Courses Descriptions
--MSc--
BENG505 Current Topics in Molecular Biology
Current Topics in Molecular Biology is an advanced course on recent developments of molecular biology and its translational aspects.
BENG506 Bioinformatics
The course covers computational techniques for mining large amount of information produced by recent advances in biology, including genome sequencing and microarray technologies. The main topics of the course include DNA and protein sequence alignment, sequence motifs/patterns, phylogenetic trees, protein structures, microarray data analysis and biological networks.
BENG507 Human Molecular Genetics
Advanced molecular biology is an advanced course on the molecular biology of pro- and eukaryotic organisms. Topics include chromosome structure and organization, RNA transcription, selected aspects of the molecular regulation of gene expression, protein synthesis and post-translational regulation, DNA synthesis, repair and recombination.
BENG508 Advanced Cell Biology
Advanced Cell Biology course deals with the biology of cells of higher organisms: The structure, function, and biosynthesis of cellular membranes and organelles; cell growth and oncogenic transformation; transport, receptors, and cell signaling; the cytoskeleton, the extracellular matrix, and cell movements; chromatin structure and RNA synthesis.
BENG512 Biotechnology and Biosafety
Modern Biotechnological approach. Historical development of biotechnology and biosafety. Transgenic applications. Biosafety of transgenic applications. Assessment methods to evaluate the effects of genetically changed organisms for food safety and environment. Biosafety systems. Biotechnological applications. Comparison of specific similarity and precaution principle approaches. Effect of biotechnological applications to human health and biological variation. Biosafety control systems. Risk assessment and risk management for biosafety systems. International biosafety protocols and rules in different countries. Socioeconomical and ethical issues in Biotechnology.
BENG514 Cancer Biology and Treatment
Provides an integrated lecture series summarizing current knowledge in cancer biology and integrating current literature with basic concepts. Topics include molecular mechanisms of cancer initiation, progression and metastasis, signal transduction, types of cancer, pathology, sources of carcinogens, genetic and epigenetic mechanisms and consequences, therapeutic resistance, cancer markers and therapeutic targets, statistics of incidence/survival. Students will learn to use online databases to develop independent strategies for analyzing datasets. There will be several writing assignments and in class oral presentations of research articles.
BENG515 Introduction to Tissue Engineering
Description of tissue engineering. Fundamentals; importance of cell-scaffold-biosignal molecule integration. Scaffold characteristics, general design criteria will be covered. Selection of cell sources and stem cells, in vitro culture conditions, and tissue engineered products and problems in their clinical utilization will be discussed. Organ tissue engineering.
BENG517 Polymeric Biomaterials
Basics of polymer structure. Classification of polymers by source, chemistry, shape, end-use, etc. Natural and synthetic polymers. Criteria of polymer type selection. Types of natural polymers, structures, isolation-purification, applications (chitosan, alginate, cellulose, collagen, starch, gelatin); types of synthetic polymers, synthesis-purification, applications (biodegradable polymers, silicones, PET, PTFE, PU, polyamides, acrylate-based polymers). Applications of biomedical polymers; dental, orthopedical applications, adhesives, sutures, vascular grafts, wound dressings, controlled release materials, carriers for drug/gene delivery.
BENG518 Biomaterials
Description and history of biomaterials. Criteria for the success of a biomaterial. Biocompatibility definition. Classification and general application types will be discussed. Biomaterials surface characteristics, investigation techniques: FTIR-ATR, SEM, surface tension, ESCA, etc. Mechanical properties and measurement, optical and diffusion properties. Material types, advantages and disadvantages: metals, ceramics, composites, polymers. Material fabrication techniques. Material- tissue interaction; coagulation, immune response, foreign body reaction. Discussion of a biomaterial journey: from lab to body.
BENG521 Biomedical Electronics
Introduction of biomedical system. Principle and design of various biomedical devices such as pacemaker, EEG, ECG, EMG, ve ICU equipment, diagnostic imaging devices, blood bank monitor, CT, MRI, mammography, ultrasound, endoscope, confocal microscope, multiphoton flourescent microscope.
