Götz, Roland Arnold, Patricia Sebastián-León, Samuel Martín-Rodríguez, Patrick Tischler, Marc-André Jehl, Joaquín Dopazo, Thomas Rattei, Ana Conesa:
B2G-FAR, a species-centered GO annotation repository. Bioinform. 27(7): 919-924 (2011) - [j53]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:
Phylemon 2.0: a suite of web-tools for molecular evolution, phylogenetics, phylogenomics and hypotheses testing. Nucleic Acids Res. 39(Web-Server-Issue): 470-474 (2011) - [j52]François Serra, Leonardo Arbiza, Joaquín Dopazo, Hernán Dopazo:
Natural Selection on Functional Modules, a Genome-Wide Analysis. PLoS Comput. Biol. 7(3) (2011) - [j51]Greet De Baets, Joke Reumers, Javier Delgado Blanco, Joaquín Dopazo, Joost Schymkowitz, Frederic Rousseau:
An Evolutionary Trade-Off between Protein Turnover Rate and Protein Aggregation Favors a Higher Aggregation Propensity in Fast Degrading Proteins. PLoS Comput. Biol. 7(6) (2011) - [c12]Daniel Lichtnow, Ronnie Alves, José Palazzo Moreira de Oliveira, Ana M. Levin, Oscar Pastor, Ignacio Medina Castello, Joaquín Dopazo:
Using Papers Citations for Selecting the Best Genomic Databases. SCCC 2011: 33-42 - 2010
- [j50]Jaime Huerta-Cepas, Joaquín Dopazo, Toni Gabaldón:
ETE: a python Environment for Tree Exploration. BMC Bioinform. 11: 24 (2010) - [j49]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:
Babelomics: an integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling. Nucleic Acids Res. 38(Web-Server-Issue): 210-213 (2010) - [j48]María José Nueda, José Carbonell, Ignacio Medina, Joaquín Dopazo, Ana Conesa:
Serial Expression Analysis: a web tool for the analysis of serial gene expression data. Nucleic Acids Res. 38(Web-Server-Issue): 239-245 (2010) - [j47]Fátima Al-Shahrour, Pablo Minguez, Tomàs Marquès-Bonet, Elodie Gazave, Arcadi Navarro, Joaquín Dopazo:
Selection upon Genome Architecture: Conservation of Functional Neighborhoods with Changing Genes. PLoS Comput. Biol. 6(10) (2010)
2000 – 2009
- 2009
- [j46]Joaquín Dopazo:
Formulating and testing hypotheses in functional genomics. Artif. Intell. Medicine 45(2-3): 97-107 (2009) - [j45]David M. Rocke, Trey Ideker, Olga G. Troyanskaya, John Quackenbush, Joaquín Dopazo:
Papers on normalization, variable selection, classification or clustering of microarray data. Bioinform. 25(6): 701-702 (2009) - [j44]María José Nueda, Patricia Sebastián, Sonia Tarazona, Francisco García-García, Joaquín Dopazo, Alberto Ferrer, Ana Conesa:
Functional assessment of time course microarray data. BMC Bioinform. 10(S-6) (2009) - [j43]Pablo Minguez, Stefan Götz, David Montaner, Fátima Al-Shahrour, Joaquín Dopazo:
SNOW, a web-based tool for the statistical analysis of protein-protein interaction networks. Nucleic Acids Res. 37(Web-Server-Issue): 109-114 (2009) - [j42]Ignacio Medina, David Montaner, Nuria Bonifaci, Miguel Angel Pujana, José Carbonell, Joaquín Tárraga, Fátima Al-Shahrour, Joaquín Dopazo:
Gene set-based analysis of polymorphisms: finding pathways or biological processes associated to traits in genome-wide association studies. Nucleic Acids Res. 37(Web-Server-Issue): 340-344 (2009) - 2008
