CSE 549 - Introduction to Computational Biology

Fall 2007
Course Time: 3:50-5:10PM Tuesday-Thursday
Place: E4315 Melville Library
Instructor: Steven Skiena

This is a course in algorithmic issues in biology, focusing current problems in genomics. Our emphasis will be algorithmic, on discovering appropriate combinatorial algorithm problems and the techniques to solve these problems. Primary topics will include DNA sequence assembly, DNA/protein sequence comparison, hybridization array analysis, RNA and protein folding, and phylogenic trees.

The prerequisites for this course will be a course in combinatorial algorithms (CSE 373/548 or equivalent) or a strong background in biology. I hope to get a mix of students from the computational and life sciences.

There is a symposium on Biomedical technology for a global age being held at Stony Brook on Wednesday September 26, 2007. Check out the program.

To study for the midterm I recommend you look at an old example midterm and the problems on the old Homeworks 1 and 2 given below.

Another course of interest being taught in Fall 2007 is AMS 535, "Introduction to Computational Structural Biology and Drug Design", taught by Robert Rizzo. He will be teaching a companion course (AMS-536, "Molecular Modeling of Biological Molecules") in Spring 2008. AMS-536 is designed for students who wish to gain hands-on experience modeling biological molecules at the atomic level. In conjunction with the participants' interest, Molecular Mechanics, molecular dynamics, Monte Carlo, Docking (virtual screening), or Quantum Mechanics software packages will be used. Projects will include setup, execution, and analysis. Students will work on individual projects outside of class.

Finally, another course of possible interest for Spring 2008 is AMS 691, Foundations of Algorithms and Numerical Methods in Computational Biology, taught by David Green. This class will survey many of the key techniques used in diverse aspects of computational biology. We will focus on how to successfully formulate a statement of the problem to be solved, and how that formulation can guide in selecting the most suitable computational approach. A set of problems from a diverse range of problems in biology will be used as examples.

The final exam will be held December 20, 2007 between 2PM-4:30PM.

Course Documents

Lecture Notes

The following lecture notes are provided in HTML and pdf, with audio:

Homework Assignments

Note: homework assignments will not be collected in Fall 2006. I do encourage all to review the assignments as preparation for the midterm and final.

Student Presentations

General Resources

Books

The textbook for this course will be:

The following books are recommended:

Additional books of possible interest are:

Related courses at other Universities

Join the Algorithm Reading Group (CSE 642) at Stony Brook!