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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 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



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.


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,, Germany

       Oligonucleotides: Insights in synthesis, purification and


   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