Calendar

Lec # TOPICS LECTURER KEY DATES
Part 1: Using DNA Sequence to Explain Mechanism
1 Course Introduction David Gifford

2 Pairwise Alignment David Gifford

3 Finding Regulatory Sequences in DNA: Motif Discovery Tommi Jaakkola

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

6 Expression Arrays, Normalization, and Error Models Tommi Jaakkola

7 Expression Profiles, Clustering, and Latent Processes Tommi Jaakkola Problem set 2 due
8 Computational Functional Genomics David Gifford

9 Stem Cells and Transcriptional Regulation David Gifford

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

12 Project Group Initial Presentations Students

13 Computational Discovery of Regulatory Networks Georg Gerber (Guest Lecturer)

14 RNA Silencing David Bartel (Guest Lecturer)

Part 3: Building Predictive Network Models of Transcriptional Regulation
15 Computational Functional Genomics (cont.) David Gifford

16 Human Regulatory Networks David Gifford

17 Protein Networks David Gifford

18 Causal Models Tommi Jaakkola

19 Causal Bayesian Networks, Active Learning Tommi Jaakkola

20 From Biological Data to Biological Insight Nir Friedman (Guest Lecturer)

21 Modeling Transcriptional Regulation Tommi Jaakkola

22 Dynamics David Gifford Problem set 4 due

Course Info

Learning Resource Types

notes Lecture Notes
group_work Projects with Examples