BIOMEDICAL ENGINEERING II

Various concepts within the field of biomedical engineering, foundational knowledge of engineering methodology applied to biological and/or medical problems through modules in biomechanics, bioinstrumentation, and biomedical imaging.

• MW 10:10 a.m.-11:25 a.m.
• 3 points

BIOMEDICAL ENGINEERING LAB II

Biomedical experimental design and hypothesis testing. Statistical analysis of experimental measurements. Analysis of experimental measurements. Analysis of variance, post hoc testing. Fluid shear and cell adhesion, neuro-electrophysiology, soft tissue biomechanics, biomecial imaging and ultrasound, characterization of excitable tissues, microfluidics.

• W 1:10 p.m.-3:40 p.m.
• R 1:10 p.m.-3:40 p.m.
• 3 points

Research Training

Research training course. Recommended in preparation for laboratory related research.

• Instructor: Gerard A Ateshian
  Info
• Instructor: Tal Danino
  Wikipedia h-index: 18 Info
• Instructor: X. Edward Guo
  CULPA: 2 h-index: 70 Info
• Instructor: Henry Hess
  CULPA: 1 h-index: 45 Info
• Instructor: Clark T Hung
  CULPA: 5 h-index: 65 Info
• Instructor: Joshua Jacobs
  Wikipedia h-index: 31 Info
• Instructor: Christoph Juchem
  CULPA: 1 h-index: 23 Info
• Instructor: Lance Kam
  CULPA: 7 h-index: 38 Info
• Instructor: Elisa Konofagou
  Wikipedia h-index: 71 Info
• Instructor: Andrew Laine
  Wikipedia h-index: 43 Info
• Instructor: Kam W Leong
  h-index: 126 Info
• Instructor: Helen Lu
  CULPA: 1 h-index: 54 Info
• Instructor: Barclay Morrison
  CULPA: 9 h-index: 42 Info
• Instructor: Elizabeth Olson
  h-index: 28 Info
• Instructor: Paul Sajda
  CULPA: 3 h-index: 47 Info
• Instructor: Kenneth Shepard
  CULPA: 2 Wikipedia h-index: 64 Info
• Instructor: Shunichi Homma
  h-index: 88 Info
• Instructor: Samuel Sia
  CULPA: 1 h-index: 39 Info
• Instructor: Milan N Stojanovic
  Info
• Instructor: Stavros Thomopoulos
  h-index: 63 Info
• Instructor: John T Vaughan
  Info
• Instructor: Gordana Vunjak-Novakovic
  Wikipedia h-index: 132 Info
• Instructor: Qi Wang
  h-index: 24 Info
• Instructor: Nandan L Nerurkar
  Info
• Instructor: Stephen H Tsang
  Wikipedia h-index: 58 Info
• Instructor: Elham Azizi
  h-index: 10 Info
• Instructor: Jose McFaline-Figuero
  Info
• Instructor: Treena L Arinzeh
  Wikipedia Info
• Instructor: Sanja Vickovic
  Info
• Instructor: Santiago Correa
  Info
• Instructor: Kaveri A Thakoor
  Info
• 0 points

BIOMEDICAL ENGIN DESIGN II

A two-semester design sequence to be taken in the senior year. Elements of the design process, with specific applications to biomedical engineering: concept formulation, systems synthesis, design analysis, optimization, biocompatibility, impact on patient health and comfort, health care costs, regulatory issues, and medical ethics. Selection and execution of a project involving the design of an actual engineering device or system. Introduction to entrepreneurship, biomedical start-ups, and venture capital. Semester I: statistical analysis of detection/classification systems (receiver operation characteristic analysis, logistic regression), development of design prototype, need, approach, benefits and competition analysis. Semester II: spiral develop process and testing, iteration and refinement of the initial design/prototype and business plan development. A lab fee of $100 each is collected.

• TR 10:10 a.m.-11:25 a.m.
• Instructor: Lauren N Heckelman
  Info
• 4 points

PROJECTS IN BIOMEDICAL ENGIN

Independent projects involving experimental, theoretical, computational, or engineering design work. May be repeated, but no more than 3 points of this or any other projects or research course may be counted toward the technical elective degree requirements as engineering technical electives.

• Instructor: Tal Danino
  Wikipedia h-index: 18 Info
• Instructor: X. Edward Guo
  CULPA: 2 h-index: 70 Info
• Instructor: Henry Hess
  CULPA: 1 h-index: 45 Info
• Instructor: Elizabeth Hillman
  Wikipedia h-index: 48 Info
• Instructor: Shunichi Homma
  h-index: 88 Info
• Instructor: Clark T Hung
  CULPA: 5 h-index: 65 Info
• Instructor: Joshua Jacobs
  Wikipedia h-index: 31 Info
• Instructor: Christoph Juchem
  CULPA: 1 h-index: 23 Info
• Instructor: Lance Kam
  CULPA: 7 h-index: 38 Info
• Instructor: Elisa Konofagou
  Wikipedia h-index: 71 Info
• Instructor: Andrew Laine
  Wikipedia h-index: 43 Info
• Instructor: Kam W Leong
  h-index: 126 Info
• Instructor: Helen Lu
  CULPA: 1 h-index: 54 Info
• Instructor: Barclay Morrison
  CULPA: 9 h-index: 42 Info
• Instructor: Elizabeth Olson
  h-index: 28 Info
• Instructor: Paul Sajda
  CULPA: 3 h-index: 47 Info
• Instructor: Kenneth Shepard
  CULPA: 2 Wikipedia h-index: 64 Info
• Instructor: Samuel Sia
  CULPA: 1 h-index: 39 Info
• Instructor: Milan N Stojanovic
  Info
• Instructor: Stavros Thomopoulos
  h-index: 63 Info
• Instructor: John T Vaughan
  Info
• Instructor: Gordana Vunjak-Novakovic
  Wikipedia h-index: 132 Info
• Instructor: Qi Wang
  h-index: 24 Info
• Instructor: Nandan L Nerurkar
  Info
• Instructor: Stephen H Tsang
  Wikipedia h-index: 58 Info
• Instructor: Elham Azizi
  h-index: 10 Info
• Instructor: Jose McFaline-Figuero
  Info
• Instructor: Treena L Arinzeh
  Wikipedia Info
• Instructor: Sanja Vickovic
  Info
• Instructor: Santiago Correa
  Info
• 1-3 points

UNDERGRADUATE FIELDWORK

May be repeated for credit, but no more than 3 total points may be used toward the 128-credit degree requirement. Only for BMEN undergraduate students who include relevant off-campus work experience as part of their approved program of study. Final report and letter of evaluation required. Fieldwork credits may not count toward any major core, technical, elective, and non-technical requirements. May not be taken for pass/fail credit or audited.

• Instructor: Lance Kam
  CULPA: 7 h-index: 38 Info
• 1-2 points

SPECIAL TOPICS IN BIOMEDICAL ENGINEERING

Orthopaedic Biomat&TisEng

Current topics in biomedical engineering. Subject matter will vary by year. Instructors may impose prerequisites depending on the topic.

• W 2:30 p.m.-5 p.m.
• Instructor: Treena L Arinzeh
  Wikipedia Info
• 3 points

SPECIAL TOPICS IN BIOMEDICAL ENGINEERING

ImmunoEng Biomat&Nanotech

Current topics in biomedical engineering. Subject matter will vary by year. Instructors may impose prerequisites depending on the topic.

• MT 10 a.m.-11:15 a.m.
• Instructor: Santiago Correa
  Info
• 3 points

QUANT PHYSIOLOGY II:ORGAN SYST

Students are introduced to a quantitative, engineering approach to cellular biology and mammalian physiology. Beginning with biological issues related to the cell, the course progresses to considerations of the major physiological systems of the human body (nervous, circulatory, respiratory, renal).

