Maroun Semaan Faculty of Engineering and Architecture (MSFEA) 317
PhD in Biomedical Engineering
Admission Requirements
The application procedures and admission requirements to the PhD program follow AUB’s
General University Academic Information as documented in the Graduate Catalogue. To
be considered for admission, applicants must hold a bachelor’s or master’s degree in
a relevant field of study from AUB or its equivalent, or from a recognized institution of
higher learning.
Acceptance into the PhD program is determined by academic performance as well
as an assessment of readiness, potential and ability to develop into independent
researchers as judged by interviews by faculty members, a written statement, letters of
recommendation, GRE scores, and other means of assessment such as publications and
industrial experience.
Accepted students are eligible to receive scholarships that fully cover their tuition fees
and provide a monthly stipend.
Degree Requirements
General requirements for master’s degree holders: Based on AUB’s guidelines, a
minimum of 48 credit hours beyond those required for the master’s degree, of which
a minimum of 18 credit hours must be in graduate level course work and a minimum
of 24 credit hours of thesis work, must be taken. Requirements also allow a maximum
of 3 credit hours out of the 18 credits of coursework as tutorial course and include a
0-credit comprehensive examination preparation course and a 0-credit thesis proposal
preparation course.
General requirements for bachelor’s degree holders: Based on AUB’s guidelines, a
minimum of 78 credit hours beyond those required for the bachelor’s degree, of which
a minimum of 36 credit hours must be in graduate level coursework and a minimum
of 30 credit hours of thesis work, must be taken. Requirements also allow a maximum
of 6 credit hours out of the 36 credits of coursework as tutorial courses and include a
0-credit comprehensive examination preparation course and a 0-credit thesis proposal
preparation course.
To earn a PhD degree in Biomedical Engineering, the student must complete the
following requirements:
• Satisfy the course and research credit requirements
• Satisfy the residence requirement and all other pertinent AUB regulations
• Have at least one international refereed journal article based on the PhD thesis
• Have at least one refereed conference paper based on the PhD thesis
• Have a cumulative average of 85 (3.7) or above
• Pass the comprehensive and oral qualifying examinations
• Successfully defend the PhD thesis
The following are the graduate level course requirements for students admitted with a
bachelor’s degree. The total number of credits is at least 36 credits divided among core,
restricted elective and free elective courses. Students admitted with a master’s degree
can waive as many courses as possible without going below the minimum required 18
credits of coursework.
Graduate Catalogue 2020–21
318 Maroun Semaan Faculty of Engineering and Architecture (MSFEA)
Core graduate courses: 21 credits of core courses from biomedical sciences and
engineering.
Required core courses (21 cr.) Credits
BIOC 321 Nucleic Acids and Basic Genetics 1
BIOC 322 Protein Biochemistry 1
BIOM 385 Research Ethics 1
BMEN 600 Biomedical Engineering Applications 3
BMEN 601 Computational Modeling of Physiological Systems 3
BMEN 671 PhD Lab Rotation1 1+1
BMEN 672 Hospital Lab Rotation 0
BMEN 673L Biomedical Engineering Lab 1
BMEN 675 Approved Experience 0
EPHD 310 Basic Biostatistics2 3
HUMR 310
Biomedical Research Techniques 1
(A, B, or C)
HUMR 314 Research Seminar 1
PHYL 346 Human Physiology 4
Restricted elective graduate courses: 9 credits restricted elective courses customized
per focus area.3
Cyber- Cardio-
Restricted elective courses (9 cr.)3 Credits Systems
netics vascular
Receptors and Signal
BIOC 325 2 R
Transduction
Bioinformatics Tools and
BIOC 326A 1 R
Applications in Genomics
BMEN 603 Tissue Engineering 3 X X
Engineering of Drug
BMEN 604 3 X X
Delivery Systems
BMEN 605 Biomedical Imaging 3 X X
BMEN 606 Nanobiosensors 3 X X
BMEN 607 Biomechanics 3 X
Biomaterials and Medical
BMEN 608 3 X X
Devices
BMEN 609 Computational Neuroscience
or or 3 X X
EECE 605 Neuromuscular Engineering
Micro and Nano Neural
BMEN 610 3 X
Interfaces
Computational Modeling in
BMEN 611 3 X X X
Biomechanics
EECE 601 or Biomedical Engineering I or
3 X X X
EECE 602 Biomedical Engineering II
1) Students are required to take two PhD lab rotation courses where each lab rotation is 1 credit (one lab rotation in MSFEA
and one lab rotation in FM).
