Introduction to
Bioinformatics
ISSP 2080
Spring 2000
Fact Sheet for Students
This
course is designed to provide an understanding of some important topics in
bioinformatics by identifying the problems in this field and commonly used
computational techniques. Students will be able to learn to access and use
databases containing biological data such as DNA/protein sequences and protein
structures. The course is intended to be flexible and adaptable to students’
needs. Prerequisites are undergraduate biology and math.
Vanathi
Gopalakrishnan, Ph.D. (Computer Science)
106
A Mineral Industries Building
Office
Hours: Wednesdays
2-3 pm
205
Mineral Industries Building
Office
Hours: By
appointment only.
The
course meets on Wednesdays from 10:00 am to 1:00 pm in 8084 Forbes Tower
conference room. The syllabus can be found below.
Students
are expected to complete the assigned readings before each class and required
to submit summaries for those indicated in class.
This
course will be graded on a standard letter grade basis, unless a student
specifically requests an S/N grade. Requests for an S/N grade must be made in
writing or email to Dr. Gopalakrishnan on or before March 15.
Most
of the learning in this course will be from the readings and class discussions.
Class attendance and participation is therefore expected. Attendance at 80% or
more of scheduled sessions and active contributions to class discussion
constitute satisfactory participation.
There
will be 2-3 homework exercises associated with accessing and searching sequence
and structure databases. These will be distributed in class along with the date
due.
Summaries
of assigned readings will be required at the beginning of several classes.
These should be brief and indicate main points of each paper. The exact
readings for which these are required will be specified one week ahead of time.
Students
are required to write individual papers in the form of a research proposal or
review paper. The paper could be a thorough review of a topic that is not
covered in much detail in class, or a research paper containing
well-thought-out ideas for enhancing state-of-the-art computation techniques
used in bioinformatics. This final paper (5-10 pages) is due on April 26.
Introduction to Bioinformatics
Spring 2000 Lecture Schedule
Date |
Topic |
Lecturer(s) |
Readings |
Notes |
|
January 5 |
Class
Survey, Challenges
and Computational Methods |
Vanathi |
Ch.
1, 2 Salzberg |
|
|
January 12 |
Introduction to Biology |
Paul |
Ch.
1, Hunter book |
|
|
January 19 |
Pairwise
Sequence Alignment I: |
Vanathi |
Smith,Waterman BLAST |
|
|
January
26 |
Pairwise
Sequence Alignment II: |
Vanathi |
FASTA, Comparison
of methods |
HW#1 out |
|
February 2 |
Multiple Sequence Alignment |
Paul |
|
Summaries #1 due |
|
February 9 |
Databases,
whole Genome |
Paul |
|
|
|
February 16 |
Gene prediction in DNA sequences |
Paul |
|
|
|
February 23 |
DNA Array Technology |
Paul |
|
|
|
March 1 |
Protein Structure
Prediction: Secondary Structure Prediction, Threading |
Vanathi Bruce Buchanan |
|
|
|
March 8 |
SPRING BREAK |
|
|
|
|
March 15 |
Protein
Structure Determination: Protein Folding + PDB |
|
|
|
|
March 22 |
Molecular Dynamics |
Vanathi
John Rosenberg |
|
|
|
March 29 |
Phylogenetic Trees |
Vanathi |
|
Due |
|
April 5 |
Structure-Function CATH database |
Vanathi
Ethan Benatan |
|
|
|
April 12 |
Linkage Analysis |
Vanathi William Forrest |
|
|
|
April 19 |
Tissueinformatics |
Guest Lecture from industry (Mary Del Brady) |
|
|
|
April 26 |
FINAL PAPERS DUE |
|
|
|