rRNA technology workshop outline
Monday 07.04.2008
8.45, Databases
Chair: Frank Oliver Glöckner
Welcome address by organizers
1. James Cole, USA
The Ribosomal Database Project
2. Todd DeSantis, USA
Integrating ribosomal sequence analysis with taxonomic
microarray data using the Greengenes database
10.00-10.30 Coffee Break
3. Peter Dawyndt, Belgium
The StrainInfo.net bioportal: reaching out to what we know
about our microorganisms
4. Frank Oliver Glöckner, Germany
The SILVA project for comprehensive, quality checked and aligned
ribosomal RNA databases
11.30-12.00 Coffee Break
12.00, Phylogeny
Chair: Wolfgang Ludwig
1. Christian von Mering, Switzerland
Protein-coding phylogenetic markers: complementing
rRNA in the analysis of environmental communities
2. Wolfgang Ludwig, Germany
rRNA based phylogeny still a backbone for taxonomy?
13.00-15.00 Lunch Break
3. Alexandros Stamatakis, Germany
Algorithms, high performance computing, and challenges for
large-scale phylogenetic inference
4. Harald Meier, Germany
Harvesting and evaluating diagnostic fruit from a molecular
phylogenetic tree - an online approach
16.00-16.30 Coffee Break
16.30, Data analysis & Biogeography
Chair: Alban Ramette
1. Anthony Lehmann, Switzerland
Generalized Regression Analysis and Spatial Predictions:
from genes to communities
2. Angelique Gobet, Germany
Contextual interpretation of 454 massive tag sequencing data.
A case study applied to coastal sediments
17.30-18.00 Coffee Break
3. Thomas Pommier, France
RAMI, a new tool to characterize and visualize the
biogeography of rRNA sequence clusters
4. Alban Ramette, Germany
Analysis of high-throughput sequencing data in their
environmental context
19.00 - 21.30, Welcome Dinner at the Max Planck Institute for Marine Microbiology
Equipment
The conference room will be equipped with an Internet connected PC and free Wireless Lan access.
Presentations can be accepted on USB-Sticks or CDs as Powerpoint or PDF files.
Sponsors
April 7-9, 2008, MPI-Bremen, Germany
Tuesday 08.04.2008
9.00, Technology
Chair: Jörg Peplies
1. Mitch Sogin, USA
Massively parallel DNA sequencing and the "Rare Biosphere"
2. Freek Bakker, The Netherlands
Global standardization & implementation of DNA barcodes:
the CBOL perspective
10.00-10.30 Coffee Break
3. Rudolf Amann, Germany
Fluorescent oligonucleotide probing of whole cells for
determinative, phylogenetic, and environmental studies
in microbiology
4. Alexander Loy, Austria
Analyzing microbes after their last meal: Raman
microspectroscopy of isotope-labeled cells and nucleic acids
11.30-12.00 Coffee Break
5. Barbara Pohl, biomers.net, Germany
Oligonucleotides: Insights in synthesis, purification and
modifications
6. Wolf Malkusch, Zeiss MicroImaging, Germany
Traditional and future scopes of image analysis in cell biology
13.00-15.00 Lunch Break
15.00, Diversity & Ecology
Chair: Bernhard Fuchs
1. Pedro Martinez-Arbizu, Euro-CoML, Germany
The Census of Marine Life in Europe
2. Erko Stackebrandt & Sylvie Cousin, Germany
Working in the underbrush: the limitations and potential
of short rRNA sequences generated in diversity studies
16.00-16.30 Coffee Break
3. Dave Stahl, USA
Nitrification: Phylotype versus ecotype revisited
4. Ramon Rossello-Mora, Spain
The Living Tree Project
18.00 Free Evening
Wednesday 09.04.2008
9.00, Diversity & Ecology cont.
Chair: Linda Amaral-Zettler
5. Stephen Giovannoni, USA
Natural variation among ecotypes of the SAR11 Clade
6. Anna-Louise Reysenbach, USA
Temporal and spatial patterns of microbial diversity at
deep-sea vents
10.00-10.30 Coffee Break
7. Gerhard Herndl, Netherlands
Prokaryotic community structure and activity in the
North Atlantic deep waters
8. Jakob Pernthaler, Switzerland
rRNA as the anchor point for investigating the
ecophysiology of aquatic bacteria at the single cell level
11.30, Roundup & Discussion
12.00, Official end of workshop
13.30-15.00, Preparation of workshop report
Organizers
Follow this link to get the Workshop Proceedings and Handout