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Fifth International Workshop on
Computational Systems Biology,

WCSB 2008
June 11-13, 2008
Leipzig, Germany


Program of WCSB 2008 (updated 27.05.2008)

The scientific program of WCSB 2008 comprises of 4 key note lectures, 21 contributed talks and 24 posters.
The conference proceedings contain 44 papers.
Social events include conference dinner (Wednesday evening) and a philharmonic concert (Thursday evening).

Wednesday June 11 - Session 1

12:30-13:00 Registration for attendance
13:00-13:50 Lunch
13:50-14:00 Korbinian Strimmer and local organisers - Welcome address
14:00-15:00 Chair:
Marja-Leena Linne
Darren Wilkinson - Keynote 1 - Bayesian inference for stochastic models of intracellular reaction networks
15:00-15:20 Antti Larjo - Active learning of Bayesian network structure in a realistic setting
15:20-15:40 Catharina Olsen - On the impact of entropy estimator in transcriptional regulatory network inference
15:40-16:20 Coffee break
16:20-16:40 Chair:
Jörg Rahnenführer
Angela Grassi - Bayesian modelling for genetic networks with topological constraints
16:40-17:00 Janis Dingel - Decoding the dynamics of gene regulatory networks under an algebraic model
17:00-17:20 Tina Müller - Finding SNP interactions
17:20-17:40 Theresa Scharl - Using neighborhood graphs for the investigation of E.coli gene clusters
17:40-18:00 Enrico Capobianco - Exploring protein interactome features
18:00-19:30 Break
19:30-22:30 Conference dinner in the city centre at Restaurant Weinstock
- Dinner speech by Heikki Huttunen
- Musical performance

Thursday June 12 - Sessions 2 & 3

09:30-10:30 Chair:
Nicole Radde
Hidde de Jong - Keynote 2 - Qualitative modeling and simulation of bacterial regulatory networks
10:30-10:50 Dora Matache - A spatial SIRS Boolean network model for the spread of H5N1 avian influenza virus among poultry farms
10:50-11:10 Thimo Rohlf - When correlations matter - response of dynamical networks to small perturbations
11:10-11:40 Coffee break
11:40-12:00 Chair:
Markus Löffler
Catherine Higham - Inference in a gene network with transcriptional time delay
12:00-12:20 Gaby Schneider - A stochastic framework for the quantification of synchronous oscillation in neuronal networks
12:20-12:40 Tiina Manninen - Stochastic kinetic simulations of activity-dependent plastic modifications in neurons
12:40-13:00Ben Calderhead - Sloppy parameters in oscillatory systems with unobserved species
13:00-13:40 Lunch break
13:40-14:40 Poster session - see list of poster contributions below
14:40-15:40 Chair:
Korbinian Strimmer
Stephane Robin - Keynote 3 - Uncovering structure and motifs in biological networks
15:40-16:20 Coffee break
16:20-16:40 Carsten Wiuf - Analysis of biological network data using likelihood-free inference techniques
16:40-17:00 Chair:
Hans Binder
Eeva Mäkiraatikka - Calcium changes induced by amyloid-beta-transmitter interactions in astrocytes: model formation
17:00-17:20 Stefan Hoehme - Towards modeling liver lobule regeneration in 3D
17:20-20:00Break
20:00- Concert in Gewandhaus Leipzig,
"Great Concert" with Mozart, Rihm and Reger
Note: For football fans we recommend to watch the EURO 2008 match Germany vs. Croatia (at 18:00) and Austria vs. Poland (at 20:45) live on screen in Moritzbastei, which is very close to the Gewandhaus.

Friday June 13 - Session 4

9:30-10:30 Chair:
Miika Ahdesmäki
Martin Lercher - Keynote 4 - Evolution of molecular networks
10:30-10:50 Eva Grafahrend-Belau - Towards systems biology of developing barley grains: a framework for modeling metabolism
10:50-11:10 Nico Scherf - Correlation patterns of cellular genealogies
11:10-11:40 Coffee break
11:40-12:00 Chair:
Konstantin Klemm
Jörg Galle - Noise-driven stem cell and progenitor population dynamics
12:00-12:20 Andre Ribeiro - Selective advantages of stochastic phenotypic determination in unpredictable environments
12:20-12:40 Peter Stadler - Rate variations, phylogenetics, and partial orders
12:40-13:00 Olli Yli-Harja - Closing
- WCSB 2008 paper awards
- Farewell
13:00- Lunch


List of Poster Contributions

Poster 1 Aho, T. et al. - Computational tool for strain design: maximizing yields in metabolic systems
Poster 2 Beaume, N. et al. - An expert-based approach for the identification of remote homologs
Poster 3 Dai, X. et al. - BGMM: Beta-Gaussian model for clustering genes with multiple data sources
Poster 4 Damaševičius, R. - Feature representation of DNA sequences for machine learning tasks
Poster 5 Erkkilä, T. et al. - Testing for differential expression in simulated and real cDNA microarray data using frequentist and Bayesian methods
Poster 6 Harju, M. et al. - Partial annealing and local structures in Boolean networks
Poster 7 Hituri, K. et al. - Stochastic modeling of Inositol-1,4,5-triphosphate receptors in Purkinje cell spine
Poster 8 Intosalmi, J. et al. - Modeling of IP3 receptor function using stochastic approaches
Poster 9 Kivinen, V. et al. - Relationships between genetic aberrations and gene expression levels in gastrointestinal tract tumors
Poster 10 Kammers, K. et al. - Survival models with expression levels of gene groups as covariates (not in the proceedings)
Poster 11 Kuryshev, V. et al. - Compression based classification of primate endogenous retrovirus sequences
Poster 12 Laurila, K. et al. - Effects of disease-related mutations on transcription factor binding
Poster 13 Lu, J. et al. - SBML ODE solver library: extensions for inverse analysis
Poster 14 Mai, J. et al. - Modelling motion of contaminant BAP in cytoplasm
Poster 15 Nikhil et al. - Evaluation of memory effects of key metabolites in a fermentative H2-production bioprocess
Poster 16 Nikkilä, J. et al. - Decomposing gene expression into regulatory and differential parts with Bayesian data fusion
Poster 17 Podwojski, K. et al. - A retention-time alignment algorithm for LC/MS data
Poster 18 Saarinen, A. et al. - Similarity measures between experiments and a model for stochastic neuronal firing
Poster 19 Sami, M.M. et al. - Quantitative analysis of the Rete process for the diagnosis of borderline malignancies in microscopic oral cancer images
Poster 20 Sandmann, W. et al. - On the statistical accuracy of stochastic simulation algorithms implemented in Dizzy
Poster 21 Schleif, F.-M. et al. - Automatic identification and quantification of metabolites in 1H-NMR measurements
Poster 22 Schober, S. - About Boolean networks with noisy inputs
Poster 23 Simeone, A. et al. - TOPModule: pathway detection in biological networks
Poster 24 Strickert, M. et al. - Adaptive matrix metrics for attribute dependence analysis in differential high-throughput data