CS3824 Introduction to Computational Biology and Bioinformatics
Spring 2010

Tuesday/Thursday 9:30 - 10:45; McBryde 231

"Everything that the living things do ... can be described as the wiggling and jiggling of atoms" Richard Feynman

"Nothing in Biology makes sense except in the light of evolution" Theodosius Dobzhansky.

Instructor:        Lenwood S. Heath
Office:              2160J Torgersen Hall
Email:               heath@vt.edu
Office Hours:    Tuesday/Thursday 11-12:30
Text Book:

Bioinformatics Algorithms, by Neil Jones and Pavel Pevzner

Syllabus

Class Calendar:

Date Topics Presenter(s) Reading Assignment
January 19, 21 Introduction Heath Jones and Pevzner
Chapters 1, 2, 3 		...
January 26, 28 Exhaustive Search
Restriction Mapping
Motif Finding 		Heath Jones and Pevzner
Chapter 4 		Homework 1
Due 2/4/2010
February 2, 4 Greedy Algorithms Heath Jones and Pevzner
Chapter 5 		Homework 2
Due 2/18/2010
February 9, 11 Structural Bioinformatics Onufriev Nucleic Acids Notes
Protein Notes 		Homework 3
Due 2/23/2010
February 16, 18 Dynamic Programming Algorithms Heath Jones and Pevzner
Chapter 6 		Homework 4
Due 3/2/2010
February 23, 25 More Dynamic Programming
Algorithms; BLAST 		Heath ... ...
March 2 Multiple Sequence Alignment;
Fitch's Algorithm 		Heath ... ...
March 4 Midterm Heath ... ...
March 16, 18 Understanding Bacterial Evolution Setubal ... Homework 5
Due 4/8/2010
March 23 Genome Evolution Zhang Lecture notes ...
March 25 Computational Systems Biology Murali ... ...
March 30 Class Project Heath ... ...
April 1 Computational Systems Biology Murali Lecture notes ...
April 6 Problem Solving Environments Shaffer Lecture notes ...
April 8 Pattern matching Heath Jones and Pevzner
Chapter 9 		...
April 13, 15 Keyword Trees; Suffix Trees Heath ... Homework 6
Due 5/4/2010
April 20, 22 Hidden Markov Models Heath Jones and Pevzner
Chapter 11 		...
April 27, 29 Public Health Epidemics
and Networks 		Marathe and
Vullikanti 		... ...
May 4 Wrap up Heath ... ...

Class Project

Resources: