Computational Functional Genomics

Lecture Notes

Lec #	TOPICS	LECTURERS
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