This course is intended for computer science graduate students that are interested in Bioinformatics and Computational Biology. In order to understand the material in this course, you should have a good working knowledge of basic algorithms, discrete structures, and probability. Knowledge of algorithms, data structures (such as hash functions), unix, and C++ or Java is required for this course.


A number of current bioinformatics research papers will be assigned for reading throughout the course. And although there is no formal textbook for the course, however, the following text is suggested for background reading: Neil C. Jones and Pavel A. Pevzner. An introduction to bioinformatics algorithms. MIT Press, 2004.


Here are the formally graded elements of the course and associated weighting:

Activity Weight
Paper Summaries and Class Participation 10 %
Presentation 30 %
Project pre-proposal 10 %
Project proposal 10 %
Final Project 40 %

Semester grades are determined by the weighted sum of points earned in each of these areas. A subjective curve (set by the instructor) is used to map points onto grades. Typically, the curve is set such that the class mean gets an B, one standard deviation above the mean is an A, one deviation below is a C, and so forth. However, the instructor retains the right to move the curve either direction. If the entire class is strong, the mean might be better than a B. Conversely, if the class as a whole is weak, the mean might be below a B...

Presentations will be completed individually and graded on an individual basis.

Late and Makeup Policy

Projects: Always check the website for due dates. The dates below are subject to change. Project proposal, related work and final projects are not allowed to be submitted after the due date and will receive an automatic zero.

Important Dates

Project Pre-proposalTuesday, September 22nd, 2015
Project ProposalTuesday, October 27th, 2015
Final ProjectTuesday, December 15th, 2015

In Class Participation

All students taking this course are expected to participate actively. For all students, this includes asking and responding to questions.

Professional Conduct

All students are expected to conduct themselves professionally. We (the instructors, fellow students, and course personel) assume you are familiar with the policies in the student information sheet for the department. Additionally, you are computing professionals, albeit perhaps just starting. You should be familiar with the code of conduct for the primary professional society, ACM. You can read the ACM Code of Conduct HERE.

We work to maintain an environment supportive of learning in the classroom and laboratory. Towards that end, we require that you be courteous to and respectful of your fellow participants (i.e., classmates, instructors, GTAs and any tutors). In particular:

  • Please turn off the ring on your cell phone. If you are expecting an emergency call, sit near the door and slide out discretely to take it.
  • In class use of electronic devices in general, and laptops specifically, is permitted as a courtesy so that you may better participate and learn. If at any time the instructor judges that an electronic device is becoming a distraction the student may be asked to to turn it off and put it away.