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.

Program

CALL FOR POSTERS

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

KEY DATES

• April 27, 2014 Due date for extended abstracts (2-3 pages) for oral presentations
• May 8, 2014 Author notification for oral presentations
• May 18, 2014 Due date for short abstracts (250 words) for poster presentations
• May 25, 2014 Author notification for poster presentations
• June 6, 2014 Early registration cut-off date
• July 12, 2014 RegGenSIG meeting

INVITED SPEAKERS

• Raluca Gordan, Department of Biostatistics and Bioinformatics, Duke University, USA
• Christina Leslie, Memorial Sloan Kettering Cancer Center, USA
• Matthew Slattery, University of Minnesota
• Stephen Montgomery, School of medicine, Stanford University, USA
• Katja Nowick, Bioinformatics Group, Department of Computer Science, University of Leipzig, Germany
• Shaun Mahony, Department of Computational Biology, Penn State University, USA
• X. Shirley Liu, Department of Biostatistics and Computational Biology, Dana-Faber Cancer Institute and Harvard School of Public Health, USA
• Marco A. Mendoza-Parra, Department of Cell Biology and Signal Transduction, CNRS (IGBMC), Illkirch, France
• Tarjei Mikkelsen, Broad Institute, USA
• Carl Herrmann, Department of Theoretical Bioinformatics (B080), German Cancer Research Center, Germany

ABSTRACTS ACCEPTED FOR ORAL PRESENTATION

• Investigating the functional role of variance-eQTL in transcriptional variation.
  Gerald Quon, Julien Ayroles, John Blangero, Andy Clark, and Manolis Kellis


• Mapping transcription factor networks that govern specific physiological processes with NetProphet and PhenoProphet.
  Michael R. Brent, Ezekiel Maier, Stacy R. Gish, and Tamara L. Doering


• An atlas of human genomic imprinting reveals global patterns of epigenetic regulation.
  Tomas Babak, Brian DeVeale, Emily Tsang, Xin Li, Kevin S. Smith, Kim R. Kukurba, Rui Zhang, Jin Billy Li, Derek van der Kooy, Stephen B. Montgomery, and Hunter B. Fraser.


• Evolution of regulation in Actinomycetes: Benefits of ChIP-Seq for evolutionary studies.
  Anna Lyubetskaya, Joshua Goldford, Hao Chen, and James Galagan


• Genome-wide analysis of enhancer-RNA transcription reveals regulatory mechanisms by an anti-diabetic drug in adipocyte.
  Hee-Woong Lim, Sonia E. Step, Jill M. Marinis, Andreas Prokesch, David J. Steger, Seo-Hee You, Mitchell A. Lazar, and Kyoung-Jae Won


• Improved computational and experimental methods for motif determination
  Gary Stormo, Shuxiang Ruan, and Zheng Zuo


• In silico prediction of mutant transcription factors function.
  Mirana Ramialison, Romaric Bouveret, Ashley Waardenberg, Nicole Schonrock, Tram Doan, Danielle de Jong, and Richard Harvey


• Deciphering gene regulatory networks using DNA sequence.
  Marc Santolini, Hervè Rouault, Thierry Mora, François Schweisguth, and Vincent Hakim


• The use of HT-SELEX to infer TF binding models: comparison to PBM and an improved algorithm.
  Yaron Orenstein and Ron Shamir


• Computational analysis of chromatin-state plasticity provides insights into cell identity.
  Luca Pinelloa, Jian Xu, Stuart H. Orkin, and Guo-Cheng Yuan


• Quantitative modeling of transcription factor binding specificities using DNA shape.
  Tianyin Zhou, Ning Shen, Lin Yang, John Horton, Harmen J. Bussemaker, Raluca Gordân, and Remo Rohs

ACCEPTED POSTERS

• Inferring the active transcription factors underlying gene expression changes with apriori gene regulation knowledge.
  Yong Fuga Li, and Russ Biagio Altman


• Empirical and computational survey of regulatory variants from multi-tissue DNase-I sensitivity data.
  Gregory Moyerbrailean, Chris Harvey, Cynthia Kalita, Xiaoquan Wen, Francesca Luca, and Roger Pique-Regi


• Joint genotyping & inference for allele specific expression of RNA-Seq data.
  Chris Harvey, Gregory Moyerbrailean, O. Davis, Xiaoquan Wen, Francesca Luca, and Roger Pique-Regi


• The role of chromatin accessibility in thermodynamics-based model of transcriptional regulation by enhancers.
  Pei-Chen Peng, Md. Abul H Samee, and Saurabh Sinha


