CS5238: Advanced Combinatorial methods in bioinformatics

2012/2013 Semester 1

Time: Thursday (6:30 to 8:30pm), COM1-0208

Click here to visit the IVLE course webpage (that is the main page).

Instructor

Aim and Objective

Biology data are too enormous. Handling them using brute-force approaches becomes impossible and efficient algorithms are required. This module has an in-depth study of some of these advance algorithms. Through the course, students not only are able to understand these algorithms in detail, but are also given chances to solve some research problems in this field.

Prerequisites: Pass CS3230 (Design and Analysis of Algorithms) or its equivalence. Note that students are expected to have good understanding in the analysis of algorithm (e.g. Recursion, Dynamic Programming, time complexity analysis, etc). From the past experience, students without good knowledge in algorithm cannot catch up with the pace of the module.

Main Text

• Wing-Kin Sung, "Algorithms in Bioinformatics: A Practical Introduction", CRC Press, 2009.

Supplementary Readings

• Pavel A. Pevner, "Computational Molecular Biology: An Algorithmic Approach", MIT Press, 2000.
• Joao Setubal and Joao Meidanis, "Introduction to Computation Molecular Biology", PWS Publishing Company, 1997.
• Dan Gusfield, "Algorithms on Strings, Trees, and Sequences - Computer Science and Computational Biology", Cambridge University Press, 1997.

Assessment

• Continuous Assessment 60%
  • Assignment
  • Mid-term test
  • Project
• Final Assessment 40%
  • Examination

Syllabus (Tentative)

For powerpoint slides, please get them from IVLE website.