Courses

• ENG BE 570: Introduction to Computational Vision
  Undergraduate Prerequisites: Working knowledge of the material covered in ENG BE 401 or EC 401, ENG BE 200 and working knowledge of MATLAB.
  . Introductory course in biological visual neuroscience and computational vision. Provides a survey of the psychophysical, neuroanatomical and neurophysiological substrates of visual mechanisms underlying perception of visual motion, depth, objects, and space and of decision making mechanisms. Discussion of theoretical, explanatory, paradigms for these visual mechanisms. Topics addressed include psychophysics, methods from single cell recording physiology and low field potentials (LFP),multimodal imaging and computational modeling of various visual tasks and their modulation by attention. We will briefly address learning mechanisms and their relationship to brain plasticity. A term project is required for graduate credit. 4 cr.
• ENG BE 575: Introduction to Neuroengineering
  Undergraduate Prerequisites: BE209, BE401, BE491, BE492 or equivalent
  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 MS, MEng and PhD students as well as qualified undergraduate seniors.
• ENG BE 605: Molecular Bioengineering
  Undergraduate Prerequisites: Required for biomedical engineering graduate students.
  Provides engineering perspectives on the building blocks of living cells and materials for biotechnology. Focuses on origins and synthesis in life and the laboratory, including biological pathways for synthesis of DNA, RNA and proteins; transduction, transmission, storage and retrieval of biological information by macromolecules; polymerase chain reaction, restriction enzymes, DNA sequencing; energetics of protein folding and trafficking; mechanisms of enzymatic catalysts and receptor-ligand binding; cooperative proteins, multi-protein complexes and control of metabolic pathways; generation, storage, transmission and release of biomolecular energy; and methods for study and manipulation of molecules which will include isolation, purification, detection, chemical characterization, imaging and visualization of structure.
• ENG BE 606: Quantitative Physiology for Engineers
  Undergraduate Prerequisites: Required for biomedical engineering graduate students.
  Course in human physiology for biomedical engineering students. Fundamentals of cellular and systems physiology, including the nervous , muscular, cardiovascular, respiratory, renal, gastrointestinal, endocrine and immune systems. Quantitative and engineering approaches will be applied to understanding physiological concepts.
• ENG BE 700: Advanced Topics in Biomedical Engineering
  Undergraduate Prerequisites: Graduate standing or consent of instructor.
  Advanced study of a specific research topic in biomedical engineering. Intended primarily for advanced graduate students.
• ENG BE 703: Numerical Methods and Modeling in Biomedical Engineering
  Undergraduate Prerequisites: Graduate standing.
  This graduate course is an introduction to the computational tools most commonly applied in biological and physiological research, with emphasis on the art of using models, programming and simulation to reach useful conclusions and insights. Specific topics include exact and iterative methods for the solution of large systems, differentiation and interpolation numerical integration, pseudorandomization, Monte Carlo methods and statistical bootstrap methods, Fourier transform and spectral methods, and also finite difference methods for the solution of ordinary and partial differential equations. Each weekly lecture is accompanied by a computer lab in which the students will gain experience in the use of the techniques under study. Interspersed with learning of methods will be a variety of specific bioengineeering applications covering the range from genes and molecules to cells, organs, and systems.
• ENG BE 705: Single Molecule Approaches for Biophysics and Bioengineering - Fundamentals and Applications
  Undergraduate Prerequisites: ENG BE 505; Statistical Thermodynamics
  The emergence of single-molecule (SM) methods in biology and bioengineering in the past decade have revolutionized the way scientists approach the molecular biology of the cell. The ability to directly probe biomolecular process in real-time, in their native cellular environment, revealed the mechanism of fundamental processes in biology with unprecedented detail and accuracy. As SM methods are refined they are increasingly recruited by bioengineers to invent the future platforms for molecular diagnostics and analytical detection. This course covers experimental methods for investigating the molecular machinery of a living cell in vitro and in live cells, and novel tools for sensing biomolecules and their application in biotechnology. Fundamental principles underlying fluorescence of single molecules, force measurements of biomolecules, ion channel kinetics, and stochastic sensing, will be covered in the context of relevant biological and biotechnological examples. There will be an emphasis on fundamental physical concepts underlying these systems, coming from statistical mechanics of soft matter. 4 cr. 1st sem.
• ENG BE 707: Quantitative Studies of Excitable Cells
  Graduate Prerequisites: ENG BE 401; graduate standing or seniors with consent of instructor.
  Focuses on the properties of the membranes of nerve and muscle cells. Classical models of resting potentials, action potentials, synaptic transmission, and sensory receptors are treated. The structure and function of single ionic channels are characterized in detail from patch-clamp recordings, neuropharmacological studies, and molecular studies. Mechanisms of muscle contraction and other forms of cellular motility are also covered.
• ENG BE 710: Neural Plasticity and Perceptual Learning
  Undergraduate Prerequisites: ENG BE 200 (or an introductory course in probability and statistics);GRS BI 755 (or any other introductory course in neuroscience). Recommended: ENG BE 570
  This course explores the capacity of cortical sensory and motor maps in the adult brain to change as a result of alterations in the effectiveness of the input, direct damage, or practice. The lectures will describe and discuss (1) the physiology and anatomy underlying adult dynamics; (2) psychophysical methods and experimental paradigms that have been used to study cortical plasticity in the early stages of the sensory and motor pathways; (3) evidence for perceptual learning; and (4) biologically plausible computational models of learning. We will discuss applications of functional neuroimaging to study perceptual learning and restorative plasticity in the human brain.
• ENG BE 726: Fundamentals of Biomaterials
  Undergraduate Prerequisites: Graduate standing.
  Provides the chemistry and engineering skills needed to solve challenges in the biomaterials and tissue engineering area, concentrating on the fundamental principles in biomedical engineering, material science, and chemistry. Covers the structure and properties of hard materials (ceramics and metals) and soft materials (polymers and hydrogels). Same as ME/MS 726. Students may not receive credit for both.
• ENG BE 727: Principles and Applications of Tissue Engineering
  Undergraduate Prerequisites: Graduate standing; ENG BE 726.
  Provides the chemistry and engineering skills needed to solve challenges in the biomaterials and tissue engineering area, concentrating on cell-biomaterial interactions, soft tissue mechanics and specific research topics. Students will write a NIH-style grant proposal on a specific research topic. Same as ME/MS 727. Students may not receive credit for both.
• ENG BE 740: Parameter Estimation and Systems Identification
  Undergraduate Prerequisites: ENG EK 500; or consent of instructor.
  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
  Undergraduate Prerequisites: Graduate standing or consent of the course directors.
  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
  Undergraduate Prerequisites: ENG BE 200 and ENG BE 401(or equivalent); graduate standing in 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 760: Structural Bioinformatics
  Undergraduate Prerequisites: ENG BE 560 or ENG BE 561 (or equivalent).
  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 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
  Undergraduate Prerequisites: ENG BE 505 or consent of instructor.
  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 768: Biological Database Analysis
  Undergraduate Prerequisites: CAS CS 112 or CAS CS 113; graduate standing or consent of instructor. Background knowledge of biochemistry and genetics.
  Describes relational data models and database management systems. Teaches the theories and techniques of constructing relational databases with emphasis on those aspects needed for various biological data, including sequences, structures, genetic linkages and maps, and signal pathways. Introduces relational database query language SQL. Summarizes currently existing biological databases and the Web-based programming tools for their access. Object-oriented modeling is introduced primarily as a design aid for dealing with the particular complexities of biological information in standard RDB design. Emphasis will be on those problems associated with dealing with data whose nomenclature and interrelationships are undergoing rapid change.
• ENG BE 773: Advanced Optical Microscopy and Biological Imaging
  Undergraduate Prerequisites: ENG BE 401 or ENG EC 401; a background in optics or photonics (ENG EC560 or equivalent) is preferable or permission of instructor.
  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
  Undergraduate Prerequisites: ENG BE 561; or consent of instructor.
  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.