Institute of Graduate Studies

Bioengineering

  1. Contact Information

Prof. Dr. Erkan Şahinkaya

E-mail: erkan.sahinkaya@medeniyet.edu.tr

Interphone: 3205

  1. About the Program

Bioengineering combines basic sciences such as biology, microbiology, molecular biology and biochemistry with engineering principles and applies them to living systems. In the 21st century, Bioengineering has become a key tool for humanity's rapid socioeconomic development. Today, this branch of science creates solutions to the problems of society and related sectors by forming a bridge between many branches of engineering such as fluid mechanics, mass and heat transfer, thermodynamics, reactor design, kinetics and basic sciences such as biology, microbiology, gene technologies, protein chemistry and metabolism. Thanks to the rapid advances in the field of bioengineering, new biotechnological methods and products are developed and used in many industries such as pharmaceutical industry, chemistry, environment and food industry. Bioengineers generally apply biotechnological methods to obtain materials compatible with biological systems such as various food materials, energy sources (hydrogen energy, bioethanol, biogas), drugs (antibiotics, vitamins, hormones) and biochemical substances (proteins and amino acids, enzymes, organic acids, pesticides and various polymers). They make necessary studies to obtain materials compatible with systems. Biotechnology in its modern sense has a recent past and rapid progress has been made in recent years. Today, it is almost impossible to think of a process without biotechnological applications.

  1. Admission Requirements

Student admission to the program will be made in accordance with the conditions specified in the Education and Training Regulation of Istanbul Medeniyet University Graduate Education Institute. Although the program is in Turkish, students are expected to have sufficient knowledge of English to be able to follow and write academic publications.

  1. Program Competencies

Due to the interdisciplinary nature of our program; those who have bachelor's and / or master's degrees from Bioengineering, Environmental Engineering, Chemical Engineering, Food Engineering, Biomedical Engineering, Biosystem Engineering, Chemistry, Biology, Molecular Biology and Genetics will be accepted to our program. In accordance with the regulations of our institute, ALES and foreign language scores are required for applications.

For students admitted with a master's degree with thesis; a minimum of 240 ECTS (not less than 60 ECTS in one academic year) and twenty-four credits in total, consisting of a minimum of eight courses, two seminars, proficiency exam, thesis proposal and thesis study are required. Students are required to take two seminar courses in order to graduate. In order for the student to be eligible for thesis defense, his/her studies within the scope of the thesis must be published or accepted for publication in a journal scanned under SCI.

  1. List of Instructors

Instructur’s Name-Surname

Academic Title

Department

Erkan ŞAHİNKAYA

Prof.

Bioengineering

Özgür AKTAŞ

Prof.

Bioengineering

Zeynep ELİBOL ÇAKMAK

Assoc. Prof.

Bioengineering

Senem TEKSOY BAŞARAN

Assist. Prof.

Bioengineering

Muhammed Erkan KARABEKMEZ

Assist. Prof.

Bioengineering

Saliha Ece ACUNER

Assist. Prof.

Bioengineering

Işık ÇOBAN

Research Assist.PhD.

Bioengineering

Songül YAŞAR YILDIZ

Research Assist. PhD.

Bioengineering

  1. Courses to be offered within the scope of the program

Course Code

Course Name

Compulsory/Elective

Theoretical (hour)

Practice (hour)

