Regulatory Genomics Special Interest Group (RegGenSIG)
Special Interest Group (SIG) at ISMB 2014
July 12, 2014, Boston, Massachusetts
SIG Hours: 8:30 a.m - 6:00 p.m.

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 RegGenSIG meeting focuses on bioinformatics for regulatory genomics. An important goal of the meeting is to foster a collaborative community wherein scientists convene to solve difficult research problems in all areas of computational regulatory genomics.

RegGenSIG will include presentations and posters that cover the broad spectrum of topics important to regulatory genomics research. The goal is to 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:

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


08:30-08:35 Introduction  
  • A quality control system for enrichment-based NGS data sets.
    Marco A. Mendoza-Parra, CNRS (IGBMC), France
  • Using ChIP-seq and DNase-seq to identify TF binding and their target genes.
    X. Shirley Liu, Dana-Faber Cancer Institute and Harvard School of Public Health, USA
  • Computational analysis of chromatin-state plasticity provides insights into cell identity.
    Guo-Cheng Yuan, Dana-Faber Cancer Institute, USA
  • Enhancer poising and regulatory locus complexity shape transcriptional programs in hematopoietic differentiation.
    Christina Leslie, Memorial Sloan Kettering Cancer Center, USA
  • Massively parallel reporter assays.
    Tarjei Mikkelsen, Broad Institute, USA
10:15-10:45 BREAK  
10:45-12:15 MOTIFS
  • Improved computational and experimental methods for motif determination.
    Gary Stormo, Washington University, USA
  • The use of HT-SELEX to infer TF binding models: comparison to PBM and an improved algorithm.
    Yaron Orenstein, Tel-Aviv University, Israel
  • Improved TF-DNA binding models challenge current hypotheses about genomic recruitment of TFs.
    Raluca Gordan, Duke University, USA
  • Quantitative modeling of transcription factor binding specificities using DNA shape.
    Remo Rohs, USC, USA
  • Deciphering gene regulatory networks using DNA sequence.
    Marc Santoni, Northeastern University, USA and École normale supérieure, France
12:15-1:45 LUNCH/POSTERS  
1:45-2:40 VARIATION
  • Transcriptome sequencing of a large human family identifies the impact of rare non-coding variants.
    Stephen Montgomery, Stanford University, USA
  • Investigating the functional role of variance-eQTL in transcriptional variation.
    Gerald Quon, MIT, USA
  • An atlas of human genomic imprinting reveals global patterns of epigenetic regulation.
    Hunter B. Fraser, Stanford University, USA
2:40 - 3:20 TFs/NETWORKS
  • Context-specificity in Drosophila developmental gene regulatory networks.
    Matthew Slattery, University of Minnesota, USA
  • Characterizing context-dependent transcription factor activity.
    Shaun Mahony, Penn State University, USA
3:20-3:50 BREAK  
3:50 - 4:30 TFs/NETWORKS (cont'd)
  • Mapping transcription factor networks that govern specific physiological processes with NetProphet and PhenoProphet.
    Michael R. Brent, Washington University, USA
  • In silico prediction of mutant transcription factors function.
    Mirana Ramialison, Victor Chang Cardiac Research Institute and Australian Regenerative Medicine Institute, Australia
4:30 - 5:10 EVOLUTION
  • Evolution of a transcription co-expression network active in the primate prefrontal cortex.
    Katja Nowick, University of Leipzig, Germany
  • Evolution of regulation in Actinomycetes: Benefits of ChIP-Seq for evolutionary studies.
    Anna Lyubetskaya, Boston University, USA
5:10 - 5:50. DISEASE
  • Transcriptional (dis)regulation in cancer.
    Carl Herrmann, German Cancer Research Center, Germany
  • Genome-wide analysis of enhancer-RNA transcription reveals regulatory mechanisms by an anti-diabetic drug in adipocyte.
    Hee-Woong Lim, University of Pennsylvania, USA
5:50-5:55 Concluding Remarks  


For poster presentations, authors should submit a 250 word abstract no later than May 18, 2014 to, including "RegGen Abstract Poster" in the subject line. Authors will be notified no later than May 25, 2014.






  Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology (NTNU)

Program Chairs:

General Chairs:

SIG Advisory Committee: