CISC 889 Bioinformatics (Spring 2004)

Time and Place

Lectures: Tuesday and Thursday 5:00- 6:15PM; Gore Hall 308

Web page: http://www.cis.udel.edu/~lliao/cis889s04

Course Description

This course will cover both the core topics and the latest development in bioinformatics. The goal is to gain a solid understanding of the concepts, methodologies, and tools in bioinformatics, and to master the essential skills in converting biological problems into computational problems and in developing algorithmic solutions for them.

 

The core topics include:

  • protein homology detection,
  • sequence signature (such as motifs and membrane domains) identification,
  • phylogenetic analysis,
  • sequence structure prediction.

The latest developments include:

  • gene expression,
  • genetic networks,
  • metabolic pathway networks, and
  • proteomics.

The major methods and techniques include:

  • dynamic programming,
  • sequence alignment,
  • hidden Markov models,
  • support vector machines,
  • stochastic grammars, and
  • Bayesian networks.

Prerequisites

No previous biology background is required. AI (CISC 481/681) and Machine Learning (CISC 889) are generally helpful, but not required as prerequisite. What are assumed are the comfort with a major programming  language (e.g., C/C++, Java, …), certain maturity in math,  and some basic knowledge of probability and statistics.

Required Textbook

Biological Sequence Analysis by R. Durbin, S. Eddy, A. Krogh and G. Mitchison, (Cambridge University Press, 1998) is

the only required book for the course.

A few other books are also useful:

  • Bioinformatics: The Machine Learning Approach. by PierreBaldi (MIT Press)
  • Bioinformatics: Sequence and Genome Analysis by David W. Mount
  • Introduction to Computational Molecular Biology by Setubal and Meidanis
  • Statistical Methods in Bioinformatics: An Introduction by Gregory R. Grant, Warren J. Ewens

There are plenty of materials about bioinformatics on-line, including

  • International Society for Computational Biology (www.iscb.org)
  • Dr. Decker's course (http://www.cis.udel.edu/~decker/courses/889d-bio)

Assignments and Grading

  • Homeworks 40% and quizzes 15%, and term project and final presentation 45%.
  • While any major programming language is allowed for the programming tasks in this course, you are strongly encouraged to learn and use PERL.
  • Late assignments will be penalized 15% per class meeting, and will not be accepted more than three class meetings late.

Policy on Academic Dishonesty

The homework assignments in this class should be performed individually. You are permitted to discuss with other students on any conceptual problems, but the work handed in must be entirely your own. For the project assignments, if it is a team work, each team member's contribution should be clearly stated in the project report. Any evidence of academic dishonesty will be handled as stated in the Official Student Handbook of the University of Delaware. If you are in doubt regarding the requirements, please consult with me before you complete any requirement of this course.

Course Staff and Contact

Staff

Name

Office

Email

Phone

Office Hours

Instructor

Li Liao

Rm 204, 77 E. Delaware Ave.

lliao@cis.udel.edu

831-3500

Tuesdays and Thursdays 1:30-3:00PM, or by appointment