Intro
Preface
Book Abstract
Contents
Part I: Genome Architecture, Evolution, and Cell Fate
Chapter 1: Networks and Islands of Genome Nano-architecture and Their Potential Relevance for Radiation Biology
1.1 Introduction to Radiation-Induced DNA Damage and Repair
1.2 Methods of Nanoscale Microscopic Analysis of the Cell Nucleus as a System at a Whole: Single-Molecule Localization Microsc...
1.3 The Cell Nucleus: A Complex System as a Whole
1.4 Radiation-Induced Chromatin Damage: A Complex System as a Whole Under Environmental Stress

1.5 Experimental Hints for System Response as a Whole After Radiation-Induced DNA Damaging
1.6 Experimental Hints for Similarity of Local System Response (Islands) After Radiation-Induced DNA Damaging
1.7 Conclusion
References
Chapter 2: A Unified Genomic Mechanism of Cell-Fate Change
2.1 Introduction: Self-Organization of Genome Expression
2.2 Classical Self-Organized Criticality Models
2.2.1 c-SOC Model
2.2.2 Rapid SOC Model
2.3 SOC Control of Genome Expression Regulation
2.4 Genome Engine: Open Thermodynamic View of Genome Expression System

2.5 Self-Organization of Whole Gene Expression Through Coordinated Chromatin Structural Transition
2.6 Synchronization Between Critical Point and Genome Attractor: CP as the Organizing Center of Cell-Fate Change
2.6.1 Critical Transition Transmitted to the Genome
2.7 Discussion
2.7.1 Different Biological Systems
2.7.1.1 MCF-7 Breast Cancer Cells: Global and Local Perturbations
2.7.1.2 HL-60 Human Leukemia Cells: Commitment to Differentiation
2.7.1.3 Human and Mouse Embryos: Developmental Oocyte-to-Embryo Transition

2.7.2 Genome Computing: CP Acting as the Center of Genome Computing
2.8 Conclusion: A Unified Genomic Mechanism
2.9 Methods
2.9.1 Biological Data Sets
2.9.2 Normalized Root Mean Square Fluctuation (nrmsf)
2.9.3 Updated Expression Flux Analysis
References
Chapter 3: Alterations to Genome Organisation in Stem Cells, Their Differentiation and Associated Diseases
3.1 Introduction
3.2 Different Types of Stem Cells
3.3 Nuclear Structures
3.3.1 The Nuclear Lamina
3.3.2 Nucleoli and Nuclear Bodies
3.4 Interphase Genome Organisation
3.5 Cellular Senescence

3.6 Alterations to Nuclear Organisation Leading to Plasticity in Differentiated Cells
3.7 Genome Behaviour in Laminopathies, Including Hutchinson-Gilford Progeria Syndrome
3.8 Chromosomal Translocations, Genome Reorganisation and Disease
3.9 Genome Behaviour in Colorectal Cancer, a Solid Tumour
3.9.1 GREM1 Duplication
3.10 Summary
References
Chapter 4: How Genomes Emerge, Function, and Evolve: Living Systems Emergence-Genotype-Phenotype-Multilism-Genome/Systems Ecol...
4.1 Introduction
4.2 A Short History of 3D Genome Organization and Its Finalization