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

2013/2014 Semester 2

Time: Wednesday (2:00pm to 4:00pm), SR@LT19

Tutorial Time: Friday (1:00pm to 2:00pm), COM2/#02-09

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


Instructor

Lecturer: Sung Wing Kin, Ken
Email: ksung@comp.nus.edu.sg
Consultation hours: Wednesday (4:00pm to 6:00pm)

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

Supplementary Readings

For more reading materials, please click this.

Assessment

Syllabus (Tentative)

Week No. Date Topics Readings
115 Jan 2014 Basic of Molecular Biology and Biotechnology Chapter 1 of the main text
222 Jan 2014 Phylogenetic comparsion and consensus tree Chapter 8 of the main text
329 Jan 2014 Phylogenetic comparsion and consensus tree Chapter 8 of the main text, Consensus Tree (SODA2013) Majority-rule consensus tree (RECOMB2013)
45 Feb 2014 Whole genome alignment Chapter 4 of the main text, MSS
512 Feb 2014 Genome rearrangement (unsigned reversal distance) Chapter 9 of the main text
619 Feb 2014 Genome rearrangement (signed reversal distance) Chapter 9 of the main text
26 Feb 2014 Recess week
75 Mar 2014 Term test and Population genetics Chapter 13 of the main text
812 Mar 2014 Population genetics Chapter 13 of the main text, Reference for CF data Reference on EM algorithm
919 Mar 2014 Population genetics Chapter 13 of the main text, Association_study_Nature_Reviews2006
1026 Mar 2014 Peptide sequencing Chapter 12 of the main text
112 Apr 2014 RNA Secondary Structure Chapter 11 of the main text
129 Apr 2014 Pathogen Chip and Differential expressed gene pathogen_chip_Genome_Bio2007, LOMA2008, PEM_jbcb2006
1316 Apr 2014 Project Presentation
7 May 2014 Examination Week

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