DOE JGI Genomics of Energy and Environment Meeting
Tuesday, March 13, 2018 |
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| 8:30 AM – 12:30 PM | KBase Workshop: Genome Analysis | Host: Bob Cottingham |
| 9:00 AM – 5:00 PM | Fungal Genomics Workshop | Host: Igor Grigoriev |
| 9:00 AM – 5:00 PM | Prokaryotic Program Workshop | Host: Nikos Kyrpides |
| 1:00 PM – 5:00 PM | KBase Workshop: Community Analysis | Host: Bob Cottingham |
| 1:00 PM – 5:00 PM | KBase Workshop: Functional Analysis | Host: Bob Cottingham |
Wednesday, March 14, 2018 |
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| 8:30 AM – 12:00 PM | KBase Workshop: How to Integrate Your Tools Into KBase Using the Software Development Kit (SDK) | Host: Bob Cottingham |
| 8:30 AM – 12:00 PM | Technology Overview Workshop | Host: Matt Blow |
| 8:30 AM – 4:00 PM | Viral EcoGenomics & Applications (VEGA) Symposium | Host: Nikos Kyrpides |
| 12:30 PM – 4:00 PM | DNA Synthesis and Metabolomics Joint Workshop | Host: Yasuo Yoshikuni / Trent Northen |
| 12:30 PM – 4:00 PM | Sample Management and Library Development Workshop | Host: Yuko Yoshinaga |
| 12:30 PM – 4:00 PM | Sequence to Science: An Overview of Analysis at JGI | Host: Alex Copeland |
| 4:00 PM – 9:00 PM | Sponsor Showcase Open | |
| 5:00 PM – 6:00 PM | Keynote Speaker Presentation: “Linking uncultivated microorganisms to biogeochemical processes” | Victoria Orphan, Caltech |
| 6:00 PM – 9:00 PM | Poster Session | |
Thursday, March 15, 2018 |
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| 8:00 AM – 5:00 PM | Sponsor Showcase Open | |
| 8:30 AM – 12:00 PM | AM Split Session #1: Viral EcoGenomics & Applications (VEGA) Symposium | |
| 8:30 AM – 12:00 PM | AM Split Session #2: Eukaryotic Functional Genomics | Session Chair: Dan Rokhsar |
| 8:30 AM – 9:00 AM | “Leveraging Genetic Variation Among Single Cells or Individuals to Understand the Cryptic Biology of Fungi” | Tim James, University of Michigan |
| 9:00 AM – 9:15 AM |
“From Single Nuclei to Whole Genome Assemblies of Arbuscular Mycorrhizal Fungi” |
Mercè Montoliu Nerín, Uppsala University |
| 9:15 AM – 9:45 AM | “Rethinking Agriculture from an Ecosystem Perspective” | Evan DeLucia, UIUC / CABBI |
| 9:45 AM – 10:00 AM | “Ice Plant Gene Atlas Resource Development” | John Cushman, University of Nevada |
| 10:00 AM – 10:30 AM | Break | |
| 10:30 AM – 11:00 AM | “Switchgrass Diversity: Identifying Signatures of Adaptation” | Jeremy Schmutz, JGI |
| 11:00 AM – 11:30 AM | “Insights into Eukaryotic Evolution from the Stress-Tolerant Red Alga Porphyra umbilicalis” | Susan Brawley, University of Maine |
| 11:30 AM – 12:00 PM | “Mushroom Forming Fungi Converting Plant Waste Streams into Novel Biomaterials” | Han Wösten, Utrecht University |
| 12:00 PM – 1:30 PM | Working Lunch – 2nd Poster Session | |
| 1:30 PM – 5:30 PM | Session: Interrogating the Microbiome | Session Chair: Susannah Tringe |
| 1:30 PM – 2:30 PM | Keynote Speaker Presentation: “Building microbial chemical factories” | Kristala Prather, MIT |
| 2:30 PM – 2:45 PM | “Automated Reconstruction of the Nitrogen Cycle along Defined Redox Gradients in Saanich Inlet Using the TreeSAPP Pipeline“ | Julia Anstett, University of British Columbia |
| 2:45 PM – 3:00 PM | “Feedback Responses of Grassland Soil Microbial Communities to Climate Warming” | Jizhong Zhou, University of Oklahoma |
| 3:00 PM – 3:30 PM | Break | |
| 3:30 PM – 4:00 PM |
“Engineering Microbial Communities for Form and Function”
