| Date | Topic | Readings | Notes |
|---|---|---|---|
| 1/21 Wed | Course policies ppt, Overview of Bioinformatics (ppt) | ||
| 1/23 Fri | Essential Prob & Stat. (ppt) | BSA Ch-1, Ch-11 | |
| 1/28 Wed | Essential Molecular Biology (ppt) | CMB Ch-13. Hunter's Book Chapter | |
|
Sequence Alignment |
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| 1/30 Fri | Pairwise sequence alignment (Basic algorithms) (note) | BSA Ch-2, CMB Ch-6 | |
| 2/4 Wed | Pairwise sequence alignment (Variations) (ppt) | BSA Ch-2, CMB Ch-6 | |
| 2/6 Fri | Pairwise sequence alignment (Signficance of scores) (ppt) | BSA Ch-2, CMB Ch-6 | Assign #1 out |
| 2/11 Wed | Multiple sequence alignment (Dynamic programming)(ppt) | BSA Ch-6, CMB Ch-7 | |
| 2/13 Fri | Multiple sequence alignment (Progressive algorithms) (ppt) | BSA Ch-6, CMB Ch-7 | Assign #1 due, Assign #2 out |
| 2/18 Wed | Multiple sequence alignment (Clustal W) (ppt) | BSA Ch-6, ClustalW paper | |
|
Hidden Markov Models |
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| 2/20 Fri | General Introduction to HMMs (ppt) | BSA Ch-3, HMM note(pdf) | |
| 2/25 Wed | General Introduction to HMMs (cont) (ppt) | BSA Ch-3, HMM note(pdf) | Assign #2 due |
| 2/27 Fri | General Introduction to HMMs (cont) (ppt) | BSA Ch-3, HMM note(pdf) | Assign #3 out |
| 3/3 Wed | Applications of HMMs (b1.tif, b2.tif, b3.tif, b4.tif, b5.tif) | BSA Ch-5 | |
| 3/5 Fri | Applications of HMMs (ppt)(cont) | BSA Ch-5, Ch-6 | |
| 3/10 Wed | Midterm | ||
| 3/12 Fri | No class (Engineering Open House) | Assign #3 due | |
| 3/17 Wed | More on HMM Applications (SAM-T98) | ISMB99 Tutorial | |
|
Microarray Data Analysis |
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| 3/19 Fri | Microarray Data Algorithms (ppt) | Survey Paper | |
| 3/24 Wed | No class (Spring Break) | ||
| 3/26 Fri | No class (Sping Break) | ||
| 3/31 Wed | Microarray Data Technologies (Guest lecture by Dr. Lei Liu) Special Location! |
Special Location: 340 ERML (Madigan Lab, 1201 W Gregory Dr), map | Assign #4 out |
|
Phylogenetic Tree Construction |
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| 4/2 Fri | Introduction (ppt) | BSA Ch 7 | |
| 4/7 Wed | Distance-based methods, Parsimony (ppt) | BSA Ch-7 | Assign #4 due |
| 4/9 Fri | Probabilistic Approaches (ppt) | BSA Ch-8 | |
|
Pattern Extraction |
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| 4/14 Wed | Deterministic Pattern Extraction (Splash)(ppt) Guest lecture by Tao Tao |
SPLASH Algorithm ( background readings) | Assign #5 out |
| 4/16 Fri | Sampling-based methods (Gibbs sampling) (ppt) | Lawrence 93 ( background readings) | |
|
Structure & Function Analysis |
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| 4/21 Wed | RNA Structure Analysis (note) | BSA Ch-10 | Assign #5 due |
| 4/23 Fri | Protein structure prediction (ppt) | Rosetta Algorithm | Assign #6 out (tentative) |
| 4/28 Wed | Bioinformatics on Networks (ppt) | ||
| 4/30 Fri | Bioinformatics on Networks (cont.)(ppt) | Assign #6 due | |
| 5/5 Wed | Review for the final exam (ppt) | ||
| 5/6 Thu | Reading Day | ||
| 5/11 Tue | Final exam (note) | Time: 7:00-10:00pm, Room: 106B6 Engineering Hall | Good luck! |
| 5/11 Tue | |||