CS3824 Introduction to Computational Biology and Bioinformatics
Fall 2015

Tuesday/Thursday 12:30 - 1:45; McBryde 308
CRN: 82197


"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 9:00-11:00
Graduate Teaching Assistant: Doaa Altarawy
Office: 2160U Torgersen Hall
Email: doaa2012@vt.edu
Office Hours: Monday 2:30-3:30
Friday 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 25, 27 Introduction Heath Jones and Pevzner
Chapters 1, 2, 3
Homework 1
Due 9/12/2015
September 1, 3 Exhaustive Search
Restriction Mapping
Motif Finding
Heath Jones and Pevzner
Chapter 4
...
September 8, 10 Greedy Algorithms Heath Jones and Pevzner
Chapter 5
Homework 2
Due 9/26/2015
September 15, 17 Dynamic Programming Algorithms
Sequence Comparison and Alignment
Heath Jones and Pevzner
Chapter 6
Homework 3
Due 10/10/2015
September 22, 24 Global Alignment
Local Alignment
Discussion of Class Project
Heath Jones and Pevzner
Chapter 6
...
September 29,
October 1
Combinatorial Pattern Matching Heath Jones and Pevzner
Chapter 9
...
October 6, 8 Combinatorial Pattern Matching Heath Jones and Pevzner
Chapter 9
Homework 4
Due 10/24/2015
October 13, 15 Hidden Markov Models Heath Jones and Pevzner
Chapter 11
...
October 20, 22 Structural Biology:
The Protein Folding Problem
Onufriev Foldit Online
Protein Puzzle
; and Foldit Gamers Solve
Riddle of HIV Enzyme
within 3 Weeks
;
protein structure lecture;
protein folding lecture
...
October 27, 29 Randomized Algorithms Heath Jones and Pevzner
Chapter 12
Homework 5
Due 11/14/2015
November 3 Applications of
Hidden Markov Models
Zhang Lecture notes;
Hidden Markov Models
and their Applications
in Biological Sequence Analysis
...
November 5 Graph Algorithms
Sequence Assembly
Heath Jones and Pevzner
Chapter 8
...
November 10, 12 Short Read Mapping Heath How to Map Billions
of Short Reads
Onto Genomes
; and
Mapping Reads on a
Genomic Sequence
Homework 6
Due 12/5/2015
November 17, 19 Clustering and Trees Heath Jones and Pevzner Chapter 10 Tuesday, November 17.
Project presentations, 10 minutes per group.
December 1, 3 Clustering and Trees Heath Jones and Pevzner Chapter 10 ...
December 8 Wrap up; projects Heath ... December 14. Final project report due by 8:00 AM.


Class Project


Resources: