8.592 - HST.452J (Fall 2024)

Statistical Physics in Biology

Lecture 21

1. Biological networks
• Protein-protein interaction networks from two hybrid assays
  • The interactome
• Gene expression networks
  • Network motif, motifs (from Milo et al, Science 2002)
• Neural connections
  • Connectome
2. Elements of networks
• Graphs: nodes, links (directed or undirected), subgraphs
• Random graphs (Erdös-Rényi) Applet 
3. Connectivity
• Giant component
• Percolation on random graph
• Percolation on square lattice (demo) (Applet)
4. Measures on a network
• Distance and diameter
• Small Worlds Network demo
• Degree distribution (applet)
5. Scale free networks :
   • Examples from the colloquium by A.-L. Barabasi
   • The world wide web- description and results
   • Yeast protein network (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

• NetLogo Models Library
• NetLearn: Interactive demonstrations of network concepts
• Barabasi Lab at Northeastern
• "Statistical mehcanics of complex networks," R. Albert and A.-L. Barabasi, RMP 74, 47 (2002).
• Yule's process, as described in paper by M.V. Simkin and V.P. Roychowdhury
• Paper: M.E.J. Newman on Power laws, Pareto distributions and Zipf’s law
• Paper: Eric J. Deeds, Orr Ashenberg, and Eugene I. Shakhnovich