Week | Date | Section | Lecture topics |

1 | 9/2 | Introduction | Class Overview |

| 9/4 | DNA sequence | Introduction to Sequence alignment |

2 | 9/9 | | Pairwise sequence alignment |

| 9/11 | | Pairwise sequence alignment |

3 | 9/16 | | Multiple sequence alignment |

| 9/18 | | Multiple sequence alignment |

4 | 9/23 | Phylogenetic Trees | Intro to Phylogenetics |

| 9/25 | | Distance-based methods (Neighbor Joining algorithm) |

5 | 9/30 | | Parsimony methods |

| 10/2 | | Probabilistic methods |

6 | 10/7 | | Phylogenetics in practice |

| 10/9 | Genome annotation | Introduction to sequence annotation/Markov models |

7 | 10/14 | Mid-term | Mid-term |

| 10/16 | | Hidden Markov models: forward/backward/viterbi algorithm |

8 | 10/21 | | Hidden Markov models: Parameter estimation |

| 10/23 | | Parameter estimation |

9 | 10/28 | | Applications of Markov models (ChromHMM) |

| 10/30 | Clustering of omic datasets | Introduction to "omic" datasets |

10 | 11/4 | | Flat clustering |

| 11/6 | | Gaussian mixture model-based clustering |

11 | 11/11 | | Hierarchical clustering |

| 11/13 | | Cluster evaluation and Clustering in practice |

12 | 11/18 | Modeling and analysis of networks | Introduction to biological networks |

| 11/20 | | Bayesian networks |

13 | 11/25 | | Bayesian networks for gene expression data |

| 11/27 | | Thanksgiving. No class. |

14 | 12/2 | | Module networks |

| 12/4 | | Dependency networks |

15 | 12/9 | | Application of networks |

| 12/11 | Class review | Class review |

16 | 12/16 | Final Exam | Final Exam |