Introduction to Systems Biology

Title: Introduction to Systems Biology Table of Contents I. Introduction 1. Scientific Challenges in Systems Biology - Hiroaki Kitano 2. Bringing Genomes to Life: The Use of Genome-Scale in silico Models - Ines Thiele and Bernhard O. Palsson 3. From Gene Expression to Metabolic Fluxes - Ana Paula Oliveira, Michael C. Jewett and Jens Nielsen II. Experimental Techniques for Systems Biology 4. Handling and Interpreting Gene Groups - Nils Bluthgen, Szymon M. Kielbasa, and Dieter Beule 5. The Dynamic Transcriptome of Mice - Yuki Hasegawa and Yoshihide Hayashizaki 6. Dissecting Transcriptional Control Networks - Vijayalakshmi H. Nagaraj and Anirvan M. Sengupta 7. Reconstruction and Structural Analysis of Metabolic and Regulatory Networks - Hong-wu Ma, Marcio Rosa Da Silva, Ji-Bin Sun, Bharani Kumar, and An-Ping Zeng 8. Cross-Species Comparison Using Expression Data - Gaelle Lelandais and Stephane Le Crom 9. Methods for Protein-Protein Interaction Analysis - Keiji Kito and Takashi Ito 10. Genome-Scale Assessment of Phenotypic Changes during Adaptive Evolution - Stephen S. Fong 11. Location Proteomics - Ting Zhao, Shann-Ching Chen, and Robert F. Murphy III. Theoretical and Modeling Techniques 12. Reconstructing Transcriptional Networks using Gene Expression Profiling and Bayesian State Space Models - Matthew J. Beal, Juan Li, Zoubin Ghahramani, and David L. Wild 13. Modeling Spatiotemporal Dynamics of Multicellular Signaling - Hao Zhu and Pawan K Dhar 14. Kinetics of Dimension Restricted Conditions - Noriko Hiroi and Akira Funahashi 15. Mechanisms Generating Ultrasensitivity, Bistability and Oscillations in Signal Transduction - Nils Bluthgen, Stefan Legewie, Hanspeter Herzel, and Boris Kholodenko 16. Employing Systems Biology to Quantify Receptor Tyrosine Kinase Signaling in Time and Space - Boris N. Kholodenko 17. Dynamic Instabilities within Living Neutrophils - Howard R. Petty, Roberto Romero, Lars F. Olsen, and Ursula Kummer 18. Efficiency, Robustness and Stochasticity of Gene Regulatory Networks in Systems Biology: Eu Switch as a Working Example - Xiaomei Zhu, Lan Yin, Leroy Hood, David Galas, and Ping Ao 19. Applications, Representation and Management of Signaling Pathway Information: Introduction to the SigPath Project - Eliza Chan and Fabien Campagne IV. Methods and Software Platforms for Systems Biology 20. SBML Models and MathSBML - Bruce E. Shapiro, Andrew Finney, Michael Hucka, Benjamin Bornstein, Akira Funahashi, Akiya Jouraku, Sarah M. Keating, Nicolas Le Novere, Joanne Matthews, and Maria J. Schilstra 21. CellDesigner: A Graphical Biological Network Editor and Workbench Interfacing Simulator - Akira Funahashi, Mineo Morohashi, Yukiko Matsuoka, Akiya Jouraku, and Hiroaki Kitano 22. DBRF-MEGN Method: An Algorithm for Inferring Gene Regulatory Networks from Large-Scale Gene Expression Profiles - Koji Kyoda and Shuichi Onami 23. Systematic Determination of Biological Network Topology: Non-Integral Connectivity Method (NICM) - Kumar Selvarajoo and Masa Tsuchiya 24. Storing, Searching and Disseminating Experimental Proteomics Data - Norman W. Paton, Andrew R. Jones, Chris Garwood, Kevin Garwood, and Stephen Oliver 25. Representing and Analyzing Biochemical Networks using BioMaze - Yves Deville, Christian Lemer, and Shoshana Wodak