[SocBIN] EMBRACE Workshop on Regulatory Sequence Motif Discovery

[David Ardell]

EMBRACE Workshop on Regulatory Sequence Motif Discovery
(apologies if you receive this mail more than once)

When : November 9-10, 2006
Where: BMC (Biomedical Center) B7:111, Uppsala, Sweden.
Web    : http://teacher.bmc.uu.se/RSMD2006

Organizers: Erik Bongcam-Rudloff and David Ardell, Linnaeus Centre  
for Bioinformatics, Uppsala, Sweden.

What: The objective of EMBRACE is to bring together a wide group of  
experts throughout Europe who use information technology in the  
biomolecular sciences. The EMBRACE Network of Excellence seeks to  
optimise informatics and information exploitation by pure and applied  
biological scientists in both the academic and commercial sectors.  
This workshop will focus on Regulatory Sequence Motif Discovery tools  
and databases and will also discuss web-services/grid aspects related  
to the presented tools and databases.

Registration: This EMBRACE workshop is open to the general public.

*** If you plan to attend, please register with Hanna Strandberg at  
Hannice at mac.com ***

Preliminary agenda:

The workshop will start Nov 10 at 8.30. BMC B7:111.

8.30 - 8.40 Welcome
- Session I. Prokaryotes: Computational Biology and Comparative Methods
* 8.40 - 9.20     Evaluation of a phylogenetic footprinting method  
designed to discover
regulatory elements in prokaryotes. Rekins Janky. Université Libre de
Bruxelles, Bruxelles, Belgium.
* 9.20 - 10.00  Adaptive potential of SIGMA-FACTOR selection.  
Ildefonso Cases.
Instituto Nacional de Tecnica Aeroespacial, Madrid, Spain.
* 10.00 - 10.30 Coffee Break

- Session II. Eukaryotes: Computational Biology and Comparative Methods
* 10.30 - 11.10 Regulation of transcript stability and post- 
transcriptional processes
from yeast to human. Reut Shalgi. The Weizmann Institute, Rehovot,  
Israel
* 11.10 - 11.50 Comparative genomics approach in promoter analysis -  
Orthologous
promoter databases and conserved motif search. Endre Barta.  
Agricultural Biotechnology Center, Hungary
* 11.50 - 13.00 Lunch

- Session III. Motif Discovery
* 13.00 - 13.40  Introduction to the Eukaryotic Promoter Database  
(EPD) and Signal
Search Analysis (SSA). Christoph Schmid and Giovanna Ambrosin.
Swiss Institute of Bioinformatics. Lausanne, Switzerland.
* 13.40 - 14.20 NestedMICA and Tiffin: finding regulatory motifs in  
large(-ish)
genomes. Thomas Down. The Sanger Institute, Hinxton, UK.
* 14.20 - 15.00 Finding regulatory modules: A statistical approach.  
Mikhail Velikanov.
The Linnaeus Centre for Bioinformatics. Uppsala, Sweden.
* 15.00 - 15.30 Coffee Break

- Session IV. Eukaryotic Regulation and Discovery
* 15.30 - 16.10 Systematic Evaluation of Matrix-Based Pattern  
Matching In
Mammals. Jean-Valery Turatsinze. Université Libre de Bruxelles,
Bruxelles, Belgium.
* 16.10 - 16.50 New paradigms and resources for promoter studies.  
Albin Sandelin.
The Bioinformatics Centre, University of Copenhagen, Copenhagen,  
Denmark.
* 16.50 - 17.30 Computational methods for genome-wide annotation of  
regulatory
sites. Erik van Nimwegen. Biozentrum, University of Basel, Switzerland.


-- 
David H. Ardell
Linnaeus Centre for Bioinformatics
Husarg. 3, Box 598
SE—751 24 Uppsala Sweden
tel: +46 (0) 18 471 6694 (fax: 6698)
http://www.lcb.uu.se/~dave