DOE Joint Genome Institute

  • COVID-19
  • About
  • Phones
  • Contacts
  • Our Science
    • DOE Mission Areas
    • Bioenergy Research Centers
    • Science Programs
    • Products
    • Science Highlights
    • Scientists
    Screencap of green algae video for PNAS paper
    Green Algae Reveal One mRNA Encodes Many Proteins
    A team of researchers has found numerous examples of polycistronic expression – in which two or more genes are encoded on a single molecule of mRNA – in two species of green algae.

    Read more

    Advances in Rapidly Engineering Non-model Bacteria
    CRAGE is a technique for chassis (or strain)-independent recombinase-assisted genome engineering, allowing scientists to conduct genome-wide screens and explore biosynthetic pathways. Now, CRAGE is being applied to other synthetic biology problems.

    Read more

    Maize can produce a cocktail of antibiotics with a handful of enzymes. (Sam Fentress, CC BY-SA 2.0)
    How Maize Makes An Antibiotic Cocktail
    Zealexins are produced in every corn variety and protect maize by fending off fungal and microbial infections using surprisingly few enzymes.

    More

  • Our Projects
    • Search JGI Projects
    • DOE Metrics/Statistics
    • Approved User Proposals
    • Legacy Projects
    Poplar (Populus trichocarpa and P. deltoides) grow in the Advanced Plant Phenotyping Laboratory (APPL) at Oak Ridge National Laboratory in Tennessee. Poplar is an important biofuel feedstock, and Populus trichocarpa is the first tree species to have its genome sequenced — a feat accomplished by JGI. (Image courtesy of Oak Ridge National Laboratory, U.S. Dept. of Energy)
    Podcast: Xiaohan Yang on A Plantiful Future
    Building off plant genomics collaborations between the JGI and Oak Ridge National Laboratory, Xiaohan Yang envisions customizing plants for the benefit of human society.

    More:

    Expansin complex with cell wall in background. (Courtesy of Daniel Cosgrove)
    Synthesizing Microbial Expansins with Unusual Activities
    Expansin proteins from diverse microbes have potential uses in deconstructing lignocellulosic biomass for conversion to renewable biofuels, nanocellulosic fibers, and commodity biochemicals.

    Read more

    High oleic pennycress. (Courtesy of Ratan Chopra)
    Pennycress – A Solution for Global Food Security, Renewable Energy and Ecosystem Benefits
    Pennycress (Thlaspi arvense) is under development as a winter annual oilseed bioenergy crop. It could produce up to 3 billion gallons of seed oil annually while reducing soil erosion and fertilizer runoff.

    Read more

  • Data & Tools
    • IMG
    • Genome Portal
    • MycoCosm
    • PhycoCosm
    • Phytozome
    • GOLD
    Artistic interpretation of CheckV assessing virus genome sequences from environmental samples. (Rendered by Zosia Rostomian​, Berkeley Lab)
    An Automated Tool for Assessing Virus Data Quality
    CheckV can be broadly utilized by the research community to gauge virus data quality and will help researchers to follow best practices and guidelines for providing the minimum amount of information for an uncultivated virus genome.

    More

    Unicellular algae in the Chlorella genus, magnified 1300x. (Andrei Savitsky)
    A One-Stop Shop for Analyzing Algal Genomes
    The PhycoCosm data portal is an interactive browser that allows algal scientists and enthusiasts to look deep into more than 100 algal genomes, compare them, and visualize supporting experimental data.

    More

    Artistic interpretation of how microbial genome sequences from the GEM catalog can help fill in gaps of knowledge about the microbes that play key roles in the Earth's microbiomes. (Rendered by Zosia Rostomian​, Berkeley Lab)
    Podcast: A Primer on Genome Mining
    In Natural Prodcast: the basics of genome mining, and how JGI researchers conducted it in IMG/ABC on thousands of metagenome-derived genomes for a Nature Biotechnology paper.

    Read more

  • User Programs
    • Calls for User Proposals
    • Special Initiatives & Programs
    • User Support
    • Submit a Proposal
    Image of Octopus Springs for the CSP annual call
    Letters of Intent are due April 12, 2021 for the annual Community Science Program (CSP) call focused on large-scale genomic science projects that address specific areas of special emphasis and exploit the diversity of JGI capabilities.

    Read more

    SIP engagement webinar
    “SIP technologies at EMSL and JGI” Webinar
    The concerted stable isotope-related tools and resources of the JGI and the Environmental Molecular Sciences Laboratory (EMSL) may be requested by applying for the annual “Facilities Integrating Collaborations for User Science” (FICUS) call.

