Introduction to Systems Biology

Part 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, Bernhard Ø. Palsson

3. From Gene Expression to Metabolic Fluxes
Ana Paula Oliveira, Michael C. Jewett, Jens Nielsen

Part II.Experimental Techniques for Systems Biology

4. Handling and Interpreting Gene Groups
Nils Blüthgen, Szymon M. Kielbasa, Dieter Beule

5. The Dynamic Transcriptome of Mice
Yuki Hasegawa, Yoshihide Hayashizaki

6. Dissecting Transcriptional Control Networks
Vijayalakshmi H. Nagaraj, Anirvan M. Sengupta

7. Reconstruction and Structural Analysis of Metabolic and Regulatory Networks
Hong-wu Ma, Marcio Rosa Silva, Ji-Bin Sun, Bharani Kumar, An-Ping Zeng

8. Cross-Species Comparison Using Expression Data
Gaëlle Lelandais, Stéphane Crom

9. Methods for Protein-Protein Interaction Analysis
Keiji Kito, Takashi Ito

10. Genome-Scale Assessment of Phenotypic Changes During Adaptive Evolution
Stephen S. Fong

11. Location Proteomics
Ting Zhao, Shann-Ching Chen, Robert F. Murphy

Part 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, David L. Wild

13. Modeling Spatiotemporal Dynamics of Multicellular Signaling
Hao Zhu, Pawan K. Dhar

14. Kinetics of Dimension-Restricted Conditions
Noriko Hiroi, Akira Funahashi

15. Mechanisms Generating Ultrasensitivity, Bistability, and Oscillations in Signal Transduction
Nils Blüthgen, Stefan Legewie, Hanspeter Herzel, 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, Ursula Kummer

18. Efficiency, Robustness, and Stochasticity of Gene Regulatory Networks in Systems Biology: ? Switch as a Working Example
Xiaomei Zhu, Lan Yin, Leroy Hood, David Galas, Ping Ao

19. Applications, Representation, and Management of Signaling Pathway Information: Introduction to the SigPath Project
Eliza Chan, Fabien Campagne

Part 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 Novère, Joanne Matthews, Maria J. Schilstra

21. CellDesigner: A Graphical Biological Network Editor and Workbench Interfacing Simulator
Akira Funahashi, Mineo Morohashi, Yukiko Matsuoka, Akiya Jouraku, Hiroaki Kitano

22. DBRF-MEGN Method: An Algorithm for Inferring Gene Regulatory Networks from Large-Scale Gene Expression Profiles
Koji Kyoda, Shuichi Onami

23. Systematic Determination of Biological Network Topology: Nonintegral Connectivity Method (NICM)
Kumar Selvarajoo, Masa Tsuchiya

24. Storing, Searching, and Disseminating Experimental Proteomics Data
Norman W. Paton, Andrew R. Jones, Chris Garwood, Kevin Garwood, Stephen Oliver

25. Representing and Analyzing Biochemical Networks Using BioMaze
Yves Deville, Christian Lemer, Shoshana Wodak

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Nyckelord: TECHNOLOGY & ENGINEERING / Biomedical TEC059000