CAP 5510 (Bioinformatics)

Instructor:	Tamer Kahveci
Email:
Location:	CSE E122
Time:	Monday/Wednesday/Friday 8th period (3:00 - 3:50 PM)
Section:	4187
Office hour:	Monday/Wednesday 2:00-2:50 PM
Contact:	E436 (office), 392-6849 (office phone)
TA:	Gunhan Gulsoy (ggulsoy @ cise) Office: Tue/Thu, 11am-noon, Rm 309

Goals:

This course will discuss the major components of bioinformatics data (such as DNA and protein sequences and protein structures) and how computer technology is used to understand this data better.

Announcements:

Homework 4 is ready. (11/06/09)
You can view class projects. (10/19/09)
Homework 3 is ready. (09/30/09)
Project milestone description is ready. (09/23/09)
Homework 2 is ready. (09/04/09)
Please sign up to course tool in order to be able to view your grade quickly. You will also use this link to submit some of your homeworks in the future. (09/04/09)
Details on project reports are ready. (08/24/09)
Details on surveys are ready. (08/24/09)
You can find course slides here. (08/24/09)
Homework 1 is ready. (08/24/09)
Check the class page regularly for announcements (08/07/09)

Prerequisites:

I will assume that you have already taken data structures and algorithms courses and you are comfortable with basic computer programming (e.g., with C or Java).

Topics:

I am planning to cover the following topics.

Biological sequences
Lossless alignments (different DP problems such as global, local alignment, etc,)
Lossy alignments (BLAST, etc)
Substitution matrices, statistics
Multiple alignment
Shotgun sequencing
Phylogeny
Protein structures and function (primary, secondary, etc.)
Structure alignment
Structure prediction
Pathways

Grading:

Grading will be based on homeworks (35 %), project (50 %), and survey (15 %). I will reward high quality projects with up to 2.5 % bonus points. You should expect both programming and paper/pen type of homeworks.

Text book:

I will teach this course from multiple books and some research papers. Therefore, I do not require any textbook. The primary book I will stick to is:

Fundamental Concepts of Bioinformatics by Dan E. Krane, Michael L. Raymer. (ISBN: 0805346333)

For interested students, I recommend the following books as further resources.

Bioinformatics: Sequence and Genome Analysis by David W. Mount. (ISBN: 0879696087)
Algorithms on Strings, Trees, and Sequences: Computer Science and Computational Biology by Dan Gusfield. (ISBN: 0521585198)
Introduction to Protein Structure by Carl-Ivar Branden, John Tooze.(ISBN: 0815323050)

Other:

Check out disability resources.
Cheating, plagiarism, and other types of academic dishonesty will be subject to punishment.
I encourage class attendence.
Please return your homeworks, project and surveys in time. Late returns will cause 20 % deduction in your grade for that homework (etc) for each late day.
Please visit only during office hours. If you really need to meet me out of the office hours email me to make an appointment. If I postpone or cancel the office hour, I will post it in the announcements section and (try to) put a note on my office door.
Please avoid any activities that will disturb the flow of the lectures: Silence your cell phones, pagers, etc.

Tamer Kahveci