Introduction to Systems Biology

Hardcover  542 pp  ISBN 9781588297068      £81.00

Informative and cutting-edge, this 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.

Of interest to: Molecular biologists, biochemical biologists, biochemists, quantitative microscopists, pharmacologists, systems biologists, neurobiologists, protein scientists.

Contents

Preface
Contributors

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 and Bernhard O. Palsson

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

Part II. Experimental Techniques for Systems Biology

4. Handling and Interpreting Gene Groups, Nils Blüthgen, 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, Gaëlle Lelandais and Stéphane 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

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, 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 Blüthgen, 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. Effi ciency, Robustness and Stochasticity of Gene Regulatory Networks in Systems Biology: l 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

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 Le Novère, 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: Nonintegral 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

Appendices
I. Software, Databases, and Websites for Systems Biology
II. Glossary
Index