CS3824 Introduction to Computational Biology and Bioinformatics
Fall 2011

Tuesday/Thursday 3:30 - 4:45; McBryde 223
CRN: 97828

"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.

Four Instructors!

Instructor: Lenwood S. Heath Yang Cao T. M. Murali Alexey Onufriev
Office: 2160J Torgersen Hall 2160L Torgersen Hall 2160B Torgersen Hall 2160C Torgersen Hall
Email: heath@vt.edu ycao@cs.vt.edu tmurali@vt.edu alexey@vt.edu
Office Hours: Tuesday/Thursday 9:30-11:00 Tuesday/Thursday 9:30-10:30 By appointment By appointment

Required Text Book:

Bioinformatics Algorithms, by Neil Jones and Pavel Pevzner

Supplementary Book:

Structural Bioinformatics


Class Calendar:

Date Topics Presenter(s) Reading Assignment
August 23, 25 Introduction Heath Jones and Pevzner
Chapters 1, 2, 3
Homework 1
Due 9/8/2011
August 30,
September 1
Exhaustive Search
Restriction Mapping
Motif Finding
Heath Jones and Pevzner
Chapter 4
September 6, 8 Greedy Algorithms Heath Jones and Pevzner
Chapter 5
Homework 2
Due 9/15/2011
September 13, 15 Modeling Biochemical Systems
with Ordinary Differential Equations
Cao Lecture1.pdf ...
September 20, 22 Case Studies: Gene Expression and
Protein Interaction Network
Cao Case Study: Cell Cycle ...
September 27, 29 Stochastic Modeling and Simulation
for Biochemical Systems
Cao Case Study: Gene Regulation

Stochastic Simulation

Homework 3
Due 10/13/2011
October 4, 6 Gene Function Prediction Murali Lecture Notes ...
October 11, 13 Gene Function Prediction in Arabidopsis Murali Lecture Notes ...
October 18, 20 Prediction of HIV Dependency Factors Murali Lecture Notes Homework 4
Due 11/10/2011
October 25, 27 Dynamic Programming Algorithms Heath Jones and Pevzner
Chapter 6
Homework 5
Due 11/17/2011
November 1, 3 Structural Bioinformatics Onufriev Bourne and Weissig, Chapter 1-2
Lecture Notes: proteins
Lecture Notes: Introduction
November 8, 10 Structural Bioinformatics Onufriev Lecture Notes: DNA, RNA Tue, Nov 8. Project presentations, 10 mins per group.
November 15, 17 Structural Bioinformatics Onufriev ... Homework 7
Due 11/15/2011
November 29,
December 1
Hidden Markov models Heath Jones and Pevzner
Chapter 11
Nov 29th. Progress report. By midnight.

Homework 6
Due 12/8/2011

December 6 Wrap up; projects Heath ... Dec 6th. Final project report by midnight.

Class Project