Workshop: Single Cell Alternatives to
Metagenomics in Environmental Microbiology
September 9-11, 2007, optional hands-on section September 12-14
Workshop hosts:
Michael Sieracki and Ramunas Stepanauskas, Bigelow Laboratory for Ocean Sciences
Steering Committee:
Martin Keller, Oak Ridge National Laboratory
Michael Sieracki, Bigelow Laboratory for Ocean Sciences
Paul Richardson, US DOE Joined Genome Institute
Ramunas Stepanauskas, Bigelow Laboratory for Ocean Sciences
Roger Lasken, JC Venter Institute
Workshop Program
Sunday, 9 September |
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| 17:00 - 19:00 | Welcome reception, dinner, and cash bar | ||
| 19:00 - 19:30 | Workshop Introduction, Michael Sieracki, Bigelow Laboratory for Ocean Sciences | ||
| 19:30 - 20:30 | The "Why" talk. Current environmental genomics - the context for single cell approach, Martin Keller, Oak Ridge National Laboratory | ||
Monday, 10 September |
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| 7:30-8:30 | Breakfast | ||
The "How" workshop. Technical aspects of single cell genomics |
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| Talk | Discussion | Topic | Speaker |
| 8:30 - 9:00 | 9:00 - 9:10 | Single cell FACS | Michael Sieracki, Bigelow Laboratory for Ocean Sciences |
| 9:10 - 9:40 | 9:40 - 10:30 | Single cell microfluidics | Yann Marcy, Stanford University |
| 10:30 - 10:45 | Coffee break | ||
| 10:45 - 11:45 | 11:45 - 12:15 | Whole genome amplification | Roger Lasken, JC Venter Institute |
| 12:15 - 13:30 | Lunch | ||
| 13:30 - 14:00 | 14:00 - 14:30 | Single cell genome sequencing and assembly | Paul Richardson, DOE JGI |
| 14:30 - 15:00 | 15:00 - 15:45 | Microbial single amplfied genome (SAG) pipeline | Ramunas Stepanauskas, Bigelow Laboratory for Ocean Sciences |
| 15:45 - 16:00 | Coffee break | ||
| 16:00 - 16:30 | 16:30 - 17:00 | Novel viral DNA polymerases from thermal aquifers | David Mead, Lucigen Corporation |
| 17:00 - 17:30 | 17:30 - 18:00 | Picoeukaryote ecology: Advances and challenges | Alexandra Worden, University of Miami |
Tuesday, 11 September |
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| 7:30-8:30 | Breakfast | ||
The "What" workshop: What are the best science questions for the single cell genomics tool? |
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| Talk | Discussion | Topic | Speaker |
| 8:30 - 9:00 | 9:00 - 9:30 | Single cell approach in microbial molecular ecology | Ramunas Stepanauskas, Bigelow Laboratory for Ocean Sciences |
| 9:30 - 10:00 | 10:00 - 10:30 | Genomics of uncultured Beggiatoa | Marc Mussman, University of Vienna, Austria |
| 10:30 - 10:45 | Coffee break | ||
| 10:45 - 11:15 | 11:15 - 11:25 | Soil TM7 bacteria: A test case for targeted genomics of the uncultured world | Mircea Podar, Oak Ridge National Laboratory |
| 11:25 - 11:55 | 11:55 - 12:45 | Single-cell genetic analysis of TM7 bacteria from the human mouth | Tina Losekann, Stanford University |
| 12:45 - 14:00 | Lunch | ||
| 14:00 - 14:30 | 14:30 - 15:00 | Marine viral ecology | William Wilson, Bigelow Laboratory for Ocean Sciences |
| 15:00 - 15:30 | 15:30 - 16:00 | Bacterial physiology in complex environments | Janet Jansson, Swedish Agriculture University |
| 16:00 - 16:15 | Coffee break | ||
| 16:15 - 16:45 | 16:45 - 17:15 | Evolution of microbial endosymbiosis | Hwan Su Yoon, Bigelow Laboratory for Ocean Sciences |
| 17:15 - 18:00 | Conclusions/synthesis: What are the pitfalls, challenges, and opportunities for microbial single cell genomics? | ||
| 18:00-19:00 | Cafe Scientifique public science discussion @ Boothbay Opera House | Diversity of Ocean Microbes - One Cell at a Time | Michael Sieracki, Bigelow Laboratory for Ocean Sciences |
Wednesday, 12 September |
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Optional hands-on section |
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| Time | Topic | Presenters | |
| 8:00 - 8:30 | Breakfast | ||
| 8:30 - 17:30 | Single cell bioinformatics: Genome assembly, annotation, and quality control | Tanja Woyke, Joel Martin, and Gary Xie, DOE JGI Sourav Chatterji, UC Davis |
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Thursday, 13 September |
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Optional hands-on section |
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| Time | Topic | Presenters | |
| 8:00 - 8:30 | Breakfast | ||
| 8:30 - 17:30 | Single cell FACS and whole genome amplification | Michael Sieracki, Nicole Poulton, Ramunas Stepanauskas, Wendy Korjeff-Bellows, and Jane Heywood, Bigelow Laboratory for Ocean Sciences, Arumugham Raghunathan, Sigma-Aldrich Corporation | |
Friday, 14 September |
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Optional hands-on section |
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| Time | Topic | Presenters | |
| 8:00 - 8:30 | Breakfast | ||
| 8:30 - 16:30 | Single cell FACS and whole genome amplification | Michael Sieracki, Nicole Poulton, Ramunas Stepanauskas, Wendy Korjeff-Bellows, and Jane Heywood, Bigelow Laboratory for Ocean Sciences, Arumugham Raghunathan, Sigma-Aldrich Corporation | |
Sponsors:
