| Week | Date | Subject | |
| 1 | 1/22 | Course Overview | |
| 1/24 | Learning Motif Models | |
| 2 | 1/29 | Learning Motif Models | |
| 1/31 | Learning Motif Models | |
| 3 | 2/5 | Learning CRM Models | |
| 2/7 | Learning CRM Models | |
| 4 | 2/12 | Learning CRM Models | |
| 2/14 | Learning CRM Models | |
| 5 | 2/19 | Gene Finding | |
| 2/21 | Gene Finding | |
| 6 | 2/26 | Gene Finding | |
| 2/28 | Gene Finding | |
| 7 | 3/5 | RNA-Seq | |
| 3/7 | RNA-Seq | |
| 8 | 3/12 | RNA Secondary Structure and SCFGs | Project Proposal Due |
| 3/14 | RNA Secondary Structure and SCFGs | |
| 9 | 3/19 | RNA Secondary Structure and SCFGs | |
| 3/21 |
| Midterm (in class) |
| Spring Break |
| 10 | 4/2 | RNA Secondary Structure and SCFGs | |
| 4/4 | RNA Secondary Structure and SCFGs
| |
| 11 | 4/9 | Large-scale alignment | |
| 4/11 | Large-scale alignment | |
| 12 | 4/16 | Large-scale alignment | Project Progress Report Due |
| 4/18 | Comparative Network Analysis | |
| 13 | 4/23 | Comparative Network Analysis | |
| 4/25 | Genotype Analysis | |
| 14 | 4/30 | Genotype Analysis | |
| 5/2 | Genotype Analysis | |
| 15 | 5/7 | Protein Structure Prediction | |
| 5/9 | Protein Structure Prediction | |
| 5/13 | | Project Report Due |
| 5/18 | | Final Exam |
