ENCODE Participants and Projects
- Production Centers
- Data Coordination Center
- Data Analysis Center
- Computational Analysis Awards
- Technology Development Effort
- Additional Participants
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 | University of Chicago | 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 | Albert Einstein College of Medicine | 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 |
---|---|---|
Timothy Hubbard | Wellcome Trust Sanger Institute |
Annotate gene features using computational methods, manual annotation, and targeted experiments. |
Last Updated: February 6, 2013