| Topic |
Date |
Lectures |
| Phylogenetics |
01/17/07 |
Lecture 1 |
| Sequence alignment |
01/24/07 |
Lecture 2 |
| Sequence alignment |
01/31/07 |
Lecture 3 |
| Perl lab |
02/06/07 |
Lecture 4 |
| Class cancelled (NJIT closed due to storm) |
02/14/07 |
|
| Student project proposal presentations |
02/21/07 |
|
| Student project proposal presentations and
alignment |
02/28/07 |
Lecture 5 |
| Alignment (HMMs) | 03/07/07 |
Lecture 6 pairwise alignment notes multiple alignment notes HMM notes |
| Alignment |
03/21/07 |
Lecture 7,
Lecture 8,
Probcons,
Probalign |
| Alignment |
03/28/07 |
Expected accuracy |
| Project talk |
04/04/07 |
1. Lawrence Drooks: Mutation Detection Probability 2. Dimitrios: A detailed study of the RSmatch algorithm for RNA secondary structure alignment and the correspondent RADAR web-server (paper) 3. Neelam: Neighbor joining additivity and error tolerance proofs |
| Project talk |
04/11/07 |
1. Sejal: Genome alignment (paper) 2. James: MUMMALS - HMMs with secondary structure states (paper) 3. Devikarani: M-GCAT: interactively and efficiently constructing large-scale multiple genome comparison frameworks in closely related species (paper) |
| Project talk |
04/20/07 |
1. Joe: Relaxed Neighbor Joining (paper)
2. Ashish: Kalign (paper) 3. Aditya: Prediction of consensus structural motifs in a family of coregulated RNA sequences (paper) |
| Project talk |
04/25/07 |
1. Justin: Using Phylogeny to Improve Genome-Wide Distant Homology
Recognition (paper)
2. Harhsa: Performance evaluation of clustering algorithms for gene expression data (paper) 3. Bhavneet: 4. Kartik: T-coffee (paper) |
| Project talk |
05/02/07 |
1. Mohan:
2. Anuradha: 3. Deepti: |