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

September 19-24, 2010

Workshop hosts:
Ramunas Stepanauskas and Michael Sieracki, 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
7:30	Breakfast
8:40	Welcome and logistics	Graham Shimmield and Ramunas Stepanauskas	Bigelow Laboratory
General topics
9:00	Dissecting environmental ecosystems with single cell genome sequencing	Stephen Quake	Stanford University
10:00	Single cell genomics at the JGI: From small symbiont genomes to massively expanding the tree of life	Christian Rinke	DOE JGI
10:30	Coffee break/discussion
10:45	Use of single cell genomics for the human microbiome project	Roger Lasken	JC Venter Institute
11:15	Putting single cell genomics to work: Scaling up to the microbial challenge	Ramunas Stepanauskas	Bigelow Laboratory
11:45	Open discussion
12:00	Lunch break
Prokaryotes
1:30	Whole genome sequencing of individual bacterial cells from the ocean	Rex Malmstrom	DOE Joint Genome Institute
2:00	Manipulation and genome sequencing of single microbial cells	Hsin-I(Sam) Chiang	Hsin-I(Sam) Chiang UC-San Diego
2:30	The use of single cell genomics for studies of reductive genome evolution in aquatic alpha-proteobacteria	Siv Andersson	Uppsala University
3:00	Coffee break/discussion
3:15	Exploring the diversity and metabolic potential of mesopelagic microbes using single cell genomics	Brandon Swan	Bigelow Laboratory
3:45	Redefining the diversity of freshwater aerobic photoheterotrophs by single cell sequencing	Manuel Martinez Garcia	Bigelow Laboratory
4:15	Marine Synechococcus ecology: do single cells matter?	Brian Palenik	U. California - San Diego
4:45	Open discussion
6:30 - 9:30 pm	Traditional Maine Lobster Bake	Location: Linekin Bay Room
Tuesday, September 21
Research presentations - Location: Pemaquid Hall
7:30	Breakfast
Protists
8:00	Single cell metagenomes reveal the dynamic world of marine protists	Debashish Bhattacharya	Rutgers University
8:30	Single cell genomics approach for the Paulinella genome sequencing	Hwan Su Yoon	Bigelow Laboratory
9:00	Sorting viruses and virus-infected cells: Lessons from a giant	Willie Wilson	Bigelow Laboratory
9:30	Exploring the genomic diversity of marine protists from the Tara Oceans expedition	Olivier Jaillon	Genoscope
10:00	Coffee break/discussion
Technologies: Cell separation
10:15	Getting cells single and clean: flow cytometry secrets revealed!	Michael Sieracki	Bigelow Laboratory
10:45	Laser microdissection: A novel approach to bacterial cell isolation	Paul Scott	Sanger Institute
11:15	Microdroplet-based single cell analysis and genomics	Michael Samuels	Raindance Technologies
11:45	Open discussion
12:00	Lunch break
Technologies: Sequence analysis
1:30	Massively Parallel sequencing has some steep start-up costs. Which one should I buy?	Paul Morrison	Harvard Medical School
2:00	Genome assembly from non-traditional data	Mihai Pop	U. Maryland
2:30	Coffee break/discussion
Technologies: Beyond DNA
2:45	Coupling function to phylogeny via single-cell phenotyping	Marina Kalyuzhnaya	U Washington
3:15	Applications of single cell transcriptomics across biology: Their relevance and feasibility	David Galbraith	U. Arizona
Single cell genomics: Challenges and opportunities
3:45	Open discussion
5:30	Concluding 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 assembly	Sergey Koren	J.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 “best” 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 genomics	Doug 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.

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