• Building regulatory networks to better understand the complex mechanisms in Diabetes Mellitus.
  Martina Kutmon, Thomas Kelder, Chris Evelo, and Susan Coort


• Phylogeny-wide discovery of bacterial transcription factor binding motifs by protein family-based approach.
  Max Shatsky, Alexey E. Kazakov, Kanchana Padmanabhan John-Marc Chandonia, and Pavel S. Novichkov


• A novel hierarchical hidden markov model for the annotation of chromatin domains.
  Eugenio Marco, Wouter Meuleman, Luca Pinello, Manolis Kellis, and Guo-Cheng Yuan


• HPV integration site selection: Association with epigenetic marks and comparison with other integrating viruses.
  Janet Doolittle, William Seaman, Danielle Cunningham, and Jennifer Webster-Cyriaque


• Quantitative modeling of transcription factor binding specificities using DNA shape.
  Tianyin Zhou, Ning Shen, Lin Yang, John Horton, Harmen J. Bussemaker, Raluca Gordân, and Remo Rohs


• Optimally choosing motif databases and sequence scanning approaches based on ChIP-seq data.
  Norbert Dojer, Michal Dabrowski, Izabella Krystkowiak, Bozena Kaminska, and Bartek Wilczynski


• GeIST: a command-line pipeline for DNA integration mapping.
  Matthew C. LaFave, Gaurav K. Varshney, Tyra G. Wolfsberg, Andreas D. Baxevanis, and Shawn M. Burgess


• Predicting human tissue-specific enhancers from diverse datasets.
  Julia Herman-Iżycka, and Bartek Wilczyński


• Induction of a human pluripotent state with distinct regulatory circuitry that resembles preimplantation epiblast.
  Jonathan Göke, Yun-Shen Chan, Jia-Hui Ng, Xinyi Lu, Kevin Andrew Uy Gonzales, Cheng-Peow Tan, Wei-Quan Tng, Zhong-Zhi Hong, Yee-Siang Lim, and Huck-Hui Ng


• TFBSshape: a motif database for DNA shape features of transcription factor binding sites.
  Lin Yang, Iris Dror, Tianyin Zhou, Anthony Mathelier, Wyeth W. Wasserman, Raluca Gordân, and Remo Rohs


• An integrative approach to identify unknown functions of a protein.
  Philge Philip


• OncoCis: An annotation tool for cis-regulatory mutations in cancer.
  Dilmi Perera, Diego Chacon, Dominik Beck, John E. Pimanda, and Jason W. H. Wong


• Global profiling of condition specific transcription factor binding with ATAC-seq.
  D. Watza, M. Estill, F. Luca, and R. Pique-Regi

SPONSORS

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

Program Chairs:

• Jason Ernst, UCLA, USA, jason.ernst@ucla.edu
• Saurabh Sinha, University of Illinois, USA, sinhas@illinois.edu
• Stein Aerts, University of Leuven, Belgium, stein.aerts@med.kuleuven.be
• Morgane Thomas-Chollier, Ecole Normale Superieure, France, mthomas@biologie.ens.fr

General Chairs:

• Finn Drabløs, Norwegian University of Science and Technology, Norway, finn.drablos@ntnu.no
• Lonnie R. Welch, Ohio University, USA, welch@ohio.edu

SIG Advisory Committee:

• Tim Bailey, University of Queensland, Australia
• Harmen Bussemaker, Columbia University
• Andrea Califano, Columbia University
• Julio Collado-Vides, National Autonomous University of Mexico
• Laura Elnitski, National Human Genome Research Institute, USA
• Ana Teresa Freitas, Technical University of Lisbon, Portugal
• Roderic Guigo, Centre for Genomic Regulation, Spain
• Alexander Hartemink, Duke University
• Manolis Kellis, MIT, USA (pending)
• Kathleen Marchal, Professor University of Ghent and K. U. Leuven, Belgium
• William Noble, University of Washington (tentative)
• Isidore Rigoutsos, Thomas Jefferson University, USA
• Sophie Schbath, Institut National de la Recherché Agronomique, France
• Gustavo Stolovitzky, IBM
• Gary Stormo, Washington University, USA
• Kai Tan, University of Iowa, USA
• Andrei Thomas-Tikhonenko, University of Pennsylvania
• Esko Ukkonen, University of Helsinki, Finland
• Martin Vingron, Max Planck Institute for Molecular Genetics, Germany
• Weixiong Zhang, Washington University, USA
• Igor Zwir, University of Granada