This course offers an introduction to
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.
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.
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.
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.
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