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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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    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.

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    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.

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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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    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.

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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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    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.

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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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    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.

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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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    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.

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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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About Us
Home › About Us › People › The JGI Leadership Team › Len Pennacchio
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Len Pennacchio

Len Pennacchio

Len Pennacchio, Deputy of Genomic Technologies, DOE Joint Genome Institute

In 2003, Dr. Pennacchio joined the DOE Joint Genome Institute and has focused on applying state-of-the-art molecular methods to address wide-ranging questions existing in biology. He holds joint appointments as a Deputy Director at the DOE Joint Genome Institute, Senior Scientist at Lawrence Berkeley Laboratory, and Adjunct Professor at UC Berkeley. Dr. Pennacchio received his Ph.D in 1998 from the Department of Genetics at Stanford University where he uncovered the genetic cause of a rare form of human epilepsy and subsequently generated one of the first mouse models for this common neurological disorder. In 1999, he was named a DOE Alexander Hollaender Distinguished Fellow where he identified a novel apolipoprotein (ApoA5) involved in human and mouse triglyceride metabolism. He is funded by DOE and through continued competitive grant support from NIH.

Education

  • BA in Biology, Sonoma State University
  • PhD in Genetics, Stanford University
  • DOE Alexander Hollaender Distinguished Fellow, Lawrence Berkeley National Laboratory

About the Deputy of Genomic Technologies

The Deputy of Genomic Technologies serves as the JGI’s primary point of contact for all High-Throughput Data Generation Platforms (Sequencing, Single Cell, DNA Synthesis, and Metabolomics) as well as Research & Development in all of these areas. Additional duties of this Deputy include interacting with users seeking to exploit new genomic technologies and providing a vision for future technical JGI directions for DOE User science.

Service, Awards, and Honors

  • 2021-  NLM Board of Regents Working Group on “NIH Comparative Genomics Resource”
  • 2021-  Co-Chair, “Advances in Genome Biology & Technology- Agriculture”
  • 2021-  Weill Neurohub Investigator
  • 2020   Elected Fellow of the American Association for the Advancement of Science (AAAS)
  • 2020- National Advisory Council, National Human Genome Research Institute, NIH
  • 2019   Lawrence Berkeley Laboratory Director’s Award for Exceptional Scientific Achievement
  • 2017-  Adjunct Professor UC-Berkeley
  • 2015-  Co-Chair, “Advances in Genome Biology & Technology-Precision Health”
  • 2013-  Instructor Leena Peltonen School of Human Genomics, Sanger Center
  • 2011-  Co-Organizer “Systems Biology of Gene Regulation and Genome Editing,” Cold Spring Harbor Asia
  • 2011-  Board of Directors, The Genome Partnership
  • 2008- Co-Chair, “Advances in Genome Biology & Technology (AGBT)”

Current research interests and ongoing projects

  • Defining the vast landscape of gene regulatory sequences in the human genome.
  • Understanding how variation in regulatory sequences influences human disease/biology.
  • Assessing and exploiting next generation sequencing technologies for applications in both the energy and health sectors.
  • Mammalian Functional Genomics Lab
  • VISTA Enhancers
  • VISTA Cardiac Enhancer Browser
  • ENCODE
  • FaceBase

Complete Publications

Genomic Technologies Program

  • The JGI Leadership Team
    • Nigel Mouncey
    • Massie S. Ballon
    • Tina Clarke
    • Nick Everson
    • Kjiersten Fagnan
    • Len Pennacchio
    • Axel Visel
    • Tanja Woyke

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