Main description:

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.

Contents:

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 ReceptorTyrosine 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: ~ 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