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Workshop "Systems Biology for Beginners"
April 8th, 2008 from 2.00 pm to 5.00 pm
organized by Philippe GLASER, Institut Pasteur, Paris, France and Benno SCHWIKOWSKI, Institut Pasteur, Paris, France
33 places available. Registration fees: 30 € (VAT included). Specific registration not included in the registrations fees for the conference.
To register,
download the registration form and send it by regular mail to
Institut Pasteur
CIS - Gestion des Colloques
28 rue du Docteur Roux
75724 Paris cedex 15
or by fax: + 33 1 40 61 37 21
Tuesday April 8th, 2008 |
| 1.30 pm-5.30 pm |
Registration |
| 2.00 pm-5.00 pm |
Workshop “Systems Biology for beginners”
organized by Philippe GLASER, Institut Pasteur, Paris, France and Benno SCHWIKOWSKI, Institut Pasteur, Paris, France |
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| Welcome addresses |
| Bernard Dujon, Senior Executive-Vice President for Scientific Affaire, Institut Pasteur, Paris, France |
| Carmen BUCHRIESER, Institut Pasteur, Paris, France |
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Opening lecture |
Chair: Jörg HACKER,Robert Koch-Institut, Berlin, Germany |
Martin J. Blaser, New York University School of Medicine, New York, USA
The extensive and changing conversations between Helicobacter pylori and human cells |
Pascale Cossart, Institut Pasteur, France
Listeria monocytogenes : RNA lessons from the genome |
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| 7.30 pm |
Welcome Reception at Institut Pasteur |
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Wednesday April 9th, 2008 |
8.30 am-10.25 am |
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| 8.30 am-8.55 am |
| 8.55 am-9.20 am |
| 9.20 am-9.45 am |
| 9.45 am-10.05 am |
| 10.05 am - 10.25 am |
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Session 1: Host - Microorganism Interactions: a) Pathogens |
Chair: Tony Pugsley, Institut Pasteur, Paris, France |
Dirk Bumann, University of Hannover, Germany
Systems Biology of Salmonella infection |
Ulla Bonas, Martin-Luther University, Halle, Germany
New insights into how the phytopathogen Xanthomonas manipulates the host |
Andrew Camilli, Tufts University, Boston, USA
Genetic Analysis of the Transmissible State of Vibrio cholerae |
Thomas Meyer, Max Planck Institute for Infection Biology, Berlin, Germany
Systematic dissection of host cell function during infection |
Sigrid De Keersmaecker, Ctre of Microbial & Plant Genetics, Leuven, Belgium
Towards systems biology, the Salmonella typhimurium luxs/ai-2 related pathway as a case study
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| 10.25 am-11.00 am |
Coffee break |
11.00 am-12.35 am |
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| 11.00 am-11.25 am |
| 11.25 am-11.50 am |
| 11.50 am-12.15 am |
| 12.15 am-12.35 am |
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Session 1: Host - Microorganism Interactions: a) Pathogens |
Chair: Birgitta Henriques Normark, Karolinska Institute Stockholm, Stockholm, Sweden |
Eliora Ron, University of Tel Aviv, Israel
Systemic E. coli infections – what can we predict from genomics? |
Stephen Lory, Harvard University, Boston, USA
Insights into the evolution of virulence in Pseudomonas aeruginosa: covering all bases |
Roland Brosch, Institut Pasteur, France
The tubercle bacilli : Molecular determinants of pathogenicity and attenuation |
Christoph Dehio, University of Basel, Basel, Switzerland
Comparative and functional genomic analysis of Bartonella identifies type iv secretion systems as host adaptability factors |
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| 12.35 pm - 2.00 pm |
Lunch at Institut Pasteur |
| 2.00 pm-3.30 pm |
| Poster session |
Company presentations |
2.00 pm-2.30 pm: Applied Biosysrems
Paolo Vatta - Comparative Whole Genome Sequencing using SOLiD™ System |
2.30 pm-3.00 pm: Cogenics
Marcel de Leeuw - Putting Next Generation sequencing of microbial genomes to work |
3.00 pm-3.30 pm: Roche Diagnostics
Andread Tauch -
Ultrafast pyrosequencing of the Human pathogens Corynebacterium urealyticum and Corynebacterium |
