CS2220: Introduction to Computational Biology
Instructor: Limsoon Wong / 2008/2009 Semester 2 / IVLE

• Lecture is held every Friday @ 2pm in COM1 Room 212
• Tutorial is held every Monday @ 2pm in COM1 Room 207
• Main references: The Practical Bioinformatician (by Wong, WSPC) and Algorithms on Strings, Trees, and Sequences (by Gusfield, CUP)

• The time/venue of lecture/tutorial got changed as below:
  • Lecture is held every Friday @ 2pm in COM1 Room 211
  • Tutorial is held every Friday @ 4pm in COM1 Room 207
• As some students went to the new room and some went to the old room (where I actually gave lecture #1), I will give a repeat of lecture #1 on 23/1/09. Lectures #2 - #4 will all be pushed back by 1 week.

• 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, 16/1/09
  Readings: Chapter 1 of The Practical Bioinformatician

  
  
  
  

• Lecture 1: Essence of Knowledge Discovery, 16/1/09
  Readings: Chapter 3 of The Practical Bioinformatician

  
  
  
  

• Lecture 2: Essence of Knowledge Discovery, 23/1/09
  Readings: Chapter 3 of The Practical Bioinformatician and Li & Wong, PKDD04, tutorial notes

  
  
  
  

• Lecture 3: Gene Feature Recognition, 30/1/09
  Readings: Chapter 4 and chapter 7 of The Practical Bioinformatician, and Koh & Wong, GIW2007, pp 73-82
  Assignment: Assignment #1 and translation initiation sites data sets

  
  
  

• Lecture 4: Gene Expression Analysis, 6/2/09
  Readings: Chapter 14 of The Practical Bioinformatician
  Assignment: Assignment #2 and gene expression data sets

  
  
  
  

• Lecture 5: ... I am still thinking about it..., 13/2/09

  
  
  
  

• Student Presentation, 20/2/09
  Target topic: Protein-Protein Interactions Reliability Assessment
  Reading list

  
  

• Lecture 6: Essence of Sequence Comparison, 6/3/09
  Readings: Chapter 10 of The Practical Bioinformatician and Chapter 11 of Algorithms for Strings, Trees, and Sequences
  Assignment: Assignment #3

  
  
  
  

• Lecture 7: Sequence Homology Interpretation, 13/3/09
  Readings: Chapter 19 of The Practical Bioinformatician

  
  
  
  

• Lecture 8: Gene Finding, 20/3/09

  
  
  
  

• Lecture 9: Phylogenetic Trees, 27/3/09
  Readings: Chapter 19 of The Practical Bioinformatician and Chapter 17 of Algoritms on Strings, Trees, and Sequences

  
  
  
  

• Student Presentation, 3/4/09
  Target topic: Protein Interaction and Protein Complex Prediction
  Reading list

  
  

• Lecture 10: ... I am still thinking about it..., 17/4/09