    Read more

    martin-adams-unsplash
    CSP Functional Genomics Call Ongoing
    The CSP Functional Genomics call helps users translate genomic information into biological function. Proposals submitted by July 31, 2021 will be part of the next review.

    Read more

  • News & Publications
    • News
    • Blog
    • Podcasts
    • Webinars
    • Publications
    • Newsletter
    • Logos and Templates
    • Photos
    Aerial photo of the switchgrass diversity panel late in the 2020 season at the Kellogg Biological Station in Michigan. (Robert Goodwin)
    A Team Effort Toward Targeted Crop Improvements
    A multi-institutional team has produced a high-quality reference sequence of the complex switchgrass genome. Building off this work, researchers at three DOE Bioenergy Research Centers have expanded the network of common gardens and are exploring improvements to switchgrass.

    More

    Artistic interpretation of how microbial genome sequences from the GEM catalog can help fill in gaps of knowledge about the microbes that play key roles in the Earth's microbiomes. (Rendered by Zosia Rostomian​, Berkeley Lab)
    Uncovering Novel Genomes from Earth’s Microbiomes
    A public repository of 52,515 microbial draft genomes generated from environmental samples around the world, expanding the known diversity of bacteria and archaea by 44%, is now available .

    More

    Green millet (Setaria viridis) plant collected in the wild. (Courtesy of the Kellogg lab)
    Shattering Expectations: Novel Seed Dispersal Gene Found in Green Millet
    In Nature Biotechnology, a very high quality reference Setaria viridis genome was sequenced, and for the first time in wild populations, a gene related to seed dispersal was identified.

    More

Our Projects
Home › Our Projects › Approved User Proposals › Approved Proposals FY12

Approved Proposals FY12

Following are the approved user proposals for fiscal year 2012.

