| Introduction to Biology |
| 1 |
The Central Dogma: Some Algorithms Introduction |
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| Enumerative Solutions: Partial Digest Problem and Median Strings |
| 2 |
Partial Digest Problem |
Problem set 1 out |
| 3 |
Motifs and Median Strings |
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| Dynamic Programming: Sequence Alignments |
| 4 |
Global Alignment |
Problem set 2 out |
| 5 |
Local Alignment |
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| 6 |
Spliced Alignment |
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| 7 |
More Efficient Alignment |
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| Graph Theory: Sequencing Genes and Proteins |
| 8 |
Genomics and SBH Graphs |
Problem set 3 out |
| 9 |
Peptide Graphs |
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| Pattern Matching: Exact Matches, Gapless Alignments, and BLAST |
| 10 |
Exact Pattern Matching |
Problem set 4 out |
| 11 |
Suffix Trees |
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| 12 |
Suffix Arrays and BWTs |
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| 13 |
BLAST |
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| Clustering: Microarrays and Phylogeny |
| 14 |
Clustering (Guest Lecturer) |
Problem set 5 out |
| 15 |
Trees |
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| Neighbor Joining |
| 16 |
Review of Phylogenetic Analysis
Coalescent Theory in Biology |
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| 17 |
Application: Microarrays (Guest Lecturer) |
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| Probabilistic Models and Machine Learning: Gene Annotation and Evolution |
| 18 |
Hidden Markov Models I |
Problem set 6 out |
| 19 |
Hidden Markov Models II |
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| 20 |
Gibbs Sampling |
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| 21 |
Random Projections |
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| 22 |
MCMC and Bayesian Networks |
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| Horizons |
| 23 |
The Future: Protein Structure (Guest Lecturer) |
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| 24 |
The Future: Haplotype Mapping (Guest Lecturer) |
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| 25 |
Presentations of Final Projects |
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| 26 |
Presentations of Final Projects (cont.) |
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