Undergraduate Course Directory

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Courses by Subject Area

Click on the links below for a list of courses in that subject area. You may then click “View Classes” to see scheduled classes for individual courses. See the Ratcliffe Hicks Courses page for a list of those courses.

1401. Honors Core: Computational Molecular Biology

Also offered as: CSE 1401, MCB 1401, PNB 1401

3.00 credits

Prerequisites: None.

Grading Basis: Honors Credit

Introduction to research in computational biology through lectures, computer lab exercises, and mentored research projects. Topics include gene and genome structure, gene regulation, mechanisms of inheritance, biological databases, sequence alignment, motif finding, human genetics, forensic genetics, stem cell development, comparative genomics, early evolution, and modeling complex systems. CA 3.

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2101. Introduction to Biomedical Engineering

3.00 credits

Prerequisites: MATH 1132Q, which may be taken concurrently; PHYS 1230 or 1501 or 1530, each of which may be taken concurrently; open to non-BME majors with instructor consent.

Grading Basis: Graded

Fundamental concepts and techniques of engineering and medical science and their integration. The art and science of medicine and the process of medical diagnosis and treatment. Topics include: diagnostic instrumentation, diagnostic measurements and their interplay; bioelectric phenomena, biomechanics, and biomaterials; biochemical engineering; computers in medicine; molecular medicine and biotechnology; medical imaging.

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3100. Physiological Modeling

3.00 credits

Prerequisites: MATH 1132, which may be taken concurrently. Open only to Biomedical Engineering majors. Recommended preparation: BIOL 1107.

Grading Basis: Graded

Techniques for analysis and modeling of biomedical systems. Application of advanced mathematics (including Differential Equations, Laplace Transforms and Statistics) and computer-aided methods to study problems at the interface of engineering and biology. Elements of physiological modeling and the solution of the transient and forced response for a variety of biomechanical, biomaterial, bioelectrical and biochemical systems.

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3120. LabVIEW Basics for Engineers

1.00 credits

Prerequisites: CSE 1010 or 1100. Open only to Biomedical Engineering majors, others by instructor consent. Not open for credits to students who have passed ENGR 3120

Grading Basis: Graded

Introduces LabVIEW programming environment. The fundamentals of using graphical programming to collect, analyze, display and store data are covered. Learn techniques for designing stand alone applications, creating interactive user interfaces and optimizing data flow.

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3193. International Study

1.00 - 6.00 credits | May be repeated for a total of 6 credits.

Prerequisites: None.

Grading Basis: Graded

Special Biomedical Engineering topics taken in an international study program. May be repeated for credit up to a maximum of six credits with change in topic.

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3300. Biochemical Engineering for Biomedical Engineers

3.00 credits

Prerequisites: BME 2101 and MATH 2410; CHEM 2443, which must be taken concurrently; open only to Biomedical Engineering majors.

Grading Basis: Graded

Introduction to chemical reaction kinetics; enzyme and fermentation technology; microbiology, biochemistry, and cellular concepts; biomass production; organ analysis; viral dynamics.

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3320. Biosensors and Nanodevices for Biomedical Applications

3.00 credits

Prerequisites: Open only to BME majors, others by instructor consent. Not open for credit to students who have passed BME 4985 when taught as Biosensors and Nanodevices for Biomedical Applications.

Grading Basis: Graded

Current and emerging technologies in biosensors for biomedical applications. Topics include principles of molecular and bio/chemical sensing, techniques for sensor integration, nano/micro electro mechanical systems (NEMS/MEMS) technologies used in biosensors, and commercial/clinical applications of biosensors.

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3401. Introduction to Computational and Systems Biology

3.00 credits

Prerequisites: MATH 2210Q, 2410Q; STAT 3025Q or 3345Q or MATH 3160.

Grading Basis: Graded

Introduction to the role of computational and mathematical analyses in biological sequence (DNA, RNA, proteins) analysis and quantitative mathematical models of cell biological processes (systems and quantitative biology). Algorithms for sequence alignment, analysis of networks involved in transcription, development, and signal transduction. Programming in the Python language will be an integral part of the course, but no prior experience with Python is necessary.

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3420. Stem Cells for Regenerative Medicine

3.00 credits

Prerequisites: Open only to BME majors, others with consent. Not open for credit to students who have passed BME 4985 when taught as Stem Cells for Regenerative Medicine.

Grading Basis: Graded

Introduces the fundamental concept and translational application of regenerative medicine such as stem cells, gene therapy, cell and tissue therapy. Topics include tissue-specific stem cells, embryonic stem cells, induced pluripotent stem cells and their potential therapeutic applications for musculoskeletal, cardiovascular and nervous systems.

