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Gaia: An AI-enabled genomic context–aware platform for protein sequence annotation
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Learning to Look
… “Where’s Waldo?” readers need to look for a number of distinguishing features. Several characters may be … first worked on a reference dataset that included genome sequences known to be affiliated with the Inoviridae. “What … in every major microbial habitat—including soil, water, and humans—around the world. By the numbers, the new approach …
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Genome Sequence of Thermofilum pendens Reveals an Exceptional Loss of Biosynthetic Pathways without Genome Reduction▿ †
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Genome Calligrapher: A Web Tool for Refactoring Bacterial Genome Sequences for de Novo DNA Synthesis
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Complete Genome Sequence for Asinibacterium sp. Strain OR53 and Draft Genome Sequence for Asinibacterium sp. Strain OR43, Two Bacteria Tolerant to Uranium
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JGI Contributes Eight to 2023 Highly Cited Researchers list
… influence in their chosen field or fields through the publication of multiple highly cited papers during the last decade” by … elements based upon their gene content and their genetic sequences. Roux was first author on a study featuring a new …
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Doubling Down on Known Protein Families
… online Oct. 11, 2023 in  Nature highlights the vast array of functional diversity of microbes through a novel approach … the process hinges on referencing to existing genome sequences.  Some of these proteins are what the scientists … Let’s say somebody is working on soil environments or the human body — they may take some of those families and try to …
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SPRUCE-ing Up Science
… his backyard in Tennessee — the birds are chirping and a soft breeze ripples through the trees in his backyard. … with renowned scientists who were involved in the Human Genome Project, or computational biologists who were … fine tune his approach. “I got a lot of that from Zhong.”   Publication: Carrell AA et al. Habitat-adapted microbial …
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Examples: Successful LOIs & Submissions
… See below for examples of successful Letters of Intent to our Community Science Program Large-Scale Call, … to soil carbon storage during simulated range shifts of plant-fungal symbionts … Elucidation of the gene regulatory networks governing terpenoid-mediated … Characterization of simplified soil communities with high and low carbon use …
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Model Fern Reveals Insight into DNA Thievery in Ferns
… Open Green Genomes hits milestone with C. richardii The Science Fern … — making it difficult to grasp a deeper understanding of fundamental aspects of fern biology and, more broadly, … richardii marks the first published manuscript of a genome sequence generated through the OGG. For a long time, C-fern …
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The Surprising Structure of a Shrub Willow Sex Chromosome
… A genetic architecture that is characteristic of the sex chromosomes of mammals is, for the first time, … first time, the sex chromosomes of shrub willow have been sequenced with sufficient resolution to analyze their … females, a development conferred by its sex chromosomes. In humans, males are “heterogametic”: they have different sex …
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Supercomputing, MetaHipMer and the Mega Dataset of Lake Mendota
… before. In 2006, the JGI produced 33 billion base pairs of sequence; by 2023, that number was almost 717 trillion. … to enable large-scale analysis. The story of a massive metagenome assembly for a time-series experiment from the … The U.S. Department of Energy Joint Genome Institute, a DOE Office of Science …
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