Publications

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Journal Article
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.
Al-Shahrour F, Minguez P, Tarraga J, et al. BABELOMICS: a systems biology perspective in the functional annotation of genome-scale experiments. Nucleic Acids Res. 2006;34:W472-6. Available at: http://nar.oxfordjournals.org/content/34/suppl_2/W472.long.
Al-Shahrour F, Carbonell J, Minguez P, et al. Babelomics: advanced functional profiling of transcriptomics, proteomics and genomics experiments. Nucleic Acids Res. 2008;36:W341-6. Available at: http://nar.oxfordjournals.org/content/36/suppl_2/W341.long.
Valls J, Grau M, Sole X, et al. CLEAR-test: combining inference for differential expression and variability in microarray data analysis. J Biomed Inform. 2008;41:33-45. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17597009.
Aguerri M, Calzada D, Montaner D, et al. Differential gene-expression analysis defines a molecular pattern related to olive pollen allergy. Journal of biological regulators and homeostatic agents. 2013;27:337-50. Available at: http://www.ncbi.nlm.nih.gov/pubmed/23830385.
Conesa A, Bro R, Garcia-Garcia F, et al. Direct functional assessment of the composite phenotype through multivariate projection strategies. Genomics. 2008;92:373-83. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18652888.
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.
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.
Al-Shahrour F, Arbiza L, Dopazo H, et al. From genes to functional classes in the study of biological systems. BMC Bioinformatics. 2007;8:114. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17407596.
Conde L, Montaner D, Burguet-Castell J, Tarraga J, Al-Shahrour F, Dopazo J. Functional profiling and gene expression analysis of chromosomal copy number alterations. Bioinformation. 2007;1:432-5. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17597935.
Minguez P, Al-Shahrour F, Montaner D, Dopazo J. Functional profiling of microarray experiments using text-mining derived bioentities. Bioinformatics. 2007;23:3098-9. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17855415.
Montaner D, Minguez P, Al-Shahrour F, Dopazo J. Gene set internal coherence in the context of functional profiling. BMC Genomics. 2009;10:197. Available at: http://www.biomedcentral.com/1471-2164/10/197.
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.
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.
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.
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.
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.
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.
Arbiza L, Duchi S, Montaner D, et al. Selective pressures at a codon-level predict deleterious mutations in human disease genes. J Mol Biol. 2006;358:1390-404. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16584746.