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2020 Agenda

JGI Genomics of Energy and Environment Meeting

Sunday, March 22rd

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

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 24th

User Meeting Kick Off

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

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

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  

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