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Sundaram AYM, Kiron V, Dopazo J, Fernandes JMO. Diversification of the expanded teleost-specific toll-like receptor family in Atlantic cod, Gadus morhua. BMC Evol Biol. 2012;12:256. doi:10.1186/1471-2148-12-256.

Lavagnino N, Serra F, Arbiza L, Dopazo H, Hasson E. Evolutionary Genomics of Genes Involved in Olfactory Behavior in the Drosophila melanogaster Species Group. Evolutionary bioinformatics online. 2012;8:89-104. doi:10.4137/EBO.S8484.

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Ventoso I, Kochetov A, Montaner D, Dopazo J, Santoyo J. Extensive translatome remodeling during ER stress response in mammalian cells. PLoS One. 2012;7(5):e35915. doi:10.1371/journal.pone.0035915.

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Nueda MJ, Ferrer A, Conesa A. ARSyN: a method for the identification and removal of systematic noise in multifactorial time course microarray experiments. Biostatistics (Oxford, England). 2011.

Minguez P, Dopazo J. Assessing the biological significance of gene expression signatures and co-expression modules by studying their network properties. PloS one. 2011;6:e17474. doi:doi:10.1371/journal.pone.0017474.

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Tarazona S, García-Alcalde F, Dopazo J, Ferrer A, Conesa A. Differential expression in RNA-seq: a matter of depth. Genome Res. 2011;21(12):2213-23. doi:10.1101/gr.124321.111.

Prieur X, Mok CYL, Velagapudi VR, et al. Differential Lipid Partitioning Between Adipocytes and Tissue Macrophages Modulates Macrophage Lipotoxicity and M2/M1 Polarization in Obese Mice. Diabetes. 2011;60:797-809.

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Huerta-Cepas J, Dopazo J, Huynen MA, Gabaldón T. Evidence for short-time divergence and long-time conservation of tissue-specific expression after gene duplication. Brief Bioinform. 2011;12(5):442-8. doi:10.1093/bib/bbr022.

Gonçalves LG, Borges N, Serra F, Fernandes PL, Dopazo H, Santos H. Evolution of the biosynthesis of di-myo-inositol phosphate, a marker of adaptation to hot marine environments. Environmental microbiology. 2011. doi:10.1111/j.1462-2920.2011.02621.x.

De Baets G, Reumers J, Blanco JDelgado, Dopazo J, Schymkowitz J, Rousseau F. An evolutionary trade-off between protein turnover rate and protein aggregation favors a higher aggregation propensity in fast degrading proteins. PLoS computational biology. 2011;7:e1002090. doi:10.1371/journal.pcbi.1002090.

Khalaf AA, Gmitter FG, Conesa A, Dopazo J, Moore GA. Fortunella margarita Transcriptional Reprogramming Triggered by Xanthomonas citri subsp. citri. BMC plant biology. 2011;11:159.

Arbiza L, Patricio M, Dopazo H, Posada D. Genome-wide heterogeneity of nucleotide substitution model fit. Genome biology and evolution. 2011;3:896-908.

Leida C, Conesa A, Llácer G, Badenes MLuisa, Ríos G. Histone modifications and expression of DAM6 gene in peach are modulated during bud dormancy release in a cultivar-dependent manner. The New phytologist. 2011. doi:10.1111/j.1469-8137.2011.03863.x.

Alloza E, Al-Shahrour F, Cigudosa JC, Dopazo J. A large scale survey reveals that chromosomal copy-number alterations significantly affect gene modules involved in cancer initiation and progression. BMC Medical Genomics. 2011;4:37. doi:10.1186/1755-8794-4-37.

Yung S, Ledran M, Moreno-Gimeno I, et al. Large-scale transcriptional profiling and functional assays reveal important roles for Rho-GTPase signalling and SCL during haematopoietic differentiation of human embryonic stem cells. Hum Mol Genet. 2011;20(24):4932-46. doi:10.1093/hmg/ddr431.

