JGI Genomics of Energy and Environment Meeting
| Please note: All listings below are Pacific Time |
Monday, August 30th |
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| 7:30AM – 7:45AM | Welcome / Kick Off | Nigel Mouncey, JGI Director |
| 7:45AM – 8:00AM | Theme 1: Beyond Sequence: Exploring the Universe of Specialized Metabolites
“Metabolomics / Secondary Metabolites at JGI” |
Session Chair: Nigel Mouncey, JGI Director / Trent Northen, Metabolomics Group Lead |
| 8:00AM – 8:45AM | Keynote Speaker – “Veridical Data Science for Biological Discovery: Detecting Epistatic Interactions with epiTree” | Bin Yu, University of California, Berkeley |
| 8:45AM – 9:00AM | Short Talk – “From Genome-Scale to Ecosystem-Level Microbial Metabolism Using KBase” | Daniel Segre, Boston University |
| 9:00AM – 9:30AM | “Fungal Secondary Metabolites and Virulence to Plants” | B. Gillian Turgeon, Cornell University |
| 9:30AM – 10:00AM | “Fungal Natural Products – Genome Mining from Fungi for New Natural Products” | Yi Tang, University of California Los Angeles |
| 10:00AM – 11:00AM | Poster Session | |
| 11:00AM – 11:15AM | Theme 2: Understanding Ecosystems: From Microbial Sequence to Environmental Function
“Microbial and Metagenome Programs at JGI” |
Session Chair: Simon Roux, DOE Joint Genome Institute /Tanja Woyke, DOE Joint Genome Institute |
| 11:15AM – 11:45AM | “Understanding the Fitness of Soil Bacteria from Genomes to Traits” | Eoin Brodie, Lawrence Berkeley National Laboratory |
| 11:45AM – 12:00PM | Short Talk – “Lytic Archaeal Viruses of the Continental Deep Biosphere Challenge a Long-Standing Paradigm” | Victoria Turzynski, University of Duisburg-Essen |
| 12:00PM – 12:30PM | “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 |
| 12:30PM – 1:00PM | “Ecosystem Effects of Viruses in Marine Oxygen Minimum Zones” | Jennifer Brum, Louisiana State University |
| 1:00PM – 2:30PM | Introducing KBase – Zoom Registration | Ben Allen, DOE Systems Biology Knowledgebase |
| Please note: All listings below are Pacific Time |
Tuesday, August 31st |
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| 7:30AM – 7:45AM | Theme 3: Of Friends and Foes: The Many Facets of Plant-Microbial Interactions
“Plant and Fungal Programs at JGI” |
Session Chair: Jeremy Schmutz, HudsonAlpha Institute for Biotechnology /Igor Grigoriev, DOE Joint Genome Institute |
| 7:45AM – 8:30AM | Keynote – “Genomics of wild and domesticated plant diversity for crop improvement” | Robert Henry, The University of Queensland |
| 8:30AM – 8:45AM | Short Talk – “From Trophic Cascade to Mutualism: Ecological Genomics Rectifies the Concept of Trichoderma – Plant Interactions” | Irina Druzhinina, Nanjing Agricultural University |
| 8:45AM – 9:15AM | “Comparative Genomics of the Xylariaceae: What are the Functional Roles of Endophytic Fungi?” | Jana U’Ren, The University of Arizona |
| 9:15AM – 9:30AM | Short Talk – “Ectomycorrhizal Fungi Regulate Rhizosphere Metal Ion Processes and Plant Ion Uptake Under High Heavy Metals” | Hui-Ling (Sunny) Liao, University of Florida |
| 9:30AM – 10:00AM |
“The Ecological and Genetic Basis of Switchgrass Microbiome Assembly and Pathogen Impacts Across North America”
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David Lowry, Michigan State University |
| 10:00AM – 11:00AM | Poster Session | |
