SCGC Workshop 2015

Third Microbial Single Cell Genomics Workshop

June 14-18, 2015

Organizing committee:

Paul Blainey, Broad Institute
David Emerson, Bigelow Laboratory for Ocean Sciences
Nicole Poulton, Bigelow Laboratory for Ocean Sciences
Ramunas Stepanauskas (chair), Bigelow Laboratory for Ocean Sciences
Tanja Woyke, DOE Joint Genome Institute

Workshop coordinator:

Brian Thompson, Bigelow Laboratory for Ocean Sciences

Sunday, June 14

6:00-8:00 PMWelcome Reception & Registration

Monday, June 15

7:30 AMBreakfast
8:30 AMWelcome and logistics(Ramunas Stepanauskas and Brian Thompson)
8:45 AMKEYNOTE Stephen Giovannoni (Oregon State University): Predicting long-term impacts of ocean desertification on microbial plankton communities


9:45 AMKatherine McMahon (University of Wisconsin): Single Cell Genomes from Freshwater Bacteria - Anchors to Study Population Expansion and Contraction
10:15 AMCoffee Break
10:30 AMMircea Podar (Oak Ridge National Laboratory): The world of the yet uncultured: from single cells to reverse genomic microbiology
11:00 AMTanja Woyke (DOE Joint Genome Institute): Insights into candidate phyla from hot springs
11:30 AMKaren Lloyd (University of Tennessee): Obtaining single cell genomes from 85 meters below the seafloor, and using them to bin metagenomic data
11:45 AMJessica Labonté (Bigelow Laboratory for Ocean Sciences): Single cell genomics reveals contrasting life strategies employed by viruses in the environment
12:00 PMLunch break (SPI)


2:00 PMJames Hicks (Cold Spring Harbor Laboratory): High depth and low depth sequencing of single cancer cells to determine lineage and heterogeneity
2:30 PM Ramiro Logares (Institute of Marine Sciences, CSIC): Exploring the marine pico-eukaryotic dark-matter using single-cell genomics
3:00 PM Coffee Break
3:15 PMPeter Countway (Bigelow Laboratory for Ocean Sciences): Sorting out ecological relationships among microbial grazers and their cyanobacterial prey: insights from small populations and single-cells
3:30 PM Nicolas Tromas (Universite de Montreal): Ecological responses of bacterial populations revealed by time-course sequencing of freshwater cyanobacterial communities
3:45 PMDavid Emerson (Bigelow Laboratory for Ocean Sciences): What single cell genomics is revealing about iron-oxidizing bacteria
4:15 PMPoster Session
6:00 PMTraditional Maine Lobster Bake (SPI)

Tuesday, June 16

7:30 AM Breakfast
8:30 AMKEYNOTE Pavel Pevzner (University of California - San Diego): Genome assembly: from single cells to metagenomes


9:30 AM Gerrit van den Engh (Center for Marine Cytometry): Flow cytometry of Prochlorococcus and Synechococcus at Station Aloha
10:00 AMCoffee Break
10:15 AM Holger Daims (University of Vienna): Raman-based sorting of microbes with defined functional properties for single-cell genomics
10:45 AMLinas Mazutis (Vilnius and Harvard Universities): Drop-Seq: Profiling transcriptome of thousands of single-cells
11:15 AMPaul Blainey (Broad Institute): Microfluidic systems for single cell sequencing
11:45 AM Emmanuelle Gerard (Institut de Physique du Globe de Paris): Laser microdissection and single cell genomics of microorganisms associated with modern microbialites
12:00 PMLunch break


2:00 PMMatthew Sullivan (University of Arizona): Emerging methods to study bacteriophage infection at the single-cell level
2:30 PM Philipp Engel (University of Lausanne): Comparative single cell genomics of honey bee gut symbionts
3:00 PM Coffee Break
3:15 PM Takuro Nunoura (JAMSTEC): Genomic insights into the niche adaptation of marine Thaumarchaeota along the water column from the sea surface to hadal ocean
3:30 PMMaria Hammond (Uppsala University): Improving whole genome amplification with droplet microfluidics
3:45 PMAndreas Bremges (Bielefeld University): Metagenomic proxy assemblies of single cell genomes
4:00 PMSteve Almo (Albert Einstein College of Medicine): Experimental strategies for functional annotation and metabolism discovery
4:15 PM Ying Zhang (University of Rhode Island): A portable system for the analysis of metabolic models
4:30 PM Tours and BBQ at Bigelow Laboratory

Wednesday, June 17

7:30 AMBreakfast
8:30 AMRamunas Stepanauskas (Bigelow Laboratory for Ocean Sciences): Bigelow Laboratory Single Cell Genomics Center: An evolving resource to the research community
9:30 AM Breakout into discussion groups and coffee
10:45 AM Breakout group presentations
11:45 AMConcluding remarks
12:00 PM Lunch break

Thursday, June 18

7:00 AMBreakfast
8:00 AM - 5:30 PM Boat trip to and hike on Monhegan Island