Monday 22 March 2010

07:30

Registration

08:30

Opening Remarks

8:40 – 9:20

Hiroaki Kitano, Systems Biology Institute, Tokyo, Japan
Biological Robustness and Drug Discovery

9:20 – 10:00

Bernhard Ø: Palsson, University of California, USA
Reconstruction of Genome-scale Transcriptional Regulatory Networks in Enterobacteria

10:00 – 10:20

Markus Uhr, ETH Zurich, Switzerland
Inference of Transcriptional Control Design of Metabolic Networks

10:20 – 10:30

Rainer Breitling, University of Groningen, the Netherlands
Metabolomic Systems Biology of Protozoan Parasites

11:00 – 11:20

Vassily Hatzimanikatis,  EPFL, Switzerland
The Process Systems Engineering of Cellular Processes

11:20 – 11:40

Ioannis Xenarios, Swiss Inst: Bioinformatics, Switzerland
Integration of Biological Knowledge: from Avalanche of Data to System Modelling

11:40 – 12:00

Edda Klipp, Humbodlt University, Germany
Integration of Different Signals in Cellular Stress Response

12:00 – 12:20

Arne Elofsson, Stockholm University, Sweden
Membrane Protein Bioinformatics

12:20 – 12:40

Tomer Shlomi, Technion, Israel
Metabolic network-based design of metabolite screening strategies for chemical production

14:00 – 14:40

Ron Weiss, MIT, USA
Synthetic Biology: from Modules to Systems

14:40 – 15:00

Sergio Bordel Velasco, Chalmers University, Sweden
New Tools for the Analysis of Metabolic Networks for the Improvement of Strain Efficiency

15:00 – 15:20

Marc Güell, Centre for Genomic Regulation, Spain
Frequency of Alternative Transcripts and Antisense RNA in Bacteria Reveal High Regulatory Complexity

15:20 – 15:30

Matthias Bujara, ETH Zurich, Switzerland
SubMeRTA:  Sub-Metabolomic Real-Time Analysis for Rapid Optimization of Multi-Enzyme in Vitro Networks

16:00 – 16:20

Victor de Lorenzo, Centro Nacional Biotecnologia, Spain
Reshaping the Architecture of the Regulatory Circuit of the TOL Plasmid of Pseudomonas Putida for an Increased Response to Environmental Pollutants

16:20 – 16:40

Christoph Wittman, TU Braunschweig, Germany
Towards Superior Cell Factories – Systems-wide Analysis and Engineering of Metabolic Pathways in Corynebacteirum glutamicum

16:40 – 17:00

Wanwipa Vongsangnak, Chalmers University of Technology, Sweden
Systems biology, Bioinformatics and Omics analysis of Aspergillus oryzae

17:00 – 17:20

Anders Blomberg, University of Gothenburg, Sweden
System-wide Functional Analysis of a Novel Class of Tentative Protein Tyrosine Phosphatases in the Yeast Saccharomyces Cerevisiae

17:20 – 17:30

Dennis Vitkup, Columbia University,USA
Global Probabilistic Reconstruction of Microbial Metabolic Networks

17:30– 17:40

Brigitte Gasser, BOKU- University of Natural Resources and Applied Life Sciences Vienna, Austria
Systems Biotechnology for Protein Production in Pichia pastoris

17:40 – 19:30

Poster Session 1 and Welcome Reception

• Technology – computational: new modeling approaches and model discrimination
• Technology – experimental: new high-throughput biology
• Microbial systems biology: biotechnology (including synthetic approaches)

Tuesday 23 March 2010

8:30 – 9:10

Sang Yup Lee, KAIST, Korea
Systems Metabolic Engineering for Chemicals and Materials

9:10 – 9:30

George Guo-Qiang Chen, Tsinghua University, China
A Systematic Study on Microbial Production of Biopolymers and Chemicals

9:30 – 9:50

Ivan Mijakovic, AgroParisTech, France
Protein Phosphorylation in Bacterial Signal Transduction

9:50 – 10:10

Paramvir Dehal, Lawrence Berkeley National Lab, USA
Creating a Systems Biology Framework for Understanding the Sulphate Reducing Microbe Desulfovibrio vulgaris

10:10 – 10:30

Christopher Henry, University of Chicago, USA
Model-driven Minimization of the B: subtilis Genome

11:00 – 11:20

Vincent Schächter, Total, France
Applications of systems and synthetic biology to biofuels and chemicals: an industrial perspective

11:20 – 11:40

Joerg Bernhardt, Greifswald University, Germany
Detection, Quantitation and Analysis of almost all Expressed Proteins of Staphylococcus Aureus

11:40 – 12:00

Oscar P: Kuipers, University of Groningen, The Netherlands
Growing Pains: Natural Stress Responses During Growth of Bacillus subtilis

12:00 – 12:10

Jörg Linde,  Hans-Knöll-Institute, Germany
Regulatory Network Modelling of Iron Acquisition by a Fungal Pathogen During Oral Infection

12:10 – 12:20

Gabriel Moreno-Hagelsieb, Wilfrid Laurier University, Canada
Exploring the Uncharted Functional Territories of a Bacterial Genome : Insights from the Functional Blueprint of Escherichia coli

12:20 – 12:30

Muriel Cocaign-Bousquet, LISBP, France
Post-transcriptional Processes Influence Lactococcus lactis Adaptation

Workshop sponsored by

Sequencing and Transcriptional analysis of bacterial genomes
Speaker: Dr: Axel Strittmatter, Eurofins MWG Operon, Ebersberg, Germany

14:00 – 14:40

Ruedi Aebersold, ETH Zurich, Switzerland
Mapping and Measuring Microbial Proteomes

14:40 – 15:00

Nicola Zamboni, ETH, Zurich, Switzerland
Deep Phenotyping by High-throughput Metabolomics

15:00 – 15:20

Federico Katzen, Life Technologies, USA
Next Generation DNA Assembly Tools for Systems Biology

15:20 – 15:30

Eric Botella, Trinity College, Dublin, Ireland
Cell Wall Metabolism in B: subtilis: a Global Analysis of Gene Expression in Growing and Phosphate Limited Cells

16:00 – 16:20

Anne Claude Gavin, EMBL, Germany
Proteome Organization in a Genome-Reduced Bacterium

16:20 – 16:40

Uwe Sauer, ETH Zürich, Switzerland
Condition-specific Transcriptional Control of Metabolic Fluxes and Computational Prediction

16:40 – 17:00

Jean Charles Portais, INSA Toulouse, France
Methylotrophy from a system perspective: genome-wide reconstruction and functional analysis of the metabolism of Methylobacterium extorquens

17:00 – 17:20

Gertien Smits, Swammerdam Institute for Life Sciences, Netherlands
Genome-wide Analysis Reveals Intracellular pH of Yeast as a Physiologically Dynamic but Genetically Tightly Controlled Cellular Property

17:20 – 17:30

Paul Wilmes, Centre de Recherche Public – Gabriel Lippmann, Luxembourg
Metabolome-proteome differentiation reflects bacterial divergence

17:30 – 19:00

Poster Session 2 and drinks

• Bottom-up systems biology: modeling individual cell subsystems (includes Dynamics of signal transduction pathways)
• Top-down systems biology: data integration & network reconstruction for a coarse-grained model of the cell
• Microbial systems biology and human health

Wednesday 24 March 2010

8:30 – 9:10

Richard Losick, Harvard University, USA
How a Single Master Regulator Generates Multiple Cell types

9:10 – 9:30

Serge Pelet, ETH Zürich, Switzerland
Transient Activation of the HOG MAPK Pathway Leads to Bimodal Protein Target Expression

9:30 – 9:50

Jörg Stülke, University of Göttingen, Germany
Organisation of Metabolism in Bacillus Subtilis: Evidence for the Presence of Protein Complexes in Central Metabolism

9:50 – 10:10

Jörg Büscher, ETH Zurich, Switzerland
Multi-Omics, Multi-Laboratory Study Reveals Bacillus' Dynamic Response to Environmental Shift

10:10 – 10:30

Pierre Nicolas, MIG, INRA, France
Genome-Scale Transcriptional Activity of Bacillus Subtilis Cells Under Various Life Styles

11:00 – 11:40

Judith Armitage, Oxford, UK
Bacterial Decision Making

11:40 – 12:00

John Helmann, Cornell University, USA
Oxidative Stress Responses in Bacillus subtilis

12:00 – 12:20

Nathalie Balaban, Hebrew University, Israel
Single cell individuality in bacterial persistence: when, how and why

12:20 – 12:30

Stefan Streif, Max Planck Institut, Germany
A predictive computational model of the kinetic mechanism of stimulus-induced transducer methylation and feedback regulation through CheY in archaeal phototaxis and chemotaxis

14:00 – 14:40

Stanislas Leibler, Rockefeller University and the Institute for Advanced Study, USA
Cooperation in bacteria: a synthetic perspective:

14:40 – 15:00

Matthias Heinemann, ETH Zurich, Switzerland
Bacterial Adaptation Through Distributed Sensing of Metabolic Fluxes

15:00 – 15:20

Filippo Menolascina, Telethon Institute of Genetics and Medicine, Italy
Controlling Gene Regulatory Networks by means of Control Systems Theory Principles and Microfluidic Devices

15:20 – 15:30

Wolfgang Hess, University of Freiburg, Germany
Deep Sequencing of Transcriptional Start Sites Provides an Experimentally Anchored Map of More than 3000 Promoters in the Model cyanobacterium Synechocystis sp: PCC 6803

16:00 – 16:40

Rick L Stevens, University of Chicago, USA
Predicting Phenotype from Genotype: Tools for Annotation, Integration, Reconstruction, and Modeling

16:40 – 17:00

Ines Thiele, University of Iceland, Iceland
An Integrated Model of Macromolecular Synthesis and Metabolism of Escherichia Coli

17:00 – 17:20

Anne Goelzer, INRA, France
Growth Rate Reflects a Bottleneck on the Resource Sharing Between Cellular Processes

17:20 – 17:40

Markus Covert, Stanford, United States
Towards a Whole-cell Model of Mycoplasma genitalium

17:40 – 17:55

Eva Yus, Centre for Genomic Regulation, Spain
Metabolic Reconstruction of Mycoplasma pneumoniae Metabolism and Insights on its Regulation

17:55 – 18:00 

Closing remarks