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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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    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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    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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    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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    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 › Partnerships Development Team (PDT)

Partnerships Development Team (PDT)

Through the Partnerships Development Team (PDT), strategic outreach efforts are targeting companies and other institutions without any prior JGI collaborations. The PDT is comprised of Director Nigel Mouncey, Chief Informatics Officer Kjiersten Fagnan, Metabolomics Technologies Group Lead and Environmental Genomics and Systems Biology Division Science Deputy Trent Northen, DNA Synthesis Science Program Head Yasuo Yoshikuni, Policy & Agreements Analyst Grace Sprehn, the Joint BioEnergy Institute (JBEI) Director of Commercialization, Biosciences Strategic Industry Engagements and Entrepreneurship Lead Robin Johnston, and Berkeley Lab Intellectual Property Office Tech Commercialization Team member Jeremy Greeter. The PDT also draws the expertise of Genomics Technologies Deputy Len Pennacchio, as needed. The PDT enables industry engagement through three primary routes: the Community Science Program call as well as less-explored mechanisms of Strategic Partnership Projects (SPP) and Cooperative Research and Development Agreements (CRADA), see below. The Business Development Team works closely with Berkeley Lab’s Intellectual Property Office to facilitate these new interactions. To set up a call or meeting to discuss partnering opportunities, contact Brooke Goodenough.

Recent Partnerships

  • Anuvia Plant Nutrients is partnering with the JGI to help drive discoveries that will render new economic advantages for farmers concerned with improving sustainable soil management practices.
  • In June 2020, the Department of Energy announced the 2020 Technology Commercialization Fund (TCF) projects. One of them supports a project between JGI and LanzaTech, a Skokie, Illinois-based company that recycles carbon emissions to make fuels and chemicals, improving air quality and promoting a circular economy.
    • Acetogenic Clostridium is considered the most efficient method of converting abundant low-cost gas feedstock into valuable bioproducts, but many Clostridium strains are difficult to engineer.
    • Yasuo Yoshikuni and his JGI colleagues have developed a technology called chassis-independent recombinase-assisted genome engineering (CRAGE), which offers single-step genomic integration and prototyping of complex pathways. The team will be working with LanzaTech to rapidly engineer a Clostridium strain for the production of biofuels and bioproducts from low-cost gas feedstock.
    • For more information about the supported Berkeley Lab TCF projects, visit the Intellectual Property Office here.

Case Study

A recent case study describing a collaboration between the JGI Metabolomics Technology Group and Brightseed can be found here.

Strategic Partnership Projects (SPPs)

SPPs enable research funded by an Industry partner to perform a defined scope of work using JGI’s unique facilities, equipment, and personnel. Sponsor may elect to obtain the entire right, title, and interest to any intellectual property generated under the agreement.

Cooperative Research and Development Agreements (CRADAs)

CRADAs enable research jointly sponsored by the Berkeley Lab and one or more partners for shared benefit. Industry partners can retain rights to their own inventions and have the first right to license Lab inventions generated through the CRADA.

For additional information about these partnering mechanisms, visit Berkeley Lab’s Innovation and Partnership Office (IPO) and read the Guide to Partnering with DOE’s National Laboratories.

  • Partnerships Development Team (PDT)
    • JGI Partnership Case Study: Brightseed

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