ENCODE 2015: Research Applications and Users Meeting

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. Feedback from participants was overwhelmingly positive, and discussions are underway for planning a second Users Meeting in 2016 on the west coast.

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

Meeting materials: Agenda | Abstracts

Tutorials and Presentations

Monday, June 29, 2015

No.	Presentation Video Link	Presenter	Organization	Additional materials
1	Using ENCODE Data to Interpret Disease-associated Genetic Variation	Mike Pazin	NHGRI	Slides
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	Slides
4	Identifying Dysregulated Genes in Autoimmune Disease	Chris Cotsapas	Yale Medical School	Slides
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	Slides
Workshop Session 1: Online Resources and Tools
7	Overview of the ENCODE Data Portal	Eurie Hong	Stanford University	Slides \| Hands-on Tutorial
8	Visualizing ENCODE Data in the UCSC Browser	Pauline Fujita	University of California, Santa Cruz	Slides & Hands-on Tutorial
Workshop Session 2: Online Resources and Tools
9	Introduction to Ensembl Regulation	Emily Perry	European Bioinformatics Institute	Slides \| Hands-on Tutorial
10	Analysing Variants with the Variant Effect Predictor (VEP)	Emily Perry	European Bioinformatics Institute	Slides \| Hands-on Tutorial\| VEP_input.vcf
11	Variant Annotation Using RegulomeDB and HaploReg	Jill Moore	University of Massachusetts Medical School	Slides \| Hands-on Tutorial

Tuesday, June 30, 2015

No.	Presentation Video Link	Presenter	Organization	Additional materials
Keynote Lecture
12	Selection and Function of Signal-Dependent Enhancers	Christopher Glass	University of California, San Diego	Slides
Scientific Session 2: Cancer, Regulation, and Mutation
13	Cancer, Genetic Predispositions, and Chromatin Architecture	Mathieu Lupien	University of Toronto	Slides
14	Mining the Genome to Understand Epigenetic Abnormalities in Cancer and Enhance Development of New Therapeutic Approaches	Stephen Baylin	Johns Hopkins University	Slides
15	Reconstructing Cancer Stem Cells from their Chromatin Landscapes	Bradley Bernstein	Harvard Medical School
16	Epigenentic Control of Genetics: the Impact of Epigenome on Mutation	Shamil Sunyaev	Harvard Medical School	Slides
17	Inference of 3D Regulatory Interactions from 2D Genomic Data	Katherine Pollard	Gladston Institutes, University of California, San Fransciso	Slides
Workshop Session 3: ENCODE Uniform Processing Pipelines
18	ENCODE Uniform Data Processing Pipelines: Introduction	J. Seth Strattan	Stanford University	Slides \| Prepare to run web-based pipelines
19	ENCODE Uniform Data Processing Pipelines: Demo and Hands-on Tutorial	Ben Hitz	Stanford University	Hands-on Tutorial
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	Handout
24	ENCODE Element Browser and the 3D Genome Browser	Yanli Wang	Pennsylvania State University	Hands-on Tutorial
25	Learning Chromatin States from ChIP-seq Data: ChromHMM	Luca Pinello	Dana-Farber Cancer Institute	Slides \| Hands-on Tutorial
26	Visualizing ENCODE Data with Self Organizing Maps: SOMatic	Camden Jensen	University of California, Irvine	Hands-on Tutorial \| Handout

Wednesday, July 1, 2015

No.	Presentation Video Link	Presenter	Organization	Additional materials
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	Slides
28	Revisiting the Human and Mouse Transcriptomes	Tom Gingeras	Cold Spring Harbor Laboratories	Slides
29	Integrative Analysis of Human and Mouse Regulomes	John Stamatoyannopoulos	University of Washington	Slides
30	Examples of how ENCODE Facilitates Biomedical Research	Richard Myers	Hudson Alpha Institute	Slides