Joaquín Dopazo Blázquez, jdopazo@cipf.es

• Mechanistic biomarkers derived from models of pathway activity

Francisco García García, fgarcia@cipf.es

• Introduction, Babelomics, Functional Profiling
• Activities, data

Francisco García García, fgarcia@cipf.es

• Clustering Analysis
• Activities, data

• Supervised Classification

• Activities, data

1. Detailed example of Affymetrix expression data analysis in Babelomics: from raw data to expression differential and functional profiling
2. Statistics Bioinformatics: handbook
3. Some R/Bioconductor packages for functional enrichment: EnrichmentBrowser, piano
4. Web tools for pathways analysis: hipathia and pathact
5. Genomic Data Analysis course

• Babelomics 5.0: functional interpretation for new generations of genomic data. Alonso R, Salavert F, Garcia-Garcia F, et al. Nucleic Acids Res. 2015;43:W117-W121.

• SNOW, a web-based tool for the statistical analysis of protein-protein interaction networks. Minguez P, Gotz S, Montaner D, Al-Shahrour F, Dopazo J. Nucl. Acids Res. 2009;37:W109-114
• Discovering the hidden sub-network component in a ranked list of genes or proteins derived from genomic experiments. García-Alonso L, Alonso R, Vidal E, Amadoz A, de María A, Minguez P, Medina I, Dopazo J. Nucleic Acids Res. 2012 Jul 27.

• FatiGO+: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments. Al-Shahrour, F., Minguez, P., Tárraga, J., Medina, I., Alloza, E., Montaner, D., & Dopazo, J. (2007). Nucleic Acids Research 35 (Web Server issue): W91-96
• FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes. Al-Shahrour, F., Díaz-Uriarte, R. & Dopazo, J. (2004). Bioinformatics 20: 578-580
• Multidimensional Gene Set Analysis of Genomic Data.. Montaner D., Dopazo J. (2010) PLoS ONE 5(4): e10348. doi:10.1371/journal.pone.0010348.
• Integrated gene set analysis for microRNA studies. Garcia-Garcia F, Panadero J, Dopazo J, Montaner D. Bioinformatics. 2016 Sep 15;32(18):2809-16. doi: 10.1093/bioinformatics/btw334. Epub 2016 Jun 20.PMID: 27324197

• High throughput estimation of functional cell activities reveals disease mechanisms and predicts relevant clinical outcomes. Hidalgo MR, Cubuk C, Amadoz A, Salavert F, Carbonell-Caballero J, Dopazo J. Oncotarget. 2017;8(3):5160-5178
• Actionable pathways: interactive discovery of therapeutic targets using signaling pathway models. Salavert F, Hidago MR, Amadoz A, Çubuk C, Medina I, Crespo D, Carbonell-Caballero J, Dopazo J. Nucleic Acids Res. 2016

• All publications.
• Computational Genomics tools