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Journal Article
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.
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.
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.
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.
Tarraga J, Medina I, Carbonell J, et al. GEPAS, a web-based tool for microarray data analysis and interpretation. Nucleic Acids Res. 2008;36:W308-14. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18508806.
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.
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.
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.
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.
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.
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.
Largo C, Alvarez S, Saez B, et al. Identification of overexpressed genes in frequently gained/amplified chromosome regions in multiple myeloma. Haematologica. 2006;91:184-91. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16461302.
Wilkinson MD, Senger M, Kawas E, et al. Interoperability with Moby 1.0–it’s better than sharing your toothbrush!. Brief Bioinform. 2008;9:220-31. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18238804.
Conde L, Montaner D, Burguet-Castell J, et al. ISACGH: a web-based environment for the analysis of Array CGH and gene expression which includes functional profiling. Nucleic Acids Res. 2007;35:W81-5. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17468499.
Reumers J, Conde L, Medina I, et al. Joint annotation of coding and non-coding single nucleotide polymorphisms and mutations in the SNPeffect and PupaSuite databases. Nucleic Acids Res. 2008;36:D825-9. Available at: http://nar.oxfordjournals.org/cgi/content/full/36/suppl_1/D825.
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.
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.
Desoignies N, Carbonell J, Moreau J-S, Conesa A, Dopazo J, Legrève A. Molecular interactions between sugar beet and Polymyxa betae during its life cycle. Annals of Applied Biology. 2014;164:244–256. doi:10.1111/aab.12095.
Montero-Conde C, Martin-Campos JM, Lerma E, et al. Molecular profiling related to poor prognosis in thyroid carcinoma. Combining gene expression data and biological information. Oncogene. 2008;27:1554-61. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17873908.
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.
Montaner D, Tarraga J, Huerta-Cepas J, et al. Next station in microarray data analysis: GEPAS. Nucleic Acids Res. 2006;34:W486-91. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16845056.
Cascon A, Ruiz-Llorente S, Rodriguez-Perales S, et al. A novel candidate region linked to development of both pheochromocytoma and head/neck paraganglioma. Genes Chromosomes Cancer. 2005;42:260-8. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15609347.
Calpena E, Martínez-Rubio D, Arpa J, et al. A novel locus for a hereditary recurrent neuropathy on chromosome 21q21. Neuromuscular disorders : NMD. 2014;24:660-5. doi:10.1016/j.nmd.2014.04.004.
Azuaje F, Al-Shahrour F, Dopazo J. Ontology-driven approaches to analyzing data in functional genomics. Methods Mol Biol. 2006;316:67-86. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16671401.