Syllabus for CMP/BIO 243 Bioinformatics

Topics for week beginning on specified date. (Note: This schedule is too ambitious. These dates will surely slip by at least a week as the quarter unfolds.)

1. (week 1): Introduction to molecular biology and biosequence databases. 9/23: What is genomics and what is bioinformatics. 9/28: Special guest lecture on proteins by Prof. Lydia Gregoret, Chemistry and Biochemistry Dept. 9/30: Special guest lecture on how genes work by Prof. Alan Zahler, Biology Dept.
2. (week 2): String searching and probability/statistical significance.
3. (week 3): pairwise alignment, profiles, Bayesian statistical methods.
4. (week 4): multiple alignment, simple Markov models, statistical models and parameter estimation.
5. (week 5): hidden Markov models, expectation maximization.
6. (week 6): neural nets, generalized HMMs for genefinding.
7. (week 7): support vector machines and analysis of gene chip data.
8. (week 8): protein and RNA structure, homology modeling, threading, energy minimization.
9. (week 9): catch up because by now we are behind the above schedule.
10. (week 10): future directions.

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