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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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    Designer DNA: JGI Helps Users Blaze New Biosynthetic Pathways
    In a special issue of the journal Synthetic Biology, JGI scientific users share how they’ve worked with the JGI DNA Synthesis Science Program and what they’ve discovered through their collaborations.

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    A genetic element that generates targeted mutations, called diversity-generating retroelements (DGRs), are found in viruses, as well as bacteria and archaea. Most DGRs found in viruses appear to be in their tail fibers. These tail fibers – signified in the cartoon by the blue virus’ downward pointing ‘arms’— allow the virus to attach to one cell type (red), but not the other (purple). DGRs mutate these ‘arms,’ giving the virus opportunities to switch to different prey, like the purple cell. (Courtesy of Blair Paul)
    A Natural Mechanism Can Turbocharge Viral Evolution
    A team has discovered that diversity generating retroelements (DGRs) are not only widespread, but also surprisingly active. In viruses, DGRs appear to generate diversity quickly, allowing these viruses to target new microbial prey.

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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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    This data image shows the monthly average sea surface temperature for May 2015. Between 2013 and 2016, a large mass of unusually warm ocean water--nicknamed the blob--dominated the North Pacific, indicated here by red, pink, and yellow colors signifying temperatures as much as three degrees Celsius (five degrees Fahrenheit) higher than average. Data are from the NASA Multi-scale Ultra-high Resolution Sea Surface Temperature (MUR SST) Analysis product. (Courtesy NASA Physical Oceanography Distributed Active Archive Center)
    When “The Blob” Made It Hotter Under the Water
    Researchers tracked the impact of a large-scale heatwave event in the ocean known as “The Blob” as part of an approved proposal through the Community Science Program.

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    A plantation of poplar trees. (David Gilbert)
    Genome Insider podcast: THE Bioenergy Tree
    The US Department of Energy’s favorite tree is poplar. In this episode, hear from ORNL scientists who have uncovered remarkable genetic secrets that bring us closer to making poplar an economical and sustainable source of energy and materials.

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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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    With a common set of "baseline metadata," JGI users can more easily access public data sets. (Steve Wilson)
    A User-Centered Approach to Accessing JGI Data
    Reflecting a structural shift in data access, the JGI Data Portal offers a way for users to more easily access public data sets through a common set of metadata.

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    Phytozome portal collage
    A More Intuitive Phytozome Interface
    Phytozome v13 now hosts upwards of 250 plant genomes and provides users with the genome browsers, gene pages, search, BLAST and BioMart data warehouse interfaces they have come to rely on, with a more intuitive interface.

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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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    Yeast strains engineered for the biochemical conversion of glucose to value-added products are limited in chemical output due to growth and viability constraints. Cell extracts provide an alternative format for chemical synthesis in the absence of cell growth by isolating the soluble components of lysed cells. By separating the production of enzymes (during growth) and the biochemical production process (in cell-free reactions), this framework enables biosynthesis of diverse chemical products at volumetric productivities greater than the source strains. (Blake Rasor)
    Boosting Small Molecule Production in Super “Soup”
    Researchers supported through the Emerging Technologies Opportunity Program describe a two-pronged approach that starts with engineered yeast cells but then moves out of the cell structure into a cell-free system.

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    These bright green spots are fluorescently labelled bacteria from soil collected from the surface of plant roots. For reference, the scale bar at bottom right is 10 micrometers long. (Rhona Stuart)
    A Powerful Technique to Study Microbes, Now Easier
    In JGI's Genome Insider podcast: LLNL biologist Jennifer Pett-Ridge collaborated with JGI scientists through the Emerging Technologies Opportunity Program to semi-automate experiments that measure microbial activity in soil.

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    A view of the mangroves from which the giant bacteria were sampled in Guadeloupe. (Hugo Bret)
    Giant Bacteria Found in Guadeloupe Mangroves Challenge Traditional Concepts
    Harnessing JGI and Berkeley Lab resources, researchers characterized a giant - 5,000 times bigger than most bacteria - filamentous bacterium discovered in the Caribbean mangroves.

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    In their approved proposal, Frederick Colwell of Oregon State University and colleagues are interested in the microbial communities that live on Alaska’s glacially dominated Copper River Delta. They’re looking at how the microbes in these high latitude wetlands, such as the Copper River Delta wetland pond shown here, cycle carbon. (Courtesy of Rick Colwell)
    Monitoring Inter-Organism Interactions Within Ecosystems
    Many of the proposals approved through JGI's annual Community Science Program call focus on harnessing genomics to developing sustainable resources for biofuels and bioproducts.

