This course is intended for 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 a programming language (such as C, C++ or Java), and a scripting language (such as perl, ruby, or python) will be a great asset in the project component of the course. Mathematics/Statistics, Biology, and Life Sciences students are also welcome and should discuss their background with the instructor in the first couple weeks of the 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
Class Participation 10 %
Paper Reviews 20 %
Presentation(s) 20 %
Project 50 %

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 and paper reviews will be individually and graded on an individual basis. Projects will be done groups of 2 or 3 students and one combined grade will be awarded to each project. All students in a group will receive the same project grade.

Late and Makeup Policy

Paper Reviews: Paper reviews are due in class on the day of the paper presentation. In the case were you are unable to attend class, please send the paper review via email one hour prior to class. No late reviews will be accepted.

Projects: Project specifics will be posted on the website and be discussed in class. Always check the website for due dates. Late projects submitted within 48 hours of the time required will receive a 10% late penalty. No projects will be allowed to be submitted after 48 hours past the due date and willreceive an automatic zero.

Important Dates

Project ProposalFriday, September 24th
Project Proposal Presentations Friday, November 5th
Final Project Due Date Monday, December 13th, 7:00 to 9:00 AM
Final Project Presentations Monday, December 13th, 7:00 to 9:00 AM

Paper Reviews

Each student must submit a review (a half a page to a full page in length), which addresses the following the three questions:

  • What are the main point(s) of the paper? Briefly summarize all the main points.
  • How could the paper be criticized? Please explain at least one criticism of the work.
  • How could the paper be extended? Give at least one follow-up research project.
These reports must be completely individually. Each will be marked out of 5. Bonus marks will be given for insightful and scientifically-creative answers.

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.