TO:
FROM:
SUBJECT:
Committee on Undergraduate Affairs
Department of Biological Sciences
Proposal for New Course in Computational Biology
The Department of Biological Sciences requests that CUA review the following proposal for a
new course entitled Computational Genomics and Molecular Biology. The Department approved
the course at its faculty meeting on 12 February 2002.
1. Title of the Course: Computational Genomics and Molecular Biology.
2. Instructor: Dr. Dannie Durand
3. Target audience:
- Advanced undergraduates who have taken 03-510 and want to learn more about computational
molecular biology.
- First and second year graduate students from Biological Sciences. All computational biology
graduate students in our department should take this course. Graduate students doing
experimental theses with sufficient computational skills are also encouraged to participate, if
interested.
- First and second year graduate students from computer science, statistics, mathematical
sciences and engineering who are interested and/or who require the background for their
research. The course number should be such that CS graduate students can take this course as
one of their electives.
4. Prerequisites:
The prerequisite will be 03-510, Computational Biology, or permission of the instructor.
5. Number of units: 9 units
6. Course Number: 03-511 and 03-711
This course will be offered as both an upper level undergraduate course (03-511) and a
graduate level course (03-711). The differential in work-load will be in the form of reading and
project based work for the 700 level students that will not be required of the 500 level students.
7. Course Description:
The proposed course is intended to be a second course in computational molecular biology,
following 03-510. The first half of the proposed course will begin with a review of pairwise
sequence alignment and dynamic programming and then focus on problems in multiple sequence
alignment and phylogeny reconstruction. The material in the second half of the course will be
drawn from recent results computational genomics.
Multiple sequence alignment and phylogeny reconstruction will be covered in the proposed
course. This material will be eliminated from 03-510, allowing additional units on hidden
Markov models and gene finding to be added to 03-510.
In 03-510, which covers the algorithmic foundations of computational molecular biology,
students are exposed to computational biology software packages through practical training and
programming assignments. The proposed course will cover computational molecular biology
algorithms in depth and will focus on problems in genomics. Course work will include problem
sets and a final project that can be a programming project or a paper.
8. Course Outline:
- Pairwise sequence alignment - review.
- Multiple sequence alignment
- Phylogeny reconstruction
- Selected topics in computational functional genomics, such as:
- Gene finding in a genomic context
- Comparative genomics and genome rearrangements
- Whole genome sequence assembly
- Gene expression array analysis
- Protein-protein interactions
- Inferring gene function from genomic context.
- SNP's
9. Suggested Text:
Pavel Pevzner, Computational Molecular Biology, MIT press
With additional material from:
W. Ewens and G. Grant, Statistical Methods in Bioinformatics
Springer-Verlag NY
R. Durbin and S. Eddy and A. Krogh and G. Mitchison, Biological Sequence
Analysis: Probabilistic Models of Proteins and Nucleic Acids. Cambridge
University Press.
Articles from the primary literature.