Sunday, August 19, 2018
15:00 - 18:00
Registration
18:00 - 19:00
Welcome Reception
19:00 - 20:00
Dinner
Monday, August 20, 2018
8:30 - 17:00
Registration
Session I: Junk or Not Junk: Structure and Sequence of Coding and Noncoding DNA
Sarah Harris, University of Leeds, United Kingdom, Chair
9:00 - 9:45
Sergei Mirkin, Tufts University, USA
RNA-DNA Hybrids Promote the Expansion of Friedreich's Ataxia (GAA)n Repeats via Break-induced Replication
9:45 - 10:30
David Levens, NIH, USA
The Regulatory Roles of DNA Topology and Conformation in Mammalian Gene Expression
10:30 - 10:50
Coffee Break
10:50 - 11:10
Anton Goloborodko, MIT, USA*
A Pathway for Mitotic Chromosome Formation
11:10 - 11:55
Charles Dorman, Trinity College, Ireland
Bacterial Decision-making Operating Through Tuneable Binary Genetic Switches
12:00 - 14:00
Lunch
Session II: Biophysical Approaches to Understanding Chromatin Structure
Stephen Levene, University of Texas at Dallas, USA, Chair
14:00 - 14:45
Wilma Olson, Rutgers University, USA
Contributions of DNA Sequence in 3D Genomic Architectures
14:45 - 15:30
Tamar Schlick, New York University, USA
Modeling Gene Elements at Nucleosome Resolution
15:30 - 15:50
Coffee Break
15:50 - 16:35
Andrzej Stasiak, University of Lausanne, Switzerland
Transcription-induced Supercoiling and TADs Formation
16:35 - 17:20
Karsten Rippe, Heidelberg University, Germany
Establishing Chromatin Subcompartments That Are Both Stable and Plastic
17:20 - 18:00
Nature Hike - Chaminade Red & Blue Trails
18:00 - 20:00
Dinner
Tuesday, August 21, 2018
8:30 - 17:00
Registration
Session III: Exploring the Physical Genome I
Wilma Olson, Rutgers University, USA, Chair
9:00 - 9:45
Javier Arsuaga, University of California, Davis, USA
Biophysical Models of DNA Organization Inside Viral Capsids
9:45 - 10:30
Shinichi Morishita, University of Tokyo, Japan
Understanding Tandem Repeats and Methylation with Long-read Sequencing
10:30 - 10:50
Coffee Break
10:50 - 11:10
Thomas Bishop, Louisiana Tech University, USA*
G-Dash: A Genomics Dashboard That Unites Physics and Informatics Studies of Chromatin
11:10 - 11:55
Alexandra Zidovska, New York University, USA
The "Self-stirred" Genome: Bulk and Surface Dynamics of the Chromatin Globule
12:00 - 14:00
Lunch
Session IV: Exploring the Physical Genome II
Stephen Levene, University of Texas at Dallas, USA, Chair
14:00 - 14:45
Xaiver Darzacq, University of California, Berkeley
Nuclear Organization and Transcription Regulation Mechanisms Studied by Live Cell Imaging
14:45 - 15:30
Martin Depken, Delft University of Technology, The Netherlands
Bottom-up Physical Modelling for CRISPR//Cas Target Prediction
15:30 - 15:50
Coffee Break
15:50 - 16:35
Laura Landweber, Columbia University, USA
RNA-programmed Genome Rearrangement in the Ciliate Oxytricha
16:35 - 16:55
Katerina Kraft, Stanford University, USA*
Genomic Rearrangement Induced Gene Activation by Architectural Stripes
17:00 - 18:00
Keynote Speaker: David Schwartz, University of Wisconsin, USA
From Big DNA Molecules to Big Data
18:00 - 20:00
Dinner
Wednesday, August 22, 2018
8:30 - 17:00
Registration
Session V: Fundamental Limits of Sequencing Accuracy, Sensitivity, and Uniqueness: What Do, and What Don't, We Know?
