CS3824 Introduction to Computational Biology and Bioinformatics
Fall 2014

Tuesday/Thursday 12:30 - 1:45; McBryde 224
CRN: 82158


"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 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


Syllabus


Class Calendar:

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.


Class Project


Resources: