Courses

The listing of a course description here does not guarantee a course’s being offered in a particular semester. Please refer to the published schedule of classes on the Student Link for confirmation a class is actually being taught and for specific course meeting dates and times.

• ENG BE 740: Parameter Estimation and Systems Identification
  Application of models with physical parameters to experimental data. Linear and non-linear systems estimation, system identifiability, time and frequency domain estimation, model sensitivity and experiment multivariate statistical analysis, and optimal design. Application predominantly to biomedical systems (e.g., cardiovascular, respiratory, and pharmokinetics). Other applications included. Same as ENG EC 740; students may not receive credit for both.
• ENG BE 745: Nanomedicine- Principles and Applications
  The use of nanoscience and technology for biomedical problems has spawned a field of applications ranging from nanoparticles for imaging and therapeutics, to biosensors for disease diagnostics. Nanomedicine is a rapidly growing field that exploits the novel properties of nanoscale materials and techniques to rapidly advance our understanding of human biology and the practice of medicine. This course focuses on the fundamental properties, synthesis and characterization of nanomaterials, coupled with their applications in nanomedicine, including: micro- and nano-particles for drug delivery and imaging, microfluidics for in vitro diagnostics, nanomaterials and platforms for biological applications. The biomedical applications include cancer, cardiovascular disease, and infectious diseases.
• ENG BE 747: Advanced Signals and Systems Analysis for Biomedical Engineering
  Introduction to advanced techniques for signals and systems analysis with applications to problems in biomedical engineering research. Time-domain and frequency-domain analysis of multiple input, multiple output systems using the fundamental matrix approach. Hilbert transform relations; applications to head- related transfer functions. Second-order characterization of stochastic processes: power density spectra, cross-spectra, auto-and cross-correlation functions. Gaussian and Poisson processes. Models of neural firing patterns. Effects of linear systems on spectra and correlation functions. Applications to models of the peripheral auditory system. Optimum processing applications. Applications to psychophysical modeling. Introduction to wavelets and wavelet transforms. Wavelet filter banks and wavelet signal processing.
• ENG BE 755: Molecular Systems and Synthetic Biology Laboratory
  Molecular Systems and Synthetic Biology Laboratory
• ENG BE 760: Structural Bioinformatics
  Principles and significance of protein structure. Protein domains and folds. Functional classification of proteins. Functional and structural annotation. Molecular modeling and simulation methods. Structure validation and refinement. Assignment of structure to genome sequences by homology modeling and fold recognition. The role of structure in functional annotation. Protein families and folds in genomes. Annotation from protein interactions. Interactions between proteins and small molecules. Structure-based drug design. Quantitative Structure-Affinity Relationships (QSAR) and the estimation of affinities. Chemoinformatics, molecular diversity, and combinatorial library design, DNA structure, protein-DNA interactions, and recognition sites. Binding of sall molecules to DNA, RNA structure prediction.
• ENG BE 764: Biophysics of Large Molecules
  Correlation between various physical properties of large molecules and their structure is considered in detail. Physical and mathematical description of polyatomic molecules and macromolecules is elaborated. Methods to study large molecules are described. A special emphasis is given to interaction of large molecules with electromagnetic radiation (visual light, ultraviolet and infrared radiation, X-rays, radiowaves). Physics of macromolecules or Polymers) is treated in detail. Numerous biomedical photosynthesis, DNA damage under irradiation, structure of major biological molecules (proteins and nucleic acids).
• ENG BE 765: Biomedical Optics and Biophotonics
  This course surveys the applications of optical science and engineering to a variety of biomedical problems, with emphasis on optical and photonics technologies that enable real, minimally-invasive clinical applications. The course teaches only those aspects of biology itself that are necessary to understand the purpose of the application. The first weeks introduce the optical properties of tissue, and following lectures cover a range of topics in three general areas: 1) Optical spectroscopy applied to diagnosis of cancer and other tissue diseases; 2) Photon migration and optical imaging of subsurface structures in tissue; and 3) Laser-tissue interactions and other applications of light for therapeutic purposes. In addition to formal lectures, recent publications from the literature will be selected as illustrative of various topical areas, and for each publication one student will be assigned to prepare an informal presentation (with overhead slides or PowerPoint) reviewing for the class the underlying principles of that paper and outlining the research results. Same as ENG EC 765; students may not receive credit for both.
• ENG BE 767: Protein and Genomic Systems Engineering
  This course will provide a critical review of current research topics in proteomics and systems biology. Emphasis will be placed on protein engineering (gross structural modifications, pathway perturbations, and biomedical applications including therapeutics and diagnostics) and genome engineering (knockout strains, conditional knockouts, and bioproductions optimization). Topics covered will include: mass spectrometry, protein microarrays, protein complex and interaction discovery, uses of antibodies as reagents and therapeutics, and pathway and network analyses.
• ENG BE 771: Introduction to Neuroengineering
  This course covers existing and future neurotechnologies for analyzing brain signals and for treating neurological and psychiatric diseases. It focuses on the biophysical, biochemical, anatomical principles governing the design of current neurotechnologies, with a goal of encouraging innovations of a new generation of therapies. Topics include basic microscopic and macroscopic architecture of the brain, the fundamental properties of individual neurons and ensemble neural networks, electrophysiology, DBS, TMS, various imaging methods, optical neural control technologies, optogenetics, neuropharmacology, gene therapy, and stem-cell therapy. Discussions of related literatures and design projects will be involved. This course is open to graduate students only and it meets with BE571.
• ENG BE 773: Advanced Optical Microscopy and Biological Imaging
