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.
KEY DATES for RegGenSIG
April 27, 2012
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Due date for extended abstracts (2-3 pages) for oral presentations
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May 11, 2012
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Author notification for oral presentations
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May 18, 2012
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Due date for short abstracts (250 words) for poster presentations
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May 25, 2012
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Author notification for poster presentations
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June 1, 2012
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Early registration cut-off date
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July 14, 2012
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RegGenSIG meeting
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Program RegGenSIG 2012
Download as PDF
7:30 a.m.
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Registration
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8:30 a.m.
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5 min
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Welcome to SIG
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40 min
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Keynote
Gary Stormo, Washington University Medical School, USA
30 years of PWMs: Where are we now and what comes next?
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20 min
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Quing Zhou, University of California, Los Angeles, USA
Constructing sparse binding landscapes by penalized posterior sampling.
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20 min
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Saurabh Sinha, University of Illinois, USA
Modeling transcription factor occupancy profiles in Drosophila.
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15 min
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Remo Rohs, University of Southern California, USA
New approaches to genome analysis based on the integration of DNA sequence and shape
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10:15 a.m.
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30 min
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Morning Coffee Break
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10:45 a.m.
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20 min
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Wei Wang, University of California, San Diego, USA
Delineation of epigenetic landscape in human cells
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20 min
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Andrew Smith, University of Southern California, USA
Precisely bounding genomic regulatory regions in mammals using high-
resolution DNA-methylation data
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15 min
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Siddarth Selvaraj, University of California, USA
Identification and Characterization of Topological Domains in Mammalian Genomes
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15 min
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Manoj Hariharan, Stanford University, USA
Context-specific Combinatorial Interaction of Transcription Factors in Gene Regulation
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15 min
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Yael Mandel-Gutfreund, Israel Institute of Technology, Israel
An integrated regulatory network reveals pervasive cross-regulation among transcription and splicing factors
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15 min
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Logan J. Everett, University of Pennsylvania, USA
Cistromic analysis reveals novel insights into hepatic CREB regulatory mechanisms
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12:30 p.m.
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60 min
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Lunch / Poster Session
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1:30 p.m.
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Joint session RegGen SIG / AS-SIG - Room 104C
Systems approaches to modeling regulatory RNAs
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5 min
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Welcome
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20 min
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Alex Hartemink, Duke University, USA
Toward a Mechanistic Understanding of Transcriptional Regulation: A
Systems Perspective on Genome Occupancy
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15 min
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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
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15 min
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Zhengqing Ouyang, Stanford University, USA
SeqFold: Accurate genome-scale RNA structure reconstruction integrating experimental measurements provides insights into gene regulation
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20 min
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Steven Brenner, UC Berkley, USA
Genome-wide analysis of RNA regulation in modENCODE
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40 min
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Panel Discussion: From bench to bedside: The future of genomic medicine.
Moderator: Klemens Hertel, University of California - Irvine, USA
Panelists:
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5 min
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Concluding remarks on joint session
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3:30 p.m.
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30 min
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Afternoon Coffee Break / Posters
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4:00 p.m.
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40 min
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Keynote
Harmen Bussemaker, Columbia University, USA
Dissecting transcription factor networks using high-throughput sequencing
and quantitative genetics
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20 min
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Roderic Guigo, Bioinformatics and Genomics, Centre for Genomic Regulation (CRG), Spain
Interrogating RNA heterogeneity
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20 min
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Igor Zwir, University of Granada, Spain
Mapping sequence to numbers: A quantitative model of promoter binding and
gene transcription kinetics under DNA accessibility constrains
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20 min
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Andrei Thomas-Tikhonenko, University of Pennsylvania, USA
Quantitative transcriptome-wide analysis of the Myc-miR-17-92 axis
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15 min
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Marit Ackermann, TU Dresden, Germany
Assessing the impact of natural genetic variation on gene expression dynamics
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5 min
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Concluding remarks on SIG
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6:00 p.m.
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SIG Ends
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SIG Chairs:
- Finn Drabløs, Norwegian University of Science and Technology, Norway, finn.drablos@ntnu.no
- Kathleen Marchal, Professor University of Ghent and K. U. Leuven, Belgium, kamar@psb.ugent.be
- Isidore Rigoutsos, Thomas Jefferson University, USA, isidore.rigoutsos@jefferson.edu
- Saurabh Sinha, University of Illinois, USA, sinhas@illinois.edu
- Lonnie R. Welch, Ohio University, USA, welch@ohio.edu
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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
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