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Lecture notes files.| SES # | TOPICS |
|---|
| L1 | Algorithms; Machine Learning; Biology (PDF - 1.9 MB)# |
| L2 | Evolutionary Models; Seq Alignment; Dynamic Programming (PDF)# |
| L3 | Local/Global Alignments; Variations on Dynamic Programming (PDF)# |
| L4 | Linear Time String Searching; Suffix Trees; String Preprocessing (PDF) |
| L5 | Database Search; Hashing; Random Projections (PDF - 2.1 MB) |
| L6 | Biological Signals; HMMs (PDF) |
| L7 | CpG Islands/Simple ORFs; Learning with HMMs (PDF) |
| L8 | Expression Analysis; Clustering (PDF) |
| L9 | Multi-dimensional Clustering; Feature Selection (PDF) |
| L10 | Regulatory Motifs; Gibbs Sampling; Expectation Maximization (PDF)# |
| L11 | Biological Networks; Graph Algorithms (PDF) |
| L12 | Phylogenetic Trees; Greedy Algorithms; Parsimony; EM (PDF) |
| L13 | Multiple Alignment; Profile Alignment; Iterative Alignment (PDF)# |
| L14 | Midterm |
| L15 | RNA Folding; Context-free Grammars; Phylo-CFGs (PDF) |
| L16 | Combine Alignment and Feature Finding; Pair HMM (PDF) |
| L17 | Gene Finding; Generalized HMMs |
| L18 | Comparative Gene Finding; Phylogenetic HMMs (PDF - 4.1 MB) |
| L19 | microRNA Regulation; Target Prediction (PDF) |
| L20 | Regulatory Relationships; Bayesian Networks |
| L21 | Generative Models of Regulation; Bayesian Graphs |
| L22 | Genome Assembly; Euler Graphs |
| L23 | Genome Duplication; Genome Rearrangements (PDF)# (Courtesy of Michael Brudno. Used with permission.) |
| L24 | Whole-genome Comparative Genomics |
| L25-L26 | Final Presentations |