Selected Topics in BioInformatics: CMPT 889

Spring  2004


Class picture 1

Class picture 2

Pub night


Cenk Sahinalp
10834 ASB
phone: x-5415

Space-time issues:

Class meeting times/location:
Tu  4:30-6:20,  AQ5016
Th  4:30-5:20,  AQ5016

Instructor's office hours/location:
Tu-Th , 3:30-4:30, 10834 ASB


This is an advanced level course on recent mathematical and computational  developments in computational molecular biology, computational genomics and proteomics.
The course is intended for graduate students in computer science, engineering, genetics, biochemistry and molecular biology who are aiming to
deepen their understanding of mathematical and algorithmic tools recently developed for problems in computational biology.

Suggested Books:

Bioinformatics, Sequence and Genome Analysis
David W. Mount
Cold Spring Harbor Lab, 2001

Algorithms on Strings, Trees and Sequences: Computer Science and Computational Biology
Dan Gusfield;
Cambridge University Press, 1997

Computational Molecular Biology: An Algorithmic Approach
Pavel Pevzner
MIT Press, 2000

Introduction to Computational Biology: Maps, Sequences and Genomes
Michael Waterman
Chapman &Hall / CRC, 1995

Biological Sequence Analysis
Durbin, Eddy, Krogh and Mitchison
Cambridge University Press, 1998


During the course of the semester the class will focus on a different research topic in genomics, proteomics and systems biology every week.
In each class, either the instructor or one of the students will give a one-hour power point presentation where the first half will provide some
background information based on text books and surveys and the second half will describe a novel approach based on one or more
research papers. Students are expected to attend all classes and should be prepared to give one or more presentations; the grades will be based on class
participation and the presentations. The students are expected to discuss with the instructor the topic and the timing of the presentation during the first two
weeks of the semester. The instructor will provide the papers as well as the background material

          Paper Lists:                                                                                                                                   Presentations: