CS3225: Combinatorial methods in bioinformatics (Post-genome informatics)

2011/2012 Semester 2

Time: Monday (12:00pm to 2:00pm), COM2/108

Tutorial Time: Tuesday (5:00pm to 6:00pm), COM2/107

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

Instructor

Aim and Objective

Computational Biology is a fast changing area. In the post-genome era, many new bio-technologies appear and classical algorithms for computational biology are no longer enough. This module is intended to cover the important algorithms related to the new technologies like microarray, SNPs, mass spectrometry, etc.

After the complete sequencing of a number of genomes, we are in the stage to understand the mystery of our body, that is, we need to understand the information encoded in the genome and its relationship with RNA and protein. This aim of this module is to cover the algorithms related to this stage.

In the module, we will cover the algorithms related to phylogenetic, RNA, proteomics, population genetics, microarray, etc.

Prerequisites: Pass CS2220 (Introduction to Computational Biology) or its equivalence.

Main Text

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

Supplementary Readings

• Neil C. Jones and Pavel A. Pevzner, "An Introduction to Bioinformatics Algorithms", MIT Press, 2004.
• 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
  • Tutorial
  • Mid-term test
  • Project
• Final Assessment 40%
  • Examination

Syllabus (Tentative)