Regulatory Genomics Special Interest Group (RegGenSIG)

Special Interest Group (SIG) at ISMB 2016 https://www.iscb.org/ismb2016

July 9, 2016, Swan and Dolphin Hotel, Orlando, Florida

 

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 is an activity of the ISCB Special Interest Group for Regulatory Systems Genomics, a community of shared interest that has multiple activities and interactions throughout the year, rather than solely meeting during the ISMB conference. An important goal of the SIG is to foster a topically-focused collaborative community wherein scientists communicate with one another on research problems and/or opportunities in the area of computational biology as it pertains to regulatory and systems genomics. The SIG holds two meetings per year, (1) RegGenSIG and (2) The RECOMB/ISCB Conference on Regulatory and Systems Genomics and DREAM Challenges.

 

 

KEY DATES

April 18, 2016     Due date for abstracts for oral presentations

May 2, 2016        Author notification for oral presentations

May 9, 2016        Due date for abstracts for poster presentation only

May 23, 2016      Author notification for poster presentations

June 3, 2016        Early registration discount cut-off date

July 9, 2016         RegGenSIG meeting

 

Program for RegGenSIG 2016

Program (pdf)


RegGenSIG
Orlando, July 9th 2016

7:30 am – 8:45 am Registration
8:30 am – 10.15 am Session Regulatory genomics in development
Chair: Saurabh Sinha

   Julia Zeitlinger (Stowers Institute) – “Elucidating enhancer mechanisms using genomics” (30 min) http://research.stowers.org/zeitlingerlab/
   Chris Rushlow (NYU) – “Activation of the Drosophila genome by the pioneer factor Zelda” (30 min) http://biology.as.nyu.edu/object/ChristineRushlow.html
   Vivekanandan Ramalingam (Stowers Institute)-“The promotor factor Lola regulates gene activation during embryogenesis by making promoters accessible over time” (20 min) Abstract
   Sushmita Roy – “CMINT: Chromatin Module inference on cellular trajectories identifies poised epigenetic states in reprogramming to induced pluripotent stem cells” (20 min) Abstract
10:15 am – 10:45 am Morning Coffee Break
10.45 am – 12.05 pm Session Regulatory genomics and epigenomics
Chair: Jason Ernst

    Anshul Kundaje (Stanford University) – “Interpretable, integrative deep learning models for regulatory genomics and epigenomics” (30 min) http://anshul.kundaje.net
   Mathieu Blanchette (McGill University) – “Studying human gene regulation using paleogenomics” (30 min) http://www.cs.mcgill.ca/~blanchem/
   Mathieu Lupien (University of Toronto) – “Chromatin context reveals the role of noncoding mutations in cancer” (30 min) https://www.pmgenomics.ca/lupienlab/index.html
12.05 am –12.15 pm Flash Talks
   Marco-Antonio Mendoza-Parra – “A functional genomics explorer for visualizing and comparing large amounts of datasets retrieved in the public domain” Abstract
   Maya Botzman – “POEM: Identifying joint additive effects on regulatory circuits” Abstract
12:30 pm - Lunch and poster session
2:00 pm – 3.30 pm Session Transcription factor specificity
Chair: Anshul Kundaje

   Ning Shen – “Determinants of differential DNA binding specificity between closely related transcription factors” (20 min) Abstract
   Yaron Orenstein – “DNA Shape Readout Specificities of Different TF Families” (20 min) Abstract
   Shuxiang Ruan – “An EM Algorithm for Binding Energy Estimation Using HT-SELEX Data” (20 min) Abstract
   Timothy Hughes (Universty of Toronto) – “Multiparameter network diversity of human C2H2 zinc finger transcription factors” (30 min) http://hugheslab.med.utoronto.ca/
3:30 pm – 4:00 pm Afternoon Coffee Break
4.00 pm – 6:00 pm Session New techniques - from enhancer assays to RNA splicing
Chair: Sushmita Roy

   Vincent Drury FitzPatrick – “Discovering the autonomous rules by which sequence drives transcription using a novel massively parallel barcoded reporter assay” (20 in) Abstract
   Jonathan Cairns – “Robust interaction detection in Capture Hi-C connects enhancers and disease SNPs to target genes” (20 min) Abstract
   R. Taylor Raborn – “Promoter architecture and sex-specific gene expression in the microcrustacean Daphnia pulex revealed by large-scale profiling of 5'-mRNA ends” (20 min) Abstract
   Logan Everett – “Deep Sequencing of Whole Transcriptomes Across the Drosophila Genetic Reference Panel” (20 min) Abstract
   Joshua Welch – “Robust Detection of Alternative Splicing in a Population of Single Cells” (20 min) Abstract



Poster abstracts

Yuichi Aoki: Involvement of evolutionary age in transcription factor mediated gene regulatory network - Abstract
Maya Botzman: POEM: Identifying joint additive effects on regulatory circuits - Abstract
Bony De Kumar: Hoxa1-TALE Gene interaction network regulates TALE cofactors, signaling pathways and pluripotency during neural differentiation - Abstract
Shlomi Dvir: Dissecting the DNA and RNA Bound Proteome of Human Embryonic Stem - Abstract
Logan Everett: Deep Sequencing of Whole Transcriptomes Across the Drosophila Genetic Reference Panel - Abstract
Marco-Antonio Mendoza-Perra: A functional genomics explorer for visualizing and comparing large amounts of datasets retrieved in the public domain - Abstract
Vivekanandan Ramalingam: The promotor factor Lola regulates gene activation during embryogenesis by making promoters accessible over time - Abstract
Ning Shen: Determinants of differential DNA binding specificity between closely related transcription factors - Abstract
Celia Siu: Bioinformatic characterization of the normal thyroid reference epigenome - Abstract



Invited Speakers

Mathieu Blanchette
Timothy Hughes
Anshul Kundaje
Mathieu Lupien
Chris Rushlow
Julia Zeitlinger

 

Program Chairs

Stein Aerts, University of Leuven, Belgium, stein.aerts@med.kuleuven.be

Jason Ernst, University of California, Los Angeles, United States, jason.ernst@ucla.edu

Saurabh Sinha, University of Illinois Urbana, United States, sinhas@illinois.edu

Julia Zeitlinger, Stowers Institute for Medical Research, United States, jbz@stowers.org

 

Steering Committee Chairs

Finn Drablos, Norwegian University of Science and Technology, Norway, finn.drablos@ntnu.no

Lonnie Welch, Ohio University Athens, United States, welch@ohio.edu

 

Steering Committee

Tim Bailey, University of Queensland, Australia

Harmen Bussemaker, Columbia University, USA

Laura Elnitski, National Human Genome Research Institute, USA

Ana Teresa Freitas, Technical University of Lisbon, Portugal

Eileen Furlong, EMBL Heidelberg, Germany

Roderic Guigo, Centre for Genomic Regulation, Spain

Alexander Hartemink, Duke University, USA

Manolis Kellis, MIT, USA

Kathleen Marchal, Professor University of Ghent and K. U. Leuven, Belgium

Pierre Nicolas, INRA, France

Isidore Rigoutsos, Thomas Jefferson University, USA

Gustavo Stolovitzky, IBM, USA

Kai Tan, Children's Hospital of Philadelphia and University of Pennsylvania, USA

Andrei Thomas-Tikhonenko, University of Pennsylvania, USA

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, Spain