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scientific program

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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
5.30 pm-6.00 pm
6.00 pm
Welcome addresses
Bernard Dujon, Senior Executive-Vice President for Scientific Affaire, Institut Pasteur, Paris, France
Carmen BUCHRIESER, Institut Pasteur, Paris, France
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
7.30 pm Welcome Reception at Institut Pasteur
Wednesday April 9th, 2008
8.30 am-10.25 am
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
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

10.25 am-11.00 am Coffee break
11.00 am-12.35 am
11.00 am-11.25 am
11.25 am-11.50 am
11.50 am-12.15 am
12.15 am-12.35 am
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
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
3.30 pm -5.05 pm
3.30 pm-3.55 pm
3.55 pm-4.20 pm
4.20 pm - 4.45 pm
4.45 pm-5.05 pm

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

5.05 pm - 5.35 pm

Coffee break

5.35 pm-6.50 pm
5.35 pm-6.00 pm
6.00 pm-6.25 pm
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
6.30 pm-8.00 pm Wine and Cheese party
Thursday April 10th, 2008
8.30 am-10.05 am
8.30 am-8.55 am
8.55 am-9.20 am
9.20 am-9.45 am
9.45 am-10.05 am
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
10.05 am-10.40 am Coffee break
10.40 am-12.15 am
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
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
12.15 pm-2.00 pm

Lunch at Institut Pasteur

2.00 pm-3.30 pm Poster session
3.30 pm-4.45 pm
3.30 pm-3.55 pm
3.55 pm-4.20 pm
4.20 pm-4.45 pm
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
4.45 pm-5.10 pm

Coffee break

5.10 pm-6.20 pm
5.10 pm-5.35 pm
5.35 pm-6.00 pm
6.00 pm-6.20 pm
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
8.00 pm Congress dinner
Friday April 11
8.30 am-10.05 am
8.30 am-8.55 am
8.55 am-9.20 am
9.20 am-9.45 am
9.45 am-10.05 am
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
10.05 am-10.35 am

Coffee break

10.35 am-12.30 am
10.35 am-11.00 am
11.00 am-11.25 am
11.25 am-11.50 am
11.50 am-12.30 am
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
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
3.00 pm-3.25 pm
3.25 pm-3.50 pm
3.50 pm-4.15 pm
4.15 pm-4.40 pm
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?
4.40 pm Poster competition award
4.40 pm-5.00 Closing lecture
Frank Kunst, Institut Pasteur, France