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    Coloring the water, the algae Phaeocystis blooms off the side of the sampling vessel, Polarstern, in the temperate region of the North Atlantic. (Katrin Schmidt)
    Climate Change Threatens Base of Polar Oceans’ Bountiful Food Webs
    As warm-adapted microbes edge polewards, they’d oust resident tiny algae. It's a trend that threatens to destabilize the delicate marine food web and change the oceans as we know them.

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News & Publications
Home › News & Publications › Publications › 2022 Publications

2022 Publications

Amundson, Kaela K. et al. (2022) Microbial colonization and persistence in deep fractured shales is guided by metabolic exchanges and viral predation. Microbiome 10(1), 5. 10.1186/s40168-021-01194-8
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Appiah-Madson, Hannah J. et al. (2022) Do Genetic Drift and Gene Flow Affect the Geographic Distribution of Female Plants in Gynodioecious Lobelia siphilitica?. Plants 11(6), 825. 10.3390/plants11060825
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Baisya, Dipankar et al. (2022) Genome-wide functional screens enable the prediction of high activity CRISPR-Cas9 and -Cas12a guides in Yarrowia lipolytica. Nature Communications 13(1), 922. 10.1038/s41467-022-28540-0
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Banerjee, Deepro et al. (2022) EnZymClass: Substrate specificity prediction tool of plant acyl-ACP thioesterases based on ensemble learning. Current Research in Biotechnology 4, 1-9. 10.1016/j.crbiot.2021.12.002
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Barnes, Elle M. et al. (2022) Exploring the roles of microbes in facilitating plant adaptation to climate change. Biochemical Journal 479(3), 327-335. 10.1042/bcj20210793
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Bewg, William P. et al. (2022) Multiplex knockout of trichome-regulating MYB duplicates in hybrid poplar using a single gRNA. Plant physiology . 10.1093/plphys/kiac128
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Bouché, Frédéric et al. (2022) EARLY FLOWERING 3 and Photoperiod Sensing in Brachypodium distachyon. Frontiers in Plant Science 12, 769194. 10.3389/fpls.2021.769194
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Bredeweg, Erin L. et al. (2022) Phenotype to genotype in Neurospora crassa: Association of the scumbo phenotype with mutations in the gene encoding ceramide C9-methyltransferase. Current Research in Microbial Sciences 3, 100117. 10.1016/j.crmicr.2022.100117
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Buijs, Valerie A. et al. (2022) Enemy or ally: a genomic approach to elucidate the lifestyle of Phyllosticta citrichinaensis. G3 (Bethesda, Md.) . 10.1093/g3journal/jkac061
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Carrell, Alyssa A. et al. (2022) Habitat‐adapted microbial communities mediate Sphagnum peatmoss resilience to warming. New Phytologist . 10.1111/nph.18072
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Chadwick, Grayson L. et al. (2022) Comparative genomics reveals electron transfer and syntrophic mechanisms differentiating methanotrophic and methanogenic archaea. PLoS Biology 20(1), e3001508. 10.1371/journal.pbio.3001508
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Chen, Song‐Can et al. (2022) Genome and proteome analyses show the gaseous alkane degrader Desulfosarcina sp. strain BuS5 as an extreme metabolic specialist. Environmental Microbiology . 10.1111/1462-2920.15956
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Chroumpi, Tania et al. (2022) Detailed analysis of the D-galactose catabolic pathways in Aspergillus niger reveals complexity at both metabolic and regulatory level. Fungal Genetics and Biology 159, 103670. 10.1016/j.fgb.2022.103670
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Ciobanu, Doina et al. (2022) Protocol for single-cell isolation and genome amplification of environmental microbial eukaryotes for genomic analysis. STAR Protocols 3(1), 100968. 10.1016/j.xpro.2021.100968
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D'Angelo, Francesca et al. (2022) Cellular assays identify barriers impeding iron-sulfur enzyme activity in a non-native prokaryotic host. eLife 11, e70936. 10.7554/elife.70936
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de Mesquita, Clifton P. Bueno et al. (2022) Methylphosphonate Degradation and Salt-Tolerance Genes of Two Novel Halophilic Marivita Metagenome-Assembled Genomes from Unrestored Solar Salterns. Genes 13(1), 148. 10.3390/genes13010148
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de Vries, Lisanne et al. (2022) pHBMT1, a BAHD-family monolignol acyltransferase, mediates lignin acylation in poplar. Plant Physiology 188(2), 1014-1027. 10.1093/plphys/kiab546
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diCenzo, George C. et al. (2022) DNA Methylation in Ensifer Species during Free-Living Growth and during Nitrogen-Fixing Symbiosis with Medicago spp. mSystems 7(1), e01092-21. 10.1128/msystems.01092-21
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Fiore-Donno, Anna Maria et al. (2022) Soil compartments (bulk soil, litter, root and rhizosphere) as main drivers of soil protistan communities distribution in forests with different nitrogen deposition. Soil Biology and Biochemistry 168, 108628. 10.1016/j.soilbio.2022.108628
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Franco, Mario E. E. et al. (2022) Ecological generalism drives hyperdiversity of secondary metabolite gene clusters in xylarialean endophytes. New Phytologist 233(3), 1317-1330. 10.1111/nph.17873
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Gao, Cheng et al. (2022) Successional adaptive strategies revealed by correlating arbuscular mycorrhizal fungal abundance with host plant gene expression. Molecular Ecology . 10.1111/mec.16343
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Garrigues, Sandra et al. (2022) Unraveling the regulation of sugar beet pulp utilization in the industrially relevant fungus Aspergillus niger. iScience 25(4), 104065. 10.1016/j.isci.2022.104065
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Gautam, Jyotshana et al. (2022) Adapted laboratory evolution of Thermotoga sp. strain RQ7 under carbon starvation. BMC Research Notes 15(1), 99. 10.1186/s13104-022-05982-9
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Gortikov, Maggie et al. (2022) Sequencing and Analysis of the Entire Genome of the Mycoparasitic Bioeffector Fungus Trichoderma asperelloides Strain T 203 (Hypocreales). Microbiology Resource Announcements 11(2), e00995-21. 10.1128/mra.00995-21
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Hill, Richard A. et al. (2022) Abscisic acid supports colonization of Eucalyptus grandis roots by the mutualistic ectomycorrhizal fungus Pisolithus microcarpus. New Phytologist 233(2), 966-982. 10.1111/nph.17825
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Hix, Gary R. et al. (2022) Characterization of Streptomyces nymphaeiformis sp. nov., and its taxonomic relatedness to other polyhydroxybutyrate-degrading streptomycetes. International journal of systematic and evolutionary microbiology 72(3). 10.1099/ijsem.0.005266
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Honeker, Linnea K. et al. (2022) Elucidating Drought-Tolerance Mechanisms in Plant Roots through 1H NMR Metabolomics in Parallel with MALDI-MS, and NanoSIMS Imaging Techniques. Environmental Science & Technology 56(3), 2021-2032. 10.1021/acs.est.1c06772
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Ke, Jing et al. (2022) Development of platforms for functional characterization and production of phenazines using a multi-chassis approach via CRAGE. Metabolic Engineering 69, 188-197. 10.1016/j.ymben.2021.11.012
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Kolton, Max et al. (2022) Defining the Sphagnum Core Microbiome across the North American Continent Reveals a Central Role for Diazotrophic Methanotrophs in the Nitrogen and Carbon Cycles of Boreal Peatland Ecosystems. mBio 13(1), e03714-21. 10.1128/mbio.03714-21
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Lamb, Austin et al. (2022) Bioenergy sorghum’s deep roots: A key to sustainable biomass production on annual cropland. GCB Bioenergy 14(2), 132-156. 10.1111/gcbb.12907
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Lanahan, Anthony et al. (2022) A Single Nucleotide Change in the polC DNA Polymerase III in Clostridium thermocellum Is Sufficient To Create a Hypermutator Phenotype. Applied and Environmental Microbiology 88(1), e01531-21. 10.1128/aem.01531-21
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Lee, Jong-Won et al. (2022) Controlling selectivity of modular microbial biosynthesis of butyryl-CoA-derived designer esters. Metabolic Engineering 69, 262-274. 10.1016/j.ymben.2021.12.001
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Lee, Sungeun et al. (2022) Soil pH influences the structure of virus communities at local and global scales. Soil Biology and Biochemistry 166, 108569. 10.1016/j.soilbio.2022.108569
