Bioinformatics for Regulatory Genomics (BioRegSIG)
Special Interest Group (SIG) at ISMB 2010
July 10, 2010, Boston
In conjunction with The Eighteenth 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. BioRegSIG is an ISMB special interest group that focuses on bioinformatics for regulatory genomics. An important goal is to foster a collaborative community wherein scientists collaborate to solve difficult research problems.

The focus of the BioRegSIG will vary from year-to-year. In 2010, the SIG will bring together researchers to consider the problem of pattern discovery for prediction/identification of functional elements in sequenced genomes. The ENCODE project identified 5 types of regulatory elements: promoters, enhancers, silencers, insulators and locus control regions. Additional categories that have yet to be fully elucidated include replication origins, structural features, and noncoding and anti-sense transcripts. Such classes of functional elements have been assessed for sequence conservation with varying levels of success. Obviously, there is a need for new computer models and algorithms that discriminate features within these classes, which can be applied toward the discovery of new genomic elements. Ultimately, the syntax and semantics of genomes need to be discovered. Comparative genomics has been used successfully for identifying individual functional elements and it holds promise for elucidating higher level functional groups. The specific topics that will be covered in the 2010 SIG include the following:

  • algorithms that are applicable to large genomes,
  • statistical models that are useful for identifying functional genomic elements, and
  • benchmarks and case studies that are useful for evaluating algorithms and statistical models.

9:00-9:15 SIG Overview
9:15-10:15 Keynote Speech 1:
ENCODE/modENCODE: Regulatory Genomics and Epigenomics in Human and Fly. Manolis Kellis, MIT, USA
10:15-10:45 coffee break
10:45 SESSION 1- Algorithms, Tools and Statistical Models(1):
Chair: Lonnie Welch, Electrical Engineering & Computer Science/Biomedical Engineering/Molecular and Cellular Biology, Ohio University, USA
  1. Computational Techniques for Motif Search. Sanguthevar Rajasekaran, University of Connecticut, USA
  2. Motif-blind computational discovery of cis-regulatory modules. Saurabh Sinha, University of Illinois, USA
  3. An SNN-GA Approach for the Prediction of Transcription Factor Binding Sites. Heike Sichtig and Alberto Riva, University of Florida, USA
  4. Discovering Novel Short RNAs and Organism-specific Aspects of Process Regulation. Isidore Rigoutsos, Thomas Jefferson University, USA
12:30-1:30 Lunch
1:30-2:30 Keynote Speech 2:
Deciphering Transcriptional Regulation via ChIP-Seq Data. Tim Bailey, University of Queensland, Australia
2:30-3:30 SESSION 2 - Algorithms, Tools and Statistical Models(2):
Chair: Sophie Schbath, Institut National de la Recherché Agrononique Unité Mathématique, Informatique & Génome, France
  1. A steganographic approach to genome-wide motif finding and its applications. Weixiong Zhang, Washington University, USA
  2. BOBRO: a new computer program for cis regulatory motif prediction in prokaryotic genomes. Ying Xu, University of Georgia, USA
3:30-4:00 Coffee Break
4:00 SESSION 3 - Benchmarks and Case Studies:
Chair: Finn Drabløs, Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Norway
  1. Inference and validation of a large Saccharomyces cerevisiae cis regulatory motif set. Matias Piipari, Wellcome Trust Sanger Institute, UK
  2. Genome-wide detection of a TFIID localization element from an initial human disease mutation. Laura Elnitski, National Human Genome Research Institute, USA
  3. The Motif Tool Assessment Pipeline (MTAP), lessons and approaches for the evaluation of transcription factor binding site detection tools for constructing regulatory networks. Daniel J. Quest, Oak Ridge National Laboratory, USA
  4. The effect of orthology and coregulation on detecting regulatory motifs. Kathleen Marchal, Katholieke Universiteit Leuven, Belgium
  5. Prediction of KOPS motifs involved in segregation of bacterial chromosomes in Lactococcus and Streptococcus. Fabrice Touzain, INRA, France
6:30 End

SIG Chairs:

Finn Drabløs, Professor
Norwegian University of Science and Technology

Sophie Schbath, Director of Research
Institut national de la recherché Agronomique

Lonnie R. Welch, Stuckey Professor
Ohio University