Francisco García

• General overview of the course.
• NGS technologies vs. analysis methods and webtools.
• Presentation

Joaquín Panadero

• Basics of the NGS technologies.
• Computing infrastructure for NGS analyses.
• Some remarks on experiment design.
• Presentation

Alejandro Alemán

• NGS data preprocessing. Handling sequence files. Quality control tools.
• Mapping. Reference genome as a concept. NGS alignment programs and algorithms. SAM/BAM and BED file formats overview. Mapped reads visualization. Quality control of the mapping. Local realignment. Computational needs.
• Variant Calling. Variant types: SNPs and InDels. Calling procedures and algorithms. VCF file formats overview. Introduction to the programs GATK, Annovar and Variant. Variant filtering. The problem of the missing data. Variant annotation. Data bases and data repositories: dbSNP, the 1000 Genomes Project and CIBERER Spanish Variant Server.
• Presentation

Will be held in the cafeteria of the CIPF.

Francisco García, Francisco Salavert, Alejandro Alemán

• Introduction to genome browsers. Presentation.
• BiERapp. Interactive web application for assisting in gene prioritization in Whole-Exome Sequencing studies.
  • Presentation
  • 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.

Mercedes Medina

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

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

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

Marta Hidalgo, Matías Marín

• Introduction to Babelomics 5: babelomics_intro.pdf
• Preprocessing of RNA-Seq data with Babelomics 5: normalization.pdf
• Differential Expression of RNA-Seq data with Babelomics 5diff_exp16.pdf

• Data for practical exercises:
  • brca_demo_counts_4babelomics.txt
  • brca_normal-basal_ed.txt
  • kirc_demo_counts_4babelomics.txt
  • kirc_demo_ed.txt

Will be held in the cafeteria of the CIPF.

Daniel Crespo

• Over Representation Analysis: FatiGO.
• Gene Set Analysis using Logistic Models.
• enrichment_gdaciberer2.pdf

• gdaciberer16_exercises.pdf
• Data:
  • apoptosis.txt
  • braf_mvswt.txt
  • dystrophy.txt
  • fa_diffexp.statistic.txt
  • fibro.txt
  • fluorouridine.txt
  • motor.txt
  • melanomavsmelanocyte_17k.txt
  • melanomavsmelanocyte_17k.fati996.txt
  • melanomavsmelanocyte_17k.fati4022.txt

Alejandro Alemán, Francisco Salavert, Asunción Gallego, Mercedes Medina, Francisco García

• NGS data preprocessing, mapping and variant calling.
• Working with all analysis webtools. Bring your data!
• NGS pipeline tutorial

• Asador Pipol. C/ Convento San Francisco, 3. Maps

José Carbonell

Functional profiling and detection of new functional candidates:

• network_analysis_gdaciber2016.pdf

• SNOW. Network Enrichment.
• Network Miner. Gene Set Network Enrichment.

Cankut Çubuk, Alicia Amadoz, Marta Hidalgo, José Carbonell

• Introduction: Signal Transduction.
  • Cell Signaling and Signaling Pathways
• Signaling Pathways Analysis:
  • hiPathia. High-throughput pathway inference analysis. Exercises
  • PathAct. Actionable pathway workshop. Exercises

Joaquín Dopazo

Will be held in the cafeteria of the CIPF.

• 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.

• More publications.
• Computational Genomics tools