Introduction to Networks

1. Elements of networks:
   • Nodes, links, subgraphs
   • Network motifs (review by Uri Alon (PDF) of transcription factor motifs)
   • Random graphs (Erdös-Rényi)
   • Percolation (Applet 1, Applet 2)
   • 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 by Prof. Mirny on Biological Networks

Some Related Links

• A course (U. Wisconsin) on Learning and modeling biological networks
• Barabasi Lab at Northeastern
• Networks group at Notre Dame
• Albert, R., and A. L. Barabasi. "Statistical Mehcanics of Complex Networks." RMP 74, no. 1 (2002): 47–97.
• Deeds, E.J., O. Ashenberg, and E.I. Shakhnovich. "A simple physical model for scaling in protein-protein interaction networks." Proc Natl Acad Sci USA 103, no. 2(2006):311-316.

(Detailed Lecture Notes (PDF))