CS 432 –
Computational Biology
Spring 2007, 10:00-10:50, MF, EPS
347
Instructor: Brendan Mumey
Email: mumey AT cs.montana.edu
Office hours: see www.cs.montana.edu/mumey/schedule.htm
Textbook: Jones and Pevzner, An Introduction to
Bioinformatics Algorithms (website)
Course Outline
We will follow a seminar
style approach examining classical and recent problems in computational
biology. We cover selected topics
from the textbook as well as other sources including recent papers from the field. Students will be expected to give some
lectures and lead discussions. A
schedule will be maintained on the course web page:
www.cs.montana.edu/courses/432
Grading Scheme
|
Class Participation |
10% |
|
Homework |
25% |
|
Lectures and discussion |
45% |
|
Quizzes |
20% |
Schedule
|
Date |
Topic |
Reading |
Leader |
HW |
|
19-Jan |
Intro |
Chapters 1-2 |
Brendan |
|
|
22-Jan |
Background on biology
and algorithms |
Chapter 3 |
Brendan |
|
|
26-Jan |
Motif finding |
4.4-4.9 |
Brendan |
|
|
29-Jan |
Restriction mapping
background |
4.1-4.3 |
Sean, Jared |
|
|
2-Feb |
Restriction mapping
algorithms |
|
Sean, Jared |
|
|
5-Feb |
Greedy and approx
algorithms |
Chapter 5 |
Ryan, William |
|
|
9-Feb |
Sorting by reversals, greedy
motif finding |
|
Ryan, William |
|
|
12-Feb |
Dynamic programming |
6.1-6.4 |
Marion, Richard |
|
|
16-Feb |
Sequence alignment |
6.5-6.8 |
Marion, Richard |
|
|
19-Feb |
President's
day |
|
|
|
|
21-Feb |
PERL basics |
|
Denbigh Starkey |
|
|
23-Feb |
class moved to Wed,
Feb 21 |
|
|
|
|
26-Feb |
PERL for
bioinformatics |
|
Denbigh Starkey |
|
|
2-Mar |
More sequence
alignment and gene prediction |
6.9-6.15 |
Mike, Jason |
|
|
5-Mar |
Divide and conquer |
7.1 |
Mike, Jason |
|
|
9-Mar |
Quiz |
|
Brendan |
|
|
12-Mar |
Spring
break |
|
|
|
|
16-Mar |
Spring
break |
|
|
|
|
19-Mar |
Graphs, dna seq. |
8.1-8.3 |
Sean, Jared |
|
|
23-Mar |
Shortest superstring |
8.4-8.5 |
Sean, Jared |
|
|
26-Mar |
SBH |
8.6-8.9 |
Ryan, William |
|
|
30-Mar |
Peptide sequencing |
8.10-8.11 |
Ryan, William |
|
|
2-Apr |
Mass spec cont. |
9.1-9.3 |
Ryan |
|
|
6-Apr |
University
day |
|
|
|
|
9-Apr |
class moved to Wed,
Apr 11 |
|
|
|
|
11-Apr |
Suffix trees |
9.4-9.5 |
Marion, Richard |
|
|
13-Apr |
BLAST, etc. |
9.6-9.8 |
Marion, Richard |
|
|
16-Apr |
Gene expression |
10.1-10.3 |
Mike, Jason |
|
|
20-Apr |
Quiz |
|
Mike, Jason |
|
|
23-Apr |
Cliques and evo. trees |
10.4-10.8 |
Sean, Jared |
|
|
27-Apr |
Parsimony, etc. |
10.9-10.11 |
William |
|
|
2-May |
HMMs overview |
Chapter 11 |
Mike, Jason |
|
|
4-May |
Randomized algs |
Chapter 12 |
Marion, Richard |
|