Intro -- Contents -- I: DEFINITIONS AND METHODOLOGY -- 1. Introduction to graphs -- 1.1 Graphs, directed graphs, and weighted graphs -- 1.2 Trees -- 1.3 Vertex correlation, assortativity -- 1.4 Hierarchical properties of graphs -- 1.5 The properties of scale-free networks -- 2. Graph structures: communities -- 2.1 Introduction -- 2.2 Typical subgraphs, motifs -- 2.3 Classes of vertices -- 2.4 Centrality measures, betweenness, and robustness -- 2.5 Clustering detection, modularity -- 2.6 Communities in graphs -- 3. Scale-invariance -- 3.1 Geometrical scale-invariance: fractals -- 3.2 Measuring the fractal dimension -- 3.3 Scale-invariance and power laws -- 3.4 Plotting a power law -- 3.5 Scale-invariance in natural sciences -- 3.6 Scale-invariance in economics and in social sciences -- 4. The origin of power-law functions -- 4.1 Random walk, Laplace equation, and fractals -- 4.2 Power laws from minimization principles -- 4.3 Multiplicative processes and normal distribution -- 4.4 Preferential attachment, the Matthew effect -- 5. Graph generating models -- 5.1 Random graph model -- 5.2 The small-world model -- 5.3 The Barabási-Albert model -- 5.4 Modifications to the Barabási-Albert model -- 5.5 Copying models -- 5.6 Fitness based model -- 5.7 Graph from optimization principles -- II: EXAMPLES -- 6. Networks in the cell -- 6.1 Basic cell biology -- 6.2 Protein-protein interaction network -- 6.3 Metabolic pathways -- 6.4 Gene regulatory networks -- |