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Department ofBioengineering

Course Descriptions

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)

203. Bio-Electromagnetics

Fundamentals of bioelectromagnetics. Tissue characterization and body phantoms, dielectrophoresis electrodes, RF/Microwave Interaction mechanisms in biological materials. Electromagnetic field absorption and SAR, Power transfer in biological environment, On-body and implant antennas, microwave hyperthermia. Also listed as ELEN 203. Prerequisite: ELEN 201 (or equivalent) or BIOE 168/268. (2 units)

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)

207. Medical Device Invention - From Ideas to Business Plan

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)

208. Biomedical Devices: Role of Polymers**

This course is designed to highlight the role of polymers play in the design and fabrication of various medical devices ranging from simple intravenous drip systems to complex cardiac defibrillator implants and transcatheter heart valves. Topics include polymer basics, biocompatibility, biodegradation and other tangentially related topics such as regulatory body approvals and intellectual property. Also listed as BIOE 108. (2 units)

209. Development of Medical Devices in Interventional Cardiology

This course will be an in-depth, case-based review of medical devices that are currently used in clinical practice, meeting the heart patient’s medical needs. Directed reading will be assigned and the in-class discussions will focus on bioengineering design considerations including: measurements of physiology vs anatomy, intracoronary blood flow vs pressure, invasive vs non-invasive imaging; as well as, the significant economic challenges facing innovative start-ups developing medical devices within our changing health care delivery system. (2 units)

210. Ethical Issues in Bioengineering

This course serves to introduce bioengineering students to ethical issues related to their work. This includes introductions to ethical theories, ethical decision-making, accessibility and social justice concerns, issues in personalized medicine, environmental concerns, and so on. This course will also cover ethical and technical issues related to biomedical devices. (2 units)

226. Biomolecular and Cellular Engineering II

This course will focus on the principle of designing, manufacturing synthetic materials and their biomedical and pharmaceutical applications. Emphasis of this class will be given to chemically synthetic materials, such as polymers, inorganic and organic compounds. Also listed as BIOE 176. Prerequisites: BIOE 22 (or BIOL 1C) and CHEM 31, or equivalent knowledge and instructor approval. BIOE 175 and 171 is recommended. (4 units)

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)

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; methods for categorical data, comparing groups (analysis of variance) and analyzing associations (linear and logistic regression). Special emphases 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)

232L. Biostatistics Laboratory**

Laboratory for BIOE 232. Also listed as AMTH 232L. Co-requisite: BIOE 232. (1 unit)

240. Biomaterials Engineering and Characterization**

This course will cover the fundamental principles of soft biomaterials characterization in terms of mechanical and rheological properties related to biocompatibility. Areas of focus in the lab include study and fabrication of implantable hydrogels for eukaryotic cell immobilization in scaffolds and microcapsules, cytotoxicity measurements in the engineered micro-environment and nutrient diffusion visualized by fluorescence microscopy. Prerequisite: CHEM 13. (2 units).

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 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, BIOE 154, BIOE 21 or BIOL 1B. (2 units)

249. Topics in Bioengineering**

An introduction to the central topics of bioengineering including physiological modeling and cellular biomechanics (e.g., modeling of the human voice production and speech biomechanics), biomedical imaging, visualization technology and applications, biosignals and analysis methods, bioinstrumentation and bio-nanotechnology. Also listed as ENGR 249. (2 units)

251. Introduction to Bioinformatics

This course provides an introduction to tools and databases important for bioengineering including DNA, RNA, and protein. Topics include but 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. Programming experience and BIOL 175 recommended. (2 units)

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)

252L. Computational Neuroscience Lab

Laboratory for BIOE 252. Co-requisite: BIOE 252. (1 unit)

256. Introduction to NanoBioengineering**

This course is designed to present a broad overview of diverse topics in nanobioengineering, 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 256. (2 units)

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 emphases will be placed on emerging applications namely Microbial Fuel Cell Technology and
Photo-bioreactors. Also listed as ENGR 257 and BIOE 157. Prerequisites: BIOE 21 (or BIOL 1B), CHEM 12, PHYS 33. (2 units)

258. Synthetic Biology & Metabolic Engineering**

This course covers current topics and trend in the emerging field of synthetic biology. These topics include applying the retro-synthetic analysis approach in classic organic chemistry, identifying and engineering metabolic pathways and mechanisms for bioproduction of antibiotics, biofuel compounds, novel bio-building blocks and non-natural proteins. Genetic regulation of biosynthetic pathways, e.g., genetic circuits will also be discussed. (2 units)

