Joint Genome Institute

DOE JGI User Meeting

2019 Agenda

Tuesday, April 2, 2019
8:30 AM – 1:00 PM Technology Mini Colloquium – See Full Agenda Here 

Golden Gate Rooms 3, 4, 5

 Host: Len Pennacchio – JGI Deputy of Genomic Technologies

Nigel Mouncey – JGI Director
9:00 AM – 12:00 PM KBase Isolate Analysis Workshop

4th Floor – Union Square Room 22

 Host: Ben Allen – Oak Ridge National Laboratory
2:00 PM – 5:00 PM KBase Microbiome Workshop

4th Floor – Union Square Room 22

 Host: Dylan Chivian – KBase

Wednesday, April 3, 2019
9:00 AM – 12:00 PM KBase Functional Genomes Analysis Workshop

4th Floor – Union Square Room 22

 Co-Hosts: Vivek Kumar, Sunita Kumari – Cold Springs Harbor Laboratory
9:00 AM – 12:00 PM KBase Office Hours

4th Floor – Union Square Rooms 19, 20

 Host: Shane Canon – KBase

Host: Paramvir Dehal – KBase
9:00 AM – 12:00 PM JGI Showcase and Future Directions – See Full Agenda Here

Continental Ballroom

 Len Pennacchio – JGI Deputy of Genomic Technologies
Matt Blow – JGI
12:00 PM – 1:00 PM Lunch – Continental Foyer

2019 User Meeting 

(Continental Ballroom)
1:00 PM – 5:00 PM Session 1:  Advancing Plant Science with Omics Session Chair: Jeremy Schmutz
1:00 PM – 1:10 PM Welcome & Introduction Nigel Mouncey, JGI Director
1:10 PM – 2:00 PM Keynote Speaker Presentation: “Selection for Gene Regulation in Rice” Michael Purugganan, New York University
2:00 PM – 2:30 PM “Understanding Plant Cell Wall Biosynthesis to Improve Plants for Biofuel Production: The Power of a Combined Fundamental and Directed Approach” Debra Mohnen, University of Georgia
2:30 PM – 3:00 PM “Plant Genome Engineering” Doane Chilcoat, DuPont Pioneer
3:00 PM – 3:30 PM Break
3:30 PM – 4:00 PM “Integrating Pan-Genomic Information with High-Resolution Phenotyping to Accelerate Sorghum Trait Discovery and Improvement” Todd Mockler, Danforth Center
4:00 PM – 4:15 PM Short Talk:  “Co-Locality to Co-Functionality: Gene Neighborhoods and Fusions as Tools for Gene Function Discovery in Green Algae” Fatima Foflonker – Brookhaven National Laboratory
4:15 PM – 4:30 PM Short Talk:  “Sex in the Salicaceae” Stephen DiFazio – West Virginia University
4:30 PM – 5:00 PM
“Why Diversity in Science is Critical for Today and for our Future”
 Geri Richmond, University of Oregon
5:00 PM – 8:00 PM Poster Session & Sponsor Showcase Reception

Thursday, April 4, 2019
8:30 AM – 12:00 PM Session 2:  Inter-Organismal Interactions Session Chair:  Susannah Tringe
8:30 AM – 9:30 AM Keynote Speaker Presentation: “Disentangling the Web of Interactions Shaping Microbial Communities in Soil” Mary Firestone, University of California, Berkeley
9:30 AM – 10:00 AM “Promoting Plant Health with Tiny Earth: Student Sourcing Antimicrobial Discovery” Amanda Hurley, University of Wisconsin, Madison
10:00 AM – 10:30 AM Break
10:30 AM – 10:45 AM Short Talk:  “Coupled Laboratory and Field Investigations Resolve Microbial Interactions that Underpin Persistence in Hydraulically Fractured Shales” Rebecca Daly – Colorado State University
10:45 AM – 11:00 AM Short Talk: “Harnessing SIP-Enhanced Metagenomics to Uncover the Carbon Cycling Capacity of Soil Microbes” Samuel Barnett – Cornell University
11:00 AM – 11:30 AM “Diving Deep: Molecular and Isotopic Insights into the Microbiology of the Deep Sea” Anne Dekas, Stanford University
11:30 AM – 12:00 PM “Towards a Decadal Multi-Omics Systems Characterization of Climate Change in a Thawing Arctic Peatland” Virginia Rich, Ohio State University
12:00 PM – 1:00 PM Industry Showcase Luncheon

  1. 12:15-12:23pm: Siva Nallasivam, Arbor Biosciences
  2. 12:24-12:32pm: Ryan Sasada, Zymo Research
  3. 12:33-12:41pm: Leandro Neves, RAPiD GENOMICS
  4. 12:42-12:50pm: Cheryl Heiner, Pacific Biosciences
  5. 12:51-12:59pm: Ivan Liachko, Phase Genomics
  
