Program

The conference programm can also be found in the abstract book
(download as pdf ).

For further information on the tours have a look at the General Information


Saturday, June 7, 2008

Arrival and individual program in Berlin

Sunday, June 8, 2008

Recovery from jet lag and evening program
Check out at ETAP Hotel, Luggage can be stored at the Charité (Monbijoustr. 2)
2.00 pm - 3.00Beginning of official program, city and boat tour
5.30 pmshuttle service to the conference hotel from Charité Institute for Biochemistry (Monbijoustr. 2)

Monday, June 9, 2008

Conference
8.45 - 9.00 amOpening Remarks
9.00 - 10.00 amSatoru Miyano
Peta Flops Computing for Systems Biology

Signalling (chair: Knapp)
10.00 - 10.20 amJózsef Bruck, Wolfram Liebermeister and Edda Klipp
The Effect of Variable Enzyme Concentrations in a Kinetic Model of Yeast Glycolysis
10.20 - 10.40 amAlexander Skupin and Martin Falcke
The Role of IP3R Clustering in Calcium Signalling
10.40 - 11.10 amCoffee Break
11.10 - 11.30 amEuna Jeong, Masao Nagasaki and Satoru Miyano
Rule-Based Reasoning for System Dynamics in Cell Systems
11.30 - 11.50 amKaname Kofima, S. Imoto, T. Shimamura, A. Fujita and S. Miyano
Estimation of non-linear Gene Regulatory Networks via L1 Regularized NVAR from Time Series Gene Expression Data

Data technology (chair: Herzel)
11.50 am - 12.10 pmMax Flöttmann, J. Schaber, E. Klipp, S. Hoops and P. Mendes
ModelMage: A Tool for the Automatic Generation and Discrimination of SBML-Models
12.10 - 12.30 pmRaymond Wan, Asa M. Wheelock and Hiroshi Mamitsuka
A Framework for Determinig Outlying Microarray Experiments
12.30 - 2.00 pmLunch Break

Saccharomyces cerevisiae (chair: Holzhütter)
2.00 - 2.20 pmClemens Kühn
Exploring the Impact of Osmoadaption on Glycolysis using Time-Varying Response-Coefficients

Networks
2.20 - 2.40 pmDavid K. Byrne, Timothy S. Gardner and Daniel Segrè
A Computational Framework for Microbial Nutrient Optimization
2.40 - 3.00 pmMoritz Schütte and Oliver Ebenhöh
A Network Evolution Model
3.00 - 3.20 pmKai Kruse
Comparing Flux Balance Analysis to Network Expansion: Producibility, Sustainability and the Scope of Compounds
3.20 - 3.50 pmCoffe Break
3.50 - 4.10 pmTimothy Hancock and Hiroshi Mamitsuka
Multiclass Semi-Supervised Graph Partitioning with Decision Trees
4.10 - 4.30 pmJorge Numata, Oliver Ebenhöh and Ernst-Walter Knapp
Measuring Statistical Coupling in Metabolic Networks Using Mutual Information
4.30 - 4.50 pmEvan Snitkin and Daniel Segrè
Optimality Criteria for the Prediction of Metabolic Fluxes in Yeast Mutants
4.50 - 5.10 pmThomas Handorf
Nutritional Requirements of Metabolic Networks
5.10 - 5.30 pmYugo Shimizu, M. Hattori, S. Goto and M. Kanehisa
Generalized Reaction Patterns for Prediction of Unknown Enzymatic Reactions
5.30 - 7.30 pmPoster session

Tuesday, June 10, 2008

Conference, Trip to Spreewald

Bioinformatics (chair: Ebenhöh)
9.00 - 9.20 amJike Cui, T. Smith, P. W. Robbins and J. Samuelson
Darwinian Selection for Sequons (Sites of Asn-Liked Glycosylation) with Thr in Phylogenetically Disparate Eukaryotes and Viruses
9.20 - 9.40 amRaphael A. Bauer, K. Rother, J. M. Bujnicki and Robert Preissner
Suffix Techniques as a Rapid Method for RNA Substructure Search
9.40 - 10.00 amStephen C. J. Parker, Elliot H. Margulies and Thomas D. Tullius
The Relationship between Fine Scale DNA Structure, GC content and Functional Elements in 1% of the Human Genome
10.00 - 10.20 amJin Hwan Do and Saturo Miyano
Secondary Metabolite Gene Cluster Analysis by the Cumulatice GC and DNA Curvature Profile in Aspergillus fumigatus Genome
10.20 - 10.50 amCoffee Break
10.50 - 11.10 amYosuke Hatanaka
A Novel Strategy to Search Concerted Transcription Factor Activities Using Gene Expression Profile and Genomic Data
11.10 - 11.30 amJonas Maaskola
How important is sequencing accuracy for next generation "deep" sequencing?
11.30 - 11.50 amChristian Waltermann, M. Krantz, S. Hohmann and E. Klipp
Sensitivity-Driven Model Discrimination in the HOG Pathway in S. Cervisiae
12.30 pmLunch Break

Trip to Spreewald

Wednesday, June 11, 2008

Conference
9.00 - 10.00 amMorihiro Hayashida
Domain-Based Model for Protein Interaction Network

Gene Regulation (chair: Falcke)
10.00 - 10.20 amLan Hu, Daniel Segrè and Temple F. Smith
Understanding the Regulatory Mechanisms of Retrotransposed Genes in the Drosophila genus
10.20 - 10.40 amManuela Benary
Modeling the Gene Expression of IL-2 in Single T cells
10.40 - 11.10 amCoffee Break
11.10 - 11.30 amMarta Luksza
Cross-species analysis of gene expression
11.30 - 11.50 amSwantje Struck, U. Schmidt, B. Grüning and R. Preissner
SuperToxic: a Systems Biology Approach to Toxicity
11.50 am - 12.10 pmMarvin Schulz and E. Klipp
Identification of Optimal Drug Targets in Differential Equation Networks
12.10 - 12.30 pmMasataka Takarabe, S. Okuda, M. Itho, Toshiaki, S. Goto and M. Kanehisa
Network analysis of adverse drug interactions
12.30 - 2.00 pmLunch Break

(chair: Günther)
2.00 - 2.20 pmAysam Gürler and Ernst-Walter Knapp
Sampling Protein-Protein Geometries in Real Space
2.20 - 2.40 pmStephan Lorenzen and Ernst-Walter Knapp
Fully Flexible Refinement of Docking Decoys
2.40 - 3.00 pmBenjamin Menküc and Christoph Gille
Computer Aided Selection of Isotopomer Labels for Tracer Experiments
3.00 - 3.20 pmChristoph Gille, Andreas Hoppe and Hermann-Georg Holzhütter
Publishing Annotated Sequence and 3D-Alignments
3.20 - 3.40 pmGyan Bhanot, H. Liu, G. Alexe, D. Juan, T. Antes, C. Delisi and L. Liou
MicroRNA Diagnostic Panels and Gene Targets in ccRCC
3.40 pm
Closing Remarks



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