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… workshop, Volkan Sevim, a computational biologist at the US Department of Energy (DOE) Joint Genome Institute (JGI), … that low sequence identity may belie. The technology he’s using is magical; transform any length of amino acid sequence into a smaller, constant-length vector using deep learning. Vector representations allow homology …

… data policies. Since completion of the HGP, the JGI has sustained its commitment to uploading sequence data generated on behalf of its user community to NCBI as well as to the  data portals that … the DOE mandate to provide data access widely to the scientific community as soon as possible after data generation …

… scant, Ace Lake’s bacteria instead go through a boom and bust cycle aligned with light availability. A long-running … cycling takes place only on a microbial level. Previous studies focused on the Southern Ocean have found that in … with a combination of marine and freshwater below. This stratified mixture holds oxygenated water up top and anoxic …

… Studying the  genomes of microorganisms is incredibly useful for understanding the microbiome of the earth, but … To access the genomes of uncultured  microbes , scientists usually employ two different methods; shotgun metagenomic … and most genomes that were acquired through it were usually only around 30% complete.  Described in  ISME …

… Researchers report a new reference genome for eucalyptus in the July edition of the journal G3 Genes | Genomes | … , with significant advances compared to the 2014 Eucalyptus grandis reference genome that has been widely adopted. … analyses.   The Impact There are 900 species of eucalyptus. The trees are fast-growing plantation crops that supply …

… The Science The first step in the deadly dance between a virus and microbial cell is an embrace. For a virus with a “head-tail” morphology, this means using proteins on its tail fibers to latch onto a specific … Energy under contract no. DE-AC02-05CH11231. This research used resources of the National Energy Research Scientific …

… Joint Genome Institute (DOE JGI), a DOE Office of Science user facility, Keedrian Olmstead was back on campus at the University of California, Merced to start … or early November, at which time they will receive certificates. With Olmstead and Lawrence back on campus, Visel …

… are made up heavily of sphagnum mosses.  New research identifies sex chromosomes in the plant and illuminates the … boggy wetlands produces an estimated 5% of annual greenhouse gas emissions. Understanding how sphagnum, a primary … their role as carbon sources. Summary Sphagnum, a genus of just under 400 mosses that can carry up to 25 times …

… have successfully automated aspects of a commonly-used process for studying microbial communities, with … method to the study of a particular fungi, researchers identified novel interactions between bacteria and the fungi. … The Impact Stable isotope probing is a long and laborious process — as well as a key way scientists study …

… The Impact Traditional methods for breaking down biomass use aerobic methods (those using oxygen) to remove lignin and transform the remaining … with JBEI. The JGI data portals and pipelines helped identify potential genes responsible for lignin deconstruction. …

… CheckV can help researchers assess virus sequence fragments and data quality. The Science Through … technologies and computational approaches, more and more virus sequences are being recovered and identified from environmental samples (metagenomes). However, …

… between the JGI and the information technology company Truss has resulted in the JGI Data Portal , a pilot download … processes from the other JGI Portals, as well. “For thousands of scientists around the world, the JGI Genome Portal … , and PhycoCosm , serve researchers with unique areas of focus and data and computational needs. Over its 23-year …