- [j41]Joan Valls, Mònica Grau, Xavier Solé, Pilar Hernández, David Montaner, Joaquín Dopazo, Miguel A. Peinado, Gabriel Capellá, Víctor Moreno, Miguel Angel Pujana:
CLEAR-test: Combining inference for differential expression and variability in microarray data analysis. J. Biomed. Informatics 41(1): 33-45 (2008) - [j40]Jaime Huerta-Cepas, Anibal Bueno, Joaquín Dopazo, Toni Gabaldón:
PhylomeDB: a database for genome-wide collections of gene phylogenies. Nucleic Acids Res. 36(Database-Issue): 491-496 (2008) - [j39]Joke Reumers, Lucía Conde, Ignacio Medina, Sebastian Maurer-Stroh, Joost J. J. van Durme, Joaquín Dopazo, Frederic Rousseau, Joost Schymkowitz:
Joint annotation of coding and non-coding single nucleotide polymorphisms and mutations in the SNPeffect and PupaSuite databases. Nucleic Acids Res. 36(Database-Issue): 825-829 (2008) - [j38]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:
GEPAS, a web-based tool for microarray data analysis and interpretation. Nucleic Acids Res. 36(Web-Server-Issue): 308-314 (2008) - [j37]Fátima Al-Shahrour, José Carbonell, Pablo Minguez, Stefan Götz, Ana Conesa, Joaquín Tárraga, Ignacio Medina, Eva Alloza, David Montaner, Joaquín Dopazo:
Babelomics: advanced functional profiling of transcriptomics, proteomics and genomics experiments. Nucleic Acids Res. 36(Web-Server-Issue): 341-346 (2008) - 2007
- [j36]Ignacio Medina, David Montaner, Joaquín Tárraga, Joaquín Dopazo:
Prophet, a web-based tool for class prediction using microarray data. Bioinform. 23(3): 390-391 (2007) - [j35]Pablo Minguez, Fátima Al-Shahrour, David Montaner, Joaquín Dopazo:
Functional profiling of microarray experiments using text-mining derived bioentities. Bioinform. 23(22): 3098-3099 (2007) - [j34]Fátima Al-Shahrour, Leonardo Arbiza, Hernán Dopazo, Jaime Huerta-Cepas, Pablo Minguez, David Montaner, Joaquín Dopazo:
From genes to functional classes in the study of biological systems. BMC Bioinform. 8 (2007) - [j33]Marc A. Martí-Renom, Andrea Rossi, Fátima Al-Shahrour, Fred P. Davis, Ursula Pieper, Joaquín Dopazo, Andrej Sali:
The AnnoLite and AnnoLyze programs for comparative annotation of protein structures. BMC Bioinform. 8(S-4) (2007) - [j32]Joaquín Tárraga, Ignacio Medina, Leonardo Arbiza, Jaime Huerta-Cepas, Toni Gabaldón, Joaquín Dopazo, Hernán Dopazo:
Phylemon: a suite of web tools for molecular evolution, phylogenetics and phylogenomics. Nucleic Acids Res. 35(Web-Server-Issue): 38-42 (2007) - [j31]Lucía Conde, David Montaner, Jordi Burguet-Castell, Joaquín Tárraga, Ignacio Medina, Fátima Al-Shahrour, Joaquín Dopazo:
ISACGH: a web-based environment for the analysis of Array CGH and gene expression which includes functional profiling. Nucleic Acids Res. 35(Web-Server-Issue): 81-85 (2007) - [j30]Fátima Al-Shahrour, Pablo Minguez, Joaquín Tárraga, Ignacio Medina, Eva Alloza, David Montaner, Joaquín Dopazo:
FatiGO +: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments. Nucleic Acids Res. 35(Web-Server-Issue): 91-96 (2007) - [j29]Marc A. Martí-Renom, Ursula Pieper, Mallur S. Madhusudhan, Andrea Rossi, Narayanan Eswar, Fred P. Davis, Fátima Al-Shahrour, Joaquín Dopazo, Andrej Sali:
DBAli tools: mining the protein structure space. Nucleic Acids Res. 35(Web-Server-Issue): 393-397 (2007) - 2006
- [j28]Fátima Al-Shahrour, Pablo Minguez, Joaquín Tárraga, David Montaner, Eva Alloza, Juan M. Vaquerizas, Lucía Conde, Christian Blaschke, Javier Vera, Joaquín Dopazo:
BABELOMICS: a systems biology perspective in the functional annotation of genome-scale experiments. Nucleic Acids Res. 34(Web-Server-Issue): 472-476 (2006) - [j27]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:
Next station in microarray data analysis: GEPAS. Nucleic Acids Res. 34(Web-Server-Issue): 486-491 (2006) - [j26]Lucía Conde, Juan M. Vaquerizas, Hernán Dopazo, Leonardo Arbiza, Joke Reumers, Frederic Rousseau, Joost Schymkowitz, Joaquín Dopazo:
PupaSuite: finding functional single nucleotide polymorphisms for large-scale genotyping purposes. Nucleic Acids Res. 34(Web-Server-Issue): 621-625 (2006) - [j25]Leonardo Arbiza, Joaquín Dopazo, Hernán Dopazo:
Positive Selection, Relaxation, and Acceleration in the Evolution of the Human and Chimp Genome. PLoS Comput. Biol. 2(4) (2006) - 2005
- [j24]Javier Santoyo, Juan M. Vaquerizas, Joaquín Dopazo:
Highly specific and accurate selection of siRNAs for high-throughput functional assays. Bioinform. 21(8): 1376-1382 (2005) - [j23]Fátima Al-Shahrour, Ramón Díaz-Uriarte, Joaquín Dopazo:
Discovering molecular functions significantly related to phenotypes by combining gene expression data and biological information. Bioinform. 21(13): 2988-2993 (2005) - [j22]Robert Hoffmann, Joaquín Dopazo, Juan C. Cigudosa, Alfonso Valencia:
HCAD, closing the gap between breakpoints and genes. Nucleic Acids Res. 33(Database-Issue): 511-513 (2005) - [j21]Fátima Al-Shahrour, Pablo Minguez, Juan M. Vaquerizas, Lucía Conde, Joaquín Dopazo:
BABELOMICS: a suite of web tools for functional annotation and analysis of groups of genes in high-throughput experiments. Nucleic Acids Res. 33(Web-Server-Issue): 460-464 (2005) - [j20]Lucía Conde, Juan M. Vaquerizas, Carles Ferrer-Costa, Xavier de la Cruz, Modesto Orozco, Joaquín Dopazo:
PupasView: a visual tool for selecting suitable SNPs, with putative pathological effect in genes, for genotyping purposes. Nucleic Acids Res. 33(Web-Server-Issue): 501-505 (2005) - [j19]Juan M. Vaquerizas, Lucía Conde, Patricio Yankilevich, Amaya Cabezón, Pablo Minguez, Ramón Díaz-Uriarte, Fátima Al-Shahrour, Javier Herrero, Joaquín Dopazo:
GEPAS, an experiment-oriented pipeline for the analysis of microarray gene expression data. Nucleic Acids Res. 33(Web-Server-Issue): 616-620 (2005) - [p3]Francisco Azuaje, Joaquín Dopazo:
Integrative Data Analysis and Visualization: Introduction to Critical Problems, Goals and Challenges. Data Analysis and Visualization in Genomics and Proteomics 2005: 1-9 - [p2]Francisco Azuaje, Joaquín Dopazo, Haiying Wang:
Data and Predictive Model Integration: An Overview of Key Concepts, Problems and Solutions. Data Analysis and Visualization in Genomics and Proteomics 2005: 29-39 - [p1]Fátima Al-Shahrour, Joaquín Dopazo:
Ontologies and Functional Genomics. Data Analysis and Visualization in Genomics and Proteomics 2005: 99-112 - [e1]Francisco Azuaje, Joaquín Dopazo:
Data Analysis and Visualization in Genomics and Proteomics. Wiley 2005, ISBN 978-0-470-09439-6 [contents] - 2004
- [j18]Fátima Al-Shahrour, Ramón Díaz-Uriarte, Joaquín Dopazo:
FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes. Bioinform. 20(4): 578-580 (2004) - [j17]Juan M. Vaquerizas, Joaquín Dopazo, Ramón Díaz-Uriarte:
DNMAD: web-based diagnosis and normalization for microarray data. Bioinform. 20(18): 3656-3658 (2004) - [j16]Lucía Conde, Juan M. Vaquerizas, Javier Santoyo, Fátima Al-Shahrour, Sergio Ruiz-Llorente, Mercedes Robledo, Joaquín Dopazo:
PupaSNP Finder: a web tool for finding SNPs with putative effect at transcriptional level. Nucleic Acids Res. 32(Web-Server-Issue): 242-248 (2004) - [j15]Javier Herrero, Juan M. Vaquerizas, Fátima Al-Shahrour, Lucía Conde, Álvaro Mateos, Javier Santoyo, Ramón Díaz-Uriarte, Joaquín Dopazo:
New challenges in gene expression data analysis and the extended GEPAS. Nucleic Acids Res. 32(Web-Server-Issue): 485-491 (2004) - [c11]Haiying Wang, Francisco Azuaje, Olivier Bodenreider, Joaquín Dopazo:
Gene expression correlation and gene ontology-based similarity: an assessment of quantitative relationships. CIBCB 2004: 25-31 - [c10]Hernán Dopazo, Javier Santoyo, Joaquín Dopazo:
Phylogenomics and the number of characters required for obtaining an accurate phylogeny of eukaryote model species. ISMB/ECCB (Supplement of Bioinformatics) 2004: 116-121 - [c9]Javier Herrero, Juan M. Vaquerizas, Fátima Al-Shahrour, Lucía Conde, Álvaro Mateos, Javier Santoyo, Ramón Díaz-Uriarte, Joaquín Dopazo:
New Challenges in Gene Expression Data Analysis and the Extended GEPAS. Spanish Bioinformatics Conference 2004: 1-5 - [c8]Leonardo Arbiza, Joaquín Dopazo, Hernán Dopazo:
Infering Non-Neutral Evolution within the Context of a Growing Genomic Framework: Preliminary Results using Human-Chimp Proteomes. Spanish Bioinformatics Conference 2004: 92-99 - [c7]Javier Santoyo, Juan M. Vaquerizas, Joaquín Dopazo:
Highly Specific and Accurate Selection of siRNAs for High-Throughput Functional Assays. Spanish Bioinformatics Conference 2004: 132-136 - [c6]Lucía Conde, Juan M. Vaquerizas, Javier Santoyo, Fátima Al-Shahrour, Joaquín Dopazo:
Finding SNPs with Putative Phenotypic Effect at Transcriptional Level. Spanish Bioinformatics Conference 2004: 157-160 - [c5]Álvaro Mateos, Joaquín Dopazo:
An Approach to the Modular Structure of Cancer. Spanish Bioinformatics Conference 2004: 161-165 - 2003
- [j14]Michal Karzynski, Álvaro Mateos, Javier Herrero, Joaquín Dopazo:
Using a Genetic Algorithm and a Perceptron for Feature Selection and Supervised Class Learning in DNA Microarray Data. Artif. Intell. Rev. 20(1-2): 39-51 (2003) - [j13]Javier Herrero, Ramón Díaz-Uriarte, Joaquín Dopazo:
Gene expression data preprocessing. Bioinform. 19(5): 655-656 (2003) - [j12]Javier Herrero, Fátima Al-Shahrour, Ramón Díaz-Uriarte, Álvaro Mateos, Juan M. Vaquerizas, Javier Santoyo, Joaquín Dopazo:
GEPAS: a web-based resource for microarray gene expression data analysis. Nucleic Acids Res. 31(13): 3461-3467 (2003) - [j11]Lucía Conde, Álvaro Mateos, Javier Herrero, Joaquín Dopazo:
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. 35(3): 245-253 (2003) - [c4]Fátima Al-Shahrour, Javier Herrero, Álvaro Mateos, Javier Santoyo, Ramón Díaz-Uriarte, Joaquín Dopazo:
Using gene ontology on genome-scale studies to find significant associations of biologically relevant terms to groups of genes. NNSP 2003: 43-52 - 2002
- [c3]Álvaro Mateos, Javier Herrero, Joaquín Dopazo:
Using Perceptrons for Supervised Classification of DNA Microarray Samples: Obtaining the Optimal Level of Information and Finding Differentially Expressed Genes. ICANN 2002: 577-582 - [c2]Lucía Conde, Álvaro Mateos, Javier Herrero, Joaquín Dopazo:
Unsupervised reduction of the dimensionality followed by supervised learning with a perceptron improves the classification of conditions in DNA microarray gene expression data. NNSP 2002: 77-86 - 2001
- [j10]Javier Herrero, Alfonso Valencia, Joaquín Dopazo:
A hierarchical unsupervised growing neural network for clustering gene expression patterns. Bioinform. 17(1): 126-136 (2001)
1990 – 1999
- 1998
- [j9]Huaichun Wang, Joaquín Dopazo, José María Carazo:
Self-organizing tree growing network for classifying amino acids. Bioinform. 14(4): 376-377 (1998) - [j8]Oswaldo Trelles, C. Ceron, Huaichun Wang, Joaquín Dopazo, José María Carazo:
New phylogenetic venues opened by a novel implementation of the DNAml algorithm. Bioinform. 14(6): 544-545 (1998) - [j7]C. Ceron, Joaquín Dopazo, Emilio L. Zapata, José María Carazo, Oswaldo Trelles:
Parallel Implementation of DNAml Program on Message-Passing Architectures. Parallel Comput. 24(5-6): 701-716 (1998) - 1997
- [j6]Joaquín Dopazo:
A new index to find regions showing an unexpected variability or conservation in sequence alignments. Comput. Appl. Biosci. 13(3): 313-317 (1997) - [c1]Joaquín Dopazo, Huaichun Wang, José María Carazo:
A New Type of Unsupervised Growing Neural Network for Biological Sequence Classification That Adopts the Topology of a Phylogenetic Tree. IWANN 1997: 932-941 - 1995
- [j5]Oswaldo Trelles-Salazar, Emilio L. Zapata, Joaquín Dopazo, A. F. Coulson, José María Carazo:
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. 11(3): 301-308 (1995) - 1993
- [j4]Joaquín Dopazo, Ana Taberner, Andrés Moya:
Quantitative characterization of antigens using monoclonal antibody reactivities. Comput. Appl. Biosci. 9(1): 101-107 (1993) - [j3]Joaquín Dopazo, A. Rodriguez, J. C. Saiz, Francisco Sobrino:
Design of primers for PCR amplification of highly variable genomes. Comput. Appl. Biosci. 9(2): 123-125 (1993) - [j2]Ana Taberner, Pedro Castanera, Enrique Silvestre, Joaquín Dopazo:
Estimation of the intrinsic rate of natural increase and its error by both algebraic and resampling approaches. Comput. Appl. Biosci. 9(5): 535-540 (1993)
1980 – 1989
- 1988
- [j1]Joaquín Dopazo:
Reducing the effect of the data order in algorithms for constructing phylogenetic trees. Comput. Appl. Biosci. 4(2): 307 (1988)
Coauthor Index
José Carbonell
aka: José Carbonell-Caballero
aka: José Carbonell-Caballero
Ignacio Medina
aka: Ignacio Medina Castello
aka: Ignacio Medina Castello
Javier Santoyo
aka: Javier Santoyo-Lopez
aka: Javier Santoyo-Lopez
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