2) EPHD 310 can be replaced by another advanced level statistics course based on JPCC’s approval.
3) Courses marked as “R” are required, and courses marked as “X” are possible elective options.
Graduate Catalogue 2020–21
Maroun Semaan Faculty of Engineering and Architecture (MSFEA) 319
Biomedical Signal and
EECE 603 3 X X
Image Processing
EECE 633 or Data Mining or
EECE 663 or System Identification or
3 X
EECE 667 or Pattern Recognition or
EECE 693 Neural Networks
HUMR 305 Cell and Tissue Biology 3 R
PHYL 300A Pulmonary Physiology 1 R
PHYL 302 Cardiovascular Physiology 2 R
Free elective graduate courses: 6 credits additional elective courses. These courses
should be taken based on the student’s specific area of research as approved by the
student’s advisor.
Course Descriptions
BMEN 600 Biomedical Engineering Applications 3 cr.
Biomedical engineering is an interdisciplinary domain which applies principles
of engineering to find solutions for biological and health problems. Biomedical
engineering aims to improve our fundamental understanding of biological processes
and develop approaches for optimized therapeutic/diagnostic healthcare procedures.
The field of biomedical engineering involves the development of materials to replace or
enhance the operation of damaged or malfunctioning biological entities, development
of diagnostic and therapeutic tools, modeling of biological systems, signal processing
and bioinformatics. This course will introduce students to biomedical engineering and
provide insight into the various applications in the biomedical engineering field. The
course will be divided into modules, and each will be given by a specialist in a certain
biomedical engineering area.
BMEN 601/ Computational Modeling of Physiological Systems 3 cr.
MECH 635
This course focuses on the quantitative modeling of different physiological systems. It
provides students with current concepts of the mathematical modeling, and different
quantitative descriptions of cellular and organ physiology. At the subcellular/cellular
level, we will examine mechanisms of regulation and homeostasis. At the system level,
the course will cover basic aspects of anatomical and pathophysiological features of
the nervous, neural, cardiovascular and respiratory systems. Several physiological
processes are treated as case studies for increasing complexity in modeling dynamical
systems. Prerequisites: MATH 202 and PHYL 346, or consent of instructor.
BMEN 602 Computational Modeling of Cardiovascular 3 cr.
and Pulmonary Systems
The need for better understanding the mechanics and tools for computational modeling
of cardiovascular and respiratory systems in healthy and diseased conditions is
constantly increasing. This is a result of the enormous advances made in the science and
engineering of both surgical and therapeutic medicine. This course covers the modeling
and simulation of cardiovascular and respiratory systems. It will provide the students with
a thorough understanding of the anatomy, physiology and mechanics of cardiovascular
and respiratory systems as well as the computational tools for modeling and simulation of
cardiac, circulatory and respiratory systems in healthy and diseased conditions.
Graduate Catalogue 2020–21
320 Maroun Semaan Faculty of Engineering and Architecture (MSFEA)
BMEN 603/ Tissue Engineering 3 cr.
CHEN 675
In a world of aging population, an ever-increasing demand for improvement of healthcare
services and need for replacement organs and tissues are arising. The limited pool
of donors together with the problem of donor organ rejection is a strong driver for
engineering tissues and other body parts. Tissue engineering is an interdisciplinary
field that uses cells, biomaterials, biochemical (e.g. growth factors) and physical (e.g.
mechanical stimulation) signals, as well as their combination to generate tissue-like
structures. The goal of tissue engineering is to provide biological substitutes that can
maintain, restore or improve the function of damaged organs in the body. This course
will introduce interested students to the new field of tissue engineering and provide
insight on cutting edge applications in this area.
