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Bachelor	TR-NQF-HE: Level 6	QF-EHEA: First Cycle	EQF-LLL: Level 6

Course Introduction and Application Information

Course Code	Course Name	Semester	Theoretical	Practical	Credit	ECTS
GEN4059	Computational Methods in Bioinformatics	Spring	3	0	3	6

This catalog is for information purposes. Course status is determined by the relevant department at the beginning of semester.

Basic information

Language of instruction:	English
Type of course:	Non-Departmental Elective
Course Level:	Bachelor’s Degree (First Cycle)
Mode of Delivery:	Face to face
Course Coordinator :	Dr. Öğr. Üyesi ELIZABETH HEMOND
Recommended Optional Program Components:	There is none.
Course Objectives:	The goal of this course is to provide an understanding of the fundamental computational methods used in bioinformatics and set of algorithms that have important applications in bioinformatics and also have several other applications outside of bioinformatics.

Learning Outcomes

The students who have succeeded in this course;
1. Recognize the fundamental models of computation useful in modeling nucleic acid and protein sequences.
2. Design and implement algorithms useful for analyzing various molecular biology data.
3. Discuss Genetic Algorithm and its applications in bioinformatics.
4. Discuss Greedy Algorithms and its applications in bioinformatics.
5. Discuss Gibbs sampling and its applications in bioinformatics.
6. Recognize Expectation Maximization and its applications in bioinformatics.
7. Recognize Hidden Markov models and its applications in bioinformatics.
8. Define Bayesian networks and its applications in bioinformatics.
9. Define graphs and its applications in bioinformatics.

Course Content

This course will provide a broad and through background in computational methods and algorithms that are widely used in bioinformatics applications. Various existing methods will be critically described and the strengths and limitations of each will be discussed.

Weekly Detailed Course Contents

Week	Subject	Related Preparation
1)	A brief introduction to computational complexity and algorithm design techniques
2)	Exact sequence search algorithms
3)	Rabin-Karp algorithm, pattern matching, suffix trees
4)	Elements of dynamic programming, Manhattan tourist problem, k-band algorithm
5)	Approximate string matching, divide and conquer algorithms
6)	Branch and bound search
7)	Genetic Algorithm
8)	Greedy Algorithms
9)	Gibbs sampling
10)	Expectation Maximization
11)	Hidden Markov models
12)	Bayesian networks
13)	Graphs
14)	Review

Sources

Course Notes / Textbooks:	Relevant course notes or hand-outs will be supplied.
References:	1)An Introduction to Bioinformatics Algorithms (Computational Molecular Biology), Neil Jones and Pavel Pevzner, MIT Press, 2004.

Evaluation System

Semester Requirements	Number of Activities	Level of Contribution
Homework Assignments	2	% 10
Project	1	% 25
Midterms	1	% 25
Final	1	% 40
Total		% 100
PERCENTAGE OF SEMESTER WORK		% 35
PERCENTAGE OF FINAL WORK		% 65
Total		% 100

ECTS / Workload Table

Activities	Number of Activities	Duration (Hours)	Workload
Course Hours	14	3	42
Study Hours Out of Class	14	7	98
Midterms	1	2	2
Final	1	2	2
Total Workload			144

Contribution of Learning Outcomes to Programme Outcomes

No Effect	1 Lowest	2 Low	3 Average	4 High	5 Highest

	Program Outcomes	Level of Contribution
1)	To be able to apply theoretical concepts related to mass communication, consumer behavior, psychology, persuasion,sociology, marketing, and other related fields to understand how advertising and brand communication works in a free-market economy.	2
2)	To be able to critically discuss and interpret theories, concepts, methods, tools and ideas in the field of advertising.	2
3)	To be able to research, create, design, write, and present an advertising campaign and brand strategies of their own creation and compete for an account as they would at an advertising agency.	2
4)	To be able to analyze primary and secondary research data for a variety of products and services.	2
5)	To be able to develop an understanding of the history of advertising as it relates to the emergence of mass media outlets and the importance of advertising in the marketplace.	2
6)	To be able to follow developments, techniques, methods, as well as research in advertising field; and to be able to communicate with international colleagues in a foreign language. (“European Language Portfolio Global Scale”, Level B1)	2
7)	To be able to take responsibility in an individual capacity or as a team in generating solutions to unexpected problems that arise during implementation process in the Advertising field.	3
8)	To be able to understand how advertising works in a global economy, taking into account cultural, societal, political, and economic differences that exist across countries and cultures.	2
9)	To be able to approach the dynamics of the field with an integrated perspective, with creative and critical thinking, develop original and creative strategies.	2
10)	To be able to to create strategic advertisements for print, broadcast, online and other media, as well as how to integrate a campaign idea across several media categories in a culturally diverse marketplace.	2
11)	To be able to use computer software required by the discipline and to possess advanced-level computing and IT skills. (“European Computer Driving Licence”, Advanced Level)	2
12)	To be able to identify and meet the demands of learning requirements.	2
13)	To be able to develop an understanding and appreciation of the core ethical principles of the advertising profession.	2