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
    A panoramic view of a lake reflecting a granite mountain.
    Genome Insider: Methane Makers in Yosemite’s Lakes
    Meet researchers who sampled the microbial communities living in the mountaintop lakes of the Sierra Nevada mountains to see how climate change affects freshwater ecosystems, and how those ecosystems work.

    Listen

    A light green shrub with spiny leaves, up close.
    Genome Insider: A Shrubbier Version of Rubber
    Hear from the consortium working on understanding the guayule plant's genome, which could lead to an improved natural rubber plant.

    Listen

    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

  • Data & Tools
    • IMG
    • Data Portal
    • MycoCosm
    • PhycoCosm
    • Phytozome
    • GOLD
    iPHoP image (Simon Roux)
    iPHoP: A Matchmaker for Phages and their Hosts
    Building on existing virus-host prediction approaches, a new tool combines and evaluates multiple predictions to reliably match viruses with their archaea and bacteria hosts.

    More

    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

  • User Programs
    • Calls for Proposals
    • Special Initiatives & Programs
    • Product Offerings
    • User Support
    • Policies
    • Submit a Proposal
    Green plant matter grows from the top, with the area just beneath the surface also visible as soil, root systems and a fuzzy white substance surrounding them.
    Supercharging SIP in the Fungal Hyphosphere
    Applying high-throughput stable isotope probing to the study of a particular fungi, researchers identified novel interactions between bacteria and the fungi.

    More

    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

    croppe image of the JGI helix sculpture
    Tips for a Winning Community Science Program Proposal
    In the Genome Insider podcast, tips to successfully avail of the JGI's proposal calls, many through the Community Science Program.

    Listen

  • 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

    image from gif that shows where in the globe JGI fungal collaborators are located.
    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

News & Publications
Home › News Releases › JGI Contributes Nine to 2022 Highly Cited Researchers List

January 31, 2023

JGI Contributes Nine to 2022 Highly Cited Researchers List

Nine headshots, one for each researcher, laid out beside a purple ribbon reading, "Home to Highly Cited Researchers 2022 Clarivate"Congratulations to the 2022 Highly Cited Researchers from the JGI recognized for their “significant influence in their chosen field or fields through the publication of multiple highly cited papers during the last decade” by Clarivate Analytics.

This year’s list features 6,900 researchers working in 21 fields. Those from the JGI whose publications rank in the top 1% by citations for field and publication year are:

  • Igor Grigoriev (Cross-field) 
  • Marcel Huntemann (Cross-field) 
  • Natalia Ivanova (Biology and Biochemistry) 
  • Nikos Kyrpides (Biology and Biochemistry) 
  • Dan Rokhsar (Cross-field) 
  • Simon Roux (Cross-field) 
  • Jeremy Schmutz (Cross-field) 
  • Susannah Tringe (Microbiology) 
  • Tanja Woyke (Biology and Biochemistry) 

Here’s a selection of studies these busy bees contributed to: 

Single filament of Ca. Thiomargarita magnifica (Jean-Marie Volland)

Single filament of Ca. Thiomargarita magnifica (Jean-Marie Volland)

Giant bacteria visible to the naked eye: Natalia Ivanova and Tanja Woyke both contributed to ground-breaking research following the discovery of bacteria 5,000 times the average size. Woyke’s Single Cells Group helped better-understand what the sulfur-oxidizing, carbon fixing bacterium was doing in the Guadeloupean mangroves where it was found. The study was featured on the New York Times 2022 List of Firsts as well as other year-end science discovery lists. 

Updates to the Genomic Encyclopedia of Bacteria and Archaea: Under the umbrella of the GEBA, the JGI is sequencing thousands of bacterial and archaeal genomes from diverse branches of the Tree of Life. 

Its latest addition — made possible in part by contributions from Ivanova, Woyke, Marcel Huntemann, Nikos Kyrpides and Simon Roux — features 600 genome sequences for Actinobacteria. 

Woyke was also one of three authors on a recent study that made the cover of Nature Reviews Microbiology, summarizing insights from three decades of work on giant viruses — providing a perspective on giant virus diversity, and how sequencing and bioinformatics have sped up the study of giant viruses. 

