Microarray Data Analysis using GEPAS and Babelomics

   Deadline for applications: May 3rd 2010 (NEW)
   Notification of acceptance dates:
        EARLY: April 6th 2010
        NORMAL: April 30th 2010
   Course date: May 10th - May 12th 2010


Joaquín Dopazo has a master degree in Chemistry (Universidad de Valencia) and a PhD in Biology (Universidad de Valencia). He is the head of the Department of Bioinformatics at the CIPF (Valencia). In previous appointments he was responsible for Bioinformatics units at the CNIO (Madrid) and at GlaxoWellcome SA (Madrid). He has supervised several large scale projects of software development, as the GEPAS or the Babelomics ( where more than 500 microarray experiments are daily analysed. He has more than one hundred papers published in international peer reviewed journals and has edited a book on genomic data analysis. His main interests include functional and comparative genomics.

Javier Santoyo-Lopez obtained his PhD in Biological Sciences from the University Autonoma of Madrid (UAM) in 1997. His PhD studies were performed at the Spanish Research Council (CSIC) Centre of Molecular Biology “Severo Ochoa” (Madrid, Spain). After his PhD he moved to Dundee (Scotland, UK) where he obtained his MSc in Bioinformatics at the University of Abertay Dundee. He was a Bioinformatician at the Wellcome Trust Biocentre (Dundee, Scotland, UK), at the Sanger Institute (Hinxton, England, UK), at the Spanish National Cancer Centre - CNIO (Madrid, Spain) and at the Division of Pathway Medicine (Edinburgh, Scotland, UK). Since 2008 he works at the Biomedical Network Research Centre for Rare Diseases (CIBERER) in The Prince Felipe Research Centre – CIPF (Valencia, Spain) where he is involved in the study of genomic variations and regulatory elements that are cause of Rare Diseases. He is also involved in the study of non-coding RNAs, in particular, the study of the RNA interference phenomenon (RNAi).

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

Course description:

DNA microarrays constitute, no doubt, a paradigm among post-genomic technologies, which are characterised for producing large amounts of data, whose analysis and interpretation is not trivial. Microarray technologies allows querying living systems in a completely new way, but at the same time present new challenges in the way hypotheses must be tested and results have to be analysed.

Since the first papers published in the latest nineties the number of questions that have been addressed through this technique have both increased and diversified. Initial interest was focused on genes coexpressing across sets of experimental conditions, implying essentially the use of clustering techniques. More recently, however, the interest has switched to find genes differentially expressed among distinct classes of experiments, or correlated to diverse parameters. There is also much interest in robust methods for building predictors of clinical outcomes. Also, CGH-arrays (Albertson and Pinkel, 2003) are recently becoming an alternative for studying the relationship between chromosomal alterations affecting to copy number (which are behind many diseases) and gene expression. In addition, there is also a clear demand for methods that allow automatic transfer of biological information to the results of microarray experiments.

This course covers the state-of-the-art in the above mentioned topics, which are of major relevance in today's gene expression data analysis. Through sessions of theory and practical examples, the students will acquire the experience necessary to address scientific questions to gene expression array datasets and solve them. Special attention will be devoted to important (despite frequently ignored) aspects in microarray data analysis, such as multiple testing or functional annotation. The course is designed to be a mixture of theoretical and practical sessions. The latter will require some familiarity with the use of web-based tools and knowledge of basics notions of statistics. Practical sessions will be carried out using the GEPAS (Herrero et al., 2003, 2004; Vaquerizas et al., 2005) environment, an integrated web tool for microarray data analysis, and the Babelomics suite (Al-Shahrour et al., 2005) for functional annotation of genome-scale experiments.

NOTE: This year this course is immediately followed by AFADM10, which is a natural choice for those that want to perform automatic annotations specially (but not exclusively) those who work with non-model organisms. You have the choice of applying to MDAGB10, AFADM10 or both, but please apply separately to each of them.

Course Pre-requisites:

basic knowledge in Molecular Biology and Statistics.

Detailed Program for MDAGB10
Detailed Program for AFADM10

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Last updated:  Feb 17th 2010