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Intro; Preface; Systems Biology; Contents; Systems Biology of Genome Structure and Dynamics; Contents; 1 Background; 2 Models of Epigenetic Modification Dynamics; 3 Protein-DNA Models; 4 Polymer-Based Models; 4.1 Models Based on Chromatin Loops; 4.2 Models Based on Supercoiling; 4.3 Integrative Models and Self-Organisation; 5 Conclusion and Outlook; References; A Systems Perspective of Complex Diseases: From Reductionism to Integration; Contents; 1 Introduction to Systems Biology; 1.1 Establishing the Need; 1.2 What Is a Model?; 1.3 Steps in Building a Model; 1.4 Modeling Methods and Tools
2 Common Methods of High-Throughput Data Generation2.1 Genomic Data; 2.2 Epigenomic Data; 2.3 Transcriptomic Data; 2.4 Regulomic Data; 2.5 Proteomic Data; 2.6 Metabolomic Data; 2.7 Metagenomic Data; 3 A Practical Example of Systems Biology Application; 4 Future Avenues; References; Systems Biology of Bacterial Immune Systems: Regulation of Restriction-Modification and CRISPR-Cas Systems; Contents; 1 Introduction; 2 Thermodynamic Modeling of Transcription Regulation; 2.1 Derivation of the Boltzmann Distribution; 2.2 Statistical Weights from Statistical Mechanics
2.3 Statistical Weights from Equilibrium Biochemical Reactions2.4 Modeling Transcription Regulation of AhdI R-M System; 3 Dynamic Modeling of Protein Expression; 4 Modeling Expression of EcoRV R-M System; 5 Inferring Effects of R-M Systems Regulatory Features on Their Dynamical Properties; 6 Assessing the Significance of CRISPR-Cas Regulatory Features; 7 Summary and Conclusion; References; Systems Biology of RNA-Binding Proteins in Amyotrophic Lateral Sclerosis; Contents; 1 Introduction; 1.1 RNA-Binding Proteins in ALS; 1.2 Application of Systems Biology to Unravel the Complexity of ALS
2 Systems Biology of ALS2.1 Genomics of ALS; 2.2 Transcriptomics of ALS; 2.3 Metabolomics of ALS; 2.4 Secretomics of ALS; 3 C9orf72 `Omics' in FTD-ALS; 4 Concluding Remarks; References; Systems Approaches to Map In Vivo RNA-Protein Interactions in Arabidopsis thaliana; Contents; 1 Introduction; 2 The Arabidopsis RBPome; 2.1 The mRNA Interactome of Arabidopsis Protoplasts; 2.2 The mRNA Interactome of Etiolated Arabidopsis Seedlings; 2.3 The mRNA Interactome of Arabidopsis Cultured Cells and Leaves of Adult Plants; 3 Toward Arabidopsis Ribonomes
3.1 HLP1, An hnRNP A/B-Like Protein Involved in Alternative Polyadenylation3.2 The Glycine-Rich RBP AtGRP7; 3.3 The Splicing Regulator SR45; 3.4 Cold Shock Protein 1; 3.5 The cpRNP Family; 3.6 The PPR Protein AtCPR1; 4 Combined Analysis of RNA-Protein Interaction and RNASecondary Structure Landscapes; 5 Achievements and Limitations of Arabidopsis In Vivo RNA-Protein Interaction; References; Systems-Level Analysis of Bacterial Regulatory Small RNA Networks; Contents; 1 Introduction; 2 Functional Consequences of Small RNA-mRNA Interactions
2 Common Methods of High-Throughput Data Generation2.1 Genomic Data; 2.2 Epigenomic Data; 2.3 Transcriptomic Data; 2.4 Regulomic Data; 2.5 Proteomic Data; 2.6 Metabolomic Data; 2.7 Metagenomic Data; 3 A Practical Example of Systems Biology Application; 4 Future Avenues; References; Systems Biology of Bacterial Immune Systems: Regulation of Restriction-Modification and CRISPR-Cas Systems; Contents; 1 Introduction; 2 Thermodynamic Modeling of Transcription Regulation; 2.1 Derivation of the Boltzmann Distribution; 2.2 Statistical Weights from Statistical Mechanics
2.3 Statistical Weights from Equilibrium Biochemical Reactions2.4 Modeling Transcription Regulation of AhdI R-M System; 3 Dynamic Modeling of Protein Expression; 4 Modeling Expression of EcoRV R-M System; 5 Inferring Effects of R-M Systems Regulatory Features on Their Dynamical Properties; 6 Assessing the Significance of CRISPR-Cas Regulatory Features; 7 Summary and Conclusion; References; Systems Biology of RNA-Binding Proteins in Amyotrophic Lateral Sclerosis; Contents; 1 Introduction; 1.1 RNA-Binding Proteins in ALS; 1.2 Application of Systems Biology to Unravel the Complexity of ALS
2 Systems Biology of ALS2.1 Genomics of ALS; 2.2 Transcriptomics of ALS; 2.3 Metabolomics of ALS; 2.4 Secretomics of ALS; 3 C9orf72 `Omics' in FTD-ALS; 4 Concluding Remarks; References; Systems Approaches to Map In Vivo RNA-Protein Interactions in Arabidopsis thaliana; Contents; 1 Introduction; 2 The Arabidopsis RBPome; 2.1 The mRNA Interactome of Arabidopsis Protoplasts; 2.2 The mRNA Interactome of Etiolated Arabidopsis Seedlings; 2.3 The mRNA Interactome of Arabidopsis Cultured Cells and Leaves of Adult Plants; 3 Toward Arabidopsis Ribonomes
3.1 HLP1, An hnRNP A/B-Like Protein Involved in Alternative Polyadenylation3.2 The Glycine-Rich RBP AtGRP7; 3.3 The Splicing Regulator SR45; 3.4 Cold Shock Protein 1; 3.5 The cpRNP Family; 3.6 The PPR Protein AtCPR1; 4 Combined Analysis of RNA-Protein Interaction and RNASecondary Structure Landscapes; 5 Achievements and Limitations of Arabidopsis In Vivo RNA-Protein Interaction; References; Systems-Level Analysis of Bacterial Regulatory Small RNA Networks; Contents; 1 Introduction; 2 Functional Consequences of Small RNA-mRNA Interactions