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ENCODE 2015: Research Applications and Users Meeting

June 29 - July 1, 2015

Bolger Center
Potomac, Md.

On June 29 - July 1, 2015, the National Human Genome Research Institute (NHGRI) sponsored the ENCODE 2015: Research Applications and Users Meeting at the Bolger Center in Potomac, Md.

The meeting featured:

  • Hands-on workshops on learning to navigate, analyze, and integrate ENCODE and mouseENCODE data into your research
  • Leading-edge research applications from distinguished invited speakers
  • Tutorials on newly-available informatics pipelines that greatly facilitate working with ENCODE data
  • Short talks selected from abstracts


YouTube video Video Playlist

View videos and slides from June 29  June 30  July 1

Monday, June 29, 2015

  Topic Moderator/Presenter
1 Using ENCODE Data to Interpret Disease-associated Genetic Variation
YouTube video Video | Slides PDF file
Mike Pazin
Keynote Lecture
2 Data Integration: Genome x Transcriptome x EMR
YouTube video Video
Nancy Cox
Vanderbilt University
Scientific Session 1: Common Disease
3 An Epigenomic and Transcriptional Basis for Insulin Resistance
YouTube video Video | Slides PDF file
Evan Rosen
Harvard Medical School
4 Identifying Dysregulated Genes in Autoimmune Disease
YouTube video Video | Slides PDF file
Chris Cotsapas
Yale Medical School
5 Enhancers: Regulatory Control Elements in Health and Disease
YouTube video Video
J. Wesley Pike
University of Wisconsin
6 Mapping the Epigenetic Basis of Kidney Disease
YouTube video Video | Slides PDF file
Katalin Susztak
University of Pennsylvania
Workshop Session 1: Online Resources and Tools
7 Overview of the ENCODE Data Portal
YouTube video Video | Slides PDF file | Handouts: ENCODE Portal Exercises PDF file
Eurie Hong
Stanford University
8 Visualizing ENCODE Data in the UCSC Browser
YouTube video Video | Slides PDF file
Pauline Fujita
University of California, Santa Cruz
Workshop Session 2: Online Resources and Tools
9 Introduction to Ensembl Regulation
YouTube video Video | Slides PDF fileHandout: Ensemble Regulation PDF file

Emily Perry
European Bioinformatics Institute

10 Analysing Variants with the Variant Effect Predictor (VEP)
YouTube video Video | SlidesPDF fileHandout: VEP WorkbookPDF file
Emily Perry
European Bioinformatics Institute

11 Variant Annotation Using RegulomeDB and HaploReg
YouTube video Video | SlidesPDF file

Handout: RegulomeDB and HaploReg Exercises PDF file
Jill Moore
University of Massachusetts Medical School



Tuesday, June 30, 2015

  Topic Moderator/Presenter
Keynote Lecture
12 Selection and Function of Signal-Dependent Enhancers
YouTube video Video | Slides PDF file
Christopher Glass
University of California, San Diego
Scientific Session 2: Cancer, Regulation, and Mutation
13 Cancer, Genetic Predispositions, and Chromatin Architecture
YouTube video Video | Slides PDF file
Matthew Lupien
University of Toronto
14 Mining the Genome to Understand Epigenetic Abnormalities in Cancer and Enhance Development of New Therapeutic Approaches
YouTube video Video | Slides PDF file
Stephen Baylin
Johns Hopkins University
15 Reconstructing Cancer Stem Cells from Their Chromatin Landscapes
YouTube video Video
Bradley Bernstein
Harvard Medical School
16 Epigenetic Control of Genetics: the Impact of Epigenome on Mutation
YouTube video Video | Slides PDF file
Shamil Sunyaev
Harvard Medical School
17 Inference of 3D Regulatory Interactions from 2D Genomic Data
YouTube video Video | Slides PDF file
Katherine Pollard
Gladstone Institutes
University of California, San Francisco
Workshop Session 3: ENCODE Uniform Processing Pipelines
18 ENCODE Uniform Data Processing Pipelines: Introduction
YouTube video Video | Handout: DNA Nexus for ENCODE PipelinesPDF file
J. Seth Strattan
Stanford University
19 ENCODE Uniform Data Processing Pipelines: Demo and Hands-on Tutorial
YouTube video Video | Handout: Running RNA-seq Pipeline on DNA Nexus PDF file
Ben Hitz
Stanford University
20 ENCODE Uniform Data Processing Pipelines:  ChIP-seq IDR Architecture
YouTube video Video
J. Seth Strattan
Stanford University
21 ENCODE Uniform Data Processing Pipelines: Demo and Hands-on Tutorial (continued)
YouTube video Video
Ben Hitz
Stanford University
22 ENCODE Uniform Data Processing Pipelines: Wrap-up
YouTube video Video
J. Seth Strattan
Stanford University
Workshop Session 4: Advanced Analysis Tools
23 ENCODE Encyclopedia and Factorbook
YouTube video Video | Handout: ENCODE Encyclopedia and Factorbook PDF file
Michael Purcaro
University of Massachusetts
24 ENCODE Element Browser and the 3D Genome Browser
YouTube video Video | Handout: ENCODE Element Browser PDF file
Yanli Wang
Pennsylvania State University
25 Learning Chromatin States from ChIP-seq Data: ChromHMM
YouTube video Video | Slides PDF fileHandout: ChromHMM Tutorial PDF file
Luca Pinello
Dana-Farber Cancer Institute
26 Visualizing ENCODE Data with Self Organizing Maps: SOMatic
YouTube video Video | Handout: SOMatic Tutorial PDF file

Handout: UCI SOMatic Browser PDF file
Camden Jensen
University of California, Irvine


Tuesday, July 1, 2015

  Topic Moderator/Presenter
Scientific Session 3: Integrative Analysis and Mouse ENCODE
Moderator: Eric Boerwinkle
27 The Integration of ENCODE Into the Study of the Complexity of Cancer Susceptibility
YouTube video Video | Slides PDF file
Stephen Chanock
National Cancer Institute
28 Revisiting the Human and Mouse Transcriptomes
YouTube video Video | Slides PDF file
Tom Gingeras
Cold Spring Harbor Laboratories
29 Integrative Analysis of Human and Mouse Regulomes
YouTube video Video | Slides PDF file
John Stamatoyannopoulos
University of Washington
30 Examples of How ENCODE Facilitates Biomedical Research
YouTube video Video | Slides PDF file
Richard Myers
Hudson Alpha Institute

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Last Updated: August 21, 2015

Last updated: August 21, 2015