Whole Exome Sequencing and RNA-seq data analysis

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   IMPORTANT DATES for this Course
   Deadline for applications: September 27th 2013
   Notification of acceptance within 72 hours of application (working days count)
   Course date: October 8th to October 11th 2013


Ignacio Medina did his Biochemistry degree at the Universidad de Valencia and a Computer Science degree at the Universidad Politecnica de Valencia. For two years he worked as a researcher in the Facultad de Medicina of the Universida de Valencia, and for another two years he worked as a researcher in the Artificial Intelligence Department of the Universidad Politecnica de Valencia. Since 2006 he is a bioinformatician at the Bioinformatics Department of the Centro de Investigacion Principe Felipe in Valencia (Spain) and since 2012 he is the Head of the Computational Biology Unit, where he is involved in several research projects and in the development of software for genome scale data analysis such as Babelomics, VARIANT, Genome Maps or HPG Aligner projects, among others. His research interests include NGS data analysis, predictors, Genomic Variant analysis as well as functional and system biology analysis of genomic data.

Affiliation: Centro de Investigacion Principe Felipe, Valencia, ES

Javier López completed his Bachelor degree in Computer Science at the University of Granada. He has a PhD in Bioinformatics from the same University (2010). He then obtained a postdoctoral position at the Barcelona Centre for International Health Research, where he developed his research from June 2010 to March 2012. During that period he was the bioinformatic component of a molecular biology research lab working on Plasmodium vivax. Since April 2012 he has been working as a bioinformatician at the Genomics and Bioinformatics Platform of Andalusia. This a high throughput sequencing centre where he is being involved in outstanding projects such as the Medical Genome Project (http://www.medicalgenomeproject.com). His research interests include the development of tools for the analysis of high throughput sequencing data, including variant analysis and prioritization with whole exome sequencing data, transcriptome analysis with RNA-seq data (differential expression, transcripts assembly, etc.).

Affiliation: Genomics and Bioinformatics Platform of Andalusia, Sevilla, ES

Course description

High-throughput technologies such as next generation sequencing (NGS) are characterized for producing massive a mounts of data. These technologies for example can allow to describe all variants in a genome or to detect the whole set of transcripts that are present in a cell or tissue. However, at the same time, posses new challenges in the way the data has to be analyzed, annotated and interpreted which are not trivial.

Whole Exome Sequencing produces sequence data using NGS assays and allows the study of genetic variations in the exonic regions of all genes that can be transformed in biological information at an unprecedented level of detail. Traditionally transcriptomic analysis has been used to find genes that are differentially expressed among distinct experimental conditions, or correlated to diverse parameters. Currently, NGS technologies such as RNA-seq can also allow to digitally quantify all, known and unknown, transcripts or to discover new isoforms and splice sites for all the genes.

However, NGS data analysis can be a major bottleneck for many researchers which are still applying inefficient tools for the processing of the data and inadequate methods for the interpretation of their results in order to have meaningful results. This course covers state-of-the-art tools and methods for NGS RNA-seq and exome variant data analysis, which are of major relevance in today's genomic and gene expression studies.

The aim of this course is to familiarise course participants with the latest analysis methodologies and to provide hands-on training on the analytical approaches implemented for RNA-seq data and whole exome variant analysis.

Target Audience

The course is oriented to experimental researchers, post-doctoral and PhD students who want to learn about the state-of-the-art of genomic variant and transcriptomics data analysis methodologies and carry out their own analysis.

Course Pre-requisites

Basic computing skills, graduate level in Life Sciences

Detailed Program

Instituto Gulbenkian de Ciência,

Apartado 14, 2781-901 Oeiras, Portugal

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Last updated:  Sept 21st 2013