JGI Genomics of Energy and Environment Meeting
Sunday, March 22rd |
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| 8:00 AM – 12:00 PM | KBase Isolate Analysis Workshop | Ben Allen, Oak Ridge National Laboratory |
| 12:00 PM – 1:00 PM | Lunch Break | |
| 1:00 PM – 5:00 PM | KBase Metabolic Modeling Workshop | Jose P. Faria, Argonne National Laboratory |
Monday, March 23th |
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| 8:00 AM – 5:00 PM | Fungal and Algal Genomics Workshop | Igor Grigoriev, DOE Joint Genome Institute |
| 8:00 AM – 12:00 PM | KBase Microbiome Workshop | Dylan Chivian, Lawrence Berkeley National Laboratory
Janaka N. Edirisinghe, Argonne National Laboratory |
| 12:00 PM – 1:00 PM | Lunch Break | |
| 1:00 PM – 5:00 PM | KBase Functional Genomics Analysis Workshop | Sunita Kumari, Cold Spring Harbor Laboratory
Vivek Kumar, Cold Spring Harbor Laboratory |
Tuesday, March 24thUser Meeting Kick Off |
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| 8:30 AM – noon | Session 1: Beyond Sequence: Exploring the Universe of Specialized Metabolites | Session Chair: Nigel Mouncey, JGI Director / Trent Northen, Metabolomics Group Lead |
| 8:30 AM – 8:45 AM | Metabolomics / Secondary Metabolites at JGI | |
| 8:45 AM – 9:00 AM | Short Talk | |
| 9:00 AM – 9:30 AM | “(Meta)-Genomic Tools for Antibiotic Discovery” | Nadine Ziemert, German Centre for Infection Research |
| 9:30 AM – 10:00 AM | “Harnessing Genomic Information and Synthetic Biology to Engineer the Biosynthesis of Novel Antibiotics”. | Lucy Foulston, Ginkgo Bioworks |
| 10:00 AM – 10:30 AM | Break | |
| 10:30 AM – 10:45 Am | Short Talk | |
| 10:45 AM – 11:00 AM | Short Talk | |
| 11:00 AM – 11:30 AM | “GenoChemetics – blending synthetic biology with synthetic chemistry, enabling access to new to nature natural products” | Rebecca Goss, University of St. Andrews |
| 11:30 AM – 12:00 PM | “Genome Mining from Fungi for New Natural Products” | Yi Tang, University of California Los Angeles |
| 12:00 PM – 1:00 PM | Industry Showcase Luncheon | |
| 1:00 PM – 5:00 PM | Session 2: Understanding Ecosystems: From Microbial Sequence to Environmental Function | Session Chair: Simon Roux, DOE Joint Genome Institute /Tanja Woyke, DOE Joint Genome Institute |
| 1:00 PM – 1:15 PM | Microbial and Metagenome Programs at JGI | |
| 1:15 PM – 1:30 PM | “Preparing the Next Generation of Users: Bringing JGI Data into the Classroom, Generating New Discoveries” | Matthew Escobar, CSU San Marcos |
| 1:30 PM – 2:00 PM | “Small Ripples Make Big Tides: Genomics Informed Biogeochemistry of River Sediments” | Kelly Wrighton, Colorado State University |
| 2:00 PM – 2:30 PM | “An Archaeon at the Prokaryote–Eukaryote Interface: Isolation, Genomics, and New Insights into Eukaryogenesis” | Masaru K. Nobu, National Institute of Advanced Industrial Science and Technology |
| 2:30 PM -3:00 PM | “Ecosystem Effects of Viruses in Marine Oxygen Minimum Zones” | Jennifer Brum, Louisiana State University |
| 3:00 PM – 3:30 PM | Break | |
| 3:30 PM – 4:00 PM | “Understanding the Fitness of Soil Bacteria from Genomes to Traits” | Eoin Brodie, Lawrence Berkeley National Laboratory |
| 4:00 PM – 5:00 PM | Keynote Speaker | Bin Yu, University of California, Berkeley |
| 5:00 PM – 5:30 PM | Sponsor Lightning Talks | |
| 5:30 PM – 8:00 PM | Poster Session & Sponsor Showcase Reception | |
Wednesday, March 25th |
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| 8:30 AM – noon | Session 3: Of Friends and Foes: The Many Facets of Plant-Microbial Interactions | Session Chair: Jeremy Schmutz, HudsonAlpha Institute for Biotechnology /Igor Grigoriev, DOE Joint Genome Institute |