BMEN 604/ Engineering of Drug Delivery Systems 3 cr.
CHEN 673
This course focuses on recent advances in the development of novel drug delivery
systems. The fundamentals of drug delivery are discussed. Various strategies to
tune and control the release of active agents for optimized therapeutic outcomes
are explored. The course covers polymers and techniques used to produce drug
nanoparticles, with specific examples of nanoparticle-based drug delivery systems.
Prerequisites: CHEN 314 and CHEN 411, or consent of instructor.
BMEN 605 Biomedical Imaging 3 cr.
Biomedical imaging offers an unprecedented view into the structure and function of a
living body, and as such plays an essential role in medical practice and research. This
course will provide students with an overview of the key concepts underlying the primary
diagnostic biomedical imaging modalities, including: ultrasound, x-ray, computed
tomography, magnetic resonance and nuclear imaging. In particular, students will
gain an understanding of the physical principles and theoretical bases governing the
operation of each imaging modality, the technology that translates theory into practice,
and the basic methods involved in image formation. Students will also learn the
limitations of each imaging procedure, while being exposed to their vast applications
in the clinic and research.
BMEN 606 Nanobiosensors 3 cr.
This course will provide a comprehensive analysis of the field of nanoengineering with
a focus on biosensors including common modalities, basic theoretical considerations
for sensor operation, physics of detection and applications in research and medical
diagnostics. The course will cover the major types of electronic nanobiosensors for
biological signal detection (potentiometric, amperometric, and mass based sensors)
and their applications in the fields of neural engineering, DNA sequencing and
cardiovascular early disease detection. The course will enable students to have a strong
grasp of fundamentals of biosensor design, select sensors for various applications and
evaluate new and emerging technologies. Prerequisites: EECE 210 (or equivalent) and
BIOL 210 (or equivalent); or consent of instructor.
BMEN 607/ Biomechanics 3 cr.
MECH 633
A course on the study of the biomechanical principles underlying the kinetics and
kinematics of normal and abnormal human motion. Emphasis is placed on the interaction
between biomechanical and physiologic factors (bone, joint, connective tissue, and
muscle physiology and structure) in skeleto-motor function and the application of such
in testing and practice in rehabilitation. The course is designed for engineering students
Graduate Catalogue 2020–21
Maroun Semaan Faculty of Engineering and Architecture (MSFEA) 321
with no previous anatomy/physiology. Prerequisites: CIVE 210, MECH 320 or CIVE 310;
or consent of instructor.
BMEN 608/ Biomaterial and Medical Devices 3 cr.
MECH 634
A course that examines the structure-property relationships for biomaterials and the
medical applications of biomaterials and devices. The first part of the course focuses
on the main classes of biomaterials, metal, ceramic, polymeric and composite implant
materials, as well as on their interactions with the human body (biocompatibility). The
second part of the course examines the various applications of biomaterials and devices
in different tissue and organ systems such as orthopedic, cardiovascular, dermatologic
and dental applications. Experts from the medical community will be invited to discuss
the various applications. Prerequisite: MECH 340 or consent of instructor.
BMEN 609 Computational Neuroscience 3 cr.
The human brain, perhaps the most complex, sophisticated, and complicated learning
system, controls virtually every aspect of our behavior. The central assumption
of computational neuroscience is that the brain computes. What does that mean?
