CSE 549 - Introduction to Computational Biology
Course Time: 4-5:20PM Tuesday-Thursday
Place: W4535 Melville Library
Instructor: Steven Skiena
This is a course in algorithmic issues in biology, focusing
current problems in genomics.
Our emphasis will be algorithmic, on discovering appropriate
combinatorial algorithm problems and the techniques to solve these problems.
Primary topics will include DNA sequence assembly,
DNA/protein sequence comparison, hybridization array
analysis, RNA and protein folding, and phylogenic trees.
The prerequisites for this course will be a course in combinatorial
algorithms (CSE 373/548 or equivalent) or a strong background
I hope to get a mix of students from the computational and life sciences.
The course TA may be Rukhsana Yeasmin.
His office hours are Tuesday and Thursday: 2-3.30PM in room 350 Life Sciences.
Contact her by email at
by David Green
on computational protein design (9/5/12).
There will be a talk by Ralf Wanger, Founder of the synthetic biology
company GeneArt, Thursday 9/13 at 1:30PM 038 Life Sciences
For those interested in Project 1: check out the
informative webpage Michael Schatz produced on data and resources for
He will be available by Skype from my office on Thursday 11/15
at 1PM for those who want to
talk with him.
The CS 549 Final Exam will Be Monday 12/17 from 2:15-5:00 pm in Lt. Eng 102 (note the room change).
The class lab tour has been cancelled -- come to class as usual on
Tuesday, November 13th.
Homework 1: Assembly and Data Bases
The answer key is now available.
Homework 2: Sequence Comparison and Gene Prediction
Source code for a C language dynamic programming program for edit distance
computation is is available here.
The textbook for this course will be:
The following books are recommended:
Additional books of possible interest are:
Algorithms on Strings, Trees, and Sequences : Computer Science and Computational Biology,
Cambridge University Press, 1997.
Durbin, Eddy, Krogh, and Mitchison,
Biological Sequence Analysis : Probabilistic Models of Proteins and Nucleic Acids
Cambridge University Press, 1998.
Setabal and Meidanis
Introduction to Computational Biology
Claverie and Notredame,
Bioinfomatics for Dummies,
For Dummies Press, 2003.
Computational Molecular Biology: An Algorithmic Approach,
MIT Press, 2000.
Cambridge Univ. Press, 2003
Bioinformatics: Sequence and Genome Analysis,
Cold Spring Harbor Laboratory, 2001
Bishop and Rawlins
DNA and Protein Sequence Analysis : A Practical Approach
Oxford University Press, 1997.
Baxevanis and Ouellette,
Sankoff and Kruskal,
Time Warps, String Edits, and Macromolecules
CSLI Publications 1999 (reprint).
Watson, Gilman, Witkowski, and Zoller,
Scientific American Press, 1992.
The Algorithm Design Manual
Springer Verlag, 1998.
Related courses at other Universities
Algorithm Reading Group (CSE 642)
at Stony Brook!