Hunting for Genes and Promoters

   IMPORTANT DATES for this Course
   Deadline for applications: May 31st 2011
   Notification of acceptance dates:
        EARLY:  May 28th 2011
        NORMAL:  June 26th 2011
   Course date: June 27th to June 30th 2011


Alexander Kel holds the position of Senior Vice President Research and Development. Dr. Kel is one of the originator of computational approaches for recognition and analysis of promoters and enhancers in genomes. During his career Dr. Kel was involved in research in practically all fields of bioinformatics, from molecular evolution, and structural biology to database development, application of machine learning techniques and sequence analysis. In the recent years his main research topics are in various fields of system biology including structural analysis of signal transduction and gene regulatory pathways and dynamic modelling of regulatory circuits of such complex cellular processes as cell cycle, differentiation and apoptosis. Alexander Kel has taught Bioinformatics courses at the IGC, both in PGBIOINF and GTPB. He is also a founding member of the PathProt forum on Patthway Analysis in Proteomics.

Affiliation:Genexplain GmbH, Wolfenbuettel, Germany

Enrique Blanco obtained the five-year degree on Computer Science from the Facultat d'Informatica de Barcelona, developing the gene prediction program GeneID together with Roderic Guigo and Genis Parra during the last year. From 2001 to 2006, he joined to the Genome Informatics Research Lab in the Center for Genomic Research (CRG/IMIM, Barcelona). Under the supervision of Dr. Roderic Guigo and Dr. Xavier Messeguer, he obtained the PhD in Computer Science (bioinformatics) from the Universitat Politecnica de Catalunya (UPC) in July, 2006. His PhD thesis work was the design of novel sequence alignment tools to characterize gene regulatory regions in eukaryotes. In 2006, he published the software meta and mmeta (TF-map alignments) and the ABS database of annotated binding sites to aid in the annotation of promoter sequences. Since January 2007, he is working as a post-doctoral researcher in the Developmental genetics and biology Drosophila group led by Dr. Montserrat Corominas and Dr. Florenci Serras of the Genetics department in the Universitat de Barcelona (UB). Here, he has focused on the determination of regulatory regions developmentally activated by chromatin remodellers (Trx/PcG proteins) or induced by regenerative events (imaginal discs), applying different bioinformatics techniques based on comparative genomics using multiple Drosophila genomes, ChIP-Seq/high-throughput data on histone/polymerase modifications and computational pattern discovery. Enrique Blanco has also taught the "Gene Finding and Identification" course, together with Genis Parra, in the scope of the PGBIOINF MSc at the IGC.

Affiliation: Departament de Genetica, Universitat de Barcelona (UB), Barcelona, ES

Course description

This course is set-up to review the basic principles of the gene and promoter prediction and the analysis of their structure. Gene structure analysis and prediction are, again, becoming a hot topic since as a result of the growth of the number of newly sequenced genomes, and the result of high throughput sequencing methodologies becoming commonplace. Effective and robust methods for annotation of new genomes are urgently needed now. But the most intriguing parts of genomes, still hiding from clear understanding, are the gene regulatory regions -- promoters and enhancers. Recognition and analysis of these areas in the new and existing genomes becomes one of the most important parts of understanding the mechanisms of genome functioning. In this course, the attendees will learn several techniques of finding genes and promoters and the principles on which these methods are based. Through "hands on" exercises, several analytical tools will be displayed and the results citicized in the light of assessing their reliability and the possibilities that they open of assigning gene function based on automatic prediction.
The course will consist of lectures that lay out the conceptual framework as needed and and "hands on" exercises will provide the practical insight on the use of the methods, gradually, in order to produce skills that can be used with a relatively high degreee of independence. Participants will know how to set-up some of the programs, and use publicly available servers for more complex analytical jobs, in an informed fashion, so that they fully understand the output generated and how its quality can be assesed. Participants will also learn the novel principles of organization of gene regulatory regions, which will help them to interpret their results of genomics and transcriptomics studies.

Target Audience

Bench biologists seeking ways to deal with sequencing data in order to discover what is hidden there in terms of genes, promoters and repressors.

Course Pre-requisites

basic knowledge of biochemistry and molecular biology. No programming skills are required.

Detailed Program

Instituto Gulbenkian de Ciência,

Apartado 14, 2781-901 Oeiras, Portugal

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Last updated:  April 7th 2011