Table of Contents
Cover
Related Titles
Title Page
Copyright
List of Contributors
About the Series Editors
Chapter 1: Integrative Analysis of Omics Data
Summary
1.1 Introduction
1.2 Omics Data and Their Measurement Platforms
1.3 Data Processing: Quality Assessment, Quantification, Normalization, and Statistical Analysis
1.4 Data Integration: From a List of Genes to Biological Meaning
1.5 Outlook and Perspectives
References
Chapter 2: 13C Flux Analysis in Biotechnology and Medicine
2.1 Introduction
2.2 Theoretical Foundations of
13
C MFA
2.3 Metabolic Flux Analysis in Biotechnology
2.4 Metabolic Flux Analysis in Medicine
2.5 Emerging Challenges for
13
C MFA
2.6 Conclusion
Acknowledgments
Disclosure
References
Chapter 3: Metabolic Modeling for Design of Cell Factories
Summary
3.1 Introduction
3.2 Building and Refining Genome-Scale Metabolic Models
3.3 Strain Design Algorithms
3.4 Case Studies
3.5 Conclusions
Acknowledgments
References
Chapter 4: Genome-Scale Metabolic Modeling and In silico Strain Design of Escherichia coli
4.1 Introduction
4.2 The COBRA Approach
4.3 History of
E. coli
Metabolic Modeling
4.4
In silico
Model-Based Strain Design of
E. coli
Cell Factories
4.5 Future Directions of Model-Guided Strain Design in
E. coli
References
Chapter 5: Accelerating the Drug Development Pipeline with Genome-Scale Metabolic Network Reconstructions
Summary
5.1 Introduction
5.2 Metabolic Reconstructions in the Drug Development Pipeline
5.3 Species-Level Microbial Reconstructions
5.4 The Human Reconstruction
5.5 Community Models
5.6 Personalized Medicine
5.7 Conclusion
References
Chapter 6: Computational Modeling of Microbial Communities
Summary
6.1 Introduction
6.2 Ecological Models
6.3 Genome-Scale Metabolic Models
6.4 Concluding Remarks
References
Chapter 7: Drug Targeting of the Human Microbiome
Summary
7.1 Introduction
7.2 The Human Microbiome
7.3 Association of the Human Microbiome with Human Diseases
7.4 Drug Targeting of the Human Microbiome
7.5 Future Perspectives
7.6 Concluding Remarks
Acknowledgments
References
Chapter 8: Toward Genome-Scale Models of Signal Transduction Networks
8.1 Introduction
8.2 The Potential of Network Reconstruction
8.3 Information Transfer Networks
8.4 Approaches to Reconstruction of ITNs
8.5 The rxncon Approach to ITNWR
8.6 Toward Quantitative Analysis and Modeling of Large ITNs
8.7 Conclusion and Outlook
Acknowledgments
References
Chapter 9: Systems Biology of Aging
Summary
9.1 Introduction
9.2 The Biology of Aging
9.3 The Mathematics of Aging
9.4 Future Challenges
Conflict of Interest
References
Chapter 10: Modeling the Dynamics of the Immune Response
10.1 Background
10.2 Dynamics of NF-κB Signaling
10.3 JAK/STAT Signaling
10.4 Conclusions
Acknowledgments
References
Chapter 11: Dynamics of Signal Transduction in Single Cells Quantified by Microscopy
11.1 Introduction
11.2 Single-Cell Measurement Techniques
11.3 Microscopy
11.4 Imaging Signal Transduction
11.5 Conclusions
References
Chapter 12: Image-Based In silico Models of Organogenesis
Summary
12.1 Introduction
12.2 Typical Workflow of Image-Based
In silico
Modeling Experiments
12.3 Application: Image-Based Modeling of Branching Morphogenesis
12.4 Future Avenues
References
Chapter 13: Progress toward Quantitative Design Principles of Multicellular Systems
Summary
13.1 Toward Quantitative Design Principles of Multicellular Systems
13.2 Breaking Multicellular Systems into Distinct Functional and Spatial Modules May Be Possible
13.3 Communication among Cells as a Means of Cell–Cell Interaction
13.4 Making Sense of the Combinatorial Possibilities Due to Many Ways that Cells Can Be Arranged in Space
13.5 From Individual Cells to Collective Behaviors of Cell Populations
13.6 Tuning Multicellular Behaviors
13.7 A New Framework for Quantitatively Understanding Multicellular Systems
Acknowledgments
References
Chapter 14: Precision Genome Editing for Systems Biology – A Temporal Perspective
Summary
14.1 Early Techniques in DNA Alterations
14.2 Zinc-Finger Nucleases
14.3 TALENs
14.4 CRISPR-Cas9
14.5 Considerations of Gene-Editing Nuclease Technologies
14.6 Applications
14.7 A Focus on the Application of Genome-Engineering Nucleases on Chromosomal Rearrangements
14.8 Future Perspectives
References
Index
End User License Agreement
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