Garrido-Gomez T, Dominguez F, Lopez JAntonio, et al. Modeling human endometrial decidualization from the interaction between proteome and secretome. The Journal of clinical endocrinology and metabolism. 2011;96:706-16.

del Pozo MGonzález-, Borrego S, Barragán I, et al. Mutation screening of multiple genes in Spanish patients with autosomal recessive retinitis pigmentosa by targeted resequencing. PLoS One. 2011;6(12):e27894. doi:10.1371/journal.pone.0027894.

Jimenez RC, Salazar GA, Gel B, Dopazo J, Mulder N, Corpas M. myKaryoView: a light-weight client for visualization of genomic data. PLoS One. 2011;6(10):e26345. doi:10.1371/journal.pone.0026345.

Serra F, Arbiza L, Dopazo J, Dopazo H. Natural selection on functional modules, a genome-wide analysis. PLoS Comput Biol. 2011;7(3):e1001093. doi:10.1371/journal.pcbi.1001093.

Bañó-Polo M, Baldin F, Tamborero S, Marti-Renom MA, Mingarro I. N-glycosylation efficiency is determined by the distance to the C-terminus and the amino acid preceding an Asn-Ser-Thr sequon. Protein science : a publication of the Protein Society. 2011;20:179-86.

García-Alcalde F, García-López F, Dopazo J, Conesa A. Paintomics: a web based tool for the joint visualization of transcriptomics and metabolomics data. Bioinformatics (Oxford, England). 2011;27:137-9.

Sánchez R, Serra F, Tárraga J, et al. Phylemon 2.0: a suite of web-tools for molecular evolution, phylogenetics, phylogenomics and hypotheses testing. Nucleic Acids Res. 2011;39(Web Server issue):W470-4. doi:10.1093/nar/gkr408.

Cardona F, Sánchez-Mut JVicente, Dopazo H, Pérez-Tur J. Phylogenetic and in silico structural analysis of the Parkinson disease-related kinase PINK1. Human mutation. 2011;32:369-78. doi:10.1002/humu.21444.

Durban J, Juárez P, Angulo Y, et al. Profiling the venom gland transcriptomes of Costa Rican snakes by 454 pyrosequencing. BMC genomics. 2011;12:259.

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Martín-Trillo M, Grandío EGonzález, Serra F, et al. Role of tomato BRANCHED1-like genes in the control of shoot branching. The Plant journal : for cell and molecular biology. 2011;67:701-14. doi:10.1111/j.1365-313X.2011.04629.x.

Lüke L, Vicens A, Serra F, et al. Sexual selection halts the relaxation of protamine 2 among rodents. PloS one. 2011;6:e29247. doi:10.1371/journal.pone.0029247.

Baù D, Marti-Renom MA. Structure determination of genomic domains by satisfaction of spatial restraints. Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology. 2011;19:25-35.

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Huerta-Cepas J, Dopazo J, Gabaldón T. ETE: a python Environment for Tree Exploration. BMC Bioinformatics. 2010;11:24. doi:10.1186/1471-2105-11-24.

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Minguez P, Dopazo J. Functional genomics and networks: new approaches in the extraction of complex gene modules. Expert Rev Proteomics. 2010;7(1):55-63. doi:10.1586/epr.09.103.

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Németh A, Conesa A, Santoyo-López J, et al. Initial genomics of the human nucleolus. PLoS genetics. 2010;6:e1000889. doi:10.1371/journal.pgen.1000889.

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Montaner D, Dopazo J. Multidimensional gene set analysis of genomic data. PLoS One. 2010;5(4):e10348. doi:10.1371/journal.pone.0010348.

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Capriotti E, Marti-Renom MA. Quantifying the relationship between sequence and three-dimensional structure conservation in RNA. BMC bioinformatics. 2010;11:322.

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Nueda MJosé, Carbonell J, Medina I, Dopazo J, Conesa A. Serial Expression Analysis: a web tool for the analysis of serial gene expression data. Nucleic Acids Res. 2010;38(Web Server issue):W239-45. doi:10.1093/nar/gkq488.

Rattei T, Tischler P, Götz S, et al. SIMAP?a comprehensive database of pre-calculated protein sequence similarities, domains, annotations and clusters. Nucleic acids research. 2010;38:D223-6.

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E. Lewintre J, C. Martin R, Montaner D, et al. Analysis of chronic lymphotic leukemia transcriptomic profile: differences between molecular subgroups. Leuk Lymphoma. 2009;50:68-79. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=19127482.

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Nobre LS, Al-Shahrour F, Dopazo J, Saraiva LM. Exploring the antimicrobial action of a carbon monoxide-releasing compound through whole-genome transcription profiling of Escherichia coli. Microbiology (Reading). 2009;155(Pt 3):813-824. doi:10.1099/mic.0.023911-0.

Nobre LS, Al-Shahrour F, Dopazo J, Saraiva LM. Exploring the antimicrobial action of a carbon monoxide-releasing compound through whole-genome transcription profiling of Escherichia coli. Microbiology. 2009;155:813-24. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=19246752.

Dopazo J. Formulating and testing hypotheses in functional genomics. Artif Intell Med. 2009;45:97-107. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18789659.

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Montaner D, Minguez P, Al-Shahrour F, Dopazo J. Gene set internal coherence in the context of functional profiling. BMC Genomics. 2009;10:197. doi:10.1186/1471-2164-10-197.

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van Heerden JH, Conesa A, Stein DJ, Montaner D, Russell V, Illing N. Parallel changes in gene expression in peripheral blood mononuclear cells and the brain after maternal separation in the mouse. BMC Res Notes. 2009;2:195.

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Martin-Coello J, Dopazo H, Arbiza L, Ausio J, Roldan ER, Gomendio M. Sexual selection drives weak positive selection in protamine genes and high promoter divergence, enhancing sperm competitiveness. Proc Biol Sci. 2009. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=19364735.

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Dopazo J. On the Use of Functional Module Definitions in the Analysis of Genomic Experiments. Molecular and Cellular Toxicology. 2009;5:47-47.

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Horcajadas JA, Minguez P, Dopazo J, et al. Controlled ovarian stimulation induces a functional genomic delay of the endometrium with potential clinical implications. J Clin Endocrinol Metab. 2008;93:4500-10. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18697870.

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Botton A, Galla G, Conesa A, Bachem C, Ramina A, Barcaccia G. Large-scale Gene Ontology analysis of plant transcriptome-derived sequences retrieved by AFLP technology. BMC Genomics. 2008;9:347. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18652646.

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Huerta-Cepas J, Bueno A, Dopazo J, Gabaldón T. PhylomeDB: a database for genome-wide collections of gene phylogenies. Nucleic Acids Res. 2008;36(Database issue):D491-6. doi:10.1093/nar/gkm899.

Huerta-Cepas J, Bueno A, Dopazo J, Gabaldón T. PhylomeDB: a database for genome-wide collections of gene phylogenies. Nucleic Acids Res. 2008;36:D491-6. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17962297.

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Dopazo H. Selective Constraints on Human Disease Mutations and Polymorphisms. In:  Handbook of Human Molecular Evolution. Handbook of Human Molecular Evolution. UK: Hildegard Kehrer-Sawatzki & David N. Cooper. John Wiley & Sons, Ltd; 2008. Available at: http://eu.wiley.com/WileyCDA/WileyTitle/productCd-0470517468,descCd-description.html.

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Stierum R, Conesa A, Heijne W, et al. Transcriptome analysis provides new insights into liver changes induced in the rat upon dietary administration of the food additives butylated hydroxytoluene, curcumin, propyl gallate and thiabendazole. Food Chem Toxicol. 2008;46:2616-28. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18539377.

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Terol J, Conesa A, Colmenero JM, et al. Analysis of 13000 unique Citrus clusters associated with fruit quality, production and salinity tolerance. BMC Genomics. 2007;8:31. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17254327.

