Chapter 8: Department of Bioengineering
Professors: Prashanth Asuri (Department Chair), Biao (Bill) Lu, Yuling Yan
Associate Professors: Ismail Emre Araci, Unyoung (Ashley) Kim, Zhiwen (Jonathan) Zhang
Assistant Professor: Hamed Akbari
Teaching Professor: Maryam Mobed-Miremadi
Lecturers: Eun Ju (Emily) Park, Julia Scott
Quarterly Lecturers: Murat Baday, Frankie Myers, Paul Nauleau, Erhan Yenilmez
Overview
Bioengineering is the fastest-growing area of engineering and holds the promise of improving the lives of all people in straightforward and diverse ways. Bioengineering focuses on the application of electrical, chemical, mechanical, and other engineering principles to understand, modify, or control biological systems. As such, the curriculum teaches principles and practices at the interface of engineering, medicine, and the life sciences. The Department of Bioengineering currently offers an M.S. degree program with a focus on biodevice engineering, biomaterials and tissue engineering, and biomolecular engineering.
Our faculty offers research projects to bioengineering students that are engaging and involve problem-solving at the interface of engineering, medicine, and biology. The list of the current faculty and their research interests is as follows:
Dr. Hamed Akbari, M.D., Ph.D., integrates medicine and engineering to enhance medical imaging and patient care, with a focus on neuro-oncology. His expertise in medical AI, pattern recognition, and machine learning drives innovative solutions for personalized disease diagnosis and treatment.
Dr. Araci’s research goals are directed toward the development and application of novel microfluidic and optofluidic technologies for biomedical applications. His work is focused on two major areas: i) implantable and miniaturized devices for telemedicine and ii) microfluidic large-scale integration (mLSI) for single molecule protein counting.
Dr. Asuri’s research interests focus on the design and development of biomaterial-based in vitro platforms to understand complex in vivo phenomena. As the Director of the Healthcare Innovation and Design program, he also partners with industry professionals to address complex challenges in healthcare.
Dr. Kim investigates the application of integrated microfluidic systems for multiple uses in diagnostics as well as experimental science.
Dr. Lu’s research focuses on medical translations of protein engineering that includes protein therapeutics and drug delivery as well as molecular sensor and imaging technology.
Dr. Mobed-Miremadi's research interests are in the areas of simulation, optimization, and statistical validation across multiscale biomaterials-related platforms.
Dr. Scott investigates and designs interventions for brain health using immersive technology and neurotechnology. In this applied form of affective computing, the research program studies how and why these technologies modulate brain function.
Dr. Yan's research centers on bioimaging, image and signal analysis, and AI-assisted diagnostics. In collaboration with a local hospital, she is working on multi-modal deep learning models to offer transparent diagnostic outcomes, with the ultimate goal of translating AI into clinical practice.
Dr. Zhang is currently engaged in interdisciplinary research programs intersecting biomolecular and biodevice engineering, synthetic biology, and drug discovery and development (protein and small molecule), enhanced by the integration of GenAI.
Degree Program
The Bioengineering graduate program at Santa Clara University is designed to accommodate the needs of students interested in advanced study in the areas of medical devices/bioinstrumentation and molecular and cellular bioengineering. An individual may pursue the degree of Master of Science (M.S.), either as a full-time or part-time student, through a customized balance of coursework, directed research, and/or thesis research. Students are also required to supplement their technical work with coursework on other topics that are specified in the graduate engineering core curriculum.
Master of Science in Bioengineering
To be considered for admission to the graduate program in bioengineering, an applicant must meet the following requirements:
- A bachelor’s degree in bioengineering or related areas from an ABET-accredited four-year B.S. degree program or its equivalent
- An overall grade point average (GPA) of at least 3.000 (based on a 4.000 maximum scale)
- Graduate Record Examination (GRE) general test
- For students whose native language is not English, Test of English as a Foreign Language (TOEFL) or the International English Language Testing Systems (ILETS) exam scores are required before the application is processed
Applicants who have taken graduate-level courses at other institutions may qualify to transfer a maximum of nine quarter units of approved credit to their graduate program at Santa Clara University.
Upon acceptance to the graduate program in bioengineering, a student will be required to select a graduate advisor (full-time faculty member) from within the Department of Bioengineering. The student’s advisor will be responsible for approving the student’s course of study. Any changes to a student’s initial course of study must have the written approval of the student’s advisor.
To qualify for the degree of Master of Science in Bioengineering, students must complete a minimum of 46 quarter units, including required core and elective courses, within the School of Engineering. Required and elective courses for the bioengineering programs are provided below. Students undertaking thesis work are required to engage in research that results, for example, in the development of a new method or approach solving a bioengineering-related problem, or a technical tool, design criteria, or a biomedical application. This work should be documented in a journal publication, conference, or research report, and must also be included in a Master’s thesis. Alternatively, students may elect to take only courses to fulfill the requirement for the M.S. degree.
