Biomedical Engineering

APBM E4650 ANATOMY FOR PHYSICISTS ＆ ENGR. 3.00 points.

Lect: 3.

Prerequisites: Engineering or physics background.
Systemic approach to the study of the human body from a medical imaging point of view: skeletal, respiratory, cardiovascular, digestive, and urinary systems, breast and womens issues, head and neck, and central nervous system. Lectures are reinforced by examples from clinical two- and three-dimensional and functional imaging (CT, MRI, PET, SPECT, U/S, etc.)

BINF GU4001 INTRO COMP BIOMED ＆ HEALTH. 3.00 points.

This course offers a comprehensive introduction to the core computational methods driving modern biomedical research and health data science. As biological and clinical datasets grow in scale and complexity—from genomic sequences and molecular profiles to electronic health records (EHRs) and consumer health data—this course equips students with the essential computational foundations to model, analyze, and interpret high-dimensional biomedical data. Organized around key algorithmic challenges spanning Clinical Informatics, Consumer Health Informatics, and Bioinformatics, the course focuses on the design and application of algorithms and statistical models to solve real-world biomedical problems. Lectures emphasize practical techniques and showcase their use across diverse biomedical data types. Designed for advanced undergraduates and graduate students in biomedical informatics, computer science, biomedical engineering, applied mathematics, and related fields, this course builds a rigorous understanding of computational biomedicine. It serves as a core requirement for the Biomedical Informatics PhD and master’s programs and is cross-listed with Computer Science. Students interested in careers in bioinformatics, health data science, computational biology, or biomedical AI will find this course especially valuable. As biomedical data continue to expand in size, diversity, and impact, this course provides a critical foundation in the algorithmic, statistical, and computational tools needed to advance the future of research at the intersection of computation and human health

BMCS E4480 Statistical machine learning for genomics. 3.00 points.

Prerequisites: Proficiency in Python/R programming, and background in probability/statistics. Recommended: COMS W4771.
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 high-dimensional 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

BMCS E4575 High-dimensional statistics for biomedical data. 3.00 points.

Prerequisites: (APMA E2000 and COMS W4771 and MATH UN2010) or (APMA E2101) Strong background in Python (or R) programming- Background in probability/statistics is recommended.

Statistical machine learning techniques and advanced mathematical concepts for analysis of high-dimensional biomedical data. Topics include optimal transport and probabilistic modeling for multi-modal genomic and imaging data integration and analysis of spatial and temporal dynamics. Programming assignments, problem sets, and a final project will be required.

BMEB W4020 Computational neuroscience: circuits in the brain. 3 points.

Lect: 3.

Prerequisites: (ELEN E3801) or (BIOL UN3004) ELEN E3801 OR BIOL W3004

The biophysics of computation: modeling biological neurons, the Hodgkin-Huxley neuron, modeling channel conductances and synapses as memristive systems, bursting neurons and central pattern generators, I/O equivalence and spiking neuron models.  Information representation and neural encoding: stimulus representation with time encoding machines, the geometry of time encoding, encoding with neural circuits with feedback, population time encoding machines.  Dendritic computation: elements of spike processing and neural computation, synaptic plasticity and learning algorithms, unsupervised learning and spike time-dependent plasticity, basic dendritic integration.  Projects in MATLAB.

BMEE E4030 NEURAL CONTROL ENGINEERING. 3.00 points.

Lect: 3.

Prerequisites: (ELEN E3801) ELEN E3801
Topics include basic cell biophysics, active conductance and the Hodgkin-Huxley model, simple neuron models, ion channel models and synaptic models, statistical models of spike generation, Wilson-Cowan model of cortex, large-scale electrohysiological recording methods, sensorimotor integration and optimal state estimation, operant conditioning of neural activity, nonlinear modelling of neural systems, sensory systems: visual pathway and somatosensory pathway, neural encoding model; spike triggered average (STA) and spike triggered covariance (STC) analysis, neuronal response to electrical micro-stimulation, DBS for Parkinson's disease treatment, motor neural prostheses, and sensory neural prostheses

BMEE E4740 BIOINSTRUMENTATION. 3.00 points.

Lect: 1. Lab: 3.

Prerequisites: (ELEN E1201) and (COMS W1005) COMS W1005 AND ELEN E1201
Hands-on experience designing, building, and testing the various components of a benchtop cardiac pacemaker. Design instrumentation to measure biomedical signals as well as to actuate living tissues. Transducers, signal conditioning electronics, data acquisition boards, the Arduino microprocessor, and data acquisition and processing using MATLAB will be covered. Various devices will be discussed throughout the course, with laboratory work focusing on building an emulated version of a cardiac pacemaker

BMEN E3010 BIOMEDICAL ENGINEERING I. 3.00 points.

Lect: 3.

Prerequisites: (BIOL UN2005) and (BIOL UN2006) or BIOL C2005 AND BIOL C2006; BMEN E3810 AND BMEN E4001 OR BMEN E4001; or instructor's permission.
Corequisites: BMEN E3810,BMEN E4001
Various concepts within the field of biomedical engineering, foundational knowledge of engineering methodology applied to biological and/or medical problems through modules in biomechanics, biomaterials, and cell ＆ tissue engineering

BMEN E3020 BIOMEDICAL ENGINEERING II. 3.00 points.

