LECTURES
Class Notes
The link to the ongoing class notes can be found here.
Note Sign-up
The link to sign up for taking class notes is here. This is required for participation credit. The link to submit your notes is here.
Videos
If the video isn’t linked yet, check Brown Panopto or the Media Library in Canvas.
| Date | Topic | Video | Extra Material |
|---|---|---|---|
| 9/8/22 | Welcome to CS 181! | video | slides |
| 9/13/22 | Introduction to Alignment Algorithms | video | slides |
| 9/15/22 | Global Alignment | video | |
| 9/20/22 | Needleman-Wunsch Algorithm and BLOSUM Matrices | video | |
| 9/22/22 | Local Alignment | video | |
| 9/27/22 | Introduction to Affine Gap Alignment | video | |
| 9/29/22 | Affine Gap Alignment Algorithm | video | slides |
| 10/4/22 | Sequence Alignment + Graph Theory | video | |
| 10/6/22 | Topological Sort and Intro to Pattern Matching | video | |
| 10/11/22 | Finite Automata and Knuth-Morris-Pratt (KMP) Algorithm | video | |
| 10/13/22 | No Lecture today | ||
| 10/18/22 | KMP continued, Nondeterministic Finite Automata | video | |
| 10/20/22 | Failure Functions and Deterministic Finite Automata | video | |
| 10/25/22 | Failure Function Algorithm | video | |
| 10/27/22 | Knuth-Morris-Pratt Algorithm | video | |
| 11/1/22 | Suffix Trees | video | |
| 11/1/22 | Suffix Trees | video | |
| 11/3/22 | No Lecture (Midterm) | ||
| 11/8/22 | No Lecture (Election Day) | ||
| 11/10/22 | Phylogenetic Trees | video | phylogeny slides |
| 11/15/22 | UPGMA Algorithm | video | |
| 11/17/22 | Neighbor-Joining Algorithm | video | |
| 11/22/22 | Neighbor-Joining Algorithm and Intro to HMMs | video | |
| 11/29/22 | Hidden Markov Models | video | |
| 12/1/22 | Hidden Markov Models - Viterbi | video | Viterbi slides |
| 12/6/22 | Viterbi, Genome Assembly | video | |
| 12/8/22 | Burrows-Wheeler Transform, Regulatory Genomics, Genomic Privacy | video |