| February |
Topic |
Professor |
| 5 |
Introduction to the course. A simple
exercise in bioinformatics. |
Sorger |
| 7 |
Principles of computational biology
and areas of application. Introduction to systems design.
What are the questions in computational biology? What
are the data? |
Sorger |
| 12 |
Pairwise sequence comparisons and
dynamic programming I. |
Yaffe |
| 14 |
Multiple sequence comparisons and
dynamic programming II. |
Yaffe |
| 19 |
(President's Day Holiday) |
|
| 21 |
Protein secondary structure prediction,
motif finding and peptide libraries. |
Yaffe |
| 26 |
Genome sequencing and assembly, DNA
motif finding. |
Burge |
| 28 |
Markov and Hidden Markov models. |
Burge |
|
| March |
|
|
| 5 |
Literature discussion |
Burge |
| 7 |
Predicting Structure & Function of DNA/RNA |
Burge |
| 12 |
Guest Lecture |
Burge/Yaffe |
| 14 |
Critical protein structure analysis
and classification |
Keating |
| 19 |
Modeling proteins with molecular mechanics |
Tidor |
| 21 |
Applications of molecular mechanics:
X-ray and NMR refinement, conformational search |
Tidor |
| 26 |
(Spring Break) |
|
| 28 |
(Spring Break) |
|
|
| April |
|
|
| 2 |
Applications of molecular mechanics:
modeling mutant structures and homology modeling |
Keating |
| 4 |
Protein structure prediction: threading,
ab initio prediction |
Keating |
| 9 |
Literature discussion |
Keating/Tidor |
| 11 |
Special topic: electrostatics and
protein interactions |
Tidor |
| 16 |
(Patriot's Day holiday) |
|
| 18 |
Special topic: protein design |
Keating |
| 23 |
Special topics lecture: Trey Ideker |
Tidor/Endy |
| 25 |
Biochemical network analysis |
Tidor/Endy |
| 30 |
DNA microarrays: technology and data
analysis |
Tidor |
|
| May |
|
|
| 2 |
Non-linear systems |
Tidor |
| 7 |
Literature discussion |
Tidor |
| 9 |
Special topics lecture |
Endy |
| 14 |
Databases and wrap-up |
Sorger |
| 16 |
(no class) |
|
| |
|
|
Syllabus 