Course Requirements
- Graduate Core - See descriptions in Chapter 6.
- Applied Mathematics (4 units) Select from AMTH 200 & 201 (or 202), 210 & 211 (or 212), or AMTH 245 & 246
- Focus Areas (10 or 16* units) - Students must take six units from one of the five primary focus areas and four units from other focus areas. An additional six units are required for Computational Bioengineering (Applied Mathematics courses) or Translational Bioengineering (Capstone).
- Bioengineering Core (9 units) - Students must take three units from biostatistics (BIOE 232 L&L), two quarter research seminar units (BIOE 200, 2 x 1 unit), and 4 units from Applied Mathematics.
- Bioengineering Technical Electives (13* or 19 units)
- Five primary focus areas are:
(1) Biomolecular Engineering
- BIOE 257, 263, 282, 283, 286, 288, 300, 301
(2) Biomaterials and Tissue Engineering
- BIOE 258(L+L), 258(L+L), 269, 273, 378
(3) Microfluidics/Biosensors and Imaging
- BIOE 203, 216, 260, 267, 268, 276, 277, 308
(4) Computational Bioengineering
- BIOE 277A&B, 251, 252, 261, 281, 312
- Advanced Applied Mathematics*- AMTH 240, 364, 370, 371, 377
(5) Translational Bioengineering
-BIOE 206, 263, 279, 285, 302, 307, 320, 380
-Graduate Capstone Project* BIOE 294, 295, 296
*additional six units required for primary focus in Computational Bioengineering or Translational Bioengineering
All graduate-level BIOE courses (except BIOE 210) may count as Technical Elective (TE) units. Selected graduate courses from ECEN, MECH, or CSEN may be credited as TEs upon approval by a faculty advisor. A maximum of 3 units of BIOE 297 is allowed if also taking BIOE 397, otherwise, a maximum of 6 units of BIOE 297 is allowed. Submission of a M.S. Thesis is required for BIOE 397 (max. 9 units)
For students in Accelerated B.S./M.S. program, a maximum of 20 units may be transferred. Courses used to meet the 46-unit minimum total for the Master of Science in Bioengineering degree cannot include courses that were used to satisfy a previous undergraduate degree program requirement. This includes cross-listed undergraduate courses at Santa Clara University and/or their equivalent courses at other institutions. If some required courses in the SCU graduate bioengineering program have been completed prior to graduate-level matriculation at SCU, additional elective courses will be required to satisfy the minimum unit total requirement as necessary.
Ph.D. in Bioengineering
The Doctor of Philosophy (Ph.D.) degree is pursued by those who wish to specialize in a particular area of bioengineering. The work for the degree involves conducting in-depth bioengineering research, preparing a thesis based on the research findings, and a program of advanced studies in engineering, mathematics, and related physical sciences. The Bioengineering Department also offers an “industrial track” for working professionals as an option to facilitate collaboration between academia and industry. Student’s work is directed by the degree-conferring department, subject to the general supervision of the School of Engineering.
Preliminary Examination
The preliminary examination will be in written format and include subject matter deemed by the major department to represent sufficient preparation in depth and breadth for advanced study in the major. Only those who pass the written examination may take the oral qualifying examination.
Students currently studying at Santa Clara University for a master’s degree who are accepted to the Ph.D. program and who are at an advanced stage of the M.S. program may, with the approval of their academic advisor, take the preliminary examination before completing the M.S. degree requirements. Students who have completed the M.S. degree requirements and have been accepted to the Ph.D. program should take the preliminary examination as soon as possible but not more than two years after beginning the program.
Students are expected to pass an exam in biostatistics as well as one each in two areas from the following list: biodevices and bioimaging, biomolecular and bioprocess engineering, biomaterials and biofabrication, and computational bioengineering. At the thesis advisor’s discretion, students may be expected to take and pass an exam in three areas (in addition to biostatistics) from the above list. Students opting to pursue the computational bioengineering focus may choose a different exam topic instead of biostatistics. Only those students who pass the preliminary examination shall be allowed to continue in the doctoral program. The preliminary examination may be retaken once, and any additional retakes are at the discretion of the thesis advisor.
Doctoral Advisor
It is the student’s responsibility to obtain consent from a full-time faculty member in the student’s major department to serve as his/her prospective thesis advisor. It is strongly recommended that Ph.D. students find a doctoral advisor before taking the preliminary examination. After passing the preliminary examination, Ph.D. students must have a doctoral advisor before the beginning of the next quarter following the preliminary examination. Students currently pursuing a master’s degree at the time of their preliminary examination should have a doctoral advisor as soon as possible after being accepted as a Ph.D. student.
