Transcriptome Assembly, Automatic Annotation and Data Mining

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   Deadline for applications: September 26th 2014
   Notification of acceptance dates:
        EARLY: Sept 19th 2014
        NORMAL: September 26th 2014
   Course date: October 6th - October 9th 2014


Stefan Götz completed his Computer Science studies in Germany in 2004. He began his work in bioinformatics within the Biomedical Informatics group at the Polytechnic University of Valencia. There, he started to work in the area of Functional Annotation of novel sequence data. He then became the main developer of the Blast2GO project. In March 2007, he joined the Bioinformatics and Genomics Department of the Prince Felipe Research Centre (CIPF) where he concluded his PhD studies in 2010, and continued to work as a staff scientist until 2011. In recent years, he has been involved in various bioinformatics projects related to the analysis and visualisation of genomics data, protein interaction networks, modelling of phenotype information and NGS data processing. He is founder and the managing director of BioBam Bioinformatics.

Affiliation BioBam, Valencia, ES

Riccardo Aiese Cigliano took a bachelor and a master degree in Biotechnological Sciences in Italy in 2005 and 2008 respectively. In 2008 he attended to an advanced course on plant genomics and post-genomics, coordinated by the Institute of Plant Genetics (IGV) - National Council Research (CNR). He has attended several courses about the application of bioinformatics and molecular biology to the study of plant genomes and transcriptomes. In 2011 he concluded his PhD with a thesis on the role of histone modifiers in plant reproduction and in 2012 he joined the Gregor Mendel Institute (Austria) for a post-doc fellowship to study the role of chromatin remodeling in DNA double strand breaks. In 2013 he founded Sequentia Biotech in Barcelona where he is also the scientific director and he is managing the transcriptomics and epigenomics department.

Affiliation: Sequentia Biotech, Barcelona, ES

Course description:

This is a combined course in RNA-seq and functional annotation aimed at scientists working in next generation sequencing transcriptomics who want to extract the best possible information from their data. The course covers all aspects of RNA-seq analysis, from quality control, to mapping, reconstruction of transcripts and differential expression. Participants will learn how to deal with RNA-seq data both in the presence and absence of a reference genome.

The second part of the course is a practical workshop on Blast2GO, the most popular framework for functional annotation of sequence data. Participants will learn how to generate de novo functional labels, such as GO terms and KEGG pathways, for their sequence data and how to extract relevant information from these annotations, i.e. visualisation and enrichment analysis using the Gene Ontology. This part will be based on the use of the Blast2GO application and will mainly comprise exercises and practical cases. Participants may bring their own data.

Who should attend? Experimentalists and bioinformaticians working on EST, NextGeneration Sequencing and microarray design projects, specially (but not exclusively) of non-model species. No programming knowledge is required.

Course Pre-requisites:

basic knowledge in Molecular Biology and Statistics.

Detailed Program / Timetable

Instituto Gulbenkian de Ciência,

Apartado 14, 2781-901 Oeiras, Portugal

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Last updated:  September 4th 2014