Trevino V, Tadesse MG, Vannucci M, et al. Analysis of normal-tumour tissue interaction in tumours: prediction of prostate cancer features from the molecular profile of adjacent normal cells. PloS one. 2011;6:e16492.

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.

Javierre BM, Fernandez AF, Richter J, et al. Changes in the pattern of DNA methylation associate with twin discordance in systemic lupus erythematosus. Genome research. 2010;20:170-9.

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.

Medina I, Montaner D, Bonifaci N, et al. Gene set-based analysis of polymorphisms: finding pathways or biological processes associated to traits in genome-wide association studies. Nucl. Acids Res. 2009;37:W340-344. doi:10.1093/nar/gkp481.

Minguez P, Gotz S, Montaner D, Al-Shahrour F, Dopazo J. SNOW, a web-based tool for the statistical analysis of protein-protein interaction networks. Nucl. Acids Res. 2009;37:W109-114. doi:10.1093/nar/gkp402.

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.

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.

Marti-Renom MA, Rossi A, Al-Shahrour F, et al. The AnnoLite and AnnoLyze programs for comparative annotation of protein structures. BMC Bioinformatics. 2007;8 Suppl 4:S4. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17570147.

Marti-Renom MA, Pieper U, Madhusudhan MS, et al. DBAli tools: mining the protein structure space. Nucleic Acids Res. 2007;35:W393-7. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17478513.

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.

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.

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.

Minguez P, Al-Shahrour F, Dopazo J. A function-centric approach to the biological interpretation of microarray time-series. Genome Inform. 2006;17:57-66.

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.

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.

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.

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.

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.

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.

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.

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.

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.