CIS 4930 / CIS 6930: Recent Advances in Bioinformatics

Instructor:	Tamer Kahveci
Email:
Section:	0936 / 7613
Location:	Tuesday CSE 220 / Thursday CSE 221
Time:	Tuesday 7th period (1:55-2:45pm) / Thursday 7-8th periods (1:55-3:50pm)
Office hour:	Tuesday 8th period / Thursday 9th period
Contact:	E436 (office), 505-1554 (office phone)

Goals:

This course will discuss the cutting edge developments in bioinformatics and computational biology. The course also aims to provide exposure to existing bioinformatics software and databases. In this class, we will discuss recent publications on computational biology and bioinformatics with emphasis on computer science challenges and contributions. Each student will be responsible from presenting one or more such papers in class and joining discussions on papers presented by the other people in class. Also each student will do a class project that has the largest impact on the final grade.

Announcements:

You can reach the class projects and details on project reports from here. The projects are listed in the order at which you will present them. (04/11/2011)
Details on project proposals are here. You can find sample project pages containing proposals from my Bioinformatics class in Fall 2010 here. (02/24/2011)
First homework is to review A 13 in our reading list. Use the review form here. Due date is February 10, 2011 in class hour. Bring a hard copy and upload soft copy in Sakai. (02/03/2011)
The introductory slides I used in the class are here. (01/25/2011)
First quiz on January 27 - at the first half of the first lecture. Quiz will include the topics we covered on interaction networks until (including) January 25. (01/20/2011)
Paper presentation schedule is here. (01/20/2011)
The class location has changed. New locations are Tuesday CSE 220 / Thursday CSE 221. (01/18/2011)
Reading assignment one: Papers 1 and 2 in "Group All" here. (01/06/2011)
No class on January 6th, 2011. Dr. Kahveci will be away on that day. (01/04/2011)
You can find the course slides for my bioinformatics class here. (01/03/2011)
A brief reading list is here. I will update the list throughout the semester.
You can find course syllabus here.
Check the announcements regularly

Prerequisites

Algorithms and Data Structures are required. Bioinformatics (CAP 5510) is strongly recommended (not required). I will assume that the students already have basic knowledge on these topics and are comfortable with basic computer programming (e.g., with C or Java).

Topics:

This course will cover the most recent developments in a broad range of bioinformatics problems. I would like to put more focus on analysis of pathways. The topics are as follows:

Comparison of biological networks
Network motifs
Essentiality in networks
Network reconstruction

Grading:

(Subject to minor changes till the first day of the semester) Grading will be based on project (50 %), presentations (15 %), homeworks and quizzes (35 %). Class participation and novelty in projects will be rewarded by bonus (5 % each). Late returns will cause deduction of 20 % of the points for each late day.

Text book:

There is no text book for this class since we will use papers as our main source.

Other:

Check out disability resources.
Cheating, plagiarism, and other types of academic dishonesty will be subject to punishment.
I encourage class attendence.
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.

Tamer Kahveci