Handbook of Systems Biology
Concepts and Insights
- 1st Edition - October 30, 2018
- Latest edition
- Editors: Marian Walhout, Marc Vidal, Job Dekker
- Language: English
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… Read more
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.
- 2013 Honorable Mention for Single Volume Reference in Science from the Association of American Publishers' PROSE Awards
- Emphasizes the interdisciplinary nature of systems biology with contributions from leaders in a variety of disciplines
- Includes the latest research developments in human and animal models to assist with translational research
- Presents biological and computational aspects of the science side-by-side to facilitate collaboration between computational and biological researchers
Current researchers and recent graduates in genetics, molecular biology, cell biology, biomedical science, and systems engineering who can integrate systems biology concepts into their work
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
Index
- Edition: 1
- Latest edition
- Published: October 30, 2018
- Language: English
MW
Marian Walhout
Affiliations and expertise
UMass Medical School, Worcester, MAMV
Marc Vidal
Affiliations and expertise
Dana-Farber Cancer Institute, Boston, MA,and Harvard Medical School, Cambridge, MA, USAJD
Job Dekker
Affiliations and expertise
University of Massachusetts Medical School, Worcester, MA, USARead Handbook of Systems Biology on ScienceDirect