CMSC 423: Lecture Slides

    Introduction to Computers and Biology

  1. Introduction and computational successes (9/1/2011)
  2. Quick biology introduction (9/6/2011)

    Dynamic Programming & Sequence Alignment

  3. Global Sequence Alignment (9/6/2011 and 9/8/2011)
  4. Local Sequence Alignment (9/13/2011)
  5. General & Affine Gap Penalties (9/15/2011 and 9/20/2011)
  6. Multiple Sequence Alignment (9/22/2011)

    7. Genome Sequencing & Assembly

  7. DNA sequencing & Lander-Waterman statistics (9/27/2011)
  8. Genome Assembly Paradigms (9/29/2011 and 10/4/2011)
  9. Comparing whole genomes with MUMmer (10/6/2011)

    10. Data Structures for String Queries

  10. Suffix Tries & Trees (10/11/2011, 10/18/2011, and 10/25/2011)
  11. Homework Review (10/13/2011)
  12. Suffix Arrays (10/27/2011)
  13. Borrows-Wheeler Transform (11/1/2011 and 11/3/2011)

    14. Structural Biology

  14. Protein Folding (11/8/2011)
  15. Side-chain Positioning (11/10/2011 and 11/15/2011)
  16. RNA Folding (11/17/2011)

    17. Pattern Discovery

  17. Motif Finding with Gibbs Sampling (11/22/2011)
  18. Bacterial Gene Finding (11/29/2011)
  19. Hidden Markov Models and Eukaryotic Gene Finding (12/1/2011 & 12/6/2011))
  20. Profile Hidden Markov Models (12/6/2011)

    21. Other topics

  21. Phylogenetics (12/8/2011)
  22. Biological Networks (12/13/2011)