CS 590B: Computational Molecular Biology, Fall 2003

Instructor Chris Bailey-Kellogg, CS 164D, 494-9025
Class time TR 1:30-2:45 in room REC 226
Office hours By appointment
Textbook No textbook is required. Appropriate materials will be listed on the schedule page, and will include the following:
  • My high-level lecture notes introducing the topics.
  • Primary papers from the literature, available electronically.
  • Selected chapters from computational biology texts, as well as introductory texts in molecular biology and biochemistry. These texts are available at the Life Science Library reserves in Lilly Hall.
  • Related resources on the web.
These should be sufficient for you to get the basics required for this class. If you're interested or confused, PubMed, Google, etc. can help you find additional resources. Please point out appropriate ones to me by email or on the course WebCT page.


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 sequences (what genes encode an organism, and how are genes related across organisms?), structures (what do the protein constructed for these genes look like, and what does that imply about their functions?), interactions (how are proteins helping and hindering each other in complex networks?), and the underlying experimental data. The computational techniques applied include all your favorites -- dynamic programming, graph search, hidden Markov models, clustering, optimization, simulation, ....

The schedule (subject to change) details the topics we'll cover. Note that there is a democratic component at the end of the semester, where I'll take suggestions for topics of interest, and you'll present your own projects.

Prereqs This course is targeted at CS graduate and advanced undergraduate students. A background in biology is not required, but students should be interested in catching up quickly on some basic molecular biology and biochemistry. Non-CS students with an interest in computational issues are invited as well; please speak with me about your background first. In general, I expect some background in design and implementation of algorithms, since the class will build on that without substantial review.
Coure requirements

The goals of this course include both broad exposure to some important algorithmic challenges in computational biology, as well as relatively deeper experience with a few example algorithms. The breadth will be achieved through lectures and associated readings (with incentive provided by some short homeworks); the depth will be achieved through three instructor-defined projects and one student-defined term project.

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

Assignments and grades will be handled electronically, through WebCT (590B page).

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

CS 590B CS 590B
Chris Bailey-Kellogg
Last modified: Mon Aug 25 17:10:28 EST 2003