Dates

Week 1

01-09

Introduction to Computational Biology

[Bio Hypertext Book]

01-11

[Optimization in Bio]

Week 2

01-16

Pooling Designs: Simple Models and error-correcting models

[Intro]

01-18

Pooling Designs: Inhibitor models

Form the groups

[Decoding]

Week 3

01-23

Pooling Designs: Complexes models

[Hwang(*)][Complexes], 

01-25

Week 4

01-30

Non-unique Probe Selection

 [Schliep(*)(except section 2.3)]

02-01

Non-unique Probe Selection

[Klau(*)],[Minimum Test Collection]

Week 5

02-06

No class, work on project  proposal

Project proposal due by 4pm via email

02-08

Multi-Sequence Alignment

[Iterative MSA(*)]

Week 6

02-13

   Multi-Sequence Alignment

[Gusfield(*)],

[NP-complete of MSA]

02-15

 [MSA via Genetic Alg(*)]

Week 7

02-20

Constrained Multi-Sequence Alignment

 [Constrained MSA(*)], [Improvement(*)]

02-22

[Space Efficiency(*)]

Week 8

02-27

Community Structure

[Girvan], [Pujol]

03-01

[Moore]

Week 9

03-06

Community Structure

[Chen]

[Local Community(*)]

03-08

[Local Community 2(*)]

Week 10

03-13

03-15

Week 11

03-20

Midterm report due (no class)

03-22

Midterm Presentation

Each team presents their results for 25 mins

Week 12

03-27

Intro to Protein Structure

[Hypertext Book]

[Survey]

03-29

Experimental Determination: X-ray Crystallography and Nuclear Magnetic Resonance (NMR)  (via my presentation)

Week 13

04-03

Protein Structure Prediction -Secondary

[Surveyl], [Rost (*)], [Local]

04-05

[Combine], [Improvement]

Week 14

04-10

Protein Structure Prediction - Threading to Tertiary

[Prob], [Lathrop(*)], [Alignment], [Rost(*)]

04-12

[via Tree Decomposition]

Week 15

04-17

Protein Structure Prediction - Lattice

[Hinds], [Overview (Required to read but no need to submit a review report)]

04-19

[Inverse Folding]

Week 16

04-24

Final Project Presentation

 Each team presents their results for 50 mins

04-26

No Class

Week 17

05-03

Submit Final Reports by 4pm at my office