259. Engineering In Drug Delivery

Engineering is a major contributor to the advancement of drug delivery systems, which improves treatment and enhances patients quality of life. In this course, we will explore engineering principles, applications, and techniques in drug delivery systems. The purpose of this course is to identify roles of engineers in the pharmaceutical industry and how to propose a solution to emerging topic in this subject. (2 units)

260. Selected Topics in Bio-Transport Phenomena**

This course will cover the principles of mass and oxygen transport across extra-corporeal devices, bio-membrane design principles, dialyzers, blood-oxygenators, hollow-fiber based bio-artificial organs, and PK/PD. Prerequisites: BIOE 155 or equivalent, BIOE 232 preferred. (2 units)    

261. Omics: Global  High-throughput Technologies in Life Sciences Discovery Research**

This course provides a practical application focused survey of global high-throughput technologies in life sciences discovery research. The impact of all facets of study design and execution on obtaining valuable molecular insights from genomics, metagenomics, transcriptomics, metabolomics, and proteomics methods will be explored. Strategies for integration and interpretation of data-rich read-outs will be applied to case studies focused on research and development of companion diagnostics. Prerequisite: BIOE 21. (2 units)

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 system. Key applications will be discussed in a comparative fashion to better understand the advantages/disadvantages of each system. In addition, informatics’ tools that facilitate the application design, implementation, data analysis will be covered. Prerequisites: BIOE 22 or BIOL 1C or equivalent. (2 units)

266. Advanced Nano-Bioengineering**

In Introduction to Nano-bioengineering (BIOE 256), students were introduced to how nanomaterials  offer the unique possibility of interacting with biological entities (cells, proteins, DNA, etc) at their most fundamental level. This course will provide a detailed overview of nanobioengineering approaches that support research in life sciences and medicine. Topics will include nanotopographical control of in vivo and in vitro cell fate, miniaturization and parallelization of biological assays, and early diagnosis of human disease. Prerequisite: BIOE 256. (2 units)

267. Introduction to Medical Imaging

This course will cover 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)

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)

268L. Biophotonics and Bioimaging Laboratory

The lab will provide the 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)

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 aim of this graduate level course is 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)

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. Prerequisite: BIOE 154. (2 units)

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)

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)

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)

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. (2 units)

279. Stem Cell & Regenerative Medicine

Few events in science have captured the same level of sustained interest and imagination of the nonscientific community as Stem Cells and Regenerative Medicine. The fundamental concept of Regenerative Medicine is appealing to scientists, physicians, and lay people alike: to heal tissue or organ defects that the current medical practice deems difficult or impossible to cure. Regenerative medicine is a new branch of medicine that attempts to change the course of chronic disease, in many instances regenerating failing organ systems lost due to age, disease, damage, or congenital defects. The area is rapidly becoming one of the most promising treatment options for patients suffering from tissue failure. This course covers principles and real cases of stem cell and regenerative medicine. Its major applications will be discussed in a comparative fashion to better understand the advantages/disadvantages of each system. Overall, this course provides a deeper exploration of the next generation biotechnology - a wide variety of cells, biomaterials, interfaces and applications for tissue engineering. Prerequisite: BIOE 269. (2 units)

280. Special Topics in  Bio-therapeutic Engineering **

This class will cover current topics on the engineering of biomimetic drugs, particularly protein drugs, and the development of vaccine, therapeutic antibody and biomarkers. Prerequisite: BIOE 270 or equivalent. (2 units)

281. Deep Learning in Medical Image Analysis and Disease Classification

This course covers the fundamentals of deep learning and methods for medical image analysis with focus on Convolutional Neural Network (CNN) and its applications in image-based disease classifications. The analysis of high-dimensional datasets with still images and volumetric data will be discussed. (2 units)

282. BioProcess Engineering**

This course will cover the principles of designing, production and purification of biologicals using living cells in a large scale and industrial scale, including bio-reactor design. Prerequisite: BIOE 21 (or BIOL 1B), BIOE 10, AMTH 106 or equivalent. (2 units)

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)

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)

