Advances in Systems Biology

Abstract

The analysis of complex biological networks has traditionally reliedon decomposition into smaller, semi-autonomous units such as individualsignaling pathways. With the increased scope of systems biology (models),rational approaches to modularization have become an important topic.With increasing acceptance of \emph{de facto} modularity in biology,widely different definitions of what constitutes a module have sparkedcontroversies. Here, we therefore review prominent classes of modularapproaches based on formal network representations. Despite somepromising research directions, several important theoretical challengesremain open on the way to formal, function-centered modular decompositionsfor dynamic biological networks. Modular Analysis of Biological Networks Modeling Signaling Networks Using High-throughput Phospo-proteomics An Integrated Bayesian Framework for Identifying Phosphorylation Networks in Stimulated Cells Signaling Cascades: Consequences of Varying Substrate and Phosphatase Levels Heterogeneous Biological Network Visualization System: Case Study in Context ofMedical Image Data Evolution of the Cognitive Proteome: From Static to Dynamic Network Models Molecular Systems Biology of Sic1 in Yeast Cell Cycle Regulation ThroughMultiscaleModeling Regulatory Dynamics for the Differentiation of Mouse Embryonic Stem Cells Using PriorKnowledge ......................... 247 Dominik Lutter, Philipp Bruns, and Fabian J. Theis 15 Cell Death and Life in Cancer:MathematicalModeling of Cell Fate Decisions....................................................... 261 Andrei Zinovyev, Simon Fourquet, Laurent Tournier, Laurence Calzone, and Emmanuel Barillot 16 Theoretical Aspects of Cellular Decision-Making and Information-Processing ............................................... 275 Tetsuya J. Kobayashi and Atsushi Kamimura 17 Zooming in on Yeast Osmoadaptation ................................... 293 Clemens K¨ uhn and Edda Klipp