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

Course Info

Learning Resource Types

notes Lecture Notes
group_work Projects with Examples