1. Measurements
   • Gene expression
   • Protein-protein interactions
   • Protein-DNA interactions
2. Analysis
   • Expression
   • Interactions/Reactions
3. Modelling
   • Yule's process, as described in paper by M.V. Simkin and V.P. Roychowdhury
   • Paper by M.E.J. Newman on Power laws, Pareto distributions and Zipf’s law
   • Paper by Eric J. Deeds, Orr Ashenberg, and Eugene I. Shakhnovich

1. Elements of networks:
   • Nodes, links, subgraphs
   • Network motifs (review by Uri Alon of transcription factor motifs)
   • Random graphs (Erdös-Rényi) Applet
   • Percolation (Applet 1, Applet2)
   • Distance, Diameter, and Degree distribution
2. Scale free networks :
   • Examples from the colloquium by A.-L. Barabasi
   • The world wide web- description and results
   • Yeast protein network (Two hybrid assays, A. Wagner: Fig. 1, Fig.2)
   • Food web
   • Metabolic network
   • p53 network- description and results
   • The Barabasi-Albert (BA) model (Applet)
   • The degree distribution of the BA model

[Lecture Notes]

[Exercises]

Related links

• A course (U. Wisconsin) on Learning and modeling biological networks
• NetLearn: Interactive demonstrations of network concepts
• Barabasi Lab at Northeastern
• Networks group at Notre Dame
• "Statistical mehcanics of complex networks," R. Albert and A.-L. Barabasi, RMP 74, 47 (2002).