CS 4491/CS 7990

SPECIAL TOPICS IN BIOINFORMATICS

Mingon Kang, PhD

Computer Science, Kennesaw State University
Self Introduction
 Instructor: Mingon Kang
 http://ksuweb.kennesaw.edu/~mkang9
 Or Google “Mingon Kang” and click the first one.
 Research interests:
 Bioinformatics, Machine Learning, Data Mining, and Big
Data Analytics
 Projects you may be interested in:
 Several Genomics projects in Bioinformatics
 Medical image classification
Course Information
 Instructor: Mingon Kang, PhD
 Office: J-339
 Email: [email protected] include ‘CS4991’ or ‘CS7790’
in the subject of your message when you email.
 Office Hours:
 Tuesday: 2-4pm, Wednesday: 10am-noon
 By appointment
 Lecture slides, Homework, and other materials are posted
on the course web page at:
http://ksuweb.kennesaw.edu/~mkang9/?menu=CS4491_
7990
 lecture recordings will be in D2L
Choice of Language
 You can use your favorite language, but R, Matlab,
Python are highly recommended.
 The course will briefly introduce R in case you have no
experience of those script languages.

 Better for file I/O of textual biological data

 Better to do matrix manipulation
 Fast Prototyping
Expected Background
 For graduate students: Coursework in data structures and
algorithms, or CS 5040 as per admissions analysis.
 For undergraduate students: CS 3304, CS 3410

 Statistics: good if you’ve had some background, but not

required
 Molecular biology: no knowledge assumed, but an interest in
learning some basic molecular biology is mandatory
What is Bioinformatics
 Application of computer and information technology to
problems in biology, particular molecular biology. NIH
definitions:

“Bioinformatics applies principles of information sciences and technologies

to make the vast, diverse, and complex life sciences data more
understandable and useful.
Computational biology uses mathematical and computational approaches
to address theoretical and experimental questions in biology. Although
bioinformatics and computational biology are distinct, there is also
significant overlap and activity at their interface.”

 sometimes used synonymously with computational biology or

computational molecular biology
Other Terminologies
 Biomedical informatics?
It is defined by National Library of Medicine (NLM) as
“the intersection of basic informational and computing
sciences with an application domain in biomedicine.”
 Biometrics?
It is the science of using biological properties to identify
individuals; for example, face recognition, finger prints, a
retina scan, and voice recognition.
Goal of this Course
 Understanding the types and sources of data
available for computational biology.
 Understanding the important computational problems
in molecular biology.
 Understanding the most significant & interesting
algorithms.
 Identifying opportunities in this field, and perhaps
formulating projects to explore further.
What this course will do
 Give you an understanding of main issues in
molecular biological computing: sequence, structure,
and function.
 Give you an opportunity to implement some widely
used algorithms.
 Give you exposure to classic computational problems,
as manifested in biology.
 Give you exposure to classic biological problems, as
represented computationally.
 Practice How to read and write research papers
Topics in Bioinformatics
 Computational Biology
 Gene Expression Analysis
 Gene Regulatory Network Inference
 Markov Chain Model for Gene Identification
 Genome-Wide Association Studies (GWAS) and expression
Quantitative Trait Loci (eQTL) analysis
 Next Generation Sequencing Data Analysis
 Deep Learning in Bioinformatics
Reference Books
 N. Jones & P. Pevzner, "An Introduction to Bioinformatics
Algorithms," 2004, ISBN 0262101068
 Supratim Choudhuri, Bioinformatics for Beginners: Genes,
Genomes, Molecular Evolution, Databases and Analytical Tools,
2014, ISBN: 0124104711
Evaluation (tentative)
 Homework Assignment (4-5 assignments: 40%)
 Mainly writing codes for algorithm implementation
 Late assignments will be accepted up to 24 hours after the due date
for 50% credit.
 Midterm (20%) + Final (20%)
 Allows two pages of cheat sheets
 Two research papers (5% and 15%)
 Using Latex
Academic Integrity
 Academic dishonesty
 Cheating

 Plagiarism

 Collusion

 The submission for credit of any work or materials that are

attributable in whole or in part to another person
 Taking an examination for another person

 Any act designed to give unfair advantage to a student or

the attempt to commit