Training

Is it right for me?

The main objective of this course is to introduce the participants to advanced bioinformatics, statistical methodologies and software tools for analyzing and managing transcriptomics data.

This course is aimed at advanced PhD students and post-doctoral researchers who are applying or planning to apply microarray, next generation sequencing technologies and bioinformatics methods in their research. Participants who have already performed microarray based experiments are encouraged to bring their own data to analyze it during the last practical session of the course.

Over the past few years, microarrays have become an established technology in molecular biology, used in an increasing number of laboratories, for studying a cell's transcriptome — the collection of all RNA transcripts produced at a specific time. The newly emerging next generation sequencing methods promise to change the landscape of gene-expression analysis, posing new analytical challenges.

A growing wealth of data analysis tools is available to researchers of different levels of expertise, and several courses on data analysis are given annually by EMBO and other organizations. Nevertheless, data analysis is still a major bottleneck for many researchers which are still applying inadequate statistical methods for the interpretation of their results. At the same time new, increasingly more sophisticated methodologies are introduced and new analysis methods are being developed.

The aim of this course is to familiarize the participants with such advanced methodologies and provide hands-on training on the latest analytical approaches.    

The European Bioinformatics Institute (EBI) is one of the acknowledged leaders in microarray informatics and data analysis. The co-organizers of this course are internationally acknowledged experts in the transcriptomics field. All trainers involved have extensive experience in teaching data analysis at both introductory and advanced levels.

References and links

• http://www.ebi.ac.uk/microarray/
• Bioconductor Case Studies. Series: Use R! Hahne, F; Huber, W.; Gentleman, R.; Falcon, S. Springer, 2008, 284 p.
• Microarray Technology in Practice. Russell, S.; Meadows, L.A., Russell, R.R. Academic Press, 2008, 464 p.
• Bioinformatics and Computational Biology Solutions Using R and Bioconductor. Series: Statistics for Biology and Health, Gentleman, R.; Carey, V.; Huber, W.; Irizarry, R.; Dudoit, S. (Eds.). Springer, 2005, 460 p.
• Microarray Gene Expression Data Analysis – a Beginner’s Guide. Causton H., Quackenbush J., Brazma A. Wiley-Blackwell, 2003, 160 p.

What will it cover?

The proposed course will consist of:

• Lectures from distinguished speakers;
• Demonstrations of microarray and next-generation sequencing data analysis software and other relevant bioinformatics resources;
• Practical sessions using the demonstrated software/resources to analyze both data provided by the trainers and the participants own data;
• Discussion of the results obtained during the practical sessions;
• Poster presentations from the participants describing their research in the transcriptomics field.

There will be 8-10 lectures (~25% of the course) which will give insight into how biological knowledge can be generated from microarray and sequencing experiments, illustrating different ways of analyzing such data.

The practical sessions (~75% of the course) will consist of computer exercises that will enable the participants to apply statistical methods to the analysis of microarray and sequencing data, under the guidance of the lecturers and teaching assistants. On the last day, participants will have the chance to analyze their own data and discuss the results with the trainers.

Each participant will be asked to prepare a poster display of their research which will be presented and discussed over the course of two poster sessions.

Trainers

• Benilton Carvalho, Cancer Research UK
• Angela Goncalves, EBI
• Hedi Peterson, University of Tartu
• Jonh Quackenbush, Dana-Faber Cancer Institute
• Oscar Rueda, Cancer Research UK
• Roslin Russell, Cancer Research UK
• Gabriella Rustici, EBI