Introduction to Systems Biology

Scientific Challenges in Systems Biology.- Bringing Genomes to Life: The Use of Genome-Scale In Silico Models.- From Gene Expression to Metabolic Fluxes.- Experimental Techniques for Systems Biology.- Handling and Interpreting Gene Groups.- The Dynamic Transcriptome of Mice.- Dissecting Transcriptional Control Networks.- Reconstruction and Structural Analysis of Metabolic and Regulatory Networks.- Cross-Species Comparison Using Expression Data.- Methods for Protein-Protein Interaction Analysis.- Genome-Scale Assessment of Phenotypic Changes During Adaptive Evolution.- Location Proteomics.- Theoretical and Modeling Techniques.- Reconstructing Transcriptional Networks Using Gene Expression Profiling and Bayesian State-Space Models.- Modeling Spatiotemporal Dynamics of Multicellular Signaling.- Kinetics of Dimension-Restricted Conditions.- Mechanisms Generating Ultrasensitivity, Bistability, and Oscillations in Signal Transduction.- Employing Systems Biology to Quantify Receptor Tyrosine Kinase Signaling in Time and Space.- Dynamic Instabilities Within Living Neutrophils.- Efficiency, Robustness, and Stochasticity of Gene Regulatory Networks in Systems Biology: ? Switch as a Working Example.- Applications, Representation, and Management of Signaling Pathway Information: Introduction to the SigPath Project.- Methods and Software Platforms for Systems Biology.- SBML Models and MathSBML.- CellDesigner: A Graphical Biological Network Editor and Workbench Interfacing Simulator.- DBRF-MEGN Method: An Algorithm for Inferring Gene Regulatory Networks from Large-Scale Gene Expression Profiles.- Systematic Determination of Biological Network Topology: Nonintegral Connectivity Method (NICM).- Storing, Searching, and Disseminating Experimental Proteomics Data.- Representing andAnalyzing Biochemical Networks Using BioMaze.