Tuesday/Thursday 12:30 - 1:45; McBryde 224
CRN: 82158
| Instructor: | Lenwood S. Heath |
| Office: | 2160J Torgersen Hall |
| Email: | heath@vt.edu |
| Office Hours: | Tuesday/Thursday 10:00-12:00 |
| Graduate Teaching Assistant: | Doaa Altarawy |
| Office: | 2160Q Torgersen Hall |
| Email: | doaa2012@vt.edu |
| Office Hours: | Thursday 2:30-4:30 |
Required Text Book:
An Introduction to Bioinformatics Algorithms, by Neil Jones and Pavel Pevzner
| Date | Topics | Presenter(s) | Reading | Assignment |
| August 26, 28 | Introduction | Heath |
Jones and Pevzner
Chapters 1, 2, 3 |
Homework 1
Due 9/13/2014 |
| September 2, 4 |
Exhaustive Search Restriction Mapping Motif Finding |
Heath |
Jones and Pevzner
Chapter 4 |
... |
| September 9, 11 | Greedy Algorithms | Heath |
Jones and Pevzner
Chapter 5 |
Homework 2
Due 9/27/2014 |
| September 16, 18 |
Dynamic Programming Algorithms
Sequence Comparison and Alignment |
Heath |
Jones and Pevzner
Chapter 6 |
Homework 3
Due 10/11/2014 |
| September 23, 25 |
Global Alignment
Local Alignment Discussion of Class Project |
Heath |
Jones and Pevzner
Chapter 6 |
... |
|
September 30, October 2 |
Combinatorial Pattern Matching | Heath |
Jones and Pevzner
Chapter 9 |
... |
| October 7, 9 | Combinatorial Pattern Matching | Heath |
Jones and Pevzner
Chapter 9 |
Homework 4
Due 10/25/2014 |
| October 14, 16 | Hidden Markov Models | Heath |
Jones and Pevzner
Chapter 11 |
... |
| October 21, 23 | Randomized Algorithms | Heath |
Jones and Pevzner
Chapter 12 |
... |
| October 28, 30 |
Graph Algorithms
Sequence Assembly |
Heath |
Jones and Pevzner
Chapter 8 |
Homework 5
Due 11/15/2014 |
| November 4, 6 | Short Read Mapping | Heath |
How to Map Billions of Short Reads Onto Genomes; and Mapping Reads on a Genomic Sequence |
... |
| November 11, 13 |
Structural Biology: The Protein Folding Problem |
Onufriev |
Foldit Online Protein Puzzle; and Foldit Gamers Solve Riddle of HIV Enzyme within 3 Weeks |
Homework 6
Due 12/6/2014 |
| November 18, 20 | Clustering and Trees | Heath | Jones and Pevzner Chapter 10 |
Tuesday, November 18.
Project presentations, 10 minutes per group. |
| December 2, 4 | Clustering and Trees | Heath | Jones and Pevzner Chapter 10 | ... |
| December 9 | Wrap up; projects | Heath | ... | December 15. Final project report due by 8:00 AM. |