ENCODE 2016: Research Applications and Users Meeting

ENCODE 2016: Research Applications and Users Meeting

June 8-10, 2016

Li Ka Shing Center
Stanford University
Palo Alto, CA

On June 8-10, 2016, the National Human Genome Research Institute (NHGRI) sponsored the ENCODE 2016: Research Applications and Users Meeting at Stanford University in Palo Alto, Calif.

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

All slides and tutorials are in  format.

 Video Playlist
 

Wednesday, June 8, 2016

• Welcome Overview of ENCODE data types
  Mike Pazin, NHGRI
  Video - Slides

• Keynote Lecture

• Integrating Genome, Transcriptome and EMR to Build a Gene to Medical Phenome Catalog
  Nancy Cox, Vanderbilt University
  Video - Slides

• Scientific Session 1: Common Disease

• Genetic regulation of gene expression variation
  Barbara Stranger, University of Chicago
  Video - Slides
• Regulation of bone and vitamin metabolism: Insights from ENCODE
  J. Wesley Pike, University of Wisconsin
  Video - Slides
• Common disease burden in non-coding regions
  Chris Cotsapas, Broad Institute/Yale University
  Video - Slides

• Workshop Session 1: ENCODE Encyclopedia

• The ENCODE Encyclopedia
  Zhiping Weng, University of Massachusetts
  Video - Slides

• Workshop Session 2: The ENCODE Data Coordinating Center

• DCC Tutorial, Part 1: The Portal
  Cricket Sloan, Stanford University
  Video - Slides - Tutorial

• Workshop Session 3: Web-based Analysis Tools

• ENCODE element browser and 3D browser
  Feng Yue, Pennsylvania State University
  Video - Slides
• RBP database
  Brenton Gravely, University of Connecticut
  Eric van Nostrand, University of California, San Diego
  Video - Slides
• Regulome DB
  Collin Melton, Stanford University
  Video - Slides
• HaploReg
  Wouter Meuleman, Massachusetts Institute of Technology
  Video - Slides

• Scientific Session 2: Non-coding RNA

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

• Lightning Talks: Moderated by Feng Yue

• 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
  Video - Slides
• The role of transcript-specific translation in human neuronal Differentiation
  Stephen Floor, University of California, Berkeley
  Video - Slides
• Crowdsourced analysis, curation, and visualization of ENCODE data with Quilt
  Aneesh Karve, Quilt Data
  Video - Slides
• 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
  Video - Slides
• Spectacle: fast chromatin state annotation using spectral learning
  Kevin Chen, Rutgers University
  Video - Slides
• Integration of Genomic Big Data: Efficient Queries on ENCODE (Meta)data 
  Stefano Perna, Politecnico di Milano
  Slides
• Genome-wide association between transcription factor expression and chromatin accessibility reveals chromatin state regulators
  David Lamparter, Verge Genomics
  Video - Slides
• Identification of non-coding risk variants associated with complex diseases based on multi-omics profiles
  Steve Qin, Emory University
  Video - Slides
• Reconstruction and analysis of tissue-specific transcriptional regulatory networks with TRENA
  Seth Ament, Institute for Systems Biology
  Video - Slides
• GWAS of QT interval in Hispanics/Latinos generalizes 13 loci and identifies population-specific signals
  Raúl Méndez-Giráldez, University of North Carolina
  Video - Slides
• ChromNet: Learning the human chromatin network from all ENCODE ChIP-seq data
  Scott Lundberg, University of Washington
  Slides
• Comprehensive characterization of the genome sequences of K562 and HepG2
  Bo Zhou, Stanford University
  Slides

 

Thursday, June 9, 2016

• Scientific Session 3: Cancer

• Regulatory variation in breast cancer
  Mathieu Lupien, University of Toronto
  Video - Slides
• Non-coding cancer drivers
  Michael Snyder, Stanford University
  Video - Slides
• Using ENCODE to interpret mutational patterns in cancer genomes
  Shamil Sunyaev, Harvard Medical School
  Video - Slides
• Tools for analyzing cancer variation
  Ekta Khurana, Cornell University
  Video - Slides

• Scientific Session 4: Functional Validation of ENCODE Elements

• Comprehensive functional testing of ChIP seq binding sites with ChIP reporter assays
  Tim Reddy, Duke University
  Video - Slides
• Using ENCODE to inform genome editing
  Matthew Freedman, Dana-Farber Cancer Institute/Harvard Medical School

• Workshop Session 4: ENCODE Uniform Processing Pipelines

• DCC tutorial Part II: Pipeline overview
  J. Seth Stattan, Stanford University
  Video - Slides - Preparing to Run ENCODE Pipelines - ChiP-sec Transcription Factor Tutorial
  ChiP-seq Histone Tutorial - RNA-seq Tutorial

• Workshop Session 5: Advanced Analysis Tools

• ChromHMM
  Jason Ernst, University of California, Los Angeles
  Video - Slides
• Segway
  Max Libbrecht, University of Washington
  Slides - PDF Tutorial
• epilogos
  Wouter Meuleman, MIT
  Video - Slides
• Deep learning for genomics
  Anshul Kundaje, Stanford University
  Video - Slides - Website

 

Friday, June 10, 2016

• Scientific Session 5: RNA Binding Proteins

• Comprehensive characterization of functional RNA element encoded in the human genome
  Brenton Graveley, University of Connecticut
  Video - Slides
• Genetic variants and associated proteins in the regulation of pre-mRNA splicing 
  Grace Xiao, University of California, Los Angeles
  Video - Slides

• Scientific Session 6: 3D Genome Organization

• Organization and Regulation of Human Genome
  Bing Ren, University of California, San Diego
  Video - Slides
• Players and Models of Transcription Regulation in 3D genome?
  Yijun Ruan, The Jackson Laboratory Cancer Institute
  Slides
• Many transcription factors recognize DNA shape
  Katie Pollard, Gladstone Institute, University fo California, San Francisco
  Videos - Slides