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 and Analyzing Biochemical Networks Using BioMaze. Introduction to Systems Biology is an introductory text for undergraduate and graduate students who are interested in comprehensive biological systems. The authors provide a broad overview of the field using key examples and typical approaches to experimental design. The volume begins with an introduction to systems biology and then details experimental omics tools. Other sections introduce the reader to challenging computational approaches to help understand biological dynamic systems. The final sections of the volume provide ideas for theoretical and modeling optimization in systemic biological researches, presenting most algorithms as implementations, including an up-to-date full range of bioinformatic programs and available successful applications. Informative and cutting-edge, this volume presents a clear and intuitive illustration of the biological systemic approaches and introduces ideal computational methods for research. Introduction to Systems Biology is an indispensable resource, providing a first glimpse into the state-of-the-art in systems biology.