Generally speaking, a computer is a dynamical system whose state variables encode
information about the external world. In short, computation equals coding plus
dynamics. Some neuroscientists study the way that information is encoded in neural
activity and other dynamical variables of the brain. Others try to characterize how these
dynamical variables evolve with time. The study of neural dynamics can be subdivided
into two separate strands. One tradition, exemplified by the work of Hodgkin and
Huxley, focuses on the biophysics of single neurons. The other focuses on the dynamics
of networks, concerning itself with phenomena that emerge from the interactions
between neurons. Therefore computational neuroscience can be divided into three sub-
specialties: neural coding, biophysics of neurons, and neural networks. This course will
introduce engineers, physicists, computational scientists, mathematicians and other
audiences to the neurosciences from the cellular level and the network level as seen
from computational lenses. Prerequisites: BIOL 201 (or equivalent) and Math 202, or
consent of instructor.
BMEN 610 Micro and Nano Neural Interfaces 3 cr.
Neural interfaces are micro and nano devices that form the connection between the
biological neural tissue and the external electronic devices. These devices are designed
for mapping, assisting, augmenting, or repairing neural pathways. The course will
focus on physical, chemical and neurophysiological principles of neural interfaces,
theoretical and functional basis for their design, micro and nano fabrication techniques
and applications in neural prosthesis for Brain Machine Interface. Topics covered in
class will include; Neural Engineering, Brain Machine Interface, Microfabrication,
Nanofabrication, Soft-lithography, Electrokinetics, Electrochemistry, Neural probes,
Biocompatibility, Microelectrodes, NeuroMEMS (neuro microelectromechanical
systems, BioMEMS (biomedical microelectromechanical systems).
BMEN 611 Computational Modeling in Biomechanics 3 cr.
This course provides students with a glimpse into the world of computational finite
element modeling and simulation in biomechanics to investigate and solve biomedical
problems. Students will take a journey through the processes involved in producing a
computational finite element model in the biomedical field; starting at construction of
model geometry, particularly from medical imaging data (CT/MRI), through to model
creation, simulation and visualization using finite element analysis software (ANSYS
Workbench). Students will also be exposed to a selection of experimental lab techniques
Graduate Catalogue 2020–21
322 Maroun Semaan Faculty of Engineering and Architecture (MSFEA)
in biomechanics and physiology to acquire data required for model development and
validation. In pursuit of developing an appreciation for the areas covered, the course
will incorporate a mix of theory, demonstrations, practice, real-world modeling
applications and research seminars. In addition to skills gained in modeling and basic
experimentation, the course will provide students with an opportunity to enhance vital
skills in scientific writing and oral communication.
BMEN 671 PhD Lab Rotation 1 cr.
PhD students in Biomedical Engineering are required take two laboratory rotations
(1 credit each) in different faculty research laboratories within the MSFEA and/or FM.
Students may also enroll in a third elective laboratory rotation. This aims to familiarize
students with potential thesis mentors and expose them to different research
environments.
BMEN 672 Hospital Lab Rotation 0 cr.
MS and PhD students in Biomedical Engineering are required to do a lab rotation in
the Medical Engineering Department at AUB Medical Center (AUBMC). This aims to
familiarize students with the typical activities and responsibilities of a biomedical
engineer in a working environment and expose them to different equipment and tools.
BMEN 673L Biomedical Engineering Lab 1 cr.
This laboratory course aims to introduce students to the practical issues in the areas
of biomedical instrumentation design and biological signal processing. A particular
emphasis will be placed on signal transduction, electronic circuit design for recording
and conditioning physiological signals. The lab will introduce hand-on laboratory
experiments on biomedical sensors, analog signal amplifiers and filters, digital
acquisition and transmission, and basic digital filtering. In addition, some experiments
cover topics that demonstrate the various levels of complexity that characterize
biological signals. Signal processing tools include spectral and cepstral analysis,
de-noising and artifact removal, filter banks and wavelet decompositions, Hilbert
transforms, and information-theoretic measures.
BMEN 675 Approved Experience 0 cr.
BMEN 796 Special Project in Biomedical Engineering 3 cr.
BMEN 797 Special Topics in Biomedical Engineering 1 cr.
BMEN 798 Special Topics in Biomedical Engineering 3 cr.