The student and the doctoral advisor jointly develop a complete program of studies for research in a particular area. The complete program of studies (and any subsequent changes) must be filed with the Graduate Services Office and approved by the student’s doctoral committee. Until this approval is obtained, there is no guarantee that the courses taken will be acceptable toward the Ph.D. course requirements.
Doctoral Committee
After passing the Ph.D. preliminary exam, a student requests their doctoral advisor to form a doctoral committee. The committee consists of at least five members, each of which must have earned a doctoral degree in a field of engineering or a related discipline. This includes the student’s doctoral advisor, at least two other current faculty members of the student’s major department at Santa Clara University, and at least one current faculty member from another appropriate academic department at Santa Clara University. The committee reviews the student’s program of study, conducts an oral comprehensive exam, conducts the dissertation defense, and reviews the thesis. Successful completion of the doctoral program requires that the student’s program of study, performance on the oral comprehensive examination, thesis defense, and thesis itself meet with the approval of all committee members.
Residence
The doctoral degree is granted on the basis of achievement, rather than on the accumulation of units of credit. However, the candidate is expected to complete a minimum of 72 quarter units of graduate credit beyond the master’s degree. Of these, 36 quarter units may be earned through coursework and independent study, and 36 through the thesis. All Ph.D. thesis units are graded on a Pass/No Pass basis. A maximum of 18 quarter units (12 semester units) may be transferred from other accredited institutions at the discretion of the student’s advisor.
Ph.D. students must undertake a minimum of four consecutive quarters of full-time study at the University; spring and fall quarters are considered consecutive. The residency time shall normally be any period between passing the preliminary examination and completion of the thesis. For this requirement, full-time study is interpreted as a minimum registration of eight units per quarter during the academic year and four units during the summer session. Any variation from this requirement must be approved by the doctoral committee.
Comprehensive Examinations and Admission to Candidacy
After completion of the formal coursework approved by the doctoral committee, the student shall present their research proposal for comprehensive oral examinations on the coursework and the subject of their research work. The student should make arrangements for the comprehensive examinations through the doctoral committee. A student who passes the comprehensive examinations is considered a degree candidate. The comprehensive examinations normally must be completed within four years from the time the student is admitted to the doctoral program. Comprehensive examinations may be repeated once, in whole or in part, at the discretion of the doctoral committee.
Dissertation Research and Defense
The period following the comprehensive examinations is devoted to research for the dissertation, although such research may begin before the examinations are complete. After successfully completing the comprehensive examinations, the student must pass an oral examination on their research and thesis, conducted by the doctoral committee and whomever they appoint as examiners. The dissertation must be made available to all examiners one month prior to the examination. The oral examination shall consist of a presentation of the results of the dissertation and the defense. This examination is open to all faculty members of Santa Clara University, but only members of the doctoral committee have a vote.
Dissertation and Publication
At least one month before the degree is to be conferred, the candidate must submit one copy of the final version of the dissertation to the department. The dissertation will not be considered as accepted until a copy signed by all committee members has been submitted to the library and one or more refereed articles based on it are accepted for publication in a professional or scientific journal approved by the doctoral committee.
Time Limit for Completing Degrees
All requirements for the doctoral degree must be completed within eight years following initial enrollment in the Ph.D. program. Extensions will be allowed only in unusual circumstances and must be recommended in writing by the student’s doctoral committee, and approved by the dean of engineering in consultation with the Graduate Program Leadership Council.
Additional Graduation Requirements
The requirements for the doctoral degree in the School of Engineering have been made to establish the structure in which the degree may be earned. Upon written approval of the provost, the dean of the School of Engineering, the doctoral committee, and the chair of the major department, other degree requirements may be established. The University reserves the right to evaluate the undertakings and the accomplishments of the degree candidate in total, and award or withhold the degree as a result of its deliberations.
Bioengineering Laboratory Facilities
The Anatomy & Physiology Laboratory provides a full range of activities to study human anatomy and organ function. Through computational modeling, organ dissection, and design projects, students will develop essential skills in conceiving and implementing engineering solutions to medical problems.
The Bioimaging/Image and Signal Analysis Laboratory carries out fundamental and translational research on voice. Current research in the laboratory includes the development of imaging modalities to study laryngeal dynamics and function, and novel approaches for image/biosignal-based analysis and assessment of voice pathologies. The lab also supports the development of new detection and analytical methods using optical probes for applications in high-contrast fluorescence imaging in cells and tissues.
The Biological Micro/Nanosystems Laboratory supports research and teaching activities in the broad areas of microfluidics/biosensing. Utilizing microfluidic technologies, spectroscopy, and microfabrication techniques, we develop innovative microfluidic platforms for applications in basic biology, diagnostics, and cellular engineering.
The Biomaterials Engineering Laboratory focuses on the use of hydrogels to develop in vitro platforms that explore the role of in vivo-like microenvironmental cues on controlling protein structure and function and regulating cell fate. The lab also supports the design and characterization of biomaterial nanocomposites for applications in tissue engineering.
The Biomolecular Engineering Laboratory conducts “bioengineering towards therapy.” The idea is to engineer novel materials (particularly proteins and peptides) and devices and apply them to study basic biological and medical questions that ultimately lead to drug discovery and disease diagnosis.
The Biophotonics & Bioimaging Laboratory supports research and teaching on portable imaging systems for wearable/implantable biosensors as well as on optical coherence tomography (OCT) probes for stereotactic neurosurgery. The time-lapse fluorescence
microscopy setup is used for measuring enzyme activity and single-cell protein expression at the single molecular level.
The Biosignals Laboratory provides a full range of measurement and analysis
capabilities including electrocardiography (ECG), electroencephalography (EEG), and electromyography (EMG) measurement systems, vocal signal recording, and analysis software.
The Micro-devices & Microfluidics Laboratory focuses on the fabrication and testing of microfluidic devices for biomedical research and teaching. The soft-lithography room is equipped with the necessary instruments (e.g., mixer, spinner, plasma cleaner) to build
micro-devices using a wide variety of materials and processes. Multiple microfluidic test setups (i.e., computer-controlled solenoid valves and microscopes) allow several tests to be run simultaneously.
The Tissue Engineering Laboratory supports research and teaching activities related to mammalian cell and tissue culture. Activities include but are not limited to 2D and 3D mammalian cell culture, investigation of the role of biophysical cues on cancer cell migration and response to drugs, and genetic manipulation of mammalian cells.
Course Descriptions
The list of undergraduate courses can be found in the Undergraduate Bulletin. https://www.scu.edu/bulletin/undergraduate-bulletin/
Graduate Courses
BIOE 200. Graduate Research Seminar
Seminar lectures on the progress and current challenges in fields related to bioengineering. P/NP grading. Also listed as BIOE 100. (1 unit)
BIOE 206. Design Control for Medical Devices
This course will cover the principles behind design control. All of the essential elements required in the regulated medical device environment will be covered from design planning, inputs and outputs to verification, validation, risk management, and design transfer. A problem-based learning approach will be utilized so that students will develop proficiency to apply the principles. Knowledge will be acquired through lectures, class activities, industry guest lectures, and field trips. Also listed as BIOE 106. (4 units)
BIOE 207. Medical Device Product Development
This course will introduce students to various tools and processes that will improve their ability to identify and prioritize clinical needs, select the best medical device concepts that address those needs, and create a plan to implement inventions. (2 units)
BIOE 210. Ethical Issues in Bioengineering
This course serves to introduce bioengineering students to ethical issues related to their work which includes introductions to ethical theories, ethical decision-making, accessibility, and social justice concerns, questions in personalized medicine, environmental concerns, and so on. This course will also cover ethical and technical issues related to biomedical devices. (2 units)
BIOE 227A. Machine Learning and Applications in Biomedical Engineering
This course covers theoretical foundations and methods that form the core of modern machine learning. Topics include supervised methods for regression and classification (linear regression, logistic regression, support vector machine, instance-based and ensemble methods, neural networks) and unsupervised methods for clustering and dimensionality reduction. Selected biomedical applications will be presented. Also listed as BIOE 177A. (2 units)
BIOE 227B. Machine Learning and Algorithm Implementation
This course introduces programming in Python and focuses on building machine learning projects with Numpy, TensorFlow, and Keras. Also listed as BIOE 177B. Prerequisite: BIOE 227A. (2 units)
BIOE 230. Immune System for Engineers
This course will discuss two significant aspects of human immune systems in bioengineering: 1) Complex hurdles associated with the body’s immune systems for biomaterials, biodevice, and implants; and 2) profound opportunities with engineered therapeutics. Also listed as BIOE 130. (4 units)
BIOE 232. Biostatistics
This course will cover the statistical principles used in Bioengineering encompassing distribution-based analyses and Bayesian methods applied to biomedical device and disease testing including methods for categorical data, comparing groups (analysis of variance), and analyzing associations (linear and logistic regression). Special emphasis will be placed on computational approaches used in model optimization, test-method validation, sensitivity analysis (ROC curve), and survival analysis. Also listed as AMTH 232. Prerequisite: AMTH 108 or BIOE 120 or equivalent. (2 units)
BIOE 232L. Biostatistics Laboratory
Laboratory for BIOE 232. Also listed as AMTH 232L. Co-requisite: BIOE 232. (1 unit)
BIOE 238. Medicinal Chemistry and Drug Design I
Small molecule medicines are coming back! In two seminal courses, principles of medicinal chemistry will be discussed in detail, as well as the related drug designs. Medicines and their designs in the following categories will be studied in the part I: Acid-Base disorders; antihistamines; anticholinergics; anti-inflammation (NSAIDs and Glucocorticoids). The contents of the course are offered at the same level as in pharmacy schools. Students are encouraged to have a strong background in biology, organic chemistry and physiology. Also listed as BIOE 138. Prerequisites: BIOE 22 (or BIOL 1C) and CHEM 31. (2 units)
BIOE 239. Medicinal Chemistry and Drug Design II
This is part II of the seminal courses – Medicinal Chemistry and Drug Design. Students will study the principles of medical chemistry in detail, as well as the pharmacology for drug design. Medicines and their design will be studied in the following categories: Non-steroidal anti-inflammatory drugs (NSAIDs), Glucocorticoids, Thyroid and Thyroid Drugs, Estrogens and Progestins. On top of the understanding of the principles of drugs, the sequel will be concluded with the “rules” of drug discovery and clinical therapy. Also listed as BIOE 139. Prerequisites: BIOE 22 (or BIOL 1C) and CHEM 31. (2 units)
BIOE 245. Introductory Biotribology for Orthopedic Implants
This course will provide an introduction to surface mechanics and tribology as applied to biological systems and medical devices, with a specific focus on orthopedic tissues and implants. Students will learn about the mechanisms of friction, lubrication, and wear in tissues and considerations for the design of implants to minimize adverse interactions in vivo while maximizing lifespan. Topics will include dry, lubricated, and mixed-mode contact and the physiological conditions resulting in each case. Class discussions will primarily center around assigned readings of published literature guided by lecture topics. Prerequisites: BIOE 240 or BIOE 153, 154, BIOE 21 (or BIOL 1B). (2 units)
BIOE 249. Topics in Bioengineering
An introduction to the central topics of bioengineering including physiological modeling and cellular biomechanics, biomedical imaging, visualization technology and applications, biosignals and analysis methods, bioinstrumentation, and bio-nanotechnology. (2 units)
BIOE 250. Genetic and Therapeutic Bioengineering
This course covers the fundamental principles and practical skills of genetic manipulation and therapeutic medicine, with an emphasis on advanced genome editing technologies and applications of gene and cell therapy, drug delivery, and vaccination. Students will be able to implement biomedical solutions in the following areas: Production of recombinant protein drugs; gene therapy; RNA therapeutics and vaccines; targeted gene editing; knockout animal, and disease modeling. Credit is not allowed for both BIOE 250 and 302 (or 263). Also listed as BIOE 150. (4 units).
BIOE 251. Introduction to Bioinformatics
This course provides an introduction to tools and databases essential for bioengineering including DNA, RNA, and protein. Topics include but are not limited to pairwise sequence alignment, multiple sequence alignment, hidden Markov models and protein sequence motifs, phylogenetic analysis, and fragment assembly. Protein structure and domain analysis, as well as genome rearrangement and DNA computing, are also covered. Students will become proficient in searching multiple databases (Genome, GenBank, Protein, and Conserved Domain), retrieving and analyzing sequences, and working with metadata. Students will design a new gene/protein or write an original program to complete an independent search project. Prerequisite: BIOE 22 or BIOL 1C and BIOE 45 (2 units)
BIOE 252. Computational Neuroscience I
This course provides a foundation in cellular and molecular neuroscience and applied computational techniques for the purpose of modeling neuronal and whole-brain structural and functional network organization. The central ideas, methods, and practice of modern computational neuroscience will be discussed in the context of relevant applications in biomedical interventions. (2 units)
BIOE 252L. Computational Neuroscience Lab
Laboratory for BIOE 252. Co-requisite: BIOE 252. (1 unit)
BIOE 256. Introduction to Nano Bioengineering
This course is designed to present a broad overview of diverse topics in nano bioengineering, with emphasis on areas that directly impact applications in biotechnology and medicine. Specific examples that highlight interactions between nanomaterials and various biomolecules will be discussed, as well as the current status and future possibilities in the development of functional nanohybrids that can sense, assemble, clean, and heal. Also listed as ENGR/GREN 256. (2 units)
BIOE 257. Introduction to Biofuel Engineering
This course will cover the basic principles used to classify and evaluate biofuels in terms of thermodynamic and economic efficiencies as well environmental impact for resource recovery. Special emphasis will be placed on emerging applications namely Microbial Fuel Cell Technology and Photo-bioreactors. Also listed as ENGR/GREN 257 and BIOE 157. Prerequisites: BIOE 21 (or BIOL 1B), CHEM 13, PHYS 33. (2 units)
BIOE 258. Soft Biomaterials Characterization
This course will cover the fundamental principles of characterization and biodegradation of soft implantable/injectable biomaterials including polymers, hydrogels, liquid crystalline colloids starting with the linkage of microscopic to macroscopic properties and, emphasis on elasticity, adhesion, diffusion and light scattering. Also listed as BIOE 158. Prerequisite: BIOE 153. Co-requisite: BIOE 258L. (4 units)
BIOE 258L. Soft Biomaterials Characterization Laboratory
Laboratory for BIOE 258. Also listed as BIOE 158L. Co-requisite: BIOE 258. (1 unit)
BIOE 259. Hard Biomaterials Characterization
This course will cover the fundamental principles of characterization and biodegradation of hard biomaterials including bioceramics and metals starting with the linkage of microscopic to macroscopic properties and, emphasis on corrosion, coatings, (nano/micro)-indentation, and accelerated implant analysis. Instruction will be complemented by software-enabled simulation of prototyping and driving forces analysis. Also listed as BIOE 159. Prerequisite: BIOE 153. Co-requisite: BIOE 259L. (4 units)
BIOE 259L. Hard Biomaterials Characterization Laboratory
Laboratory for BIOE 259. Also listed as BIOE 159L. Co-requisite: BIOE 259. (1 unit)
BIOE 260. Selected Topics in Bio-Transport Phenomena
This course will cover the principles of mass and oxygen transport and across extra-corporeal devices and bio-membrane design principles, dialyzers, blood-oxygenators, hollow-fiber-based bio-artificial organs, and PK/PD. Prerequisite: BIOE 155 or equivalent. BIOE 232 preferred. (2 units)
BIOE 263. Applications of Genome Engineering and Informatics in Mammalian System
Advances in genome engineering technologies offer versatile solutions to systematic interrogation and alteration of mammalian genome function. Among them, zinc finger transcription factor nuclease (ZNF), transcription activator-like effector nuclease (TALEN), and CRSPR-associated RNA-guided Cas9 endonuclease (CRISPR/Cas9) have become major drivers for innovative applications from basic biology to biotechnology. This course covers principles and real cases of genome engineering using either ZFN/TALEN or CRSPR/Cas9-based systems. Key applications will be discussed comparatively to understand the advantages/disadvantages of each system better. In addition, informatics tools that facilitate the application design, implementation, and data analysis will be covered. Prerequisites BIOE 22 or BIOL 1C or equivalent. (2 units)
BIOE 267. Introduction to Medical Imaging
This course will cover the basics of technical aspects and clinical applications of medical imaging. Practicing radiologists will introduce the students to the history of radiology and medical imaging, as well as specific modalities such as X-ray, CT, MR, ultrasound, nuclear medicine, and interventional radiology. A brief discussion of applications of information technology to radiology is also included. Also listed as BIOE 167. (2 units)
BIOE 268. Biophotonics and Bioimaging
This course starts with an introduction of optics and basic optical components (e.g. lenses, mirrors, diffraction grating, etc.), then focuses on light propagation and propagation modeling to examine interactions of light with biological matter (e.g. absorption, scattering). Other topics that will be covered in this course are laser concepts, optical coherence tomography, microscopy, confocal microscopy, polarization in tissue, absorption, diffuse reflection, light scattering, Raman spectroscopy, and fluorescence lifetime imaging. Graduate students will prepare a presentation/report on one of the state-of-the-art biophotonics technologies. Also listed as BIOE 168. Prerequisite: PHYS 33. (4 units)
BIOE 268L. Biophotonics and Bioimaging Laboratory
The lab will provide hands-on experience for basic imaging and microscopy techniques as well as advanced techniques such as fiber optics and optical coherence tomography. Some of the experiments that will be conducted are: measuring the focal length of lenses and imaging using a single lens and a lens system, determining the magnification of optical systems (e.g. of a microscope), interference in Young’s double slit and in Michelson configuration, diffraction, polarization, and polarization rotation. Also listed as BIOE 168L. (4 units)
BIOE 269. Stem Cell Bioengineering
A majority of recent research in bioengineering has focused on engineering stem cells for applications in tissue engineering and regenerative medicine. The graduate-level course aims to illuminate the breadth of this interdisciplinary research area, with an emphasis on engineering approaches currently being used to understand and manipulate stem cells. The course topics will include basic principles of stem cell biology, methods to engineer the stem cell microenvironment, and the potential of stem cells in modern medicine. (2 units)
BIOE 270. Mechanobiology
This course will focus on the mechanical regulation of biological systems. Students will gain an understanding of how mechanical forces are converted into biochemical activity. The mechanisms by which cells respond to mechanical stimuli and current techniques to determine these processes will be discussed. Class discussions will primarily center around assigned readings of published literature guided by lecture topics. Also listed as Bioe 170. Prerequisite: BIOE 154. (2 units)
BIOE 273. Advanced Topics in Tissue Engineering
Overview of the progress achieved in developing tools, technologies, and strategies for tissue engineering-based therapies for a variety of human diseases and disorders. Lectures will be complemented by a series of student-led discussion sessions and student-team projects. Also listed as BIOE 173. Prerequisite: BIOE 172 (or with the consent of the instructor). (2 units)
BIOE 275. Introduction to Neural Engineering