  This course will present a rigorous and detailed overview of the theory of optical microscopy starting from basic notions in light propagation and covering advanced concepts in imaging theory such as Fourier optics and partial coherence. Topics will include basic geometric optics, photometry, diffraction, optical transfer functions, phase contrast microscopy, 3D imaging theory, basic scattering and fluorescence theory, imaging in turbid media, confocal microscopy, optical coherence tomography (OCT), holographic microscopy, fluorescence correlation spectroscopy (FCS), fluorescence resonant energy transfer (FRET), and nonlinear-optics based techniques such as two-photon excited fluorescence (TPEF) and second-harmonic generation (SHG) microscopy. Biological applications such as calcium and membrane-potential imaging will be discussed. A background in optics is preferable. A background in signals and analysis is indispensable. In particular, the student should be comfortable with Fourier transforms, complex analysis, and transfer functions. Meets with ENGEC773. Students may not receive credit for both.
• ENG BE 777: Computational Genomics
  A case-study approach to current topics in computational genomics. Mathematical and engineering tools for analyzing genomic data are reviewed. The relationships between sequence, structure, and function in complex biological networks are studied using quantitative modeling. Whole genome analysis is performed. Completion of a series of projects emphasizing real-life data, integrated approaches, practical applications, hands-on analysis, and collaboration. Course projects aim at improving current approaches and involve C and/or PERL programming to interface with existing software packages. The course will be offered in a computer laboratory equipped with one laptop per student.
• ENG BE 780: Brain Machine Interfaces
  Brain Machine Interfaces introduces major approaches and central challenges in BMI applications. An initial overview will cover low-level details of interfacing with neural tissue, including electrode and optical designs, types of neural signals, and issues of biocompatibility and signal degradation. The core of the course will consider applications, with topics focused on (1) signal decoding approaches in motor control applications, signal to noise requirements, and effects of training and plasticity, and (2) neural stimulation, including choice of peripheral vs. central targets, consequences of topographic organization, types of perceptual responses, and limits to control of distributed systems. Special emphasis will be placed on comparing and critiquing the expanding range of applicable technologies, from in-dwelling microelectrodes to cutting edge neurophotonic tools. To follow rapid changes in the field, course materials will be drawn primarily from research literature. In addition to readings, discussion and computational exercises, students will complete a final project. This is a 4 credit course.
• ENG BE 788: Soft Tissue Biomechanics
  This course will introduce students to the mechanics of soft biological tissue. In particular, the response of the heart, vasculature, and tissue scaffolds to mechanical loads from the perspective of nonlinear solid mechanics will be studied. Constitutive models for hyperelastic materials will be adapted to biomaterials to handle mechanical characteristics such as nonlinearity, viscoelasticity, and orthotropy. Basic experimental methods, and anatomy and physiology of particular tissue types will also be introduced. Emphasis is placed on integrating the basic analytical, experimental, and computational methods for a more complete understanding of the underlying mechanobiology. Meets with ENG ME788. Students may not receive credit for both.
• ENG BE 790: Biomedical Engineering Seminar
  Discussion of current topics in biomedical engineering. Students are expected to read assigned journal articles and to participate actively in weekly discussion meetings. Meetings organized around presentations by invited guests of their research problems, strategy, and technique.
• ENG BE 791: PhD Biomedical Engineering Laboratory Rotation System
  This course allows PhD students to take part in a laboratory rotation system. During these rotations, students become familiar with research activity within departmental laboratories that are of interest to them. These rotations help students identify the laboratory in which they will perform their dissertation research. PhD students must complete three rotations: one in their first semester of matriculation, and two in their second semester. Normally each rotation will last up to seven weeks.
• ENG BE 792: Critical Literature Review
  Peer-reviewed publications in the area of biomedical engineering will be critically evaluated. Scientific ethics and the process of review and publication of manuscripts will be discussed. The classes will be a mix of didactic information and group discussion. Methodological issues covered will include study design, techniques used, and interpretation of research findings. Students completing this course will understand the principles underlying preparation and publication of scientific manuscripts and will be able to apply these principles as they read the scientific literature.
• ENG BE 795: Biomedical Innovation Strategies
  This lecture and discussion course will introduce BME graduate students to advanced analylical and strategic planning tools and techniques used by biomedical, biotech, and healthcare companies to anticipate, evaluate, and incorporate breakthrough medical innovations. Senior executives and strategic planners, along with investors, advisors, and clinical innovators will share insights through guest lectures, cases, interviews, and discussions with BME PhD and Masters students interested in biomedical research and product development in the private sector.
• ENG BE 801: Teaching Practicum
  This course cannot be used to meet the structured course requirements. Practical teaching experience for an assigned course, includes some combination of running discussion sections, managing laboratory sections, providing some lectures, preparing homework and solution sets, exams, and grading. Attend lectures/seminars on best teaching practices.
• ENG BE 802: Teaching Practicum II
  Practical teaching experience.
• ENG BE 810: PhD Internship in Biomedical Engineering
  This course provides BME PhD students the opportunity to include a full-time (30-40 hours/week, for at least 12 weeks) paid internship experience as part of their professional training. The internship must be related to the student's area of study. International students require CPT authorization. Written summary required. Graded P/F. Prerequisite: Permission of advisor and an approved, full-time internship offer; at least two complete semesters in the BME PhD program.

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