| 11:00AM – 11:15AM | Theme 4: Smarter Than Us: Machine Learning and Artificial Intelligence for Biology
“Data Science and Informatics at JGI” |
Session Chair: Kjiersten Fagnan, DOE Joint Genome Institute / Nikos Kyrpides, DOE Joint Genome Institute |
| 11:15AM – 11:45AM | “Introduction to Graph Neural Networks” | Brenda Ng, Lawrence Livermore National Laboratory |
| 11:45AM – 12:00PM | Short Talk – “Methods for Fast and Sensitive Meta-Genome Annotation with Confidence Assessment, and a New Lightweight and Flexible Javascript Visualization Library” | Travis Wheeler, University of Montana |
| 12:00PM – 12:30PM | “FAIR and more, boosting Insights for Life Sciences” | Berenice Wulbrecht, Ontoforce |
| 12:30PM – 1:00PM | “A Metagenomic Compendium of DNA Viruses from the Human Gut Microbiome” | Stephen Nayfach, DOE Joint Genome Institute |
| Please note: All listings below are Pacific Time |
Wednesday, September 1st |
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| 7:30AM – 7:45AM | Theme 5: Building Better: Integrative Omics-Inspired Plant and Microbe Engineering
“DNA Synthesis Science at JGI” |
Session Chair: Yasuo Yoshikuni, DOE Joint Genome Institute / Ian Blaby, DOE Joint Genome Institute |
| 7:45AM – 8:30AM | Keynote Speaker – “Bio-manufacturing in green algae – Food and Fuel for the 21st Century” | Stephen Mayfield, University of California, San Diego |
| 8:30AM – 8:45AM | Short Talk – “Optimizing the Thermotolerance of Photorespiration in Higher Plants Through Robust Parameterization of Pathway Kinetics and in Plant Validation” | Berkley Walker, Michigan State University
Aaron Leipmen, Michigan State University |
| 8:45AM – 9:15AM | “An Integrated Cell / Cell-free Metabolic Engineering Approach for Rapid Prototyping of Genes and Pathways” | Hal Alper, University of Texas at Austin |
| 9:15AM – 9:30AM | Short Talk – “Developing a Novel Microbial Host and Synthetic Biology Tools for Valorizing Waste Polyethylene Terephthalate and Lignin” | Tae Seok Moon, Washington University St. Louis |
| 9:30AM – 10:00AM | “GenoChemetics: Blending Synthetic Biology with Synthetic Chemistry for Molecule Making” | Rebecca Goss, University of St. Andrews |
| 10:00AM – 11:00AM | Poster Session | |
| 11:00AM – 11:15AM | Theme 6: The Cutting Edge: Technology Highlights
“New Technologies at JGI” – Ronan O’Malley / DOE Joint Genome Institute |
Session Chair: Susannah Tringe, DOE Joint Genome Institute / Axel Visel, DOE Joint Genome Institute |
| 11:15AM – 11:25AM | JGI Data Policies | Tanja Woyke, DOE Joint Genome Institute |
| 11:25AM – 11:30AM | Poster Prize Announcement | Susannah Tringe, DOE Joint Genome Institute |
| 11:30AM – 11:45AM | Short Talk – ” SIP-OMICS: A Semi-Automated Pipeline for Isotopically-Targeted Community Analysis and Metagenomics” | Erin Nuccio, Lawrence Livermore National Laboratory |
| 11:45AM – 12:15PM | “Widespread polycistronic gene expression in green algae” | Sabeeha Merchant, University of California, Berkeley |
| 12:15PM – 12:30PM | Short Talk – “The Root of the Problem: Transferring Knowledge from Model to Crop”
Short Talk – “Exploring and Visualizing a Panicum Hallii Mutant Library” |
Maria Mendoza, and Lorenzo Scaturchio, University of California Merced
Beryl Arinda, University of California Merced |
| 12:30PM – 1:00PM | “Window into the soil methane cycle: new outlooks on the metabolically active reservoir in wetlands” | Kelly Wrighton,Colorado State University |