MATHEMATICS
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
MBG4057	Special Topics 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
Course Objectives:	This course aims to discuss technical papers from the recent bioinformatics literature, examine their algorithms and conduct an intensive study on a specific bioinformatics problem.

Learning Outcomes

The students who have succeeded in this course;
1. Define the open research questions in bioinformatics.
2. Discuss current solutions to tackle bioinformatics problems.
3. Develop an ability to discuss open research issues in computational biology.
4. Acquire an understanding of existing bioinformatics solutions for genomics.
5. Acquire an understanding of existing bioinformatics solutions for proteomics.
6. Develop an ability to focus on several bioinformatics articles and present their findings.
7. Obtain a familiarity with emerging topics in bioinformatics.
8. Obtain a familiarity with emerging topics in computational biology.
9. Develop an ability to find, read and discuss scientific articles published in the bioinformatics field.

Course Content

This discussion-based bioinformatics course will expose students to the latest developments in bioinformatics analyses and algorithms.

Weekly Detailed Course Contents

Week	Subject	Related Preparation
1)	Genomics (genome sequencing, storage and study of genome information, genome databases)
2)	Genomics (polymorphism in the human genome and association with diseases)
3)	Comparative genomics (genome subtraction method, whole-genome alignment methods, genome-context methods, gene-fusion method)
4)	Structural genomics (the scientific program of structural genomics, target selection in structural genomics)
5)	Functional genomics (integration of experimental and computational methods)
6)	Functional genomics (gene-expression data and DNA micro-arrays)
7)	Functional genomics (regulatory networks, protein-protein interaction networks)
8)	Proteomics, Protein folding and fold recognition
9)	Epigenomics
10)	Cancer informatics
11)	Non-coding RNA identification and search
12)	Emerging topics in bioinformatics
13)	Emerging topics in computational biology
14)	Presentations

Sources

Course Notes / Textbooks:	Haftalık ders notları iletilecektir. Course notes will be supplied.
References:	Articles from the primary literature (scientific journals, e.g. Nature Reviews Genetics, Nature, Science, Genome Research, Nature Genetics, Nature Methods, Bioinformatics, Molecular Systems Biology etc.)

Evaluation System

Semester Requirements	Number of Activities	Level of Contribution
Homework Assignments	2	% 15
Project	1	% 25
Midterms	1	% 10
Final	1	% 50
Total		% 100
PERCENTAGE OF SEMESTER WORK		% 25
PERCENTAGE OF FINAL WORK		% 75
Total		% 100

ECTS / Workload Table

Activities	Number of Activities	Duration (Hours)	Workload
Course Hours	14	3	42
Study Hours Out of Class	14	8	112
Midterms	1	2	2
Final	1	2	2
Total Workload			158

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 have a grasp of basic mathematics, applied mathematics and theories and applications in Mathematics
2)	To be able to understand and assess mathematical proofs and construct appropriate proofs of their own and also define and analyze problems and to find solutions based on scientific methods,
3)	To be able to apply mathematics in real life with interdisciplinary approach and to discover their potentials,
4)	To be able to acquire necessary information and to make modeling in any field that mathematics is used and to improve herself/himself,	4
5)	To be able to tell theoretical and technical information easily to both experts in detail and non-experts in basic and comprehensible way,
6)	To be familiar with computer programs used in the fields of mathematics and to be able to use at least one of them effectively at the European Computer Driving Licence Advanced Level,
7)	To be able to behave in accordance with social, scientific and ethical values in each step of the projects involved and to be able to introduce and apply projects in terms of civic engagement,
8)	To be able to evaluate all processes effectively and to have enough awareness about quality management by being conscious and having intellectual background in the universal sense,	4
9)	By having a way of abstract thinking, to be able to connect concrete events and to transfer solutions, to be able to design experiments, collect data, and analyze results by scientific methods and to interfere,
10)	To be able to continue lifelong learning by renewing the knowledge, the abilities and the competencies which have been developed during the program, and being conscious about lifelong learning,
11)	To be able to adapt and transfer the knowledge gained in the areas of mathematics ; such as algebra, analysis, number theory, mathematical logic, geometry and topology to the level of secondary school,
12)	To be able to conduct a research either as an individual or as a team member, and to be effective in each related step of the project, to take role in the decision process, to plan and manage the project by using time effectively.