Francisco García García, fgarcia@cipf.es

• General overview of the sessions. Studies of genomic variation. Prioritization of variants and genes. Presentation.
• BiERapp. Interactive web application for assisting in gene prioritization in Whole-Exome Sequencing studies. BiERapp exercises
• CSVS (CIBERER Spanish Variant Server). This database provides information about the variability of the Spanish population. It is very useful for filtering polymorphisms and local variations when prioritizing candidate disease genes.

Francisco García García, fgarcia@cipf.es

• Management of panels of genes for targeted enrichment and massive sequencing for diagnostic applications.
• How to design panels of genes.
• TEAM (Targeted Enrichment Analysis and Management):

• Activity 1:
  • activity1_team.pdf
  • data_activity1_team.zip

• Activity 2:
  • activity2_team.pdf
  • data_activity2_team.zip

Alicia Amadoz Navarro, aamadoz@cipf.es

• RNA-Seq Data Analysis. transcriptomics_upvmbb2016.pdf
• Introduction to Babelomics 5.
• Data for practical exercises:
  • Normalization exercise: brca_demo_counts_4babelomics.txt
  • Normalization exercise: brca_normal-basal_ed.txt
  • Single Enrichment exercise: brca_diffexp_toplist50.txt
  • Clustering exercise: brca_tmm_normalized_results_sel200.txt
  • Pipeline exercise: kirc_demo_counts_4babelomics.txt
  • Pipeline exercise: kirc_demo_ed.txt

Marta Hidalgo García, mhidalgo@cipf.es

• Introduction: Signal Transduction.
• Signaling Pathways Analysis:
  • hiPathia. High-throughput pathway inference analysis. hipathia_15-12-16.pdf
  • PathAct. Actionable pathway workshop. pathact_15-12-16.pdf

• 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.
• 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 May 2. DOI 10.1093/nar/gkw369.

• More publications.
• Computational Genomics tools