There will not be a required book for this class, most topics will be covered by handouts, websites, ot research papers. This is mainly due to the fact that the field changes rapidly and many books are dated by the time they hit the shelves.
| Lec # | Topic | Date | Reading | Lecture Notes | Comments |
| 1. | Overview & Genomes | Sept 10 |
EBI's Intro to Biology: Sections 1-3 JGI's Intro to Genomics | ||
| Sequences | |||||
| 2. | Sequence Alignment | Sept 12 |
Wikipedia page
on Sequence Alignment (Through section 3) Longest Common Subsequence Problem | Notes on Sequence Alignment | |
| 3. | Various faces of Prallelization | Sept 17 | Tutorial on Parallel Computing Through Section 5. | ||
| 4. | BLAST & Heuristic Sequence Alignmemnt | Sept 19 | |||
| 5. | BLAST & Karlin-Altschul Statistics | Sept 24 | Reading handed out in class, available from the instructor via e-mail | ||
| Lecture Cancelled | Sept 26 | ||||
| 6. | Parsers, Scripting & Unix Tools | Oct 1 |
Unix Shell Scripting Unix Tools |
||
| 7. | Evolutionary Trees | Oct 3 | Notes on Phylogenetic Trees | ||
| Structures | |||||
| 8. | Structures of Molecules | Oct 10 | |||
| 9. | Representation of Structures | Oct 15 | |||
| 10. | Secondary Structure Prediction | Oct 15 | |||
| 11. | Structural Classification of Proteins (SCOP) | Oct 17 | |||
| 12-13. | Tertiary Structure: | Oct 22 & 24 | |||
| Microarrays | |||||
| 14-15. | Microarray: Data, Normalization, and Scaling | Oct 29 & 31 | |||
| 16-17. | Hypothesis testing: p-values, corrections, false discovery rates | Nov 5 & 7 | |||
| 18. | Clustering: k-means | Nov 12 | |||
| 19. | Classification: Gene Function Prediction | Nov 14 | |||
| Networks | |||||
| 20. | Biological Networks: Physical & Genetic | Nov 19 | |||
| 21-22. | Algorithms for Network Visualization & Analysis | Nov 21 & 26 | |||
| 25. | Conclusion | Dec 5 |