UMD

CMSC 858L: Network Algorithms for Biology

Lectures

These lectures were given in CMSC 858L "Network Algorithms for Biology" graduate class in the Computer Science Department at the University of Maryland, College Park. Many of the algorithms are described in the papers listed here.

    Biological Background and Network Construction

  1. Lecture 1: Introduction
  2. Lecture 2: Yeast 2-hybrid
  3. Lecture 3: Other experimental protocols (TAP-MP, SSL, ChIP-seq)
  4. Lecture 4: Computational Edge Prediction
  5. Function prediction and graph clustering

  6. Lecture 5: Function Prediction (Min Multiway Cut, FuncFlow)
  7. Lecture 6: Graph Summarization
  8. Lecture 7: VI-CUT
  9. Lecture 8: Modularity
  10. Lecture 9: Kernighan-Lin & Distance-based Clustering
  11. Lecture 10: RNSC, MCODE, & MCL
  12. Network Alignment

  13. Lecture 11: Network Alignment
  14. Lecture 12: Color Coding
  15. Lecture 13: IsoRank
  16. Random Networks & Motifs

  17. Lecture 14: Models of Network Evolution
  18. Lecture 15: Attack/Failure Response
  19. Lecture 16: Network motifs & Symmetry Breaking
  20. Other Topics

  21. Lecture 17: Dynamics of gene networks
  22. Lecture 18: Side-chain positioning
  23. PCP theorem & hardness of approximation

Slides for the Spring 2009 lectures can be found here.

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