Joaquín Dopazo Vis

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53EEJoaquín Dopazo: Formulating and testing hypotheses in functional genomics. Artificial Intelligence in Medicine 45(2-3): 97-107 (2009)
52EEMaría José Nueda, Patricia Sebastián, Sonia Tarazona, Francisco García-García, Joaquín Dopazo, Alberto Ferrer, Ana Conesa: Functional assessment of time course microarray data. BMC Bioinformatics 10(S-6): (2009)
51EEDavid M. Rocke, Trey Ideker, Olga G. Troyanskaya, John Quackenbush, Joaquín Dopazo: Papers on normalization, variable selection, classification or clustering of microarray data. Bioinformatics 25(6): 701-702 (2009)
50EEPablo 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 Research 37(Web-Server-Issue): 109-114 (2009)
49EEIgnacio 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 Research 37(Web-Server-Issue): 340-344 (2009)
48EEJoan 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. Journal of Biomedical Informatics 41(1): 33-45 (2008)
47EEJaime Huerta-Cepas, Anibal Bueno, Joaquín Dopazo, Toni Gabaldón: PhylomeDB: a database for genome-wide collections of gene phylogenies. Nucleic Acids Research 36(Database-Issue): 491-496 (2008)
46EEJoke 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 Research 36(Database-Issue): 825-829 (2008)
45EEJoaquín 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 Research 36(Web-Server-Issue): 308-314 (2008)
44EEFátima 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 Research 36(Web-Server-Issue): 341-346 (2008)
43EEFátima 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 Bioinformatics 8: (2007)
42EEMarc 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 Bioinformatics 8(S-4): (2007)
41EEPablo Minguez, Fátima Al-Shahrour, David Montaner, Joaquín Dopazo: Functional profiling of microarray experiments using text-mining derived bioentities. Bioinformatics 23(22): 3098-3099 (2007)
40EEIgnacio Medina, David Montaner, Joaquín Tárraga, Joaquín Dopazo: Prophet, a web-based tool for class prediction using microarray data. Bioinformatics 23(3): 390-391 (2007)
39EEJoaquín 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 Research 35(Web-Server-Issue): 38-42 (2007)
38EEMarc 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 Research 35(Web-Server-Issue): 393-397 (2007)
37EELucía 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 Research 35(Web-Server-Issue): 81-85 (2007)
36EEFátima 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 Research 35(Web-Server-Issue): 91-96 (2007)
35EEFátima 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 Research 34(Web-Server-Issue): 472-476 (2006)
34EEDavid 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 Research 34(Web-Server-Issue): 486-491 (2006)
33EELucía 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 Research 34(Web-Server-Issue): 621-625 (2006)
32EEFátima Al-Shahrour, Ramón Díaz-Uriarte, Joaquín Dopazo: Discovering molecular functions significantly related to phenotypes by combining gene expression data and biological information. Bioinformatics 21(13): 2988-2993 (2005)
31EEJavier Santoyo, Juan M. Vaquerizas, Joaquín Dopazo: Highly specific and accurate selection of siRNAs for high-throughput functional assays. Bioinformatics 21(8): 1376-1382 (2005)
30EERobert Hoffmann, Joaquín Dopazo, Juan C. Cigudosa, Alfonso Valencia: HCAD, closing the gap between breakpoints and genes. Nucleic Acids Research 33(Database-Issue): 511-513 (2005)
29EEFátima 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 Research 33(Web-Server-Issue): 460-464 (2005)
28EELucía 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 Research 33(Web-Server-Issue): 501-505 (2005)
27EEJuan 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 Research 33(Web-Server-Issue): 616-620 (2005)
26EEHernán 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
25 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
24 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
23 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
22 Álvaro Mateos, Joaquín Dopazo: An Approach to the Modular Structure of Cancer. Spanish Bioinformatics Conference 2004: 161-165
21 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
20EEJuan M. Vaquerizas, Joaquín Dopazo, Ramón Díaz-Uriarte: DNMAD: web-based diagnosis and normalization for microarray data. Bioinformatics 20(18): 3656-3658 (2004)
19EEFátima Al-Shahrour, Ramón Díaz-Uriarte, Joaquín Dopazo: FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes. Bioinformatics 20(4): (2004)
18 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 Research 32(Web-Server-Issue): 242-248 (2004)
17 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 Research 32(Web-Server-Issue): 485-491 (2004)
16EEMichal 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)
15 Javier Herrero, Ramón Díaz-Uriarte, Joaquín Dopazo: Gene expression data preprocessing. Bioinformatics 19(5): 655-656 (2003)
14 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 Research 31(13): 3461-3467 (2003)
13EELucía 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. VLSI Signal Processing 35(3): 245-253 (2003)
12EEÁlvaro 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
11 Javier Herrero, Alfonso Valencia, Joaquín Dopazo: A hierarchical unsupervised growing neural network for clustering gene expression patterns. Bioinformatics 17(1): 126-136 (2001)
10 Huaichun Wang, Joaquín Dopazo, José María Carazo: Self-organizing tree growing network for classifying amino acids. Bioinformatics 14(4): 376-377 (1998)
9 Oswaldo Trelles, C. Ceron, Huaichun Wang, Joaquín Dopazo, José María Carazo: New phylogenetic venues opened by a novel implementation of the DNAml algorithm. Bioinformatics 14(6): 544-545 (1998)
8 C. Ceron, Joaquín Dopazo, Emilio L. Zapata, José María Carazo, Oswaldo Trelles: Parallel Implementation of DNAml Program on Message-Passing Architectures. Parallel Computing 24(5-6): 701-716 (1998)
7EEJoaquín 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
6 Joaquín Dopazo: A new index to find regions showing an unexpected variability or conservation in sequence alignments. Computer Applications in the Biosciences 13(3): 313-317 (1997)
5 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. Computer Applications in the Biosciences 11(3): 301-308 (1995)
4 Joaquín Dopazo, A. Taberner, A. Moya: Quantitative characterization of antigens using monoclonal antibody reactivities. Computer Applications in the Biosciences 9(1): 101-107 (1993)
3 Joaquín Dopazo, A. Rodriguez, J. C. Saiz, F. Sobrino: Design of primers for PCR amplification of highly variable genomes. Computer Applications in the Biosciences 9(2): 123-125 (1993)
2 A. Taberner, P. Castanera, E. Silvestre, Joaquín Dopazo: Estimation of the intrinsic rate of natural increase and its error by both algebraic and resampling approaches. Computer Applications in the Biosciences 9(5): 535-540 (1993)
1 Joaquín Dopazo: Reducing the effect of the data order in algorithms for constructing phylogenetic trees. Computer Applications in the Biosciences 4(2): 307 (1988)

