| Part 1: Using DNA Sequence to Explain Mechanism |
| 1 |
Course Introduction (PDF) |
David Gifford |
| 2 |
Pairwise Alignment (PDF) |
David Gifford |
| 3 |
Finding Regulatory Sequences in DNA: Motif Discovery (PDF) |
Tommi Jaakkola |
| 4 |
Finding Regulatory Sequences in DNA: Motif Discovery (cont.) (PDF) |
Tommi Jaakkola |
| Part 2: Observing the Mechanism of Transcriptional Regulation |
| 5 |
Microarray Technology (PDF) |
David Gifford |
| 6 |
Expression Arrays, Normalization, and Error Models (PDF) |
Tommi Jaakkola |
| 7 |
Expression Profiles, Clustering, and Latent Processes (PDF) |
Tommi Jaakkola |
| 8 |
Computational Functional Genomics (PDF) |
David Gifford |
| 9 |
Stem Cells and Transcriptional Regulation |
David Gifford |
| 10 |
Part One: An Example of Clustering Expression Data (PDF)
Part Two: Computational Functional Genomics (cont.) (PDF) |
David Gifford |
| 11 |
Project Group Meetings |
|
| 12 |
Project Group Initial Presentations |
Students |
| 13 |
Computational Discovery of Regulatory Networks (PDF - 2.3 MB) (Courtesy of Georg Gerber. Used with permission.) |
Georg Gerber (Guest Lecturer) |
| 14 |
RNA Silencing (PDF) |
David Bartel (Guest Lecturer) |
| Part 3: Building Predictive Network Models of Transcriptional Regulation |
| 15 |
Computational Functional Genomics (cont.) (PDF) |
David Gifford |
| 16 |
Human Regulatory Networks (PDF) |
David Gifford |
| 17 |
Protein Networks |
David Gifford |
| 18 |
Causal Models (PDF) |
Tommi Jaakkola |
| 19 |
Causal Bayesian Networks, Active Learning (PDF) |
Tommi Jaakkola |
| 20 |
From Biological Data to Biological Insight (PDF) |
Nir Friedman (Guest Lecturer) |
| 21 |
Modeling Transcriptional Regulation (PDF) |
Tommi Jaakkola |
| 22 |
Dynamics |
David Gifford |