CS2220: Introduction to Computational Biology
Instructors: Limsoon Wong and Lisa Tucker-Kellogg / 2009/2010 Semester 2 / IVLE

• Lecture is held every Thursday @ 2pm in COM1 Room 211
• Tutorial is held every Thursday @ 4pm in COM1 Room 207
• Main references: The Practical Bioinformatician (by Wong, WSPC), Algorithms in Bioinformatics: A Practical Introduction (by Sung, CRC), and Algorithms on Strings, Trees, and Sequences (by Gusfield, CUP)

• 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

• Click here for related courses offerred in SOC

Lecture Slides, Assignments, and Notes

• Course Briefing, 14/1/10 (Lisa)
  Readings: Chapter 1 of The Practical Bioinformatician

  
  
  
  

• Lecture 1: Essence of Knowledge Discovery, 14/1/10 (Lisa)
  Readings: Chapter 3 of The Practical Bioinformatician

  
  
  
  

• Lecture 2: Essence of Knowledge Discovery, 21/1/10 (Limsoon)
  Readings: Chapter 3 of The Practical Bioinformatician and Li & Wong, PKDD04, tutorial notes

  
  
  
  

• Lecture 3: Gene Feature Recognition, 28/1/10 (Limsoon)
  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, 4/2/10 (Limsoon)
  Readings: Chapter 14 of The Practical Bioinformatician
  Assignment: Assignment #2 and gene expression data sets

  
  
  
  

• Lecture 5: Phylogenetic Trees, 11/2/10 (Limsoon)
  Readings: Chapter 19 of The Practical Bioinformatician and Chapter 17 of Algoritms on Strings, Trees, and Sequences

  
  
  
  

• Student Presentation, 25/2/10
  Target topic: Protein-Protein Interactions Reliability Assessment
  Reading list

  
  

• Lecture 6: Essence of Sequence Comparison, 4/3/10 (Lisa)
  Readings: Chapter 10 of The Practical Bioinformatician and Chapter 11 of Algorithms for Strings, Trees, and Sequences
  Assignment: Assignment #3

  
  
  
  

• Lecture 7: Protein Sequence, Structure, and Applications of Optimization, 11/3/10 (Lisa)
  

  
  
  
  

• Lecture 8: Sequence Homology Interpretation, 18/3/10 (Limsoon)
  Readings: Chapter 19 of The Practical Bioinformatician

  
  
  
  

• Lecture 9: Gene Finding, 25/3/10 (Lisa)

  
  
  
  

• Student Presentation, 1/4/10
  Target topic: Protein Interaction and Protein Complex Prediction
  Reading list

  
  

• Student Presentation, 8/4/10
  Target topic: Host-Pathogen Protein Interactions
  Reading list

  
  
  
  

• Lecture 10: ... I am still thinking about it..., 15/4/10