Results

Decomposing a San Francisco estuary microbiome using long-read metagenomics reveals species- and strain-level dominance from picoeukaryotes to viruses
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A Natural Mechanism Can Turbocharge Viral Evolution
… Understanding how a fundamental mechanism of evolution allows microbes to adapt to changing environments. The … sampled all at once from the same environment, called metagenomes. Why? Simon Roux, who led the research team and … the dice. There’s some evidence to support the idea. Study coauthor Stephen Nayfach, a JGI bioinformatics …
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Filling in the Plant Tree of Life
… plants and how they adapt to their ever-changing environments better? We could unlock new innovations to drive more productive food, medicine, and bioenergy … genomes are from narrow swaths of the plant tree of life. One project aims to change that. …
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Sequencing Submission Requirements for DNA Synthesis
… Sequence files for all constructs should be emailed to  Miranda Harmon-Smith, Synthetic Biology Project Manager . … File There are several easy-to-use open source tools for converting DNA sequence files into well-formed GenBank files. ApE is an open source desktop application written by M. Wayne Davis or commercial options include …
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Taking Stock of the Known and Unknown Microbial Space
… of Science User Facility located at Lawrence Berkeley National Laboratory Berkeley Lab), have taken stock of the … sequence data generated over the past three decades, their study assesses what fraction of the microbial diversity we … genes on nearly 2 million genomes, including isolates, metagenome-assembled genomes (MAGs) with varying quality …
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Long-term excess nitrogen fertilizer increases sensitivity of soil microbial community to seasonal change revealed by ecological network and metagenome analyses
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High-Quality Draft Genome Sequences of the Uncultured Delta3 Endosymbiont (Deltaproteobacteria) Assembled from Metagenomes of the Gutless Marine Worm Olavius algarvensis
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Metagenomic and Metatranscriptomic Analyses Reveal the Structure and Dynamics of a Dechlorinating Community Containing Dehalococcoides mccartyi and Corrinoid-Providing Microorganisms under Cobalamin-Limited Conditions
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Refinement of the “Candidatus Accumulibacter” genus based on metagenomic analysis of biological nutrient removal (BNR) pilot-scale plants operated with reduced aeration
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A Community Resource for Secondary Metabolite Researchers
… The Secondary Metabolism Collaboratory encourages user engagement. … and secondary metabolites information from isolate and metagenome data.   The SMC ( smc.jgi.doe.gov ) is designed … Expansion of the SMC to include fungal, plant, viral, and metagenome data is currently underway. …
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The Megadata of Lake Mendota - Part 2: Souped Up Computing
… This series is the story of a giant metagenome assembly from Wisconsin’s Lake Mendota. In this episode: a look at the … with the assembler program MetaHipMer2. Oak Ridge National Lab is home to two supercomputers — Summit and Frontier …
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JGI Part of Berkeley Lab Team Awarded Best Use of HPC in Life Sciences
… “ Berkeley Lab Receives Multiple 2021 HPCwire Awards ” on the Berkeley Lab Computing Sciences site. Lawrence Berkeley National Laboratory (Berkeley Lab), the National Energy Research Scientific Computing Center (NERSC), … of Science User Facility  located at Lawrence Berkeley National Laboratory, is committed to advancing genomics in …
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