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

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

    11. Network Alignment

  11. Lecture 11: Network Alignment
  12. Lecture 12: Color Coding
  13. Lecture 13: IsoRank

    14. Random Networks & Motifs

  14. Lecture 14: Models of Network Evolution
  15. Lecture 15: Attack/Failure Response
  16. Lecture 16: Network motifs & Symmetry Breaking

    17. Other Topics

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

Slides for the Spring 2009 lectures can be found here.

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