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Automated group assignment in large phylogenetic trees using GRUNT: GRouping, Ungrouping, Naming Tool
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Microbiome engineering for sustainable agriculture: using synthetic biology to enhance nitrogen metabolism in plant-associated microbes
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A Practical Approach to Using the Genomic Standards Consortium MIxS Reporting Standard for Comparative Genomics and Metagenomics
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Extracting Protein-Protein Interactions (PPIs) from Biomedical Literature using Attention-based Relational Context Information
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Genome-wide fitness profiling reveals molecular mechanisms that bacteria use to interact with Trichoderma atroviride exometabolites
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W. Berkeley Kauffman
… Berkeley is responsible for receiving and processing user samples. His R&D work focuses on the development of new applications utilizing a variety of technologies to improve the JGI’s capabilities in the areas of metagenomics, …
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Mining Public Databases Yields Largest Map of Fungal Mitochondrial Genomes to Date
… By leveraging new tools and large-scale data mining, JGI researchers nearly tripled the available fungal … (DOE) Joint Genome Institute (JGI), a DOE Office of Science user facility at Berkeley Lab, addressed this gap in a … (https://ror.org/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the …
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Promoting the Power of Viral Metagenomics
… summarizing the field of viral metagenomics, authored by JGI researchers Lee Call,  Stephen Nayfach and  Nikos … published in the journal  Annual Review of Biomedical Data Science . The following guest piece was written by Call, a postdoctoral fellow in the JGI Microbiome Data Science Group led by Kyrpides. Since early 2020, people …
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Supercharging SIP in the Fungal Hyphosphere
… and fungi The Science Researchers have successfully automated aspects of a commonly-used process for studying … of Energy Joint Genome Institute, a DOE Office of Science User Facility at Lawrence Berkeley National Laboratory, have … HT-SIP is a capability available to request through  the JGI proposal calls . …
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New Lineages of Life Group
… Our research is focused on the discovery and characterization of novel bacterial, archaeal and eukaryotic microbes and viruses in environmental sequence data. We use multi-omics (metagenomics, metatranscriptomics, single cell genomics and phylogenomics) … Exploring the fascinating world of giant viruses, which challenge our …
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Identification of beneficial and detrimental bacteria impacting sorghum responses to drought using multi-scale and multi-system microbiome comparisons
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Identification of Cellulose-Responsive Bacterial and Fungal Communities in Geographically and Edaphically Different Soils by Using Stable Isotope Probing
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