Handbook Of Systems Biology: Concepts And Insights

Description

ELSEVIER Handbook Of Systems Biology: Concepts And Insights by Marc Vidal and Job Dekker and Marian Walhout

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 Chapter 1. Proteomic Analysis of Cellular Systems Introduction MS-Based Proteomics Workflow Computational Proteomics Deep Expression Proteomics Interaction Proteomics Large-Scale Determination of Post-Translational Modifications Outlook and Future Challenges References Chapter 2. The Coding and the Non-coding Transcriptome Introduction The Pathway from DNA to Protein Sequences Methods to Determine the Reference Transcriptome The Human Transcriptome Conclusions and Future Challenges References Section II: Network Properties of Biological Systems Chapter 3. Interactome Networks Introduction Towards a Reference Protein–Protein Interactome Map Drawing Inferences from Interactome Networks Towards Dynamic Interactomes Concluding Remarks Acknowledgements References Chapter 4. Gene Regulatory Networks Cells are Computers Gene Regulation Transcription Gene Regulatory Networks (GRNs) Future Challenges Acknowledgements References Chapter 5. Analyzing the Structure, Function and Information Flow in Signaling Networks using Quantitative Cellular Signatures The Concept of Linear Cassettes and Modularity in Signal Transduction Genetic Dissection of Signal Transduction Pathways Systems Approaches to Identify the ‘Parts’ of Cellular Signaling Networks Quantitative RNAi Signatures or Phenoprints to Infer Context Dependent Information Flow Through Cellular Signaling Networks Concluding Remarks References Chapter 6. Genetic Networks Introduction Defining Genetic Interactions Experimental Approaches to Map Genetic Interaction Networks in Yeast Exploring Genetic Interaction Networks Integrating Genetic Interactions with Other Biological Networks Mapping Genetic Interactions in Other Organisms Genetic Network Conservation Expanding Genetic Networks: Mutant Alleles, Conditions and Phenotypes Genetic Interactions and Genome-Wide Association Studies Acknowledgements References Chapter 7. The Spatial Architecture of Chromosomes Introduction The Basic Material: the Chromatin Fiber The Polymer Physics of Chromosomes Nuclear Confinement and Formation of Chromosome Territories Anchoring of the Genome to Fixed Scaffolds The Internal Organization of Chromosomes: Long-Range Interactions Along and Between Chromosomes A Stochastic Interaction-Driven Model for Genome Folding and Nuclear Organization Future Challenges References Chapter 8. Chemogenomic Profiling: Understanding the Cellular Response to Drug Impact of the Human Genome Project on Healthcare and Biology Impact of Genomics: Shifting the Perceptions of Drug and Cellular Behavior Chemogenomics HIPHOP Conclusions and Future Challenges References Chapter 9. Graph Theory Properties of Cellular Networks Introduction Biological Systems as Graphs The Tools of Graph Theory Successes and Failures of the Erdős–Rényi Model Scale-Free Nature of Cellular Networks Hierarchy and Modularity Party vs. Date Hubs Degree Correlations Human Disease Network The Building Blocks of Cellular Networks Going Beyond Topology From Structure to Dynamics References Section III: Dynamic and Logical Properties of Biological Systems Chapter 10. Boolean Models of Cellular Signaling Networks Introduction Boolean Networks and Biological Systems Boolean Network Modeling Application Examples Conclusions and Future Directions References Chapter 11. Transcriptional Network Logic: The Systems Biology of Development Development is a System-Wide Direct Output of the Genome GRN Structural Components and Model Representation The Regulatory State Concept System-Wide and Deep Information Flow in Development General Features of the Developmental Process Developmental GRN Dynamics Examples of GRN-Mediated Spatial Control in Development Conclusion: The Explanation of Development Note Added in Proof Acknowledgement References Chapter 12. Reconstruction of Genome-Scale Metabolic Networks Introduction The Reconstruction Process Reconstruction Standards Applications Future Directions Glossary Acknowledgments References Chapter 13. Genotype Networks and Evolutionary Innovations in Biological Systems Introduction Metabolic Networks and Their Innovations Regulatory Circuits and Their Innovations Macromolecules and Their Innovations Towards a Systematic Understanding of Innovation Genotype Spaces and the Phenotypes Therein References Chapter 