Ā Workshop: Single Cell Alternatives to
Metagenomics in Environmental Microbiology
SeptemberĀ 9-11, 2007, optional hands-on section September 12-14
Workshop hosts:Ā
Michael SierackiĀ andĀ Ramunas Stepanauskas,Ā Bigelow Laboratory for Ocean Sciences
Ā Steering Committee:
Ā Martin Keller, Oak Ridge National Laboratory
Ā Michael Sieracki, Bigelow Laboratory for Ocean SciencesĀ
Paul Richardson, US DOE Joined Genome Institute
Ramunas Stepanauskas, Bigelow Laboratory for Ocean SciencesĀ
Roger Lasken, JC Venter Institute
Workshop ProgramĀ
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:
