ELEC5810  Introduction to Bioinformatics Algorithms

 

                                           Time:        Tuesday 6:00PM-8:50PM, Spring 2012

                                           Venue:      Room 3408

                                           Instructor: Weichuan Yu (eeyu AT ust DOT HK)

                                          

 

 

This is an introductory course on bioinformatics.  It will cover basic biological knowledge, common biological data acquisition techniques, popular data analysis algorithms and their applications. The major content of this course is computation-oriented.  

 

This course is designed for graduate students and senior undergraduate students who are interested in the emerging area of bioinformatics and computational biology. Basic knowledge in applied mathematics, probability, algorithms and programming is required. Knowledge in biology is a plus but not a must.

 

The course consists of lectures, homework,  mid-term exam, and a final project.  Grade is based on homework (20%), mid-term exam (20%),  and final project (60%, including the course presentation).  The final project is a literature review study in which each student focuses on one specific bioinformatics problem. He/she will complete a comprehensive literature survey with his/her own comments on pros and cons of the methods and/or suggestions on how to improve the existing methods. The project consists of a written report (20-25 pages) and a class presentation (25-30 minutes duration). Topic of the project will be assigned or chosen by himself/herself (with the instructor’s approval).

 

A tentative schedule is described as follows. More materials (lecture notes, homework assignment, etc.) can be found at http://lmes2.ust.hk/portal/:

 

Week 1           Fundamentals of Molecular Biology

Week 2           Genome Sequencing I

Week 3           Genome Sequencing II

Week 4           Sequence Analysis I

Week 5           Sequence Analysis II

Week 6           Sequence Analysis III

Week 7           Genome-Wide SNP Data Analysis I

Week 8           Genome-Wide SNP Data Analysis II

Week 9           Midterm

Week 10         Proteomics I

Week 11         Proteomics II

Week 12         Proteomics III

Week 13         Course presentation

Week 14         Course presentation / Final review

 

Textbook
An Introduction to Bioinformatics Algorithms.
Neil C. Jones and Pavel A. Pevzner, The MIT Press, 2004.

 

References
1. Algorithms on Strings, Trees, and Sequences.
   Dan Gusfield.  Cambridge University Press, 1997
2. Bioinformatics: Genes, Proteins and Computers
   C.A. Orengo, D.T. Jones & J.M. Thornton, BIOS Scientific Publishers, 2003
3. Bioinformatics Basics: Applications in Biological Sciences and Medicine
   H. H. Rashidi and L. K. Buehler, CRC Press, 2000
4. Introduction to Proteomics: Tools for the New Biology
   Daniel C. Liebler, Humana Press, 2002
5. L. Hunter, Artificial Intelligence and Molecular Biology
   http://www.aaai.org/AITopics/pmwiki/pmwiki.php/AITopics/ArtificialIntelligenceAndMolecularBiology