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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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Our Projects
Home › Our Projects › Approved User Proposals › Approved Proposals FY15

Approved Proposals FY15

Following are the approved user proposals for fiscal year 2015 including CSP and JGI-EMSL Collaborative Science Initiative projects.

FY 2015 Community Science Program (CSP) Plans

Proposer Affiliation Project Description
Baliga, Nitin Institute of Systems Biology Genome-wide analysis of chromatin accessibility and miRNA-mediated transcriptional regulation of lipid accumulation in Chlamydomonas reinhardtii
Banfield, Jill University of California, Berkeley Genome-resolved metagenomic analysis of microbial function in the subsurface
Banfield, Jill University of California, Berkeley Tree-driven diel microbial carbon dynamics in the vadose zone
Barrasa, Jose Maria University of Alcala  (Spain) Study of the lignocellulolytic machinery in saprobic wood and leaf litter degrading Agaricales
Busby, Posy University of Washington Mechanisms of interaction in the foliar fungal microbiome of Populus trichocarpa
Cadillo-Quiroz, Hinsby Arizona State University Microbial composition and metagenomic functional potential across tropical peatlands: comparative evaluation and modeling of C decomposition to greenhouse gases
Campbell, Barbara Clemson University Biogeochemical cycling links between terrestrial and marine systems
Cavicchioli, Rick University of New South Wales (Australia) Seasonal variation in Antarctic microbial communities: ecology, stability and susceptibility to ecosystem change
Chistoserdova, Ludmila University of Washington Methane oxidation as a community function: defining partnerships and strategies through sequencing metagenomes and metatranscriptomes of laboratory manipulated microcosms
DiFazio, Steven West Virginia University Sex determination in the Salicaceae
Frank, Carolin University of California, Merced Diazotrophic aboveground endophytes in native pines, poplar and willow
Fredrickson, Jim PNNL Spatio-temporal functional profiling in model microbial communities
Hallam, Steven University of British Columbia (Canada) Microbial engines driving organic matter transformations in the dark ocean: an integrated biological and chemical perspective
James, Timothy University of Michigan Revealing the ecological function of uncultured fungal dark matter in freshwater ecosystems using single cell genomics
Klassen, Jonathan University of Connecticut Metagenomic mining of natural product diversity and understanding its contribution to ecosystem function in the cellulolytic fungus-growing ant symbiosis
Klenk, Hans-Peter; Goker, Markus University of Newcastle (UK); DSMZ (Germany) Exploiting the genomes of the Actinobacteria: plant growth promoters and producers of natural products and energy relevant enzymes united in a taxonomically unresolved phylum
Lamendella, Regina Juniata College Systems biology approach to fracking for environmental monitoring
Laudencia-Chingcuanco, Debbie USDA-ARS Creating a genome-wide sequence-indexed collection of grass mutants
Liu, Wen-Tso University of Illinois Shedding light on the anaerobic wastewater treatment “black-box” in anthropogenic carbon cycling: exploring the uncharted ecological function of uncultured microbial taxa through next-generation sequencing technology
Loper, Joyce USDA-ARS Exploring the genomic diversity of the Pseudomonas fluorescens group
Medina-Munoz, Monica Penn State University How do coral hosts communicate with their associated microbial community?
Peay, Kabir Stanford University Coprophilous fungi as a model system for understanding the metagenomics of carbon cycling in microbial eukaryote communities
Simon, Holly Oregon Health & Science University A systems approach to evaluate physical constraints and microbial controls on fluxes of nutrients and energy in a coastal ecosystem
Sorek, Rotem Weizmann Institute of Science (Israel) Comparative genomics of a single organism: In search of acquired immunity in trees
Swaminathan, Kankshita University of Illinois Understanding variance in allele specific expression in the polyploid Saccharinae
Thon, Michael University of Salamanca (Spain) Evolution and adaptation of carbohydrate utilization in the Colletotrichum acutatum species complex
Treseder, Kathleen University of California, Irvine Genomes and transcriptomes of decomposer fungi responding to warming in Alaskan boreal forest
Wildermuth, Mary University of California, Berkeley Comparative genomics of powdery mildews and associated host plants
Wosten, Han Utrecht University (Netherlands) Functional genomics of lignocellulose degradation by Agaricomycete fungi
Wurzbacher, Christian IGB (Germany) Whole genome sequencing of aquatic fungi responsible for the degradation of recalcitrant substrates in liquid environments
Young, Erica University of Wisconsin Metagenome and metatranscriptome of complex algal communities growing in wastewater: Bioremediation, nutrient transformation, carbon sequestration
Zhang, Baohong East Carolina University Panicum virgatum small RNA sequencing to identify gene expression changes related to biofuel traits

JGI-EMSL Facilities Integrating Collaborations for User Science (FICUS) Plans

Proposer Affiliation Project Description
Colwell, Frederick Oregon State University Integrated Biogeochemical Modeling of Microbial Consortia Mediating Anaerobic Oxidation of Methane in Dynamic Methane Hydrate-bearing Sediments
Crump, Byron Oregon State University Decoding DOM Degradation: How Does Carbon Source and Sunlight Exposure Alter Microbial Metabolism and Expression of Genome-Encoded Metabolic Degradation of Permafrost Organic Matter?
Cumming, Jonathan West Virginia University Mapping the Metabolism of Nutrient and Carbon Exchange in the Plant-Microbe Symbiosis
de Vries, Ronald CBS-KNAW Fungal Biodiversity Centre Dissecting Intraspecies Diversity in Fungal Wood Decay
DiChristina, Thomas Georgia Institute of Technology Sensing External Metals by Outer Membrane Beta-Barrel Proteins
Lebeis, Sarah University of Tennessee Uncovering the Composition and Function of the Aquatic Microbiome for Duckweeds
Luthey-Schulten, Zaida University of Illinois at Urbana-Champaign Quantifying Differential Expression and Identifying Bottlenecks in Methanogenic Pathways
Magnuson, Jon Pacific Northwest National Laboratory Elucidating the Influences of Engineered N-glycosylation Motifs in Bacterial Biomass Hydrolyzing Enzymes upon Heterologous and Native Gene Expression, Secretion and Degradation in Aspergillus niger
Rich, Virginia University of Arizona Systems-level Insights into Carbon Transformations in Thawing Permafrost by Parallel High-resolution Organic Matter and Microbial Community Characterizations
Stegen, James Pacific Northwest National Laboratory Coupling Microbial Communities to Carbon and Contaminant Biogeochemistry in the Groundwater-Surface Water Interaction Zone
Vilgalys, Rytas Duke University Integrated Genomic/Transcriptomic/Secretomic Study of Plant-Fungal Interactions Between Pines and Their Symbiotic Ectomycorrhizal Fungi in the Mushroom Genus Suillus
Wrighton, Kelly The Ohio State University Microbial Controls on Biogeochemical Cycling in Deep Subsurface Shale Carbon Reservoirs
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