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
    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

    Artist rendering of genome standards being applied to deciphering the extensive diversity of viruses. (Illustration by Leah Pantea)
    Expanding Metagenomics to Capture Viral Diversity
    Along with highlighting the viruses in a given sample, metagenomics shed light on another key aspect of viruses in the environment — their sheer genetic diversity.

    More

    Photograph of a stream of diatoms beneath Arctic sea ice.
    Polar Phytoplankton Need Zinc to Cope with the Cold
    As part of a long-term collaboration with the JGI Algal Program, researchers studying function and activity of phytoplankton genes in polar waters have found that these algae rely on dissolved zinc to photosynthesize.

    More

  • Data & Tools
    • IMG
    • Data Portal
    • MycoCosm
    • PhycoCosm
    • Phytozome
    • GOLD
    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

    HPCwire Editor's Choice Award (logo crop) for Best Use of HPC in the Life Sciences
    JGI Part of Berkeley Lab Team Awarded Best Use of HPC in Life Sciences
    The HPCwire Editors Choice Award for Best Use of HPC in Life Sciences went to the Berkeley Lab team comprised of JGI and ExaBiome Project team, supported by the DOE Exascale Computing Project for MetaHipMer, an end-to-end genome assembler that supports “an unprecedented assembly of environmental microbiomes.”

    More

  • User Programs
    • Calls for Proposals
    • Special Initiatives & Programs
    • Product Offerings
    • User Support
    • Policies
    • Submit a Proposal
    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

    CSP New Investigators FY23 R1
    JGI Announces First Round of 2023 New Investigator Awardees
    Twice each year we look for novel research projects aligned with DOE missions and from PIs who have not led any previously-accepted proposals through the CSP New Investigator call.

    More

    screencap from Amundson and Wilkins subsurface microbiome video
    Digging into Microbial Ecosystems Deep Underground
    JGI users and microbiome researchers at Colorado State University have many questions about the microbial communities deep underground, including the role viral infection may play in other natural ecosystems.

    Read more

  • 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

    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 FY16

Approved Proposals FY16

Following are the approved user proposals for fiscal year 2016 including CSP, CSP Small-Scale, Synthesis, and FICUS projects.

FY 2016 Community Science Program (CSP) Plans

PI Affiliation Project Description
Catcheside, David Flinders University (Australia) Acquisition of the sequestrate (truffle like) habit by basidiomycete macrofungi
Cooper, Elizabeth Clemson University Comparative transcriptomics of sweet and grain sorghum to understand the mechanism and timing of sugar accumulation in an important bioenergy crop
de Vries, Ronald CBS-KNAW Fungal Biodiversity Centre (Netherlands) Dissecting the different approaches of ascomycete fungi to degrade plant biomass
DeLong, Ed University of Hawaii at Manoa Going long and going deep: Comprehensive open ocean community single cell genome sequencing at the model open ocean time series study site, station ALOHA
Dollhofer, Veronika Bavarian State Research Center for Agriculture (Germany) Anaerobic fungi and assessment of their potential for biogas production
Duplessis, Sebastien INRA (France) Sequencing a reference genome for Phakopsora pachyrhizi, the fungal pathogen responsible for the Asian Soybean Rust
Francis, Christopher Stanford University Metagenomic characterization of nitrogen-cycling microbial communities impacting uranium release in the Upper Colorado River Basin
Hamelin, Richard University of British Columbia (Canada) Pathobiome of bioenergy trees
Hibbett, David Clark University Comparative and functional genomics of shiitake mushrooms: an international collaboration to resolve evolutionary relationships, substrate specificity, growth profiles, and routes to domestication in the amphi-Pacific genus Lentinula
Juenger, Tom University of Texas at Austin Exploring natural genetic diversity in switchgrass (Panicum virgatum) and its microbiome
Kalyuzhnaya, Marina University of Washington Systems level insights into methane cycling in arid and semi-arid ecosystems via community metagenomics and metatranscriptomics
Lorito, Matteo University of Naples (Italy) Supporting the development of microbial probiotics for grasses useful in sustainable bioenergy production
Martin, Francis INRA (France) 1KFG: Deep sequencing of ecologically-relevant Dikarya
Mayali, Xavier Lawrence Livermore National Laboratory Influence of phycosphere-associated bacteria on microalgal biofuel production
McMahon, Katherine University of Wisconsin-Madison Diel cycles of gene expression in oligotrophic, dystrophic, and eutrophic lakes to identify new gene functions and dissect carbon cycling metabolisms
Merchant, Sabeeha University of California, Los Angeles Comparative genomics and expression profiling of snow algae Chlamydomonas cribrum and Chloromonas nivalis
Niyogi, Kris University of California, Berkeley Functional genomics of photosynthesis in Chlamydomonas, JGI’s flagship alga
O’Malley, Michelle University of California, Santa Barbara Genomic basis for syntrophic interactions between anaerobic gut fungi and methanogenic archaea
Pires, J. Chris University of Missouri-Columbia Investigating the diversity of mycorrhizal fungi to understand the evolution and function of symbiosis with orchids
Plett, Jonathan University of Western Sydney (Australia) Exploring the genomic basis for the global diversification by the ectomycorrhizal genus Pisolithus
Poland, Jesse Kansas State University The Intermediate Wheatgrass Genome: A resource for understanding mechanisms of perenniality and accelerating the development of perennial crops
Rappe, Michael University of Hawaii at Manoa Metagenomics of viral and microbial communities inhabiting warm, anoxic fluids of the sediment-buried deep ocean crust
Schachtman, Daniel University of Nebraska Systems analysis of the physiological and molecular mechanisms of Sorghum nitrogen use efficiency, water use efficiency and interactions with the soil microbiome
Spatafora, Joey Oregon State University Genomics of the early diverging lineages of fungi and their transition to terrestrial, plant-based ecologies
Umen, James Donald Danforth Plant Science Center Single cell and population dynamics of chromatin across the diurnal cycle in the model alga Chlamydomonas
Walsh, David Concordia University (Canada) Microbial metagenomics of carbon cycling communities in northern aquatic ecosystems
Wrighton, Kelly Ohio State University Life in the extreme deep terrestrial subsurface: microbial metabolism before and after shale gas extraction

