CISC 889 Bioinformatics
Spring semester 2004
Tentative schedule
|
Date |
Topic |
|
Handouts |
Notes |
|
2/10 |
Overview of the course |
|
syllabus |
|
|
2/12 |
Biology |
|
Dr. Adam Marsh |
|
|
2/17 |
Genome sequencing |
|
|
|
|
2/19 |
Sequence pairwise alignment: concepts and algorithms |
Chapter 2 |
|
|
|
2/24 |
Sequence pairwise alignment: statistics |
Chapter 2 |
|
|
|
2/26 |
Sequence pairwise alignment: heuristics |
|
|
HW1 out |
|
3/2 |
Multiple sequence alignment |
Chapter 6 |
|
|
|
3/4 |
Hidden Markov models |
Chapter 3 |
|
|
|
3/9 |
Hidden Markov models |
Chapter 4 |
|
|
|
3/11 |
Hidden Markov models |
Chapter 5 |
|
HW2 out (HW1 due) |
|
3/16 |
Gene finding, and motif and domain identification |
|
|
|
|
3/18 |
Protein Secondary structure prediction |
|
|
|
|
3/23 |
Spring break |
|
|
|
|
3/25 |
Spring break |
|
|
|
|
3/30 |
Phylogenetic analysis |
Chapter 7 |
|
|
|
4/1 |
Phylogenetic analysis |
Chapter 8 |
|
|
|
4/6 |
Phylogenetic analysis |
|
|
HW3 out (HW2 is due) |
|
4/8 |
Stochastic grammars |
Chapter 9 |
|
|
|
4/13 |
RNA alignment and |
Chapter 10 |
|
|
|
4/15 |
DNA microarray |
|
|
HW4 out (HW3 is due) |
|
4/20 |
Gene expression profiling (Support vector machines) |
|
|
|
|
4/22 |
Genetic networks (modeling by Boolean networks) |
|
|
|
|
4/27 |
Genetic networks (modeling by Bayesian networks) |
|
|
|
|
4/29 |
Metabolic pathways reconstruction |
|
|
HW4 is due |
|
5/4 |
Proteomics |
|
|
|
|
5/6 |
TBA |
|
|
|
|
5/11 |
TBA |
|
|
|
|
5/13 |
Presentations |
|
|
|
|
5/18 |
Presentations |
|
|
|