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

Our Projects
Home › Our Projects › Approved User Proposals › Approved Proposals FY19

Approved Proposals FY19

Following are the approved user proposals for fiscal year 2019, including CSP, CSP New Investigator, Synthesis, and FICUS JGI-EMSL.

Community Science Program (CSP)

Proposer Affiliation Project Description
Airo, Alessandro Berlin Institute of Technology (Germany) Past and modern microbial communities in million-year-old Atacama Desert and their role in biogeochemical cycling in hyperarid environments
Blanchard, Jeffrey University of Massachusetts-Amherst Molecular responses to a short-term temperature shift in a long-term soil warming experiment at Harvard Forest
Bowen, Jennifer Northeastern University Nitrate in coastal waters: shifting the balance from carbon sink to carbon source
Brown, Judith The University of Arizona Characterizing infections and host-pathogen interactions of Chlorella spp. by the predatory algal bacterial pathogen, Vampirovibrio chlorellavorus
Carini, Paul The University of Arizona Adaptive strategies in a cosmopolitan and abundant soil bacterium: metabolic flexibility or genome divergence?
D’Hont, Angelique CIRAD (France) Genomic diversity in the Saccharum complex for improvement of sugarcane as an energy crop
Freitag, Michael Oregon State University The curse of being first meets the need to be complete: Finishing genomes to leverage additional information from completed and ongoing JGI CSPs
Gladieux, Pierre INRA (France) Comparative genomics and association mapping in Sordariales: insights into functional diversity in Neurospora and its relatives
Greenham, Katie University of Minnesota Leveraging pan-genomes to investigate diel transcriptomic and metabolomic responses to abiotic stress in B. rapa and B. napus diversity panels.
Hazen, Samuel University Of Massachusetts-Amherst Regulatory Genomics of Plant Biomass Accumulation
Leakey, Andrew University of Illinois at Urbana-Champaign Transcriptomics of water use efficiency traits in Sorghum and Setaria
Liao, Hui-Ling NFREC/University of Florida Genetic, community, and ecosystem consequences of co-introduction of mycorrhizal fungi with exotic pines
Malagnac, Fabienne University Paris Sud (France) Linking epigenomic regulation of carbon acquisition to nutrient use in fungi
McMahon, Trina University of Wisconsin-Madison Extended temporal dynamics of microbially-mediated freshwater carbon processing as revealed through time-series metagenomes
Moore, Bradley University of California, San Diego Exploring algal biodiversity for the production of chemical feedstocks and other biotechnological applications
Nagy, Laszlo Biological Research Center (Hungary) Fungal Comparative ENCODE Project: FUNCODE
Rodrigues, Jorge University of California, Davis Partitioning the Biological Causes of Methane Flux Variation in the Amazon Rainforest
Salome, Patrice University of California, Los Angeles Control of mRNA half-life Across the Diurnal Cycle in the Model Alga Chlamydomonas
Van de Peer, Yves Ghent University/VIB (Belgium) Marine Angiosperm Genome Initiative (MAGI)
Weston, David Oak Ridge National Laboratory Elucidating Sphagnum Microbiome Genetic Interactions for Improved Plant Growth to Warming
Whitman, William University of Georgia Genome Encyclopedia of Bacteria and Archaea VI: Functional Genomics of Type Strains
Wilhelm, Steven The University of Tennessee Algal, Bacterial and Viral Interactions as the Backdrop to Marine Carbon and Trace Metal Cycling
Wrighton, Kelly Colorado State University From genomes to updated biogeochemical models: Targeting critical knowledge gaps in methanogenesis from soil systems

CSP New Investigator

Proposer Affiliation Project Description
Bouskill, Nicholas Lawrence Berkeley National Laboratory Microbial environmental feedbacks and the evolution of soil organic matter
Carlos-Shanley, Camila Texas State Univeristy Functional genomics of gut bacteria from endangered species of beetles from the Edwards Aquifer
Dassanayake, Maheshi Louisiana State University A transcriptome atlas enabling discovery of genes evolved as adaptations to environmental stress in a model extremophyte, Schrenkiella parvula
Davis, Richard Jacobs Engineering/JETS Temporal and Spatial Exploration of Fumarolic Ice Cave Microbial Communities
Emerson, Joanne University of California, Davis Elucidating depth-resolved viral links to soil carbon chemistry and crop yields in agricultural systems
Fabiano, Elena IIBCE Searching for New Bacterial Functions in Antarctic Lithobionts
Hughes, Karen University of Tennessee Utilizing microbial functional responses to follow soil carbon and nutrient cycling recovery and resilience following the November 2016 fire in the Great Smoky Mountains National Park
Kluge, Mariana SLU – Swedish University of Agricultural Sciences (Sweden) The fungal contribution to the carbon cycle of Subarctic and Arctic permafrost areas
Moghe, Gaurav Cornell University High-throughput annotation of metabolic enzymes in Brachypodium distachyon using correlated transcriptomics and metabolomics
Rivers, Adam USDA – Agricultural Research Service Developing probabilistic graphical models and analysis software to integrate multi-omics data
 

Schultzhaus, Zachary

Naval Research Laboratory Functional Genomics and Transcriptomics to Target Mechanisms of Radiation Resistance in Melanized Fungi
Searcy, Christopher University of Miami Fire selection and the carbon cycling potential of the soil microbiome
Strack, Maria University of Waterloo (Canada) Microbial processes in restored and unrestored post-extraction peatlands: key to understanding greenhouse gas emissions from managed wetland ecosystems

FY 2019 Facilities Integrating Collaboration for User Science (FICUS) JGI-EMSL Plans

Proposer Affiliation Project Description
Boye, Kristin Stanford Linear Accelerator Center Microbial Metabolic Activity and Biogeochemical Reaction Networks in Redox Cycled Alluvial Systems
de Vries, Ron Westerdijk Fungal Biodiversity Institute Validation of The Transfer of Metabolic Models From Aspergillus niger to Other Fungi Using an Orthology-Based Approach
Hom, Erik University of Mississippi Probing Microbial Interactions and Coordinated Trophic Responses in Biological Soil Crusts
Moran, James Pacific Northwest National Laboratory Linking Phosphorus and Carbon in Rhizosphere Nutrient Cycling
O’Malley, Michelle University of California, Santa Barbara Deciphering the Structure & Function of Secondary Metabolites from Anaerobic Fungi
Oono, Ryoko University of California, Santa Barbara Plant Litter Degradation and Microbial Defense by Host-Specific Fungal Endophytes
Shaked, Yeala Hebrew University of Jerusalem Interactive Mechanisms of Mineral Dissolution by A Microbial Consortia
Solomon, Kevin Purdue University Epigenetic Regulation of Anaerobic Fungi for Increased Lignocellulose Degradation
Trinh, Cong University of Tennessee Understanding and Harnessing the Robustness of Undomesticated Yarrowia lipolytica Strains for Biosynthesis of Designer Bioesters
Weston, David Oak Ridge National Laboratory Consequences of Plant Genetic Variation and The Surrounding Microbiome on Nitrogen Fixation
Wilkins, Michael Colorado State University Hydrobiogeochemical Feedbacks Across Seasonal and Decadal Time-Scales: Implications For Solute Fate and Transport in Riverbed Ecosystems
Zimmerman, Richard Old Dominion University Experimental Impacts of Climate Warming and Ocean Acidification on Metabolic Function and Blue Carbon Accumulation by Eelgrass

 

  • Approved Proposals FY23
  • Approved Proposals FY22
  • 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
  • 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