| Lecture | Date | Instructor | Topic | Assignment |
|---|---|---|---|---|
| 1 | Wed, Sep 1 | AH | Course introduction; Structure of SARS genome | |
| 2 | Fri, Sep 3 | AH | Molecular biology primer: DNA, RNA and protein | Problem Set 1 out |
| 3 | Wed, Sep 8 | AH | Gene/genome organization; SARS genome revisited | |
| 4 | Fri, Sep 10 | AH | Algorithm analysis and design | |
| 5 | Wed, Sep 15 | AH | Divide-and-conquer | |
| 6 | Fri, Sep 17 | AH | Divide-and-conquer fails; Memoization | Problem Set 1 due; Problem Set 2 out |
| 7 | Wed, Sep 22 | AH | Memoization; Dynamic programming | |
| 8 | Fri, Sep 24 | AH | Greedy algorithms; Sequence variation | |
| 9 | Wed, Sep 29 | AH | The alignment problem; Aligning sequences globally | |
| 10 | Fri, Oct 1 | AH | Aligning sequences with affine gap scores; Local alignment | Problem Set 2 due; Problem Set 3 out |
| 11 | Wed, Oct 6 | NA | Class cancelled | |
| 12 | Fri, Oct 8 | LB | Tour of the Duke Genome Sequencing facility | |
| 13 | Wed, Oct 13 | AH | DNA and genome sequencing; HGP and Celera | |
| 14 | Fri, Oct 15 | AH | Genome assembly; FASTA and BLAST heuristics | Problem Set 3 due; Problem Set 4 out |
| 15 | Wed, Oct 20 | AC | Next-gen sequencing; Indexes and short-read alignment | |
| 16 | Fri, Oct 22 | AH | Finish FASTA and BLAST; Start review of probability | |
| 17 | Wed, Oct 27 | AH | Discrete and continuous distributions; Joint, marginal, conditional | |
| 18 | Fri, Oct 29 | AH | Parameter estimation; Model selection | Problem Set 4 due; Problem Set 5 out |
| 19 | Wed, Nov 3 | AH | Markov and hidden Markov models (HMMs) | |
| 20 | Fri, Nov 5 | AH | Estimating HMMs; Viterbi decoding | |
| 21 | Wed, Nov 10 | AH | Posterior decoding; optimization and Baum-Welch | |
| 22 | Fri, Nov 12 | AH | HMMs for gene finding in higher eukaryotes | Problem Set 5 due; Problem Set 6 out |
| 23 | Wed, Nov 17 | AH | Multiple sequence alignment | |
| 24 | Fri, Nov 19 | AH | Profile HMMs; HMM variations; motif finding | |
| Wed, Nov 24 | Thanksgiving break | |||
| Fri, Nov 26 | Thanksgiving break | Problem Set 6 due (originally due Tuesday) | ||
| 25 | Wed, Dec 1 | AH | Comparative genomics; Tree of life; Phylogenetics | Problem Set 7 out |
| 26 | Fri, Dec 3 | AH | Building phylogenetic trees (UPGMA and NJ) | |
| 27 | Wed, Dec 8 | AH | Unsupervised learning: Clustering; Course evaluations | |
| 28 | Fri, Dec 10 | AH | Supervised learning: Classifying; Course summary | Problem Set 7 due |
AH: Alex Hartemink, AC: Abrita Chakravarty, LB: Lisa Bukovnik, NA: not applicable
