Bioinformatics for Regulatory Genomics (BioRegSIG)
Special Interest Group (SIG) at ISMB 2011
July 16, 2011, Vienna
In conjunction with The Nineteenth International Conference on Intelligent Systems for Molecular Biology (ISMB)

Regulatory genomics involves the study of the genomic 'control system,' which determines how, when and where to activate the 'blueprint' encoded in the genome. Due to the importance of computational methods in the study of gene regulation, BioRegSIG unites scientists to consider bioinformatics methods in the context of regulatory genomics. The international organizing committee of BioRegSIG 2011 has constructed an exciting program, featuring two keynote speakers and 15 research presentations.

Program BioRegSIG 2011

Download BioRegSIG Program (pdf) (office word)
Download Abstracts (pdf)

7:30 a.m. Registration
8:30 a.m. 10 min Welcome: Lonnie Welch

8:40 a.m.

45 min
Chair: Isidore Rigoutsos
Keynote: Alexander Stark
Research Institute of Molecular Pathology (IMP), Vienna, Austria
Regulatory genomics in Drosophila
9:25 a.m. 25 min


25 min
Invited: Benoit Ballester
European Bioinformatics Institute, Hinxton, UK
Five-vertebrate ChIP-seq reveals the evolutionary dynamics of transcription factor binding
Invited: Kjetil Klepper
Dept. of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
MotifLab: A tools and data integration workbench for motif discovery and regulatory sequence analysis
10:15 a.m. 30 min Coffee break

10:45 a.m.

25 min


20 min

20 min

20 min

20 min
Chair: Saurabh Sinha
Invited: Ana Teresa Freitas
CSE Department, INESC-ID/IST Technical University of Lisbon, Portugal
Identification of regulatory signals using graph modularity analysis
Contributed: Kathleen Marchal
Unveiling combinatorial regulation through the combination of ChIP information and in silico cis-regulatory module detection
Contributed: Ivan V. Kulakovskiy
Preferred pair distance templates reveal functional transcription factor binding sites
Contributed: Bram Van de Sande
Discovery of regulators for co-expressed human genes using large sequence search spaces
Contributed: Pieter Monsieurs
Transcriptional cross-regulation as survival mechanism in bacteria
12:30 p.m. 60 min Lunch

1:30 p.m.

45 min
Chair: Kathleen Marchal
Keynote: Martin Vingron
Max Planck Institute for Molecular Genetics, Berlin, Germany
Transcription factor binding sites, histone modifications, and two promoter classes
2:15 p.m. 25 min


25 min



25 min
Invited: Esko Ukkonen
Department of Computer Science, University of Helsinki, Finland
Modeling regulatory complexes using both TF-DNA and TF-TF interactions
Invited: Virginie Bernard
Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics - University of British Columbia, Vancouver BC, Canada
The functional importance and detection of regulatory sequence variants
Invited: Roderic Guigo
Center for Genomic Regulation, Barcelona, Catalonia, Spain
Alternative splicing variability in human populations
3:30 p.m. 30 min Coffee break

4:00 p.m.

25 min


25 min


25 min



20 min

20 min
Chair: Ana Teresa Freitas
Invited: Tim Hubbard
Wellcome Trust Sanger Institute, Hinxton, UK
TBA
Invited: Ivo L. Hofacker
Institut für Theoretische Chemie, Universität Wien, Austria
Prediction of bacterial small RNA targets
Invited: Pål Sætrom
Dept. of Computer and Information Science and Dept. of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
Analyzing and designing small RNA-mediated gene regulation
Contributed: Pieter Meysman
Use of structural DNA properties for the prediction of regulator binding sites with conditional random fields
Contributed: Heike Sichtig
A computational paradigm for more specific TFBS detection
5:55 p.m. 5 min
Concluding remarks: Finn Drabløs
6:00 p.m. end

SIG Chairs:

  1. Finn Drabløs, Norwegian University of Science and Technology, Norway, finn.drablos@ntnu.no
  2. Sophie Schbath, Director of Research, Institut national de la recherché Agronomique, France, Sophie.Schbath@jouy.inra.fr
  3. Lonnie R. Welch, Ohio University, USA, welch@ohio.edu

SIG Organizing Committee:

  • Herbert Auer, Institute for Research in Biomedicine, Spain
  • Tim Bailey, University of Queensland, Australia
  • Laura Elnitski, National Human Genome Research Institute, USA
  • Roderic Guigo, Centre for Genomic Regulation, Spain
  • Manolis Kellis, MIT, USA
  • Kathleen Marchal, Katholieke Universiteit Leuven, Belgium
  • Gerhard Mittler, Max Planck Institute, Germany
  • Matias Piipari, Wellcome Trust Sanger Institute, UK
  • Daniel J. Quest, Oak Ridge National Laboratory, USA
  • Isidore Rigoutsos, Thomas Jefferson University, USA
  • Saurabh Sinha, University of Illinois, USA
  • Gary Stormo, Washington University, USA
  • Weixiong Zhang, Washington University, USA