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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 PDF format.


Wednesday, June 8, 2016

  • Welcome Overview of ENCODE data types
    Mike Pazin, NHGRI
  • Keynote Lecture
  • Integrating Genome, Transcriptome and EMR to Build a Gene to Medical Phenome Catalog
    Nancy Cox, Vanderbilt University
  • Scientific Session 1: Common Disease
  • Genetic regulation of gene expression variation
    Barbara Stranger, University of Chicago
  • Regulation of bone and vitamin metabolism: Insights from ENCODE
    J. Wesley Pike, University of Wisconsin
  • Common disease burden in non-coding regions
    Chris Cotsapas, Broad Institute/Yale University
  • Workshop Session 1: ENCODE Encyclopedia
  • The ENCODE Encyclopedia
    Zhiping Weng, University of Massachusetts
  • Workshop Session 2: The ENCODE Data Coordinating Center
  • DCC Tutorial, Part 1: The Portal
    Cricket Sloan, Stanford University
    VideoSlides - Tutorial
  • Workshop Session 3: Web-based Analysis Tools
  • ENCODE element browser and 3D browser
    Feng Yue, Pennsylvania State University
  • RBP database
    Brenton Gravely, University of Connecticut
    Eric van Nostrand, University of California, San Diego
  • Regulome DB
    Collin Melton, Stanford University
  • HaploReg
    Wouter Meuleman, Massachusetts Institute of Technology
  • Scientific Session 2: Non-coding RNA
  • Comparative Analysis of Non-Coding Transcription using ENCODE and modENCODE data
    Joel Rozowsky, Yale University
  • Human cellular identity considered in the context of organ of origin
    Thomas Gingeras, Cold Spring Harbor Laboratory
  • 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
  • The role of transcript-specific translation in human neuronal Differentiation
    Stephen Floor, University of California, Berkeley
  • Crowdsourced analysis, curation, and visualization of ENCODE data with Quilt
    Aneesh Karve, Quilt Data
  • 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
  • Spectacle: fast chromatin state annotation using spectral learning
    Kevin Chen, Rutgers University
  • Integration of Genomic Big Data: Efficient Queries on ENCODE (Meta)data 
    Stefano Perna, Politecnico di Milano
  • Genome-wide association between transcription factor expression and chromatin accessibility reveals chromatin state regulators
    David Lamparter, Verge Genomics
  • Identification of non-coding risk variants associated with complex diseases based on multi-omics profiles
    Steve Qin, Emory University
  • Reconstruction and analysis of tissue-specific transcriptional regulatory networks with TRENA
    Seth Ament, Institute for Systems Biology
  • GWAS of QT interval in Hispanics/Latinos generalizes 13 loci and identifies population-specific signals
    Raúl Méndez-Giráldez, University of North Carolina
  • ChromNet: Learning the human chromatin network from all ENCODE ChIP-seq data
    Scott Lundberg, University of Washington
  • Comprehensive characterization of the genome sequences of K562 and HepG2
    Bo Zhou, Stanford University


Thursday, June 9, 2016

  • Scientific Session 3: Cancer
  • Regulatory variation in breast cancer
    Mathieu Lupien, University of Toronto
  • Non-coding cancer drivers
    Michael Snyder, Stanford University
  • Using ENCODE to interpret mutational patterns in cancer genomes
    Shamil Sunyaev, Harvard Medical School
  • Tools for analyzing cancer variation
    Ekta Khurana, Cornell University
  • Scientific Session 4: Functional Validation of ENCODE Elements
  • Comprehensive functional testing of ChIP seq binding sites with ChIP reporter assays
    Tim Reddy, Duke University
  • 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
    VideoSlides - 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
  • Segway
    Max Libbrecht, University of Washington
    Slides - PDF Tutorial
  • epilogos
    Wouter Meuleman, MIT
  • Deep learning for genomics
    Anshul Kundaje, Stanford University
    VideoSlides - 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
  • Genetic variants and associated proteins in the regulation of pre-mRNA splicing 
    Grace Xiao, University of California, Los Angeles
  • Scientific Session 6: 3D Genome Organization
  • Organization and Regulation of Human Genome
    Bing Ren, University of California, San Diego
  • Players and Models of Transcription Regulation in 3D genome?
    Yijun Ruan, The Jackson Laboratory Cancer Institute
  • Many transcription factors recognize DNA shape
    Katie Pollard, Gladstone Institute, University fo California, San Francisco

Last Updated: November 6, 2016