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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 Bornstein,Akira Funahashi, Akiya Jouraku, Sarah M. Keating, Nicolas Le Novère,Joanne 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