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

Problem Set 1 (PDF)

Problem Set 2 (PDF)

Code (ZIP) (The ZIP file contains: 22 .m files.)

Data (ZIP - 1.9 MB) (The ZIP file contains: 2 .fasta files.)

Code Diagram (JPG)

Bound ORFs (FA)

Revised Load Sequences (M)

Problem Set 3 (PDF)

Problem Set 4 (PDF)

Code and Data (ZIP) (The ZIP contains: 1 .ps file, 1 .pdf file, 2 .mat files, and 11 .m files.)

Bayes Net Toolbox (BNT) for MATLAB®