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Aragues R, Sali A, Bonet J, Marti-Renom MA, Oliva B. Characterization of protein hubs by inferring interacting motifs from protein interactions. PLoS Comput Biol. 2007;3:1761-71. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17941705.

Dopazo J. Clustering - Class discovery in the post-genomic era. In:  Fundamentals of data mining in genomics and proteomics. Fundamentals of data mining in genomics and proteomics. New York, USA: Springer-Verlag, W. Dubitzky, M. Granzow and D.P. Berrar; 2007.

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Nueda MJ, Conesa A, Westerhuis JA, et al. Discovering gene expression patterns in time course microarray experiments by ANOVA-SCA. Bioinformatics. 2007;23:1792-800. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17519250.

Hernandez P, Huerta-Cepas J, Montaner D, et al. Evidence for systems-level molecular mechanisms of tumorigenesis. BMC Genomics. 2007;8:185. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17584915.

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Robledo M, González-Neira A, Dopazo J. f single nucleotide polymorphism arrays: Design, tools and applications. In:  Microarray Technology Through Applications. Microarray Technology Through Applications. New York, USA: Taylor & Francis, F. Falciani; 2007.

Al-Shahrour F, Minguez P, Tarraga J, et al. FatiGO +: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments. Nucleic Acids Res. 2007;35:W91-6. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17478504.

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Gabaldón T, Huynen MA. From endosymbiont to host-controlled organelle: the hijacking of mitochondrial protein synthesis and metabolism. PLoS Comput Biol. 2007;3:e219. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17983265.

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Dopazo J, Al-Shahrour F. Functional annotation of microarray experiments. In:  Microarray Technology Through Applications. Microarray Technology Through Applications. New York, USA: Taylor & Francis, F. Falciani; 2007.

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Minguez P, Al-Shahrour F, Montaner D, Dopazo J. Functional profiling of microarray experiments using text-mining derived bioentities. Bioinformatics. 2007;23(22):3098-9. doi:10.1093/bioinformatics/btm445.

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Huerta-Cepas J, Dopazo H, Dopazo J, Gabaldón T. The human phylome. Genome Biol. 2007;8:R109. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17567924.

Rico D, Vaquerizas JM, Dopazo H, Bosca L. Identification of conserved domains in the promoter regions of nitric oxide synthase 2: implications for the species-specific transcription and evolutionary differences. BMC Genomics. 2007;8:271. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17686182.

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Medina I, Montaner D, Tarraga J, Dopazo J. Prophet, a web-based tool for class prediction using microarray data. Bioinformatics. 2007;23:390-1. Available at: http://bioinformatics.oxfordjournals.org/cgi/content/full/23/3/390?view=long&pmid=17138587.

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Gandia M, Conesa A, Ancillo G, et al. Transcriptional response of Citrus aurantifolia to infection by Citrus tristeza virus. Virology. 2007;367:298-306. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17617431.

Melo F, Marti-Renom MA. Accuracy of sequence alignment and fold assessment using reduced amino acid alphabets. Proteins. 2006;63:986-95. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16506243.

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Dopazo J. Bioinformatics and cancer: an essential alliance. Clin Transl Oncol. 2006;8:409-15. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16790393.

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Goni JR, Vaquerizas JM, Dopazo J, Orozco M. Exploring the reasons for the large density of triplex-forming oligonucleotide target sequences in the human regulatory regions. BMC Genomics. 2006;7:63. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16566817.

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Rossi A, Marti-Renom MA, Sali A. Localization of binding sites in protein structures by optimization of a composite scoring function. Protein Sci. 2006;15:2366-80. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16963645.

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Conde L, Vaquerizas JM, Dopazo H, et al. PupaSuite: finding functional single nucleotide polymorphisms for large-scale genotyping purposes. Nucleic Acids Res. 2006;34:W621-5. Available at: http://nar.oxfordjournals.org/cgi/content/full/34/suppl_2/W621.

Topf M, Baker ML, Marti-Renom MA, Chiu W, Sali A. Refinement of protein structures by iterative comparative modeling and CryoEM density fitting. J Mol Biol. 2006;357:1655-68. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16490207.

