Dates

Week 1

01-06

Introduction to Computational Biology

[Optimization in Bio]

01-08

Week 2

01-13

Pooling Designs: Simple Models and error-correcting models

[Intro], [Matrix]

[Decoding]

01-15

Pooling Designs: Inhibitor models

Form the groups

Week 3

01-20

Class project discussion

No lecture

01-22

Pooling Designs: Complexes models

HW1 out

Week 4

01-27

Non-unique Probe Selection

[Thai(*)]

01-29

Non-unique Probe Selection

[Klau],  [Wang(*)]

Week 5

02-03

No class, work on project  proposal

Project proposal due by 4pm via email

02-05

Non-unique Probe

HW1 due

No reading assignment

Week 6

02-10

   Community Structure

[Survey],[Network Properties]

02-12

 [Protein Complexes(*)],[Cancer Metastasis(*)], [Clique Percolation]

Week 7

02-17

Community Structure

 [Modularity(*)]

02-19

[Limit (*)],[Density(*)]

Week 8

02-24

Community Structure

[Semidefinite (*)]

02-26

[NP-hard(*)], [Evolution]

Week 9

03-03

Community Structure

Finish the NP-hard paper

03-05

[Local Modularity], [Local Shell]

Week 10

03-10

03-12

Week 11

03-17

Midterm report due (no class)

03-19

Midterm Presentation

Each team presents their results for 25 mins

Week 12

03-24

Multi-Sequence Alignment (MSA)

HW2 out

[MSA-Just (*)]

03-26

[MSA-Metric], [MSA-ClustalW]

Week 13

03-31

Multi-Sequence Alignment

[MSA-Genetic (*)]

04-02

[MSA-Gusfield (*)], [Constrain]

Week 14

04-07

HW2 due (04-07)

Protein Structure Prediction

[Overview and Survey]

04-09

[Secondary],[Threading]

Week 15

04-14

Protein Structure Prediction

[Threading]

04-16

Each team presents their results for 25 mins

Week 16

04-21

No Class

Week 17

04-25

Submit Final Reports by 4pm via email