CS 5263 Bioinformatics
News and Announcements
11/26 Homework 3 and data files online
11/8 Possible topics for a term paper
10/20 Homework 2 and data files online
10/9 Project 1 material online
9/4: Homework 1 and data files online
9/4:Reading material added
8/28: The Jones & Pevzner book is available online through UTSA library. (You can access it from on campus, or have VPN installed at home).
Overview
This course is a survey of algorithms and methods in bioinformatics and computational biology, approached from a computational viewpoint. Topics covered include: sequence alignment (dynamic programming, heuristic search), motif finding (greedy algorithms, randomized algorithms), pattern matching (suffix trees), gene prediction (Hidden Markov Models), RNA structure prediction (stochastic context free grammar), microarray analysis (statistics, data mining), and gene network/pathway analysis (graph algorithms).
Prerequisite
This course is primarily designed for graduate students and advanced undergraduate in the Computer Science department. Although there are no formal prerequisites for the course, fundamental understanding of data structure, algorithms, programming experience in C/C++/Java as well as some knowledge of mathematics and statistics are expected. Some prior exposure to molecular biology is preferred, but not required, as we will introduce basic biological concepts and terms along the way. Students that are from other background but are comfortable with programming and algorithms are also welcomed. Talk to me if you are not sure.
Goals
The goal is to provide you with all the theoretical background you need to understand the methods used in computational biology and the difficulties surrounding them. Your part is to work hard and learn a lot.
Time and Location: We meet in room BB 3.03.14. Lecturers are Tuesday and Thursday, 8:30-9:45 PM.
Instructor:
Dr. Jianhua Ruan
Office location: S.B. 4.01.48
Office hours: Tuesday 6:30-7:30pm, Wednesday 3:00-4:00pm, or by appointment
Email:
jruan@cs.utsa.edu
Phone: (210) 458-6819