ENCODE 2016: Research Applications and Users Meeting

On June 08 - June 10, 2015, the National Human Genome Research Institute (NHGRI) will sponsor the ENCODE 2016: Research Applications and Users Meeting at the Stanford University in Palo Alto, CA. This page features the some of the material from the upcoming hands-on workshops, and will be updated as more material becomes available.

*Note: Dr. Freedman requested the ENCODE Consortium to not put his own slides in our tutorial page.

The meeting will feature:

  • Hands-on workshops on learning to navigate, analyze, and integrate ENCODE and mouse ENCODE 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

   Wednesday, June 08, 2016

No.

Presentation Video Link (coming soon!)

Presenter

Organization

Additional materials

1

Welcome Overview of ENCODE data types

Mike Pazin

NHGRI

Slides

Keynote Lecture

2

Integrating Genome, Transcriptome and EMR to Build a Gene to Medical Phenome Catalog

Nancy Cox

Vanderbilt University

Slides

Scientific Session 1: Common Disease

3

Genetic regulation of gene expression variation

Barbara Stranger

University of Chicago

Slides 

4

Regulation of bone and vitamin metabolism: Insights from ENCODE

J. Wesley Pike

University of Wisconsin

Slides

5

Common disease burden in non-coding regions

Chris Cotsapas

Broad Institute/Yale University

Slides

Workshop Session 1: ENCODE Encyclopedia

6

The ENCODE Encyclopedia

Zhiping Weng

University of Massachusetts

Slides 

Workshop Session 2: The ENCODE Data Coordinating Center

7

DCC Tutorial, Part I: The Portal

Cricket Sloan

Stanford University

Slides | PDF Tutorial

Workshop Session 3: Web-based Analysis Tools

8

ENCODE element browser and 3D browser

Feng Yue

Pennsylvania State University

Slides

9

RBP database

Brenton Graveley, Eric van Nostrand

University of Connecticut, MIT UCSD

Slides

10 RegulomeDB 

Collin Melton

Stanford University Slides 
11 HaploReg Wouter Meuleman MIT Slides

Scientific Session 2: Non-coding RNA

12 Comparative Analysis of Non-Coding Transcription using ENCODE and modENCODE data  Joel Rozowsky Yale University Slides
13 Human cellular identity considered in the context of organ of origin  Thomas Gingeras Cold Spring Harbor Laboratory Slides

Lightning Talks: Moderated by Feng Yue

14 Decoding Brain Epigenome Maps with Broad H3K4me3 Signals: Discovering Functional Epigenetic Patterns and         Their Dynamics in Gene Regulatory Networks  Aslihan Dincer Icahn School of Medicine, Mt. Sinai Slides
15 The role of transcript-specific translation in human neuronal Differentiation Stephen Floor University of California, Berkeley Slides
16 Crowdsourced analysis, curation, and visualization of ENCODE data with Quilt Aneesh Karve Quilt Data Slides
17  Evaluation of U12-type non-canonical splicing events in human ENCODE RNA-Seq datasets and analysis of biological functions for spliced sequences by Read-Spit-Fly algorithm  Yongsheng Bai Indiana State University Slides
18  Spectacle: fast chromatin state annotation using spectral learning Kevin Chen Rutgers University Slides
19 Integration of Genomic Big Data: Efficient Queries on ENCODE (Meta)data  Stefano Perna Politecnico di Milano Slides
20 Genome-wide association between transcription factor expression and chromatin accessibility reveals chromatin state regulators David Lamparter Verge Genomics Slides
21 Identification of non-coding risk variants associated with complex diseases based on multi-omics profiles Steve Qin Emory University Slides
22 Reconstruction and analysis of tissue-specific transcriptional regulatory networks with TRENA Seth Ament Institute for Systems Biology Slides
23 GWAS of QT interval in Hispanics/Latinos generalizes 13 loci and identifies population-specific signals Raúl Méndez-Giráldez University of North Carolina Slides
24 ChromNet: Learning the human chromatin network from all ENCODE ChIP-seq data Scott Lundberg University of Washington Slides
25 Comprehensive characterization of the genome sequences of K562 and HepG2 Bo Zhou Stanford University Slides

 

   Thursday, June 09, 2016

No.

Presentation Video Link

Presenter

Organization

Additional materials

Scientific Session 3: Cancer

1

Regulatory variation in breast cancer

Mathieu Lupien

University of Toronto

Slides

2

Non-coding cancer drivers

Michael Snyder

Stanford University

Slides

3

Using ENCODE to interpret mutational patterns in cancer genomes

Shamil Sunyaev

Harvard Medical School

Slides 

4

Tools for analyzing cancer variation

Ekta Khurana

Cornell University

Slides

Scientific Session 4: Functional validation of ENCODE elements

5

Comprehensive functional testing of ChIP-seq binding sites with ChIP-reporter assays

Tim Reddy

Duke University

Slides

6

Using ENCODE to inform genome editing

Matthew Freedman

Dana-Farber Cancer Institute/Harvard Medical School

N/A*

Workshop Session 4: ENCODE Uniform Processing Pipelines

7

DCC tutorial Part II: Pipeline overview

J. Seth Strattan

Stanford University

SlidesPreparing to Run ENCODE Pipelines | ChIP-seq Transcription Factor tutorial | ChIP-seq Histone tutorial | RNA-seq tutorial

Workshop Session 5: Advanced Analysis Tools

8

ChromHMM

Jason Ernst

University of California, Los Angeles

Slides

9

Segway

Max Libbrecht

University of Washington

SlidesPDF Tutorial

10

epilogos

Wouter Meuleman

MIT

Slides

11 Deep learning for genomics Anshul Kundaje Stanford University Slides | Website

 

   Friday, June 10, 2016

No.

Presentation Video Link

Presenter

Organization

Additional materials

Scientific Session 5: RNA Binding Proteins

 1 Comprehensive characterization of functional RNA element encoded in the human genome  Brenton Graveley University of Connecticut Slides
 2 Genetic variants and associated proteins in the regulation of pre-mRNA splicing   Grace Xiao  UCLA  Slides

Scientific Session 6: 3D Genome Organization

4

Organization and Regulation of Human Genome

Bing Ren

University of California, San Diego

Slides

5

Players and Models of Transcription Regulation in 3D genome​

Yijun Ruan

The Jackson Laboratory Cancer Center

Slides

6 Many transcription factors recognize DNA shape Katie Pollard Gladstone Institute, UCSF Slides