ENCODE 2015: Research Applications and Users Meeting
June 29 - July 1, 2015
Bolger Center
Potomac, Md.
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
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
| Mike Pazin NHGRI |
| Keynote Lecture | ||
| 2 | Data Integration: Genome x Transcriptome x EMR
| Nancy Cox Vanderbilt University |
| Scientific Session 1: Common Disease | ||
| 3 | An Epigenomic and Transcriptional Basis for Insulin Resistance
| Evan Rosen Harvard Medical School |
| 4 | Identifying Dysregulated Genes in Autoimmune Disease
| Chris Cotsapas Yale Medical School |
| 5 | Enhancers: Regulatory Control Elements in Health and Disease
| J. Wesley Pike University of Wisconsin |
| 6 | Mapping the Epigenetic Basis of Kidney Disease
| Katalin Susztak University of Pennsylvania |
| Workshop Session 1: Online Resources and Tools | ||
| 7 | Overview of the ENCODE Data Portal
| Eurie Hong Stanford University |
| 8 | Visualizing ENCODE Data in the UCSC Browser
| Pauline Fujita University of California, Santa Cruz |
| Workshop Session 2: Online Resources and Tools | ||
| 9 | Introduction to Ensembl Regulation
| Emily Perry European Bioinformatics Institute |
| 10 | Analysing Variants with the Variant Effect Predictor (VEP)
| Emily Perry European Bioinformatics Institute |
| 11 | Variant Annotation Using RegulomeDB and HaploReg
| Jill Moore University of Massachusetts Medical School |
Tuesday, June 30, 2015
| Topic | Moderator/Presenter | |
|---|---|---|
| Keynote Lecture | ||
| 12 | Selection and Function of Signal-Dependent Enhancers
| Christopher Glass University of California, San Diego |
| Scientific Session 2: Cancer, Regulation, and Mutation | ||
| 13 | Cancer, Genetic Predispositions, and Chromatin Architecture
| Matthew Lupien University of Toronto |
| 14 | Mining the Genome to Understand Epigenetic Abnormalities in Cancer and Enhance Development of New Therapeutic Approaches
| Stephen Baylin Johns Hopkins University |
| 15 | Reconstructing Cancer Stem Cells from Their Chromatin Landscapes
| Bradley Bernstein Harvard Medical School |
| 16 | Epigenetic Control of Genetics: the Impact of Epigenome on Mutation
| Shamil Sunyaev Harvard Medical School |
| 17 | Inference of 3D Regulatory Interactions from 2D Genomic Data
| Katherine Pollard Gladstone Institutes University of California, San Francisco |
| Workshop Session 3: ENCODE Uniform Processing Pipelines | ||
| 18 | ENCODE Uniform Data Processing Pipelines: Introduction
| J. Seth Strattan Stanford University |
| 19 | ENCODE Uniform Data Processing Pipelines: Demo and Hands-on Tutorial
| Ben Hitz Stanford University |
| 20 | ENCODE Uniform Data Processing Pipelines: ChIP-seq IDR Architecture
| J. Seth Strattan Stanford University |
| 21 | ENCODE Uniform Data Processing Pipelines: Demo and Hands-on Tutorial (continued)
| Ben Hitz Stanford University |
| 22 | ENCODE Uniform Data Processing Pipelines: Wrap-up
| J. Seth Strattan Stanford University |
| Workshop Session 4: Advanced Analysis Tools | ||
| 23 | ENCODE Encyclopedia and Factorbook
| Michael Purcaro University of Massachusetts |
| 24 | ENCODE Element Browser and the 3D Genome Browser
| Yanli Wang Pennsylvania State University |
| 25 | Learning Chromatin States from ChIP-seq Data: ChromHMM
| Luca Pinello Dana-Farber Cancer Institute |
| 26 | Visualizing ENCODE Data with Self Organizing Maps: SOMatic
| 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
| Stephen Chanock National Cancer Institute |
| 28 | Revisiting the Human and Mouse Transcriptomes
| Tom Gingeras Cold Spring Harbor Laboratories |
| 29 | Integrative Analysis of Human and Mouse Regulomes
| John Stamatoyannopoulos University of Washington |
| 30 | Examples of How ENCODE Facilitates Biomedical Research
| Richard Myers Hudson Alpha Institute |
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