Transcriptome Assembly, Automatic Functional Annotation and Data Mining

   Deadline for applications: Feb 20th 2012
   Notification of acceptance dates:
        EARLY: Feb 14th 2012
        NORMAL: Feb 20th 2012
   Course date: Feb 27th - Mar 1st 2012


Ana Conesa is a senior scientist at the Bioinformatics and Genomics Department of the CIPF. She did her PhD in Fungal Genetics at the Dutch Institute for Applied Sciences (TNO), followed by a Bioinformatics Project Leider position a the Toxicology Department. Then she moved to the Valencia Agricultural Research Institute to step-up a Bioinformatics service until April 2007, when she joined the CIPF. Her research activity is in the Field of Functional Genomics, developing bioinformatics methods for the functional annotation of non-model organisms, the statistical analysis of transcriptomics data and the integration of systems biology data. In particular, Blast2GO.

Affiliation Centro de Investigacion Principe Felipe, Valencia, ES

Fernando García-Alcalde after finishing his Computer Science studies in 2005, he started his PhD studies in Bioinformatics in the area of transcription regulation. He obtained his PhD in from the University of Granada (Spain) in 2010. After his PhD he moved to Valencia (Spain) to work as a Post-Doc in the Genomics of Gene Expression Lab headed by Ana Conesa at the Bioinformatics department of the Centro de Investigación Príncipe Felipe (CIPF). He conducted research on Next Generation Sequencing data analysis with a specialization in RNA-Seq. Currently he works at the Max Planck Institute for Infection Biology in Berlin (Germany) where he is involved in the study of the epigenetic changes occured in the host upon bacterial infection and their implications in cancer development.

Affiliation: Max Planck Institute for Infection Biology, Berlin, DE

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, form quality control, to mapping, reconstruction of transcripts and differential expression. Participants will learn how to deal with RNAseq data both in the presence and absence of a reference genome. The second part of the course is a practical tutorial on Blast2GO, the most popular framework for functional annotation of sequences. Participants will also 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. visualization and enrichment analysis using the Gene Ontology.

The course will be based on the use of 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

In collaboration with INTERBIO

Sponsorship available for members of the following INTERBIO Nodes:
- Université Paul Sabatier Toulouse - UPS (Midi-Pyrénées - France) (www.ups-tlse.fr)
- Fundación Privada BioRegió de Catalunya - BIOCAT (Catalonia - Spain), (www.biocat.cat)
- Institut Européen de Chimie et Biologie - IECB (Aquitaine - France), (www.iecb.u-bordeaux.fr)
- Fundación de la Comunidad Valenciana para la Innovación Urbana y Economía del Conocimiento - FIVEC (Valencia - Spain), (www.fivec.org).

If you wish to apply as a member of one of these institutions, please contact your local INTERBIO representative.

Instituto Gulbenkian de Ciência,

Apartado 14, 2781-901 Oeiras, Portugal

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Last updated:  Feb 29th 2012