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Introduction to Systems Biology
Introductory text for undergraduate and graduate students who are interested in comprehensive biological systems. The authors provide 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...
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Totowa, N.J
Humana Press
2007
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Table of Contents:
- Introduction
- Scientific challenges in systems biology / Hiroaki Kitano
- Bringing genomes to life: the use of genome-scale in silico models / Ines Thiele, Bernhard O. Palsson
- From gene expression to metabolic fluxes / Ana Paula Oliveira, Michael C. Jewett Jens Nielson
- Experimental techniques for systems biology
- Handling and interpreting gene groups / Nils Bluthgen, Szymon M. Kielbasa, Dieter Beule
- The dynamic transcriptome of mice / Yuki Hasegawa, Yoshihide Hayashizaki
- Dissecting transcriptional control networks / Hong-wu Ma, Marcio Rosa da Silva, Ji-Bin Sun [and others]
- Cross-species comparison using expression data / Gaelle Lelandais, Stephane Le Crom
- Methods for protein-protein interaction analysis / Keiji Kito, Takashi Ito
- Genome-scale assessment of phenotypic changes during adaptive evolution / Stephen S. Fong
- Location proteomics / Ting Zhao, Shann-Ching Chen, Robert F. Murphy
- Theoretical and modeling techniques
- Reconstructing transcriptional networks using gene expression profiling and Bayesian state-space models / Matthew J. Beal, Juan Li, Zoubin Ghahramani [and others]
- Modeling spatiotemporal dynamics of multicellular signaling / Hao Zhu, Pawan K. Dhar
- Kinetics of dimension-restricted coditions / Noriko Hiroi, Akira Funahashi
- Mechanisms generating ultrasensitivity, bistability, and oscillations in signal transduction / Nils Bluthgen, Stefan Legewie, Hanspeter Herzel [and others] Employing systems biology to quantify receptor tyrosine kinase signaling in time and space / Boris N. Kholodenko
- Dynamic instabilities within living neutrophils / Howard R. Petty, Roberto Romero, Lars F. Olsen [and others]
- Efficiency, robustness and stochasticity of gene regulatory networks in systems biology: (A) switch as a working example / Xiaomei Zhu, Lan Yin, Leroy Hood [and others]
- Applications, representation, and management of signaling pathway information: introduction to the SigPath project / Eliza Chan, Fabien Campagne
- Methods and software platforms for systems biology
- SBML models and mathSBML / Bruce E. Shapiro, Andrew Finney, Michael Hucka [and others]
- Celldesigner: a graphical biological network editor and workbench interfacing simulator / Akia Funahashi, Mineo Morohashi, Yukiko Matsuoka [and others]
- DBRF-MEGN method: an algorithm for inferring gene regulatory networks from large-scale gene expression profiles / Koji Kyoda, Shuichi Onami
- Systematic determination of biological network topology: nonintegral connectivity method (NICM) / Kumar Selvarajoo, Masa Tsuchiya
- Storing, searching, and disseminating experimental proteomics data / Norman W. Paton, Andrew R. Jones, Chris Garwood [and others]
- Representing and analyzing biochemical networks using biomaze / Yves Deville, Christian Lemer, Shoshana Wodak.