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