• MW 8:40 a.m.-9:55 a.m.
• Instructor: Barclay Morrison
  CULPA: 9 h-index: 42 Info
• 3 points

ELECTROPHYS OF HUM MEMORY * NAVIGATION

ELECTROPHYS OF HUM MEM&NV

Human memory, including working, episodic, and procedural memory. Electrophysiology of cognition, noninvasive and invasive recordings. Neural basis of spatial navigation, with links to spatial and episodic memory. Computational models of memory, brain stimulation, lesion studies.

• M 1:10 p.m.-3:40 p.m.
• Instructor: Joshua Jacobs
  Wikipedia h-index: 31 Info
• 3 points

SOLID BIOMECHANICS

Applications of continuum mechanics to the understanding of various biological tissues properties. The structure, function, and mechanical properties of various tissues in biolgical systems, such as blood vessels, muscle, skin, brain tissue, bone, tendon, cartilage, ligaments, etc. are examined. The establishment of basic governing mechanical principles and constitutive relations for each tissue. Experimental determination of various tissue properties. Medical and clinical implications of tissue mechanical behavior.

• T 1:10 p.m.-3:40 p.m.
• Instructor: X. Edward Guo
  CULPA: 2 h-index: 70 Info
• 3 points

Biomechanics of Developmental Biology

BIOMECHANICS DEVELOPMENTA

Biophysical mechanisms of tissue organization

during embryonic development: conservation laws, reaction-diffusion, finite elasticity, and fluid mechanics are reviewed and applied to a broad range of topics in developmental biology, from early development to later organogenesis of the central nervous, cardiovascular, musculoskeletal, respiratory, and gastrointestinal systems. Subdivided into modules on patterning (conversion of diffusible cues into cell fates) and morphogenesis (shaping of tissues), the course will include lectures, problem sets, reading of primary literature, and a final project.

• MW 1:10 p.m.-2:25 p.m.
• Instructor: Nandan L Nerurkar
  Info
• 3 points

PRIN OF ULTRASOUND IN MEDICINE

Fourier analysis. Physics of diagnostic ultrasound and principles of ultrasound imaging instrumentation. Propagation of plane waves in lossless medium; ultrasound propagation through biological tissues; single-element and array transducer design; pulse-echo and Doppler ultrasound instrumentation, performance evaluation of ultrasound imaging systems using tissue-mimicking phantoms, ultrasound tissue characterization; ultrasound nonlinearity and bubble activity; harmonic imaging; acoustic output of ultrasound systems; biological effects of ultrasound.

• W 2:30 p.m.-5 p.m.
• Instructor: Elisa Konofagou
  Wikipedia h-index: 71 Info
• 3 points

SIGNAL MODELING

Fundamental concepts of signal processing in linear systems and stochastic processes. Estimation, detection and filtering methods applied to biomedical signals. Harmonic analysis, auto-regressive model, Wiener and Matched filters, linear discriminants, and independent components. Methods are developed to answer concrete questions on specific data sets in modalities such as ECG, EEG, MEG, Ultrasound. Lectures accompanied by data analysis assignments using MATLAB.

• T 1:10 p.m.-3:40 p.m.
• Instructor: Paul Sajda
  CULPA: 3 h-index: 47 Info
• 3 points

PRIN OF MAG RESONANCE IMAGING

Fundamental principles of Magnetic Resonance Imaging (MRI), including the underlying spin physics and mathematics of image formation with an emphasis on the application of MRI to neuroimaging, both anatomical and functional. The examines both theory and experimental design techniques.

• R 4:10 p.m.-6:40 p.m.
• Instructor: Christoph Juchem
  CULPA: 1 h-index: 23 Info
• 3 points

Deep Learning in Biomedical Imaging

Deep Learning in BME / Im

Introduction to methods in deep learning, with focus on applications to quantitative problems in biomedical imaging and Artificial Intelligence (AI) in medicine. Network models: Deep feedforward networks, convolutional neural networks and recurrent neural networks. Deep autoencoders for denoising. Segmentation and classification of biological tissues and biomarkers of disease. Theory and methods lectures will be accompanied with examples from biomedical image including analysis of neurological images of the brain (MRI), CT images of the lung for cancer and COPD, cardiac ultrasound. Programming assignments will use tensorflow / Pytorch and Jupyter Notebook. Examinations and a final project will also be required.

• R 1:10 p.m.-3:40 p.m.
• Instructor: Andrew Laine
  Wikipedia h-index: 43 Info
• 3 points

Statistical machine learning for genomic

Statistical ML for genomi

Introduction to statistical machine learning methods using applications in genomic data and in particular high-dimensional single-cell data. Concepts of molecular biology relevant to genomic technologies, challenges of highdimensional genomic data analysis, bioinformatics preprocessing pipelines, dimensionality reduction, unsupervised learning, clustering, probabilistic modeling, hidden Markov models, Gibbs sampling, deep neural networks, gene regulation. Programming assignments and final project will be required.

• T 4:10 p.m.-6:40 p.m.
• Instructor: Elham Azizi
  h-index: 10 Info
• 3 points

MICRO/NANO STRUCT CELL ENG

Design, fabrication, and application of micro-/nanostructured systems for cell engineering. Recognition and response of cells to spatial aspects of their extracellular environment. Focus on neural, cardiac, coculture, and stem cell systems. Molecular complexes at the nanoscale.

• M 2:10 p.m.-4 p.m.
• Instructor: Lance Kam
  CULPA: 7 h-index: 38 Info
• 3 points

FOUND OF NANOBIOSCI/NANOBIOTECH

Fundamentals of nanobioscience and nanobiotechnology, scientific foundations, engineering principles, current and envisioned applications. Includes discussion of intermolecular forces and bonding, of kinetics and thermodynamics of self-assembly, of nanoscale transport processes arising from actions of biomolecular motors, computation and control in biomolecular systems, and of mitochondrium as an example of a nanoscale factory.

• TR 11:40 a.m.-12:55 p.m.
• Instructor: Henry Hess
  CULPA: 1 h-index: 45 Info
• 3 points

BIOMEMS:CELL/MOLECULAR APPLIC

Topics include biomicroelectromechanical, microfluidic, and lab-on-a-chip systems in biomedical engineering, with a focus on cellular and molecular applications. Microfabrication techniques, biocompatibility, miniaturization of analytical and diagnostic devices, high-throughput cellular studies, microfabrication for tissue engineering, and in vivo devices.

• T 4:10 p.m.-6:40 p.m.
• Instructor: Samuel Sia
  CULPA: 1 h-index: 39 Info
• 3 points

Research Training

Research training course. Recommended in preparation for laboratory related research.

• Instructor: Gerard A Ateshian
  Info
• Instructor: Tal Danino
  Wikipedia h-index: 18 Info
• Instructor: X. Edward Guo
  CULPA: 2 h-index: 70 Info
• Instructor: Henry Hess
  CULPA: 1 h-index: 45 Info
• Instructor: Elizabeth Hillman
  Wikipedia h-index: 48 Info
• Instructor: Clark T Hung
  CULPA: 5 h-index: 65 Info
• Instructor: Joshua Jacobs
  Wikipedia h-index: 31 Info
• Instructor: Christoph Juchem
  CULPA: 1 h-index: 23 Info
• Instructor: Lance Kam
  CULPA: 7 h-index: 38 Info
• Instructor: Elisa Konofagou
  Wikipedia h-index: 71 Info
• Instructor: Andrew Laine
  Wikipedia h-index: 43 Info
• Instructor: Kam W Leong
  h-index: 126 Info
• Instructor: Helen Lu
  CULPA: 1 h-index: 54 Info
• Instructor: Barclay Morrison
  CULPA: 9 h-index: 42 Info
• Instructor: Elizabeth Olson
  h-index: 28 Info
• Instructor: Paul Sajda
  CULPA: 3 h-index: 47 Info
• Instructor: Kenneth Shepard
  CULPA: 2 Wikipedia h-index: 64 Info
• Instructor: Shunichi Homma
  h-index: 88 Info
• Instructor: Samuel Sia
  CULPA: 1 h-index: 39 Info
• Instructor: Milan N Stojanovic
  Info
• 0 points