BMEN 799T MS Comprehensive Exam 0 cr.
Every term.
BMEN 799 MS Thesis 6 cr.
Every term. Prerequisite: BMEN 799T.
BMEN 980 Qualifying Exam Part I: Comprehensive Exam 0 cr.
Every term.
BMEN 981 Qualifying Exam Part II: Defense of Thesis Proposal 0 cr.
Every term. Prerequisite: BMEN 980.
Graduate Catalogue 2020–21
Maroun Semaan Faculty of Engineering and Architecture (MSFEA) 323
BMEN 982 PhD Thesis 3 cr.
Every term. Taken while total required credit hours have been completed.
BMEN 983 PhD Thesis 6 cr.
Every term. Taken while total required credit hours have not been completed.
BMEN 984 PhD Thesis 9 cr.
Every term. Taken while total required credit hours have not been completed.
BMEN 985 PhD Thesis 12 cr.
Every term. Taken while total required credit hours have not been completed.
BMEN 986 PhD Thesis 0 cr.
Every term. Taken while total required credit hours have not been completed.
BMEN 987 PhD Thesis Defense 0 cr.
Every term. Prerequisite: BMEN 981.
BIOC 321 Nucleic Acids and Basic Genetics 15.0; 1 cr.
This course discusses the principles of nucleic acid structure and function in eukaryotes.
It includes the information for basic genetics in terms of genome structure as well as
the diversity of gene regulation. Required from MS and PhD students in biomedical
Sciences. requires consent of coordinator for other graduate disciplines. First term.
BIOC 322 Protein Biochemistry 10.10; 1 cr.
This course deals with the biochemistry of proteins including their basic units, different
structures, folding process and protein-protein interactions. It focuses on how changes
at the structural level modify function. The course also covers the principles of protein
purification and sequencing, and introduces students to protein database, molecular
modeling and systems biology. Required from MS and PhD students in biomedical
sciences. Requires coordinator approval for other graduate disciplines. First term.
BIOC 325 Receptors and Signal Transduction 25.10; 2 cr.
This course covers classical pathways involved in receptor signaling and activation of
downstream targets and the molecular mechanisms involved. It deals with the inter-
and intracellular communication, from the generation of signaling molecules through
the cellular responses. Required from MS and PhD students in biomedical sciences.
Requires consent of coordinator for other graduate disciplines. First term.
BIOC 326A Bioinformatics Tools and Applications in Genomics 1 cr.
This course will discuss the relationships among sequence, structure and function in
biological networks, as well as advances in modeling of quantitative, functional and
comprehensive genomics analyses. It will assess computational issues arising from
high-throughput techniques recently introduced in biomedical sciences, and cover very
recent developments in computational genomics, including genome structural variant
discovery, epigenome analysis, cancer genomics and transcriptome analysis.
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324 Maroun Semaan Faculty of Engineering and Architecture (MSFEA)
BIOM 385 Research Ethics 15.0; 1 cr.
This course introduces the fundamentals of responsible conduct of research,
emphasizing the ethical practice of human research. The course recaps history of
ethical principles, the development of research codes of conduct and ethical practices,
familiarizes students with the different kinds of ethical issues that they might come
across throughout their careers and allows scholars to reflect critically on what it means
to be an ethical and responsible researcher. Summer term.
EECE 601 Biomedical Engineering I 3 cr.
This course includes an introduction to: general instrumentation configuration and
performance of instrumentation systems; types and characteristics of transducers;
sources and characteristics of bioelectric signals; types and characteristics of electrodes;
temperature regulation and measurement; cardiovascular system, measurements and
diagnostic equipment; blood instruments; patient care and monitoring; and electrical
safety of medical equipment. Prerequisites: BIOL 210 or BIOL 202 or PHYL 246, and EECE
210; or PHYS 228 and PHYS 228L; or consent of instructor.
EECE 603 Biomedical Signal and Image Processing 3 cr.
