Advances in Systems Biology

Front Matter....Pages i-xxii
Front Matter....Pages 1-1
Modular Analysis of Biological Networks....Pages 3-17
Modeling Signaling Networks Using High-throughput Phospho-proteomics....Pages 19-57
An Integrated Bayesian Framework for Identifying Phosphorylation Networks in Stimulated Cells....Pages 59-80
Signaling Cascades: Consequences of Varying Substrate and Phosphatase Levels....Pages 81-94
Heterogeneous Biological Network Visualization System: Case Study in Context of Medical Image Data....Pages 95-118
Evolution of the Cognitive Proteome: From Static to Dynamic Network Models....Pages 119-134
Molecular Systems Biology of Sic1 in Yeast Cell Cycle Regulation Through Multiscale Modeling....Pages 135-167
Proteome-Wide Screens in Saccharomyces cerevisiae Using the Yeast GFP Collection....Pages 169-178
Unraveling the Complex Regulatory Relationships Between Metabolism and Signal Transduction in Cancer....Pages 179-189
Front Matter....Pages 191-191
The Cell as a Thermostat: How Much does it Know?....Pages 193-198
Stem Cell Differentiation as a Renewal-Reward Process: Predictions and Validation in the Colonic Crypt....Pages 199-209
A Dynamic Physical Model of Cell Migration, Differentiation and Apoptosis in Caenorhabditis elegans ....Pages 211-233
A Modular Model of the Apoptosis Machinery....Pages 235-245
An Ensemble Approach for Inferring Semi-quantitative Regulatory Dynamics for the Differentiation of Mouse Embryonic Stem Cells Using Prior Knowledge....Pages 247-260
Cell Death and Life in Cancer: Mathematical Modeling of Cell Fate Decisions....Pages 261-274
Theoretical Aspects of Cellular Decision-Making and Information-Processing....Pages 275-291
Zooming in on Yeast Osmoadaptation....Pages 293-310
Front Matter....Pages 311-311
Receptor Dynamics in Signaling....Pages 313-323
A Systems-Biology Approach to Yeast Actin Cables....Pages 325-335
Modeling Morphodynamic Phenotypes and Dynamic Regimes of Cell Motion....Pages 337-358
Front Matter....Pages 311-311
Time-Structure of the Yeast Metabolism In vivo....Pages 359-379
Coarse Graining Escherichia coli Chemotaxis: From Multi-flagella Propulsion to Logarithmic Sensing....Pages 381-396
Self-Feedback in Actin Polymerization....Pages 397-406
Front Matter....Pages 407-407
Global Optimization in Systems Biology: Stochastic Methods and Their Applications....Pages 409-424
Mathematical Modeling of the Human Energy Metabolism Based on the Selfish Brain Theory....Pages 425-440
Identification of Sensitive Enzymes in the Photosynthetic Carbon Metabolism....Pages 441-459
Formal Methods for Checking the Consistency of Biological Models....Pages 461-475
Global Parameter Identification of Stochastic Reaction Networks from Single Trajectories....Pages 477-498
A Systems Biology View of Adaptation in Sensory Mechanisms....Pages 499-516
Leveraging Modeling Approaches: Reaction Networks and Rules....Pages 517-530
Front Matter....Pages 531-531
Why and How to Expand the Role of Systems Biology in Pharmaceutical Research and Development....Pages 533-542
Multiscale Mechanistic Modeling in Pharmaceutical Research and Development....Pages 543-561
Re-analysis of Bipolar Disorder and Schizophrenia Gene Expression Complements the Kraepelinian Dichotomy....Pages 563-577
Bringing Together Models from Bottom-Up and Top-Down Approaches: An Application for Growth of Escherichia coli on Different Carbohydrates....Pages 579-595
A Differential Equation Model to Investigate the Dynamics of the Bovine Estrous Cycle....Pages 597-605
Reducing Systems Biology to Practice in Pharmaceutical Company Research; Selected Case Studies....Pages 607-615
System-Scale Network Modeling of Cancer Using EPoC....Pages 617-643
Early Patient Stratification and Predictive Biomarkers in Drug Discovery and Development....Pages 645-653
Biomedical Atlases: Systematics, Informatics and Analysis....Pages 655-677
Back Matter....Pages 679-682