BENG525 Instrumental Analysis
Students will develop an understanding of the analytical capabilities of a number of instrumental methods and be able to suggest suitable instrumental methods for particular analytical problems. The main objective of instrumental analysis is to learn the theory of operation for several types of instruments used for chemical measurements in the analytical sciences. Lecture topics cover spectrophotometric and chromatographic methods. In the laboratory, students gain hands-on experience both by performing selected basic chemical determinations and by undertaking special projects.
BENG526 Basic Patent Principles in Science and Engineering
This course will provide an introduction to the basic principles of the national and international patent systems. It covers the function of the patent system; the nature of patents as property and as legal instruments; comparisons with other forms of intellectual property; subject matter eligible for patenting; the conditions for patentability of an invention; and the disclosure requirements for a patent application. This course mainly focuses on the preparation technics of a patent application. The students will each be assigned an case study, and will write a patent application draft. Students will be instructed as to best practices drafting the application, and then will be critiqued regarding written patent applications. The patent applications will be written in stages, including invention disclosure considerations, drawings, claims, and specification, with critique on each step in the process.
BENG531 Biosignal and Image Analysis
Fundamentals of signal processing (linear time invariant systems, Fourier transforms for continuous and discrete signals, sampling, filter design; Imaging system: Point spread function, resolution (pixel, voxel, spatial, temporal); Image quality and uncertainties in image formation (digitization, quantum efficiency, calibration, CNR, SNR); Image registration, filtering and noise removal; Basic clustering methods; Time –frequency analysis; Compressed sensing; Applications for biomedical signal and images.
BENG535 Molecular & Statistical Mechanics
This course covers statistical mechanics theory and its applications to molecular systems, and computer simulation methods to study the dynamics/energetics of macromolecules. No background is required. Upon completion of this course, students should be able to: 1) explain the concepts of statistical mechanics; 2) use computational methods. Topics include: Maxwell-Boltzmann distributions, ensembles, partition functions, energy optimization, Monte Carlo methods, and molecular dynamics simulations.
BENG536 Linux for Scientific Research
Linux is a computer operating system that appears in many different architectures: mainframes, servers, desktops, and laptops. Researchers in any fields may encounter a situation in which Linux knowledge is required to pursue their studies. This course is primarily designed for would-be users of Linux. Topics include common Linux commands, bash shell, user environment, editors (vim and emacs), filters (grep, sed, and awk), document-preparation tools (LaTeX, cvs, and make). Upon completion of the course, students should be intermediate-level Linux users who possess a good working knowledge of Linux and can keep developing their Linux knowledge and skills by themselves.
BENG537 Stem Cells
It will introduce important biological concepts like stem cell biology, pluripotency, adult and embryonic and cancer stem cell and the barriers to regenerative medicine, including scientific, ethical, regulatory and proprietary issues. We will also consider the potential consequences and limitations of stem cell therapy, particularly the connection between stem cells and cancer. Students will have a comprehensive overview of this exciting new field of research and its clinical relevance.
BENG539 Nanocarriers and Drug Delivery
Definiton of drug delivery. Criteria for a nanocarrier design. Physiochemical characteristics. Types of nanocarriers: lipid-based, inorganic-based, polymer-based nanoparticles, biological nanoparticles (viruses). Quantum dots for nuclear and cytoplasmic visualization. Targeting and biodistribution of nanoparticles, EPR effect, renal clearance, etc. Toxicological issues. Examples of FDA approved nanodrugs in addition to nano formulations at the pre-clinical and clinical stages.
BENG542 Molecular Basis of Disease
The main aim of this course is to provide an insight into the molecular mechanisms underlying human disease processes and help the development of targeted therapies and drugs. To provide an opportunity for students to: learn genetics and biochemical processes leading to a range of diseases; learn the molecular details of protein folding diseases; learn the modelling human diseases; learn diseases caused by enzyme deficiency; learn how the immune system works and autoimmune diseases.
BENG543 Computational Biology
This course will provide up-to-date theories and methodologies in computational biology with emphasis on structural and dynamical aspects of biological systems at atomic scale. The classes consist of both classroom lectures and computer labs. Upon completion of the course, the students should be able to perform various computational analyses on biological systems. The topics include Linux basics, molecular modelling and visualization, molecular dynamics, search algorithms, statistical analysis of biological data.
