- 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
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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
- Examples from the colloquium by A. L. Barabasi
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.