| No. | date | topic | notes etc. |
| 1 | Jan 10 (Tu) | Lect0 (Course Overview) Getting R and Matlab ready |
slides R, Intro to genome biology, Basic lab techiques, |
| 2 | Jan 12(Tr) | Lect1 (Microarray technology) | slides short movie, paper homework assignmrnt 1 |
| 3 | Jan 17 (Tu) | Lect2 (Introduction to R) | slides |
| 4 | Jan 19 (Tr) | Lect3 (Review of satistics 1) | slides |
| 5 | Jan 24(Tu) | Lect4 (Review of satistics 2) | slides homework assignment 2 |
| 6 | Jan 26(Tr) | Lect5 (Review of satistics 3) |
slides |
| 7 | Jan 31 (Tu) | Lect6 (Pre-processing: cDNA microarrays) | slides, papers [1], [2], [3], [4] |
| 8 | Feb 2 (Tr) | Lect7 (Pre-processing: Affymetrix GeneChip arrays) | slides papers [1], [2], [3], [4] |
| 9 | Feb 7 (Tu) | Lect8 (Pre-processing with Bioconductor) | slides,
Bioconductor-Overview, Bioconductor-URL project1, tutorial for projec1 |
| 10 | Feb 9 (Tr) | Lect9( Differentially expressed genes) | slides papers [1], [2], [3],[4],[5] |
| 11 | Feb 14 (Tu) | Lect10 (Multiple testing ) | slides papers [1], [3] |
| 12 | Feb 16 (Tr) | Lect11 (Multiple testing - SAM ) | slides papers [1] |
| 13 | Feb 21 (Tu) | Lect12 (Annotation-1) | slides homework assignment 3 |
| 14 | Feb 23 (Tr) | Lect13 (Annotation-2) | slides |
| 15 | Feb 28 (Tu) | Lect14 (Clustering 1) | slides |
| 16 | March 2 (Tr) | Lect15 (Clustering 2) | slides |
| 17 | March 7 (Tu) | Lect16 | slides |
| 18 | March 9 (Tr) | Lect17 | papers [1], [2],
[3], [4], [5] homework assignment 4 (due 3/16/2006)) |
| 19 | March 14 (Tu)) | Lect18 (PCA) | slides |
| 20 | March 16 (Tr) | presentation | |
| 21 | March 21 (Tu) | Spring break, No class | |
| 23 | March 24 (Tr) | Spring break, No class | |
| 23 | March 28 (Tu) | Lect20 (Classification1) | slides |
| 24 | March 30 (Tr) | Lect21 (Classification2) | slides |
| 25 | April 4 (Tu) | Lect22 (Classification3) | slides tutorial by Bernhard Schölkopf |
| 26 | April 6 (Tr) | Lect23 ((Classification3 - continue) |
slides |
| 27 | April 11 (Tu) | Lect24 (applicaton) |
slides , paper |
| 28 | April 13 (Tr) | Lect25 (identification of motifs ) | slides Homework assignment 5, assignment 6 |
| 29 | April 18 (Tu) | Lect26 ( ) | |
| 30 | April 20 (Tr) | Lect27 (Identification of genetic network) | slides |
| 31 | April 25 (Tu) | review | slides |
| 32 | April 27 (Tr) | Final Exam |