Download CS4491_CS7990_Syllabus_Spring2017_Mingon

CS4491/CS7990: Special Topics in Bioinformatics
Spring 2017
M/W 6:30-7:45pm J211
Instructor Name: Mingon Kang
Lecture Time: M/W 6:30-7:45pm
Phone: (470) 578-4311
Email: [email protected]
Office: Atrium Building J339, Marietta Campus
Course Description
Biological sciences are undergoing a revolution in how they are practiced. In the last decade, a vast
amount of biological data has become available, and computational methods are playing a
fundamental role in transforming this data into scientific understanding. Bioinformatics involves
developing and applying computational methods for managing and analyzing information about the
sequence, structure and function of biological molecules and systems. This course covers a wide
range of machine learning, data mining, and computational algorithms to solve various
bioinformatics research problems.
Credit hours 3-0-3.
Prerequisites
For graduate students: Coursework in data structures and algorithms, or CS 5040 as per admissions
analysis.
For undergraduate students: CS 3304, CS 3410
Course Learning Objectives
Upon completion of this course, the students will be able to.
1. implement various machine learning, data mining, and computational algorithms in
bioinformatics
2. solve various current research problems in bioinformatics
3. develop scientific thinking for research
4. read and write research papers
Course Topics
1.
2.
3.
4.
5.
6.
7.
Introduction to Bioinformatics
Data Preprocessing
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
8.
Deep learning in Bioinformatics
Required Texts
Not required, but there are reference textbooks:


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
The grade will be based on:
Attendance
Assignments
Final Project
Research Paper
5%
35%
30%
30%
Score ≥ 90
Score ≥ 80 & Score < 90
Score ≥ 70 & Score < 80
Score ≥ 60 & Score < 70
Score < 60
A
B
C
D
F
Course Requirements/Assignments: (subject to change)
During the first week, students will choose topics for a semester long research paper, submit
abstract, then outline, then the first draft before the midterm. The final paper will be due at the end
of the semester.
Assignment 1: Data Visualization
Assignment 2: Gene Regulatory Network Inference
Assignment 3: Markov Chain Model for Gene identification
Research Project & Research Paper
University Policies
Academic Honesty Statement:
Every KSU student is responsible for upholding the provisions of the Student Code of Conduct, as
published in the Undergraduate and Graduate Catalogs. Section II of the Student Code of Conduct
addresses the University's policy on academic honesty, including provisions regarding plagiarism
and cheating, unauthorized access to University materials, misrepresentation/falsification of
University records or academic work, malicious removal, retention, or destruction of library
materials, malicious/intentional misuse of computer facilities and/or services, and misuse of student
identification cards. Incidents of alleged academic misconduct will be handled through the
established procedures of the University Judiciary Program, which includes either an "informal"
resolution by a faculty member, resulting in a grade adjustment, or a formal hearing procedure,
which may subject a student to the Code of Conduct's minimum one semester suspension
requirement.
Reference Requirement
When you quote or base your ideas on other people’s work (e.g., from articles, journals, magazines,
books, websites, etc.) in the technical report, you MUST cite the source you used. When you direct
quote, you must put others’ words in quotation marks and cite the source(s). When reading that
source contributed to the ideas presented in your paper, you must give the authors proper credit.
Students are recommended to user APA style for their references. APA style guide:
http://owl.english.purdue.edu/owl/resource/560/01/