Introduction to Systems Biology

ISBN-13: 9781617377297 / Angielski / Miękka / 2010 / 542 str.

Sangdun Choi

Opis

Introduction to Systems Biology is an 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 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 researches, presenting most algorithms as implementations, 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. Introduction to Systems Biology is an indispensable resource, providing a first glimpse into the state-of-the-art in systems biology.

Spis treści

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 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 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 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 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: 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