The minimum number of credits that must successfully be completed to get a degree in Master of Science in Biomedical Engineering are given in the Table below:

  National Credit ECTS Credit
Compulsory Course 9 24
Elective Course 12 32
Seminar 4
Thesis 60
Total 21 120

The list of compulsory and elective courses in the Master of Science in Biomedical Engineering Program is presented in Table-1 and Table-2, respectively.

Table 1. Compulsory Courses in the Master of Science in Biomedical Engineering Program.

 FBE Code  BME Code Course Name National Credit ECTS Credit
802500735010 BME 501 Advances in Biomedical Engineering (3 0)3 8
802500735020 BME 502 Advanced Engineering Mathematics (3 0)3 8
802500735030 BME 503 Fundamentals of Biological Sciences (3 0)3 8
802500735040 BME 504 Fundamentals of Engineering Sciences (3 0)3 8
805101735000 BME 500 Research Methods (1 0)1 3
  • BME 501 course will be taken by all students.
  • Minumum of 2 courses will be selected among courses BME 502, BME 503 and BME 504.
  • BME 500 is a joint compulsory course that is given by the Institute of Natural and Applied Sciences.


Table 2. Elective Courses in the Master of Science in Biomedical Engineering Program.

 FBE Code BME Code Course Name National Credit ECTS Credit
802500735051 BME 505 Magnetic Resonance Imaging (3 0)3 8
802500735061 BME 506 Digital Image Processing (3 0)3 8
802500735071 BME 507 Functional Neuroimaging (2 2)3 8
802500735081 BME 508 Data Mining and Machine Learning in Bioinformatic Field (3 0)3 8
802500735091 BME 509 Viscoelasticity (3 0)3 8
802500735101 BME 510 Biomechanics (3 0)3 8
802500735111 BME 511 Bioreactor Design (3 0)3 8
802500735121 BME 512 3D Printing in Medical Applications (3 0)3 8
802500735131 BME 513 Microscopic Techniques in Biomedical Engineering (2 2)3 8
802500735141 BME 514 Advances in Tissue Engineering (3 0)3 8
802500735151 BME 515 Nanotechnology Applications in Biomedical Engineering (3 0)3 8
802500735161 BME 516 Cell and Gene Therapy (3 0)3 8
802500735171 BME 517 Thermodynamics of Biological Systems (3 0)3 8
802500735181 BME 518 Advanced Computational Methods for Biomaterial Modelling (2 2)3 8
802500735191 BME 519 Physics of Medical Imaging (3 0)3 8
802500735201 BME 520 Biostatistics for Biomedical Engineering (2 2)3 8
802500735211 BME 521 Animal Models in Biomedical Engineering (3 0)3 8
802500735221 BME 522 Regenerative Medicine (3 0)3 8
802500735231 BME 523 Advanced Genetics and Genomics (3 0)3 8
802500735241 BME 524 Applications of Bioinformatics in Biomedical Engineering (3 0)3 8
802500735251 BME 525 Trends in Biomedical Research Focused on Proteomics (2 2)3 8
  • Minumum of 4 Elective Courses will be selected.

Course Contents:

Advances in Biomedical Engineering

Recent research topics in biomedical engineering, industrial developments in biomedical engineering, biomedical engineering ethics, entrepeneurship, research paper analysis in a wide variety of biomedical engineering topics, writing a research paper, preparing a research proposal, patents.

Advanced Engineering Mathematics

Ordinary differential equations, basic concepts, first-order ODEs, second-order linear ODEs; linear algebra, vector calculus, matrix eigenvalue problems, vector differential calculus, vector integral calculus; Fourier analysis; partial differential equations; complex analysis, complex numbers, complex functions; numeric analysis, numeric linear algebra, numerics for ODEs and PDEs; optimization, uncontrained optimization, linear programming; data analysis, probability theory, mathematical statistics.

Fundamentals of Biological Sciences

Biomolecules (proteins, nucleic acids, carbohydrates, lipids), life and organization in living systems (cells, tissues, organs), cell metabolism, genetics, principles of cell physiology, neural system, biosignals.

