These researchers received NHGRI funds for the large-scale application of existing technologies to determine functional elements across all ENCODE target regions.

• Ian Dunham, David Vetrie, and Nigel Carter, The Wellcome Trust Sanger Institute, Hinxton, U.K.
           Detecting human functional sequences with microarrays
• Anindya Dutta, University of Virginia, Charlottesville
           Mapping replication elements on human chromosomes
• Thomas Gingeras, Affymetrix, Inc., Santa Clara, California
           Mapping sites of transcription and regulation
• Roderic Guigo, Municipal Institute of Medical Research, Barcelona, Spain
           Encyclopedia of genes and gene variants
• Richard Myers, Stanford University, Palo Alto, California
           The Stanford ENCODE Project
• Bing Ren, Ludwig Institute for Cancer Research, University of California, San Diego
           Mapping transcriptional regulatory elements in human DNA
• Michael Snyder, Yale University, New Haven, Connecticut
           Transcription and regulatory elements in ENCODE regions
• George Stamatoyannopoulos, University of Washington, Seattle
           Identification of functional DNA elements by HSqPCR

These researchers received NHGRI funds to improve or develop new technologies for finding functional elements in genomic DNA, and will employ them across all ENCODE target regions. Groups that are also participating in the ENCODE Pilot Phase are marked with a star (*).

• Job Dekker, University of Massachusetts Medical School, Worcester
           Structural annotation of the human genome
• Xiang-Dong Fu, University of California, San Diego
           A novel chIP-chip technology for ENCODE
• Roland Green *, Nimblegen Systems, Inc., Madison, Wisconsin
           Discovery of binding sites for transcription factors
• Robert Kingston, Massachusetts General Hospital, Boston
           Long-range, high-resolution mapping of chromatin
• Mark McCormick, Nimblegen Systems, Inc., Madison, Wisconsin
           DNA array-based exon detection and linkage mapping
• Zhiping Weng *, Boston University
           Alternative promoter usage in tissue-specific gene expression

Second round of technology development grantees (September 2004):

• Joseph Ecker, Salk Institute
           Genome Wide Analysis of DNA Methylation
• Vishwanath Iyer, University of Texas, Austin
           STAGE and FAIRE for Regulatory Element Identification
• Madaiah Puttaraju, Intronn, Inc.
           Use of RNA trans-splicing to identify splice sites
• Yijun Ruan, Genome Institute of Singapore
           Ditag technologies for complete transcriptome annotation
• Scott Tenenbaum, SUNY Albany
           Identifying functional regulatory elements in RNA
• Tom Tullius, Boston University
           Structure of genomic DNA at single-nucleotide resolution

These researchers provided infrastructure development to support ENCODE-related research.

• Andreas D. Baxevanis, NHGRI Division of Intramural Research
           Coordination of the database for other data types
• Pieter De Jong, Children's Hospital Oakland Research Institute
           Clone resources to support comparative sequencing.
• Eric Green, NIH Intramural Sequencing Center
           Comparative sequencing
• Ross Hardison, Webb Miller, Pennsylvania State University
           Computational tools for comparative genomics; collaboration with UCSC
• Jim Kent, David Haussler, Kate Rosenbloom, Daryl Thomas, Ting Wang, and the UCSC Genome Bioinformatics staff
           Coordination of the Genome Browser website and the database for all sequence-related data
• Kerstin Lindblad-Toh, Michele Clamp, Broad Institute
           Computational tools for comparative genomics and prediction of cis-regulatory elements
• Marco Marra, British Columbia Cancer Agency Genome Sciences Center
           Generation of maps and contigs for ENCODE BACs
• Greg Schuler, National Center for Biotechnology Information (NCBI)
           Coordination of ENCODE data with NCBI

Additional ENCODE pilot phase participants:

• Greg Crawford, Francis Collins, NHGRI Intramural Program
           Identification of DNAse hypersensitive sites
• Steven Jones, British Columbia Cancer Agency Genome Sciences Center
           Computational tools for comparative genomics, visualization of genome, features, and prediction of cis-regulatory elements
• Steven Salzberg, Center for Bioinformatics and Computational Biology, University of Maryland
           Computational tools for comparative genomics