ENCODE

Comparative encyclopedia of DNA elements in the mouse genome, enabling cross-species analysis of regulatory element conservation and divergence. Provided the foundation for understanding which functional elements are evolutionarily constrained.

ENCODE Pilot Project launched by NHGRI to identify functional elements in 1% (30 Mb) of the human genome. 35 research groups across 80 institutions used multiple experimental and computational approaches to annotate genes, regulatory elements, and chromatin features.

Landmark ENCODE pilot results demonstrating that the majority of the human genome is biochemically functional, with pervasive transcription, abundant regulatory elements, and complex chromatin landscapes. Challenged the traditional view of 'junk DNA' and established ENCODE as a foundational genomics resource.

Comprehensive guide to the ENCODE resource, describing data types, experimental protocols, analysis pipelines, and data access tools. Provided the framework for understanding the full-genome ENCODE project and the upcoming 2012 Nature publications.