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Learning to Look
… by scientists at the U.S. Department of Energy (DOE) Joint Genome Institute (JGI), a DOE Office of Science User … are filamentous viruses with small, single-stranded DNA genomes and a unique chronic infection cycle. “We’re not … and metagenome datasets, ultimately identifying more than 10,000 inovirus-like sequences compared to the 56 previously …
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Exploring the Diversity of the American Prairie’s Switchgrass
… potential biofuel feedstock. But switchgrass has a complex genome and, as a species, encompasses dizzying diversity. …
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Crysten Blaby-Haas
… user capability between the JGI and Molecular Foundry for genome-encoded biomaterial discovery, design, and … the heme-binding split-barrel family. J Biol Chem  300(11), 107888. Grosjean N, Yee EF, Kumaran D, Chopra K, Abernathy … into the red algae and eukaryotic evolution from the genome of Porphyra umbilicalis (Bangiophyceae, Rhodophyta). …
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Extracting the Secrets of Secondary Metabolites
… Repeats) is the leading tool for accurately editing genomes, its effectiveness has historically been limited due … CRAGE (Chassis-independent Recombinase-Assisted Genome Engineering) is a technique researchers can use to … users of the U.S. Department of Energy (DOE) Joint Genome Institute (JGI), a DOE Office of Science User …
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A User-Centered Approach to Accessing JGI Data
… When we have a calculation for automatically determining which datasets are unrestricted and which are not, we … metadata criteria. Wilson said that the Data Portal and  Genome Portal will continue to run in parallel for now. Eventually, he added, the Genome Portal will be retired once the same features are …
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An Age of CRAGE: Advances in Rapidly Engineering Non-model Bacteria
… that allows researchers to quickly modify diverse bacterial genomes. In 2019, the JGI’s Yasuo Yoshikuni and his team  … of DNA (up to 60 kb) in a single step, directly into the genome. “CRAGE is central to our ability to offer … engineering system that allows scientists to conduct genome-wide screens and explore biosynthetic pathway. Thus …
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Integrating Experimentation with Data
… $250     Industry: $700    Thanks for joining the Joint Genome Institute (JGI) and the Environmental Molecular …
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2025 Progress Report
… Biological and Environmental Research program, the Joint Genome Institute provides advanced genomic capabilities, …
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Mapping Heat Resistance in Yeasts
… A new approach for improving functional annotation in fungal genomes. The Science In a proof-of-concept study, … closest relative S. paradoxus at high temperatures (39°C/102°F). The Impact One of the challenges in understanding … including biofuel production. Efforts such as the 1000 Fungal Genomics Project led by the DOE Joint Genome …
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JGI Early Career Researchers Featured in mSystems Special Issue
… Micro-Scale Applications head Rex Malmstrom and Metagenome Program head Emiley Eloe-Fadrosh outline more … processes. A third approach steps away from reconstructing genomes directly from the environment and focuses on … planet’s viral diversity has advanced drastically, aided by genome assembly from metagenomes. This is a critical step …
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Doubling Down on Known Protein Families
… of scientists at the U.S. Department of Energy (DOE) Joint Genome Institute (JGI), a DOE Office of Science User … families. From there they focused on families with at least 100 members.  “If you have 100 sequences, the quality of the cluster is significantly …
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Accelerating Metagenomics Discoveries with Deep Learning
… biologist at the US Department of Energy (DOE) Joint Genome Institute (JGI), presented on generating vector … to vectorize protein sequences. Sevim is part of the JGI Genome R&D Group and is one of more than 100 scientists and systems engineers involved in …
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