Joaquín Dopazo

	2009
53		Joaquín Dopazo: Formulating and testing hypotheses in functional genomics. Artificial Intelligence in Medicine 45(2-3): 97-107 (2009)
52		María 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)
51		David 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)
50		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 Research 37(Web-Server-Issue): 109-114 (2009)
49		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 Research 37(Web-Server-Issue): 340-344 (2009)
	2008
48		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. Journal of Biomedical Informatics 41(1): 33-45 (2008)
47		Jaime 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)
46		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 Research 36(Database-Issue): 825-829 (2008)
45		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 Research 36(Web-Server-Issue): 308-314 (2008)
44		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 Research 36(Web-Server-Issue): 341-346 (2008)
	2007
43		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 Bioinformatics 8: (2007)
42		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 Bioinformatics 8(S-4): (2007)
41		Pablo Minguez, Fátima Al-Shahrour, David Montaner, Joaquín Dopazo: Functional profiling of microarray experiments using text-mining derived bioentities. Bioinformatics 23(22): 3098-3099 (2007)
40		Ignacio Medina, David Montaner, Joaquín Tárraga, Joaquín Dopazo: Prophet, a web-based tool for class prediction using microarray data. Bioinformatics 23(3): 390-391 (2007)
39		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 Research 35(Web-Server-Issue): 38-42 (2007)
38		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 Research 35(Web-Server-Issue): 393-397 (2007)
37		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 Research 35(Web-Server-Issue): 81-85 (2007)
36		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 Research 35(Web-Server-Issue): 91-96 (2007)
	2006
35		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 Research 34(Web-Server-Issue): 472-476 (2006)
34		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 Research 34(Web-Server-Issue): 486-491 (2006)
33		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 Research 34(Web-Server-Issue): 621-625 (2006)
	2005
32		Fátima 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)
31		Javier Santoyo, Juan M. Vaquerizas, Joaquín Dopazo: Highly specific and accurate selection of siRNAs for high-throughput functional assays. Bioinformatics 21(8): 1376-1382 (2005)
30		Robert 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)
29		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 Research 33(Web-Server-Issue): 460-464 (2005)
28		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 Research 33(Web-Server-Issue): 501-505 (2005)
27		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 Research 33(Web-Server-Issue): 616-620 (2005)
	2004
26		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
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
20		Juan M. Vaquerizas, Joaquín Dopazo, Ramón Díaz-Uriarte: DNMAD: web-based diagnosis and normalization for microarray data. Bioinformatics 20(18): 3656-3658 (2004)
19		Fátima 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)
	2003
16		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)
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)
13		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. VLSI Signal Processing 35(3): 245-253 (2003)
	2002
12		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
	2001
11		Javier Herrero, Alfonso Valencia, Joaquín Dopazo: A hierarchical unsupervised growing neural network for clustering gene expression patterns. Bioinformatics 17(1): 126-136 (2001)
	1998
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)
	1997
7		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
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)
	1995
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)
	1993
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)
	1988
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

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

Colors in the list of coauthors