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3500. Biomedical Engineering Measurements

4.00 credits

Prerequisites: ECE 3101, which may be taken concurrently; open only to BME majors, others by instructor consent.

Grading Basis: Graded

A lecture and laboratory course that covers fundamentals of biomedical measurement and patient safety. Measurements of physical quantities by means of electronic instruments, mechanical devices and biochemical processes. Analysis of measurement systems using mathematical models. Methods of measuring signals in the presence of noise. Use of computers in measurement systems.

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3520. Developing Mobile Apps for Healthcare

3.00 credits

Prerequisites: Open only to BME majors, others with consent. Not open for credit to students who have passed BME 4985 when taught as Developing Mobile Apps for Healthcare.

Grading Basis: Graded

Mobile apps are changing the way doctors and patients approach health care. Designed for use by doctors, patients or both, the apps available range from handy databases about drugs and diseases to sophisticated monitors that read a person's physiological signals. Students will learn the basic elements of apps development on Android platforms, including XML, and Java, UI amongst others. Topics include how to handle patient data in the cloud using HIPAA-Compliant web service and how to integrate machine learning models in app development. No previous programming experience is needed.

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3600. Biomechanics

4.00 credits

Prerequisites: BME 3150 or CE 2110; open only to Biomedical Engineering majors; others by instructor consent.

Grading Basis: Graded

Application of solid mechanics theory to describe and analyze mechanical behaviors of biological tissues. Basic concepts in mechanics of materials, including the essential mathematics, kinematics of deformation and motion, stress, constitutive relations. Biomechanics principles; identifying, formulating and solving problems related to bone, cartilage, tendon, cardiac and vascular tissues. Introduction of experimental methods and computational modeling of biological tissues. A separate laboratory component will introduce students to experimental methods in more detail. Laboratory reports with revisions are required.

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3700. Biomaterials

4.00 credits

Prerequisites: MSE 2101 and MATH 2410; open only to BME majors. Cannot be taken for credit after passing MSE 3700.

Grading Basis: Graded

A lecture and laboratory course that introduces a series of implant materials including metals, ceramics, glass ceramics, polymers, and composites. These materials are compared with the natural materials, with consideration given to issues of mechanical properties, biocompatibility, degradation of materials by biological systems, and biological response to artificial materials. Particular attention is given to the materials for the total hip prosthesis, dental restoration, and implantable medical devices.

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3720. Drug Delivery

3.00 credits

Prerequisites: BME 3700; open only to BME majors, others with consent. Not open for credit to students who have passed BME 4985 when taught as Drug Delivery.

Grading Basis: Graded

Introduction to drug delivery systems that provide pharmaceutical agents at target tissues, the mechanism of pharmacokinetic regulation, the basics, technology, and applications of drug delivery systems. Emphasis on understanding the principles of pharmacokinetics and drug delivery systems to improve clinical efficacy as well as to reduce side effects.

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3740. Introduction to Microscopy and Biophotonics

3.00 credits

Prerequisites: ECE 3101; open only to BME majors, others with consent. Not open for credit to students who have passed BME 4985 as Introduction to Microscopy and Biophotonics.

Grading Basis: Graded

Basic principles of modern light microscopy and related biophotonics techniques. Matlab will be used to model various imaging platforms. Topics include geometrical optics; image processing in spatial and Fourier domain; lensless microscopy imaging; light scattering and absorption in tissue; wave propagation; coherent and incoherent imaging; lens-based imaging systems; optical aberrations; phase retrieval; brightfield, darkfield, phase-contrast, and confocal microscopy; holographic imaging; light field microscopy; 3D tomographic imaging; autofocusing for whole slide imaging; two-photon imaging; structured illumination and other super-resolution techniques; Fourier ptychographic imaging; detectors and photon transfer curve; image denoising via regularization; optical coherent tomography.

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3810. Computational Genomics

Also offered as: CSE 3810

3.00 credits

Prerequisites: BIOL 1107; CSE 1010 or 1100 or 1729; STAT 3025 or 3345; open only to students in the School of Engineering and declared Computer Science minors.

Grading Basis: Graded

Computational methods for genomic data analysis. Topics covered include statistical modeling of biological sequences, probabilistic models of DNA and protein evolution, expectation maximization and Gibbs sampling algorithms, genomic sequence variation, and applications in genomics and genetic epidemiology.

