Part I Models in Systems Biology and Parameters Identification
1. Identifying Key In Silico Knockout for Enhancement of Limonene Yield through Dynamic Metabolic Modelling Jasmeet Kaur Khanijou, Yan Ting Hee, and Kumar Selvarajoo
2. The Search for System’s Parameters: A Statistical and Dynamical Description from Complex Network Analysis Alessandro Giuliani
3. Untargeted Analysis of Short-Chain Peptides in Urine Samples Short Peptides Analysis SaraElsa Aita, Andrea Cerrato, Aldo Laganà, Carmela Maria Montone, Enrico Taglioni, and Anna Laura Capriotti
4. Metastasis Models: Thermodynamics and Complexity A. Guerra, J.A. Betancourt-Mar, J.A. Llanos-Pérez, R. Mansilla, and J.M. Nieto-Villar
5. Metabolomics: Challenges and Opportunities in Systems Biology Studies Ahmed Mediani and Syarul Nataqain Baharum
6. Optical Estimation of Bioelectric Patterns in Living Embryos Patrick McMillen and Michael Levin
Part II Computational Methods
7. Mathematical Modeling in the Study of Organisms and Their Parts Maël Montévil
8. Systems Biology Modelling of Cancer Non-Linear Dynamics Abdallah Alameddine
Part III Critical Transition States Across Waddington’s Like Landscapes
9. From Cell States to Cell Fates: Control of Cell State Transitions Masa Tsuchiya, Alessandro Giuliani, and Paul Brazhnik
10. Understanding Cell Differentiation through Single-Cell Approaches: Conceptual Challenges of the Systemic Approach Laëtitia Racine and Andras Paldi
11. Modelling Mammary Organogenesis from Biological First Principles: A Systems Biology Approach Cheryl M. Schaeberle, Victoria A. Bouffard, Carlos Sonnenschein, and Ana M. Soto
Part IV Specific Field of Investigation
12. Systems Biology and Inborn Error of Metabolism: Analytical Strategy in Investigating Different Biochemical/Genetic Parameters Aurora Piombarolo, Cristiano Ialongo, Mariano Bizzarri, and Antonio Angeloni
13. Systems Biology Approach in Investigating Epithelial-Mesenchymal Transition (EMT) Noemi Monti, A. Querqui, Guglielmo Lentini, M. Tafani, and Mariano Bizzarri
14. An Enhanced Quantitative Reverse Transcription-PCR Approach for Measuring Circulating MicroRNAs Mahmoud Tavallaie and Mostafa Khafaei
15. Systems Biology Approaches to Understanding COVID-19 Spread in the Population Sofija Marković, Igor Salom, and Marko Djordjevic
Subject Index List…
This second edition volume expands on the previous edition with discussions of the latest advancements and methods used by scientists to study systems biology. The chapters in this book are organized into four parts. Part One looks at models in systems biology and parameters identification such as short peptide analysis, metastasis models, and metabolomics. Part Two covers computational methods in the study of organisms, and cancer non-linear dynamics. Part Three discusses critical transition states across Waddington’s like landscapes such as understanding cell differentiation through single-cell approaches and modeling mammary organogenesis from biological first principles. Part Four talks about specific fields of investigation including inborn errors of metabolism, system biology approach in epithelial-mesenchymal transition, and an approach to understanding how COVID-19 spreads in the population. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.
Cutting-edge and comprehensive, Systems Biology, Second Edition is a valuable tool for any researcher looking to learn more about this important and developing field.