286. Biotechnology**

The course is designed to introduce basic 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 the real cases in lectures. Also listed as BIOE 186. Prerequisite: BIOE 22 or BIOL 1B. (2 units)

287. Pharmaceutical Drug Development & Chemical Analysis

This course will introduce the fundamental principles of drug discovery and development, also discussing important drug targets in drug discovery. While discussing analytical-chemical characteristics of selected drug substances, basic concepts for the common analytical methods that are used in the quantitative and qualitative chemical analysis of pharmaceutical drugs will be addressed. International Pharmacopoeias, Regulations, and Guidelines will also be reviewed briefly. (2 units)

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. Biotechnology III - 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)

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)

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)

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)

297. Directed Research

By arrangement. (1–6 units)

300. Antibody Bioengineering**

This course will cover major 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. Anti-body 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. Prerequisites: BIOE 176 or equivalent. (2 units)

301. Protein Engineering and Therapeutics**

Protein-based therapeutics has 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)

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 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)

307. Medical Device Product Development

The purpose of this course is to provide background information and knowledge to start or enhance a career in medical device product development. Discusses medical device examples, product development processes, regulation, industry information, and intellectual property. Also listed as BIOE 107 and EMGT 307. (2 units)

308. Wearable Sensors and Actuators for Biomedical Applications

The wearable sensor and robotics technologies have the potential to extend the range of health care 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. (2 units)

310. Machine Learning in Biomedical Engineering

This course presents an overview of Machine Learning, the study of computing systems that improve their performance with learning abilities. The basic ideas and intuition behind modern methods, concepts, techniques, and algorithm are presented. The course has a special emphasis on deep learning as the most representative machine learning method. The applications of machine learning in biomedical engineering are presented and discussed during the course. (2 units)

312. Deep Learning

This course is an introduction to deep learning, a cutting-edge artificial intelligence concerned with the structure, development, and application of modern neural networks. A range of topics from basic neural networks, convolutional architectures, unsupervised learning, recurrent network structures, non-convex optimization, and the mathematical, statistical and computational challenges of building stable representations and analysis for high-dimensional data, such as images and text are discussed. Programming and building projects in TensorFlow, Keras, and NumPy will be discussed. (4 units)

320. Immunotherapy

The goal of this course is to provide conceptual, preclinical and clinical background necessary to understand the strengths and limits of the main types of cancer immunotherapy and to assess efficacy of the treatment using immunoassays. Emphasis will be given to antibody-drug conjugates, checkpoint blockade, CAR-T cell therapy, cancer vaccines, cytokines and interferon, through lectures and journal club presentations. (2 units)

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)

378. Advanced Biomaterials

The objective of this course is to examine the range of new biomaterials potentially applicable to medical and biotechnology devices. The content will focus on chemistry and fabrication of polymeric biomaterials, surface properties, nano-scale analytical tools, effects of the biological environment and interaction with cells and tissues. In teams of 2 to 4, students will prepare and orally present a design study for a solution to a medical problem requiring one or more biomaterials, using tissue engineering and regenerative approaches. Students should be familiar with or prepared to learn medical, anatomical and physiological terminology. Written assignments are an annotated bibliography drawn from research literature on the topic of the design study and an individually-written section of the team’s report. Material from lectures and student presentations will be covered in short quizzes and a final examination. (2 units)

380. Clinical Trials: Design, Analysis, and Ethical Issues

This course will cover the principles behind the logistics of design and analysis of clinical trials from the statistical  and ethical perspectives. Topics include methods used for quantification of treatment effect(s) and associated bias interpretation, cross-over designs used in randomized clinical trials and clinical equipoise. Also listed as BIOE 180. Prerequisites: BIOE 10, AMTH 108 or BIOE 120 or with consent of the instructor. (4 units)

397. Master’s thesis research

By arrangement. (1–9 units)

642. Computational and Medical Imaging

Algorithms for indirect image formation using both optimization and model-based methods. Applications include computed tomography, magnetic resonance imaging, microscopy, remote sensing, super-resolution. Analysis of accuracy and resolution of image formation based on measurement geometry and statistics. Offered in alternate years. Also listed as ELEN 642. Prerequisites: AMTH 211 and either ELEN 233, AMTH 358, or equivalent. (2 units)


** These courses are eligible for the technical stem in Engineering Management

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Chair: Zhiwen Zhang
Administrative Assistant: Matthew Blanco

Santa Clara University
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