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3900. Junior Design

3.00 credits

Prerequisites: BME 3500 and 3600; or CE 2110, ECE 2001, and MSE 2101

Grading Basis: Graded

Students work through a structured process that emulates an open-ended, real-world design of a biomedical engineering product. Project definition and product specifications, project scheduling and management, team interactions, failure and safety criteria, progress reporting, marketing concepts, ethical issues, prototype development, proper documentation and technical presentation of the final project outcomes. Includes a significant writing component, makes use of computers and design software, and involves hands-on design explorations. Students will complete a semester-long design project that demonstrates the skills and knowledge learned during the course in preparation for the capstone design experience.

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4120. Neural Information Processing and Sensory Coding

3.00 credits

Prerequisites: ECE 3101; open only to BME majors, others with consent. Not open for credit to students who have passed BME 4985 as Neural Information Processing

Grading Basis: Graded

Processing, transmission, and storage of information in the central and peripheral nervous systems. Mechanisms of signal generation, transmission and coding by neurons and dendrites. Analysis of invertebrate and vertebrate visual and auditory systems, including: mechanisms of neurosensory transduction, coding, and signal-to-noise ratio enhancement. Neural spatio-temporal filters for feature extraction and pattern recognition. Information theoretic analysis of signal encoding and transmission in the nervous system. Assumes a background in linear systems and feedback control systems.

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4130. Neural Prostheses

3.00 credits

Prerequisites: Open only to Biomedical Engineering majors, others by instructor consent.

Grading Basis: Graded

Development of neural prostheses. Topics will cover physiology of neurological disorders, key concepts of neural prostheses, electrode designs and materials, fabrication methodologies, measurement techniques, histological evaluations, and clinical translations. Students will also learn to critique journal articles and to write their own NIH research proposal.

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4201. Introduction to Medical Imaging

3.00 credits

Prerequisites: PHYS 1502, BME 3500, and ECE 3101. Open only to Biomedical Engineering majors, others by instructor consent.

Grading Basis: Graded

Introduction to spatial signals including spatial impulse response, spatial sampling and filtering, spatial Fourier transforms, and back projection. Principles, systems and clinical applications of X-ray, X-ray CT, ultrasound, Positron Emission Tomography (PET) and Single Photon Emission Tomography (SPECT), and MRI imaging.

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4300. Physiological Control Systems

3.00 credits

Prerequisites: BME 3400 or ECE 3101; open only to BME majors.

Grading Basis: Graded

Analysis of human physiological control systems and regulators through the use of mathematical models. Identification and linearization of system components. Systems interactions, stability, noise, and the relation of system malfunction to disease. The analysis and design of feedback systems to control physiological states through the automatic administration of drugs.

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4400. Dynamical Modeling of Biological Networks

3.00 credits

Prerequisites: ECE 3101, Open only to BME majors, others by Instructor Consent.

Grading Basis: Graded

Construction and analysis of biochemical pathway models. Mass action kinetics and the S-matrix formalism, nonlinear differential equations, bistability, bifurcations, linear stability analysis, and nonlinear oscillations. Possible applications include kinetic proofreading, classical enzyme kinetics, biological switches, and dynamical behavior of simple biochemical circuits.

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4401. Computational Foundations of Systems Biology

3.00 credits

Prerequisites: Open only to Biomedical Engineering majors, others by instructor consent.

Grading Basis: Graded

Introduction to computational systems biology, which focuses on studying the dynamic and intelligent features (e.g., adaptation and robustness) of biological systems. Through a variety of assignments and projects using MATLAB, LabVIEW and C#, students will obtain a deeper understanding of physical and engineering principles and methods (e.g., computational physics, digital signal processing, control engineering, and digital logic) applied to biological systems.

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4500. Bioinstrumentation

3.00 credits

Prerequisites: BME 3500; open only to BME majors.

Grading Basis: Graded

Modeling, analysis, design, and operation of transducers, sensors, and electrodes, for physiological systems; operational and instrumentation amplifiers for bioelectric event signal conditioning, interfacing and processing; A/D converters and hardware and software principles as related to sampling, storing, processing, and display of biosignals and digital computers.

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4520. Digital Image Processing for Biomedical Engineering

3.00 credits

Prerequisites: ECE 3101; open only to BME majors, others with consent. Not open for credit to students who have passed BME 4985 as Digital Image Processing for BME.

Grading Basis: Graded

Fundamentals of digital signal processing with particular emphasis on problems in biomedical research and clinical medicine. Principles and algorithms for processing both deterministic and random signals. Topics include ECG, image modalities, discrete Fourier transform, Fast Fourier transform, data acquisition, sampling, filtering, denosing, regularization, coding, feature extraction and modeling, image segmentation and registration, and machine learning. Includes the training of a neural network to classify images with different diseases.

