Computational Functional Genomics

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