Introduction to Computers and Biology
- Introduction and computational successes (9/1/2011)
- Quick biology introduction (9/6/2011)
Dynamic Programming & Sequence Alignment
- Global Sequence Alignment (9/6/2011 and 9/8/2011)
- Local Sequence Alignment (9/13/2011)
- General & Affine Gap Penalties (9/15/2011 and 9/20/2011)
- Multiple Sequence Alignment (9/22/2011)
Genome Sequencing & Assembly
- DNA sequencing & Lander-Waterman statistics (9/27/2011)
- Genome Assembly Paradigms (9/29/2011 and 10/4/2011)
- Comparing whole genomes with MUMmer (10/6/2011)
Data Structures for String Queries
- Suffix Tries & Trees (10/11/2011, 10/18/2011, and 10/25/2011)
- Homework Review (10/13/2011)
- Suffix Arrays (10/27/2011)
- Borrows-Wheeler Transform (11/1/2011 and 11/3/2011)
Structural Biology
- Protein Folding (11/8/2011)
- Side-chain Positioning (11/10/2011 and 11/15/2011)
- RNA Folding (11/17/2011)
Pattern Discovery
- Motif Finding with Gibbs Sampling (11/22/2011)
- Bacterial Gene Finding (11/29/2011)
- Hidden Markov Models and Eukaryotic Gene Finding (12/1/2011 & 12/6/2011))
- Profile Hidden Markov Models (12/6/2011)
Other topics
- Phylogenetics (12/8/2011)
- Biological Networks (12/13/2011)