Joaquin Dopazo

Personal Home Page

http://bioinfo.cipf.es/jdopazo/

Articles in Scholarly Journals [Incomplete List]

  1. ISACGH: a web-based environment for the analysis of Array CGH and gene expression which includes functional profiling
    Nucleic Acids Research, vol. 35, no. Web Server, pp. W81–W85, 2007
  2. FatiGO +: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments
    Nucleic Acids Research, vol. 35, no. Web Server, pp. W91–W96, 2007
  3. Association Study of 69 Genes in the Ret Pathway Identifies Low-penetrance Loci in Sporadic Medullary Thyroid Carcinoma
    Cancer Research, vol. 67, no. 19, pp. 9561–9567, 2007
  4. Phylemon: a suite of web tools for molecular evolution, phylogenetics and phylogenomics
    Nucleic Acids Research, vol. 35, no. Web Server, pp. W38–W42, 2007
  5. ERCC4 Associated with Breast Cancer Risk: A Two-Stage Case-Control Study Using High-throughput Genotyping
    Cancer Research, vol. 66, no. 19, pp. 9420–9427, 2006
  6. BMC Genomics, vol. 7, no. 1, p. 63, 2006
  7. Positive Selection, Relaxation, and Acceleration in the Evolution of the Human and Chimp Genome
    PLoS Computational Biology, vol. 2, no. 4, p. e38, 2006
  8. Functional Interpretation of Microarray Experiments
    OMICS: A Journal of Integrative Biology, vol. 10, no. 3, pp. 398–410, 2006
  9. Selective Pressures at a Codon-level Predict Deleterious Mutations in Human Disease Genes
    Journal of Molecular Biology, vol. 358, no. 5, pp. 1390–1404, 2006
  10. Prophet, a web-based tool for class prediction using microarray data
    Bioinformatics, vol. 23, no. 3, pp. 390–391, 2006
  11. PupaSuite: finding functional single nucleotide polymorphisms for large-scale genotyping purposes
    Nucleic Acids Research, vol. 34, no. Web Server, pp. W621–W625, 2006
  12. BABELOMICS: a systems biology perspective in the functional annotation of genome-scale experiments
    Nucleic Acids Research, vol. 34, no. Web Server, pp. W472–W476, 2006
  13. Next station in microarray data analysis: GEPAS
    Nucleic Acids Research, vol. 34, no. Web Server, pp. W486–W491, 2006
  14. A novel candidate region linked to development of both pheochromocytoma and head/neck paraganglioma
    Genes, Chromosomes and Cancer, vol. 42, no. 3, pp. 260–268, 2005
  15. Phenotypic characterization of BRCA1 and BRCA2 tumors based in a tissue microarray study with 37 immunohistochemical markers
    Breast Cancer Research and Treatment, vol. 90, no. 1, pp. 5–14, 2005
  16. BABELOMICS: a suite of web tools for functional annotation and analysis of groups of genes in high-throughput experiments
    Nucleic Acids Research, vol. 33, no. Web Server, pp. W460–W464, 2005
  17. PupasView: a visual tool for selecting suitable SNPs, with putative pathological effect in genes, for genotyping purposes
    Nucleic Acids Research, vol. 33, no. Web Server, pp. W501–W505, 2005
  18. Discovering molecular functions significantly related to phenotypes by combining gene expression data and biological information
    Bioinformatics, vol. 21, no. 13, pp. 2988–2993, 2005
  19. GEPAS, an experiment-oriented pipeline for the analysis of microarray gene expression data
    Nucleic Acids Research, vol. 33, no. Web Server, pp. W616–W620, 2005
  20. PupaSNP Finder: a web tool for finding SNPs with putative effect at transcriptional level
    Nucleic Acids Research, vol. 32, no. Web Server, pp. W242–W248, 2004
  21. FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes
    Bioinformatics, vol. 20, no. 4, pp. 578–580, 2004
  22. DNMAD: web-based diagnosis and normalization for microarray data
    Bioinformatics, vol. 20, no. 18, pp. 3656–3658, 2004
  23. Phylogenomics and the number of characters required for obtaining an accurate phylogeny of eukaryote model species
    Bioinformatics, vol. 20, no. suppl_1, pp. i116–i121, 2004
  24. Highly specific and accurate selection of siRNAs for high-throughput functional assays
    Bioinformatics, vol. 21, no. 8, pp. 1376–1382, 2004
  25. Gene expression analysis of chromosomal regions with gain or loss of genetic material detected by comparative genomic hybridization
    Genes, Chromosomes and Cancer, vol. 41, no. 4, pp. 353–365, 2004
  26. HCAD, closing the gap between breakpoints and genes
    Nucleic Acids Research, vol. 33, no. Database issue, pp. D511–D513, 2004
  27. New challenges in gene expression data analysis and the extended GEPAS
    Nucleic Acids Research, vol. 32, no. Web Server, pp. W485–W491, 2004
  28. Gene expression data preprocessing
