This book provides an entry point into Systems Biology for researchers in genetics, molecular biology, cell biology, microbiology and biomedical science to understand the key concepts to expanding their work. Chapters organized around broader themes of Organelles and Organisms, Systems Properties of Biological Processes, Cellular Networks, and Systems Biology and Disease discuss the development of concepts, the current applications, and the future prospects. Emphasis is placed on concepts and insights into the multi-disciplinary nature of the field as well as the importance of systems biology in human biological research. Technology, being an extremely important aspect of scientific progress overall, and in the creation of new fields in particular, is discussed in 'boxes' within each chapter to relate to appropriate topics.

Table of Contents

• List of Contributors
• Preface
• Reviewers
• Section I Components of Biological Systems
• 1. Proteomic Analysis of Cellular Systems - Marco Y. Hein, Kirti Sharma, Jürgen Cox and Matthias Mann
• 2. The Coding and the Non-coding Transcriptome - Roderic Guigó
• Section II Network Properties of Biological Systems
• 3. Interactome Networks - Anne-Ruxandra Carvunis, Frederick P. Roth, Michael A. Calderwood, Michael E. Cusick, Giulio Superti-Furga and Marc Vidal
• 4. Gene Regulatory Networks - Martha L. Bulyk and A.J. Marian Walhout
• 5. Analyzing the Structure, Function and Information Flow in Signaling Networks using Quantitative Cellular Signatures - Meghana M. Kulkarni and Norbert Perrimon
• 6. Genetic Networks - Michael Costanzo, Anastasia Baryshnikova, Benjamin VanderSluis, Brenda Andrews, Chad L. Myers and Charles Boone
• 7. The Spatial Architecture of Chromosomes - Job Dekker and Bas van Steensel
• 8. Chemogenomic Profiling: Understanding the Cellular Response to Drug - Anna Y. Lee, Gary D. Bader, Corey Nislow and Guri Giaever
• 9. Graph Theory Properties of Cellular Networks - Baruch Barzel, Amitabh Sharma and Albert-László Barabási
• Section III Dynamic and Logical Properties of Biological Systems
• 10. Boolean Models of Cellular Signaling Networks - Zhongyao Sun and Réka Albert
• 11. Transcriptional Network Logic: The Systems Biology of Development - Isabelle S. Peter and Eric H. Davidson
• 12. Reconstruction of Genome-Scale Metabolic Networks - Hooman Hefzi, Bernhard O. Palsson and Nathan E. Lewis
• 13. Genotype Networks and Evolutionary Innovations in Biological Systems - Andreas Wagner
• 14. Irreversible Transitions, Bistability and Checkpoint Controls in the Eukaryotic Cell Cycle: A Systems-Level Understanding - John J. Tyson and Béla Novák
• 15. Phenotypes and Design Principles in System Design Space - Michael A. Savageau
• 16. System Biology of Cell Signaling - Chiara Mariottini and Ravi Iyengar
• 17. Spatial Organization of Subcellular Systems - Malte Schmick, Hernán E. Grecco and Philippe I.H. Bastiaens
• Section IV Systems and Biology
• 18. Yeast Systems Biology: Towards a Systems Understanding of Regulation of Eukaryotic Networks in Complex Diseases and Biotechnology - Juan I. Castrillo, Pinar Pir and Stephen G. Oliver
• 19. Systems Biology of Caenorhabditis elegans - Andrew Fraser and Ben Lehner
• 20. Arabidopsis as a Model for Systems Biology - Philip N. Benfey and Ben Scheres
• 21. The Role of the Circadian System in Homeostasis - Anand Venkataraman, Heather Ballance and John B. Hogenesch
• 22. Biological and Quantitative Models for Stem Cell Self-Renewal and Differentiation - Huilei Xu, Dmitri Papatsenko, Avi Máayan and Ihor Lemischka
• Section V Multi-Scale Biological Systems, Health and Ecology
• 23. Systems Medicine and the Emergence of Proactive P4 Medicine: Predictive, Preventive, Personalized and Participatory - Leroy Hood, Mauricio A. Flores, Kristin R. Brogaard and Nathan D. Price
• 24. Cancer Systems Biology: A Robustness-Based Approach - Hiroaki Kitano
• 25. Systems Immunology: From Cells and Molecules to a Dynamic Multi-Scale System - Mark M. Davis and Shai S. Shen-Orr
• 26. Causal Inference and the Construction of Predictive Network Models in Biology - Eric E. Schadt
• 27. Social Networks, Contagion Processes and the Spreading of Infectious Diseases - Bruno Gonc¸ alves, Nicola Perra and Alessandro Vespignani