ENCODE 2016: Research Applications and Users Meeting
On June 08 - June 10, 2016, 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
Video recordings of presentations are available here on the NHGRI website
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 |
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Keynote Lecture |
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2 |
Integrating Genome, Transcriptome and EMR to Build a Gene to Medical Phenome Catalog |
Nancy Cox |
Vanderbilt University |
Slides |
|
Scientific Session 1: Common Disease |
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3 |
Genetic regulation of gene expression variation |
Barbara Stranger |
University of Chicago |
|
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4 |
Regulation of bone and vitamin metabolism: Insights from ENCODE |
J. Wesley Pike |
University of Wisconsin |
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5 |
Common disease burden in non-coding regions |
Chris Cotsapas |
Broad Institute/Yale University |
Slides |
|
6 |
The ENCODE Encyclopedia |
Zhiping Weng |
University of Massachusetts |
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Workshop Session 2: The ENCODE Data Coordinating Center |
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|
7 |
DCC Tutorial, Part I: The Portal |
Cricket Sloan |
Stanford University |
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Workshop Session 3: Web-based Analysis Tools |
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|
8 |
ENCODE element browser and 3D browser |
Feng Yue |
Pennsylvania State University |
|
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9 |
RBP database |
Brenton Graveley, Eric van Nostrand |
University of Connecticut, MIT UCSD |
|
| 10 | RegulomeDB |
Collin Melton |
Stanford University | Slides |
| 11 | HaploReg | Wouter Meuleman | MIT | Slides |
|
Scientific Session 2: Non-coding RNA |
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| 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 |
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| 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 |
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|
1 |
Regulatory variation in breast cancer |
Mathieu Lupien |
University of Toronto |
|
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2 |
Non-coding cancer drivers |
Michael Snyder |
Stanford University |
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3 |
Using ENCODE to interpret mutational patterns in cancer genomes |
Shamil Sunyaev |
Harvard Medical School |
|
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4 |
Tools for analyzing cancer variation |
Ekta Khurana |
Cornell University |
|
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Scientific Session 4: Functional validation of ENCODE elements |
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|
5 |
Comprehensive functional testing of ChIP-seq binding sites with ChIP-reporter assays |
Tim Reddy |
Duke University |
|
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6 |
Using ENCODE to inform genome editing |
Matthew Freedman |
Dana-Farber Cancer Institute/Harvard Medical School |
N/A* |
|
7 |
DCC tutorial Part II: Pipeline overview |
J. Seth Strattan |
Stanford University |
Slides | Preparing to Run ENCODE Pipelines | ChIP-seq Transcription Factor tutorial | ChIP-seq Histone tutorial | RNA-seq tutorial |
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Workshop Session 5: Advanced Analysis Tools |
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|
8 |
ChromHMM |
Jason Ernst |
University of California, Los Angeles |
|
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9 |
Segway |
Max Libbrecht |
University of Washington |
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10 |
epilogos |
Wouter Meuleman |
MIT |
|
| 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 |
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| 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 |
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Scientific Session 6: 3D Genome Organization |
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|
4 |
Organization and Regulation of Human Genome |
Bing Ren |
University of California, San Diego |
|
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5 |
Players and Models of Transcription Regulation in 3D genome |
Yijun Ruan |
The Jackson Laboratory Cancer Center |
|
| 6 | Many transcription factors recognize DNA shape | Katie Pollard | Gladstone Institute, UCSF | Slides |