Table of Contents
Wednesday 16
11:00 – 11:15 Registration
11:15 – 11:45 Welcome, course overview and networking
Francisco García García
11:45 – 13:30 Introduction
11:45 – 12:45 Introduction to Biostatistics
Marta Hidalgo García
12:45 – 13:30 High throughput technologies and clinical and biological databases
Irene Pérez Díez
13:30 – 14:30 Lunch break
14:30 – 16:00 Visualization of omics data
José F. Català Senent
- Tools:
- BoxPlotR (http://boxplot.tyerslab.com)
- Heatmapper (http://heatmapper.ca)
16:00 – 16:15 Break
16:15 – 18:00 Omics-based biomarkers detection I
Thursday 17
9:30 – 11:00 Omics-based biomarkers detection II
Francisco García García
11:00 – 11:30 Coffee break
11h30 – 13:30 Functional profiling: over-representation and GSA methods
Rubén Grillo Risco
13:30 – 14:30 Lunch break
14:30 – 16:00 Functional profiling: protein-protein interaction
Raúl Pérez Moraga
16:00 – 16:15 Break
16:15 – 18:00 Prioritization of genes
Sandra Alandes Esteve
Friday 18
9:30 – 11:00 Single-cell analysis
Antonio Jordán Pla
11:00 – 11:30 Coffee break
11:30 – 13:00 Models of signaling pathway activity: HiPathia
Marta Hidalgo
- Tool: HiPathia
13:00 – 13:15 Course feedback and wrap up
Francisco García García
References and links
- 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
