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An Integrated Computer-Aided Design and Manufacturing Workflow for Synthetic Biology
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Integrative analysis of multimodal mass spectrometry data in MZmine 3
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Designer DNA: JGI Helps Users Blaze New Biosynthetic Pathways
… cell is key to interrogating what genes do, how they work, and applying them to environmental and energy challenges. … the JGI enables large-scale synthesis support, sequencing, integrative -omics, and data mining, empowering research … more than 10 papers, including two Nature Plants publications, in five years, have come out of the …
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Open Frameworks Training the Next Generation of Scientists
… Educational training technologies provide opportunities for students and professors alike The Science In  PLoS Pathogens , a team … and discovery environment designed for reproducible computational biology analysis. KBase also supports  … MycoEd receives organizational and developmental support from KBase (The …
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Simon Roux
… His responsibilities include the development of novel computational tools to identify virus sequences, the design of new experimental approaches to link viruses to their host(s), collaboration with JGI users for analyzing viral datasets, and the organization of …
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Finding the Fermenters
… Harnessing BER-funded data resources, researchers built an interactive and comprehensive database of fermentative prokaryotes. The Science Most organisms use … the range of bacteria and archaea that rely on this form of metabolism, researchers recently compiled a list of …
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JGI@25: Using Team Science to Build Communities Around Data
… In honor of the JGI's 25th anniversary in 2022, we have revisited a number of notable … a 2012 Community Science Program proposal. Joseph Spatafora of Oregon State University led the effort to sequence … genomes that are both large and complex. The first publication of a genome generated by the OGG initiative — …
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Natural Prodcast Episode 2: The Primer, Part 2
… DAN: You’re listening to the US Department of Energy Joint Genome Institute’s “Natural Prodcast,” a … so secondary metabolism is throughout nature, except maybe for animals and humans, not as much. You know, we have this … Episode Transcript … continues a conversation from the first episode . You can go to part 3 here . You can find the podcast on  Apple ,  …
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Mapping the Earth’s Hidden Fungal Kingdom
… comparative genomics to decode millions of mystery genes and lay a future-ready foundation     Over the past billion … Earth's fungal kingdom. The manuscript reviews about 200 publications linking evolutionary history and innovations … be used for machine learning and artificial intelligence approaches for prediction of fungal lifestyles based on …
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For the Tiniest Archaea, A Genomic Switch of Friend or Foe
… mutualism or parasitism between some archaeal hosts and their hitchhikers. The Science Within the archaeal domain, there is a group of tiny hitchhikers. These organisms are abundant and yet … how these hosts and hitchhikers coexist is key for understanding their impact on wider ecosystems, but …
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Fishing for Novel Cellulose Degraders
… A “bait and hook” single-cell genomic approach to bioprospecting. The Science One of the most vital pieces of equipment for fly fishing is a boxful of lures. Designed with feathers … of Energy, Office of Science, Office of Biological and Environmental Research, through contract …
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DAP-seq Drives Robust Mapping of Gene Regulation
… Multi-species assays yield an unprecedented view of plant evolution and adaptation.    … maps. Together, the scale of data enabled by these approaches creates a vast resource offering researchers the … said Sharon Greenblum, a co-first author on the paper and computational biologist at the JGI. “We had to work really …
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