Week | Date | Section | Lecture topics | HW assigned | HW due |
1 | 9/7 | Introduction | Class Overview |
2 | 9/12 | | Molecular biology 101 |
| 9/14 | Sequence assembly | Sequence assembly | HW0 |
3 | 9/19 | | Sequence assembly | HW1 | HW0 |
| 9/21 | | Sequence assembly |
4 | 9/26 | Sequence alignment | Pairwise sequence alignment |
| 9/28 | | Pairwise sequence alignment |
5 | 10/3 | | Intro to Probability for Discrete Variables |
| 10/5 | | Heuristic methods | HW2 | HW1 |
6 | 10/10 | | Multiple sequence alignment |
| 10/12 | | Multiple sequence alignment |
7 | 10/17 | Phylogenetic Trees | Intro to Phylogenetics |
| 10/19 | | Distance-based methods (Neighbor Joining algorithm) | HW3 | HW2 |
8 | 10/24 | | Parsimony methods |
| 10/26 | | Probabilistic methods | | HW3 |
9 | 10/31 | Mid-term | Mid-term |
| 11/2 | Genome annotation | Introduction to sequence annotation/Markov models |
10 | 11/7 | | Hidden Markov models: forward/backward/viterbi algorithm | HW4 |
| 11/9 | | Hidden Markov models: Parameter estimation |
11 | 11/14 | | Applications of Markov models (ChromHMM) |
| 11/16 | Clustering of omic datasets | Introduction to "omic" datasets and Flat Clustering |
12 | 11/21 | | Gaussian mixture model-based clustering | HW5 | HW4 |
| 11/23 | | Thanksgiving. No class. |
13 | 11/28 | | Hierarchical clustering, Cluster evaluation, and Clustering in practice |
| 11/30 | Modeling and analysis of networks | Introduction to biological networks |
14 | 12/5 | | Bayesian networks | HW6 | HW5 |
| 12/7 | | Bayesian networks |
15 | 12/12 | | Bayesian networks | | HW6 |
| 12/21 | Final Exam | Final Exam |