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3.30 pm -5.05 pm |
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| 3.30 pm-3.55 pm |
| 3.55 pm-4.20 pm |
| 4.20 pm - 4.45 pm |
| 4.45 pm-5.05 pm |
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Session 2: Host - Microorganism Interactions: b) Symbionts, Commensals |
Chair: Peter SEBO, Czech Academy of Science, Prague, Czech Republic |
Oded Beja, Technion - Israel Institute of Technology, Haifa, Israel
Metagenomics of viral 'photosynthesis' |
Dusko Ehrlich, INRA, Jouy en Josass, France
Metagenomics of the human digestive tract – insights into commensal bacteria |
Richard FFrench-Constant, University of Bath, United Kingdom
Rapid Virulence Annotation of Bacterial Genomes: Lessons from the insect pathogen Photorhabdus |
Sascha Stoll, University of Wüerzburg, Wüerzburg, Germany
The transcriptome of the endosymbiont Blochmannia floridanus in the different life stages of its holometabolous host
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| 5.05 pm - 5.35 pm |
Coffee break |
5.35 pm-6.50 pm |
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| 5.35 pm-6.00 pm |
| 6.00 pm-6.25 pm |
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Session 3: Host Genomics and Vaccines |
Chair: Agnès ULLMANN, Institut Pasteur, Paris, France |
Catharina Svanborg, University of Lund, Sweden
Innate immune response genetics and susceptibility to urinary tract infection |
Philippe Sansonetti, Institut Pasteur, France
How Shigella hijacks host-cell gene transcription and signalling pathways to modulate the innate immune response |
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| 6.30 pm-8.00 pm |
Wine and Cheese party |
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Thursday April 10th, 2008 |
8.30 am-10.05 am |
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| 8.30 am-8.55 am |
| 8.55 am-9.20 am |
| 9.20 am-9.45 am |
| 9.45 am-10.05 am |
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Session 4: New Technologies – What are the Results |
Chair: Antoine DANCHIN, Institut Pasteur, Paris, France |
Michael Hecker, University of Greifswald, Greifswald, Germany
Towards the entire proteome of gram-positive bacteria |
Amos Bairoch, Swiss Institute of Bioinformatics, Geneva, Switzerland
UniProtKB and microbial proteomes: status and future developments |
Julian Parkhill, Sanger Center, Cambridge, United Kingdom
Variation detection in highly monomorphic bacteria using new sequencing technologies |
Trent Northen, The Scripps Research Institute, La Jolla, United States
High Throughput Mass Spectrometry Based Metabolomic and Enzymatic Assays for Functional Genomics |
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| 10.05 am-10.40 am |
Coffee break |
10.40 am-12.15 am |
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| 10.40 am-11.05 am |
| 11.05 am-11.30 am |
| 11.30 am-11.55 am |
| 11.55 am-12.20 pm |
| 12.20 pm-12.40 pm |
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Session 5: Functional Genomics |
Chair: Brendan WREN, London, United Kingdow |
Susan Gottesman, Nat. Cancer Inst., Bethesda, USA
Small RNAs and E. coli regulatory circuits |
Peer Bork, EMBL, Heidelberg, Germany
Predicting biological function at different scales |
Tracy Palmer, University of Dundee, Dundee, United Kingdom
Functional genomic analysis of protein secretion in Streptomyces species |
Mariagrazia Pizza, Novartis Vaccines, Italy
Microbial genomes as basis of vaccine discovery: the Meningococcus B challenge |
Athanasios Typas, University of California at San Francisco, San Francisco, USA
The first high-throughput system for quantitatively assessing genetic interactions in bacteria |
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| 12.15 pm-2.00 pm |
Lunch at Institut Pasteur |
| 2.00 pm-3.30 pm |
Poster session |
3.30 pm-4.45 pm |
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| 3.30 pm-3.55 pm |
| 3.55 pm-4.20 pm |
| 4.20 pm-4.45 pm |
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Session 6: Microbial Metagenomics |
