Joint Genome Institute

JGI Annual User Meeting

2016 Agenda

Genomics of Energy & Environment Meeting

March 21 – 24, 2016 in Walnut Creek, California

Speakers/Talk titles:

  • Orli Bahcall, Nature Publishing: “The Nature of Scientific Publishing”
  • Chris Bowler, École Normale Supérieure (France): “Tara Oceans: Eco-systems Biology at Planetary Scale”
  • Charles Chiu, University of California, San Francisco: “Deep Sequencing Methods for Detecting Infectious Agents”
  • Manpreet Dhami, Stanford University: “The Competitive Edge: Genetic Basis of Fitness in Floral Yeasts”
  • José Dinneny, Carnegie Institution for Science: “The Divining Root: Understanding How Roots Find Water in a Heterogeneous Environment”
  • Tim Donohue, Great Lakes Bioenergy Research Center: “Mining Genomes for Producing Fuels and Chemicals from Biomass”
  • Kirsten Hofmockel, Pacific Northwest National Laboratory: “Microbial Drivers of Cellulose Cycling in Biofuel Crop Soils”
  • Sarah Lebeis, University of Tennessee: “Characterizing Plant Growth Promoting Members of the Duckweed Microbiome”
  • Christopher Mason, Weill Cornell Medical College: “Engineered Metagenomes for Superfund Sites, Subways, and Space Stations”
  • Margaret McFall-Ngai, University of Hawaii: “Nature’s Toolkit: Evolutionary ‘Experiments’ in Host-Microbe Interactions”
  • Gene Myers, Max Planck Institute of Molecular Cell Biology and Genetics (Germany): “Towards Perfect Sequence Assembly”
  • Dianne Newman, California Institute of Technology: “Primary Roles for Secondary Metabolites”
  • Jeanine Olsen, Groningen Institute of Evolutionary Life Sciences: “Return to the sea: the genome of the seagrass Zostera marina”
  • Michelle O’Malley,University of California, Santa Barbara: “Deciphering the Biomass-Degrading Abilities of Anaerobic Gut Fungi”
  • Christine Queitsch, University of Washington: “Mapping and Dynamics of Regulatory DNA in Plants”
  • Jeffrey Ross-Ibarra, University of California, Davis: “Adaptation in Plant Genomes: The Importance of Demographic History and Genome Size”
  • Reshma Shetty, Ginkgo Bioworks: “Developing plant-inspired cultured aromas using a foundry for organism engineering”
  • Hamilton Smith, JCVI: “Design and Synthesis of a Minimal Bacterial Genome”
  • Mary Voytek, NASA: “Searching for Life on Earth and Beyond”
  • Kelly Wrighton, The Ohio State University: “Life in the Deep Subsurface: What’s Shale Got to Do With It?”

Complete 2016 Agenda

All functions were held at the Walnut Creek Marriott unless otherwise noted.

MONDAY, March 21
9:00 AM – 4:00 PM Fungal Genomics Workshop Host: Igor Grigoriev, JGI
 9:00 AM – 4:00 PM NERSC Workshop: Reproducible Bioinformatics Pipelines Host: Kjiersten Fagnan, JGI/NERSC
12:00 PM – 4:00 PM Synthetic Biology Workshop Host: Yasuo Yoshikuni, JGI

TUESDAY, March 22
8:30 AM – 2:30 PM Genomic Technologies Workshop Host: Len Pennacchio, JGI
9:00 AM – 3:00 PM KBase Workshop Host: Oak Ridge National Laboratory
2:30 PM – 4:00 PM Sample QC Workshop Host: Matt Blow, JGI
5:00 PM – 5:10 PM Welcome and Introduction Eddy Rubin, JGI
5:10 PM – 6:10 PM Opening Keynote Presentation                                             Primary Roles for Secondary Metabolites Dianne Newman, Caltech
6:10 PM – 9:00 PM Opening Reception and Poster Session

