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).


Lecturer: Sung Wing Kin, Ken
Email: ksung@comp.nus.edu.sg
Consultation hours: Thursday (5:00 to 6:30pm)
Office: COM2 #02-06

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

Supplementary Readings


Syllabus (Tentative)

Week No. Date Topics Remark
116 Aug 2012 Basics of Molecular Biology
223 Aug 2012 Suffix Tree (1)
330 Aug 2012 No class
46 Sept 2012 Suffix tree (2)
513 Sept 2012 Genome Assembly (1)
620 Sept 2012 Genome Assembly (2)
27 Sept 2012 Short Tag mapping Recess week
74 Oct 2012 Structural variation + Midterm
811 Oct 2012 ChIP-seq analysis
918 Oct 2012 Motif finding (1)
1025 Oct 2012 Motif finding (2)
111 Nov 2012 RNA secondary structure prediction
128 Nov 2012 RNA secondary structure comparison
1315 Nov 2012 Project Presentation
22 Nov 2012 Reading period
4 Dec 2012 Examination

For powerpoint slides, please get them from IVLE website.

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