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Madhusudhan MS, Marti-Renom MA, Sanchez R, Sali A. Variable gap penalty for protein sequence-structure alignment. Protein Eng Des Sel. 2006;19:129-33. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16423846.

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Al-Shahrour F, Minguez P, Vaquerizas JM, Conde L, Dopazo J. BABELOMICS: a suite of web tools for functional annotation and analysis of groups of genes in high-throughput experiments. Nucleic Acids Res. 2005;33:W460-4. Available at: http://nar.oxfordjournals.org/content/33/suppl_2/W460.long.

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Huynen MA, Spronk CA, Gabaldón T, Snel B. Combining data from genomes, Y2H and 3D structure indicates that BolA is a reductase interacting with a glutaredoxin. FEBS Lett. 2005;579:591-6. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15670813.

McMahon SA, Miller JL, Lawton JA, et al. The C-type lectin fold as an evolutionary solution for massive sequence variation. Nat Struct Mol Biol. 2005;12:886-92. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16170324.

Azuaje F, Dopazo J. Data analysis and visualisation in genomics and proteomics. In:  Wiley, F. Azuaje and J. Dopazo; 2005.

Azuaje F, Dopazo J, Wang H. Data and Predictive Model Integration: an Overview of Key Concepts, Problems and Solutions. In:  Data analysis and visualisation in genomics and proteomics. Data analysis and visualisation in genomics and proteomics. Wiley, F. Azuaje and J. Dopazo; 2005.

Espadaler J, Aragues R, Eswar N, et al. Detecting remotely related proteins by their interactions and sequence similarity. Proc Natl Acad Sci U S A. 2005;102:7151-6. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15883372.

Forment J, Gadea J, Huerta L, et al. Development of a citrus genome-wide EST collection and cDNA microarray as resources for genomic studies. Plant Mol Biol. 2005;57:375-91. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15830128.

Al-Shahrour F, Diaz-Uriarte R, Dopazo J. Discovering molecular functions significantly related to phenotypes by combining gene expression data and biological information. Bioinformatics. 2005;21:2988-93. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15840702.

Gabaldón T. Evolution of proteins and proteomes: a phylogenetics approach. Evol Bioinform Online. 2005;1:51-61. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=19325853.

Dopazo H, Dopazo J. Genome-scale evidence of the nematode-arthropod clade. Genome Biol. 2005;6:R41. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15892869.

Vaquerizas JM, Conde L, Yankilevich P, et al. GEPAS, an experiment-oriented pipeline for the analysis of microarray gene expression data. Nucleic Acids Res. 2005;33:W616-20. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15980548.

Hoffmann R, Dopazo J, Cigudosa JC, Valencia A. HCAD, closing the gap between breakpoints and genes. Nucleic Acids Res. 2005;33:D511-3. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15608250.

Santoyo J, Vaquerizas JM, Dopazo J. Highly specific and accurate selection of siRNAs for high-throughput functional assays. Bioinformatics. 2005;21:1376-82. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15591357.

Azuaje F, Dopazo J. Integrative Data Analysis and Visualization: Introduction to Critical Problems, Goals and Challenges. In:  Data analysis and visualisation in genomics and proteomics. Data analysis and visualisation in genomics and proteomics. Wiley, F. Azuaje and J. Dopazo; 2005:3-9.

Gabaldón T, Huynen MA. Lineage-specific gene loss following mitochondrial endosymbiosis and its potential for function prediction in eukaryotes. Bioinformatics. 2005;21 Suppl 2:ii144-50. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16204094.

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Al-Shahrour F, Dopazo J. Ontologies and functional genomics. In:  Data analysis and visualisation in genomics and proteomics. Data analysis and visualisation in genomics and proteomics. Wiley, F. Azuaje and J. Dopazo; 2005:99-102.

Palacios J, Honrado E, Osorio A, et al. Phenotypic characterization of BRCA1 and BRCA2 tumors based in a tissue microarray study with 37 immunohistochemical markers. Breast Cancer Res Treat. 2005;90:5-14. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15770521.