Community Science Program (CSP) Plans

Proposer Affiliation Project Description
Acinas, Silvia ICM-CSIC, Spain Microbial metagenomics and transcriptomics from a global deep-ocean expedition
Andresson, Olafur University of Iceland Sequencing of the three cultured partners of the lichen Lobaria pulmonaria and the sequencing of the transcriptomes from the natural tripartite lichen under selected and controlled conditions.
Banfield, Jill University of California, Berkeley Terabase sequencing for comprehensive genome reconstruction to assess metabolic potential for environmental bioremediation
Brodie, Eoin DOE JGI Mediterranean Grassland Soil Metagenome (MGSM): Enabling a systems view of soil carbon and nitrogen biogeochemistry under a changing climate.
Brutnell, Thomas Boyce Thompson Institute for Plant Research Development of sequence-based community tools for Setaria viridis-a model genetic system for C4 grasses
Bucking, Heike South Dakota State University Exploring the transcriptome of perennial grasses in association with beneficial microorganisms to increase biomass production and environmental sustainability of bioenergy production
Cary, Stephen University of Delaware Understanding terrestrial microbial biocomplexity in an Antarctic desert landscape: resolving universal drivers of community structure and function in a trophically simple system
Crouch, Jo Anne USDA-ARS Genomic signatures of pathogenicity and endophytism in five species of grass-associated Colletotrichum impacting the health and production of bioenergy feedstocks, agriculture and the environment
Dangl, Jeff University of North Carolina at Chapel Hill Plant associated metagenomes–Microbial community diversity and host control of community assembly across model and emerging plant ecological genomics systems.
DeAngelis, Kristen University of Massachusetts Microbial ecology and genomics of carbon-storing bacteria in rhizosphere soils
Dubilier, Nicole & Kleiner, Manuel Max Planck Institute for Marine Microbiology, Germany Understanding novel pathways for energy and carbon use in bacterial symbionts of gutless marine worms
Emerson, David Bigelow Laboratory for Ocean Sciences Single cell genome sequencing of biomineralizing bacteria
Fierer, Noah University of Colorado Cross-site metagenomic analyses to assess the impacts of experimental nitrogen additions on belowground carbon dynamics
Fredrickson, Jim Pacific Northwest National Laboratory Microbial Interactions in Extremophilic Mat Communities
Gilbert, Jack Argonne National Laboratory Creating a successional model for carbon remediation in the Gulf of Mexico
Gross, Stephen DOE JGI The Agave Microbiome: Exploring the role of microbial communities in plant adaptations to desert environments
Hazen, Samuel University of Massachusetts Creating a multi-functional library of grass transcription factors for the energy crop model system Brachypodium distachyon
Hess, Matthias Washington State University Expression profile of biomass-degrading fungi inhabiting the cow rumen
Kelly, William AgResearch, New Zealand The Hungate 1000. A catalogue of reference genomes from the rumen microbiome.
Kerfeld, Cheryl DOE JGI Enhancing Bacterial Carbon Capture and Sequestration: Synthesis of Building Blocks for the Carboxysome, A Metabolic Module for CO2 Fixation
Kyrpides, Nikos DOE JGI Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes (KMG) project
Laplaze, Laurent Institut de Recherche pour le Developpement (IRD), France Transcriptome Analysis of Salt Tolerance in Casuarina trees
Martin, Francis INRA, France Metatranscriptomics of Soil Forest Ecosystems
McKay, Robert Bowling Green State University Metagenomics and metatranscriptomics of the Lake Erie ‘dead zone’: a seasonal source of greenhouse gases
McMahon, Katherine University of Wisconsin, Madison Dynamics of microbial carbon processing pathways across a decade in a freshwater eutrophic lake revealed through metagenomic sequencing
Mock, Thomas University of East Anglia, UK Sea of Change: Eukaryotic Phytoplankton Communities in the Arctic Ocean
Mohn, William University of British Columbia, Canada Metagenomic and metatranscriptomic analysis of forest soil communities across North America
Moran, Mary Ann University of Georgia The Genetic Basis for Heterotrophic Carbon Processing in the Sea
Murray, Alison Desert Research Institute Lake Vida brine microbial community (LVBMCo) genomics and transcriptomics – a window into diversity, adaptation and processes in extreme cold
Gerard Muyzer Delft University of Technology Genome sequencing of 100 strains of the haloalkaliphilic chemolithoautotrophic sulfur-oxidizing bacterium Thioalkalivibrio
Nealson, Kenneth University of Southern California Life at the edge: community cooperation and success in a very extreme (ultrabasic and ultra-reducing) environment
Ohm, Robin DOE JGI Towards functional genomics: development of Schizophyllum commune as a model system to study lignocellulose degradation
Pester, Michael University of Vienna, Austria Targeted metagenomics and metatranscriptomics of a sulfate-reducing rare biosphere member and potentially novel sulfate reducers that impact methane emission from peatlands
Powell, Amy Sandia National Laboratories A Phylogenomic Framework to Investigate Fungal Thermophily
Pukkila, Patricia University of North Carolina at Chapel Hill Functional genomics in the model mushroom Coprinopsis cinerea
Rodrigues, Jorge University of Texas at Arlington Profiling metagenomic consequences of Amazon deforestation at different spatial scales
Schadt, Christopher Oak Ridge National Laboratory Defining the Populus Microbiome: Role of Genotype by Environment Interactions in Shaping the Rhizosphere Microbiome of Populus trichocarpa
Schrenk, Matthew East Carolina University Metagenome-enabled Investigations of Carbon and Hydrogen Fluxes within the Serpentinite-hosted Subsurface Biosphere
Spatafora, Joseph Oregon State University 1000 Fungal Genomes
Stepanauskas, Ramunas Bigelow Laboratory for Ocean Sciences Dark ocean microbial single cell genomics
Wing, Rod University of Arizona Empowering functional plant genomics with genomes and transcriptomes of the top 20 Brassicales
  • Approved Proposals FY21
  • Approved Proposals FY20
  • Approved Proposals FY19
  • Approved Proposals FY18
  • Approved Proposals FY17
  • Approved Proposals FY16
  • Approved Proposals FY15
  • Approved Proposals FY14
  • Approved Proposals FY13
  • Approved Proposals FY12
  • Approved Proposals FY11
  • Approved Proposals FY10
  • Approved Proposals FY09
  • Approved Proposals FY08
  • Approved Proposals FY07
  • Approved Proposals FY06
  • Approved Proposals FY05
  • ETOP Projects

More topics:

  • COVID-19 Status
  • News
  • Science Highlights
  • Blog
  • Podcasts
  • Webinars
  • CSP Plans
  • Featured Profiles
  • Careers
  • Contact Us
  • Events
  • User Meeting
  • MGM Workshops
  • Internal
  • Disclaimer
  • Credits
  • Emergency Info
  • Accessibility / Section 508 Statement
  • RSS feed
  • Flickr
  • LinkedIn
  • 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

© 1997-2021 The Regents of the University of California