LSM3241: Bioinformatics and Biocomputing

Prerequisite: Pass in LSM2104, LSM2102, LSM1101

This module provides fundamental knowledge in bioinformatics and its applications. It emphasizes on the learning of problem-solving skills in real-case studies. Topics include viral genome analysis, database construction, sequence analysis and applications, molecular modeling. Students learn basic algorithm and practice the use of commonly-used bioinformatics tools in real-life problems in biology, virology, and drug design.

Instructor

Dr. Chen Yu Zong
Department of Computational Science
National University of Singapore
Office: Blk S17 Room 07-24
Tel: 6874-6877. Fax: 6774-6756
E-mail: yzchen@cz3.nus.edu.sg
Web: http://bidd.nus.edu.sg (Lots of info about biocomputing)

Schedule (Right click to save)

• Lectures:
  • Lecture 1: Introduction, bioinformatics in biological study and drug development (week 1).(Right click to save)
  • Lecture 2: Bioinformatics of viral genomes (week 2).(Right click to save)
  • Lecture 3: Molecular database development (week 3).(Right click to save)
  • Lecture 4: Sequence analysis methods revisited. PSI-BLAST for protein function prediction (week 4).(Right click to save)
  • Lecture 5: Support vector machines for protein function prediction (week 5).(Right click to save)
  • Lecture 6: Fundamentals of molecular modeling. (week 6).(Right click to save)
  • Lecture 7: Molecular modeling software (week 8)(Right click to save)
  • Lecture 8: Gene Expression Profiles and Microarray Data Analysis (week 9).(Right click to save)
  • Lecture 9: Biological Pathway Simulation (week 10).(Right click to save)
• TEXT BOOK (Reference books):
  • Main reference book
    • Introduction to Bioinformatics. Arthur M. Lesk. 2002. Oxford University Press; ISBN: 0199251967
  • Other reference book
    • Bioinformatics: The Machine Learning Approach (Adaptive Computation and Machine Learning). Pierre Baldi, Soren Brunak. 2001. The MIT Press; ISBN: 026202506X
    • Molecular modelling : principles and applications. Andrew R. Leach. Imprint Harlow, England; Singapore: Pearson Education, c2001.
• MODE OF ASSESSMENT:
  • Project 1 (25%); Project 2 (25%); Final (50%)
• Tutorials
  • No. of sessions: 3
    • Session 1: Molecular database development (week 2-3).
    • Session 2: Functional prediction of proteins in viral genome by means of PSI-BLAST and SVM (week 4-10).
    • Session 3: Clustering analysis of microarray data from GEO database (week 11 and 14).
  • location of tutorials: LS Lab 5, 8 and CZ Lab
  • technologists-in-charge: Ng Hwee Lang (CZ), and lab tech at LS Lab 5, 8.
• Lab (Project-Based) Sessions
  • No. of sessions: 3
    • Session 1: Molecular database development (week 2-3, due date: week 3)
    • Session 2: Functional prediction of proteins in viral genome (week 4-10, due date: week 10)
    • Session 3 (optional): Modeling software (week 11 and 14)
  • location of labs: LS Lab 5, 8 and CZ Lab
  • technologists-in-charge: Ng Hwee Lang (CZ), and lab tech at LS Lab 5, 8