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Cynthia Collins, Rensselaer Polytechnic Institute |
| 4:00 PM – 4:30 PM | “The Deep Blue (Inland) Seas: Illuminating Microbial Activity in Earth’s Largest Freshwater Ecosystem” | Maureen Coleman, University of Chicago |
| 4:30 PM – 5:00 PM | “Applications of Genomic Standards for Microbiome Science” | Lynn Schriml, University of Maryland |
| 5:00 PM – 5:30 PM | “Chemical Communication in the Soil Microbiome” | Kriti Sharma, University of North Carolina at Chapel Hill |
| 6:30 PM – 9:00 PM | Keynote Speaker Presentation: “Reproducible research: challenges and improvements” & Banquet Dinner |
John Ioannidis – Stanford University |
Friday, March 16, 2018 |
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| 8:00 AM – 1:30 PM | Sponsor Showcase Open | |
| 8:30 AM – 12:00 PM | Session: Complementary Technologies | Session Chair: Len Pennacchio |
| 8:30 AM – 9:00 AM | “Assessing Soil Microbial Responses to Land Use Change” | Krista McGuire, University of Oregon |
| 9:00 AM – 9:30 AM | “Linking Omics and Structural Biology” | James Evans, EMSL |
| 9:30 AM – 9:45 AM | “Exploring Metabolite Production from Tryptophan Precursors in Two Algal Associated Bacteria, Algoriphagus sp. ARW1R1 and Marinobacter sp. 19DW” | Ty Samo, Lawrence Livermore National Laboratory |
| 9:45 AM – 10:00 AM | “High-Throughput Sequencing and Metabolomics Enabled Phenomics to Investigate the Integration of Heat and Circadian Responses in the Model Green Alga Chlamydomonas reinhardtii“ | Ru Zhang, Danforth Center |
| 10:00 AM – 10:30 AM | Break | |
| 10:30 AM – 11:00 AM | “Social Life of Microbial Communities: Structural Studies of Contact-Dependent Signaling in Bacteria” | Andrzej Joachimiak, Argonne National Laboratory |
| 11:00 AM – 11:30 AM | “Exploring Microbial Ecology with Isotopes and Imaging” | Jennifer Pett-Ridge, Lawrence Livermore National Laboratory |
| 11:30 AM – 12:00 PM | “Effective Solutions for Diversity and Inclusion, Going Beyond Gender and Race” | Sheena Becker, DowDuPont |
| 12:20 PM – 1:20 PM | Working Lunch: Industry Showcase Presentations | |
| 1:30 PM – 5:00 PM | Session: Use-inspired “Omics” | Session Chair: Yasuo Yoshikuni |
| 1:30 PM – 2:00 PM | “Establishing Cell-Free Systems for Rapid Biosynthetic Pathway Prototyping and Biomanufacturing” | Mike Jewett, Northwestern University |
| 2:00 PM – 2:30 PM | 200 Fungal Genomes: Accelerating Insights into Genomic Drivers of Fungal Symbioses with Plants | Daniela Pignatta, Indigo Agriculture |
| 2:30 PM – 2:45 PM | “CRISPR-Cas9 Genome Editing and CRISPRa/i Tools for Engineering the Oleaginous Yeast Yarrowia lipolytica“ | Ian Wheeldon, UC Riverside |
| 2:45 PM – 3:00 PM | “Novel Cyclic Triterpenoid Biosynthesis Enzymes from Environmental Metagenomes“ | Amy Banta, Stanford University |
| 3:00 PM – 3:30 PM | Break | |
| 3:30 PM – 3:45 PM | “Transcription Start Site Sequencing Reveals Distinct Feature of Zymomonas mobilis Sigma 70 Promoter Elements” | Jessica Vera, GLBRC, University of Wisconsin-Madison |
| 3:45 PM – 4:00 PM | “A metaproteomics method to determine carbon sources and assimilation pathways of species in microbial communities” | Manuel Kleiner, North Carolina State University |
| 4:00 PM – 4:30 PM | “Genomics and Engineering of Non-Conventional Yeasts for Biotechnical Applications” | Tom Jeffries, Xylome |
| 4:30 PM – 5:00 PM | “From Oat Genomics to Biosynthetic Gene Clusters” | Aymeric Leveau, John Innes Centre |
| 5:00 PM | End of JGI User Meeting | |