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4600. Biosolid Mechanics

3.00 credits

Prerequisites: BME 3600; open only to BME majors.

Grading Basis: Graded

Mechanical behavior of biological solids. Applications of the theories of elasticity, viscoelasticity, and poroelasticity to bones, ligaments and tendons, skeletal muscle, and articular cartilage. Axial, bending, shearing and torsional loadings. Bone morphology and growth. Biphasic theory. Failure theories. Topics may be modified slightly to accomodate student interests.

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4701. Advanced Biomaterials

3.00 credits

Prerequisites: BME 3700; open only to BME majors. Not open to students who have passed MSE 4701.

Grading Basis: Graded

Offers opportunity to gain in-depth knowledge of a series of biomaterials for various applications. Topics include calcium phosphates and composites for hard tissue replacement, drug delivery systems, issues unique to the biomedical field, and regulations for new products and standards.

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4710. Tissue Engineering

3.00 credits

Prerequisites: BME 3700; open only to BME majors.

Grading Basis: Graded

Presents basic principles of biological, medical, and material science as applied to implantable medical devices, drug delivery systems and artificial organs.

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4720. Cellular Engineering

3.00 credits

Prerequisites: None.

Grading Basis: Graded

Cellular engineering emphasizes the navigation and understanding of discoveries in stem cell, molecular, and developmental biology from an engineering perspective. Student projects and an active learning approach enable students to practice the complex and open-ended process of synthesizing and translating basic discoveries for the rational design of tissue regeneration therapies.

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4800. Bioinformatics

Also offered as: CSE 3800

3.00 credits

Prerequisites: BIOL 1107; CSE 1010 or 1100 or 1729; STAT 3025 or 3345; open only to Biomedical Engineering majors, Computer Science, and Computer Science and Engineering majors, others by instructor consent.

Grading Basis: Graded

Fundamental mathematical models and computational techniques in bioinformatics. Exact and approximate string matching, suffix trees, pairwise and multiple sequence alignment, Markov chains and hidden Markov models. Applications to sequence analysis, gene finding, database search, phylogenetic tree reconstruction.

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4900. Biomedical Engineering Design I

3.00 credits

Prerequisites: Open only to Biomedical Engineering majors; prerequisites vary by track as follows: Biomaterials and Tissue Engineering, BME 3500, 3600, 3700, and 3900; Biomechanics and Mechanobiology, BME 3600 and 3900; Computational and Systems Biology, BME 3900; Systems, Imaging and Instrumentation, BME 3500 and 3900; no track: BME 3500, 3600, and 3700.

Grading Basis: Graded

Discussion of the design process; project statement, specifications project planning, scheduling and division of responsibility, ethics in engineering design, safety, environmental considerations, economic constraints, liability, manufacturing, and marketing. Projects are carried out using a team-based approach. Selection and analysis of a design project to be undertaken in BME 4910 is carried out. Written progress reports, a proposal, an interim project report, a final report, and oral presentations are required.

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4910. Biomedical Engineering Design II

3.00 credits

Prerequisites: BME 4900; open only to BME majors.

Grading Basis: Graded

Design of a device, circuit system, process, or algorithm. Team solution to an engineering design problem as formulated in BME 4900, from first concepts through evaluation and documentation. Written progress reports, a final report, and oral presentation are required.

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4910W. Biomedical Engineering Design II

3.00 credits

Prerequisites: BME 4900; ENGL 1010 or 1011 or 2011; open only to Biomedical Engineering majors

Grading Basis: Graded

Design of a device, circuit system, process, or algorithm. Team solution to an engineering design problem as formulated in BME 4900, from first concepts through evaluation and documentation. Written progress reports, a final report, and oral presentation are required.

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4985. Special Topics in Biomedical Engineering

1.00 - 6.00 credits | May be repeated for credit.

Prerequisites: Open only to BME majors. Prerequisites and/or consent announced separately for each topic.

Grading Basis: Graded

Classroom and/or laboratory courses in special topics as announced for each semester. With a change of topic, this course may be repeated for credit.

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4999. Independent Study

1.00 - 6.00 credits | May be repeated for credit.

Prerequisites: Open only to Biomedical Engineering majors.

Grading Basis: Graded

Independent study project carried on by the student under the guidance of a faculty member. The student is required to submit a report on the study at the end of the semester. With a change in content, this course may be repeated for credit.

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