Lect: 3.

Prerequisites: (BIOL UN2005) and (BIOL UN2006) or BIOL C2005 AND BIOL C2006; BMEN E3820 AND BMEN E4002 OR BMEN E4002; or instructor's permission.
Corequisites: BMEN E3820,BMEN E4002
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

BMEN E3810 BIOMEDICAL ENGINEERING LAB I. 3.00 points.

Lab: 4.

Fundamental considerations of wave mechanics; design philosophies; reliability and risk concepts; basics of fluid mechanics; design of structures subjected to blast; elements of seismic design; elements of fire design; flood considerations; advanced analysis in support of structural design

BMEN E3820 BIOMEDICAL ENGINEERING LAB II. 3.00 points.

Lab: 4.

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

BMEN E3899 Research Training. 0.00 points.

Prerequisites: Instructor's permission.
Research training course. Recommended in preparation for laboratory related research

BMEN E3910 BIOMEDICAL ENGINEERING DESIGN. 4.00 points.

Lect: 1. Lab: 3.

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

BMEN E3920 BIOMEDICAL ENGIN DESIGN II. 4.00 points.

Lect: 1. Lab: 3.

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

BMEN E3998 PROJECTS IN BIOMEDICAL ENGIN. 1.00-3.00 points.

Hours to be arranged.

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

BMEN E3999 UNDERGRADUATE FIELDWORK. 1.00-2.00 points.

Prerequisites: Obtained internship and approval from faculty adviser. BMEN undergraduate students only.
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

BMEN E4000 SPECIAL TOPICS IN BIOMEDICAL ENGINEERING. 3.00 points.

Lect: 3.

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

BMEN E4001 QUANTITATIVE PHYSIOLOGY I. 3.00 points.

Lect: 3.

Prerequisites: (BIOL UN2005) and (BIOL UN2006) BIOL C2005 AND BIOL C2006; BMEN E3010 AND BMEN E3810 OR BMEN E3010 OR BMEN E4490 OR BMEN E6505
Corequisites: BMEN E3010,BMEN E3810
Physiological systems at the cellular and molecular level are examined in a highly quantitative context. Topics include chemical kinetics, molecular binding and enzymatic processes, molecular motors, biological membranes, and muscles

BMEN E4002 QUANT PHYSIOLOGY II:ORGAN SYST. 3.00 points.

Lect: 3.

Prerequisites: (BIOL UN2005) and (BIOL UN2006) BIOL C2005 AND BIOL C2006; BMEN E3020 AND BMEN E3820 OR BMEN E3020 OR BMEN E4490 OR BMEN E6505
Corequisites: BMEN E3020,BMEN E3820
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)

BMEN E4050 ELECTROPHYS OF HUM MEMORY * NAVIGATION. 3.00 points.

Lect: 3.

Prerequisites: Instructor's permission.

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.

BMEN E4110 BIOSTATISTICS FOR ENGINEERS. 4.00 points.

Lect: 3.

Prerequisites: (APMA E2000 and APMA E2101 and MATH UN1202

Fundamental concepts of probability and statistics applied to biology and medicine. Probability distributions, hypothesis testing and inference, summarizing data and testing for trends. Signal detection theory and the receiver operator characteristic. Lectures accompanied by data analysis assignments using MATLAB as well as discussion of case studies in biomedicine.

BMEN E4210 DRIVING FORCES OF BIOLOGICAL SYSTEMS. 4.00 points.

Lect: 4.

Prerequisites: (CHEM UN1404) and (MATH UN1202) BIOL C2005; or equivalent.
Corequisites: BIOL UN2005
Introduction to the statistical mechanics and thermodynamics of biological systems, with a focus on connecting microscopic molecular properties to macroscopic states. Both classical and statistical thermodynamics will be applied to biological systems; phase equilibria, chemical reactions, and colligative properties. Topics in modern biology, macromolecular behavior in solutions and interfaces, protein-ligand binding, and the hydrophobic effect

BMEN E4302 BIOMECHANICS OF MUSCULOSKELETAL SOFT TIS. 3.00 points.

Lect.: 3.

Prerequisites: (ENME E3113) or ENME E3113; or equivalent. Restricted to seniors and graduate students.
Biomechanics of orthopaedic soft tissues (cartilage, tendon, ligament, meniscus, etc.). Basic and advanced viscoelasticity applied to the muscoskeletal system. Topics include mechanical properties, applied viscoelasticity theory, and biology of orthopaedic soft tissues

BMEN E4310 SOLID BIOMECHANICS. 3.00 points.

Lect.: 3.

Prerequisites: (ENME E3105) and (ENME E3113) and ENME E3105 AND ENME E3113
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

BMEN E4330 Cellular Bioengineering ＆ Therapeutics. 3.00 points.

