Network Analysis and Modeling in Systems Biology
Introduction
1 Justification, outline and contributions
2 State of the Art
2.1 Molecular systems biology
2.1.1 Systems biology
2.1.2 Molecular Biology
2.1.3 Modelling biology
2.1.4 Experimental data integration
2.2 Biological networks
2.2.1 Networks
2.2.2 Metabolic networks
2.2.3 Protein-protein interaction networks
2.3 Modelling tools
2.3.1 Graph theory
2.3.2 Constraint-based modelling
2.3.3 Multivariate statistics
3 Potyvirus network analysis
3.1 Introduction
3.2 Potyvirus-Arabidopsis thaliana protein-protein interaction network
3.3 Potyvirus data fusion
3.4 Conclusions
4 Constraint-based approaches for metabolic analysis of E. coli
4.1 Introduction
4.2 Summary
4.3 Background
4.4 Materials
4.5 Methodology
4.6 Results and discussion
4.7 Conclusions
5 Metabolic graph analysis of E. coli
5.1 Introduction
5.2 Summary
5.3 Background
5.4 Methodology
5.5 Results and discussion
5.5.1 Graphs of metabolic networks: constructing graphs that incorporate directionality and context
5.5.2 Graph analysis of the core E. coli metabolic model
5.5.3 Structure of FBGs at multiple resolutions
5.6 Conclusions
6 Conclusions
References
Community Detection in E. coli Metabolic Network using Markov Stability and Constrain-based Modelling
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5.5 Results and discussion
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