DOE Joint Genome Institute

  • COVID-19
  • About Us
  • Contact Us
  • Our Science
    • DOE Mission Areas
    • Science Programs
    • Science Highlights
    • Scientists
    A vertical tree stump outdoors with about a dozen shiitake mushrooms sprouting from its surface.
    Tracing the Evolution of Shiitake Mushrooms
    Understanding Lentinula genomes and their evolution could provide strategies for converting plant waste into sugars for biofuel production. Additionally, these fungi play a role in the global carbon cycle.

    More

    Soil Virus Offers Insight into Maintaining Microorganisms
    Through a collaborative effort, researchers have identified a protein in soil viruses that may promote soil health.

    More

    Data yielded from RIViT-seq increased the number of sigma factor-gene pairs confirmed in Streptomyces coelicolor from 209 to 399. Here, grey arrows denote previously known regulation and red arrows are regulation identified by RIViT-seq; orange nodes mark sigma factors while gray nodes mark other genes. (Otani, H., Mouncey, N.J. Nat Commun 13, 3502 (2022). https://doi.org/10.1038/s41467-022-31191-w)
    Streamlining Regulon Identification in Bacteria
    Regulons are a group of genes that can be turned on or off by the same regulatory protein. RIViT-seq technology could speed up associating transcription factors with their target genes.

    More

  • Our Projects
    • Search JGI Projects
    • DOE Metrics/Statistics
    • Approved User Proposals
    • Legacy Projects
    A panoramic view of a lake reflecting a granite mountain.
    Genome Insider: Methane Makers in Yosemite’s Lakes
    Meet researchers who sampled the microbial communities living in the mountaintop lakes of the Sierra Nevada mountains to see how climate change affects freshwater ecosystems, and how those ecosystems work.

    Listen

    A light green shrub with spiny leaves, up close.
    Genome Insider: A Shrubbier Version of Rubber
    Hear from the consortium working on understanding the guayule plant's genome, which could lead to an improved natural rubber plant.

    Listen

    The switchgrass diversity panel growing at the Kellogg Biological Station in Michigan. (David Lowry)
    Mapping Switchgrass Traits with Common Gardens
    The combination of field data and genetic information has allowed researchers to associate climate adaptations with switchgrass biology.

    More

  • Data & Tools
    • IMG
    • Data Portal
    • MycoCosm
    • PhycoCosm
    • Phytozome
    • GOLD
    iPHoP image (Simon Roux)
    iPHoP: A Matchmaker for Phages and their Hosts
    Building on existing virus-host prediction approaches, a new tool combines and evaluates multiple predictions to reliably match viruses with their archaea and bacteria hosts.

    More

    Abstract image of gold lights and squares against a black backdrop
    Silver Age of GOLD Introduces New Features
    The Genomes OnLine Database makes curated microbiome metadata that follows community standards freely available and enables large-scale comparative genomics analysis initiatives.

    More

    Graphical overview of the RNA Virus MetaTranscriptomes Project. (Courtesy of Simon Roux)
    A Better Way to Find RNA Virus Needles in the Proverbial Database Haystacks
    Researchers combed through more than 5,000 data sets of RNA sequences generated from diverse environmental samples around the world, resulting in a five-fold increase of RNA virus diversity.

    More

  • User Programs
    • Calls for Proposals
    • Special Initiatives & Programs
    • Product Offerings
    • User Support
    • Policies
    • Submit a Proposal
    Green plant matter grows from the top, with the area just beneath the surface also visible as soil, root systems and a fuzzy white substance surrounding them.
    Supercharging SIP in the Fungal Hyphosphere
    Applying high-throughput stable isotope probing to the study of a particular fungi, researchers identified novel interactions between bacteria and the fungi.

    More

    Digital ID card with six headshots reads: Congratulations to our 2022 Function Genomics recipients!
    Final Round of 2022 CSP Functional Genomics Awardees
    Meet the final six researchers whose proposals were selected for the 2022 Community Science Program Functional Genomics call.

    More

    croppe image of the JGI helix sculpture
    Tips for a Winning Community Science Program Proposal
    In the Genome Insider podcast, tips to successfully avail of the JGI's proposal calls, many through the Community Science Program.

    Listen

  • News & Publications
    • News
    • Blog
    • Podcasts
    • Webinars
    • Publications
    • Newsletter
    • Logos and Templates
    • Photos
    2022 JGI-UC Merced interns (Thor Swift/Berkeley Lab)
    Exploring Possibilities: 2022 JGI-UC Merced Interns
    The 2022 UC Merced intern cohort share how their summer internship experiences have influenced their careers in science.

    More

    image from gif that shows where in the globe JGI fungal collaborators are located.
    Using Team Science to Build Communities Around Data
    As the data portals grow and evolve, the research communities further expand around them. But with two projects, communities are forming to generate high quality genomes to benefit researchers.

    More

    Cow Rumen and the Early Days of Metagenomics
    Tracing a cow rumen dataset from the lab to material for a hands-on undergraduate research course at CSU-San Marcos that has since expanded into three other universities.

    More

All JGI Features
Home › Archives for David Gilbert
Page 1 of 1612345...10...»Last »

January 7, 2016

JGI at PAG XXIV

JGI will be sharing a booth (#202) at The Plant and Animal Genome XXIV Conference (PAG) in San Diego from Sunday, January 10 through Tuesday, January 12, 2016 with our colleagues from KBase: The Department of Energy Systems Biology Knowledgebase. Also, on Tuesday, January 12, 2016 from 4:00-6:10 pm in the San Diego Room, join us… [Read More]

February 6, 2014

A cool glass of clean drinking water

A new system called ScanDrop could revolutionize how we identify pathogens in drinking water. The Science: Researchers from Lawrence Berkeley National Laboratory (the Joint BioEnergy Institute and the DOE Joint Genome Institute) and Northeastern University and the Massachusetts General Hospital/Harvard Medical School) have developed a portable, network-enabled system for testing drinking water contamination. The system, called ScanDrop, developed by… [Read More]

January 30, 2014

Ocean sponge-dwelling bacteria have hidden talents

Ocean sponge-dwelling bacteria have hidden talents. The kidney-red coral reef sponge, Theonella swinhoei, is a source of several anti-fungal and anti-cancer drug candidates. These compounds aren’t produced by the sponge itself, but by symbiotic bacteria that live inside it. The compounds in question are called polyketides, secondary metabolites that happen to be made by just two… [Read More]

January 28, 2014

Faster, bigger, stronger: improvements to two of JGI’s genome databases

Capacities for DOE JGI’s twin genome analysis systems, IMG and IMG/M have both been expanded in the last two years. The Science: The DOE Joint Genome Institute maintains the Integrated Microbial Genomes (IMG) data warehouse, which contains a rich collection of genomes from all three domains of life. IMG/M provides a similar collection of microbial… [Read More]

January 17, 2014

Fresh water and marine SAR11 bacteria – distant relatives and different lives

Researchers assembled genomes from several single-cell isolates of the SAR11 group of Alphaproteobacteria and found that they form microclusters within the freshwater clade. [Read More]

January 10, 2014

ENVO brings structure to biological “environments”

New tool aims to help life science researchers formalize naming conventions for the environments they study. The Science: Biological and biomedical research is increasingly referencing and compiling data from environmental samples, leading to a growing need for a formal and standardized approach to describing those environments. The Environment Ontology (ENVO; www.environmentontology.org) is a community-led, open-access… [Read More]

January 6, 2014

Out with the old, in with the new, improved Genome Portal

The newest iteration of the DOE Joint Genome Institute’s and analytical tools sports improved user interface and infrastructure. The Science: The DOE Joint Genome Institute’s massive genomic database and data management system, the Genome Portal (http://genome.jgi.doe.gov), has recently been upgraded with a more robust infrastructure to manage the torrent of genomic data available and a… [Read More]

December 20, 2013

Surprising finds in a rare plant’s mitochondrial genome

Rare and ancient plant gobbles up entire mitochondria from other plants and holds onto them for eons. The Science: One of the oldest flowering plants, Amborella trichopoda, split off from the lineage of other flower plants about 200 million years ago. Analysis reveals that it has a record-setting amount of foreign DNA in its mitochondria,… [Read More]

December 20, 2013

A gluttonous plant reveals how its cellular power plant devours foreign DNA

Amborella trichopoda, a sprawling shrub that grows on just a single island in the remote South Pacific, is the only plant in its family and genus. It is also one of the oldest flowering plants, having branched off from others about 200 million years ago. Now, researchers from Indiana University, with the U.S. Department of… [Read More]

December 13, 2013

One big family: Understanding the Polyporales phylogenetic and phylogenomic trees

Looking at a combination of whole genomes and gene databases suggests a new way to examine this fungus family tree. The Science: Researchers reviewed 10 currently available whole genomes, comparing them to known gene datasets. They reported family trees for several taxonomic subgroupings called clades. They also analyzed several single-copy genes to assess them for… [Read More]
Page 1 of 1612345...10...»Last »

More topics:

  • COVID-19 Status
  • News
  • Science Highlights
  • Blog
  • Webinars
  • CSP Plans
  • Featured Profiles
  • Careers
  • Contact Us
  • Events
  • User Meeting
  • MGM Workshops
  • Internal
  • Disclaimer
  • Credits
  • Policies
  • Emergency Info
  • Accessibility / Section 508 Statement
  • Flickr
  • LinkedIn
  • RSS
  • Twitter
  • YouTube
Lawrence Berkeley National Lab Biosciences Area
A project of the US Department of Energy, Office of Science

JGI is a DOE Office of Science User Facility managed by Lawrence Berkeley National Laboratory

© 1997-2023 The Regents of the University of California