Contents-Report-41

From Ticsp

Preface

The Workshop on Computational Systems Biology has been organized annually by the Computational Systems Biology research group in the Department of Signal Processing at Tampere University of Technology (TUT). The history of the workshop traces back to 2003, when it was organized for the first time as an internal meeting with some invited international collaborators. Since then the meeting has grown each year witnessing a rapid development in experimental biosciences and growth in the research of computational methods in systems biology.

This year the program committee set the target to making the event more international, as well as emphasizing the quality and significance of the research papers published in this proceedings book. Therefore in 2008 the workshop is organized in Leipzig, Institute for Medical Informatics, Statistics and Epidemiology (IMISE), Germany, together with collaborators from University of Leipzig and Dortmund University of Technology. The joint organization has proved to be smooth and successful - we are having a record number of international participants. We have brought together the various communities involved in the different aspects of computational systems biology research, e.g. experimental biology, machine learning, signal processing, statistics and theoretical physics. The workshop program together with the range of published papers demonstrate an increasing sphere of influence of WCSB.

This volume is the collection of the research papers and short abstracts submitted to WCSB2008. We would like to thank the authors and the reviewers for their contribution to this workshop. We are also grateful for the contribution of organizers in Finland and Germany for their efforts. We would also like to thank Finnish Academy of Sciences, Tampere Graduate School in Information Science and Engineering (TISE), Tampere International Center for Signal Processing (TICSP), Research Training Group "Statistical Modelling", Department of Statistics, Dortmund University of Technology, and Max Planck Institute for Evolutionary Anthropology for their support.

On behalf of the WCSB 2008 Scientific committee,

Olli Yli-Harja

Contents

Abstracts

Qualitative Modeling and Simulation of Bacterial Regulatory Networks Hidde de Jong, INRIA Grenoble-Rhône-Alpes, France |3

Evolution of Molecular Networks Martin Lercher, Heinrich-Heine-Universität, Germany |5

Uncovering Structure and Motifs in Biological Networks Stéphane Robin, AgroParisTech / INRA Appl. Math. Comput. Sc., France | 7

Bayesian Inference for Stochastic Models of Intracellular Reaction Networks Darren Wilkinson, Newcastle University, UK | 9

Regular papers

Computational Tool for Strain Design: Maximizing Yields in Metabolic Systems Tommi Aho, Tampere University of Technology, Finland; Roger Mallol Parera, Tampere University of Technology, Finland and Escola Tècnica Superior d'Enginyeria, Spain; Antti Larjo, Olli Yli-Harja, Tampere University of Technology, Finland | 13

An Expert-Based Approach for the Identification of Remote Homologs Nicolas Beaume, INSERM, France and LINA, France; Gerard Ramstein, LINA, France; Yannick Jacques, INSERM, France | 17

Sloppy Parameters in Oscillatory Systems with Unobserved Species Ben Calderhead, Mark Girolani, University of Glasgow, Scotland | 21

BGMM: A Beta-Gaussian Mixture Model for Clustering Genes with Multiple Data Sources Xiaofeng Dai, Harri Lähdesmäki, Olli Yli-Harja, Tampere University of Technology, Finland | 25

Feature Representation of DNA Sequences for Machine Learning Tasks Robertas Damaševičius, Kaunas University of Technology, Lithuania | 29

Decoding the Dynamics of Gene Regulatory Networks Under an Algebraic Expression Model Janis Dingel, Technische Universität München, Germany; Olgica Milenkovic, University of Illinois at Urbana-Champaign, USA | 33

Testing for Differential Expression in Simulated and Real cDNA Microarray Data Using Frequentist and Bayesian Methods Timo Erkkilä, Matti Nykter, Harri Lähdesmäki, Miika Ahdesmäki, Olli Yli-Harja, Tampere University of Technology, Finland | 37

Towards Systems Biology of Developing Barley Grains: A Framework for Modeling Metabolism E. Grafahrend-Belau, B. H. Junker, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Germany; D. Koschützki, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Germany and Furtwangen University of Applied Sciences, Germany; C. Klukas, S. Weise, U. Scholz, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Germany; F. Schreiber, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Germany and Martin-Luther-University Halle-Wittenberg, Germany | 41

Bayesian Modelling for Genetic Networks with Topological Constraints Angela Grassi, Italian National Research Council, Italy and University of Padova, Italy; Ernst Wit, Lancaster University, UK | 45

Partial Annealing and Local Structures in Boolean Networks Manu Harju, Juha Kesseli, Olli Yli-Harja, Tampere University of Technology, Finland | 49

Inference in a Gene Network with Transcriptional Time Delay Catherine F. Higham, University of Glasgow, Scotland, UK | 53

Stochastic Modeling of Inositol-1,4,5-Trisphosphate Receptors in Purkinje Cell Spine Katri Hituri, Tampere University of Technology, Finland; Pablo Achard, University of Antwerp, Belgium; Stefan Wils, University of Antwerp, Belgium and Okinawa Institute of Science and Technology, Japan; Marja-Leena Linne, Tampere University of Technology, Finland; Erik De Schutter, University of Antwerp, Belgium and Okinawa Institute of Science and Technology, Japan | 57

Towards Modeling Liver Lobule Regeneration in 3D Stefan Hoehme, University of Leipzig, Germany; Jan G. Hengstler, Marc Brulport, Alexander Bauer, University of Dortmund, Germany; Dirk Drasdo, University of Leipzig, Germany, and Institut National de Recherche en Informatique et en Automatique (INRIA), France | 61

Noise-Driven Stem Cell and Progenitor Population Dynamics Martin Hoffmann, Joerg Galle, University of Leipzig, Germany | 65

Modeling IP3 Receptor Function Using Stochastic Approaches Jukka Intosalmi, Tiina Manninen, Katri Hituri, Keijo Ruohonen, Marja-Leena Linne, Tampere University of Technology, Finland | 69

A Spatial SIRS Boolean Network Model for the Spread of H5N1 Avian Influenza Virus Among Poultry Farms Alexander Kasyanov, Federal Centre for Animal Health, Russia; Leona Kirkland, GR Exypnos, Inc., USA; Mihaela Teodora Matache, University of Nebraska at Omaha, USA | 73

Relationships Between Genetic Aberrations and Gene Expression Levels in Gastrointestinal Tract Tumors Virpi Kivinen, Tampere University of Technology, Finland; Matti Nykter, Tampere University of Technology, Finland and Institute for Systems Biology, USA; Antti Ylipää, Tampere University of Technology, Finland; Limei Hu, David Cogdell, Kelly Hunt, Wei Zhang, The University of Texas M.D. Anderson Cancer Center, USA; Olli Yli-Harja, Tampere University of Technology, Finland | 77

Compression Based Classification of Primate Endogenous Retrovirus Sequences Vladimir Kuryshev, Max Planck Inst. for Ornithology and Technische Universität München, Germany; Pavol Hanus, Technische Universität München, Germany | 81

Active Learning of Bayesian Network Structure in a Realistic Setting Antti Larjo, Harri Lähdesmäki, Tampere University of Technology, Finland; Marc Facciotti, Nitin Baliga, Institute for Systems Biology, USA; Olli Yli-Harja, Tampere University of Technology, Finland; Ilya Shmulevich, Institute for Systems Biology, USA | 85

Effects of Disease-Related Mutations on Transcription Factor Binding Kirsti Laurila, Harri Lähdesmäki, Tampere University of Technology, Finland | 89

SBML ODE Solver Library: Extensions for Inverse Analysis James Lu, Stefan Müller, Austrian Academy of Sciences, Austria; Rainer Machné, Christoph Flamm, University of Vienna, Austria | 93

Modeling Motion of Contaminant BaP in Cytoplasm Juliane Mai, Sabine Attinger, Helmholtz-Centre for Environmental Research, Germany | 97

Stochastic Kinetic Simulations of Activity-Dependent Plastic Modifications in Neurons Tiina Manninen, Marja-Leena Linne, Tampere University of Technology, Finland | 101

Exploring Protein Interactome Features Elisabetta Marras, Enrico Capobianco, Science and Technology Park of Sardinia, Italy | 105

Finding SNP Interactions Tina Mueller, Holger Schwender, Katja Ickstadt, Technische Universität Dortmund, Germany | 109

Calcium Changes Induced by Amyloid-β-Neurotransmitter Interactions in Astrocytes: Model Formation Eeva Mäkiraatikka, Tampere University of Technology, Finland; Amit K. Nahata, Kidney Care Center at DCI, USA; Tuula O. Jalonen, University of Jyväskylä, Finland, Marja-Leena Linne, Tampere University of Technology, Finland | 113

Evaluation of Memory Effects of Key Metabolites in a Fermentative H2-Production Bioprocess Nikhil, Perttu E.P. Koskinen, Ari Visa, Jaakko A. Puhakka, Olli Yli-Harja, Tampere University of Technology, Finland | 117

