# 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 US A 103, no. 2(2006):311-316.

(Detailed Lecture Notes (PDF))