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Conde L, Vaquerizas JM, Ferrer-Costa C, de la Cruz X, Orozco M, Dopazo J. PupasView: a visual tool for selecting suitable SNPs, with putative pathological effect in genes, for genotyping purposes. Nucleic Acids Res. 2005;33:W501-5. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15980522.

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Gabaldón T, Rainey D, Huynen MA. Tracing the evolution of a large protein complex in the eukaryotes, NADH:ubiquinone oxidoreductase (Complex I). J Mol Biol. 2005;348:857-70. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15843018.

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Vaquerizas JM, Dopazo J, Diaz-Uriarte R. DNMAD: web-based diagnosis and normalization for microarray data. Bioinformatics. 2004;20:3656-8. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15247094.

Martinez-Delgado B, Meléndez B, Cuadros M, et al. Expression profiling of T-cell lymphomas differentiates peripheral and lymphoblastic lymphomas and defines survival related genes. Clinical cancer research : an official journal of the American Association for Cancer Research. 2004;10:4971-82. Available at: http://clincancerres.aacrjournals.org/content/10/15/4971.long.

Al-Shahrour F, Diaz-Uriarte R, Dopazo J. FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes. Bioinformatics. 2004;20:578-80. Available at: http://bioinformatics.oxfordjournals.org/content/20/4/578.abstract.

Melendez B, Diaz-Uriarte R, Cuadros M, et al. Gene expression analysis of chromosomal regions with gain or loss of genetic material detected by comparative genomic hybridization. Genes Chromosomes Cancer. 2004;41:353-65. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15382261.

Wang H, Azuaje F, Bodenreider O, Dopazo J. Gene expression Correlation and Gene Ontology-Based Similarity: An Assessment of Quantitative Relationship. In:  IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology. IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology.; 2004:25-31.

Pieper U, Eswar N, Braberg H, et al. MODBASE, a database of annotated comparative protein structure models, and associated resources. Nucleic Acids Res. 2004;32:D217-22. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=14681398.

Herrero J, Vaquerizas JM, Al-Shahrour F, et al. New challenges in gene expression data analysis and the extended GEPAS. Nucleic Acids Res. 2004;32:W485-91. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15215434.

Vella F, Mietchen D, Gabaldón T. Perceptions about postdocs. EMBO Rep. 2004;5:1104. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15577920.

Dopazo H, Santoyo J, Dopazo J. Phylogenomics and the number of characters required for obtaining an accurate phylogeny of eukaryote model species. Bioinformatics. 2004;20 Suppl 1:i116-21. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15262789.

Gabaldón T, Huynen MA. Prediction of protein function and pathways in the genome era. Cell Mol Life Sci. 2004;61:930-44. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15095013.

Conde L, Vaquerizas JM, Santoyo J, et al. PupaSNP Finder: a web tool for finding SNPs with putative effect at transcriptional level. Nucleic Acids Res. 2004;32:W242-8. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15215388.

Gabaldón T, Huynen MA. Shaping the mitochondrial proteome. Biochim Biophys Acta. 2004;1659:212-20. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15576054.

Mirkovic N, Marti-Renom MA, Weber BL, Sali A, Monteiro AN. Structure-based assessment of missense mutations in human BRCA1: implications for breast and ovarian cancer predisposition. Cancer Res. 2004;64:3790-7. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15172985.

Herrero J, Diaz-Uriarte R, Dopazo J. An approach to inferring transcriptional regulation among genes from large-scale expression data. Comp Funct Genomics. 2003;4:148-54. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18629097.

Martin MJ, Herrero J, Mateos A, Dopazo J. Comparing bacterial genomes through conservation profiles. Genome Res. 2003;13:991-8. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12695324.

Koh IY, Eyrich VA, Marti-Renom MA, et al. EVA: Evaluation of protein structure prediction servers. Nucleic Acids Res. 2003;31:3311-5. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12824315.

