Systems Biology.

Intro -- Related Titles -- Title Page -- Copyright -- Table of Contents -- 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 13C MFA -- 2.3 Metabolic Flux Analysis in Biotechnology -- 2.4 Metabolic Flux Analysis in Medicine -- 2.5 Emerging Challenges for 13C 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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Electronic reproduction. Ann Arbor, Michigan : ProQuest Ebook Central, 2024. Available via World Wide Web. Access may be limited to ProQuest Ebook Central affiliated libraries.