This course provides a foundation in the neural principles underlying existing and upcoming neurotechnologies. The goal is to understand the design criteria necessary for engineering interventions in neural structure and function with application to neurological diseases, disorders, and injuries. Topics include brain imaging and stimulation, neural implants, nanotechnologies, stem cell and tissue engineering. This course includes lectures, literature critiques, and design projects. Also listed as BIOE 179. Prerequisites: BIOE 21 (or BIOL 21). BIOE 171 recommended. (2 units)
BIOE 276. Microfluidics and Lab-on-a-Chip
The interface between engineering and miniaturization is among the most intriguing and active areas of inquiry in modern technology. This course aims to illuminate and explore microfluidics and LOC (lab-on-a-chip) as an interdisciplinary research area, with an emphasis on emerging microfluidics disciplines, LOC device design, and micro/nanofabrication. Prerequisite: BIOE 155 or instructor approval. (2 units)
BIOE 277. Biosensors
This course focuses on underlying engineering principles used to detect DNA, small molecules, proteins, and cells in the context of applications in diagnostics, fundamental research, and environmental monitoring. Sensor approaches include electrochemistry, fluorescence, optics, and impedance with case studies and analysis of commercial biosensors. Also listed as BIOE 182 (2 units)
BIOE 280. Clinical Trials: Design, Analysis and Ethical Issues
This course will cover the principles behind the logistics of design and analysis of clinical trials from statistical and ethical perspectives. Topics include methods used for quantification of treatment effect(s) and associated bias interpretation, crossover designs used in randomized clinical trials, and clinical equipoise. Also listed as BIOE 180. Prerequisites: BIOE 120 (or AMTH 108), or with consent of the instructor. (4 units)
BIOE 281. Deep Learning for Bioengineering I
This course covers a spectrum of topics ranging from the fundamentals of neural networks to state-of-the-art deep learning methods, and applications in biomedical engineering with focus on medical image analysis and disease identification. (2 units)
BIOE 282. Bioprocess Engineering
This course will cover the principles of designing, production, and purification of biologicals using living cells on a large scale and industrial scale, including bio-reactor design. Prerequisite: BIOE 21 (or BIOL 1B), AMTH 106 or equivalent. (2 units)
BIOE 283. Bioprocess Engineering II
This course will cover principles of bio-separation processes. Driving forces behind upstream and downstream separation processes from post-culture cell collection to end-stage purification will be analyzed. Special emphasis will be placed on scale-up and economics of implementation of additional purification processes vs. cost illustrated by the use of Simulink software. Prerequisite: BIOE 282 or equivalent. (2 units)
BIOE 285. Physiology and Disease Biology
The course will provide a molecular-level understanding of physiology and disease biology, an overview of gastrointestinal diseases, and an introduction to medical devices used in the diagnosis and treatment as well as challenges in this field. The course will include lectures, class discussions, case studies, and team projects. Also listed as BIOE 185. Prerequisite: BIOE 21 (or BIOL 1B). BIOE 171 recommended. (2 units)
BIOE 286. Biotechnology
The course is designed to introduce fundamental and practical biotechniques to the students with minimum training and background in biomolecular engineering. The basic principles and concepts of modern biotechniques will be illustrated and highlighted by studying real cases in lectures. Also listed as BIOE 186. Prerequisite: BIOE 22 or BIOL 1C. (2 units)
BIOE 288. Biotechnology II
The course is designed to discuss practical applications of recombinant DNA technologies, data science, and other modern technologies in the biotechnology industry beyond pharmaceutical development. Specific topics include microbial, industrial, agricultural, environmental biotechnologies, and forensic science. The technical principles and concepts will be highlighted by reviewing real-world cases in lectures. The course will also discuss critical issues such as ethics, regulations, market, and business. Also listed as BIOE 187. (2 units)
290. Drug Development Process
This course is designed to discuss an overview of the modern pharmaceutical development process, from drug discovery and development, manufacturing, and the regulatory approval process. Specific topics will include current concepts of drug discovery, advanced drug screening methods, preclinical studies and requirements, and the four major phases of clinical development. There will be an emphasis on product development and manufacturing processes for biologics, such as monoclonal antibody-based drugs. Also listed as BIOE 190. (2 units)
BIOE 294. Graduate Capstone Project I
Specification of a translational bioengineering project, selected with the mutual agreement of the student and the project advisor, completion of initial design and feasibility analysis, and submission of a preliminary study report. (2 units)
BIOE 295. Graduate Capstone Project II
Continued design and development of the project (system or prototype), and submission of a draft project report. Prerequisite: BIOE 294. (2 units)
BIOE 296. Graduate Capstone Project III
Continued design and development of the project (system or prototype), and submission of the final project report. Prerequisite: BIOE 295. (2 units)
