DOE Joint Genome Institute

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    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.

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

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    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.

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    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.

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    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.

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    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.

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    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.

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    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.

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    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.

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    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.

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    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.

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    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.

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    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.

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    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.

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    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.

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User Programs
Home › User Programs › Special Initiatives & Programs

Special Initiatives & Programs

Biological and Environmental Research Support Science (BERSS) | Emerging Technologies Opportunity Program (ETOP) | Visiting Scientist Program

Partnerships Development Team (PDT)

The vast majority of the JGI’s over 2,000 Users come from the public sector – academic and government institutions. As such, the capabilities and expertise of the JGI are largely unknown and underutilized by industry. With the arrival of JGI Director Nigel Mouncey, who joined the JGI with 20 years of industry experience in 2017, an opportunity emerged to expand JGI’s portfolio of user companies by establishing a Partnerships Development Team (PDT). Other targets of PDT’s activities include other academic, governmental, and non-governmental institutions that have not yet partnered with the JGI. Learn more about the PDT.

Bioenergy Research Centers (BRCs):

The JGI performs sequencing on behalf of the U.S. Department of Energy Bioenergy Research Centers. The Centers are intended to accelerate basic research in the development of cellulosic ethanol and other biofuels, advancing the federal initiative that seeks to reduce U.S. gasoline consumption by 20% within 10 years through increased efficiency and diversification of clean energy sources. The four Centers are located in geographically distinct areas and use different plants both for laboratory research and for improving feedstock crops.

Center for Advanced Bioenergy and Bioproducts Innovation (CABBI) led by University of Illinois at Urbana-Champaign. Announced in July 2017, CABBI is a collaboration between Illinois’ Institute for Sustainability, Energy, and Environment (iSEE) and the Carl R. Woese Institute for Genomic Biology (IGB), and it will include 17 partner institutions. CABBI researchers will develop fuels and products by integrating three highly interconnected DOE priority areas of Feedstock Development, Conversion, and Sustainability.

Center for Bioenergy Innovation (CBI) led by DOE’s Oak Ridge National Laboratory in Oak Ridge, Tennessee. CBI will pursue a host of new technologies to alleviate critical cost barriers to sustainable, economically viable production of bio-based products and advanced biofuels. The center will focus on creating robust high-yielding feedstock plants, using advanced genetic technology to accelerate the domestication of perennials. CBI will create methods for high-yield production of advanced biofuels that can be blended with existing transportation fuels. Researchers will also study ways to develop valuable byproducts from lignin left over after biomass processing.

Great Lakes Bioenergy Research Center (GLBRC) led by the University of Wisconsin in Madison, Wisconsin, in close collaboration with Michigan State University in East Lansing, Michigan. This center is studying a range of plants and, in addition to exploring plant fiber breakdown, aims to increase plant production of starches and oils, which are more easily converted to fuels. This Center also has a major focus on sustainability, examining the environmental and socioeconomic implications of moving to a biofuels economy.

Joint BioEnergy Institute (JBEI) led by DOE’s Lawrence Berkeley National Laboratory. This center will concentrate on “model” crops of rice and Arabidopsis, in the search for game-changing breakthroughs in basic science, and is exploring microbial-based synthesis of fuels beyond ethanol.

Biological and Environmental Research Support Science (BERSS):

Overview

JGI provides sequencing, synthesis, and targeted metabolomics support for DOE-BER funded awards, including awards funded through BER Funding Opportunity Announcements, Science Focus Areas (SFA) opportunities, and the Office of Science Early Career Research Program.  FAIR, RENEW, and Energy Earthshot proposals are NOT eligible for BERSS support.

Available Resources

Eligible product types include those listed here:  https://jgi.doe.gov/our-science/product-offerings/

Proposals may not exceed 3 Tbp sequencing, 500 kbp synthesis, and 200 polar/500 nonpolar metabolomics samples, and should generally conform to the guidelines for current annual Community Science Program proposals.

Process

Proposals may be submitted at any time.  Support is limited to work included in the BER-funded proposal, and PIs must provide an award number and contact information for their DOE program officer. Submitters are strongly encouraged to contact JGI to determine general feasibility prior to submitting a BER proposal that includes a JGI request. Proposals whose scope was not previously negotiated with the JGI will only be accepted pending available capacity, technical review, and scope negotiation at JGI.

Investigators with grants funded by DOE-BER requiring support from JGI capabilities may submit proposals here.

Investigators preparing grant applications to DOE-BER and requesting an optional letter of feasibility to accompany their proposal may contact Tanja Woyke (twoyke@lbl.gov), Deputy for User Programs, with a proposed scope.

Investigators wishing to expand on their DOE-BER funded work with additional sequencing, synthesis, or metabolomics should apply to one of the JGI’s calls for user proposals.

 

Emerging Technologies Opportunity Program (ETOP)

The ETOP identifies and funds partnerships to develop new technical capabilities that could be provided to JGI users.  Projects targeted for 2018 include development of methods for rapid prototyping of gene and pathway function targeting organisms found in natural environments:

  • High-throughput cell-based systems for biological and metabolic characterization
  • Cell-free technologies that enable scaleable in vitro gene and pathway functional analyses
  • Sensor-based technologies, biological or non-biological, that enable in vivo reporting of metabolic activity and/or activity-based cell sorting

Deadline for proposal submission has passed. For more information, check out the solicitation.

See a list of previously supported projects.

 

Visiting Scientist Program

The JGI Visiting Scientist Program (VSP) provides an opportunity for faculty-level scientists who are seeking to build upon their line of scientific inquiry by leveraging JGI experimental, computational, and personnel resources for genomic research and sequence-based science. Projects include de novo generation of genome data, assistance in interpreting and/or building on an existing data set, or the refining of new technology (e.g., single-cell genomics; metagenomics, etc.). Length of stay depends on complexity of the project being considered and availability of data and other resources. Investigators, postdocs, and graduate students participating in approved JGI User Projects are also invited to apply for on-site access to JGI resources and capabilities. For more information, contact Tanja Woyke (twoyke@lbl.gov), Deputy for User Programs.

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