| Lecture |
Date |
Topic
|
Refs |
| |
|
|
|
| 1 |
08/26 |
Course Overview, Biological Background
Scribe: Pankaj Agarwal
Notes Additional
Readings |
GG*
[Ch 2-4] |
| 2 |
08/28 |
Biological Background, Computation Intro
Scribe: Pankaj Agarwal
Notes Additional
Readings |
GG* |
| |
|
|
|
| 3 |
09/02 |
Mathematical Foundation, Model of Computation
Scribe: Leelavati Narlikar
Notes
|
CLR
[Ch 1-3] |
| 4 |
09/04 |
Divide and conquer, Greedy Algorithms
Scribe: Leelavati Narlikar
Notes |
CLR
[Ch 1, 4] |
| 5 |
09/09 |
Dynamic Programing
Scribe: David Vaughn
Notes |
CLR
[Ch 16,17] |
| 6 |
09/11 |
Graphs, Representation of Graphs, Traversal Algorithms
Scribe: Sukhendu Chakraborty
Notes
Homework
1 |
CLR
[Ch 23] |
| 7 |
09/16 |
Minimum Spanning Trees, Shortest Paths
Guest Lecturer: Yusu Wang
Scribe: Joe Volpe
Notes Readings |
CLR
[Ch 24,25] |
| |
09/18 |
No Class |
|
| |
|
|
|
| 8 |
09/23 |
Sequence Alignment I: Global Alignment
Scribe: Avik Bhattacharya
Notes Readings |
M
[Ch 3]
P
|
| 9 |
09/25 |
Sequence Alignment II: Global
and Semiglobal Alignment
Scribe: Jeff Phillips
Notes Readings |
M [Ch 3]
P |
| 10 |
09/30 |
Local Alignment and Substitution Matrices
Scribe: Madhuwanti Vaidya
Notes Homework 2 |
P
EG
SM
|
| 11 |
10/02 |
Sequence Database Search: BLAST and FASTA
Scribe: Dmitri Morozov
Notes Readings |
EG
SM
|
| |
|
|
|
| 12 |
10/07 |
Genome Assembly
Scribe: Philippe Luedi
Notes Readings |
SM
W
|
| 13 |
10/09 |
Probabilistic and Stochastic Modeling
Scribe: Tingting Jiang
Notes Readings |
DE*
[Ch 11]
EG |
| |
10/14 |
Fall Break |
|
| 14 |
10/16 |
Hidden Markov Models (Guest Lecture)
Guest Lecturer: Ron Parr
Scribe: Wenbin Pan
Slides Notes Readings |
DE* [Ch 3] |
| 15 |
10/21 |
Multiple Sequence Alignment
Scribe: David Orlando
Notes Readings |
DE*
[Ch 5,6]
M
|
| 16 |
10/23 |
Profile HMM and multiple alignment
Scribe: Sarah Roberts
Notes Readings |
P
M [Ch 8] |
| |
|
|
|
| 17 |
10/28 |
Gene Prediction
Scribe: Haige Shen
Notes Homework 3 |
|
| 18 |
10/30 |
Analyzing Gene Expression Data: Clustering &
classification
Scribe: Dajun Hou
Notes Readings |
|
| |
|
|
|
| 19 |
11/04 |
Proteins, Primary Strucure
Scribe: Quihua Liu
Notes Readings |
L
BT |
| 20 |
11/06 |
Secondary Structure Prediction
Scribe: Jeff Headd
Notes Readings |
L
St |
| 21 |
11/11 |
Tertiary Strucure (Guest Lecture)
Guest Lecturer: Leelavati Narlikar
Scribe: Curtis Layton
Notes Readings |
L
St |
| 22 |
11/13 |
Space Filling Diagrams
Scribe: Pankaj Agarwal
Notes Readings |
|
| 23 |
11/18 |
Shape Analysis
Scribe:Pankaj Agarwal
Notes Readings |
|
| |
|
|
|
| 24 |
11/20 |
Protein Folding
| |
| 25 |
11/25 |
Protein-Protein Interaction
Scribe: Li Liu
Notes Readings |
|
| 26 and 27 |
12/02 and 12/04 |
Project Presentations
Schedule |
|
