CS 5263 Bioinformatics
11/19: HW4 is due on Wed, Dec 5th.
11/11: Final Project Description (update on due dates).
10/29: HW3 is due on Wednesday, Nov 14th.
9/27: HW2 is due on Wednesday, Oct 17th.
9/24: Slides on multiple sequence alignment and exact string matching posted
9/5: HW1 is due on Sept 24th.
8/28: Welcome to CS5263!
This course is a survey of algorithms and methods in bioinformatics and computational biology, approached from a computational viewpoint. Topics covered include: sequence comparison (dynamic programming), motif finding (combinatorial algorithms, stochastic heuristic search algorithms, suffix trees), next-generation sequencing (Burrows Wheeler transform), RNA secondary structure prediction (dynamic programming), microarray analysis (data mining), and gene network/pathway analysis (graph algorithms).
This course is primarily designed for graduate students in the Computer Science department. Although there are no formal prerequisites for the course, fundamental understanding of data structure, algorithms, excellent programming experience in at least one programming language, as well as some knowledge of probability 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 without background in Algorithms or Statistics should consult the instructor prior to taking the course.
Time and Location
We meet in room SB 3.02.07 . Lecturers are Monday and Wednesday, 8:30-9:45 PM.
Instructor: Dr. Jianhua Ruan
Office location: S.B. 4.01.48
Office hours: Tuesdays 1:00-2:00pm, or by appointment
Email: jruan 'at' cs 'dot' utsa 'dot' edu
Phone: (210) 458-6819
Teaching Assistant: Jessica Sherette
Office location: SB 1.04.02
Office hours: Mondays 7:00-8:15pm or by appointment
Email: jlsherette 'at' satx 'dot' rr 'dot' com
There is no textbook required for this course. Parts of the course are based on the text:
Number of weeks
|Introduction to molecular biology||
|Pairwise sequence alignment||
|Multiple sequence alignment||
|String matching algorithms and applications||
|Microarray data analysis||