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… Highlighting the latest interactive version of the JGI’s plant data portal. On August 6, 2021,  version … and only, version of Phytozome accessible as an interactive website. Since May 2019, v12 has not had any additional … v13. Why is it necessary to retire Phytozome v12? The codebase for Phytozome v12 was first deployed (as the foundation …

… In a special issue of mSystems , out May 14, 2019, JGI researchers are among the authors who offer … uncultivated, Roux outlines what’s been achieved thus far based on computational predictions, and future directions … sequencing and computational analysis that enable systems-based scientific approaches to these challenges.  DOE’s …

… how these microbes respond and adapt to environmental changes. Summary Researchers have been utilizing metagenomics as a way to study a collection of hard-to-culture microbes, but the efficacy of this … of the Emerging Technologies Opportunity Program in 2013, a team of researchers has been working on improving …

… to expression, scientists can now opt for various shades of grey. The ability to fine-tune the level of gene … Laboratory (Berkeley Lab). Researchers used a library-based approach to fine-tune gene expression. They tested … Alper and his team also applied this method to a production-based scenario, in this case, the production of …

… in their chosen field or fields through the publication of multiple highly cited papers during the last decade” by … Those from the JGI whose publications rank in the top 1% by citations for field and publication year are: Igor … that identifies and classifies mobile genetic elements based upon their gene content and their genetic sequences. …

… For the first time, a team analyzes the transcriptomes of a lichen fungus and alga to understand their partnership … Asterochloris glomerata . To see how gene expression changes when living together versus apart, the team grew the … including those involved in carbon and nitrogen exchange between the lichen partners. This genomic and …

… In honor of the JGI's 25th anniversary in 2022, we have revisited a … to more sustainable energy production.  However, less than 10% of the microbes found in any environment can be grown in … over 27,000 microbial genes. These genes were identified based on their potential to efficiently degrade …

… annotation in fungal genomes. The Science In a proof-of-concept study, researchers demonstrated that a new … closest relative S. paradoxus at high temperatures (39°C/102°F). The Impact One of the challenges in understanding … The work conducted by the US Department of Energy Joint Genome Institute, a DOE Office of Science …

… Interns contributed to a number of projects, from refining lab protocols at the bench to … a DOE Office of Science User Facility. This year, the 12th JGI-UC Merced cohort consisted of three undergraduate … Brandon Barana Mentor: Zhong Wang Project:  Embeddings Based Clustering of Biosynthetic Gene Cluster for Novel …

… to replicate themselves and spread from cell to cell. Two of the most common forms of MGEs are viruses and plasmids. … called geNomad identifies and classifies MGEs based upon their gene content and their genetic sequences. … the JGI’s  IMG Virus Resource (IMG/VR) , now with more than 15 million viral genomes. It was also key to developing the …

… data portal allows anyone to freely investigate the genes of more than 100 algae. The Science Interested in the genomes of algae? … built-in connection to the DOE Systems Biology Knowledgebase (KBase) also allows researchers to study how …

… and researchers more about the patterns and functions of environmental microbes. Researchers can use the tool to … activity in microbiomes. The initial analysis used over 12,000 metagenomes from diverse environments and grouped … similar microbial communities together. Those similarities, based on their ratios of small DNA sequence fragments called …