Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
- E. Birney, J. Stamatoyannopoulos, P. D. de Jong
- BiologyNature
- 14 June 2007
Functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project are reported, providing convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts.
The ENCODE (ENCyclopedia Of DNA Elements) Project
- E. Feingold, P. Good, S. Harvey
- Biology, EngineeringScience
- 22 October 2004
The ENCyclopedia Of DNA Elements (ENCODE) Project is organized as an international consortium of computational and laboratory-based scientists working to develop and apply high-throughput approaches for detecting all sequence elements that confer biological function.
Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences
- R. Strausberg, E. Feingold, M. Marra
- BiologyProceedings of the National Academy of Sciences…
- 11 December 2002
The National Institutes of Health Mammalian Gene Collection (MGC) Program is a multiinstitutional effort to identify and sequence a cDNA clone containing a complete ORF for each human and mouse gene.…
Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE
- Sushmita Roy, J. Ernst, Manolis Kellis
- BiologyScience
- 1 December 2010
Two studies identified regions of the nematode and fly genomes that show highly occupied targets (or HOT) regions where DNA was bound by more than 15 of the transcription factors analyzed and the expression of related genes were characterized.
An integrated encyclopedia of DNA elements in the human genome
- I. Dunham, A. Kundaje, L. Lochovsky
- Biology
- 1 September 2012
Panel C shows several SNPs associated with Crohn’s disease and other inflammatory diseases that reside in a large gene desert on chromosome 5, along with some epigenetic features suggestive of function.
A comparative encyclopedia of DNA elements in the mouse genome
By comparing with the human genome, this work not only confirms substantial conservation in the newly annotated potential functional sequences, but also finds a large degree of divergence of sequences involved in transcriptional regulation, chromatin state and higher order chromatin organization.
A User's Guide to the Encyclopedia of DNA Elements (ENCODE)
- R. Myers, J. Stamatoyannopoulos, B. Risk
- Biology, Computer SciencePLoS Biology
- 1 April 2011
An overview of the project and the resources it is generating and the application of ENCODE data to interpret the human genome are provided.
Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project
- M. Gerstein, Z. Lu, R. Waterston
- BiologyScience
- 24 December 2010
These studies identified regions of the nematode and fly genomes that show highly occupied targets (or HOT) regions where DNA was bound by more than 15 of the transcription factors analyzed and the expression of related genes were characterized, providing insights into the organization, structure, and function of the two genomes.
An encyclopedia of mouse DNA elements (Mouse ENCODE)
- J. Stamatoyannopoulos, M. Snyder, Leslie B. Adams
- BiologyGenome Biology
- 13 August 2012
The Mouse E NCODE Consortium is applying the same experimental pipelines developed for human ENCODE to annotate the mouse genome to enable a broad range of mouse genomics efforts.
Defining functional DNA elements in the human genome
- Manolis Kellis, B. Wold, R. Hardison
- BiologyProceedings of the National Academy of Sciences
- 21 April 2014
The strengths and limitations of biochemical, evolutionary, and genetic approaches for defining functional DNA segments, potential sources for the observed differences in estimated genomic coverage, and the biological implications of these discrepancies are reviewed.
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