Hunting for Promoters with NGS data

   Deadline for applications: Oct 1st 2012
   Notification of acceptance in 72 hours after application
   Acceptance on meeting requirements for up to 20 seats
   Course date: Oct 22nd - Oct 25th 2012


Alexander Kel holds the position of Senior Vice President Research and Development. Alexander Kel is one of the originators of computational approaches for recognition and analysis of promoters and enhancers in genomes. During his career Alexander 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 Pathway Analysis in Proteomics.

Affiliation: geneXplain GmbH, Wolfenbuettel, DE

Martin Enge received his PhD from Karolinska Institutet in 2009, within the framework of the Research school of Genomics and Bioinformatics, after completing a Bachelor in science with a Master in Biomedicine at the same university in 2002. His research includes small-molecule screens for cancer therapy, and genome-scale methods for transcription and chromatin architecture. He has consistently published in top-tier journals including articles in Science, Nature Medicine and Cancer Cell. Martin currently holds an assistant professorship position in the systems biology lab at Novum, Karolinska Institutet, where his main focus is large-scale analysis of ChIP-seq data and development of emerging technologies for studying chromatin structure and genome organization.

Affiliation: Karolinska Institutet, Stockholm, SE

Christian Zinser heads the consulting and training department at Genomatix. Before he joined the company, he was working in database development in a biotech start-up company. His background is in Biology, with a PhD from the University of Munich.

Affiliation: Genomatix Software GmbH, Munich, DE Germany

Course description:

This course is set-up to review the basic principles of gene regulation, first of all, by prediction of promoters and distant enhancers and silencers and by analysis of structure of the gene regulatory regions and identification of binding sites for transcription factors. The most intriguing parts of genomes, still hiding from clear understanding, are the gene regulatory regions -- promoters and enhancers. Analysis and prediction of the regulatory sites in the genome, which is now a hot topic as a result of the growth of the number of newly sequenced genomes, and the result of high throughput sequencing methodologies becoming commonplace. Also, the introduction of high throughput-sequencing based techniques for genome-wide epigenetic analysis such as ChIP-seq has revolutionized our ways for studying the gene regulatory mechanisms. First of all, effective and robust methods for annotation of new genomes are urgently needed now.But also, 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 promoters and enhancers 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. Also, the course will include an overview of the state of the art in lab techniques for studying gene regulation as well as a detailed account of data analysis for the more commonly used techniques such as ChIP-seq.
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 assessed. 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:
The course is directed to researchers in biology, bioinformatics, biochemistry and medicine. Background knowledge in elementary bioinformatics is not absolutely necessary, but can be very useful.
Please note that the PathProt brainstorming event takes place on the week just before this course. You will need to register in PathProt separately, though. Please use its specific PathProt website

Course Pre-requisites:
Basic biochemistry. Elementary computing skills

Detailed Program

Instituto Gulbenkian de Ciência,

Apartado 14, 2781-901 Oeiras, Portugal

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Last updated:  September 10th 2012