CS438 Bioinformatics Algorithms

Course Web Site: www.cs.siu.edu/~dche/courses/CS438

 

INSTRUCTOR

 

Dr. Dunren “Daren” Che

Office: Faner 2128
Hours: 10am – 12pm MWF
Phone: 618-453-6046
Email: dche@cs.siu.edu (preferred!)



TA

 

Mr. Dabin Ding

Office: Faner 3131

Office Hrs: 2-4pm TR & 4-5pm F

Phone: 453-6037

Email: dabin@siu.edu (private email: sendtoding@gmail.com)

 

 

OBJECTIVE

 

This course is an introductory course on bioinformatics algorithms and the computational ideas that have driven them. The course includes a primer of molecular biology, an introduction/review of algorithms and complexity, and a series of lectures & discussions of different techniques that can be used to solve important and practical computing problems in biology, i.e., bioinformatics.

 

FEATURE OF THE SUGJECT

 

It’s not simply an application of existing algorithm design principles to biological problems, but really calls for rethinking of algorithm design issues and recreation of novel design ideas because of the high challenges and uniqueness of compressing bioinformatics problems.

 

CHALLENGES

 

A bioinformatician is expected to be an expert in both biology and computer science (especially computing algorithms and information/data management). However, even mastering only one of the two would take a lot of work and effort.

 

PREREQUISITES

 

CS330 with a grade of C or better (biology background is helpful but not necessary as a molecular biology primer will be provided).

 

TEXTs

 

An Introduction to Bioinformatics Algorithms (for both 438 and 591)

Neil C. Jones and Pavel A. Pevzner

ISBN 0-262-10106-8 / August 2004, The MIT Press.

 

Bioinformatics Algorithms: Techniques and Applications (for 591 only)

by Ion Mandoiu, Alexander Zelikovsky

February 2008, Hardcover (E-Book also available)


 

GRADING POLICY (subject to minor change/adjustment)

 

Your final grades (for CS438 students) will depend on three parts: 2 term exams (each taking up 30%), about 5 or 6 assignments (homework and implementation projects, taking 40%); For CS591 students, a presentation is required (taking 15% from the percentage allocated to assignments).

 

A letter grade (of A, B, C, D, or F) will be assigned to each student at the end based on one’s overall average percentage of grades according to the following scales:

 

A ---- above 90

B ---- 80 --- 89

C ---- 70 --- 79

D ---- 60 --- 69

F ---- below 60

 

Tentative Exam Dates

 

Exam 1: March 9, Friday (right before spring break).

Exam 2: May 4 or follow officially scheduled time for final.

 

 

SYLLABUS

 

The course is planned to have about 40 lectures, including selected topics that may be assigned to each student to present with the professor’s guidance and supervision. The purpose for arranging student presentation is to inspire students and get them fully involved in an active learning process. Book 2 can be used as the major source for choosing your presentation topics.

 

1.

Molecular Biology Primer

7

2.

Exhaustive Search

6

3.

Greedy Algorithms

3

4.

Dynamic Programming Algorithms

6

5.

Divide-and-Conquer Algorithms

3

6.

Graph Algorithms

6

7.

Clustering and Trees

6

8.

Randomized Algorithms

3

 

Total

40