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program [2016/12/19 13:42]
mhidalgo 		program [2017/05/24 14:23] (current)
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 +====== Day 1: Dec 12th ======
 +=====17:30-19:30 Genomics =====
 +Francisco García García, fgarcia@cipf.es
 +  *General overview of the sessions. Studies of genomic variation. Prioritization of variants and genes. {{:presentation.pdf|Presentation}}.  
 +  ***[[http://courses.babelomics.org/bierapp|BiERapp]]**. Interactive web application for assisting in gene prioritization in Whole-Exome Sequencing studies.  [[bierapp_exercises|  BiERapp exercises]]
 +  ***[[http://csvs.babelomics.org/|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. 
  
 +
 +
 +====== Day 2: Dec 14th ======
 +=====15:30-17:00 Genomics =====
 +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.
 +     ***[[http://courses.babelomics.org/team|TEAM]]** (Targeted Enrichment Analysis and Management): 
 +
 +    * Activity 1:
 +      * {{:activity1_team.pdf|}}
 +      * {{:data_activity1_team.zip|}}
 +
 +    * Activity 2:
 +      * {{:activity2_team.pdf|}}
 +      * {{:data_activity2_team.zip|}}
 +
 +=====17:30 – 19:30 Transcriptomics  =====
 +Alicia Amadoz Navarro, aamadoz@cipf.es
 +
 +
 +    * RNA-Seq Data Analysis. {{:transcriptomics_upvmbb2016.pdf|}}
 +    * Introduction to [[http://courses.babelomics.org/|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|}}
 +
 +
 +====== Day 3: Dec 15th ======
 +=====17:30-19:30 Transcriptomics =====
 +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|}} 
 +
 +
 +====== References and links ======
 +  * **Babelomics 5.0: functional interpretation for new generations of genomic data.** Alonso R, Salavert F, Garcia-Garcia F, et al. [[http://nar.oxfordjournals.org/content/43/W1/W117|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. [[http://nar.oxfordjournals.org/content/early/2015/04/16/nar.gkv349.full|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.  [[http://www.biomedcentral.com/1752-0509/8/121/abstract|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. [[http://nar.oxfordjournals.org/content/41/W1/W213|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.  [[http://nar.oxfordjournals.org/content/42/W1/W88|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.  [[http://nar.oxfordjournals.org/content/42/W1/W83.long|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.  [[http://nar.oxfordjournals.org/content/early/2009/05/19/nar.gkp402.full|Nucl. Acids Res. 2009;37:W109-114]] 
 +  * **Genome Maps, a new generation genome browser.** Medina I, Salavert F, Sanchez R, et al.  [[http://nar.oxfordjournals.org/content/41/W1/W41|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, [[http://nar.oxfordjournals.org/content/early/2016/05/02/nar.gkw369.full|Nucleic Acids Res. 2016 May 2. DOI 10.1093/nar/gkw369]].
 +
 +  *[[http://bioinfo.cipf.es/publications|More publications]].
 +  *[[http://bioinfo.cipf.es/tools|Computational Genomics tools]]