Spring 2008

3/17 – The fourth assignment is now posted on CMS. It is due either in class or through CMS by 1:25pm on 4/3/08.

2/29 – The third assignment is now posted on CMS. It is due either in class or through CMS by 1:25pm on 3/13/08.

2/14 – The second assignment is now posted on CMS. It is due either in class or through CMS by 1:25pm on 2/29/08.

1/31 – The first assignment is now posted on CMS. It is due either in class or through CMS by 1:25pm on 2/14/08.

1/21 – Lecture notes, homework assignments and other material will be available through CMS. To log in you need your netID. Please email me your netID if you do not see the course listed among your courses or if you can't log into the system.

**Instructor:**Uri Keich, 4159 Upson Hall, 5-7017 <keich@cs> (Office hour: Tuesdays 3-4pm, or by email appointment)

**Administrative assistant:**Cindy Robinson, 4146 Upson Hall, 5-0985, <cindy@cs>

Genomes / T.A. Brown

An introduction to bioinformatics algorithms / Neil C. Jones, Pavel A. Pevzner

Biological sequence analysis : probabilistic models of proteins and nucleic acids / Richard Durbin et al.

Statistical methods in bioinformatics : an introduction / Warren Ewens, Gregory Grant.

A draft syllabus is available here. Deviations are expected but it does give the big picture.

Nothing written in stone, but the following concepts will be used with minimal or no explanations: trees, algorithms, complexity, basic probability (terms such as: distribution and density functions, binomial random variable, expectation). You should also be able to program at least in a scriptable language such as Matlab or Perl.

There will be a final on Friday, May 16 2:00 - 4:30 pm in Hollister 372.

There will be biweekly homework sets, generally due on Tuesdays. Homework should be handed in class just before it starts on the day it is due.

Late submissions will not receive credit. (If a **genuine**
emergency situation prevents you from handing in an assignment on
time, come talk to me and we can work something out.)

You are allowed to collaborate on the homework to the extent of formulating ideas as a group. However, you must write up the solutions to each problem set completely on your own. You must also list the names of everyone that you discussed the problem set with.

The overall course grade course grade will be the arithmetic mean of your final grade and your average normalized homework score.

You are expected to maintain the utmost level of academic integrity in the course. Any violation of the code of academic integrity will be penalized severely.

You are allowed to collaborate on the homework to the extent of formulating ideas as a group. However, you must write up the solutions to each problem set completely on your own. You must also list the names of everyone that you discussed the problem set with.