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Lewin, Harris A. et al. (2022) The Earth BioGenome Project 2020: Starting the clock. Proceedings of the National Academy of Sciences 119(4), e2115635118. 10.1073/pnas.2115635118
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Liu, Furong et al. (2022) Silencing of Dicer‐like protein 2a restores the resistance phenotype in the rice mutant, sxi4 (suppressor of Xa21‐mediated immunity 4). The Plant Journal . 10.1111/tpj.15692
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Looney, Brian et al. (2022) Evolutionary transition to the ectomycorrhizal habit in the genomes of a hyperdiverse lineage of mushroom‐forming fungi. New Phytologist . 10.1111/nph.17892
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Macdonald, Spencer S. et al. (2022) A Synthetic Gene Library Yields a Previously Unknown Glycoside Phosphorylase That Degrades and Assembles Poly-β-1,3-GlcNAc, Completing the Suite of β‑Linked GlcNAc Polysaccharides. ACS Central Science . 10.1021/acscentsci.1c01570
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Matson, Morgan M. et al. (2022) Adaptive laboratory evolution for improved tolerance of isobutyl acetate in Escherichia coli. Metabolic Engineering 69, 50-58. 10.1016/j.ymben.2021.11.002
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Mazzoli, Roberto et al. (2022) In vivo evolution of lactic acid hyper-tolerant Clostridium thermocellum. New Biotechnology 67, 12-22. 10.1016/j.nbt.2021.12.003
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Meng, Jiali et al. (2022) GalR, GalX and AraR co‐regulate d‐galactose and l‐arabinose utilization in Aspergillus nidulans. Microbial Biotechnology . 10.1111/1751-7915.14025
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Muleta, Kebede T. et al. (2022) The recent evolutionary rescue of a staple crop depended on over half a century of global germplasm exchange. Science advances 8(6), eabj4633. 10.1126/sciadv.abj4633
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Niu, Puhua et al. (2022) Protocol for condition-dependent metabolite yield prediction using the TRIMER pipeline. STAR Protocols 3(1), 101184. 10.1016/j.xpro.2022.101184
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Palma, Margarida et al. (2022) Genome Sequence and Analysis of the Flavinogenic Yeast Candida membranifaciens IST 626. Journal of Fungi 8(3), 254. 10.3390/jof8030254
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Persoons, Antoine et al. (2022) Genomic Signatures of a Major Adaptive Event in the Pathogenic Fungus Melampsora larici-populina. Genome Biology and Evolution 14(1), evab279. 10.1093/gbe/evab279
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Pudlo, Nicholas A. et al. (2022) Diverse events have transferred genes for edible seaweed digestion from marine to human gut bacteria. Cell Host & Microbe 30(3), 314-328.e11. 10.1016/j.chom.2022.02.001
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Rasmussen, Anna N. et al. (2022) Genome-Resolved Metagenomic Insights into Massive Seasonal Ammonia-Oxidizing Archaea Blooms in San Francisco Bay. mSystems 7(1), e01270-21. 10.1128/msystems.01270-21
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Reichart, Nicholas J. et al. (2022) Metagenomes and Metagenome-Assembled Genomes from Substrate-Amended Hot Spring Sediment Incubations from Yellowstone National Park. Microbiology Resource Announcements , e01065-21. 10.1128/mra.01065-21
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Rodríguez-Gijón, Alejandro et al. (2022) A Genomic Perspective Across Earth’s Microbiomes Reveals That Genome Size in Archaea and Bacteria Is Linked to Ecosystem Type and Trophic Strategy. Frontiers in Microbiology 12, 761869. 10.3389/fmicb.2021.761869
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Rubinstein, Rebecca L. et al. (2022) ORT: A workflow linking genome-scale metabolic models with reactive transport codes. Bioinformatics (Oxford, England) 38(3), 778-784. 10.1093/bioinformatics/btab753
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Ruhl, Ilona A. et al. (2022) GAL08, an Uncultivated Group of Acidobacteria, Is a Dominant Bacterial Clade in a Neutral Hot Spring. Frontiers in Microbiology 12, 787651. 10.3389/fmicb.2021.787651
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Rybnicky, Grant A. et al. (2022) Development of a Freeze-Dried CRISPR-Cas12 Sensor for Detecting Wolbachia in the Secondary Science Classroom. ACS Synthetic Biology 11(2), 835-842. 10.1021/acssynbio.1c00503
