KEYNOTE LECTURE

Enhancing Genetically-Predicted Gene Expression Using ENCODE Data
Nancy Cox, Vanderbilt U.

SESSION 1 — RNA / Transcriptomes

Roles of RNA Binding Proteins and Chromatin in RNA Processing
Beatrice Borsari, Centre for Genomic Regulation (Barcelona)

Analysis of ENCODE Long-Read RNA Transcriptome Data — Slides
Gabriela Balderrama, U. California Irvine

Single Cell and Ensemble RNA Transcriptomes
Brian Williams, Cal Tech

Large-Scale Mapping and Analysis of Human RNA Binding Proteins — Slides
Eric Van Nostrand, UCSD

SESSION 2 — Regulatory DNA & RNA

Analysis of the Rapidly Expanding ENCODE Transcription Factor Maps
Eric Mendenhall, Hudson Alpha Institute

Chromatin Partitioning Reveals the Nature of Non-Coding Mutations in Cancer
Mathieu Lupien, U. Toronto

Profiling Nascent RNA Transcription Using Bru-seq —​ Slides
Mats Ljungman, U. Michigan

Index and vocabulary of accessible DNA elements in the human genome
Wouter Meuleman, Altius Institute

Accessing ENCODE's 15,000+ Datasets: Portal, API, & more — Workshop Materials
Khine Lin, Jennifer Jou, Paul Sud, ENCODE DCC, Stanford University

Navigating the ENCODE Encyclopedia with SCREEN — Workshop Materials
Jill Moore, DAC, UMass Med

Using ENCODE in the cloud: Uniform Processing Pipelines — Workshop Materials
Otto Jolanki, ENCODE DCC, Stanford University

Using the GENCODE reference annotation of human and mouse genes and transcripts — Workshop Materials
Jane Loveland, European Bioinformatics Institute

KEYNOTE LECTURE

Genome-wide mapping of protein-DNA interaction dynamics —​ Slides
Steve Henikoff, Fred Hutchinson Cancer Research Center

SESSION 3 — Technology

Functional Studies of Candidate Enhancers Using CRISPR & Massively Parallel Reporter Assays
Jay Shendure, U. Washington

Integrating Multi-Omic Single Cell Data Sets — Slides
William Greenleaf, Stanford

Large-Scale Structure-Function Studies
Lea Starita, UW

Inferring the Epigenetic Landscape of Polygenic Disease —​ Slides
Tiffany Amariuta, Raychaudhuri Lab/Harvard

SESSION 4 — Functional Analysis

Dissecting Genome Function and Drug-Responsive Regulation
Tim Reddy, Duke

Leveraging ENCODE to Reveal the Role of Regulatory Variants in Neuropsychiatric Disorders — Slides
Yin Shen, UCSF

ENCOTE - Encyclopedia of Transposable Elements
Ting Wang, Washington University

RAPID-FIRE TALKS I

Jason Underwood, UW / PacBio (Abstract 05)

Timothy Cherry, Harvard (Abstract 01)

WORKSHOPS II

Engaging ENCODE data using the WashU Epigenome Browser — Workshop Materials
Ting Wang, Wash U

Exploring ENCODE Hi-C Data with Juicebox and Juicebox.JS — Workshop Materials
Muhammad Shamim, Baylor

Neural Networks and Deep Learning: Applications to Genomics and Gene Regulation — Workshop Materials / Slides
Anna Shcherbina, Kundaje lab/Stanford

RAPID-FIRE TALKS II

Dan Zhou, Vanderbilt (Abstract 02)

Colin Shew, UC Davis (Abstract 07)

Alison Paquette, ISB (Abstract 09)

Stephanie Ni, UC Davis (Abstract 10)

Michael Meers, FHCRC (Abstract 11)

Alireza Lorzadeh, UBC (Abstract 12)

Wei Zhou, UW (Abstract 22)

James Thomas, FHCRC (Abstract 24)

SESSION 5 — Disease Genetics

Genetic and epigenetic analyses of multiple sclerosis —​ Slides
Chris Cotsapas, Broad Institute / Yale

Sex differences in the human transcriptome
Barbara Stranger, U. Chicago

Genetics and functional genomics of inflammatory diseases
Soumya Raychaudhuri, Harvard / Brigham & Women's

SESSION 6 — Regulation

Regulatory interactions
Michael Snyder, Stanford

Mapping nuclear architecture
Erez Aiden, Baylor

Mapping long-range regulatory interactions
Yijun Ruan, Jackson Laboratories

Footprinting the human genome
Jeff Vierstra, Altius

SESSION 7 — AI / Machine Learning

Imputation of epigenomic and transcriptomic experiments —​ Slides
​William Noble, U. Washington

Using deep learning to gain insights into genome regulation —​ Slides
Anshul Kundaje, Stanford

Deciphering regulatory DNA codes using machine learning
Mike Beer, Johns Hopkins