    Bioinformatics, vol. 19, no. 5, pp. 655–656, 2003
  29. Artificial Intelligence Review, vol. 20, no. 1/2, pp. 39–51, 2003
  30. An approach to inferring transcriptional regulation among genes from large-scale expression data
    Comparative and Functional Genomics, vol. 4, no. 1, pp. 148–154, 2003
  31. Improved Class Prediction in DNA Microarray Gene Expression Data by Unsupervised Reduction of the Dimensionality followed by Supervised Learning with a Perceptron
    The Journal of VLSI Signal Processing-Systems for Signal, Image, and Video Technology, vol. 35, no. 3, pp. 245–253, 2003
  32. GEPAS: a web-based resource for microarray gene expression data analysis
    Nucleic Acids Research, vol. 31, no. 13, pp. 3461–3467, 2003
  33. Comparing Bacterial Genomes Through Conservation Profiles
    Genome Research, vol. 13, no. 5, pp. 991–998, 2003
  34. Systematic Learning of Gene Functional Classes From DNA Array Expression Data by Using Multilayer Perceptrons
    Genome Research, vol. 12, no. 11, pp. 1703–1715, 2002
  35. Bioinformatics methods for the analysis of expression arrays: data clustering and information extraction
    Journal of Biotechnology, vol. 98, no. 2-3, pp. 269–283, 2002
  36. Journal of Proteome Research, vol. 1, no. 5, pp. 467–470, 2002
  37. Methods and approaches in the analysis of gene expression data
    Journal of Immunological Methods, vol. 250, no. 1-2, pp. 93–112, 2001
  38. A hierarchical unsupervised growing neural network for clustering gene expression patterns
    Bioinformatics, vol. 17, no. 2, pp. 126–136, 2001
  39. Self-organizing tree growing network for classifying amino acids
    Bioinformatics, vol. 14, no. 4, pp. 376–377, 1998
  40. Parallel implementation of DNAml program on message-passing architectures
    Parallel Computing, vol. 24, no. 5-6, pp. 701–716, 1998
  41. A procedure for detecting selection in highly variable viral genomes: evidence of positive selection in antigenic regions of capsid protein VP1 of foot-and-mouth disease virus
    Journal of Virological Methods, vol. 74, no. 2, pp. 215–221, 1998
  42. A RT-PCR assay for the differential diagnosis of vesicular viral diseases of swine
    Journal of Virological Methods, vol. 72, no. 2, pp. 227–235, 1998
  43. Genetic Characterization of Populations of a De Novo Arisen Sugar Beet Pest, Aubeonymus mariaefranciscae (Coleoptera, Curculionidae), by RAPD Analysis
    Journal of Molecular Evolution , vol. 45 , no. 1 , pp. 24 –31 , 1997
  44. Phylogenetic Reconstruction Using an Unsupervised Growing Neural Network That Adopts the Topology of a Phylogenetic Tree
    Journal of Molecular Evolution , vol. 44 , no. 2 , pp. 226 –233 , 1997
  45. Contribution of Mutation and RNA Recombination to the Evolution of a Plant Pathogenic RNA
    Journal of Molecular Evolution , vol. 44 , no. 1 , pp. 81 –88 , 1997
  46. Phylogenetic relationships of European strains of porcine reproductive and respiratory syndrome virus (PRRSV) inferred from DNA sequences of putative ORF-5 and ORF-7 genes
    Virus Research, vol. 42, no. 1-2, pp. 159–165, 1996
  47. Comparative study of the genetic variability in thymidine kinase and glycoprotein B genes of herpes simplex viruses by the RNase A mismatch cleavage method
    Virus Research, vol. 35, no. 2, pp. 205–214, 1995
  48. Large deletions in the 5'-untranslated region of foot-and-mouth disease virus of serotype C
    Virus Research, vol. 35, no. 2, pp. 155–167, 1995
  49. Immunogenicity of non-structural proteins of foot-and-mouth disease virus: differences between infected and vaccinated swine
    Archives of Virology, vol. 136, no. 1-2, pp. 123–131, 1994
  50. Evolutionary relationships among bean common mosaic virus strains and closely related potyviruses
    Virus Research, vol. 31, no. 1, pp. 39–48, 1994
  51. Analysis of genetic variability of populations of herpes simplex viruses
    Virus Research, vol. 28, no. 3, pp. 249–261, 1993
  52. Estimates by computer simulation of genetic distances from comparisons of RNAse A mismatch cleavage patterns
    Journal of Virological Methods, vol. 45, no. 1, pp. 73–82, 1993
  53. A computer program for the design of PCR primers for diagnosis of highly variable genomes
    Journal of Virological Methods, vol. 41, no. 2, pp. 157–165, 1993
  54. Gene Encoding Capsid Protein VP1 of Foot-And-Mouth Disease Virus: A Quasispecies Model of Molecular Evolution
    Proceedings of the National Academy of Sciences, vol. 85, no. 18, pp. 6811–6815, 1988