This book provides an introductory text for undergraduate and graduate students who are interested in comprehensive biological systems. The authors offer 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. The final sections provide ideas for theoretical and modeling optimization in systemic biological researches. The book is an indispensable resource, providing a first glimpse into the state-of-the-art in systems biology.

This book provides an introductory text for undergraduate and graduate students who are interested in comprehensive biological systems. Informative and cutting-edge, the volume presents a clear and intuitive illustration of the biological systemic approaches and introduces ideal computational methods for research. The book is an indispensable resource, providing a first glimpse into the state-of-the-art in systems biology. The authors offer a broad overview of the field. The volume begins with an introduction to systems biology and then details experimental omics tools. Other sections introduce the reader to challenging computational approaches. 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.

Title: Introduction to Systems BiologyTable of ContentsI. Introduction1. Scientific Challenges in Systems Biology Hiroaki Kitano2. Bringing Genomes to Life: The Use of Genome-Scale in silico Models Ines Thiele and Bernhard O. Palsson3. From Gene Expression to Metabolic Fluxes Ana Paula Oliveira, Michael C. Jewett and Jens NielsenII. Experimental Techniques for Systems Biology4. Handling and Interpreting Gene Groups Nils Blüthgen, Szymon M. Kielbasa, and Dieter Beule5. The Dynamic Transcriptome of Mice Yuki Hasegawa and Yoshihide Hayashizaki6. Dissecting Transcriptional Control Networks Vijayalakshmi H. Nagaraj and Anirvan M. Sengupta7. Reconstruction and Structural Analysis of Metabolic and RegulatoryNetworks Hong-wu Ma, Marcio Rosa Da Silva, Ji-Bin Sun, Bharani Kumar, andAn-Ping Zeng8. Cross-Species Comparison Using Expression Data Gaëlle Lelandais and Stéphane Le Crom9. Methods for Protein-Protein Interaction Analysis Keiji Kito and Takashi Ito10. Genome-Scale Assessment of Phenotypic Changes during AdaptiveEvolution Stephen S. Fong11. Location Proteomics Ting Zhao, Shann-Ching Chen, and Robert F. MurphyIII. Theoretical and Modeling Techniques12. Reconstructing Transcriptional Networks using Gene ExpressionProfiling and Bayesian State Space Models Matthew J. Beal, Juan Li, Zoubin Ghahramani, and David L. Wild13. Modeling Spatiotemporal Dynamics of Multicellular Signaling Hao Zhu and Pawan K Dhar14. Kinetics of Dimension Restricted Conditions Noriko Hiroi and Akira Funahashi15. Mechanisms Generating Ultrasensitivity, Bistability andOscillations in Signal Transduction Nils Blüthgen, Stefan Legewie, Hanspeter Herzel, and Boris Kholodenko16. Employing Systems Biology to Quantify ReceptorTyrosine KinaseSignaling in Time and Space Boris N. Kholodenko17. Dynamic Instabilities within Living Neutrophils Howard R. Petty, Roberto Romero, Lars F. Olsen, and Ursula Kummer18. Efficiency, Robustness and Stochasticity of Gene RegulatoryNetworks in Systems Biology: ¿ Switch as a Working Example Xiaomei Zhu, Lan Yin, Leroy Hood, David Galas, and Ping Ao19. Applications, Representation and Management of Signaling PathwayInformation: Introduction to the SigPath Project Eliza Chan and Fabien CampagneIV. Methods and Software Platforms for Systems Biology20. SBML Models and MathSBML Bruce E. Shapiro, Andrew Finney, Michael Hucka, Benjamin BornsteinAkira Funahashi, Akiya Jouraku, Sarah M. Keating, Nicolas Le NovèreJoanne Matthews, and Maria J. Schilstra21. CellDesigner: A Graphical Biological Network Editor and WorkbenchInterfacing Simulator Akira Funahashi, Mineo Morohashi, Yukiko Matsuoka, Akiya Jouraku, andHiroaki Kitano22. DBRF-MEGN Method: An Algorithm for Inferring Gene RegulatoryNetworks from Large-Scale Gene Expression Profiles Koji Kyoda and Shuichi Onami23. Systematic Determination of Biological Network Topology:Non-Integral Connectivity Method (NICM) Kumar Selvarajoo and Masa Tsuchiya24. Storing, Searching and Disseminating Experimental Proteomics Data Norman W. Paton, Andrew R. Jones, Chris Garwood, Kevin Garwood, andStephen Oliver25. Representing and Analyzing Biochemical Networks using BioMaze Yves Deville, Christian Lemer, and Shoshana Wodak