How cells, tissues and organisms interpret the information encoded in the genome has vital implications for our understanding of development, health and disease. Launched in 2003, the ENCyclopedia Of DNA Elements (ENCODE) project aims to map the functional elements in the human genome (later expanded to include model organisms).

This Collection showcases the main articles and related content resulting from the third phase of ENCODE, during which almost 6,000 new experiments were performed (4,834 involving human samples and 1,158 with mouse samples) and an online registry of more than one million human and mouse candidate cis-regulatory elements (cCREs) was curated. The Encyclopedia paper gives an overview of the various assays and describes the registry of cCREs, and in the companion articles, individual data types are analysed in more detail and the development of novel methodology is reported. This dedicated collection also contains a Perspective, News & Views articles and links to other resources

Mouse Epigenetics and Gene Expression

Human Transcripts and RNA Regulation

Computational Analysis and Tools

An exhaustive list of all ENCODE and community publications can be found on the ENCODE portal: https://www.encodeproject.org/publications/