MEDICINE
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
MBG1002	Introduction to Bioinformatics	Spring	3	0	3	5

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 Lecturer(s):	Prof. Dr. SÜREYYA AKYÜZ Dr. Öğr. Üyesi SERKAN AYVAZ
Recommended Optional Program Components:	There is none.
Course Objectives:	This course aims to prepare the students to work in the interdisciplinary area, bioinformatics that marry the advances in high-performance computing with the exploiting information resources of the human genome and related data.

Learning Outcomes

The students who have succeeded in this course;
1. Recognize the working in interdisciplinary teams of biologists, biochemists, medical researchers, geneticists, and computer engineers.
2. Perform sophisticated searches over enormous databases, and to interpret results.
3. Perform genomic comparisons, display genes and large genomic regions in Genome Browsers.
4. Recognize the basic bioinformatics problems and their solutions, including: fragment assembly, gene finding, protein folding and microarray studies.
5. Anayze the results in probabilistic terms using statistical significance.
6. Recognize the sequencing techniques, inherent computational problems, possible solutions.
7. Define Markov Model building and its usage for gene prediction.
8. Define computational methods for analysis of microarray data, and discuss the interpretations of gene expression from this data.
9. Discuss ethical, legal, and social issues associated with the Human Genome Project and its outcomes.

Course Content

Bioinformatics is a rapidly growing field that integrates molecular biology, statistics, and computer science. This course is devoted to the mathematical models and computer algorithms of DNA and protein sequence analysis. In this course, the students will learn many of the popular tools for performing bioinformatics analysis and you will be introduced to the thinking that drives these algorithms. Various existing bioinformatics methods will be critically described and the strengths and limitations of each will be discussed.

Weekly Detailed Course Contents

Week	Subject	Related Preparation
1)	Introduction: Probability and statistics in a nut shell.
2)	Analysis of nucleic acid and protein sequences.
3)	Molecular Biology Databases on the Web.
4)	Bioinformatics softwares on the internet
5)	How the Genome is Studied, Maps and Sequences, The Human Genome Project
6)	Sequencing: Next Gen, Exome, Shotgun
7)	Fragment Assembly Problem; Sequence Alignment Models: Shortest Common Superstring, Reconstruction, Multicontig, Graph Model
8)	Restriction mapping: a) Double Digest Problem, b) Partial Digest Problem
9)	Computational Gene Hunting, Gene finding methods; sequence patterns, Hidden Markov Models.
10)	Bioinformatics approaches to gene expression
11)	Protein folding problem
12)	Genome Rearrangements
13)	Suffix trees I
14)	Suffix trees II

Sources

Course Notes / Textbooks:	Biyoinformatik ders notları haftalık olarak verilecektir. Course material will be supplied weekly.
References:	1) Pevsner J., Bioinformatics and Functional Genomics, Wiley-Liss, 2009 2) Mount D.W., Bioinformatics: Sequence and Genome Analysis (2nd edition), Cold Spring Harbor Laboratory Press, 2004 3) Krane D.E., Raymer M.L., Fundamental Concepts of Bioinformatics, Benjamin Cummings, 2003 4) Setubal C., Meidanis J., Introduction to Computational Molecular Biology, PWS Publishing, 1997"

Evaluation System

Semester Requirements	Number of Activities	Level of Contribution
Homework Assignments	2	% 15
Project	1	% 20
Midterms	1	% 25
Final	1	% 40
Total		% 100
PERCENTAGE OF SEMESTER WORK		% 40
PERCENTAGE OF FINAL WORK		% 60
Total		% 100

ECTS / Workload Table

Activities	Number of Activities	Duration (Hours)	Workload
Course Hours	14	3	42
Study Hours Out of Class	14	5	70
Project	1	10	10
Midterms	1	2	2
Final	1	2	2
Total Workload			126

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)	Integrates the knowledge, skills and attitudes acquired from basic and clinical medical sciences, behavioral sciences and social sciences, and uses them in health service delivery.
2)	In patient management, shows a biopsychosocial approach that takes into account the socio-demographic and sociocultural background of the individual, regardless of language, religion, race and gender.
3)	In the provision of health services, prioritizes the protection and development of the health of individuals and society.
4)	Taking into account the individual, societal, social and environmental factors affecting health; does the necessary work to maintain and improve the state of health.
5)	By recognizing the characteristics, needs and expectations of the target audience, provides health education to healthy/sick individuals and their relatives and other healthcare professionals.
6)	Shows a safe, rational and effective approach in health service delivery, prevention, diagnosis, treatment, follow-up and rehabilitation processes.
7)	Performs invasive and/or non-invasive procedures in diagnosis, treatment, follow-up and rehabilitation processes in a safe and effective way for the patient.
8)	Provides health services by considering patient and employee health and safety.
9)	In the provision of health services, takes into account the changes in the physical and socioeconomic environment on a regional and global scale, as well as the changes in the individual characteristics and behaviors of the people who apply to it.
10)	Takes good medical practice into account while carrying out his/her profession.
11)	Fulfills its duties and obligations within the framework of ethical principles, rights and legal responsibilities required by its profession.
12)	Demonstrates decisive behavior in providing high-quality health care, taking into account the integrity of the patient.
13)	Evaluates his/her performance in his/her professional practice by considering his/her emotions and cognitive characteristics.
14)	Advocates improving the provision of health services by considering the concepts of social reliability and social responsibility for the protection and development of public health.
15)	Can plan and carry out service delivery, training and consultancy processes related to individual and community health in cooperation with all components for the protection and development of health.
16)	Evaluates the impact of health policies and practices on individual and community health indicators and advocates increasing the quality of health services.
17)	The physician attaches importance to the protection of his/her own physical, mental and social health, and does what is necessary for this
18)	Shows exemplary behavior and leads the healthcare team during service delivery.
19)	Uses resources cost-effectively, for the benefit of society and in accordance with the legislation, in the planning, implementation and evaluation processes of health services in the health institution he/she is the manager of.
20)	Establishes positive communication within the health team it serves and assumes different team roles when necessary.
21)	Is aware of the duties and responsibilities of the health workers in the health team and acts accordingly.
22)	In the professional practices, works in harmony and effectively with the colleagues and other professional groups.
23)	Communicates effectively with patients, their relatives, healthcare professionals, other professional groups, institutions and organizations.
24)	Communicates effectively with individuals and groups that require a special approach and have different socio-cultural characteristics.
25)	In the diagnosis, treatment, follow-up and rehabilitation processes, shows a patient-centered approach that associates the patient with the decision-making mechanisms.
26)	Plans and implements scientific research, when necessary, for the population it serves, and uses the results and/or the results of other research for the benefit of the society.
27)	Reaches and critically evaluates current literature knowledge about his/her profession.
28)	Applies the principles of evidence-based medicine in clinical decision making.
29)	Uses information technologies to increase the effectiveness of its work on health care, research and education.
30)	Effectively manages individual work processes and career development.
31)	Demonstrates skills in acquiring and evaluating new knowledge, integrating it with existing knowledge, applying it to professional situations and adapting to changing conditions throughout professional life.
32)	Selects the right learning resources to improve the quality of the health service it offers, organizes its own learning process