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Rybnicky, Grant A. et al. (2022) Spacer2PAM: A computational framework to guide experimental determination of functional CRISPR-Cas system PAM sequences. Nucleic Acids Research 50(6), 3523-3534. 10.1093/nar/gkac142
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Sasaki, Yusuke et al. (2022) Metabolic engineering for valorization of macroalgae biomass. Metabolic Engineering 71, 42-61. 10.1016/j.ymben.2022.01.005
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Scarborough, Matthew J. et al. (2022) Metagenome-Assembled Genomes from a Microbiome Converting Xylose to Medium-Chain Carboxylic Acids. Microbiology Resource Announcements , e01151-21. 10.1128/mra.01151-21
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Schweitzer, Hannah D. et al. (2022) Subsurface hydrocarbon degradation strategies in low- and high-sulfate coal seam communities identified with activity-based metagenomics. npj Biofilms and Microbiomes 8(1), 7. 10.1038/s41522-022-00267-2
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Seidel, Laura et al. (2022) Weakened resilience of benthic microbial communities in the face of climate change. ISME Communications 2(1), 21. 10.1038/s43705-022-00104-9
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Shahan, Rachel et al. (2022) A single-cell Arabidopsis root atlas reveals developmental trajectories in wild-type and cell identity mutants. Developmental Cell 57(4), 543-560.e9. 10.1016/j.devcel.2022.01.008
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Sharon, Itai et al. (2022) Structure and Function of the β‑Asp-Arg Polymerase Cyanophycin Synthetase 2. ACS Chemical Biology 17(3), 670-679. 10.1021/acschembio.1c01007
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Sønstebø, Jørn Henrik et al. (2022) Population genomics of a forest fungus reveals high gene flow and climate adaptation signatures. Molecular Ecology 31(7), 1963-1979. 10.1111/mec.16369
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Strenkert, Daniela et al. (2022) An optimized ChIP‐Seq framework for profiling histone modifications in Chromochloris zofingiensis. Plant Direct 6(3), e392. 10.1002/pld3.392
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Sun, Yi-Fei et al. (2022) Phylogenomics and Comparative Genomics Highlight Specific Genetic Features in Ganoderma Species. Journal of Fungi 8(3), 311. 10.3390/jof8030311
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Traving, Sachia J. et al. (2022) On Single-Cell Enzyme Assays in Marine Microbial Ecology and Biogeochemistry. Frontiers in Marine Science 9. 10.3389/fmars.2022.846656
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Van Houghton, Brett D. et al. (2022) Membrane Bioreactor Pretreatment of High-Salinity O&G Produced Water. ACS ES&T Water 2(3), 484-494. 10.1021/acsestwater.1c00436
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Weiner, Agnes K. M. et al. (2022) Examining the Relationship Between the Testate Amoeba Hyalosphenia papilio (Arcellinida, Amoebozoa) and its Associated Intracellular Microalgae Using Molecular and Microscopic Methods. Protist 173(1), 125853. 10.1016/j.protis.2021.125853
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Wimmer, Franziska et al. (2022) A TXTL-Based Assay to Rapidly Identify PAMs for CRISPR-Cas Systems with Multi-Protein Effector Complexes. , 391-411. 10.1007/978-1-0716-1998-8_24
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Wimmer, Franziska et al. (2022) Rapid cell-free characterization of multi-subunit CRISPR effectors and transposons. Molecular Cell 82(6), 1210-1224.e6. 10.1016/j.molcel.2022.01.026
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Wint, Rhondene et al. (2022) Kingdom-Wide Analysis of Fungal Protein-Coding and tRNA Genes Reveals Conserved Patterns of Adaptive Evolution. Molecular Biology and Evolution 39(2), msab372. 10.1093/molbev/msab372
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Wong-Bajracharya, Johanna et al. (2022) The ectomycorrhizal fungus Pisolithus microcarpus encodes a microRNA involved in cross-kingdom gene silencing during symbiosis. Proceedings of the National Academy of Sciences 119(3), e2103527119. 10.1073/pnas.2103527119
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Wu, Gang et al. (2022) Evolutionary innovations through gain and loss of genes in the ectomycorrhizal Boletales. New Phytologist 233(3), 1383-1400. 10.1111/nph.17858
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