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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    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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    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.

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    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.

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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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    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.”

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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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    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.

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    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.

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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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    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 › User Program Info › Review Process and Scoring Criteria

Review Process and Scoring Criteria

Review Process

Proposals go through a two-step review process. First, they are evaluated for technical feasibility by JGI scientific staff. Second, proposals are considered by the scientific review panel. Each proposal is reviewed by three reviewers who each prepare written comments on the proposal’s strengths and weaknesses, keyed to the review criteria (listed below). The reviews are made available to the applicants.  The mean score is used to rank proposals. Recommendations on which proposals will be approved are made by JGI senior management based on the rank order established by the scientific reviewers, and projected resource availability.  Final approval of the proposal list is made by the DOE after review of mission relevance.  The Project Manager for each project then begins a consultative process with the proposer that culminates in the creation of a Statement of Work.

Scoring Criteria

Proposals will be judged on the following scoring criteria:

  • Scientific merit. An important goal of this program is to direct JGI’s sequencing, synthesis, metabolomics and informatics capacity to scientific problems of great importance and of high impact on science and society. Scientific merit will be one of the most important criteria for scoring proposals, and scoring will include an evaluation of the importance of the scientific questions to be addressed and the likelihood that genomic sequencing efforts will answer them.
  • Relevance to DOE mission. Relevance to the DOE missions of carbon cycling, biogeochemistry, or alternative energy sources will be considered during the review of all proposals. Projects of strictly biomedical relevance will not be considered.
  • Demonstrated capability of the applicant(s) and/or the scientific community to use the resource generated. Large-scale projects should be followed up in a timely fashion with analyses or further studies that answer important scientific questions. Proposals will be evaluated on whether scientists with expertise and the necessary skills will be ready to perform follow-up research and publications. The size and productivity of the user community will also be considered.
  • Amount of DOE JGI resources to be allocated. The scale of each proposal should be commensurate with its stated scientific goals.  Weight will be given to the effort required for each project in order to optimize the JGI’s overall contribution to scientific discovery.  The JGI may suggest focusing or expanding the scope of the proposal to improve feasibility and/or project output.
  • Technical feasibility. Proposed projects will be evaluated  for compatibility with JGI capabilities and potential sources of technical difficulty.
  • Calls for User Proposals
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