Title: Introduction to Systems BiologynnnTable of ContentsnnnI. Introductionnn1. Scientific Challenges in Systems Biologyn- Hiroaki Kitanonn2. Bringing Genomes to Life: The Use of Genome-Scale in silico Modelsn- Ines Thiele and Bernhard O. Palssonnn3. From Gene Expression to Metabolic Fluxesn- Ana Paula Oliveira, Michael C. Jewett and Jens NielsennnnII. Experimental Techniques for Systems Biologynn4. Handling and Interpreting Gene Groupsn- Nils Blüthgen, Szymon M. Kielbasa, and Dieter Beulenn5. The Dynamic Transcriptome of Micen- Yuki Hasegawa and Yoshihide Hayashizakinn6. Dissecting Transcriptional Control Networksn- Vijayalakshmi H. Nagaraj and Anirvan M. Senguptann7. Reconstruction and Structural Analysis of Metabolic and RegulatorynNetworksn- Hong-wu Ma, Marcio Rosa Da Silva, Ji-Bin Sun, Bharani Kumar, andnAn-Ping Zengnn8. Cross-Species Comparison Using Expression Datan- Gaëlle Lelandais and Stéphane Le Cromnn9. Methods for Protein-Protein Interaction Analysisn- Keiji Kito and Takashi Itonn10. Genome-Scale Assessment of Phenotypic Changes during AdaptivenEvolutionn- Stephen S. Fongnn11. Location Proteomicsn- Ting Zhao, Shann-Ching Chen, and Robert F. MurphynnnIII. Theoretical and Modeling Techniquesnnn12. Reconstructing Transcriptional Networks using Gene ExpressionnProfiling and Bayesian State Space Modelsn- Matthew J. Beal, Juan Li, Zoubin Ghahramani, and David L. Wildnn13. Modeling Spatiotemporal Dynamics of Multicellular Signalingn- Hao Zhu and Pawan K Dharnn14. Kinetics of Dimension Restricted Conditionsn- Noriko Hiroi and Akira Funahashinn15. Mechanisms Generating Ultrasensitivity, Bistability andnOscillations in Signal Transductionn- Nils Blüthgen, Stefan Legewie, Hanspeter Herzel, and Boris Kholodenkonn16. Employing Systems Biology to Quantify ReceptorTyrosine KinasenSignaling in Time and Spacen- Boris N. Kholodenkonn17. Dynamic Instabilities within Living Neutrophilsn- Howard R. Petty, Roberto Romero, Lars F. Olsen, and Ursula Kummernn18. Efficiency, Robustness and Stochasticity of Gene RegulatorynNetworks in Systems Biology: ~ Switch as a Working Examplen- Xiaomei Zhu, Lan Yin, Leroy Hood, David Galas, and Ping Aonn19. Applications, Representation and Management of Signaling PathwaynInformation: Introduction to the SigPath Projectn- Eliza Chan and Fabien CampagnennnIV. Methods and Software Platforms for Systems Biologynn20. SBML Models and MathSBMLn- Bruce E. Shapiro, Andrew Finney, Michael Hucka, Benjamin Bornstein,nAkira Funahashi, Akiya Jouraku, Sarah M. Keating, Nicolas Le Novère,nJoanne Matthews, and Maria J. Schilstrann21. CellDesigner: A Graphical Biological Network Editor and WorkbenchnInterfacing Simulatorn- Akira Funahashi, Mineo Morohashi, Yukiko Matsuoka, Akiya Jouraku, andnHiroaki Kitanonn22. DBRF-MEGN Method: An Algorithm for Inferring Gene RegulatorynNetworks from Large-Scale Gene Expression Profilesn- Koji Kyoda and Shuichi Onaminn23. Systematic Determination of Biological Network Topology:nNon-Integral Connectivity Method (NICM)n- Kumar Selvarajoo and Masa Tsuchiyann24. Storing, Searching and Disseminating Experimental Proteomics Datan- Norman W. Paton, Andrew R. Jones, Chris Garwood, Kevin Garwood, andnStephen Olivernn25. Representing and Analyzing Biochemical Networks using BioMazen- Yves Deville, Christian Lemer, and 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. 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.
This book provides an introductory text for undergraduate and graduate students who are interested in comprehensive biological systems. Informative and cutting-edge, the 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. The authors offer a broad overview of the field. 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 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.