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2015 Agenda

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Genomics of Energy & Environment Meeting

March 23 – 26, 2015 in Walnut Creek, California

Thanks for making our 10th Annual User Meeting a resounding success!

Event Location: Marriott Hotel, 2355 North Main Street Walnut Creek, CA 94596

Who should attend? Any and all researchers and students interested in energy and environmental genomics.

Need some inspiration to participate? See/hear these testimonials from a previous meeting.

Topics: 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 impact of technological advances. State-of-the-art presentations by invited speakers as well as short talks selected from poster abstracts.

Speakers/talk titles:

  • Joan Bennett, Rutgers, Do Fungi have a ‘Volatome’?
  • Steve Briggs, UC San Diego, Protein Regulatory Networks
  • Tom Brutnell, Danforth Center, Dissecting C4 Photosynthetic Differentiation Through Comparative Transcriptomics in the Grasses
  • Mark Burk, Genomatica, A Rational Approach to Driving the Development of Commercial Production Strains Through Systems Biology          
  • Atul Butte, Stanford University, Translating a Trillion Points of Data into Therapies, Diagnostics, and New Insights into Disease
  • Rick Cavicchioli, University of South Wales, Australia, Antarctic Microbial Omics–A Path to Learning About Life in the Cold
  • Michelle Chang, UC Berkeley, Designing New Biosynthetic Pathways for Biofuel Production
  • Edward DeLong, University of Hawaii, Ocean Basin-Wide Patterns and Processes Revealed by High Resolution Microbial Community Transcriptome Networks
  • Jack Gilbert, Argonne National Laboratory, Genome-Enabled Flux Balance Metabolic Networks From Periodically Flooded Soils   
  • Barbara Jasny, Science Magazine, Data and Science Publishing in the 21st Century
  • Shawn Kaeppler, Great Lakes Bioenergy Research Center, Analysis of Natural Variation for Biofuel Traits in Grasses
  • Sophien Kamoun, Sainsbury Lab, UK, The Two-Speed Genomes of Filamentous Plant Pathogens
  • Susan Lynch, UC San Francisco, The Microbiome–A New Frontier in Human Health
  • Francis Martin, INRA, Harnessing Genomics for Understanding Tree-Microbe Interactions in Forest Ecosystems
  • Marton Palatinszky, University of Vienna, Raman Microspectroscopy Based Sorting of Active Microbial Cells for Single Cell Genomics
  • Sue Rhee, Carnegie Institution for Science, Genome-enabled Prioritization of Candidate QTL Causal Genes Using Machine Learning
  • Antonis Rokas, Vanderbilt University, Evolution of Fungal Chemodiversity
  • Blake Simmons, Joint BioEnergy Institute, Function-Based Genomic Screening for the Discovery and Manipulation of Lignocellulolytic Enzymes and Pathways
  • Rotem Sorek, Weizmann Institute, The Immune System of Bacteria–CRISPR and Beyond
  • Jerry Tuskan, BioEnergy Science Center, Identification and Isolation of Populus Genes that Trigger Laccaria Colonization
  • Stephen Wright, University of Toronto, Comparative and Population Genomics in the Brassicaceae: Understanding Genome-Wide Natural Selection

Agenda

MONDAY, March 23  (Room TBD)

9:00 AM – 4:00 PM Fungal Genomics Workshop Host: Igor Grigoriev

TUESDAY, March 24

9:00 AM – 4:00 PM Genomic Technologies Workshop Host: Len Pennacchio
9:00AM – 4:00 PM KBase Workshop Host: Oak Ridge National Laboratory
4:00PM – 5:00 PM Sample QC Workshop Host: Mansi Chovatia
5:00 PM – 5:10 PM Welcome and Introduction Eddy Rubin, JGI
 5:10 PM – 6:10 PM Opening Keynote Presentation  
Function-Based Genomic Screening for the Discovery and Manipulation of Lignocellulolytic Enzymes and Pathways Blake Simmons, Joint BioEnergy Institute (JBEI)
Analysis of Natural Variation for Biofuel Traits in Grasses Shawn Kaeppler,Great Lakes Bioenergy Research Center (GLBRC)
Identification and Isolation of Populus Genes that Trigger Laccaria Colonization Jerry Tuskan, BioEnergy Science Center (BESC)
6:10 PM – 6:20 PM van Niel Award Ceremony  
6:20 PM – 9:00 PM Opening Reception and Poster Session  

