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Decoding the massive genome of loblolly pine using haploid DNA and novel assembly strategies
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Mining Public Databases Yields Largest Map of Fungal Mitochondrial Genomes to Date
… (DOE) Joint Genome Institute (JGI), a DOE Office of Science user facility at Berkeley Lab, addressed this gap in a … in the JGI's IMG portal for mitochondrial ribosomal RNA sequences. The next step applied metagenomic binning … genome assemblies in the National Center for Biotechnology Information's GenBank. This led to identifying 6,467 of …
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Biotech Partners Summer Intern Co-Authors NAR Paper
… “This exercise helped us in filling or updating geographic information for nearly 1,100 samples,” said Reddy. Kaushal also reviewed and assigned … name and IDs for nearly 20,000 public/private mtagenome biosamples in GOLD. “Besides these, he curated several small …
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Ray Turner Completes Last Tour of Lab Duty at JGI
… wife Deb, delivered a mask for Ray to wear and a red carnation lei flown in from Maui, care of the Admin Group’s … Officer). “You define the word ‘collegial’” “Every user facility at this Laboratory needs to have a great … to the ever-shifting landscape of funding Federal for programs, noted that “Ray is someone who just will get it …
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From Berkeley to Binghamton: Tracking Strawberry Evolution
… missing from the analysis (due to extinction or you didn’t sample it). But once we deciphered the subgenomes we came up …
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JGI@25: Cow Rumen and the Early Days of Metagenomics
… biofuels . Since one of the challenges of developing alternative fuels from plants is the high cost and resource … and then extrapolating data obtained from environmental samples — to identify over 27,000 microbial genes. These … into genes and even into genomes — from these environmental samples,” said Matthias Hess, first author on the paper and …
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Help from Citrus’ Bitter, Hardier Cousin
… (DOE) Joint Genome Institute (JGI), a DOE Office of Science User Facility located at Lawrence Berkeley National … authors of the  recent study published in  The Plant Journal.  this study included the discovery of candidate genes … of Energy Joint Genome Institute, a DOE Office of Science User Facility  located at Lawrence Berkeley National …
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Tracking the roots of cellulase hyperproduction by the fungus Trichoderma reesei using massively parallel DNA sequencing
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Busting the Unbreakable Lignin
… of Energy Joint Genome Institute, a DOE Office of Science User Facility at Lawrence Berkeley National Laboratory, and … for lignin deconstruction. (The JGI also conducted RNA sequencing and alignment to the reference fungal  genome … (https://ror.org/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the …
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Inspiring STEM Careers Through a Hands-on Everglades Microbiome Study
… Journal publication caps JGI pilot project with fledgling … (DOE) Joint Genome Institute (JGI), a DOE Office of Science User Facility located at Lawrence Berkeley National … with the proper permits, to the refuge to collect soil samples from multiple locations. Back in the classroom, JGI …
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An Automated Tool for Assessing Virus Data Quality
… are being recovered and identified from environmental samples (metagenomes). However, the quality and completeness … (DOE) Joint Genome Institute (JGI), a DOE Office of Science User Facility located at Lawrence Berkeley National … and guidelines for providing the minimum amount of information for an uncultivated virus genome. CheckV has …
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Dan Rokhsar
… Program (2010-2019), and JGI Chief Informatics Officer (2013-2016). Dr. Rokhsar joined the faculty of University of …
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