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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 |