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| SES # | TOPICS | SCRIBE NOTES | SLIDES |
|---|---|---|---|
| L1 | Introduction: biology, algorithms, machine learning | (PDF) | (PDF - 1.7MB) |
| L2 | Global / local alignment, dynamic programming | (PDF) | (PDF) |
| L3 | String search, BLAST, database search | (PDF) | (PDF - 1.4MB) |
| L4 | Clustering basics, gene expression, sequence clustering | (PDF) | |
| L5 | Classification, feature selection, SVM | (PDF) | (PDF) |
| L6 | HMMs 1: evaluation, parsing | (PDF) | (PDF) |
| L7 | HMMs 2: posterior decoding, learning | (PDF) | (PDF) |
| L8 | Generalized HMMs and gene prediction | (PDF) | (PDF - 1.5MB) |
| L9 | Regulatory motifs, Gibbs sampling, EM | (PDF) | |
| L10 | Gene evolution: phylogenetic algorithms, NJ, ML, parsimony | (PDF) | (PDF) |
| L11 |
Molecular evolution, coalescence, selection, Ka/Ks Guest lecturer: Daniel Neafsey, Broad Institute | (PDF) | (PDF) (Courtesy of Daniel Neufsey. Used with permission.) |
| L12 |
Population genomics: fundamentals Guest lecturer: Pardis Sabeti, Harvard Systems Biology | (PDF) | |
| L13 |
Population genomics: association studies Guest lecturer: Pardis Sabeti, Harvard Systems Biology | (PDF) | |
| L14 | Midterm | ||
| L15 | Genome assembly, Euler graphs | (PDF) | |
| L16 | Comparative genomics 1: biological signal discovery, evolutionary signatures | (PDF) | |
| L17 | Comparative genomics 2: phylogenetics, gene and genome duplication | ||
| L18 | Conditional random fields, gene finding, feature finding | (PDF) | (PDF) |
| L19 | Regulatory networks, Bayesian networks | (PDF) | |
| L20 | Inferring biological networks, graph isomorphism, network motifs | (PDF) | |
| L21 | Metabolic modeling 1: dynamic systems modeling | (PDF) | (PDF - 1.1MB) |
| L22 | Metabolic modeling 2: flux balance analysis and metabolic control analysis | (PDF) | |
| L23 |
Systems biology Guest lecturer: Uri Alon, Weizmann Institute of Science | ||
| L24 |
Module networks Guest lecturer: Aviv Regev, Broad Institute | (PDF) | |
| L25 |
Synthetic biology Guest lecturer: Tom Knight, MIT Computer Science and Artificial Intelligence Laboratory | (PDF) | |
| L26 | Final presentations |
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