| Date | Topic |
Readings |
|
PHASE 1: ALGORITHMIC CONCEPTS FOR BIOINFORMATICS PROBLEMS
|
| 8/23 Thu | Molecular Biology Primer.
ppt
| |
| 8/28 Tue | Introduction to bioinformatics.
ppt
| |
| 8/30 Thu | Enumerative algorithms. Restriction Mapping and Motif finding.
ppt
| 4.1 - 4.6 |
| 9/04 Tue | Enumerative algorithms continued.
ppt
pdf
| 4.7 - 4.9, 5.5 |
| 9/06 Thu | Greedy algorithms. Genome rearrangement and breakpoints.
ppt
pdf
| 5.1 - 5.4 |
| 9/11 Tue | Dynamic programming. Pairwise sequence alignment & local alignment.
ppt
pdf
| 6.3 - 6.9.
DEKM 2.1 - 2.3 |
| 9/13 Thu | Dynamic programming. Gene prediction.
ppt
pdf
| 6.11 - 6.14 |
| 9/18 Tue | Dynamic programming. RNA secondary structure. Energy minimization.
ppt
pdf
| DEKM 10.1 - 10.2 (parts) |
| 9/20 Thu | Graphs. DNA sequencing.
ppt
pdf
| 8.1 - 8.9 |
| 9/25 Tue | Graphs. Protein sequencing.
ppt
ppt
| 8.10 - 8.15 |
| 9/27 Thu | Combinatorial Pattern Matching.
ppt
pdf
| 9.1 - 9.7 |
| 10/02 Tue | No class.
| |
| 10/04 Tue | Clustering. Gene expression.
ppt
pdf
| 10.1 - 10.4 |
| 10/09 Thu | Trees. Phylogeny reconstruction.
ppt
pdf
| 10.5 - 10.11 |
| 10/11 Thu | Midterm examination | |
|
PHASE 2: BIOINFORMATICS IN ACTION
|
| 10/16 Tue | HMM.
ppt
pdf
| 11.1 - 11.3 |
| 10/18 Thu | Motif finding. Gibbs sampling.
ppt
pdf
| Lawrence et al. |
| 10/23 Tue | Gene Finding. GeneMark.hmm.
ppt
pdf
| Lukashin & Borodovsky |
| 10/25 Thu | Local sequence alignment. BLAST.
ppt
pdf
| Altschul et al. 1990 |
| 10/30 Thu | Multiple alignment.
ppt
pdf
| Blanchette et al. |
| 11/01 Tue | Gene expression. Cancer microarrays.
ppt
pdf
| Segal et al. |
| 11/06 Thu | Cross species comparison & ChIP-chip data. Yeast regulation.
ppt
pdf
| Harbison et al. |
| 11/08 Tue | Gene function prediction from microarray data. Classification. SVM.
ppt
pdf
| Brown et al. |
| 11/13 Thu | Protein structure prediction. Neural networks. PSIPRED.
ppt
pdf
| Jones |
| 11/15 Thu | Previous lecture continued. | |
| 11/27 Tue | Metabolic networks.
ppt
pdf
| Jeong et al. |
| 11/29 Thu | Biological literature mining.
ppt
pdf
| Ling et al. |
| 12/04 Tue | Statistical Testing with Genes.
ppt
pdf
|
|
| 12/06 Thu | Evolutionary Models.
ppt
pdf
|
|
| 12/10 Mon | Final examination | |
