Course Name: Bioinformatics

Credits: 2.0

Level: Undergraduate

Pre-requisite: Basic knowledge in: Biochemistry and Molecular biology, Computer Language, Data Structure and Algorithm, Probability and Statistics

Lecture Time: 9 weeks, 2 sessions/week, 2 hours/session

Instructors: ???

Course Description

Bioinformatics is a field to process genome sequences and many other types of –omics data, by the combined use of computational and statistical tools, with a focus on sequence information management, signal processing and pattern recognition, and knowledge discovery. One example is to use computer to study the structure, function and evolution of genomes based on high throughput data. Bioinformatics is a rapidly evolving and developing field following the advances of data generation technologies. This course focuses on basic theory and tools in sequence analysis, phylogenetic analysis and network analysis, methods for analysis of high-throughput data, and how to access biological databases.

Topics and Schedule

  1. Introduction (4 hrs)

1.1.   Concepts and definitions

1.2.   Computer data structure and algorithms

1.3.   Statistical modeling

  1. Sequence alignment and database search (8 hrs)

2.1.   Pairwise sequence alignment and substitution matrix

2.2.   BLAST database search

2.3.   Multiple sequence alignment and motif discovery

  1. Genome assembly and annotation (6 hrs)

3.1.   Genome sequencing and assembly

3.2.   Gene prediction and functional annotation

3.3.   Annotation of repetitive sequences

  1. Transcriptome analysis (4 hrs)

4.1.   Quantification and normalization of gene expression

4.2.   Differential gene expression analysis

4.3.   Gene expression clustering analysis

  1. Phylogenetic analysis (6 hrs)

5.1.   Basic concepts of evolution

5.2.   Methods for constructing phylogenetic trees

5.3.   Introduction to phylogenetic software packages

  1. Biomolecular networks (4 hrs)

6.1.   Basic concepts

6.2.   Protein interaction networks

6.3.   Gene regulatory networks

  1. Introduction to biological database (4 hrs)

6.1.   General databases

6.2.   Special databases

6.3.   Biocuration and literature mining

Grading Information

Grades will be based on homework assignments and two exams. Homework assignments will be due most weeks. Exams will be based on module materials, textbook readings, supplemental readings, homework exercises, and the provided on-line resources. These exams will include multiple choice, short answer, and essay questions.

Assignments: 30%.

Midterm exam: 30%

Final exam: 40%

TOTAL 100%


Supplemental Readings

[1]   Understanding Bioinformatics, Marketa Zvelebil, Jeremy O. Baum. ISBN: 9780815340249. Publication Date: September 05, 2007

[2]   Introduction to Bioinformatics, 4th Edition, Arthur Lesk. ISBN-13: 978-0199651566

[3]   Bioinformatics for Beginners: Genes, Genomes, Molecular Evolution, Databases and Analytical Tools, Supratim Choudhuri, ISBN-13: 978-0124104716

[4]   Chen, Luonan, BIOMOLECULAR NETWORKS Methods and Applications in Systems Biology, 2009 by John Wiley & Sons, Inc.

Course Website

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