Francisco García García

• Overview course

Marta Hidalgo García

• Clinical and biological databases, Statistics and high throughput technologies

Will be held in the cafeteria of the CIPF.

Francisco García García

• Omics-based biomarkers detection in Metabolomics, Proteomics, Transcriptomics from arrays,...
• Tool: Babelomics (http://babelomics.bioinfo.cipf.es/ from Firefox browser)
• Exercises

José F. Català Senent

• Presentation
• Exercises
• Tools:
  • BoxPlotR (http://boxplot.tyerslab.com)
  • Heatmapper (http://heatmapper.ca)

Francisco García García

• Omics-based biomarkers detection in Transcriptomics: RNA-Seq, microRNA-Seq,...
• Tool: Babelomics (http://babelomics.bioinfo.cipf.es/ from Firefox browser)
• Exercises

Sandra Alandes Esteve

• How to prioritize from Endeavour?
• Exercises

Will be held in the cafeteria of the CIPF.

Francisco García García

• Presentation
• Tools:
  • PANTHER: Classification System
  • Babelomics (http://babelomics.bioinfo.cipf.es/ from Firefox browser)
• Exercises

Francisco García García

• Presentation
• Tool: STRING: functional protein association networks
• Exercises

Antonio Jordán Pla

• Single cell RNA-seq data analysis with ASAP.
• Tool: ASAP: Automated Single-cell Analysis Pipeline

Marta Hidalgo, Francisco García, José F. Català, Sandra Alandes, Antonio Jordán

• During this session you can analyze your data with us.
• You can also do the exercises of other sessions.
• If you do not have any data, this will not be a problem and here we have a full practice for you.

Francisco García García, fgarcia@cipf.es

• 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
• 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
• 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;44:W212-W216
• 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.
• Assessing the impact of mutations found in next generation sequencing data over human signaling pathways. Hernansaiz-Ballesteros RD, Salavert F, Sebastián-León P, Alemán A, Medina I, Dopazo J. Nucleic Acids Res. 2015;43:W270-W275.
• Understanding disease mechanisms with models of signaling pathway activities. Sebastian-Leon P, Vidal E, Minguez P, et al. BMC Syst Biol. 2014;8(1):121.
• Inferring the functional effect of gene expression changes in signaling pathways. Sebastián-León P, Carbonell J, Salavert F, Sanchez R, Medina I, Dopazo J. Nucleic Acids Res. 2013;41:W213-W217.
• A web-based interactive framework to assist in the prioritization of disease candidate genes in whole-exome sequencing studies. Alemán A, Garcia-Garcia F, Salavert F, Medina I, Dopazo J. Nucleic Acids Res. 2014;42:W88-W93.
• A web tool for the design and management of panels of genes for targeted enrichment and massive sequencing for clinical applications. Alemán A, Garcia-Garcia F, Medina I, Dopazo J. Nucleic Acids Res. 2014;42:W83-W87.
• 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
• Genome Maps, a new generation genome browser. Medina I, Salavert F, Sanchez R, et al. Nucleic Acids Res. 2013;41:W41-W46.
• Heatmapper: web-enabled heat mapping for all. Babicki S, Arndt D, Marcu A, el al. Nucleic Acids Res. 2016;44:W147-W153
• 40 years of boxplots. Wickman H & Stryjewski L. http://vita.had.co.nz/papers/boxplots.pdf

• More publications.
• Software list