Kyrpides and the JGI’s IMG/M Data Portal were instrumental to a study that looked into how soil viruses, and in particular a chitosanase protein, can contribute to soil health. He also contributed to an update of the JGI’s Genome OnLine Database (GOLD) database that also marked the platform’s 25th anniversary, published in Nucleic Acids Research. 

ID’ing RNA viruses with ease: Searching for RNA sequences within a database can be like combing for the proverbial need in a haystack — until now. Scientists have recently created a computational pipeline that scans specifically for RNA virus sequences, initially using it to comb through more than 5,000 data sets and thereby increasing RNA virus diversity five-fold. 

Ivanova, Roux and Kyrpides are all authors on the study. Huntemann, Woyke, Igor Grigoriev and Susannah Tringe also contributed as part of the study’s RNA Virus Discovery Consortium. 

Grigoriev contributed to a cover article detailing how forest floors, in particular the soil microbiome, recover post-wildfire. He and Tringe were also involved in a study that applied metagenomic capabilities to studying phytoplankton microbiomes from polar and non-polar oceans.  

A green fern against a black backdrop

As it turns out, Ceratopteris richardii has been hoarding and co-opting genes for millenia — making it both enormous and complex.(David Randall and Zhonghua Chen)

The reasons behind C-fern’s size and complexity revealed: C-fern is typical of most ferns in many ways, including its large genome with numerous chromosomes. This recent study, including work from Jeremy Schmutz, reveals that C-fern’s size and complexity is not due to whole-genome duplication, as was previously thought. Instead, it turns out this fern has been co-opting genes from bacteria.

Schmutz was also involved in a switchgrass study that delved into the nuances of the plant’s genome. A candidate bioenergy feedstock, switchgrass has adapted to expand its habitat range —but at what cost? 

Dan Rokshar contributed to the demystification of cassava related to recent advances in genome assemblies for the heterozygous staple crop, as well as the discussion of key cassava genomic resources. Genome annotations for cassava are available on the JGI plant portal Phytozome.

Share this:

  • Click to share on Facebook (Opens in new window)
  • Click to share on LinkedIn (Opens in new window)
  • Click to share on Pinterest (Opens in new window)
  • Click to share on Twitter (Opens in new window)
  • Click to print (Opens in new window)

The U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility at Lawrence Berkeley National Laboratory, is committed to advancing genomics in support of DOE missions related to clean energy generation and environmental characterization and cleanup. JGI provides integrated high-throughput sequencing and computational analysis that enable systems-based scientific approaches to these challenges. Follow @jgi on Twitter.

DOE’s Office of Science is the largest supporter of basic research in the physical sciences in the United States, and is working to address some of the most pressing challenges of our time. For more information, please visit science.energy.gov.

Filed Under: News Releases

More topics:

  • COVID-19 Status
  • News
  • Science Highlights
  • Blog
  • Webinars
  • CSP Plans
  • Featured Profiles

Related Content:

You can move, but you can’t hide

Illustration of a magnifying glass identifying viruses and plasmids.

JGI announces second round of 2023 New Investigator awardees

From left to right: [above] Emma Bell, Mallory Choudoir, Sneha Couvillion, Tobin Hammer, Christina Hazard, Rachel Mackelprang, Brook Moyers, Mei, Ran,; [below] Benjamin Peterson, Dacheng Ren, Allison Rober, Neal Scott, Chikae Tatsumi, Vojtech Tlaskal, Fernando Torralbo, Luis Felipe Valdez-Nuñez

A Collaboration to Improve Plant Genome Annotations Across Species

A tiled collage of square photos of different plants - soybeans, and sorghum, for example.

From Berkeley to Binghamton: Tracking Strawberry Evolution

iPHoP: A Matchmaker for Phages and their Hosts

iPHoP image (Simon Roux)

Supercharging SIP in the Fungal Hyphosphere

Green plant matter grows from the top, with the area just beneath the surface also visible as soil, root systems and a fuzzy white substance surrounding them.
  • 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