| SES # | tOPICS | KEY DATES |
|---|---|---|
| L1 | Algorithms; Machine Learning; Biology | |
| R1 | Running Times, Molecular Biology and Probability | |
| L2 | Evolutionary Models; Sequence Alignment; Dynamic Programming | Problem set 1 out |
| L3 | Local/Global Alignments; Variations on Dynamic Programming | |
| R2 | Python and Dynamic Programming and Alignments | |
| L4 | Linear Time String Searching; Suffix Trees; String Preprocessing | |
| L5 | Database Search; Hashing; Random Projections | |
| R3 | Randomization, Modulus, Hashing, Random Projections, BLAST, Suffix Trees | |
| L6 | Biological Signals; HMMs | Problem set 1 due one day before Lec #6 Problem set 2 out |
| L7 | CpG Islands/Simple ORFs; Learning with HMMs | |
| R4 | Hidden Markov Models | |
| L8 | Expression Analysis; Clustering | |
| L9 | Multi-dimensional Clustering; Feature Selection | |
| L10 | Regulatory Motifs; Gibbs Sampling; Expectation Maximization | Problem set 2 due three days before Lec #10 Problem set 3 out |
| R5 | Motif Finding Using EM and Gibbs Sampling | |
| L11 | Biological Networks; Graph Algorithms | |
| L12 | Phylogenetic Trees; Greedy Algorithms; Parsimony; EM | |
| R6 | UPGMA, Neighbor Joining, Parsimony | |
| L13 | Multiple Alignment; Profile Alignment; Iterative Alignment | Problem set 3 due one day before Lec #13 Practice midterm out |
| L14 | Midterm | |
| L15 | RNA Folding; Context-free Grammars; Phylo-CFGs | Problem set 4 out |
| L16 | Combine Alignment and Feature Finding; Pair HMM | |
| R7 | RNA Folding, Context Free Grammars and Related Algorithms | |
| L17 | Gene Finding; Generalized HMMs | |
| L18 | Comparative Gene Finding; Phylogenetic HMMs | |
| L19 | microRNA Regulation; Target Prediction | Problem set 4 due one day before Lec #19 Project proposals due one day before Lec #19 Problem set 5 out |
| L20 | Regulatory Relationships; Bayesian Networks | |
| R8 | Sequencing by Hybridization | |
| L21 | Generative Models of Regulation; Bayesian Graphs | Problem set 5 due one day after Lec #21 Revised project proposals due one day after Lec #21 |
| L22 | Genome Assembly; Euler Graphs | |
| L23 | Genome Duplication; Genome Rearrangements | |
| L24 | Whole-genome Comparative Genomics | |
| L25-L26 | Final Presentations | Final projects due one day after Lec #26 |