Marc Salit, NIST, USA, Chair
9:00 - 9:45
Marc Salit, NIST, USA
Metrology of Genome-Scale Measurements: Standards and Systematics to Get Comparability and Confidence
9:45 - 10:05
Miten Jain, University of California, Santa Cruz, USA*
A Reference Human Transcriptome Based on Native RNA Sequencing
10:05 - 10:25
Idan Gabdank, Stanford University, USA*
Portable and Reproducible Computational Analyses
10:25 - 10:50
Coffee Break
10:50 - 11:10
Stephen Lincoln, Invitae, USA*
Complexgenetic Variants: Implications for Clinical Sequencing Methods and Validation Approaches
11:10 - 12:00
Formal Discussions
12:00 - 14:00
Lunch
Session VI: Single-cell Genomics and Single-molecule Sequencing
Tim J. Stevens, MRC Laboratory of Molecular Biology, United Kingdom, Chair
14:00 - 14:45
Tim J. Stevens, MRC Laboratory of Molecular Biology, United Kingdom
Computing the 3D Single-cell Structures of Whole Mammalian Genomes
14:45 - 15:30
Bo Wang, Stanford University, USA
Self-organization of Single-cell RNA Sequencing Data
15:30 - 16:15
Cristian Micheletti, SISSA Trieste, Italy
Nanopore Translocation of Knotted DNA
16:15 - 18:00
Poster Session
18:00 - 20:00
Dinner
20:00
Pool Night
Thursday, August 23, 2018
8:30 - 17:00
Registration
Session VII: The RNA World: Structure, Dynamics, and Interaction
Andrew Fire, Stanford University, USA, Chair
9:00 - 9:45
Andrew Fire, Stanford University, USA
Long-term RNA-based Transmission of Biological States
9:45 - 10:30
Alan Lambowitz, University of Texas at Austin, USA
Thermostable Group II Intron Reverse Transcriptases (TGIRTs) and Their Use in RNA-seq
10:30 - 10:50
Coffee Break
10:50 - 11:10
Priscilla L. Boon, National University of Singapore*
How Dengue Capsid Protein Assists in Organizing Dengue Virus Genomic RNA
11:10 - 11:55
Sarah Woodson, Johns Hopkins University, USA
Sequential Folding of RNA
12:00 - 14:00
Lunch
Session VIII: Genomics of Gene Regulation
Massa Shoura, Stanford University, USA, Chair
14:00 - 14:45
Nadav Ahituv, University of California, San Francisco, USA
Functional Characterization of Gene Regulatory Elements
14:45 - 15:30
Polly Fordyce, Stanford University, USA
Quantitative Mapping of Transcription Factor Binding Energy Landscapes
15:30 - 15:50
Coffee Break
15:50 - 16:35
Zeba Wunderlich, University of California, Irvine, USA
Noise in the Shadows
16:35 - 16:55
Ariel Afek, Duke University, USA*
Mismatched Base-pairs Locally Distort DNA Structure and can Induce Increased DNA-binding by Transcription Factor Proteins
16:55 - 17:15
Alexander Wood, Newcastle University, United Kingdom*
What Gene Expression Noise Tells About the Spatiotemporal Organization of Gene Regulatory Networks
17:15 - 18:00
Illumina Workshop
18:00 - 20:00
Dinner
Friday, August 24, 2018
8:30 - 12:00
Registration
Session IX: Extreme Genomes
Massa Shoura, Stanford University, USA, Chair
9:00 - 9:45
Ami Bhatt, Stanford University, USA
Culture-free Microbial Genome Assembly and Tracking in Hospitalized Patients
9:45 - 10:05
Jason DeRouchey, University of Kentucky, USA*
DNA in Tight Spaces: Linking Structure, Stability and Protection in Sperm Chromatin
10:05 - 10:50
Joanna Kelley, Washington State University, USA
Eukaryotic Genome Evolution in Extreme Environments
10:50 - 11:20
Closing Remarks
12:00 - 14:00
Lunch
*Contributed talks selected from among submitted abstracts.