Course Announcement - Spring 2007

Math 127: Mathematics for Computational Biology

Instructor: Bernd Sturmfels

Office hours: Wednesdays 9:00-11:00am and by appointment
Contact: bernd at math, 925 Evans, 642 4687

Time and Place: Tuesdays and Thursdays, 12:30-2:00pm, 70 Evans Hall

Prerequisites: Some basics of Discrete Mathematics, Statistics and Abstract Algebra. An interest in Molecular Biology is encouraged. A crucial prerequisite is willingness to work hard and to interact with other students, who have different backgrounds from your own. If you are unsure whether this course is suitable for you, please talk to the instructor. In the past, this course was taught by Lior Pachter.

Course text: Algebraic Statistics for Computational Biology,
edited by Lior Pachter and Bernd Sturmfels, Cambridge University Press, 2005.

Syllabus: This course offers an introduction to mathematical foundations which we believe are relevant for computational biology, in particular, for biological sequence analysis. The emphasis lies on algebraic statistics (e.g. hidden Markov models) and discrete algorithms (e.g. neighbor-joining for tree construction). We will have an occasional guest speaker discussing biological problems and applications.

Consultants: Jason Morton and Dustin Cartwright.

This class does not have a teaching assistent but the two experts listed above kindly agreed to act as ''consultants''.
Jason and Dustin will be available for your questions, and they will help by mentoring some of the course projects.
Extra office hours: One of Jason, Dustin or Anne Shiu will be available for your questions on
Mondays between 2:00pm and 3:00pm in 1015 Evans. Feel free to stay for tea afterwards.

Homework: There will be biweekly homework during the first half of the course. It is posted here in pdf format:
Homework 1 (due January 30) Here are some solutions provided by Shaowei Lin.
Homework 2 (due February 15) Here are some solutions provided by Shaowei Lin.
Homework 3 (due February 27) Here are some solutions provided by Shaowei Lin.
Homework 4 (due March 20) Here are some solutions provided by Shaowei Lin.

Course projects: In the middle of February, we shall form research teams, consisting of two or three students. By the middle of March, the homework will stop, so everyone can fully concentrate on their project. Here are specific dates and deadlines:
Thursday, February 8: Discussion about Projects
Thursday, February 22: Project Proposal is Due
Tuesday, April 3: Preliminary Report is Due
Tuesday, May 1: Final Paper is Due
All teams will be given the opportunity to present their findings in class.

Participants: The students in this class come from mathematics and from other departments (MCB, IB, Stat, EECS, etc....). This is a truly interdisciplinary opportunity. Participants will greatly benefit from working with each other.

Grading: The course grade will be based on both the homework and the course projects.
Your background will be taken into consideration when assigning the final grades.

Further Reading:
D. Gusfield: Algorithms on Strings, Trees, and Sequences, Cambridge University Press, 1997
R. Durbin, S. Eddy, A. Korgh and G. Mitchison: Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids, Cambridge University Press, 1998