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Syllabus cs2220 14aug2023

The goals of the course CS2220 Introduction to Computational Biology are to develop problem solving skills, understand bioinformatics problems, familiarize students with databases and techniques, and explore applications. The course covers topics like protein structure prediction, sequence analysis, databases, and computer aided drug design through case studies.

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20 views

Syllabus cs2220 14aug2023

The goals of the course CS2220 Introduction to Computational Biology are to develop problem solving skills, understand bioinformatics problems, familiarize students with databases and techniques, and explore applications. The course covers topics like protein structure prediction, sequence analysis, databases, and computer aided drug design through case studies.

Uploaded by

Pawandeep Singh
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
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Download as PDF, TXT or read online on Scribd
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CS2220: Introduction to Computational Biology

Instructor: Michael Gromiha/2023/2024 Semester 1

Overview
The goals of CS2220 (Introduction to Computational Biology) are: (i) development of flexible and
logical problem-solving skills; (ii) understanding main bioinformatics problems; (iii) familiar with
databases, techniques, algorithms and approaches to bioinformatics and (iv) potential applications.
To achieve the goals above, students are exposed to a series of case studies spanning extracting
hidden information in protein and gene sequences, protein structure prediction, sequence
homology interpretation, phylogeny analysis, mutation-phenotype association, development of
databases, computer aided drug design etc.

Topics
• Essence of Bioinformatics [2 hours, integrated into various lectures]
o Overview of biomolecules and molecular biology
o Overview of major aspects in bioinformatics
o Overview of themes and applications of bioinformatics

• Essence of Knowledge Discovery [3-4 hours]


o Basic classification performance measures and techniques
o Introduction to feature-selection techniques
o Introduction to machine-learning techniques
o [Brief overview only. No algorithmic details]

• Concepts and development of databases [3-4 hours]


o Basics on databases
o Case study of databases on nucleic acids
o Case study of databases for proteins
o Development of biological databases
o [Concentrate on importance and applications]

• Extracting hidden features in protein sequences [3-4 hours]


o Basics on protein structures
o Case study of classifying proteins based on structure and function.
o Case study of recognizing patterns in protein sequences
o Case study of identifying conserved amino acids
o [Concentrate on methodologies, not algorithms]
• Protein structure Analysis and prediction [3-4 hours]
o Statistical analysis of protein structure
o Case study of predicting protein secondary structure
o Development of features from protein three-dimensional structures
o Case study of protein three-dimensional structure prediction
o Cast study of stabilizing residues in protein structures
o [Concentrate on methodologies, not algorithms.]

• Essence of Sequence Comparison [3-4 hours]


o Dynamic programming basics
o Sequence comparison and alignment basics
o Case study of the Needleman-Wunsch global alignment algorithm
o Case study of the Smith Waterman local alignment algorithm
o Case study of the BLAST heuristic-based similarity search method
o [Basic concepts only]

• Sequence Homology Interpretation [3-4 hours]


o Case study of protein function prediction by sequence alignment
o Case study of active site and domain prediction
o Case study of key mutation sites prediction

• Computer Aided Drug Design (3-4 hours]


o Basics on the necessity of computational techniques in drug design
o Computational algorithms in drug design
o Case study on identifying drug like compounds.
o Case study on covid-19 and other diseases

• Some additional topics: E.g., phylogenetic trees, disease/phenotype mutations (may be


discussed if there is sufficient time).

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