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Nontargeted virus sequence discovery pipeline and virus clustering for metagenomic data
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JGI@25: Cow Rumen and the Early Days of Metagenomics
… In honor of the JGI's 25th anniversary in 2022, we have revisited a number of notable achievements that showcase our collaborations and …
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Mindfully Moving JGI
… JGI is in the process of shifting its operations from Walnut … than 100 at its peak, all the machines were switched off. Over the next two weeks, they were crated, shipped to, and … runs before the end of the week. “One week up and operating is a great story and a testament to our extensive …
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JGI Contributes Eight to 2023 Highly Cited Researchers list
… to the 2023 Highly Cited Researchers from the JGI recognized for their “significant influence in their chosen field or fields through the publication of multiple highly cited papers during the last decade” by …
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SIPs with Standards
… catch: SIP labwork and analysis can be very demanding.  The JGI offers SIP analysis to make these experiments accessible to … ways they're working to make this technique, SIP, more standardized -- more reproducible, more reusable, and more …
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A standardized quantitative analysis strategy for stable isotope probing metagenomics
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FunGAP: Fungal Genome Annotation Pipeline using evidence-based gene model evaluation.
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A global metagenomic map of urban microbiomes and antimicrobial resistance
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Improved Assemblies Using a Source-Agnostic Pipeline for MetaGenomic Assembly by Merging (MeGAMerge) of Contigs
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How to Target a Microbial Needle within a Community Haystack
… A workflow for capturing the genetic make-up of specific uncultivated microbes from complex environmental … worked with researchers at the U.S. Department of Energy (DOE) Joint Genome Institute (JGI), a DOE Office of Science … in situ hybridization (HCR-FISH). In contrast to standard FISH where a one probe adds one fluorescent …
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Toward a Standards-Compliant Genomic and Metagenomic Publication Record
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Rex Malmstrom
… Dr. Malmstrom is a Staff Scientist and leader of the Microscale Applications group. Before joining the JGI in 2010, he made the first ever measurements of in situ … that require fluorescence activated cell sorting and non-standard molecular protocols.  Finally, his team utilizes …
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