HPND12 Hunting for Promoters with NGS data |
IMPORTANT DATES for HPND12
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Instructors: |
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.
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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.
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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.
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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.
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Target Audience:
Course Pre-requisites: |
Detailed Program |
Instituto Gulbenkian de Ciência, Apartado 14, 2781-901 Oeiras, Portugal Last updated: September 10th 2012 |