Chunguang Du

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BIOL 497 - Genomics

Spring 2008
Dr. Chunguang Du
Department of Biology and Molecular Biology
Montclair State University

Course Description

Genomics has been defined as the science of examining the structure and function of genes and proteins through the use of computational analysis, statistics, and pattern recognition. This course is designed to introduce genomics/bioinformatics at a level appropriate for biology majors having completed the lower-division core, and for chemistry, computer science, and math majors with an interest in biology. This course is designed so that the content and curricula can rapidly adjust as required to meet changing circumstances during the course of the semester and to evolve with the topics of interest in genomics/bioinformatics over time. Students will learn to use conventional software, web-based applications, and software, which they download to their machine. By using the well-tested and successful approach of problem-based learning, students will learn through applying the strategies and tools used in bioinformatics to topical problems drawn from ongoing research and applications in a variety of fields. There is to be an integration of the basics of computation and analysis along with molecular biology throughout the course.

The fields of study in molecular and cell biology continue to grow rapidly. The field of bioinformatics changes so rapidly that it is nearly impossible to keep up with all the different areas of progress. It is therefore necessary to learn how to access new information and how to assimilate it into the whole, in order to continue to learn beyond the limits of this course. It is also necessary to become aware of the tools and techniques used in research and in applications. Therefore, while learning the essentials of bioinformatics, you will also begin to learn to use some of these tools. In doing so, you should find that they help you in learning beyond this course and to see the connections in other courses.


1) Integrate a research project that involves students enrolled in Genoimcs class
2) Teach students the critical techniques of genomics while allowing them to understand the importance of basic research.
3) Allow students to gain a better understanding of DNA sequence annotation, alignment, and comparison analysis.

Course Content

• Introduction to Research Project
• Genome Sequencing
• Retrotransposon Identification
• Introduction to Biological Databases – GenBank
• Pairwise Sequence Alignment
• Multiple Sequence Alignment
• Basic Local Alignment Search Tool
• Finding genes: promoters, introns, exons
• Marking Genomes
• Mapping Genomes
• Molecular Phylogeny and Evolution

Course Grading: Final grade will be based on the following components: attendance, participation in discussions, 10%; report on finishing fosmid clone, 20%; report on genes/pseudogenes, 10%; final report on maize genome (analysis and annotation), written 20%, and oral 20%; final exam, 20%.
Office hours: My office hours are Monday 1:00 – 3:30 in SH110.