BIE 3300 - Bioinformatics

3 lecture hours 2 lab hours 4 credits

Course Description
This course will introduce Chemical and Biomolecular Engineering students to bioinformatics and its ever-increasing power in solving various complex problems in medicine and drug development. 1) Students will explore in detail the building blocks of biomolecules and their physicochemical properties to lay the foundation for better understanding the constantly “breathing” biomolecules and their delicate - intramolecular and intermolecular - interactions with their working partners in action. 2) Students will learn how to navigate the human genome as well as its organization and dynamics, determine any given gene’s exact chromosomal location, and explore the gene. 3) Students will learn how to search against a wide array of specialized bioinformatics databases and retrieve their desired information effectively and efficiently. 4) Students will learn various sequence alignment algorithms in use today and practice them in processing of biosequences. 5) Students will learn and practice comparative sequence analysis and covariation analysis to build a phylogenetic tree for a set of biosequences, together with principal component analysis. This course meets the following Raider Core CLO requirement: Integrate Learning. (prereq: BIE 2300, CHM 2310) (quarter system prereq: CH 223, EB 2420, and EB 2430)

Course Learning Outcomes
Upon successful completion of this course, the student will be able to:

Acknowledge the ever-increasing power of bioinformatics
Apply the physicochemical properties to understand biomolecular structures
Navigate the human genome browser to determine the exact chromosomal location of a gene
Understand search algorithms to search for similar biosequences
Search a query against various specialized bioinformatics databases
Unambiguously differentiate similarity and homology of biosequences
Understand various biosequence alignment algorithms
Understand the fundamental concept of comparative sequence analysis
Align a set of compiled biosequences with Jalview
Understand the fundamental concepts of covariation analysis of biosequences
Understand the fundamental concept of principal component analysis
Build a phylogenetic tree based on well-aligned biosequences

Prerequisites by Topic

None

Course Topics

Introduction to bioinformatics
Bioinformatics of nucleic acids
Bioinformatics of proteins
Browsing genomes and their data
Sequence similarity search
Bioinformatics databases
Human genome organization and dynamics
Sequence alignment algorithms
Comparative analysis of biosequences
Covariation analysis of biosequences
Principal component analysis of biosequences

Laboratory Topics

Introduction lab
Understanding nucleic acid structure and function
Understanding protein structure and function
Browsing genomes and genes
Searching NCBI Entrez databases
BLAST similarity search
Jalview - a sequence alignment editor
Comparative analysis of protein sequences - 1
Comparative analysis of protein sequences - 2
Comparative analysis of RNA sequences
The Tree of Life and phylogenetic analysis - 1
The Tree of Life and phylogenetic analysis - 2

Coordinator
Dr. Jung Lee

Announcement

The Raider Return

Milwaukee School of Engineering

Connect With MSOE

BIE 3300 - Bioinformatics