CS2220: Introduction to Computational Biology
Instructor: Limsoon Wong / 2022/2023 Semester 1

Overview

The goals of CS2220 (Introduction to Computational Biology) are: (i) developmen of flexible and logical problem-solving skills; (ii) understanding of main bioinformatics problems; and (iii) appreciation of main techniques and approaches to bioinformatics. To achieve the goals above, students are exposed to a series of case studies spanning gene feature recognition, gene expression and proteomic analysis, sequence homology interpretation, phylogeny analysis, mutation-phenotype association, etc.

Topics

• Essence of Bioinformatics [1 hour, integrated into various lectures]
  
  • Overview of molecular biology
  • Overview of tools and instruments for molecular biology
  • Overview of themes and applications of bioinformatic

• Essence of Knowledge Discovery [3-4 hours]
  
  • Basic classification performance measures and techniques
  • Introduction to feature-selection techniques
  • Introduction to machine-learning techniques
  • [Brief overview only. No algorithmic details]

• Gene-Feature Recognition from Genomic DNA [3-4 hours]
  
  • The ``feature generation, feature selection, feature integration'' approach
  • Case study of translation initiation site (TIS) recognition
  • Case study of transcription start site (TSS) recognition
  • [Some other gene feature recognition problems may be used in the lecture instead of TIS and TSS.]
  • [Concentrate on methodologies, not algorithms.]

• Gene Expression Analysis [3-4 hours]
  
  • Microarray & transcriptomics basics
  • Case study of classification of gene expression profiles
  • Case study of clustering of gene expression profiles
  • Case study of molecular network reconstruction by gene expression profiles
  • [Some other gene expression analysis problems may be used in the lecture instead of molecular network reconstruction, e.g., batch effects.]
  • [Concentrate on methodologies, not algorithms.]

• Essence of Sequence Comparison [3-4 hours]
  
  • Dynamic programming basics
  • Sequence comparison and alignment basics
  • Case study of the Needleman-Wunsh global alignment algorithm
  • Case study of the Smith-Waterman local alignment algorithm
  • Case study of the BLAST heuristic-based similarity search method
  • [Basic concepts only]

• Sequence Homology Interpretation [3-4 hours]
  
  • Case study of protein function prediction by sequence alignment
  • Case study of protein function prediction by phylogenetic profiling
  • Case study of active site and domain prediction
  • Case study of key mutation sites prediction

• Phylogenetic Trees [3-4 hours]
  
  • Phylogeny reconstruction method basics
  • Case study on the origin of Polynesians
  • Case study on the origin of Europeans
  • Reconciliation of phlogenetic trees

• Some additional topics---e.g. disease/phenotype mutations---may be discussed if there is sufficient time.