Fundamentals of Engineering Sciences

Basic engineering calculations (dimensions, dimensionless groups, stoichiometry,  presentation and analysis of data, open and close systems, steady and un-steady state systems), fundamentals of momentum, mass and energy balances, concepts of thermodynamics, fundamentals of kinetics, separation methods in bioprocesses, circuits, signals, mathematical models for biological systems

Research Methods

Research terminology in biomedical engineering, ethical principles and challenges of biomedical research, approval processes, quantitative, qualitative and mixed methods approaches to research, literature review process, critical analysis of published research

Magnetic Resonance Imaging

Temel MRI fiziği, nükleer spin, manyetik moment, dış manyetik alanlarla etkileşim; MRI donanımı bileşenleri; görüntü oluşturmada temel kavramlar, radyofrekansı ile uyarma, gradyan manyetik alanlar, görüntüleme denklemi, Fourier Dönüşümü, k-uzayı, iki-boyutlu uzaysal kodlama; uygulamalar, görüntü arfefaktları, hızlı gmrüntüleme yöntemleri, sinyal-gürüntü oranı, kontrast-görüntü oranı, çözünürlük

Digital Image Processing

Human visual system; digital image fundamentals using MATLAB; image acquisiton, sampling theory, optimal quantization; histogram processing, contrast and brightness adjustment; arithmetic/logic operations; spatial filtering, contrast enhancement, edge sharpening; 2D transforms, Fourier Transform, frequency domain processing, ringing artifact, pixel operations, geometric processing image restoration, denoising, deblurring; image segmentation, edge detection, edge, linking, hough transform, thresholding; segmentation, region based segmentation, watershed segmentation, motion-based segmentation; morphological image processing; multi-resolution processing, discrete wavelet transform; image format and standards in medical images; biomedical applications.

Functional Neuroimaging

Basics of functional brain imaging and introduction to the brain imaging techniques, basic physical principles of Magnetic Resonance Imaging (MRI), introduction to MR contrast mechanisms introduction to physiology of functional MRI (fMRI), fMRI data analysis principles, definition of noise in fMRI, precprocessing of the fMRI data, statistical inference in subject and group level, introduction to fMRI experimental design.

Data Mining and Machine Learning in Bioinformatic Field

Biomedical data types, preprocessing, feature extraction, visulalizaiton, fundamentals of machine learning, linear regression, decision trees, random forest, support vector machine (SVM), rule-based classifier, nearest neighbor classifier, Naive Bayes, ensemble classifier, Bioinformatic models using classifiers, unsupervised learning, clustering algoritms, clustering algoritms in bioinformatics, sem supervised learning, introduction to deep learning, artificial neural networks, CNN.


Viscoelastic stress-strain constitutive relations, polymer behavior, viscoleastic models, elastic-viscoelastic correspondence principle, initial/boundary value problems, wave propagation, thermoviscoelasticity.


Motion dynamics, vibrations, internal and external flow, flying, swimming, blood flow in heart, arteries, veins, lung, micro- and macrocirculation, respiratory gas flow, mass transport in capillaries, tissues, force and deformation, stress, strain and stability of organs, fluid solid interaction

Bioreactor Design

Engineering, biochemical and physiological considerations in bioreactor design, Enzyme and microbial kinetics, mass transfer limitations in enzyme and microbial systems, Bioreactor types, selection and design, Scale-up, Analysis and design of bioreactors for the generation of tissue culture and stem cell culture

3D Printing in Medical Applications

Fundamentals of 3D printing, biomaterials for medical 3D printing, 3D printing methods based on different production techniques, patient-specific 3D modelling and 3D printing, direct 3D printing of tissues and organs, computational modelling, design, simulation and measurement activities involving 3D printed products and 3D models, 3D printing in the development of personalized therapeutics, disease models, surgical models and educational materials.