Yi X, Conesa A, Punt PJ, Hager LP. Examining the role of glutamic acid 183 in chloroperoxidase catalysis. J Biol Chem. 2003;278:13855-9. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12576477.

Herrero J, Diaz-Uriarte R, Dopazo J. Gene expression data preprocessing. Bioinformatics. 2003;19:655-6. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12651726.

Herrero J, Al-Shahrour F, Diaz-Uriarte R, et al. GEPAS: A web-based resource for microarray gene expression data analysis. Nucleic Acids Res. 2003;31:3461-7. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12824345.

Dopazo H, Gordon MB, Perazzo R, Risau-Gusman S. A model for the emergence of adaptive subsystems. Bull Math Biol. 2003;65:27-56. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12597115.

Ilyin VA, Pieper U, Stuart AC, Marti-Renom MA, McMahan L, Sali A. ModView, visualization of multiple protein sequences and structures. Bioinformatics. 2003;19:165-6. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12499313.

Gabaldón T, Huynen MA. Reconstruction of the proto-mitochondrial metabolism. Science. 2003;301:609. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12893934.

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Díaz-Uriarte R, Al-Shahrour F, Dopazo J. Use of GO Terms to Understand the Biological Significance of Microarray Differential Gene Expression Data. In:  Microarray data analysis III. Microarray data analysis III. Kluwer Academic, K. F. Johnson and S. M. Lin; 2003:233-247.

Al-Shahrour F, Herrero J, Mateos A, Santoyo J, Díaz-Uriarte R, Dopazo J. Using Gene Ontology on genome-scale studies to find significant associations of biologically relevant terms to group of genes. In:  Neural Networks for Signal Processing XIII. Neural Networks for Signal Processing XIII. New York, USA: IEEE Press; 2003:43-52.

Tamames J, Clark D, Herrero J, et al. Bioinformatics methods for the analysis of expression arrays: data clustering and information extraction. J Biotechnol. 2002;98:269-83. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12141992.

Conesa A, Jeenes D, Archer DB, van den Hondel CA, Punt PJ. Calnexin overexpression increases manganese peroxidase production in Aspergillus niger. Appl Environ Microbiol. 2002;68:846-51. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11823227.

Herrero J, Dopazo J. Combining hierarchical clustering and self-organizing maps for exploratory analysis of gene expression patterns. J Proteome Res. 2002;1:467-70. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12645919.

Punt PJ, van Biezen N, Conesa A, Albers A, Mangnus J, van den Hondel C. Filamentous fungi as cell factories for heterologous protein production. Trends Biotechnol. 2002;20:200-6. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11943375.

Conesa A, Punt PJ, van den Hondel CA. Fungal peroxidases: molecular aspects and applications. J Biotechnol. 2002;93:143-58. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11738721.

Tracey L, Villuendas R, Ortiz P, et al. Identification of genes involved in resistance to interferon-alpha in cutaneous T-cell lymphoma. Am J Pathol. 2002;161:1825-37. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12414529.

Mateos A, Herrero J, Tamames J, Dopazo J. Methods of Microarray Data Analysis IISupervised Neural Networks for Clustering Conditions in DNA Array Data After Reducing Noise by Clustering Gene Expression Profiles. (Lin SM, Johnson KF, eds.). Boston: Kluwer Academic Publishers; 2002:91 - 103. doi:10.1007/b11298210.1007/0-306-47598-7_7.

Dopazo J. Microarray Data Processing And Analysis. In:  Microarray data analysis II. Microarray data analysis II. Kluwer Academic; 2002:43-63.

Marti-Renom MA, Madhusudhan MS, Fiser A, Rost B, Sali A. Reliability of assessment of protein structure prediction methods. Structure. 2002;10:435-40. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12005441.

Mateos A, Herrero J, Tamames J, Dopazo J. Supervised Neural Networks For Clustering Conditions In DNA Array Data After Reducing Noise By Clustering Gene Expression Profiles. In:  Microarray data analysis II. Microarray data analysis II. Kluwer Academic; 2002:91-103.