Credit

ECTS

BYM 701

Scientific Research Methods and Ethics

C

3

0

3

7

BYM 702

Bioengineering Applications

C

3

0

3

7

BYM 703

Structural Biology

E

3

0

3

7

BYM 704

Structural Bioinformatics and Modeling

E

3

0

3

7

BYM 705

System Biomedicine

E

3

0

3

7

BYM 706

Network Biology

E

3

0

3

7

BYM 707

Industrial Biotechnology

E

3

0

3

7

BYM 708

Advanced Reaction Engineering

E

3

0

3

7

BYM 709

Industrial Applications of Environmental Biotechnology

E

3

0

3

7

BYM 710

Bioengineering Applications of Membrane Processes

E

3

0

3

7

BYM 711

Advanced Statistics

E

3

0

3

7

BYM 712

Advanced Metabolic Engineering

E

3

0

3

7

BYM 713

Drug Repositioning

E

3

0

3

7

BYM 714

Integrated Bioprocesses and Applications

E

3

0

3

7

BYM 715

Enzymatic Analysis Methods

E

3

0

3

7

BYM 716

Bioreactor Design

E

3

0

3

7

BYM 717

Biosensors

E

3

0

3

7

BYM 718

Biosafety and Bioeconomics

E

3

0

3

7

BYM 719

Seminar 1

C

1

2

0

4

BYM 720

Seminar 2

C

1

2

0

4

BYM 721

Specialization Field Course

C

4

0

0

15

BYM 722

PhD Qualifying Exam

C

0

0

0

30

BYM 723

PhD Thesis Proposal

C

0

0

0

30

BYM 724

PhD Thesis

C

0

0

0

45

I. SEMESTER (FALL TERM)

Course Code

Course Name

Compulsory/Elective

Theoretical (hour)

Practice (hour)

Credit

ECTS

BYM 701

Scientific Research Methods and Ethics

C

3

0

3

7

BYMXXX

Elective 1

E

3

0

3

7

BYMXXX

Elective 2

E

3

0

3

7

TOTAL

9

0

9

21

II. SEMESTER (SPRING TERM)

Course Code

Course Name

Compulsory/Elective

Theoretical (hour)

Practice (hour)

Credit

ECTS

BYM 702

Bioengineering Applications

C

3

0

3

7

BYMXXX

Elective 3

E

3

0

3

7

BYMXXX

Elective 4

E

3

0

3

7

BYM 719

Seminar 1

C

1

2

0

4

TOTAL

10

2

9

25

III. SEMESTER (FALL TERM)

Course Code

Course Name

Compulsory/Elective

Theoretical (hour)

Practice (hour)

Credit

ECTS

BYMXXX

Elective 5

E

3

0

3

7

BYMXXX

Elective 6

E

3

0

3

7

BYM 720

Seminar 2

C

1

2

0

4

TOTAL

5

2

0

18

IV. SEMESTER (SPRING TERM)

Course Code

Course Name

Compulsory/Elective

Theoretical (hour)

Practice (hour)

Credit

ECTS

BYM 722

PhD Qualifying Exam

C

0

0

0

30

BYM 723

PhD Thesis Proposal

C

0

0

0

30

TOTAL

4

0

0

60

V. SEMESTER (FALL TERM)

Course Code

Course Name

Compulsory/Elective

Theoretical (hour)

Practice (hour)

Credit

ECTS

BYM 721

Specialization Field Course

C

4

0

0

15

BYM 724

PhD Thesis

C

0

0

0

45

TOTAL

4

0

0

60

VI. SEMESTER (SPRING TERM)

Course Code

Course Name

Compulsory/Elective

Theoretical (hour)

Practice (hour)

Credit

ECTS

BYM 721

Specialization Field Course

C

4

0

0

15

BYM 724

PhD Thesis

C

0

0

0

45

TOTAL

4

0

0

60

Course Contents:

BYM 701-Scientific Research Methods and Ethics

In this course, students will be taught how scientific research should be done. Basic information such as novelty of the research subject, creating a timeline and method for the study, evaluating the results obtained, preparing a thesis proposal, preparing a project, writing an article will be given. In addition, awareness about scientific ethics will be raised.

BYM 702-Bioengineering Applications

In this course, examples within the scope of bioengineering applications, such as below, will be examined. Basic components of cell culture systems (cell structure, reproduction, differentiation, transformation, aging), cell production environments (composition of the medium, the effect of the culture system on the medium selection, preparation of the medium, sterilization, quality control), cell culture sources, contamination of cell cultures ( resources, results, measures, elimination), commercial scale micropropagations, the importance of plant tissue cultures in plant breeding, bioprocess kinetics, kinetic models and performance estimation, yield, efficiency concepts, different biocatalysts, bioreactor principles and scaling up in cell cultures.

