Computer
Science 458/558
Introduction
to Bioinformatics
3 credits
Instructor:
Office:
SS 412
Phone:
243-5605
Office
Hours:Tues./ Thurs. 10:30am-noon or by appointment
Email:
cwyoo@cs.umt.edu
Description:
This course will introduce and use biological data
sources available in the post human
genome project era. Topics will include basic algorithms for alignment of
genome sequences and prediction of protein structures, as well as more advanced
representational and algorithmic issues in protein structure, genome sequence
computation, and systems biology. Also this course
will discuss of state of the art bioinformatics projects that are being
developed between the department of computer science and the school of pharmacy
and allied sciences.
Format: Two classes per week.
Offered: Fall semester 2007
Prerequisites: Consent of Instructor
Materials: Articles
and a text book:
Bioinformatics:
Sequence and Genome Analysis by David W. Mount
Publisher: Cold Spring Harbor Laboratory; 2nd edition (July, 2004)
ISBN: 0879696877
Assessment of Student
Performance:
CS458: Attendance (20%) /
Homework (40%) / Small Projects (40%)
CS558: Attendance (15%) /
Homework + Small Projects (40%) / Class Project + Presentations (45%)
Meetings (2007): Tues/Thurs 3:40pm-5:00pm
(GBB 201)
Plagiarism on homework assignments, cheating on
tests, use of inappropriate language (oral or written), or misuse of the
computer facilities will not be tolerated.
Offenders will be prosecuted to the fullest extent of the University
Student Conduct Rules.
Tentative
Schedule
|
Date |
Topic |
Required |
|
|
Aug 28 |
Introduction to
Bioinformatics and Computational Genomics / Course Overview |
|
|
|
Aug 30 |
Introduction to
Bioinformatics and Computational Genomics (cont.) |
|
|
|
Sep 4 |
Dynamic
Programming Sequence Alignment |
|
|
|
Sep 6 |
Intro to Microarrays |
|
|
|
Sep 11 |
Microarray
Clustering and Classification |
|
|
|
Sep 13 |
Microarray
Clustering and Classification (cont.) |
|
|
|
Sep 18 |
Protein structure
prediction |
|
|
|
3D
structure computations, NMR, Xtallography |
|||
|
Sep 20 |
Protein structure
prediction (cont.) |
|
|
|
Sep 25 |
Phylogenetic
algorithms |
|
|
|
Sep 27 |
1D Motifs,
Algorithms and Databases |
|
|
|
Oct 2 |
RNA secondary structure |
|
|
|
Oct 4 |
Multiple Sequence
Alignment |
|
|
|
Oct 9 |
Multiple Sequence
Alignment (cont.) |
|
|
|
Oct 11 |
Genetic
networks |
KEGG database of genes and gene
pathways/networks/nEcoCYC database of metabolic
pathways in E. Coli |
|
|
3D
structure computations, NMR, Xtallography |
|||
|
Oct 16 |
Comparative
genomics algorithms, Genome Alignment |
|
|
|
Oct 18 |
Comparative
genomics algorithms, Genome Alignment (cont.) |
|
|
|
Oct 23 |
Project Proposal
Presentation (CS558) |
|
|
|
Oct 25 |
|
|
|
|
Probability and
Statistical Analysis |
Project Proposal DUE |
||
|
Oct 30 |
Hidden Markov
models |
|
|
|
Nov 1 |
Perl
Bioinformatics Modules |
Chapter 12 |
|
|
Nov 6 |
Proteomics, 3D
motifs |
|
|
|
Nov 8 |
3D structure
alignment |
|
|
|
Nov 13 |
Natural Language
Processing |
||
|
Nov 15 |
Microarray
Clustering and Classification (cont.) |
|
|
|
Nov 20 |
Thanksgiving break |
|
|
|
Nov 22 |
|
|
|
|
Nov 27 |
Genetic
networks (cont.) |
Pacific Symposium on
Biocomputing, session on Gene Networks 1998 |
|
|
Pacific Symposium on
Biocomputing, session on Gene Networks 1999 |
|||
|
Pacific Symposium on
Biocomputing, session on Gene Networks 2000 |
|||
|
Nov 29 |
Recent
Bioinformatics Research |
Asbestos Modeling |
|
|
Systems Biology |
|||
|
Dec 4 |
Recent
Bioinformatics Research and Final Thoughts |
Asbestos Modeling |
|
|
Systems Biology |
|||
|
Dec 6 |
No Class |
|
|
|
Dec 8 |
Final Project
Presentation |
|
|
|
Dec 13 |
Final Project
Presentation |
Final project documentation DUE |
|