Chair: Didier MAZEL, Institut Pasteur, Paris, France |
Jean Weissenbach, Genoscope, Paris, France
Mining metagenomes |
Victor de Lorenzo, Centro Nacional de Biotecnología, Madrid, Spain
Debugging and reconstructing regulatory networks of Pseudomonas putida for environmental release |
George Weinstock, Baylor College, Huston, USA
Approaching the Human Microbiome |
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| 4.45 pm-5.10 pm |
Coffee break |
5.10 pm-6.20 pm |
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5.10 pm-5.35 pm |
| 5.35 pm-6.00 pm |
6.00 pm-6.20 pm |
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Session 6: Microbial Metagenomics |
Chair: Hilde DE REUSE, Institut Pasteur, Paris, France |
Karl O. Stetter, University of Regensburg, Germany
The Hyperthermophilic Archaea |
Virginia Armbrust, University of Washington, USA
Life in the sea: new insights from diatom genomes |
Lena Tasse, INSA Toulouse, Toulouse, France
Screening of the human intestinal microbiota for the discovery of new enzymes specific for fiber degradation |
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| 8.00 pm |
Congress dinner |
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Friday April 11 |
8.30 am-10.05 am |
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| 8.30 am-8.55 am |
| 8.55 am-9.20 am |
| 9.20 am-9.45 am |
| 9.45 am-10.05 am |
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Session 7: Computational, Structural Genomics and Systems Biology |
Chair: BennoSCHWIKOWSKI, Institut Pasteur, Paris, France |
Russel L Finley Jr, Wayne State University, Detroit, USA
Generating protein interaction maps for pathogens using yeast two-hybrid |
Jörg Stelling, ETH Zürich, Switzerland
Systems analysis of signal transduction pathways |
Fiona Brinkman, Simon Fraser University, Burnaby, Canada
Insights into the evolution of pathogens using improved bioinformatics approaches |
Alexei Savchenko, University of Toronto, Toronto, Canada
Genomewide structural and biochemical annotation of uncharacterised proteins from pathogenic bacteria |
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| 10.05 am-10.35 am |
Coffee break |
| 10.35 am-12.30 am |
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| 10.35 am-11.00 am |
| 11.00 am-11.25 am |
| 11.25 am-11.50 am |
| 11.50 am-12.30 am |
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Session 8: Comparative Genomics and Evolution |
Chair: Agnès LABIGNE, Institut Pasteur, Paris, France |
Erick Denamur, Medical Faculty Xavier Bichat, Paris, France
Population phylogenomics of the Escherichia coli species |
Carmen Buchrieser, Institut Pasteur, Paris, France
Comparative genomics of Legionella pneumophila and Legionella longbeachae, two human pathogens that coevolved with protozoa |
Tim Stinear, Monash University, Victoria, Australia
Insight into tuberculosis and Buruli ulcer from the complete genome sequence of Mycobacterium marinum |
| Pathogenomics PhD award |
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| 12.30 am-2.00 pm |
Lunch at the Institut Pasteur |
| 2.00 pm-3.00 pm |
Poster session |
3.00 pm-4.40 pm |
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| 3.00 pm-3.25 pm |
| 3.25 pm-3.50 pm |
| 3.50 pm-4.15 pm |
| 4.15 pm-4.40 pm |
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Session 8: Comparative Genomics and Evolution |
Chair: Xavier Nassif, Necker Hospital, Paris, France |
Hilde De Reuse, Institut Pasteur, Paris, France
Nickel trafficking in the gastric pathogen Helicobacter pylori |
Uri Gophna, University of Tel Aviv, Tel Aviv, Israel
Complexity, connectivity, and the fate of laterally acquired genes |
Mark Pallen, The University of Birmingham, Birmingham, United Kingdom
Escherchia coli: Pathogenomics of a model organism |
Ben Adler, Monash University, Victoria, Australia
What can we learn from comparative genomics of Leptospira species? |
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| 4.40 pm |
Poster competition award |
| 4.40 pm-5.00 |
Closing lecture
Frank Kunst, Institut Pasteur, France |
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