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Toward More Reproducible, Reusable Stable Isotope Probing Experiments
… As SIP experiments shed more light on microbial communities than ever before — especially with … participation — is especially important in microbial ecosystems. These communities harbor tens of thousands of … microbes cycle nitrogen and carbon, or how freshwater ecosystems process methane and organic matter.  However, to get …
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Introducing New Members of the JGI User Executive Committee
… Committee (UEC) – Jack Gilbert, Ashley Shade, and Jason Stajich! They join six other JGI users already serving on the UEC – go here to view the full roster of members. … efforts with diversity, equity and inclusion in mind. Microbiome ecologist Shade became Director of Research at …
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Promoting the Power of Viral Metagenomics
… piece was written by Call, a postdoctoral fellow in the JGI Microbiome Data Science Group led by Kyrpides. Since early 2020, people all over the world have been forced to confront the awesome power that viruses have to affect nearly … sequencing and computational analysis that enable systems-based scientific approaches to these challenges.  …
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RECAP: Multi-Omic Journeys with 2023 JGI Annual Meeting Keynotes
… attendees joined the JGI Annual Genomics of Energy & Environment Meeting.  A wide array of invited speakers shared how … the conference, sharing the journeys of their research careers, and showcasing the broad applications of their … and new views of how nutrients cycle through ecosystems. Of course, some of those collaborators, like Jennifer …
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Discovery of a novel filamentous prophage in the genome of the Mimosa pudica microsymbiont Cupriavidus taiwanensis STM 6018
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Dealing with Drought: Uncovering Sorghum’s Secrets
… Over 40 percent of the cereal crop’s genes respond to drought stress. The Science Fields of drooping stalks and cracked earth are becoming common images in many regions due to more extreme weather events … and how these conditions impact the crop and its microbiome. For three consecutive years (2016-2018), …
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JGI Contributes Nine to 2022 Highly Cited Researchers List
… list features 6,900 researchers working in 21 fields.  Congratulations to the  2022 Highly Cited Researchers from the JGI … article detailing how forest floors, in particular the soil microbiome, recover post-wildfire . He and  Tringe were also … sequencing and computational analysis that enable systems-based scientific approaches to these challenges.  …
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JGI Launches Latest Strategic Plan
… Genome Institute, the end of 2018 was marked by a celebration of contributing over one “petabase” – a quadrillion nucleotide … JGI supports, include JGI’s emerging leadership role in a Microbiome Data Science effort (pages 37-39) and the …
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Mining Metagenomes for Cas Proteins
… mining the datasets in the Integrated Microbial Genomes and Microbiomes (IMG/M) suite of tools managed by the U.S. … to accurately edit genomes (that is, repair gene mutations, and either delete or add genes in a precise fashion) … on genome editing has focused on the seminal CRISPR-Cas9 system, which targets double-stranded DNA. The discovery of …
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A Sorghum Pangenome Opens More Doors to Discovery
… holds keys to drought and flood resilience, biomass production for fuels, and growth in poor soils. In addition to … and Environmental Research (BER) program to apply systems biology approaches to plants relevant to national … when picked. Wild plants will ‘shatter’ their seeds off a stem to distribute them, but domesticated lines were …
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Forming Scientific Connections and Building Community
… and seven graduate students from UC Merced through their long standing internship program. In just two months, the … and what they’ll take with them as they go forward in their careers.   Listed below are the interns, their mentors, and … Project: “ Development of a multiplex genomic integration system for the selection of genes essential for specialized …
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Supercomputing, MetaHipMer and the Mega Dataset of Lake Mendota
… over the last  25-plus years since the JGI’s inception, making it possible for researchers to get a close look at more ecosystems and organisms than ever before. In 2006, the JGI … They may also provide a basic understanding of the roles microbiomes play in determining the behavior of the physical …
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