Formatted contents note |
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. |