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Sixth International Workshop on
Computational Systems Biology,

WCSB 2009
June 10-12, 2009
Aarhus (Århus), Denmark

Lindhard lecture

Stuart Kauffman from the University of Calgary, Calgary, Canada, will give a Lindhard lecture organised by Centre for Theory in Natural Science on Tuesday 9th of June at 15:00 in the Large Anatomy Lecture Theatre 115 located in building 1232. See abstract here.

Program of WCSB 2009

The scientific program of WCSB 2009 comprises of 5 keynote lectures, 18 contributed talks and 21 posters.
The conference proceedings contain 38 papers.
Social events include Old town tour and conference dinner on Wednesday evening and reception and Sculpture by the Sea exhibition on Thursday evening.

Wednesday June 10 - Session 1

11:00-12:00 Registration for attendance outside the lecture theatre 011 situated in building 1324 (Bartholins Alle) at the campus of Aarhus University
12:00-12:50 Lunch break
12:50-13:00 Carsten Wiuf - Welcome address
13:00-14:00 Chair:
Harri Lähdesmäki
Ilya Shmulevich - Keynote 1 - Modeling and inference of transcriptional regulatory networks
14:00-14:20 Reinhard Heckel - A Boolean genetic regulatory network created by whole genome duplications
14:20-14:40 Marco Grzegorczyk - Modelling non-stationary gene regulatory processes with a non-homogeneous dynamic Bayesian network and the change point process
14:40-15:10 Coffee break
15:10-16:40 Poster session 1 - see list of poster contributions below
16:40-17:00 Frédéric Boyer - Extracting transcriptional regulatory modules from a large microarray compendium using a graph-based approach: application to the response of Arabidopsis Thaliana under stress conditions
17:00-17:20 Miika Ahdesmäki - Comparison of the Gaussian process classification approach with classical penalised classification methods in high dimensional omics data
17:20- Old town tour, group photo, and conference dinner at restaurant Prins Ferdinand
- Dinner speech by Stuart Kauffman

Thursday June 11 - Sessions 2 & 3

09:30-10:30 Chair:
Marja-Leena Linne
Erik De Schutter - Keynote 2 - What can Computational Neuroscience learn from Systems Biology and vice versa?
10:30-11:00 Coffee break
11:00-11:20 Katri Hituri - Comparison and validation of two stochastic models of the cerebellar IP3 receptor
11:20-11:40 Heinz Koeppl - Rule-based modeling for protein-protein interaction networks - the cyanobacterial circadian clock as a case study
11:40-12:00 Nicole Radde - A comparison of likelihoods for dynamic stochastic models of biological networks
12:00-12:20 Kirsti Laurila and Tarmo Äijö - Techila GRID demo
12:20-13:20 Lunch break
13:20-14:50 Poster session 2 - see list of poster contributions below
14:50-15:50 Chair:
Marco Grzegorczyk
Jean-Philippe Vert - Keynote 4 - Inferring and using biological networks
15:50-16:20 Coffee break
16:20-16:40 Evgenia Freis - Effects of metagene calculation on survival: an integrative approach using cluster and promoter analysis
16:40-17:00 Antti Larjo - Combined dynamic modeling of metabolism and gene regulation
17:00-17:20 Catherine F. Higham- Modelling dynamic DNA in Myotonic Dystrophy
17:20-17:40 Antti Häkkinen - Effects of transcriptional time delays on gene expression dynamics
17:40-19:00 Reception at the university
19:00- Sculpture by the Sea exhibition

Friday June 12 - Sessions 4 & 5

09:00-10:00 Chair:
Miika Ahdesmäki
Stephen T. C. Wong - Keynote 3 - Image-oriented systems biology methods in drug development and interventional medicine
10:00-10:30 Coffee break
10:30-10:50 Pekka Ruusuvuori - Image analysis tool for fat tissue quantification in histological sections
10:50-11:10 Verena Zuber - Correlation-adjusted t-scores in application to functional magnetic resonance imaging data
11:10-11:30 Sven Nahnsen - A geometric matching approach improves throughput and accuracy in DIGE based proteomics
11:30-12:50 Lunch break
12:50-13:40 Chair:
Carsten Wiuf
Lucas Pelkmans - Keynote 5 - Challenges in image based siRNA virus screens (presentation given by Pauli Rämö)
13:40-14:00 Michael Knudsen - Modeling cis- and trans-regulation in Drosophila species
14:00-14:20 Kirsti Laurila - A probabilistic model for competitive binding of transcription factors
14:20-14:40 Olli-Pekka Smolander - Stochastic model of bacterial bioluminescence at the single cell, single molecule level
14:40-15:00 Olli Yli-Harja - Closing
- WCSB 2009 paper awards
- Farewell

List of posters in Poster session 1

Poster 1 Jugoslava Acimovic et al. - Computational models for assessing the properties of spontaneous activity in cell cultures
Poster 2 Sharif Chowdhury et al. - Automated cell tracking and cell lineage construction with improved performance
Poster 3 Xiaofeng Dai et al. - A unified probabilistic framework for clustering genes from gene expression and protein-protein interaction data
Poster 4 João B. Destro-Filho et al. - A simple model of the electromagnetic field associated with ionic channels at rest
Poster 5 Timo Erkkilä et al. - A generic class density estimation framework using Dirichlet processes
Poster 6 Saadia Faisal et al. - Discrete time modeling of protein networks by Zhegalkin polynomials
Poster 7 Manu Harju et al. - Branching process models of regulatory networks with arbitrary out-degree distributions
Poster 8 Merja Heinäniemi et al. - Nuclear receptor regulatory modules in cellular metabolism, cellular growth and differentiation (Poster presentation without paper in the proceedings)
Poster 9 Jukka Intosalmi et al. - Modeling protein kinase C activation in the presence of calcium ion fluctuations
Poster 10 Heinz Koeppl et al. - Motifs, algebraic connectivity and computational performance of two data-based cortical circuit templates
Poster 11 Heinz Koeppl et al. - Semi-quantitative stability analysis constrains saturation levels in metabolic networks

List of posters in Poster session 2

Poster 1 Heinz Koeppl et al. - A statistical analysis of receptor clustering using random graphs
Poster 2 Lingjia Kong et al. - Evaluating the effects of different library files in analysing Affymetrix exon array expression data
Poster 3 Juliane Mai et al. - Analysis of spatio-temporal dynamics by FRAP
Poster 4 João F. Mari et al. - Three-dimensional visualization of rat hippocampal cultured neurons based on images of multielectrode arrays (MEA)
Poster 5 Elisabetta Marras et al. - Inference by mixture models in protein interactome networks
Poster 6 Vijayanarasimha H. Pakka et al. - Correlated fluctuations probe dynamics of transcriptional regulation
Poster 7 Mustafa M. Sami et al. - Twin rete ridge analysis for histopathological diagnosis in H&E stained microscopic images of the oral mucosa
Poster 8 Steffen Schober et al. - Inference of Boolean networks using spectral techniques
Poster 9 Leonid Yaroslavsky et al. - Optics-less imaging sensors as a model of early vision
Poster 10 Antti Ylipää et al. - A gene copy number based classifier for gastrointestinal stromal tumors and leiomyosarcomas