BIOE 297. Directed Research
By arrangement. (1–6 units)
BIOE 300. Antibody Bioengineering
This course will cover significant areas of antibody engineering, including recent progress in the development of antibody-based products and future direction of antibody engineering and therapeutics. The product concept and targets for antibody-based products are outlined and basic antibody structure, and the underlying genetic organization which allows easy antibody gene manipulation, and the isolation of novel antibody binding sites will be described. Antibody library design and affinity maturation techniques and deep-sequencing of antibody responses, together with biomarkers, imaging, and companion diagnostics for antibody drug and diagnostic applications of antibodies, as well as clinical design strategies for antibody drugs, including phase one and phase zero trial design, will be covered. Prerequisite: BIOE 176 or equivalent. (2 units)
BIOE 301. Protein Engineering and Therapeutics
Protein-based therapeutics have played an increasingly important role in medicine. Future protein drugs are likely to be more extensively engineered to improve their efficacy in patients. Such technologies might ultimately be used to treat cancer, neurodegenerative diseases, diabetes, and cardiovascular or immune disorders. This course will provide an overview of protein therapeutics and its enabling technology, protein engineering. Topics will cover the following areas of interest: therapeutic bioengineering, genome, and druggable genes, classification of pharmacological proteins, advantages and challenges of protein-based therapeutics, principles of recombinant protein design, approaches of protein production, and potential modifications. Specific applications will include drug delivery, gene therapy, vaccination, tissue engineering, and surface engineering. Students will work on teams where they will take examples of concepts, designs, or models of protein therapeutics from literature and determine their potential in specific engineering applications. Prerequisite: BIOE 176 or equivalent. (2 units)
BIOE 302. Gene and Cell Therapy
This course covers principles and applications of gene and cell therapy. Key concepts and technologies such as gene and gene expression, gene variation and genetic defect, therapeutic vector design and construction, as well as ex vivo and in vivo gene delivery will be discussed. The course will culminate in a design project focused on implementing gene or cell-based solutions for a specific disease. After taking this course, participants will: 1) Know the concepts and principles of gene therapy; 2) Understand multiple aspects of gene therapy, including disease gene identification, therapeutic gene design, and expression vector construction, as well as gene delivery strategy and efficacy evaluation; 3) Gain skills to use analytical software to aid design; 4) Gain skills to use sequence manipulation software in expression vector design; 5) Gain skills to use genome database and other related databases; and 6) Present and critically analyze original research concerning gene and cell therapy. (2 units)
BIOE 307. Medical Device Product Development
The course purpose is to discuss and practice product development using medical devices as the model. The course includes identification of product need, invention, development, and implementation or commercialization. Also listed as BIOE 107 and EMGT 307.
BIOE 308. Wearable Sensors and Actuators for Biomedical Applications
Wearable sensor and robotics technologies have the potential to extend the range of the healthcare system from hospitals to the community, improving diagnostics and monitoring, and maximizing the independence and participation of individuals. In this course, we will cover operation principles, challenges, and promises of wearables for physiological and biochemical sensing, as well as for motion sensing, in-depth. Also listed as BIOE 148. (2 units)
BIOE 312. Deep Learning for Bioengineering II
This course focuses on convolutional and recurrent network structures, non-convex optimization problems, and the mathematical, statistical, and computational challenges of building stable representations and analysis for high-dimensional data, such as images and text. Programming and building projects in TensorFlow, Keras, and NumPy will be discussed. Prerequisite: BIOE 281 or equivalent. (2 units)
BIOE 357. Root Cause Analysis (RCA) Effective Problem Solving
Solving problems is one of the main functions of engineering and one of the main concerns of engineering managers. This course will focus on a step-by-step problem-solving approach, used by the best engineering practitioners in the world, designed to improve the efficiency and effectiveness of the problem-solving process. Topics will include proper methods of problem description, identification, correction, and containment. Also listed as EMGT 357. (2 units)
BIOE 381. Sampling Plans in Biomedical Engineering
Statistical sampling plans are used from bench top to scale up in diagnostics, biodevice manufacturing for defect sampling by the FDA. Starting from a review of the Central Limit Theorem, continuity correction, and moment-generating functions, the course transitions into discrete variable distributions used in single, multiple, and rectifying sampling plans. Instruction will be completed by JMP/SAS software. Also listed as BIOE 181. Prerequisites: BIOE 180 or 380 or BIOE 232. (2 units)
BIOE 397. Master’s Thesis Research
By arrangement. (1–9 units)