1:00 PM – 5:00 PM Session 3:  Eukaryotic Microbiology Session Chair:  Dan Rokhsar
1:00 PM – 1:30 PM “Host Factors in Plant-Pathogen Interactions” Mary Wildermuth, University of California, Berkeley
1:30 PM – 1:45 PM Short Talk: “Evolution of Heavy Metal Tolerance in a Mycorrhizal Fungus” Sara Branco – Montana State University
1:45 PM – 2:00 PM Short Talk: “Multi-Omics Investigation of a Green Microalga Scenedesmus sp. NREL 46B-D3 Response to Temperature Stress” Sara Calhoun – DOE Joint Genome Institute
2:00 PM – 2:30 PM “Using Symbiogenic Technology to Generate Climate Resilient, Nutritionally Independent, and Pathogen Resistant Crop Plants” Rusty Rodriguez, Symbiogenics/Adaptive Symbiotic Technologies
2:30 PM – 3:00 PM “Fungal Synthetic Biology: Optogenetics, Circuitry and Transcriptional Memory” Luis Larrondo,  Universidad Catolica de Chile
3:00 PM – 3:30 PM Break
3:30 PM – 4:00 PM “Resilience of Wild Microbial Communities” Ashley Shade, Michigan State University
4:00 PM – 4:30 PM User Facility Flash Talks

  1. Environmental Molecular Sciences Laboratory (EMSL) – Nancy Hess, PNNL
  2. DOE Systems Biology Knowledgebase (KBase) – Adam Arkin, LBNL
  3. National Energy Research Supercomputing Center (NERSC) – Debbie Bard, LBNL
  4. Structural Molecular Biology, Stanford Synchrotron Radiation Lightsource (SLAC) – Riti Sarangi, SLAC
  5. Advanced Light Source (ALS) – Corie Ralston, LBNL
4:30 PM – 5:00 PM “Molecular Switch for Oxygenic Photosynthesis and Metabolism in a Green Alga” Melissa Roth, University of California, Berkeley
5:00 PM – 8:00 PM Poster Session & Sponsor Showcase Reception

Friday, April 5, 2019
8:30 AM – 12:00 PM Session 4:  Engineering Biology Session Chair:  Yasuo Yoshikuni
8:30 AM – 9:00 AM “Olfactory Receptor-Based Sensors for Chemical Detection” Pamela Peralta-Yahya, Georgia Tech
9:00 AM – 9:30 AM “Development of Genetic and Epigenetic Strategies to Optimize Biomass-Degrading Capabilities in Anaerobic Fungi” Kevin Solomon, Purdue University
9:30 AM – 10:00 AM “Host Engineering for Robust and Scalable Production of Biofuels and Bioproducts” Aindrila Mukhopadhyay, Joint BioEnergy Institute
10:00 AM – 10:30 AM Break  
10:30 AM – 11:00 AM “Skill and Practical Knowledge in the Automated Laboratory” Emma Frow, Arizona State University
11:00 AM – 11:15 AM Short Talk: “Consequences of Diversity on Microbial Responses to Exometabolite-Mediated Interactions in a Synthetic Microbial Community” John Chodkowski – Michigan State University
11:15 AM – 11:30 AM Short Talk: “Exploiting and Engineering the Natural CO2 Binding Potential of Propionyl-CoA Synthase” Iria Bernhardsgrutter – Max Planck Institute
 11:30 AM – 12:00 PM “Persistent Connections Between Researchers and Their Contributions: Making Research Results Findable and Citable” George Garrity, Michigan State University
 12:00 PM – 1:00 PM Industry Showcase Luncheon

  1. 12:15-12:23pm: Pamela Lussier, Illumina
  2. 12:24-12:32pm: Emily Leproust, Twist Bioscience
  3. 12:33-12:41pm: Iain MacLaren-Lee, Oxford Nanoporetech
  4. 12:42-12:50pm: Keith Brown, iGenomX
1:00 PM – 3:00 PM Session 5:  Data-Intensive Biology Session Chair:  Kjiersten Fagnan
1:00 PM – 1:30 PM “Exascale Biology:  From Genome to Climate With a Few Stops Along the Way” Dan Jacobson, Oak Ridge National Laboratory
1:30 PM – 2:00 PM “Interesting Insights on Gene Networks Associated with Agronomic Gain Via An EMS-treated Sorghum Population” Doreen Ware, USDA ARS, Cold Springs Harbor Laboratory
2:00 PM – 3:00 PM Keynote Speaker Presentation:   “On the Origin of Virulence of Pathogenic Microbes” Arturo Casadevall, Johns Hopkins University
3:00 PM End of JGI User Meeting