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ENCODE/Roadmap Epigenomics Tutorial - October 2015, ASHG

On October 11, 2015, ENCODE and the Common Fund-supported Roadmap Epigenomics Mapping Centers (REMC) held a workshop at the American Society of Human Genetics (ASHG) annual meeting.

This advanced workshop began with brief overviews of the ENCODE and Roadmap Epigenomics projects. Hands-on tutorials were provided on how to perform integrative analysis with a variety of data sets as seen in recent ENCODE and Roadmap Epigenomics publications, with a special focus on how it can be used to improve the annotation of genetic variants underlying disease.

Workshop attendees received hands-on experience using the following resources:

  • Searching for datasets using the ENCODE portal []
  • Browsing and downloading Encyclopedia annotations from ENCODE and REMC
  • Using RegulomeDB and HaploReg to query ENCODE and REMC data
  • Using the ENCODE element browser and 3D Genome Browser
  • Using ChromHMM to predict regulatory states in the genome

This workshop educated researchers, clinicians and genetic counselors on how to use ENCODE data to generate hypotheses for further biological investigation.

Agenda and Resources

  Topic Presenter
1 Workshop Introduction
YouTube video Video
Feng Yue
Pennsylvania State University
2 A Brief Tour of ENCODE
YouTube video Video | Slides PDF file
Mike Pazin
3 The NIH Roadmap Epigenomics Program
YouTube video Video | Slides PDF file
Kim McAllister
National Institute of Environmental Health Sciences
4 ENCODE Standards, Data and Access
YouTube video Video | Slides PDF file
J. Michael Cherry
Stanford University
5 The ENCODE Encyclopedia and Variant Annotation Using RegulomeDB and HaploReg
YouTube video Video | Slides PDF file
Jill E. Moore
University of Massachusetts Medical School
6 ENCODE Element Browser and the 3D Genome Browser
YouTube video Video | Slides PDF file
Yanli Wang
Pennsylvania State University
7 ChromHMM Tutorial
YouTube video Video | Slides PDF file
Jason Ernst
University of California, Los Angeles
8 Concluding Remarks
YouTube video Video
Manolis Kellis
Massachusetts Institute of Technology
For questions or more information contact:

Michael Pazin, Ph.D.

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Last Reviewed: May 11, 2016

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