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Deeplasmid: deep learning accurately separates plasmids from bacterial chromosomes
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IMG/PR: a database of plasmids from genomes and metagenomes with rich annotations and metadata
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Metabolomics Program
… The JGI’s Metabolomics Program works to uncover the roles of small molecules in biological systems, linking them with genomic data to enhance our understanding of genome science, organisms, and ecosystems at the … Integrating genomics with metabolomics fuels the discovery  of novel metabolites, genes, and proteins. It also enables …
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Natural Prodcast Episode 2: The Primer, Part 2
… DAN: You’re listening to the US Department of Energy Joint Genome Institute’s “Natural Prodcast,” a podcast about the science and scientists of secondary metabolism.  DAN: Hi, again. This is Dan, and … is a bacterial sacred metabolite, and ergot alkaloids come from fungi, and Taxol from plants. Plants, fungi, bacteria, …
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You Can Move, But You Can’t Hide
… and accurately identify mobile genetic elements like plasmids and viruses. The Science Mobile genetic elements … seek to replicate themselves and spread from cell to cell. Two of the most common forms of MGEs are viruses and plasmids. … The U.S. Department of Energy Joint Genome Institute …
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Plasmids captured in C. metallidurans CH34: defining the PromA family of broad-host-range plasmids
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Who We Are
…   The U.S. Department of Energy (DOE) Joint Genome Institute (JGI) is a national … at Lawrence Berkeley National Laboratory. The JGI consists of 225 researchers and support staff in the Integrative … The U.S. Department of Energy (DOE) Joint Genome Institute (JGI) is a …
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User Programs
… and analysis will be paid for by the Department of Energy’s funding of the JGI. There is no cost to the user … Letters of Intent and must use a variety of capabilities at two or more user facilities. Proposals must be preceded by … and metabolomics. Proposals must request capabilities from both JGI and the Molecular Foundry.  Submission …
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DOE Metrics
… (Trillions) Operating Hours Goal  Actual Total*   Actual % of Goal   Goal (hours)**   Actual Total   Actual % Goal   FY … platforms. **Operating Hours target is based on 98% of the total available hours.   FY 2025 DOE Metrics There … Hours reflect a delay in implementation of the LIMS from Q2 to Q3. As a result of the delay in the LIMS …
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Unveiling plasmid diversity in nature
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Natural Prodcast Episode 3: The Primer, Part 3
… DAN: You’re listening to the US Department of Energy Joint Genome Institute’s “Natural Prodcast,” a … out, you probably want to go back and listen to the first two parts ( part 1 is here and part 2 is here ) so you … maybe it’s a new culture of a new bacteria that you pulled from the soil, maybe it’s, you know, we talked about …
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JGI@25: Tracking & Subduing the Plague of California’s Oak Woodlands
… sojae, which imperils soybean harvests. The subsequent comparative analysis of these two pathogens, led by the JGI … was released to the public in a highly-cited 2006 publication in the journal Science . This provided a … to their lab in Mulford Hall. There, they conducted DNA analyses of samples collected on recent SOD Blitz …
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