Coauthor Index

1Fátima Al-Shahrour [14] [17] [18] [19] [23] [25] [27] [29] [32] [34] [35] [36] [37] [38] [41] [42] [43] [44] [45] [49] [50]
2Eva Alloza [34] [35] [36] [44] [45]
3Leonardo Arbiza [21] [33] [39] [43]
4Christian Blaschke [35]
5Nuria Bonifaci [49]
6Anibal Bueno [47]
7Jordi Burguet-Castell [34] [37]
8Amaya Cabezón [27]
9Gabriel Capellá [48]
10José María Carazo [5] [7] [8] [9] [10]
11José Carbonell [44] [45] [49]
12P. Castanera [2]
13C. Ceron [8] [9]
14Juan C. Cigudosa [30]
15Lucía Conde [13] [17] [18] [23] [25] [27] [28] [29] [33] [34] [35] [37] [46]
16Ana Conesa [44] [45] [52]
17A. F. Coulson [5]
18Xavier de la Cruz [28]
19Fred P. Davis [38] [42]
20Ramón Díaz-Uriarte [14] [15] [17] [19] [20] [25] [27] [32]
21Hernán Dopazo [21] [26] [33] [39] [43]
22Joost J. J. van Durme [46]
23Pablo Escobar [45]
24Narayanan Eswar [38]
25Alberto Ferrer [52]
26Carles Ferrer-Costa [28]
27Toni Gabaldón [39] [47]
28Francisco García-García [45] [52]
29Stefan Götz [44] [45] [50]
30Mònica Grau [48]
31Pilar Hernández [48]
32Javier Herrero [11] [12] [13] [14] [15] [16] [17] [25] [27] [34]
33Robert Hoffmann [30]
34Jaime Huerta-Cepas [34] [39] [43] [45] [47]
35Trey Ideker [51]
36Michal Karzynski [16]
37Mallur S. Madhusudhan [38]
38Marc A. Martí-Renom [38] [42]
39Álvaro Mateos [12] [13] [14] [16] [17] [22] [25]
40Sebastian Maurer-Stroh [46]
41Ignacio Medina [36] [37] [39] [40] [44] [45] [46] [49]
42Pablo Minguez [27] [29] [34] [35] [36] [41] [43] [44] [45] [50]
43David Montaner [34] [35] [36] [37] [40] [41] [43] [44] [45] [48] [49] [50]
44Víctor Moreno [48]
45A. Moya [4]
46Sach Mukherjee [34]
47María José Nueda [52]
48Modesto Orozco [28]
49Miguel A. Peinado [48]
50Ursula Pieper [38] [42]
51Miguel A. G. Pujana [34]
52Miguel Angel Pujana [48] [49]
53John Quackenbush [51]
54Joke Reumers [33] [46]
55Mercedes Robledo [18]
56David M. Rocke [51]
57A. Rodriguez [3]
58Andrea Rossi [38] [42]
59Frederic Rousseau [33] [46]
60Sergio Ruiz-Llorente [18]
61J. C. Saiz [3]
62Andrej Sali [38] [42]
63Javier Santoyo [14] [17] [18] [23] [24] [25] [26] [31]
64Joost Schymkowitz [33] [46]
65Patricia Sebastián [52]
66E. Silvestre [2]
67F. Sobrino [3]
68Xavier Solé [48]
69A. Taberner [2] [4]
70Sonia Tarazona [52]
71Joaquín Tárraga [34] [35] [36] [37] [39] [40] [44] [45] [49]
72Oswaldo Trelles (Oswaldo Trelles-Salazar) [5] [8] [9]
73Olga G. Troyanskaya [51]
74Alfonso Valencia [11] [30]
75Joan Valls [34] [48]
76Juan M. Vaquerizas [14] [17] [18] [20] [23] [24] [25] [27] [28] [29] [31] [33] [34] [35]
77Susana Vegas-Azcárate [45]
78Javier Vera [34] [35]
79Huaichun Wang [7] [9] [10]
80Patricio Yankilevich [27]
81Emilio L. Zapata [5] [8]

Colors in the list of coauthors

Copyright © Tue Nov 3 08:52:44 2009 by Michael Ley (ley@uni-trier.de)