| Instructor: | Prof. Yechiam Yemini (YY) |
| Email: | yemini via cs.columbia.edu |
| Office Hours: | Tuesdays 6-7, or by appointment, 519 CSB |
| Date | Topic | Slides PDF | Updated | Notes/Assignments | |
| 9/4 | Ch1: Biology Primer |
1.0 Course intro slides ;
1.1 Biology Primer |
9/3 4PM | Welcome to the new academic year and to W4761!! | |
| 9/6 | Ch1: Biology Primer | 1.2 Basic Experimental Methods |
9/6 11AM | -- | |
| 9/11 | Ch2: Sequence Alignment |
2.1 Pairwise Sequence Alignment |
9/10 7PM | Assignment 2.1: Pairwise Alignment Assignment 2.1: Solutions |
|
| 9/13 | Rosh Hashana; Happy New Year!! |
No Class |
-- | -- | |
| 9/18 | Ch2: Sequence Alignment |
2.2 Scoring Matrices |
9/18 12:30PM | -- | |
| 9/20 | Ch2: Sequence Alignment |
2.3 Searching Sequence Databases |
9/25 1:30AM | -- | |
| 9/25 | Ch2: Sequence Alignment |
2.4 Multiple Sequence Alignment |
9/25 1:30PM | Assignment 2.4: Multiple Sequence Alignment (Posted 9/27) Assignment 2.4: Solutions |
|
| 9/27 | Ch3: Phylogenetics |
3.1 Introduction to Phylogenetics |
9/27 11:00AM | -- | |
| 10/2 | Ch3: Phylogenetics |
3.2 Computing Phylogeny |
10/2 3:00PM | -- | |
| 10/4 | Ch3: Phylogenetics |
3.3 Markovian Models |
10/4 2:00PM | -- | |
| 10/9 | Ch4: Hidden Markov Models (HMM) |
4.1 HMM Introduction 4.2 Computing Likelihood 4.3 HMM Training |
Updated 4.3; 2PM 10/11 | -- | |
| 10/11 | Ch4: Hidden Markov Models (HMM) |
4.4 HMM Applications |
3PM 10/18 updated | Assignment 4.4: Hidden Markov Modeling (Posted 10/16) Assignment 4.4: Solutions | |
| 10/16 | Ch5: Microarrays |
5.1 Microarrays Introduction |
11:45AM 10/16 | -- | |
| 10/18 | Ch5: Microarrays |
5.2 Microarrays Basic Analysis |
2PM 10/18 | -- | |
| 10/23 | Ch5: Microarrays |
5.3 Microarrays Advanced Analysis |
12:30PM 10/25 | Assignment 5.3: SVM classification (Posted 11/1) | |
| 10/25 | Ch6: Regulatory Networks |
6.1 Introduction to Regulatory Mechanisms |
12:30PM 10/25 | -- | |
| 10/30 | Ch6: Regulatory Networks |
6.2 Analyzing Regulation |
2PM 10/30 | -- | |
| 11/1 | Ch6: Regulatory Networks |
6.3 Boolean Network Models |
1:30PM 11/8 | -- | |
| 11/6 | Elections Day |
University Holiday |
-- | -- | |
| 11/8 | Ch6: Regulatory Networks |
6.4 Synthetic Biology |
1:30PM 11/8 | -- | |
| 11/13 | Ch 7: Bayesian Networks Techniques |
Prof. D. Pe'er's notes | Spring 07 | Slides by Prof D. Pe'er | |
| 11/15 | Ch7: Bayesian Networks Techniques | Spring 07 | -- | ||
| 11/20 | Ch8: Network Topology |
8.1 Introduction |
12:30 11/20 | -- | |
| 11/22 | Happy ThanksGiving!!! |
University Holiday |
Spring 07 | -- | |
| 11/27 | Ch8: Network Topology |
8.2 Network Motifs |
11/27 2PM | -- | 11/29 | Ch8: Network Topology |
8.3 Network Dynamics |
11/29 2:30PM | -- |
| 12/4 | Ch9: Metabolic Networks |
Project PPT Template 9.1 Introduction; Flux Based Analysis |
12/4 12:30PM | -- | |
| 12/6 | Ch9: Metabolic Networks |
9.2 Applications ; Concluding Notes |
12/6 1PM | -- |