Microscopic Techniques in Biomedical Engineering

Basic physical principles behind microscopic techniques and imaging, introduction to optics, basic principles of light and image formation, light microscopy techniques, prisms and lenses, objectives, principles of histological analysis, fixation, sectioning, staining, immuncytochemistry, immunhistochemistry, fluorescence and digital imaging techniques, fluorescent labelling techniques, confocal microscopy, two-photon fluorescence microscopy,  scanning probe microscopy, atomic force microscopy, scanning and transmission electron microscopy, X-ray microscopy and and microCT.

Advances in Tissue Engineering

Basics of biomaterials and cell biology, tissue engineered graft development, production and characterization techniques and case studies on tissue engineered grafts that find clinical application, biomimetic strategies in tissue engineering, techniques to improve graft functionality and principles of clinical tissue engineering

Nanotechnology Applications in Biomedical Engineering

Brief introduction on nanotechnology applications in medicine, principles of nanomedicine and regenerative medicine, nanorobots and nanodevices, nanotechnological applications in orthopaedics, cardiology, cancer therapy and theranostics.

Cell and Gene Therapy

Brief introduction to cell and gene therapy, viral or non-viral delivery systems, gene expression, regulation and modifications monitoring during a therapeutic application, cell and gene based therapy applications for different diseased conditions.

Thermodynamics of Biological Systems

Thermodynamics of biological systems, with a focus on connection microscopic molecular properties to macroscopic states. Both classical and statistical thermodynamics will be applied to biological systems; phase equilibria, chemical reactions, and colligative properties. Topics in modern biology, macromolecular behavior in solutions and interfaces, protein-ligand binding, and the hydrophobic effect.

Advanced Computational Methods for Biomaterial Modelling

Computational methods and algorithms in general and particularly in biomaterial area, Monte Carlo methods, Molecular  Dynamic method for polymer and protein modeling, practical information about the softwares for protein folding problems.

Physics of Medical Imaging

Introduction to medical imaging, X-ray production and X-ray generators, Film-Screen systems, Image quality (Contrast,  Noise, Spatial resolution), Mammography imaging techniques, Fluoroscopy imaging technique, New digital detectors used for medical imaging, Computed tomography, Quality control and performace test for medical imaging systems.

Biostatistics for Biomedical Engineering

Types of variables and descriptive measures, Preparing data set in SPSS, Obtaining descriptive measures in SPSS, Introduction to hypothesis tests and confidence intervals, selection of appropriate hypothesis tests, universe mean/ratio valuability test, sampling and assessmet of sample size, Mann-Whitney U Test, SPSS, importance test of the difference between a pair and Wilcoxon paired sample test, one way analysis of variance and multiple comparison tests, Analysis of Kruskal-Wallis variance, Chi-square test, correlaion coefficient, regression analysis.

Animal Models in Biomedical Engineering

Basic principles of an animal research (what is animal research, types of animal research, experimental design, legal requirements and ethical approval). Basic anatomy of the animals. General classification of the experimental animals (laboratory animals, farm animals, pets and exotic animals). Selection criteria of the suitable animal model (research factors, animal care factors, animal-related factors, environmental factors, financial support).

Regenerative Medicine

Regenerative and restorative medicine, translational research, in-vitro tissue regeneration, cell-extracellular matrix interactions, regenerative medicine and tissue engineering, biocompatibility and biodegradation, vasculogenesis and angiogenesis, bioreactors, mechanical stimulators of tissue regeneration, epithelial, orthopedic, cardiovasular applications, nerve regeneration, neural applications, methabolic organ applications, plastic and reconstructive surgery applications, regenerative surgery, other current developments.

Advanced Genetics and Genomics

Basis of omics technologies and corner stone omic projects.

Applications of Bioinformatics in Biomedical Engineering

Frequently used bioinformatics tools and basic concepts of bioinformatics.

Trends in Biomedical Research Focused on Proteomics

Proteins that can be used in diagnosis, predictive selection and prognosis of complex diseases especially metabolic syndrome and cancer, current technologies during practical applications