Fundamentals of digital signal processing as implemented in biomedical applications. It
provides a concise treatment of the tools utilized to describe deterministic and random
signals as the basis of analyzing biological signals: data acquisition; imaging; denoising
and filtering; feature extraction; modeling. The course is tightly coupled with a practical
component through laboratory projects. Examples include the auditory system, speech
generation, electrocardiogram, neuronal circuits and medical imaging. Students should
have reasonable software skills in Matlab. Prerequisites: STAT 230 and EECE 340, or
equivalent; or consent of instructor.
EECE 633 Data Mining 3 cr.
This course is an introduction to data mining. Data mining refers to knowledge discovery
from huge amounts of data to find non-trivial conclusions. Topics will range from
statistics to machine learning to database, with a focus on analysis of large data sets.
The course will target at least one new data mining problem involving real data for which
the students will have to find a solution. Prerequisite: EECE 330 or consent of instructor.
EECE 663 System Identification 3 cr.
This course introduces the basic mathematical tools to fit models into empirical input-
output data. General time-series modeling and forecasting, such as stock prices,
biological data and others. Topics include nonparametric identification methods: time
and frequency response analysis; parametric identification: prediction error, least
squares, linear unbiased estimation and maximum likelihood; convergence, consistency
and asymptotic distribution of estimates; properties and practical modeling issues:
bias distribution, experiment design and model validation.
EECE 667 Pattern Recognition 3 cr.
The course provides an overview of the algorithms used in machine learning. The
course discusses modern concepts for model selection and parameter estimation,
decision-making and statistical learning. Special emphasis will be given to regression
and classification for a supervised mode of learning. Students will be assigned typical
machine learning problems to investigate as projects.
Graduate Catalogue 2020–21
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EECE 693 Neural Networks 3 cr.
The course provides a comprehensive foundation to artificial neural networks and
machine leaning with applications to pattern recognition and data mining; learning
processes: supervised and unsupervised, deterministic and statistical; clustering;
single layer and multilayer perceptrons; least-mean-square, back propagation and
Al-Alaoui algorithms; radial-basis function networks; committee machines; principal
component analysis; self-organizing maps; and current topics of interest.
EPHD 310 Basic Biostatistics 2.2; 3 cr.
An introductory biostatistics course that covers basic concepts in statistical methods.
The course demonstrates methods of exploring, organizing and presenting data. The
course presents the foundation of statistical inference from estimation, to confidence
interval and testing of hypothesis. Applications include comparing population means
or proportions via data obtained from paired or independent samples, one-way ANOVA.
Also, it introduces simple linear regression, correlations, logistic regression and
nonparametric methods for data analysis.
HUMR 305 Cell and Tissue Biology 30.33; 3 cr.
Consists of the first half of Basic Histology, HUMR 209, covering cells and tissues. Open
to graduate students outside the department.
HUMR 310 Biomedical Research Techniques 1 cr.
(A, B, or C)
A guided laboratory course in research methods used in cell biology and physiology.
HUMR 310A covers Cell Biology Techniques; HUMR 310B covers Genomics and
Proteomics; HUMR 310C covers Mouse Models and In Vivo Studies. Used in cell biology
and physiology.
HUMR 314 Research Seminar 0.32; 1 cr.
Presentation and discussion of timely research topics designated by members of the
department.
PHYL 302 Cardiovascular Physiology 31.6; 2 cr.
Presents the cardiovascular system with clear reference to pathophysiological and
clinical events. Didactic lectures and seminar sessions define physiological concepts
and emphasize structure-function relationships. Laboratory sessions familiarize the
student with instrumentation and techniques in the cardiovascular field. Open to all
graduate students in the department.
PHYL 346 Human Physiology for Paramedical 48; 4 cr.
and Undergraduate Students
Outlines fundamental principles of human physiology and the mechanisms governing
the function of different body organs. Prerequisites: BIOC 246 and BIOL 201
(or BIOL 210).
Graduate Catalogue 2020–21
