| Date | Topic |
Readings |
|
PHASE 1: ALGORITHMIC CONCEPTS FOR BIOINFORMATICS PROBLEMS
|
| 8/26 Tue | Introduction to bioinformatics.
ppt
pdf
| |
| 8/28 Thu | Molecular Biology Primer.
ppt
pdf
| |
| 9/02 Tue | Enumerative algorithms. Restriction Mapping and Motif finding.
ppt
pdf
| 4.1 - 4.4 |
| 9/04 Thu | Enumerative algorithms continued.
ppt
pdf
| 4.5 - 4.9 |
| 9/09 Tue | Greedy algorithms. Genome rearrangement and breakpoints.
ppt
pdf
| 5.1 - 5.5 |
| 9/11 Thu | Dynamic programming. Pairwise sequence alignment & local alignment.
ppt
pdf
| 6.3 - 6.9.
DEKM 2.1 - 2.3 |
| 9/16 Tue | Dynamic programming. Gene prediction.
ppt
pdf
| 6.11 - 6.14 |
| 9/18 Thu | No class
| |
| 9/23 Tue | Dynamic programming. RNA secondary structure. Energy minimization.
ppt
pdf
| DEKM 10.1 - 10.2 (parts) |
| 9/25 Thu | Graphs. DNA sequencing.
ppt
pdf
| 8.1 - 8.9 |
| 9/30 Tue | Combinatorial Pattern Matching.
ppt
pdf
| 9.1 - 9.7 |
| 10/02 Thu | Clustering. Gene expression.
ppt
pdf
| 10.1 - 10.4 |
| 10/07 Tue | Trees. Phylogeny reconstruction.
ppt
pdf
| 10.1 - 10.4 |
| 10/09 Thu | Trees. Phylogeny reconstruction. (Cont'd)
| 10.5 - 10.11 |
| 10/14 Tue | HMM.
ppt
pdf
| 11.1 - 11.3 |
| 10/16 Thu | Midterm examination | |
|
PHASE 2: BIOINFORMATICS IN ACTION
|
| 10/21 Tue | Gene Finding. GeneMark.hmm.
ppt
pdf
| Lukashin & Borodovsky |
| 10/23 Thu | Motif finding. Gibbs sampling.
ppt
pdf
| Lawrence et al. |
| 10/28 Tue | Local sequence alignment. BLAST.
ppt
pdf
| Altschul et al. 1990 |
| 10/30 Thu | BLAST continued.
| No paper |
| 11/04 Tue | No class |
| 11/06 Thu | Gene expression. Cancer & microarrays.
ppt
pdf
| Segal et al. |
| 11/11 Tue | Statistical Testing with Genes.
ppt
pdf
|
|
| 11/13 Thu | Gene function prediction from microarray data. Classification. SVM.
ppt
pdf
| Brown et al. |
| 11/18 Tue | Protein structure prediction. Neural networks. PSIPRED.
ppt
pdf
| Jones |
| 11/20 Thu | Biological literature mining
ppt
pdf
| Ling et al. |
| 12/02 Tue | Metabolic networks.
ppt
pdf
| Jeong et al. |
12/04 Thu | Cross species comparison & ChIP-chip data. Yeast regulation.
ppt
pdf
| Harbison et al. |
| 12/09 Tue | Open |
| 12/18 Thu | Final examination | |
