Handbook of Systems Biology

Handbook of Systems Biology

Concepts and Insights

1st Edition - November 20, 2012
  • Editors: Marian Walhout, Marc Vidal, Job Dekker
  • eBook ISBN: 9780123859457
  • Hardcover ISBN: 9780123859440

Purchase options

Purchase options
DRM-free (PDF, Mobi, EPub)
Available
Sales tax will be calculated at check-out

Institutional Subscription

Free Global Shipping
No minimum order

Description

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.

Key Features

  • 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

Readership

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

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

    Index

Product details

  • No. of pages: 552
  • Language: English
  • Copyright: © Academic Press 2012
  • Published: November 20, 2012
  • Imprint: Academic Press
  • eBook ISBN: 9780123859457
  • Hardcover ISBN: 9780123859440

About the Editors

Marian Walhout

Affiliations and Expertise

UMass Medical School, Worcester, MA

Marc Vidal

Affiliations and Expertise

Dana-Farber Cancer Institute, Boston, MA,and Harvard Medical School, Cambridge, MA

Job Dekker

Affiliations and Expertise

University of Massachusetts Medical School, Worcester, MA