| 8:30 AM – 8:45 AM | Plant and Fungal Programs at JGI | |
| 8:45 AM – 9:00 AM | Short Talk | |
| 9:00 AM – 9:30 AM | “The Ecological and Genetic Basis of Resistance to Switchgrass Pathogen Across North America” | David Lowry, Michigan State University |
| 9:30 AM – 10:00 AM | “Fungal Secondary Metabolites and Virulence to Plants” | B. Gillian Turgeon, Cornell University |
| 10:00 AM – 10:30 AM | Break | |
| 10:30 AM – 10:45 AM | Short Talk | |
| 10:45 AM – 11:00 AM | Short Talk | |
| 11:00 AM – 11:30 AM | “Understanding the Relation Between Genome Sequence and the Dynamic Interface Between Populus and its Mycobiome” | Jessy Labbe, Oak Ridge National Laboratory |
| 11:30 AM – 12:00 PM | “Comparative Genomics of the Xylariaceae: What are the Functional Roles of Previously Unknown Endophytic Fungi?” | Jana U’Ren, The University of Arizona |
| 12:00 PM – 1:00 PM | Industry Showcase Luncheon | |
| 1:00 PM – 5:00 PM | Session 4: Smarter Than Us: Machine Learning and Artificial Intelligence for Biology | Session Chair: Kjiersten Fagnan, DOE Joint Genome Institute / Nikos Kyrpides, DOE Joint Genome Institute |
| 1:00 – 1:15 PM | Data Science and Informatics at JGI | |
| 1:15 PM – 1:30 PM | Short Talk | |
| 1:30 PM 2:00 PM | “What Can Deep Learning Do For You?” | Brenda Ng, Lawrence Livermore National Laboratory |
| 2:00 PM – 2:30 PM | Talk Title TBD | Kathy Yelick, Lawrence Berkeley National Laboratory |
| 2:30 PM – 3:00 PM | “New Bioinformatic Methods to Recover 100s of Genomes and their Interactions from Metagenomic Chronoseries” | Kostas Konstantinidis, Georgia Institute Technology |
| 3:00 PM – 3:30 PM | Break | |
| 3:30 PM – 4:00 PM | Talk Title TBD | Berenice Wulbrecht, Ontoforce |
| 4:00 PM – 5:00 PM | Keynote Speaker – “Genomics of wild and domesticated plant diversity for crop improvement” | Robert Henry, The University of Queensland |
| 5:00 PM – 8:00 PM | Poster Session & Sponsor Showcase Reception | |
Thursday, March 26th |
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| 8:30 AM – noon | Session 5: Building Better: Integrative Omics-Inspired Plant and Microbe Engineering | Session Chair: Yasuo Yoshikuni, DOE Joint Genome Institute / Ian Blaby, DOE Joint Genome Institute |
| 8:30 AM – 8:45 AM | DNA Synthesis Science at JGI | |
| 8:45 AM – 9:00 AM | Short Talk | |
| 9:00 AM – 9:30 AM | “Ecological Assembly of Rhizosphere Microbiomes Associated with Increased Yield of Brassica Rapa” | Jenny Kao-Kniffin, Cornell University |
| 9:30 AM – 10:00 AM | “A bottom-up approach to understanding the dynamics and functions of microbial communities.” | Ophelia Venturelli, University of Wisconsin |
| 10:00 AM – 10:30 AM | Break | |
| 10:30 AM – 11:00 AM | Talk Title TBD | |
| 11:00 AM – 11:30 AM | “In vitro Synthetic Biology – Using Cell Free Extracts From Non-Model Organisms to Prototype Parts, Biosynthetic Pathways and Chemical Synthesis” | Paul Freemont, Imperial College London |
| 11:30 AM – 12:00 PM | Talk Title TBD | Karsten Temme, Pivot Bio |
| 12:00 PM – 1:00 PM | Lunch – TBD | |
| 1:00 PM – 3:00 PM | Session 6: The Cutting Edge: 2020 User Science Highlights | Session Chair: Susannah Tringe, DOE Joint Genome Institute / Axel Visel, DOE Joint Genome Institute |
| 1:00 PM – 2:00 PM | CSP User Flash Talks | |
| 2:00 PM – 3:00 PM | Keynote Speaker – “Bio-manufacturing in green algae – Food and Fuel for the 21st Century” | Stephen Mayfield, University of California, San Diego |
| 3:00 PM | End of JGI User Meeting |