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Tracking Microbial Succession in Petroleum Wells
While shifting toward more sustainable, alternative energy sources, people still rely on fossil fuels for energy and transportation fuels. Understanding how microbial communities in subsurface petroleum reservoirs are impacted by human activity, and how their responses can sour oil production, can influence oil industry practices.
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Insights into A Eukaryotic Alga
Through the DOE JGI's Community Science Program, a 50-member team led by University of Maine, Carnegie Institution for Science, and East Carolina University researchers sequenced and analyzed the genome of the red alga Porphyra umbilicalis.
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New Technology to Access Microbial Dark Matter
Enabled by the DOE JGI's Emerging Technology Opportunity Program, Stanford researchers extracted 29 novel microbial genomes from Yellowstone hot spring samples while still preserving single-cell resolution to enable accurate analysis of genome function and abundance.
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Our Projects
Comparative and Population Genomics of Xylariaceae
A genomic survey of the Xylariaceae, one of the largest and most diverse families of fungi made up of endophytic, pathogenic, and saprotrophic (including wood degrading) species.
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Gene Atlases of Grass-Microbe Interactions
This proposal seeks to build comprehensive gene atlas maps for diverse bioenergy grass-microbe interactions, including pathogenic and beneficial interactions in two grass models, Brachypodium and Setaria.
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Quantifying Cyanobacteria Interactions
The long term objective is to quantify dynamic interactions between phototrophs and their virus predators. This will help to build quantitative, dynamic and predictive models of host-viral interactions and the effect on carbon and nutrient cycling.
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Data & Tools
- IMG
- Genome Portal
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DOE JGI Database of DNA viruses and retroviruses debuts on IMG platform
In a series of four articles published in the Database issue of the Nucleic Acids Research journal, DOE JGI researchers report on the latest updates to several publicly accessible databases and computational tools that benefit the global community of microbial researchers.
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Benchmark Study for Improving Microbial Community Profiling
Researchers used synthetic and natural microbial lake communities to compare the microbial community profiles generated from high throughput short-read sequencing and high throughput long-read sequencing approaches.
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Better Microbial Genome Binning with MetaBAT
An automated tool called MetaBAT that automatically groups large genomic fragments assembled from metagenome sequences to reconstruct single microbial genomes.
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User Program Info
2018 DOE JGI Community Science Program Allocations Announced
“These new CSP projects demonstrate further growth into multi-omics and bring exciting new investigators, ideas and approaches to the application of genomics to DOE mission science."
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Meet a JGI User: C. Titus Brown
"JGI is one of the only places that invests systematically and heavily in non-biomedical sequencing. This has tremendously enriched our knowledge of everything from microbes involved in biogeochemical cycling to organisms that are very evolutionarily distant."
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DOE User Facilities Partner for Greater Scientific Impact
A total of 14 proposals were selected from a joint JGI-EMSL call for 2018 research under the Facilities Integrating Collaborations for User Science (FICUS) initiative. This is the This was the fifth FICUS call between EMSL and JGI since the collaborative science initiative was formed in 2014.
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News & Publications
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Tracking the Viral Parasites of Giant Viruses over Time
In Nature Communications, using metagenome data sets collected over several years in northern freshwater lakes, a team effectively doubled the number of virophages known since their discovery a decade ago.
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Liverwort Genes and Land Plant Evolution
Genome analysis of the common liverwort (Marchantia polymorpha) identified genes and gene families that were deemed crucial to plant evolution and have been conserved over millions of years and across plant lineages.
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Benchmarking Computational Methods for Metagenomes
Results from the Critical Assessment of Metagenome Interpretation (CAMI) Challenge, the first-ever, community-organized benchmarking assessment of computational tools for metagenomes.
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January 10, 2015

JGI @ PAG XXIII Brochure

JGI @ PAG XXIII Brochure

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