BENG544 Neuroscience
The main purpose of this course is to introduce types of nervous cells, structures of nervous cell, nerve impulse, connection between nervous cells, nerve cell formation in the brain and spinal cord; sensory systems such as vision, hearing, smell, transformation and processing of physical energy into neural signals, neurochemical basis of brain diseases, emotional, mobility, learning and memory control systems.
BENG545 Protein Expression and Purification
Overview of bacterial and eukaryotic protein expression systems and protein extraction methods from different sources. Principles of protein purification methods such as precipitation, centrifugation, electrophoresis, liquid chromatography and affinity enrichment.
BENG546 Data Mining
The course presents an introduction to popular data mining approaches. The key processes in data mining will be covered: types of attributes, common data set structures, data preprocessing (cleaning, transformation and reduction), feature selection, sampling, using different statistical and machine learning techniques (supervised and unsupervised methods) and visualization (histogram, box-plot, ROC).
BENG547- Bioconjugate Techniques
This course consists of following subjects:
- To determine the functional groups/functions in biological systems and the chemical modifications and the reactions of these targets.
- Chemicals used in bioconjugations (Functional chemical cross linkers, tags and probes) and their reactions.
- Bioconjugate applications. (Bioconjugations and modifications)
BENG548¬ Cell Culture Techniques
This course provides knowledge of basic cell culture concepts and terminology, and it aims to be a guide for the grad students to design and carry on an in vitro experiment. The topics covered in this course include aseptic working area, maintenance of cells in the culture, cell-based assays, 2D/3D cell culture strategies, transfection and hybridoma technologies, and preventative and/or corrective actions for the contamination problem.
BENG549-Genom Editing: CRISPR
The objective of this course is to introduce the concept of genome editing technology. We will be discussing the history of genome editing technologies (ZNF, TALEN and CRISPR/Cas9) and will be able to compare distinct methods for genome editing. We will design CRISPR experiments (sgRNA, vector selection or adoption of the vector-free system, screening strategy, CRISPR efficiency, specificity and safety, etc) from the beginning. CRISPR-mediated genome editing has opened doors to cure incurable human diseases and the extent to which CRISPR-mediated genome editing provides hope for these diseases will be discussed. We will discuss the applications of CRISPR/Cas9-mediated genome editing in a wide range of research. Finally, there will be a discussion of ethical aspects of genome editing technology.
BENG550-Bioengineering; A Conceptual Approach
This course reflects the critical principles and basic concepts in bioengineering which integrates the biological, physical, and chemical laws and principles enlightening bioengineering as an emerging, novel, complex approach with deep roots in the fundamental science.Topics covered in this course include cell architecture and physiology, genomics and proteomics, stem cells, drug delivery, system physiology, biomechanics, bioinstrumentation, biomaterials, nanotechnology.
--PhD--
BENG601 Emerging Topics in Biotechnology
This seminar-style, capstone course is an in-depth exploration of emerging technologies, innovations, and new products that are noteworthy to the biotechnology industry. The first half of the course focuses on examining and critiquing what new scientific discoveries will likely impact the industry and in what ways. In the second half of the course, students, working in teams, will give written and oral presentations on case studies that attempt to predict products derived from the new innovations and discoveries. The objective of the course is to give the student insight into the process of translating scientific discovery into innovative products.
BENG602 Introduction to Nanobiotechnology: Concepts and Applications
This course provides perspective for students and researchers who are interested in nanoscale physical and biological systems and their applications in medicine. It introduces concepts in nanomaterials and their use with biocomponents to synthesize and address larger systems. Applications include systems for visualization, labeling, drug delivery, and cancer research. Technological impact of nanoscale systems, synthesis, and characterizations of nanoscale materials are discussed.
BENG603 Ethics in Biotechnology
History of bioengineering, definition of bioengineering, research, publishing principles and human and animal rights in terms of technology, place of environmental consciousness on the application of bioengineering subjects and important ethical terms, legal and social laws.
BENG604 Tissue Engineering and Regenerative Medicine
Basics concepts of tissue engineering andregenerative medicine field will be covered in the first part of the course. The repair and regeneration of varying tissues for therapeutic purposes will be discussed. Mechanism of cell differentiation into specific tissues in response to biological signal molecules will be explored. Cellular mechanism involved in animal clonning. Molecular basis of cellular tissue remodelling and regeneration fort he discovery of new drugs.
BENG605 Artificial Organs
Introduction to artificial organs. Mass transfer and basic principles of fluid mechanics. Chemical reactions in biological systems. Information on biomaterials. Basic principles of artificial organ design (biomimetics). Effects of artificial organs on the development of society health. Mass transfer. Basic principles of fluid mechanics. Chemical reactions in biological systems. Chemical reactions in biological systems. Basic components of biological systems. Working principles of biological systems. Production of biomaterials used in artificial organs. Basic principles of artificial organ design (biomimetics). Artificial organ (heart, lung, kidney, etc) design Effects of artificial organs on the development of society health.
BENG606 Biomechanics
Introduction to biomechanics and muscle-skeletal system. Introduction to Biomechanics in biological systems and transport process. Dynamics of mechanical systems. Dynamics of muscle and arthrosis. Response of living tissues under the strain. Application methods of mechanical engineering on human muscle- skeletal system. Mechanical properties of tissues. Investigation of orthopedic materials and mechanical properties. Tension and deformations on materials. Analysis of fracture-crack, fracture-crack fictions, frictional, polish and overwear, process of implants. Headlines on heart dynamics and heart beating, blood circulation, microcirculation and muscle mechanics. Modern developments on biomechanics at advanced mathematical level. Main research areas and problems related with biomechanics.
BENG607 Multifunctional Polymeric Nanocarriers
Multifunctional nanocarriers and main characteristics. A typical nanocarrier. Pathways and problems in drug delivery. Types of nanocarriers: liposomes, inorganics, polymeric nanoparticles, micelles, etc. Polymeric nanoparticle preparation methods (emulsion, phase separation, coaservation). Micelle formation; controlled polymerization for uniform polymer chains (RAFT, ATRP). Cross-linked micelles. Stimuli-responsive systems. Drug-conjugated systems. Surface modification, PEGylation. Targeting ligands and targeting approaches.
BENG608 Biosensors
Underlying engineering principles used to detect small molecules, DNA, proteins, and cells in the context of applications in diagnostic testing, pharmaceutical research, and environmental monitoring. Biosensor approaches including electrochemistry, fluorescence, acoustics, and optics; aspects of selective surface chemistry including methods for biomolecule attachment to transducer surfaces; characterization of biosensor performance; blood glucose detection; fluorescent DNA microarrays; label-free biochips; bead-based assay methods. Case studies and analysis of commercial biosensors.
BENG609 Advanced Polymer Science
Polymer terminology, nomenclature. Stereochemistry in polymers, conformation, configuration, isomerization, optical activity. Morphology of polymers, crystaline, amorphous and semi-crystalline polymers, glass-transition temperature, melting temperature. Methods for the molecular weight determination of polymers, colligative properties and molecular weight, size-exclusion chromatography, light-scattering, etc. Mechanical properties and other properties of polymers. Polymerization reactions, radical polymerization, addition polymerization, condensation polymerization, etc. Polymerization processes, bulk, solution, suspension, emulsion polymerizations. Processing of polymers.
BENG610 Nanofabrication for Biological Applications
Importance of surface characteristics for biological applications (i.e., biomaterials, biosensors). Lithography, optical and e-beam lithography; X-ray lithography, focused-ion lithography, soft lithography, imprinting lithography, Thin film deposition, physical vapor deposition, chemical vapor deposition; Etching: wet and dry; Self-assembling; Microelectromechanical systems.
BENG611 Medical Imaging
General characteristics of imaging systems; X-ray and CT: general principles, interaction of X-rays with tissues, contrast agents, imaging techniques, image reconstruction, radiation dose; Nuclear Medicine: general principles, radionuclide, radioactive decay, gamma camera, imaging techniques, SPECT, PET; Ultrasound imaging: general principles, interaction of acoustic waves with tissue, acoustic impedance, instrumentation, scanning modes, artifacts, blood velocity measurements, contrast agents; MR imaging: general principles, nuclear magnetism, magnetic resonance, instrumentation, imaging sequences, contrast agents, imaging techniques, functional MRI.
BENG612 Cell Death
Throughout this course students will learn how cells decide their mode of death based on stress and pathological conditions. In addition to that, we will identify the different classification of cell death processes and mechanisms. The different cell death processes that will be covered in the course are apoptosis, extrinsic apoptosis, mitochondrial permeability transition (MPT)-driven necrosis, necroptosis, ferroptosis, pyroptosis, parthanatos, entotic cell death, NETotic cell death, lysosome-dependent cell death, autophagy-dependent cell death, immunogenic cell death, cellular senescence, and mitotic catastrophe.
BENG613 Implant-Cell Interactions
Cell response on implant strongly governs the success of the treatment. This course aims to shed light on to the molecular and cellular interactions with the implant surfaces. The changes in cell structure will be analyzed both in normal and cancer cells. Based on topics covered student will be able to design implants which would enhance the cell response and minimize the post-surgical complications.
BENG614 Mechanical Properties of Biomaterials
This course aims to bring an understanding of the fundamental relationships between the mechanical properties of a range of biomaterials and the biomedical applications. Critical properties influencing the success of the application will be discussed by analyzing the current clinical applications. Students will learn how to characterize some of the main properties and implement this knowledge into the selection of an appropriate material specific to the application.
BENG617 Glyco-protein Engineering
Glyco-protein is a protein modified with a glycan via enzymatic reaction. Majority of the proteins in human body are glycosylated. This protein glycosylations have a profound structural and functional consequences. Therefore, glycol-proteins need to be properly glycosylated. Especially, this is very important for therapeutic glyco-proteins which requires carefully control. In this course, the importance of protein glycosylation will be discussed in terms of the requirements for protein glycosylation, glycosylation machinery, techniques for characterization of glycoprotein, impact of glycosylation in human biology, and finally implication of these aspects of glycosylation in engineering of glyco-proteins for therapeutic applications.
BENG619 Proteomics and Metabolomics
Introduction to proteome and proteomics technology. General workflow for bottom-up and top-down proteomic approaches. Exploration of differential protein expression, post-translational modifications and protein-protein interactions (PPI). Introduction to metabolome and metabolomics. Metabolite identification, pathway identification and pathway integration.
BENG620 Mass Spectrometry:
Basic concepts and principles of mass spectrometry. Ion sources and ionization (ESI, APCI, FAB, MALDI and others), analyzers (Magnetic-Sector, Quadrupole, Time-of-Flight, Ion-trap, FT-ICR), and detectors. Interpretation of mass spectral data. Examples of mass spectrometry methodologies in different biological applications.
BENG621 Cell Signaling
The course will provide a detailed knowledge of molecular mechanisms of cell signaling with emphasis on the significance of signal transduction in physiology (such as apoptosis, cell cycle regulation, gene transcription) and pathophysiology (such as cancer and cardiovascular disease). The main signalling pathways and their functional properties, including different types of receptors and their signalling pathways, G proteins, protein kinases will be discussed together with their model systems and regulation. Accordingly, therapeutic strategies designed to specifically target altered signaling pathways in diseases will be discussed.
BENG622 Machine Learning
This course covers the fundamental concepts of machine learning. We will also examine implementation of widely used machine learning methods such as SVM, Decision Tree, Random Forest, Naïve Bayes, k-means clustering and hierarchical clustering on various datasets (biological, medical etc.) by using data science platforms (e.g. KNIME, Weka).
BENG624 Metastasis and Tumor Microenvironment
This course will introduce cancer, as a complex architecture comprised of different cell types and macromolecules that form intricate interactions for the good of the tumor “organ”. This course will discuss how tumor cells and other non-transformed specialized cells interact to constitute the “tumor microenvironment (TME)” and how this interaction facilitates the process of metastasis. In addition to that, the course will cover the multistages of metastasis that requires cancer cells to escape from the primary tumour, survive in the circulation, seed at distant sites and grow.