WEDNESDAY, March 23
8:30 AM – 12:00 PM SESSION I Chair: Susannah Tringe
 8:30 AM – 9:00 AM Tara Oceans: Eco-Systems Biology at Planetary Scale Chris Bowler, Institut de Biologie de I’Ecole Normale Superieure, France
9:00 AM – 9:30 AM The Competitive Edge: Genetic Basis of Fitness in Floral Yeasts Manpreet Dhami, Stanford School of Medicine
 9:30 AM – 10:00 AM Deep Sequencing Methods for Detecting Infectious Agents Charles Chiu, UCSF
10:00 AM – 10:30 AM Break  
10:30 AM – 10:45 AM Genome-wide Identification of Bacterial Plant Colonization Genes  Ben Cole, JGI
 10:45 AM – 11:15 AM Characterizing Plant Growth Promoting Members of the Duckweed Microbiome Sarah Lebeis, University of Tennessee
11:15 AM – 11:45 AM Towards Perfect Sequence Assembly Gene Myers, Max-Planck Institute for Molecular Cell Biology & Genetics
 11:45 AM – 12:00 PM Tracing Community Utilization of Light-Derived Extracellular Organic Matter in Biofilms Rhona Stuart, LLNL
12:00 PM – 1:30 PM Working Lunch  
1:30 PM – 5:00 PM SESSION II Chair: Dan Rokhsar
1:30 PM – 2:00 PM The Divining Root: Understanding How Roots Find Water in A Heterogeneous Environment Jose Dinneny, Carnegie Institution for Science
2:00 PM 2:30 PM Return to the sea: the genome of the seagrass Zostera marina Jeanine Olsen, Groningen Institute of Evolutionary Life Sciences
2:30 PM – 3:00 PM Adaptation in Plant Genomes: The Importance of Demographic History and Genome Size Jeffrey Ross-Ibarra, University of California Davis
3:00 PM – 3:30 PM Break
 3:30 PM – 3:45 PM Comparative Genomics of C4 Grasses Elizabeth Kellogg, Donald Danforth Plant Science Center
3:45 PM – 4:15 PM Mapping and Dynamics of Regulatory DNA in Plants Christine Queitsch, University of Washington, School of Medicine
4:15 PM – 4:30 PM Genetic and Genomic Studies of Local Adaptation in Panicum hallii Tom Juenger, UT Austin
4:30 PM – 5:00 PM Engineered Metagenomes for Superfund Sites, Subways, and Space Stations Christopher Mason, Cornell University
 5:00 PM – 7:00 PM Travel to JGI – Bus Service from Marriott  
6:00 PM – 9:00 PM Reception, Poster Session and Tours at JGI  
7:00 PM – 9:00 PM Travel from JGI – Bus Service to Marriott  

THURSDAY, March 24
8:30 AM – 11:45 PM SESSION III Chair: Tanja Woyke
8:30 AM – 9:00 AM Mining Genomes for Producing Fuels and Chemicals From Biomass Tim Donohue, University of Wisconsin-Madison
9:00 AM – 9:30 AM Microbial Drivers of Cellulose Cycling in Biofuel Crop Soils Kirsten Hofmockel, Pacific Northwest National Laboratory
9:30 AM – 10:00 AM Developing Plant-Inspired Cultured Aromas Using a Foundry for Organism Engineering Reshma Shetty, Gingko Bioworks, Inc.
10:00 AM – 10:30 AM Break  
10:30 AM – 10:45 AM Codon Reassignment in Yeasts Robert Riley, JGI
10:45 AM – 11:15 AM Deciphering the Biomass-Degrading Abilities of Anaerobic Gut Fungi Michelle O’Malley, UC Santa Barbara
 11:15 AM – 11:45 PM Searching for Life on Earth and Beyond Mary Voytek, NASA
 11:45 AM – 1:15 PM Working Lunch
 1:15 PM – 5:00 PM SESSION IV Chair: Len Pennacchio
1:15 PM – 2:00 PM New Technologies Overview and User Feedback Joint Genome Institute
2:00PM – 2:30 PM The Nature of Scientific Publishing Orli Bahcall, Nature
2:30 PM – 3:00 PM Break  
3:00 PM – 3:30 PM Design and Synthesis of a Minimal Bacterial Genome Hamilton Smith, J. Craig Venter Institute
3:30 PM – 4:00 PM Life in the Deep Subsurface: What’s Shale Got to do With it? Kelly Wrighton, Ohio State University
 4:00 PM – 5:00 PM Closing Keynote Presentation
Nature’s Toolkit: Evolutionary ‘Experiments’ in Host-Microbe Interactions Margaret McFall-Ngai, University of Hawaii
5:00 PM End of JGI User Meeting