Small-Scale Proposals

Proposer Affiliation Project Description
Beman, J Michael University of California, Merced Metagenomics of methane production and oxidation in high altitude lakes of Yosemite National Park
Chistoserdova, Ludmila University of Washington Understanding methane cycling through manipulation of synthetic methane-oxidizing communities
Cullings, Ken NASA Ames Extreme endosymbiosis: An investigation into a unique fungal microbiome found in geothermal ecosystems in Yellowstone National Park and New Zealand
DeAngelis, Kristen University of Massachusetts, Amherst Expanding genomic diversity of terrestrial bacteria: linking genes to metabolism in the slower-growing members of forest soil bacterial communities
Kostka, Joel Georgia Institute of Technology The role of the Sphagnum microbiome in carbon and nutrient cycling in peatlands
McMahon, Katherine University of Wisconsin-Madison Reference genomes for abundant freshwater taxa – Actinobacteria and Verrucomicrobia phase 2
Meredith, Laura Stanford University Microbial, chemical, and physical drivers of COS fluxes and 18O-CO2 exchange rates in soils
Miller, Christopher University of Colorado, Denver Developing a systems-level understanding of biotic and abiotic controls on microbial methane cycling in freshwater wetlands
Redmond, Molly University of North Carolina, Charlotte Metagenomic sequencing of methane-oxidizing mesocosms from the Gulf of Mexico and Hudson Canyon
Rich, Jeremy Brown University Metagenomic sequencing of an uncultivated bacterial phylum in marine sediments amended with organic carbon and nitrate
Saito, Mak Woods Hole Oceanographic Institution Characterizing Synechococcus dominated populations from the Costa Rica dome and surrounding waters
Shade, Ashley Michigan State University Response and recovery of surface soil microbial communities to an ongoing underground coalmine fire
Simister, Rachel University of British Columbia Linking microbial genomic capacity to geochemical process in the deep terrestrial biosphere
Slonczewski, Joan Kenyon College Cyanobacterial communities of Antarctic Lake Fryxell liftoff mats and glacier meltwater
Tolar, Bradley Stanford University Monitoring the transcriptional response of a representative low-salinity ammonia-oxidizing thaumarchaeote to shifts in environmental conditions
Walsh, Davi Concordia University Metagenomics of western Arctic Ocean microbial communities
Wilkins, Michael Ohio State University Seasonal sulfur cycling as a control on methane flux in carbon-rich prairie pothole sediment ecosystems
Wrighton, Kelly Ohio State University Identifying key genomes and metabolisms responsible for near-surface methane cycling in freshwater wetlands

Synthesis Proposals

Proposer Affiliation Project Description
Chang, Jui-Jen Biodiversity Research Center,Academia Sinica Designer Operons-A biomimic approach to the regulation of an enzyme cocktail for an artificial enzyme complex
Chen, Brandon Genomatica, Inc. Engineering efficient methanol utilization for renewable chemicals
McCourt, Peter University of Toronto Exploring the perception landscape of the strigolactone receptor
Prather, Kristala Massachusetts Institute of Technology Combinatorial assembly, screening and functional characterization of a recombinant glucaric acid pathway in S. cerevisiae
Shen, Ben The Scripps Research institute Construction of bacterial artificial chromosome (BAC) vector libraries for comparative genomics, elucidation of gene functions and heterologous expression of targeted genes
Smanski, Mike University of Minnesota Towards a mechanistic understanding of disease suppressive soils: Refactoring natural product gene clusters
Wang, Clay University of Southern California Identification of fungal secondary metabolites with novel structures
Zimmer, Jochen University of Virginia Synthesis of cellulose synthase genes implicated in primary and secondary plant cell wall formation for structural and functional analyses of plant cellulose biosynthesis

FY 2016 Facilities Integrating Collaboration for User Science (FICUS) JGI-EMSL Plans

Proposer Affiliation Project Description
Bell-Pedersen, Deborah Texas A&M University Specialized Ribosomes: A New Frontier in Gene Regulation
Cardon, Zoe Marine Biological Laboratory 3D Reality Check: Developing Structural Support for Predicting Microbial Function and Interpreting Microbial “Omics” Data
Doty, Sharon University of Washington Nitrogen fixation in Populus: Identification and localization of the key diazotrophs in planta
Duhaime, Melissa University of Michigan Building the phage-host-environment interaction data to scale from genes-to-ecosystems: Towards predictive modeling of wild microbial and viral community dynamics
Eastwood, Dan Swansea University (UK) Genomes to dynamic decay communities: Understanding fungal interactions during early decomposition events in natural lignocellulosic substrate
Neumann, Rebecca University of Washington A Rhizosphere-Scale Investigation of the Relationship Between Plant Productivity and Methane Emissions from Wetlands
Orphan, Victoria California Institute of Technology Fluorescence-based cell sorting and targeted proteomic analysis of active methane-oxidizing syntrophic consortia from environmental samples
Pan, Chongle Oak Ridge National Laboratory Integrated Omics Analyses of a Populus Pedigree for Crop Improvement
  • 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