BYM 703-Structural Biology

The aim of this course is; to learn the structures of biomolecules and the methods used to study them. The course will cover topics such as protein folding and factors involved in protein folding, structural databases, experimental techniques and computational methods used to determine and analyze the structures of biomolecules.

BYM 704-Structural Bioinformatics and Modeling

In this course; Homology modeling, molecular simulation and docking of biological molecules will be covered. Principles of protein structure, including non-covalent bonds, will be reviewed. Structural bioinformatics and genomics will be introduced.

BYM 705-System Biomedicine

Within the scope of the course, students will be informed about the basic methods and approaches used in systems biology. Then, it will be explained how these applications can be integrated and used in the field of medicine.

BYM 706-Network Biology

The topics to be studied in the scope of the course can be summarized as an introduction to data integration and statistical methods used in System Biology, Bioinformatics and Systems Pharmacology research. The course covers methods of processing raw data from genome-wide mRNA expression studies (microarrays and RNA-seq), including data normalization, differential expression, clustering, enrichment analysis, and network structure. This includes the use of the analysis tools, as well as understanding the mathematics behind the methods applied within the tools.

BYM 707-Industrial Biotechnology

Topics to be studied in this course are: Overview of Industrial Biotechnology, Microorganisms in Industrial Biotechnology, Microbial Growth and Kinetics of Bioproducts, Enzyme Technology, Biological Fuel Production, Single Cell Protein, Biotechnology and Medicine, Environmental Biotechnology, Biotechnology in Agriculture and Forestry Industries, Safety in Biotechnology of Food and Beverage, Safety in Genetic Engineering, and Social and Ethical Aspects of Biotechnology.

BYM 708-Advanced Reaction Engineering

The reaction kinetics will be explained in detail, taking into account the applications of bioengineering in different fields. In addition, by considering different reactor types, the application of reaction kinetics in different reactors will be discussed in detail. Particularly, how to write mass and energy balance in bioreactors and how to use reaction rate expressions for different reactors will be discussed.

BYM 709-Industrial Applications of Environmental Biotechnology

Undoubtedly, one of the most important problems of today is the increasing environmental problems. In the solution of these problems, environmentally friendly biotechnological solutions should be developed and adapted to the industry. Within the scope of this course, solutions will be offered with biotechnological approaches that will be developed in the bioengineering discipline by addressing environmental problems specific to industries.

BYM 710-Bioengineering Applications of Membrane Processes

Membrane processes are increasingly being used in biotechnology. This technology is used as an alternative process in both environmental biotechnology applications and production areas where biotechnology is used. In this course, bioengineering applications of membrane processes will be discussed in detail and examples on their designs will be given.

BYM 711-Advanced Statistics

The aim of this course is the gain of any statistical skills that a researcher will need. Probability, probability distributions, mathematical expectation, sample distributions, confidence intervals, hypothesis tests, linear regression, multiple nonlinear regression, ANOVA, factorial experiment design, non-parametric statistics will be covered in detail and on bioengineering examples.

BYM 712-Advanced Metabolic Engineering

Theoretical and practical skills will be gained to simulate and optimize cell growth and metabolite production/consumption using mathematical modeling approaches representing cellular metabolic networks. Students will be able to investigate the effect of bioreactor operating conditions on cellular metabolic pathways. Subjects such as metabolic flux control analysis, metabolic flux balance analysis, kinetic metabolic models, multi-strain spatial/temporal metabolic culture models will be studied and practical skills will be gained by using the relevant software tools.

BYM 713-Drug repositioning

Data integration and statistical methods used in System Biology, Bioinformatics and Systems Pharmacology research will be introduced. Afterwards, drug repositioning examples, applications and current scientific literature on this subject will be discussed.

BYM 714-Integrated Bioprocesses and Applications

Topics to be examined in this course are: related concepts, overview and roadmap, upstream processes in integrated bioprocesses, downstream processes, mass and energy balances, in situ product removal, flow diagrams, production of penicillin, bioethanol, biodiesel, amylase, chitosan, rituximab and HGH and industrial biodesigns.

BYM 715-Enzymatic Analysis Methods

Topics to be examined in this course include principles of enzymatic analysis, basic techniques used in enzymatic analysis, determination of analyte concentrations and enzyme activity, advanced enzymatic methods, sample preparation and collection for enzymatic analysis, development of new methods, improvement, modification, adaptation and problem solving, and applications of enzymatic analysis methods.

BYM 716-Bioreactor design

Within the scope of this course; fermentation kinetics, batch, continuous and batch-fed bioreactor cultures, kinetic parameters, variables; mass transfer in bioreactors, fermenter design, reactor dynamics, rheology in bioreactors, aeration and mixing; Reactor types and auxiliary equipment (pump, filter, valve, etc.) topics will be covered.

BYM 717-Biosensors

In this course; sensors and sensor technology, types and usage areas of biosensors, voltammetry, amperometry, potentiometry, conductometry, capacitive sensors, enzyme, gene and protein supported sensors, QCM gravimetric sensors, optical sensors will be covered.

BYM 718-Biosafety and Bioeconomics

In this course; definition and principles of biosafety, gains and requirements of biosafety, bioeconomy definitions, intellectual property rights, the importance of bioeconomics and real world examples will be discussed.

BYM 719, 720-Seminar (I and II)

It is planned that students will conduct literature research on current Bioengineering issues, determine a subject of interest and make a presentation about it. Thus, it is aimed that the students will be able to master the literature, create new research project ideas and gain the habit of preparing successful presentations.

BYM 721-Specialized Field Course

The aim of this course is to enable the student to acquire advanced knowledge in a field of his own choosing, to gain research experience and to start to contribute to the academic literature on the subject. The student is expected to learn the latest information in a theoretical or experimental field, and on any subject of interest, and then make an up-to-date, original and useful contribution to the relevant literature.

BYM 722-Doctoral Qualifying Exam

It is a course that covers the necessary studies to prepare for an exam in which it is determined whether a student has enough academic competence to carry out his doctoral thesis or not.

BYM 723-PhD Thesis Proposal

It is the course in which a student acquires the knowledge and gains such as determining the thesis subject, making a literature study, converting the information into practice, evaluating the results of the study, preparing a report and presenting the study.

BYM 724-Doctoral Thesis

It is a course in which the student will increase his knowledge and experience in the scientific field of interest, provide scientific ethics and study discipline, and gain the ability to follow and evaluate the current literature.

  1. Graduation Requirements

For students admitted with a master's degree with thesis; a minimum of 240 ECTS (not less than 60 ECTS in one academic year) and twenty-four credits in total, consisting of a minimum of eight courses, two seminars, proficiency exam, thesis proposal and thesis study are required. Students are required to take two seminar courses in order to graduate. In order for the student to be eligible for thesis defense, his/her studies within the scope of the thesis must be published or accepted for publication in a journal scanned under SCI.

  1. Employment Opportunities

Those who have completed the Bioengineering doctorate program can work as a researcher in hospitals and clinics, institutions with legal obligations such as Hıfsısıhha and TSE, genetic diagnosis and treatment centers, vaccine production facilities, import-export companies, public institutions, or as a lecturer in universities.

In our country, bioengineers are employed in a wide range of industrial areas from food, agriculture, health and pharmaceuticals to environmental sectors. Some example areas that Bioengineers can find employment opportunities in, are listed below:

  • Pharmaceutical companies
  • Genetic diagnostic centers
  • Hospitals
  • Biofuel production facilities
  • Chemical industry
  • Stem cell banks
  • Microbiology and biotechnology companies
  • In vitro fertilization centers
  • Biomedical companies