CS 88/188: Introduction to Bioinformatics, Fall 2005

Computation is vital for modern molecular biology, helping scientists to model, predict the behaviors of, and control the molecular machinery of the cell. This course will study algorithmic challenges in analyzing biomolecular sequences (what genes encode an organism, and how are genes related across organisms?), structures (what do the proteins constructed for these genes look like, and what does that tell us about their mechanisms?), and functions (what do these things do, and how do they interact with each other in doing it?). The course is application-driven, but focused on the underlying algorithms and information processing techniques, employing approaches from search, optimization, pattern recognition, and so forth.

Here's a fun little flyer for CS types.

This is an introductory course targeted at advanced undergraduate and beginning graduate students in computer science. A background in biology is not required, but students should be interested in catching up quickly on some basic molecular biology and biochemistry. Bruce Donald's Topics in Computational Molecular Biology is a natural successor for those who would like additional depth in the applications and algorithms.

While the course is structured from an algorithmic perspective, I very much welcome and encourage the participation of students from the life sciences, statistics, and other related disciplines. Naturally, a basic understanding of and interest in computational issues is expected. Please contact me to discuss your background and interests.

The course seeks to provide broad exposure to some important algorithmic challenges and approaches in bioinformatics. The lectures and readings will provide a fairly general (for a ten-week course) survey of the field. Since one of the best ways to learn something is by doing it, a series of labs will offer the opportunity to implement and apply some of the algorithms. Each lab will be introduced in conjunction with the relevant lecture, and a portion of the class time will be devoted to getting started on the lab. After each pair of labs on related topics (sequence, structure, and function), a class will be devoted to student presentations and discussion about the labs.

All students are expect to read, understand, and follow the course policies.

The course schedule lists due dates, topics, and readings.