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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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    (PXFuel)
    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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Home › About Us › People › The JGI Leadership Team › Tanja Woyke
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Tanja Woyke

Tanja Woyke

Tanja Woyke, Deputy of User Programs, DOE Joint Genome Institute

After studying the mechanism of action of antifungal natural products and their derivatives during her Ph.D. in Microbiology at the Eberhard Karls University Tübingen (Germany), Dr. Woyke pursued her postdoctoral research at the DOE Joint Genome Institute in 2004. The main object of her research was the symbiont community of a gutless oligochaete for which she deciphered function and host-symbiont interplay using metagenomics. Taking on a Research Scientist position in 2007, she switched gears from metagenomics to single-cell genomics, which is now her primary interest and passion. Dr. Woyke stepped into the Microbial Genomics Program Lead position in 2009 and assumed the Deputy Director of User Program position in 2021. In addition to her JGI appointment, she also holds an Adjunct Scientist appointment at the Bigelow Laboratory for Ocean Sciences since 2012 and an Adjunct Associate Professor at the University of California, Merced School of Natural Sciences since 2015.

Read more about Dr. Woyke’s Targeted Genomics lab.

Education

  • MS in Biology, Eberhard Karls University of Tübingen, Germany
  • Ph.D. in Microbiology, Eberhard Karls University of Tübingen, Germany

About the JGI Deputy of User Programs

The Deputy of User Programs provides direction, leadership, and oversight for all JGI user programs, including the Community Science Program and Emerging Technical Opportunity Program. The Deputy of User Programs also acts as a liaison to our partner institutions, funding agencies and the broader scientific community.

Awards and Service

  • 2020 van Niel International Prize for Studies in Bacterial Systematics
  • 2020 Elected fellowship in the American Academy of Microbiology
  • 2015 LBNL Women @ The Lab Award
  • 2014 LBNL 2014 Director’s Award for Exceptional Scientific Achievement
  • Advisory Board Member for Bigelow Laboratory for Ocean Sciences Single Cell Genomics Center (2013-current)
  • Science Advisory Board Member for Science Department, Berkeley City College, (2015-current)
  • Organizing Committee Board Member for Lake Arrowhead Microbial Genomics Conference (2017-current)
  • Genomic Standards Consortium Advisory Board member (2018-current)
  • France Genomique Scientific Advisory Board member (2020-current)
  • Advisory Committee member for the Center for Biotechnology and Bioinformatics at Virginia State University (2021-current). 
  • Editorial Board Member for ISME J (Senior Editor 2016-2021), Peer J (2015-2019), Scientific Data (2017-2019).
  • Reviewer for major journals and funding agencies, including Nature, Nature Biotechnology, Nature Methods, Nature Communications, Nature Protocols, Nature Reviews Genetics, ISME J, Nucleic Acids Research, DOE Small Business Innovation Research (SBIR) grants, UAEU Program for Advanced Research (UPAR) Grant Competition, ANR, ASF, Beckman Institute at Caltech Review (Member of Visiting Committee), NASA Exobiology. 

Selected Publications

  1. Nayfach et al. 2021. A genomic catalog of Earth’s microbiomes. Nature Biotechnology 39, 499-509.
  2. Schulz et al. 2020. Giant virus diversity and host interactions through global metagenomics. Nature 578, 432-436.
  3. Bowers et al. 2017. Minimum information about a single amplified genome (MISAG) and a metagenome- assembled genome (MIMAG) of bacteria and archaea. Nature Biotechnology 35, 725-731.
  4. Mukherjee et al. 2017. 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life. Nature Biotechnology 35, 676-683.
  5. Schulz et al. 2017. Giant viruses with an expanded complement of translation system components. Science 356, 82-85.
  6. Tsementzi et al. 2016. SAR11 bacteria linked to ocean anoxia and nitrogen loss. Nature 536, 179-183.
  7. Ivanova et al. 2014. Stop codon reassignments in the wild. Science 344, 909-913.
  8. Rinke et al. 2013. Insights into the phylogeny and coding potential of microbial dark matter. Nature 499, 431-437.
  9. Hess et al. 2011. Metagenomic discovery of biomass-degrading genes from cow rumen. Science 331, 463-467.
  10. Swan et al. 2011. Potential for chemolithoautotrophy amoung ubiquitous bacteria lineages in the dark ocean. Science 333, 1296-1300.
  11. Newton et al. 2007. The Calyptogena magnifica chemoautotrophic symbiont genome. Science 315, 998-1000.
  12. Woyke et al. 2006. Symbiosis insights through metagenomic analysis of a microbial consortium. Nature 443, 950-955.
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    • Massie S. Ballon
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