ENCODE Pilot Project: Participants and Projects

National Human Genome Research Institute

National Institutes of Health
U.S. Department of Health and Human Services


ENCODE Pilot Project: Participants and Projects

Groups Participating in the ENCODE Pilot Phase

Research Group Institution Research Goals
Ian Dunham Wellcome Trust Sanger Institute Map origins of replication, DNA methylation, chromatin modifications, transcription factor binding sites, primarily with ChIP-chip assays using spotted DNA microarrays.
Anindya Dutta University of Virginia Identify early and late origins of replication, sites of replication termination and pause sites for replication forks. Replication products mapped by hybridization to Affymetrix microarrays.
Thomas Gingeras Affymetrix, Inc. Map RNA transcripts, binding sites for transcription factors and chromosomal proteins using Affymetrix microarrays and ChIP-chip assays.
Roderic Guigo Municipal Institute of Medical Research Identify all protein-coding genes. Combine computational prediction with experimental RT/PCR confirmation of gene models.
Richard Myers Stanford University Identify promoters and enhancers with transfection of reporter constructs into cell lines. Identify transcription factor binding sites and chromatin modifications with ChIP-chip assays using Affymetrix arrays. Identify conserved domains with comparative genomic data. Test the function of conserved domains by mapping polymorphisms to these domains and assaying for the effect of these polymorphisms in reporter assays for enhancers in transfected cells.
Bing Ren Ludwig Institute for Cancer Research Identify promoters, enhancers, repressors/silencers using ChIP-chip assays and mapping on spotted DNA microarrays.
Michael Snyder Yale University Map RNA transcripts and binding sites for transcription factors and chromosomal proteins using DNA microarrays and ChIP-chip assays. Comparison of Affymetrix, NimbleGen and spotted DNA arrays platforms.
George Stamatoyannopoulos University of Washington Map DNase I hypersensitive sites using quantitative, real time PCR.

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Additional ENCODE Pilot Phase Participants

Research Group Institution Research Goals
Andy Baxevanis National Human Genome Research Institute Develop an ENCODE data portal for non-sequence based data including coordinated data deposition and dissemination.
Greg Crawford Duke University Identify DNase hypersensitive sites using high-throughput sequencing and microarray methods.
Pieter De Jong Children's Hospital Oakland Research Institute Create clone resources to support comparative sequencing.
Emmanouil Dermitzakis Wellcome Trust Sanger Institute Identify nucleotide variants that are associated with variations in levels of gene expression.
Laura Elnitski National Human Genome Research Institute Design and implement a publicly-accessible database for the querying and retrieval of ENCODE data.
Eric Green NIH Intramural Sequencing Center/ National Human Genome Research Institute Isolate BAC clones for ENCODE regions in multiple organisms; generate multispecies comparative genome sequence data for these ENCODE regions; develop computational tools for analysis of comparative genome sequences.
Roland Green NimbleGen Systems, Inc. Map transcription factor binding sites and identify first exons/promoters using NimbleGen microarrays and ChIP-chip assays.
Ross Hardison Pennsylvania State University Develop tools to analyze comparative genomic sequences and integrate functional data with the genome sequence.
David Haussler University of California, Santa Cruz Develop ENCODE-specific views of the human genome using the Santa Cruz UCSC Browser; develop tools to analyze comparative genomic sequences and integrate functional data with the genome sequence.
Steven Jones British Columbia Cancer Agency Genome Sciences Centre Generate whole genome data on gene expression; develop tools to identify regulatory elements from co-expressed genes.
Kerstin Lindblad-Toh/ Michelle Clamp Broad Institute Develop methodologies, algorithms and software to generate regional alignments of multiple genomes in the ENCODE regions.
Elliott Margulies National Human Genome Research Institute Develop and implement analytical methods to characterize evolutionarily constrained sequences and to establish their functional significance.
Marco Marra British Columbia Cancer Agency Genome Sciences Centre Generate fingerprint maps and tiling paths for BACs isolated from the ENCODE regions in different species; identify alternatively spliced transcripts for genes in the ENCODE regions.
Webb Miller Pennsylvania State University Develop tools to analyze comparative genomic sequences and integrate functional data with the genome sequence.
Steve Salzberg The Institute for Genomic Research Develop computational tools to analyze comparative genomic sequences, to find genes and to assemble genomes.
Greg Schuler National Center for Biotechnology Information (NCBI), National Library of Medicine Coordinate ENCODE comparative genomic sequence data with NCBI.
Zhiping Weng Boston University Use computation methods to identify cis-regulatory elements in alternative promoters.

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Groups Participating in the ENCODE Technology Development Phase

Research Group Institution Research Goals
Job Dekker* University of Massachusetts Medical School Develop PCR strategy to identify regions in chromosomes that interact through protein complex binding using the Chromosome Conformation Capture (3C) technology.
Xiang-Dong Fu* University of California, San Diego Improve sensitivity and specificity of the ChIP-chip technology using single stranded oligonucleotide microarrays and DASL (DNA Annealing Selection and Ligation) technology.
Roland Green* NimbleGen Systems, Inc. Test ability of NimbleGen's Maskless Array Synthesis technology to map transcription factor binding sites and first exon/promoter identification in ChIP and microarray assays.
Robert Kingston* Massachusetts General Hospital Develop high-throughput methods for mapping chemical and enzymatic DNA cleavage sites in chromatin at nucleotide resolution.
Mark McCormick* NimbleGen Systems, Inc. Develop "exon-linkage assay" to study alternative splicing using NimbleGen's oligonucleotide array platform.
Zhiping Weng* Boston University Develop computational methods to identify cis-regulatory elements in alternative promoters and confirm these elements by competitive PCR and reporter-construct assays in transfected cells.
Joseph Ecker** Salk Institute for Biological Studies Test multiple methylation detection methods (bisulfite treatment, restriction digest with methylation-sensitive enzymes, anti-methylcytosine antibodies, binding of proteins to methylated DNA) using whole genome microarrays.
Vishwanath Iyer** University of Texas, Austin Develop methods for Sequence Tag Analysis of Genomic Enrichment (STAGE) that combines chromatin immunoprecipitation and SAGE and Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE) to identify regulatory elements in chromatin.
Madaiah Puttaraju** Intronn, Inc Develop methods to find splice sites using pre-trans splicing molecules (Spliceosome Mediated RNA Trans-splicing (SMaRT) ExonFinder).
Yijun Ruan** Genome Institute of Singapore Develop Gene Identification Signature (GIS) analysis to generate SAGE data with linked 5' and 3' mRNA information; extend this method to analysis ChIP DNA fragments.
Scott Tenenbaum** University at Albany, State University of New York Develop methods to detect protein binding sites in mRNA by ribonucleoprotein immunoprecipitation combined with microarray hybridization (RIP-chip).
Thomas Tullius** Boston University Develop a library of hydroxyl radical cleavage patterns of random DNA and use to develop computational predictions of DNA cleavage patterns and correlation with DNA binding sites.

*Projects were initiated September 2003
**Projects were initiated September 2004

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Last Reviewed: February 19, 2012