The U.S. Department of Energy Joint Genome Institute (DOE JGI) was created in 1997 to unite the expertise and resources in DNA sequencing, informatics, and technology development pioneered at the U.S. Department of Energy (DOE) genome centers at Lawrence Berkeley National Laboratory (LBNL), Lawrence Livermore National Laboratory (LLNL), and Los Alamos National Laboratory (LANL). In 1999, to accelerate the completion of DOE’s commitment to the Human Genome Project, the University of California, which manages the DOE JGI lead laboratory in LBNL, leased laboratory and office space in a light industrial park in Walnut Creek, California, to consolidate activities. The significant economies of scale achieved in doing so enabled the DOE JGI to be the first to publish the sequence analysis of the target chromosomes 5, 16, and 19, in the journal Nature. Following this accomplishment, the DOE JGI went on to advance basic science by sequencing scores of microbial species as well as several model organisms and contributing this information freely to the public databases.
In 2004, the DOE JGI established itself as a national user facility and today there are more than 1,200 primary users worldwide. The vast majority of DOE JGI sequencing and analysis is conducted under the auspices of the Community Science Program (CSP), surveying the biosphere to characterize organisms relevant to the DOE science mission areas of bioenergy, global carbon cycling, and biogeochemistry. The DOE JGI’s largest customers are the DOE Bioenergy Research Centers (BRCs), which were launched in 2007 to accelerate basic research in the development of next generation cellulosic biofuels. The JGI continues to receive its support from the Office of Biological and Environmental Research in DOE’s Office of Science.
The DOE JGI has grown to occupy 80,000 square feet, employs over 250 staff and had been led by internationally recognized geneticist, Eddy Rubin, M.D., Ph.D. from 2002 until he stepped down in 2016. The DOE JGI’s partner laboratories include LBNL, LLNL and the HudsonAlpha Institute for Biotechnology (formerly associated with the Stanford Human Genome Center). The DOE JGI workforce draws most heavily from LBNL.
The DOE JGI is enormously productive, not only in terms of generation of DNA sequence data (in FY15 alone, over 140 trillion nucleotides) but also with respect to generating high-profile publications. Since 2004, the DOE JGI has played a role and shared co-authorship in several hundred peer-reviewed publications and played a significant role in several dozen papers in the journals Science and Nature between 2006 and the present. All of these papers have one or more DOE JGI authors and for the majority of them the DOE JGI played a leadership role in the study, reflected in first or senior authorship.