SCGC Workshop 2010

Workshop: Redefining microbial genomics:
The power of sequencing individual cells

September 19-24, 2010

Workshop hosts:
Ramunas StepanauskasĀ andĀ Michael Sieracki,Ā Bigelow Laboratory for Ocean Sciences

Workshop coordinator:
Nicole Poulton

Workshop Program

Sunday, September 19, 2010

Arrival and registration

5:00 - 7:00 pm Welcome Reception & Registration at the Spruce Point Inn -
Location: 88 Grandview - Oceanfront Dinning Room

Monday, September 20

Research presentations - Location: Pemaquid Hall

8:40Welcome and logisticsGraham Shimmield and Ramunas StepanauskasBigelow Laboratory

General topics

9:00Dissecting environmental ecosystems with single cell genome sequencingStephen QuakeStanford University
10:00Single cell genomics at the JGI: From small symbiont genomes to massively expanding the tree of lifeChristian RinkeDOE JGI
10:30Coffee break/discussion
10:45Use of single cell genomics for the human microbiome projectRoger LaskenJC Venter Institute
11:15Putting single cell genomics to work: Scaling up to the microbial challengeRamunas StepanauskasBigelow Laboratory
11:45Open discussion
12:00Lunch break


1:30Whole genome sequencing of individual bacterial cells from the oceanRex MalmstromDOE Joint Genome Institute
2:00Manipulation and genome sequencing of single microbial cellsHsin-I(Sam) ChiangHsin-I(Sam) Chiang UC-San Diego
2:30The use of single cell genomics for studies of reductive genome evolution in aquatic alpha-proteobacteria Siv AnderssonUppsala University
3:00Coffee break/discussion
3:15Exploring the diversity and metabolic potential of mesopelagic microbes using single cell genomics Brandon SwanBigelow Laboratory
3:45Redefining the diversity of freshwater aerobic photoheterotrophs by single cell sequencingManuel Martinez GarciaBigelow Laboratory
4:15Marine Synechococcus ecology: do single cells matter?Brian PalenikU. California - San Diego
4:45Open discussion
6:30 - 9:30 pmTraditional Maine Lobster Bake Location: Linekin Bay Room

Tuesday, September 21

Research presentations - Location: Pemaquid Hall



8:00Single cell metagenomes reveal the dynamic world of marine protistsDebashish BhattacharyaRutgers University
8:30Single cell genomics approach for the Paulinella genome sequencingHwan Su YoonBigelow Laboratory
9:00Sorting viruses and virus-infected cells: Lessons from a giantWillie WilsonBigelow Laboratory
9:30Exploring the genomic diversity of marine protists from the Tara Oceans expeditionOlivier Jaillon Genoscope
10:00Coffee break/discussion

Technologies: Cell separation

10:15Getting cells single and clean: flow cytometry secrets revealed!Michael SierackiBigelow Laboratory
10:45Laser microdissection: A novel approach to bacterial cell isolationPaul Scott Sanger Institute
11:15Microdroplet-based single cell analysis and genomicsMichael SamuelsRaindance Technologies
11:45Open discussion
12:00Lunch break

Technologies: Sequence analysis

1:30Massively Parallel sequencing has some steep start-up costs. Which one should I buy?Paul MorrisonHarvard Medical School
2:00Genome assembly from non-traditional dataMihai PopU. Maryland
2:30Coffee break/discussion

Technologies: Beyond DNA

2:45Coupling function to phylogeny via single-cell phenotypingMarina KalyuzhnayaU Washington
3:15Applications of single cell transcriptomics across biology: Their relevance and feasibilityDavid GalbraithU. Arizona

Single cell genomics: Challenges and opportunities

3:45Open discussion
5:30Concluding remarks

Wednesday, September 22

Excursions to Monhegan Island and Bigelow Laboratory for Ocean Sciences

Thursday-Friday, September 23-24

Bioinformatics tutorial - Location: Linekin Bay Room

Thusday AM

Genome assemblySergey KorenJ.C. Venter Institute
Syllabus: Genome assembly is a pushbutton process on isolate bacteria but challenging on next-generation sequencing and single cell amplified data. In addition, a means to choose the ā€œbestā€ assembly from a set of candidates is needed. The tutorial will include information on data preparation, assembly, and strategies for single cell amplified data. The tutorial will also include an introduction to assembly visualization and validation through a combination of lecture and hands on analysis.

Thusday PM

Genome annotation Iain Anderson DOE JGI
Syllabus: IMG provides a wide range of tools for the analysis and comparison of genomes. The tutorial will include coverage of tools that allow the user to select genes found in one set of genomes and missing in another set; abundance profile tools to compare the occurrence of domains across a group of organisms; and tools that enable analysis of synteny across a group of genomes. We will also discuss the tools available in IMG for analysis of metabolic and non-metabolic pathways. The live tutorial will be followed by a hands-on section with exercises, followed by a discussion of the answers to the exercises.

Friday AM

Comparative genomicsDoug Rusch J.C. Venter Institute
Syllabus: There are a variety of ways to analyze a genome. In many cases environmental data can be used to compare, validate, and enhance the analysis of individual genomes that annotation alone cannot provide. These tools exist in the border land between assembly and annotation and serve to enhance both. This will include methods for rapidly comparing genomes to genomes, methods for analyzing genomes using environmental data with tools like fragment recruitment, approaches for improving single cell genomes with environmental data, and other techniques. This tutorial will include a combination of lecture and hands on learning.

Major Sponsors: