Regulatory Genomics Special Interest Group (RegGenSIG)
Special Interest Group (SIG) at ISMB 2012
July 14, 2012, Long Beach, California
In conjunction with The Twentieth 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. Regulatory genomics is the topic of much research activity worldwide. Since computational methods are important in the study of gene regulation, the ISMB Regulatory Genomics Special Interest Group - RegGenSIG - focuses on bioinformatics for regulatory genomics. An important goal of the SIG is to foster a collaborative community wherein scientists convene to discuss difficult research problems in all areas of computational regulatory genomics.

RegGenSIG 2012 will include presentations and posters that cover the broad spectrum of topics important to regulatory genomics research, and a joint panel discussion with the Alternative Splicing SIG. RegGenSIG will bring together experts in experimental methods and computational methods to consider sequence-based reconstruction of regulatory networks and prediction of gene expression. Topics to be addressed in the SIG include the following:

  • inference of gene regulatory networks,
  • utilization of information pertaining to epigenetics, chromatin structure, and histone modifications,
  • determination of the roles of regulatory RNAs,
  • prediction of transcriptional regulation from RNA-seq data and ChIP-seq data,
  • pattern discovery in sequences, and
  • sequence based modeling of gene expression.


April 27, 2012 Due date for extended abstracts (2-3 pages) for oral presentations
May 11, 2012 Author notification for oral presentations
May 18, 2012 Due date for short abstracts (250 words) for poster presentations
May 25, 2012 Author notification for poster presentations
June 1, 2012 Early registration cut-off date
July 14, 2012 RegGenSIG meeting

Program RegGenSIG 2012
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7:30 a.m.


8:30 a.m.

5 min

Welcome to SIG

40 min


Gary Stormo, Washington University Medical School, USA

30 years of PWMs: Where are we now and what comes next?

20 min

Quing Zhou, University of California, Los Angeles, USA

Constructing sparse binding landscapes by penalized posterior sampling.

20 min

Saurabh Sinha, University of Illinois, USA

Modeling transcription factor occupancy profiles in Drosophila.

15 min

Remo Rohs, University of Southern California, USA

New approaches to genome analysis based on the integration of DNA sequence and shape

10:15 a.m.

30 min

Morning Coffee Break

10:45 a.m.

20 min

Wei Wang, University of California, San Diego, USA

Delineation of epigenetic landscape in human cells

20 min

Andrew Smith, University of Southern California, USA

Precisely bounding genomic regulatory regions in mammals using high- resolution DNA-methylation data

15 min

Siddarth Selvaraj, University of California, USA

Identification and Characterization of Topological Domains in Mammalian Genomes

15 min

Manoj Hariharan, Stanford University, USA

Context-specific Combinatorial Interaction of Transcription Factors in Gene Regulation

15 min

Yael Mandel-Gutfreund, Israel Institute of Technology, Israel

An integrated regulatory network reveals pervasive cross-regulation among transcription and splicing factors

15 min

Logan J. Everett, University of Pennsylvania, USA

Cistromic analysis reveals novel insights into hepatic CREB regulatory mechanisms

12:30 p.m.

60 min

Lunch / Poster Session

1:30 p.m.

Joint session RegGen SIG / AS-SIG - Room 104C

Systems approaches to modeling regulatory RNAs

5 min


20 min

Alex Hartemink, Duke University, USA

Toward a Mechanistic Understanding of Transcriptional Regulation: A Systems Perspective on Genome Occupancy

15 min

An-Yuan Guo, Huazhong Univ. of Science and Technology, China

MicroRNA and transcription factor co-regulatory network analysis reveals miR-19 inhibits CYLD in T-cell acute lymphoblastic leukemia

15 min

Zhengqing Ouyang, Stanford University, USA

SeqFold: Accurate genome-scale RNA structure reconstruction integrating experimental measurements provides insights into gene regulation

20 min

Steven Brenner, UC Berkley, USA
Genome-wide analysis of RNA regulation in modENCODE

40 min

Panel Discussion: From bench to bedside: The future of genomic medicine.

Moderator: Klemens Hertel, University of California - Irvine, USA


5 min

Concluding remarks on joint session

3:30 p.m.

30 min

Afternoon Coffee Break / Posters

4:00 p.m.

40 min


Harmen Bussemaker, Columbia University, USA

Dissecting transcription factor networks using high-throughput sequencing and quantitative genetics

20 min

Roderic Guigo, Bioinformatics and Genomics, Centre for Genomic Regulation (CRG), Spain

Interrogating RNA heterogeneity

20 min

Igor Zwir, University of Granada, Spain

Mapping sequence to numbers: A quantitative model of promoter binding and gene transcription kinetics under DNA accessibility constrains

20 min

Andrei Thomas-Tikhonenko, University of Pennsylvania, USA

Quantitative transcriptome-wide analysis of the Myc-miR-17-92 axis

15 min

Marit Ackermann, TU Dresden, Germany

Assessing the impact of natural genetic variation on gene expression dynamics

5 min

Concluding remarks on SIG

6:00 p.m.

SIG Ends

SIG Chairs:

SIG Organizing Committee:

  • Tim Bailey, University of Queensland, Australia
  • Benoit Ballester, European Bioinformatics Institute, UK
  • Laura Elnitski, National Human Genome Research Institute, USA
  • Ana Teresa Freitas, Technical University of Lisbon, Portugal
  • Roderic Guigo, Centre for Genomic Regulation, Spain
  • Tim Hubbard, Wellcome Trust Sanger Institute, UK
  • Manolis Kellis, MIT, USA
  • Sophie Schbath, Institut National de la Recherché Agronomique, France
  • Gary Stormo, Washington University, USA
  • Esko Ukkonen, University of Helsinki, Finland
  • Martin Vingron, Max Planck Institute for Molecular Genetics, Germany
  • Weixiong Zhang, Washington University, USA