New Phytologist dedicates an entire issue to various research directions based on the tree genome. The Science: Building off the Eucalyptus grandis tree genome that researchers at the DOE Joint Genome Institute helped sequence and analyze, several researchers demonstrate the utility of the reference genome in the June 2015 special issue of New Phytologist. The…
Confirming Microbial Lineages Through Cultivation-Independent Means
Collaborative work culminates in evidence of a single candidate bacterial phylum. The number of microbes found on Earth has been compared to the number of stars in the Milky Way. Yet the proportion of those microbes that can actually be grown under laboratory conditions is so small it would be akin to those stars that…
Collaborator Janet Jansson in Quanta magazine
“[S]oon after the turn of the century, new high-octane DNA sequencing methods made it possible to sequence thousands or even millions of genes almost instantly. These new, speedier methods meant researchers could easily sequence the collective genomes of the sample, known as a metagenome, for the first time. Suddenly, it was possible to scan the…
Automating Microbial Genome Sequence Decontamination
Single cell genomics and metagenomics are pioneering techniques that have helped researchers assess environmental microbial community structure and function. As projects applying these techniques scale up, however, researchers are hindered by the lack of a high-throughput process to review assembled genome sequences. Currently, sequence decontamination of the microbial genomes being uploaded to public databases is…
Data Quality, Data Sets and New Directions: Plotting IMG’s Next 10 Years
Nikos Kyrpides received the Van Niel International Prize in Bacterial Systematics for the triennium 2012-2014. His efforts to systematically describe and classify microbes in action can be seen in the Integrated Microbial Genomes (IMG) data management system.
Charting Short-Term Results of Wetlands Restoration
In mBio, JGI researchers reported on microbial community composition and carbon emissions patterns from restored wetlands.
Promoting Safety & Wellness at Work and at Home
Marking its 9th year, the annual JGI Safety and Wellness Fair took place on Wednesday, June 3, 2015, drawing around 120 attendees to our Courtyard. Over a dozen booths promoted various aspects of health and safety, both at work and at home. The JGI Safety & Wellness (SWELL) Team, a group of employees who have…
Meraculous: Genome Assembly from Months to Minutes
“Using the parallelized version of Meraculous, we can now assemble the entire human genome in about eight minutes using 15,360 computer processor cores. With this tool, we estimate that the output from the world’s biomedical sequencing capacity could be assembled using just a portion of NERSC’s Edison supercomputer,” says Evangelos Georganas, a UC Berkeley graduate…
The Most Complete Functional Map of an Entire Enzyme Family
DOE-funded researchers develop a new process for annotating cellulose-degrading enzymes. The Science: Researchers at two Department of Energy-funded Scientific User Facilities collaborated with one of three Bioenergy Research Centers to develop and analyze high-resolution crystal structures of an enzyme from the cellulose-degrading GH55 family. They then went further and were able to apply a variety…
Jillian Banfield, University of California, Berkeley
Jillian Banfield, PhD is a prominent geomicrobiologist and biochemist, a UC Berkeley Professor, a Berkeley Lab Earth Sciences Division staff scientist, and a long time user of the DOE Joint Genome Institute’s resources through the Community Science Program (CSP) and the Emerging Technologies Opportunities Program (ETOP). In this short interview, Jill shares her perspective how…