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ENCODE Phase 3: Participants and Projects

ENCODE Production Centers

Research Group Institution Major Research Goals
Bradley Bernstein Broad Institute of MIT and Harvard Map histone modifications using chromatin immunoprecipitation followed by high-throughput sequencing.
Thomas Gingeras Cold Spring Harbor Laboratory Identify protein-coding and non-protein coding RNA transcripts using high-throughput sequencing, and identify transcription start sites using cap analysis.
Brenton Graveley University of Connecticut Health Center Identify human RNA sequence elements bound by proteins, and investigate their function.
Richard Myers HudsonAlpha Institute for Biotechnology Identify transcription factor binding sites in the human genome, identify RNA transcripts in mouse and human cells, and identify DNA methylation sites in human cells.
Bing Ren LICR/University of California, San Diego

Catalog chromatin structure in mouse cells by mapping histone modifications and identifying sites of DNA methylation. Functionally characterize regulatory elements using transgenic mice.

Michael Snyder Stanford University Identify transcription factor binding sites in the human genome, and functionally characterize regulatory elements.
John Stamatoyannopoulos University of Washington, Seattle Map chromatin structure and transcription factor binding sites in human and mouse cells using DNaseI.

ENCODE Data Coordination Center

Research Group Institution Goals
Michael Cherry Stanford University Collect, organize, store, manage, and provide access to data from ENCODE and related projects.

ENCODE Data Analysis Center

Research Group Institution Research Goals
Zhiping Weng University of Massachusetts Medical School, Worcester Coordinate and assist in the integrative analysis of data produced by the ENCODE Consortium.

ENCODE Computational Analysis Awards

Research Group Institution Research Goals
Peter Bickel University of California Develop statistical methods to enable integration of high dimensional ENCODE data.
David Gifford Massachusetts Institute of Technology Improve resolution for experimental identification of functional elements, and learn enhancer grammar to predict enhancers.
Sunduz Keles University of Wisconsin, Madison Develop computational methods to annotate repetitive regions, and integrate datasets in repetitive regions.
Robert Klein Sloan-Kettering Institute for Cancer Research Develop computational methods to integrate ENCODE data with GWAS data, to find functional variants and critical cell types.
Jonathan Pritchard Stanford University Develop statistical and computational methods for interpreting ENCODE data with respect to gene expression.
Xinshu Xiao University of California, Los Angeles Provide in-depth analysis of ENCODE data to identity functional variants regulating mRNA metabolism.

ENCODE Technology Development Effort

Research Group Institution Research Goals
Christopher Burge Massachusetts Institute of Technology Develop technology for genome-wide identification of RNA branch points.
Barak Cohen Washington University in St. Louis Functionally characterize regulatory elements using high-throughput assays in cell lines and primary cells.
Peggy Farnham University of Southern California Functionally characterize transcription factor hotspots in situ using site-specific nuclease technology.
Raymond Hawkins University of Washington Improve the sensitivity of ChIP-seq assays, to increase power to identify functional elements.
Christina Leslie Memorial Sloan-Kettering Cancer Center Develop computational predictions of transcription factor binding sites and predict cell-specific gene expression.
Jason Lieb University of North Carolina, Chapel Hill Highly parallel functional characterization of enhancers, promoters, insulators, and silencers.
Mats Ljungman University of Michigan Develop new assays (BruChase-seq and BrUV-seq) to identify promoters and enhancers, and to measure RNA metabolism.
Tarjei Mikkelsen Broad Institute of MIT and Harvard Functionally characterize enhancers, silencers, insulators, splicing regulators, and RNA stability/translation, using high-throughput assays with integrated reporters.
Jay Shendure University of Washington Functionally characterize regulatory elements using massively parallel assays in cell lines and mice.
Alexey Wolfson Advanced RNA Technologies, LLC Develop improved RNAi method using self-deliverable RNAs.
Guo-Cheng Yuan Harvard School of Public Health Develop novel computational methods to characterize chromatin states and predict chromosomal interactions.

Additional ENCODE Participants

Research Group Institution Research Goals
Michael Beer Johns Hopkins University Develop sequence-based models to predict regulatory elements and determine their function.
Jennifer Harrow Wellcome Trust Sanger Institute

GENCODE Project: Annotate gene features using computational methods, manual annotation, and targeted experiments.

David Gilbert Florida State University Investigate the relationship of replication timing to other chromatin properties and developmental gene expression patterns.
Anton Valouev University of Southern California, Keck School of Medicine Generate and analyze nucleosome-binding and gene regulatory data, and develop novel computational methods for such analyses.

Last Updated: September 17, 2018