WEDNESDAY, March 25

8:30 AM – 12:00 PM SESSION I Chair: Susannah Tringe
 8:30 AM – 9:00 AM Genome-Enabled Flux Balance Metabolic Networks From Periodically Flooded Soils Jack Gilbert, Argonne National Laboratory
9:00 AM – 9:30 AM Harnessing Genomics for Understanding Tree-Microbe Interactions in Forest Ecosystems Francis Martin, Institut National de la Recherche Agronomique (INRA)
 9:30 AM – 10:00 AM Do Fungi have a ‘Volatome’? Joan Bennett, Rutgers University
10:00 AM – 10:30 AM Break  
10:30 AM – 10:45 AM Marsh Madness: Microbial Communities Driving Greenhouse Gas Cycling in Coastal Wetlands Susanna Theroux, Joint Genome Institute
 10:45 AM – 11:15 AM Evolution of Fungal Chemodiversity Antonis Rokas, Vanderbilt University
11:15 AM – 11:45 AM The Immune System of Bacteria – CRISPR and Beyond Rotem Sorek, Weizmann Institute of Science
 11:45 AM – 12:00 PM Back From The Dead: The Curious Tale of the Predatory Cyanobacterium Vampirovibrio chlorellavorus Phil Hugenholtz, University of Queensland
12:00 PM – 1:30 PM Working Lunch  
1:30 PM – 5:00 PM SESSION II Chair: Len Pennacchio
1:30 PM – 2:00 PM Data and Science Publishing in the 21st Century Barbara Jasny, AAAS
2:00 PM 2:30 PM Translating a Trillion Points of Data into Therapies, Diagnostics, and New Insights into Disease Atul Butte, Stanford University
2:30 PM – 3:00 PM A Rational Approach to Driving the Development of Commercial Production Strains Through Systems Biology Mark Burk, Genomatica
3:00 PM – 3:30 PM Break
 3:30 PM – 3:45 PM Enabling Recombinatorial Fungal Metabolic Engineering via Genome Editing and DNA Synthesis William Alexander, University of Wisconsin-Madison
3:45 PM – 4:15 PM Designing New Biosynthetic Pathways for Biofuel Production Michelle C. Chang, University of California, Berkeley
4:15 PM – 4:30 PM Kryptonia: A New Bacterial Candidate Phylum Discovered through Global Metagenomic Surveys Emiley Eloe-Fadrosh, Joint Genome Institute
4:30 PM – 5:00 PM Raman Microspectroscopy Based Sorting of Active Microbial Cells for Single Cell Genomics  Marton Palatinszky, University of Vienna
 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 26

8:30 AM – 11:45 PM SESSION III Chair:  Dan Rokhsar
8:30 AM – 9:00 AM Dissecting C4 Photosynthetic Differentiation Through Comparative Transcriptomics in the Grasses Thomas Brutnell, Danforth Center
9:00 AM – 9:30 AM Comparative and Population Genomics in the Brassicaceae: Understanding Genome-Wide Natural Selection Stephen Wright, University of Toronto
9:30 AM – 10:00 AM Genome-enabled Prioritization of Candidate QTL Causal Genes Using Machine Learning Sue Rhee, Carnegie Institution for Science
10:00 AM – 10:30 AM Break  
10:30 AM – 10:45 AM Resequencing of Switchgrass, an Outcrossing Bioenergy Crop Species Laura Bartley, University of Oklahoma
10:45 AM – 11:15 AM Keeping up with the Plant Destroyers – The Two-Speed Genomes of Filamentous Plant Pathogens Sophien Kamoun, The Sainsbury Laboratory
 11:15 AM – 11:45 PM Protein Regulatory Networks Steve Briggs, UC San Diego
 11:45 AM – 12:00 PM Tight, Inducible Gene Expression in Plants with Alternatively Spliced Suicide Exons  Tania González, UC Berkeley
 12:00 PM – 1:30 PM Working Lunch  
 1:30 PM – 5:00 PM SESSION IV Chair:  Tanja Woyke
1:30 PM – 2:30 PM New Technologies Overview and User Feedback Joint Genome Institute
2:30PM – 3:00 PM The Microbiome – A New Frontier in Human Health Susan Lynch, University of California, San Francisco
3:00 PM – 3:30 PM Break  
3:30 PM – 4:00 PM Antarctic Microbial Omics – a Path to Learning About Life in the Cold Rick Cavicchioli, University of New South Wales
 4:00 PM – 5:00 PM Closing Keynote Presentation
Ocean Basin-Wide Patterns and Processes Revealed by High Resolution Microbial Community Transcriptome Networks Edward DeLong, University of Hawaii
5:00 PM End of JGI User Meeting  

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