BNFO 602: Foundations of bioinformatics II
Spring 2008

Instructor:
Usman Roshan, GITC 3802
Ph: 973-596-2872
Office hours: Wed 3-5:30
Email: usman@cs.njit.edu

Grading: Course project. This will be a short programming project and a class presentation of the results. The project must be approved by the instructor in advance. The deadline for project approval is Feb 13th. You must have an approved project by this date in order to get a grade for this class. The project can be an implementation of a newly published algorithm or experimental study of new and existing software.

Recommended texts:

• Introduction to Bioinformatics by Arthur Lesk
• Biological Sequence Analysis by Durbin et. al.
• Algorithms on strings, trees, and sequences: computer science and computational biology by Dan Gusfield
• Introduction to computational molecular biology by Setubal and Medianis

Course plan:
   

Topic	Date	Lectures
Phylogenetics: introduction, distance-based methods (UPGMA and NJ)	01/23/08	Lecture 1
Phylogenetics: evolutionary models	01/30/08	Lecture 2
Phylogenetics: ML; Alignment	02/06/08	Lecture 3(a) Lecture 3(b)
Project proposal presentations	02/13/08
Phylogenetics: ML; Alignment	02/06/08	Lecture 3(a) Lecture 3(b)