Mateos A, Dopazo J, Jansen R, Tu Y, Gerstein M, Stolovitzky G. Systematic learning of gene functional classes from DNA array expression data by using multilayer perceptrons. Genome Res. 2002;12:1703-15. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12421757.

Conde L, Mateos A, Herrero J, Dopazo J. Unsupervised reduction of the dimensionality followed by supervised learning with a perceptron improves the classification of conditions in DNA microarray gene expression data. In:  Neural Networks for Signal Processing XII. 2002 IEEE Signal Processing Society WorkshopProceedings of the 12th IEEE Workshop on Neural Networks for Signal Processing. Neural Networks for Signal Processing XII. 2002 IEEE Signal Processing Society WorkshopProceedings of the 12th IEEE Workshop on Neural Networks for Signal Processing. Martigny, Switzerland: IEEE; 2002. doi:10.1109/NNSP.2002.1030019.

Iverson GM, Reddel S, Victoria EJ, et al. Use of single point mutations in domain I of beta 2-glycoprotein I to determine fine antigenic specificity of antiphospholipid autoantibodies. J Immunol. 2002;169:7097-103. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12471146.

Mateos A, Herrero J, Dopazo J. Using perceptrons for supervised classification of DNA microarray samples: obtaining the optimal level of information and finding differentially expressed genes. In:  ICANN 2002, LNCS 2415. ICANN 2002, LNCS 2415. J.R. Dorronsoro; 2002:577-582.

Dopazo J, Mendoza A, Herrero J, et al. Annotated draft genomic sequence from a Streptococcus pneumoniae type 19F clinical isolate. Microb Drug Resist. 2001;7:99-125. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11442348.

Mas JM, Aloy P, Marti-Renom MA, et al. Classification of protein disulphide-bridge topologies. J Comput Aided Mol Des. 2001;15:477-87. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11394740.

Conesa A, Weelink G, van den Hondel CA, Punt PJ. C-terminal propeptide of the Caldariomyces fumago chloroperoxidase: an intramolecular chaperone?. FEBS Lett. 2001;503:117-20. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11513866.

Marti-Renom MA, Ilyin VA, Sali A. DBAli: a database of protein structure alignments. Bioinformatics. 2001;17:746-7. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11524379.

Eyrich VA, Marti-Renom MA, Przybylski D, et al. EVA: continuous automatic evaluation of protein structure prediction servers. Bioinformatics. 2001;17:1242-3. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11751240.

Conesa A, van De Velde F, van Rantwijk F, Sheldon RA, van den Hondel CA, Punt PJ. Expression of the Caldariomyces fumago chloroperoxidase in Aspergillus niger and characterization of the recombinant enzyme. J Biol Chem. 2001;276:17635-40. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11278701.

Herrero J, Valencia A, Dopazo J. A hierarchical unsupervised growing neural network for clustering gene expression patterns. Bioinformatics. 2001;17:126-36. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11238068.

Nunez JI, Martin MJ, Piccone ME, et al. Identification of optimal regions for phylogenetic studies on VP1 gene of foot-and-mouth disease virus: analysis of types A and O Argentinean viruses. Vet Res. 2001;32:31-45. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11254175.

Dopazo J, Zanders E, Dragoni I, Amphlett G, Falciani F. Methods and approaches in the analysis of gene expression data. J Immunol Methods. 2001;250:93-112. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11251224.

Dopazo H, Gordon MB, Perazzo R, Risau-Gusman S. A model for the interaction of learning and evolution. Bull Math Biol. 2001;63:117-34. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11146879.

Elena SF, Dopazo J, de la Pena M, Flores R, Diener TO, Moya A. Phylogenetic analysis of viroid and viroid-like satellite RNAs from plants: a reassessment. J Mol Evol. 2001;53:155-9. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11479686.

Conesa A, Punt PJ, van Luijk N, van den Hondel CA. The secretion pathway in filamentous fungi: a biotechnological view. Fungal Genet Biol. 2001;33:155-71. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11495573.