Decomposing Gene Expression into Regulatory and Differential Parts with Bayesian Data Fusion Janne Nikkilä, Helsinki University of Technology, Finland; Timo Erkkilä, Harri Lähdesmäki, Tampere University of Technology, Finland | 121

On the Impact of Entropy Estimator in Trasncriptional Regulatory Network Inference Catharina Olsen, Patrick E. Meyer, Gianluca Bontempi, Université Libre de Bruxelles, Belgium | 125

A Retention-Time Alignment Algorithm for LC/MS Data Katharina Podwojski, Arno Fritsch, Technische Universität Dortmund, Germany and Zentrum für Angewandte Proteomik (ZAP), Germany; Daniel Chamrad, Protagen AG, Germany; Wolfgang Paul, Petra Mutzel, Katja Ickstadt, Jörg Rahnenfhrer, Technische Universität Dortmund, Germany and Zentrum für Angewandte Proteomik (ZAP), Germany | 129

Rate Variations, Phylogenetics, and Partial Orders Sonja J. Prohaska, Santa Fe Institute, USA and University of Vienna, Austria; Guido Fritzsch, University of Leipzig, Germany; Peter F. Stadler, University of Leipzig, Germany, Santa Fe Institute, USA and University of Vienna, Austria and Fraunhofer Institut for Cell Therapy and Immunology (IZI), Germany | 133

Selective Advantages of Stochastic Phenotypic Determination in Unpredictable Environments Andre S. Ribeiro, Tampere University of Technology, Finland; John J. Grefenstette, George Mason University, USA; Daniel Cloud, Princeton University, USA; Antti Hakkinen, Tiina Rajala, Olli Yli-Harja, Tampere University of Technology, Finland | 137

When Correlations Matter - Response of Dynamical Networks to Small Perturbations Thimo Rohlf, Santa Fe Institute, USA and Max-Planck-Institute for Mathematics in the Sciences, Germany; Natali Gulbahce, Northeastern University, USA and Dana Farber Cancer Institute, USA; Christof Teuscher, Los Alamos National Laboratory, USA | 141

Similarity Measures Between Experiments and a Model for Stochastic Neuronal Firing Antti Saarinen, Olli Yli-Harja, Marja-Leena Linne, Tampere University of Technology, Finland | 145

Quantitative Analysis of the Rete Processes for the Diagnosis of Borderline Malignancies in Microscopic Oral Cancer Images Mustafa M. Sami, Hisakazu Kikuchi, Takashi Saku, Niigata University, Japan | 149

On the Statistical Accuracy of Stochastic Simulation Algorithms Implemented in Dizzy Werner Sandmann, Christian Maier, University of Bamberg, Germany | 153

Using Neighborhood Graphs for the Investigation of E. Coli Gene Clusters Theresa Scharl, Vienna University of Technology, Austria and University of Natural Resources and Applied Life Sciences, Austria; Friedrich Leisch, University of Munich, Germany | 157

Correlation Patterns of Cellular Genealogies Nico Scherf, Ingo Roeder, Ingmar Glauche, University of Leipzig, Germany | 161

Automatic Identification and Quantification of Metabolites in 1H-NMR Measurements F.-M. Schleif, T. Riemer, M. Cross, T. Villmann, Leipzig University, Germany | 165

A Stochastic Framework for the Quantification of Synchronous Oscillation in Neuronal Networks Gaby Schneider, University Frankfurt, Germany; Danko Nikolic, University Frankfurt, Germany and Max-Planck-Institute for Brain Research, Germany | 169

About Boolean Networks with Noisy Inputs Steffen Schober, Ulm University, Germany | 173

TopModule: Pathway Detection in Biological Networks Angela Simeone, Jacob Michaelson, Antigoni Elefsinioti, Andreas Beyer, Technische Universität Dresden, Germany | 177

Adaptive Matrix Metrics for Attribute Dependence Analysis in Differential High-Throughput Data M. Strickert, K. Witzel, J. Keilwagen, H.-P. Mock, Leibniz Institute of Crop Plant Research, Germany; P. Schneider, M. Biehl, University of Groningen, NL; T. Villmann, University of Leipzig, Germany | 181

Analysis of Biological Network Data Using Likelihood-Free Inference Techniques Carsten Wiuf, University of Aarhus, Denmark; Oliver Ratmann, Imperial College London, UK; Michael Knudsen, University of Aarhus, Denmark | 185

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