CS2220: Introduction to Computational Biology
Instructors: Limsoon Wong / 2013/2014 Semester 1 / IVLE

• Lecture is held every Thursday @ 9am in SR@LT19
• Tutorial is held every Thursday @ 11am in SR@LT19
• Main references: The Practical Bioinformatician (by Wong, WSPC) and Algorithms in Bioinformatics: A Practical Introduction (by Sung, CRC).

• The goals of CS2220 (Introduction to Computational Biology) are: (1) development of flexible and logical problem solving skills; (2) understanding of main bioinformatics problems; and (3) appreciation of main techniques and approaches to bioinformatics. To achieve the goals above, we expose the students to a series of case studies spanning gene feature recognition, gene expression and proteomic analysis, gene finding, sequence homology interpretation, phylogeny analysis, physical mapping, and genome sequencing

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Lecture Slides, Assignments, and Notes

• Course Briefing, 15/8/13
  Readings: Chapter 1 of The Practical Bioinformatician and Chapter 1 of Algorithms in Bioinformatics
  

  
  
  
  

• Week 1: Essence of Knowledge Discovery, 15/8/13
  Readings: Chapter 3 of The Practical Bioinformatician

  
  
  
  

• Week 2: Essence of Knowledge Discovery, 22/8/13
  Readings: Chapter 3 of The Practical Bioinformatician and Li & Wong, PKDD04, tutorial notes

  
  
  
  

• Week 3: Gene Feature Recognition, 29/8/13
  Readings: Chapter 4 and chapter 7 of The Practical Bioinformatician, and Koh & Wong, GIW2007, pp 73-82
  Assignment: Assignment #1 (due on 20/9/2013) and translation initiation sites data sets

  
  
  

• Week 4 & 5: Gene Expression Analysis, 5/9/13 & 12/9/13
  Readings: Chapter 14 of The Practical Bioinformatician
  Assignment: Assignment #2 (due on 11/10/2013) and gene expression data sets

  
  
  
  

• Week 6 & 7: Essence of Sequence Comparison, 19/9/13 & 3/10/13
  Readings: Chapter 10 of The Practical Bioinformatician and Chapters 2 & 5 of Algorithms in Bioinformatics
  Assignment: Assignment #3 (due on 25/10/2013)

  
  
  
  

• Week 8 & 9: Sequence Homology Interpretation, 10/10/13 & 17/10/13
  E-learning audio file
  Readings: Chapter 19 of The Practical Bioinformatician
  Assignment: Assignment #4 (due on 12/11/2013)

  
  
  
  

• Week 10: Gene Finding, 24/10/13

  
  
  
  

• Week 11: Phylogenetic Trees, 31/10/13
  Readings: Chapter 19 of The Practical Bioinformatician and Chapters 7 & 8 of Algoritms in Bioinformatics

  
  
  
  

• Week 12 & 13: Student Presentations, 7/11/13 & 14/11/13
  Target topic: Protein function prediction
  Reading list