Joint Genome Institute

JGI Annual User Meeting

2017 Agenda

March 20-23, 2017, Walnut Creek, CA

Who should attend this meeting?

Open to all, not just current DOE JGI users. Researchers working in the areas of energy and environmental genomics and synthetic biology, as well as current and potential future users of the DOE Joint Genome Institute.  The Genomics of Energy and Environment Meeting program will feature international speakers on a range of exciting topics, but will also provide opportunities to interact with JGI users supported through the JGI Community Science Program (CSP), the Facilities Integrating Collaborations for User Science (FICUS) initiative, and the DOE Bioenergy Research Centers, as well as technical and scientific JGI staff.  Students, postdocs, and principal investigators considering future applications to the CSP or other JGI User Programs are particularly encouraged to attend.

Need some inspiration to participate? Listen to members of the JGI user community describe why you should participate in the 2017 JGI User Meeting.

Topics discussed at this meeting: Microbial genomics, fungal genomics, metagenomics, and plant genomics; genome editing, secondary metabolites, pathway engineering, synthetic biology, high-throughput functional genomics, high-performance computing applications, and societal impacts of technological advances. State-of-the-art presentations by invited speakers as well as short talks selected from poster abstracts.

DOE JGI Genomics of Energy and Environment Meeting

Keynote Speakers:

  • Tobias Erb, Max Planck Institute for Terrestrial Microbiology
  • C. Titus Brown, University of California, Davis

Plenary Speakers:

  • Cat Adams, UC Berkeley
  • Mikael Andersen, Technical University of Denmark
  • Patsy Babbitt, UC San Francisco
  • Gloria Coruzzi, New York University
  • Colleen Hansel, WHOI
  • Jan Leach, Colorado State University
  • Mary Lipton, PNNL / EMSL
  • Jonathan Lynch, Penn State University
  • Katherine (Trina) McMahon, University of Wisconsin – Madison
  • Thomas Mock, University of East Anglia
  • Chris Pires, University of Missouri
  • Andrew Roger, Dalhousie University
  • Teresa Pawlowska, Cornell University
  • Renee Wegrzyn, DARPA
  • Philipp Zerbe, UC Davis

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

Poster Abstracts (Tuesday, March 21 and Wednesday, March 22)

2017 JGI Meeting Abstract Book (Click here to download a copy)

MONDAY, March 20
8:30 AM – 12:30 PM Metabolomics Workshop Host: Trent Northen
 9:00 AM – 5:00 PM Fungal Genomics Workshop in Contra Costa 1 Host: Igor Grigoriev
 9:00 AM – 4:00 PM NERSC Computing Workshop Host: Kjiersten Fagnan
1:30 PM –  5:30 PM Synthetic Biology Workshop Host: Yasuo Yoshikuni

TUESDAY, March 21
9:30 AM – 3:30 PM Genomic Technologies Workshop Host: Len Pennacchio
9:00 AM – 3:00 PM KBase Workshop in Contra Costa 1 Host: Bob Cottingham, Oak Ridge National Laboratory
5:00 PM – 5:15 PM Welcome and Introduction JGI Director Nigel Mouncey
5:15 PM – 6:15 PM Opening Keynote Presentation: “CETCH Me if You Can – A Synthetic Pathway for the Fixation of Carbon Dioxide“ Tobias Erb, Max Planck Institute for Terrestrial Microbiology
6:15 PM – 9:00 PM Opening Reception and Poster Session – Click here for the evening’s poster abstracts

WEDNESDAY, March 22
8:30 AM – 12:00 PM SESSION I – Genomics in the environment and society. Chair: Susannah Tringe
 8:30 AM – 9:00 AM “Pieces of the Phytobiome: Multitrophic and Environmental Influences on Plant Health” Jan Leach, Colorado State University
9:00 AM – 9:30 AM  “Unconscious Bias and Fungi: Studying Microorganisms in a Macro-Focused World“ Cat Adams, University of California, Berkeley
 9:30 AM – 10:00 AM  “Manganese oxidation and Mineralization by Ascomycete Fungi“ Colleen Hansel, Woods Hole Oceanographic Institution
10:00 AM – 10:30 AM Break  
10:30 AM – 10:45 AM “Unraveling the Core Mechanisms of Suillus–Pinus Symbiosis through Time-Course RNAseq and Omics“ Sunny Liao, University of Florida
 10:45 AM – 11:15 AM “Room at the Bottom: Opportunities and Challenges in the Subsoil” Jonathan Lynch, Pennsylvania State University
11:15 AM – 11:45 AM “Setting a Safe Course for Gene Editing Research” Renee Wegrzyn, Defense Advanced Research Projects Agency
 11:45 AM – 12:00 PM “Community RNA Reveals Changes in Soil Biodiversity and Ecosystem Function in a Long-Term Soil Warming Chronosequence“ Lauren Alteio, University of Massachusetts, Amherst
12:00 PM – 1:30 PM Working Lunch  
1:30 PM – 5:00 PM SESSION II – From genomes to structure, function and metabolism. Chair: Axel Visel
1:30 PM – 2:00 PM  “How has Nature Evolved the Enzymes Required for Life“ Patsy Babbitt, University of California, San Francisco
2:00 PM 2:30 PM  “Investigating Plant Terpene Metabolic Diversity for Biotechnology Applications“ Philipp Zerbe, University of California, Davis
2:30 PM – 3:00 PM  “Whole-Genus Association Analysis–Using Hundreds of Aspergillus Genomes for Linking Phenotype to Genotypes“ Mikael Andersen, Technical University of Denmark
3:00 PM – 3:30 PM Break
 3:30 PM – 3:50 PM “Pervasive Adenine N6-Methylation of Active Genes in Fungi“ Stephen Mondo, JGI
3:50 PM – 4:20 PM “EvoNet: A Phylogenomic and  Systems Biology Approach to Identify Genes Underlying Plant Survival in Marginal, Low-Nitrogen Soils” Gloria Coruzzi, New York University
4:20 PM – 4:40 PM “eQTL Mapping in Populus“  Jay Chen, Oak Ridge National Laboratory
4:40 PM – 5:00 PM “Giant Viruses with An Unprecedented Translation System“ Frederik Schulz, JGI
 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 – Click here for the evening’s poster abstracts  
7:00 PM – 9:00 PM Travel from JGI – Bus Service to Marriott  

THURSDAY, March 23
8:30 AM – 11:45 PM SESSION III – Genome Evolution Chair: Dan Rokhsar
8:30 AM – 9:00 AM “Community Genomes Uncover Pattern and Process in Freshwater Bacterial Ecology and Evolution“ Trina McMahon, University of Wisconsin-Madison
9:00 AM – 9:30 AM “Polyploidy and the Origins of Novelty: Impact of Duplication on Genomes and Network Evolution“ J. Chris Pires, University of Missouri
9:30 AM – 10:00 AM “The Evolution and Significance of Diverged Alleles in Diatoms“  Thomas Mock, University of East Anglia
10:00 AM – 10:30 AM Break  
10:30 AM – 10:45 AM “Quantifying Genomic Exchange in Chickpea-Nodulating Mesorhizobium“ Alex Greenspan, University of California, Davis
10:45 AM – 11:15 AM  “Adaptation of Microbial Eukaryotes to Low Oxygen Conditions and the Gastrointestinal Tract“ Andrew Roger, Dalhousie University
 11:15 AM – 11:45 AM “Genomics of Fungal-Bacterial Interactions“ Teresa Pawlowska, Cornell University
 11:45 AM – 1:15 PM Working Lunch
 1:15 PM – 5:00 PM SESSION IV – Novel experimental and analytical methods. Chairs: Len Pennacchio and Tanja Woyke
1:15 PM – 2:20 PM New Technologies Overview and User Feedback Joint Genome Institute staff
2:20 PM – 2:35 PM “Disco: High Performance Scalable Assembler for Integrated Assembly of Illumina and PacBio Reads“ Abhishek Biswas, University of Tennessee
2:35 PM – 3:05 PM Break  
3:05 PM – 3:35 PM “EMSL Capabilities for Functional Genomics of Plants and Microbes“ Mary Lipton, Environmental Molecular Sciences Laboratory
3:35 PM – 3:55 PM “Omics-Enabled Discovery of a Novel Bacterial Enzyme Enabling First-Time Bio-Based Toluene Production“ Harry Beller, Joint BioEnergy Institute
 3:55 PM – 4:55 PM Closing Keynote Presentation: “Notes from the Datapocalypse“ C. Titus Brown, University of California, Davis
5:00 PM End of JGI User Meeting