14. Irreversible Transitions, Bistability and Checkpoint Controls in the Eukaryotic Cell Cycle: A Systems-Level Understanding Introduction Irreversibility and Bistability Irreversible Transitions in the Budding Yeast Cell Cycle Irreversible Transitions in the Mammalian Cell Cycle Additional Checkpoints Conclusions References Chapter 15. Phenotypes and Design Principles in System Design Space Background Phenotypes Design Principles Conclusions and Future Challenges Acknowledgements References Chapter 16. System Biology of Cell Signaling Introduction Cellular Signaling: Pathways to Networks Isoforms of Signaling Molecules, Signaling Integration and Sorting Scaffolding Proteins: Signaling Networks Form Signaling Complexes Computational Analysis of Signaling Networks Regulation By Network Motifs Properties of a Cellular Signaling Network Network Topology and Consolidation of Signals Dynamical Models Positive Feedback Loops can form Switches: The Concept of Bistability Signaling Microdomains Within Cells Conclusions and Future Challenges Glossary Acknowledgments References Chapter 17. Spatial Organization of Subcellular Systems Motivation Dimensionality Effects in Biochemical Reactions Towards a Systemic Understanding of Cellular Biology Spatiotemporal Modeling of Cellular Processes Spatiotemporal Quantification of Cellular Processes Causality From Variation and Perturbation Analysis Model-Driven Experimentation and Experimentally Driven Modeling Conclusions References Section IV: Systems and Biology Chapter 18. Yeast Systems Biology: Towards a Systems Understanding of Regulation of Eukaryotic Networks in Complex Diseases and Biotechnology Introduction Yeast for Systems Understanding of Eukaryotic Biology and Networks Applications Conclusions: Future Perspectives Acknowledgements References Chapter 19. Systems Biology of Caenorhabditis elegans Introduction: The System before the Sequence Forward and Reverse Genetics in the Worm: How 97mb says ‘Make a Worm’ Expressing and Regulating an Animal Genome Integrative and Dynamic Modeling to Link Genotype to Phenotype Outlook References Chapter 20. Arabidopsis as a Model for Systems Biology Introduction Systems Analysis of Arabidopsis Development Development and the Response to Environmental Stress Conclusions and Perspective References Chapter 21. The Role of the Circadian System in Homeostasis Introduction Evolution of Clocks Role of the clock in neurological functions Homeostasis: You Notice It When It’s Broken Clocks in Energy and Metabolic Homeostasis Conclusion References Chapter 22. Biological and Quantitative Models for Stem Cell Self-Renewal and Differentiation Current Problems and Paradigms in Stem Cell Research Examples of Quantitative Models Explaining Stem Cell Behavior Strategies for Model Construction and Validation Information Flow and Epigenetic Landscapes in Differentiation References Section V: Multi-Scale Biological Systems, Health and Ecology Chapter 23. Systems Medicine and the Emergence of Proactive P4 Medicine: Predictive, Preventive, Personalized and Participatory Introduction Systems Medicine Five Systems’ Strategies for Dealing with Biological Complexity P4 Medicine Two Big Challenges: Education and Information Technology for Healthcare Impact of P4 Medicine on Society How to Bring P4 Medicine to Patients Acknowledgments References Chapter 24. Cancer Systems Biology: A Robustness-Based Approach Introduction Mechanisms for Robustness Mechanisms for Cancer Robustness Robustness Trade-offs Theoretically Motivated Therapy Strategies A Proper Index of Treatment Efficacy Long-Tail Drug Open Pharma Conclusion Acknowledgements References Chapter 25. Systems Immunology: From Cells and Molecules to a Dynamic Multi-Scale System Introduction Cell-Focused Systems Immunology System-Focused Systems Immunology Multi-Scale-Focused Systems Immunology Conclusions and Future Challenges References Chapter 26. Causal Inference and the Construction of Predictive Network Models in Biology Introduction A Movie Analogy for Modeling Biological Systems Causality as A Statistical Inference From Assessing Causal Relationships Among Trait Pairs to Predictive Gene Networks Conclusion and Future Directions References Chapter 27. Social Networks, Contagion Processes and the Spreading of Infectious Diseases Introduction Network Thinking Contagion Phenomena in Complex Social Networks Complex Networks and the Large-Scale Spreading of Infectious Diseases Conclusions and Future Challenges References