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.

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 to help understand biological dynamic systems .The final sections of the volume provide ideas for theoretical and modeling optimization in systemic biological researchers, presenting most algorithms as implementation, including an up-to-date full range of bioinformatic programs and available successful applications. 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.