Prerequisites: General understanding of chemistry and biology.

Explores cutting-edge field of cellular bioengineering and applications of cell therapies. Comprehensive understanding of the principles, techniques, and ethical considerations involved in cells for medical applications studied.

BMEN E4350 Biomechanics of Developmental Biology. 3.00 points.

Prerequisites: Undergraduate-level course in mechanics e.g., MECE E3113, BMEN E4310 and cell biology e.g., BIOL UN2005/6 or by instructor's permission.
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

BMEN E4410 PRIN OF ULTRASOUND IN MEDICINE. 3.00 points.

Lect: 3.

Prerequisites: (MATH UN1202) and APMA E2000 or equivalent.

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.

BMEN E4420 SIGNAL MODELING. 3.00 points.

Lect: 3.

Prerequisites: or instructor's permission.

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.

BMEN E4430 PRIN OF MAG RESONANCE IMAGING. 3.00 points.

Lect: 3.

Prerequisites: (PHYS UN1403) and (APMA E2101) or APMA E2101 AND PHYS C1403; or instructor's permission.
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

BMEN E4460 Deep Learning in Biomedical Imaging. 3.00 points.

Prerequisites: APMA E2000 and APMA E2101 and MATH UN1202 Recommended: background in Python programming.

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.

BMEN E4470 Deep Learning for Biomedical Signal Processing. 3.00 points.

Prerequisites: Recommended: background in Python programming.
Introduction to methods in deep learning, focus on applications to biomedical signals and sequences. Review of traditional methods for analysis of signals and sequences. Temporal convolutional neural networks and recurrent neural networks. Long-short term memory (LSTM) models and deep state-space models. Theory and methods lectures accompanied with examples from biomedical signal and sequence analysis, including analysis of electroencephalogram (EEG), electrocardiogram (ECG/EKG), and genomics. Programming assignments use tensorflow/keras. Exams and final project required

BMEN E4480 Statistical machine learning for genomics. 3.00 points.

Prerequisites: APMA E2101 and MATH UN1202 and MATH UN2010 Proficiency in Python/R programming, and background in probability/statistics. Recommended: COMS W4771.

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.

BMEN E4490 Magnetic Resonance Spectroscopy: A Window to the Living Brain. 3.00 points.

Prerequisites: BMEN E4001 OR BMEN E4002
Introduction to use of magnetic resonance spectroscopy (MRS) with focus on brain. Covers all aspects of in vivo MRS from theory to experiment, from data acquisition to the derivation of metabolic signatures, from study design to clinical interpretation. Includes theoretical concepts, hands-on training in MRS data literacy and direct experimental experience using a 3T MR scanner

BMEN E4500 Functional Genomics: Methods and Applications. 3.00 points.

Prerequisites: BIOL C2005 AND BIOL C2006
Introduces approaches for the functional genomic analysis of biological systems and their use to define genotype-phenotype relationships. Genetic variation, gene expression and regulation at the epigenome, chromatin organization level, and link between gene and protein expression covered. Case studies covered: study of cancer and cancer-associated processes, neuro-biology, and organismal development. The presented methods study these events at the genome, epigenome, transcriptome, and proteome levels.Approaches that increase the resolution of functional genomic assays to the level of individual cells, spatial profiling, integration with genetic and chemical screening methods, and their application to chemical genomic approaches also studied. Programming assignments and a final project required

BMEN E4501 Biomaterials and Scaffold Design. 3.00 points.

Lect: 3.

An introduction to the strategies and fundamental bioengineering design criteria in the development of biomaterials and tissue ngineered grafts. Materials structuralfunctional relationships, biocompatibility in terms of material and host responses. Through discussions, readings, and a group design project, students acquire an understanding of cell-material interactions and identify the arameters critical in the design and selection of biomaterials for biomedical applications.

BMEN E4510 TISSUE ENGINEERING. 3.00 points.

Lect: 3

Prerequisites: (BIOL UN2005) and (BIOL UN2006) and (BMEN E4001) and (BMEN E4002) BIOL C2005 AND BIOL C2006 AND BMEN E4001 AND BMEN E4002
An introduction to the strategies and fundamental bioengineering design criteria behind the development of cell-based tissue substitutes. Topics include biocompatibility, biological grafts, gene therapy-transfer, and bioreactors

BMEN E4520 SYNTHETIC BIOLOGY:PRIN GENETIC CIRCUITS. 3.00 points.

Basic principles of synthetic biology and survey of the field. Fundamentals of biological circuits, including circuit design, modern techniques for DNA assembly, quantitative characterization of genetic circuits, and ODE modeling of biological circuits with MATLAB. Knowledge of biology, ordinary differential equations, and MATLAB will be assumed. Intended for advanced undergraduate and graduate students.

BMEN E4525 Advanced Cell and Tissue Engineering: From Concepts to Translation. 3.00 points.

Prerequisites: Biology and Physiology

Covers advancements in the fields of cellular and developmental biology, molecular biology and materials science towards the development of “tissue engineered” therapies. Emphasis on tissue engineering therapies applied to musculoskeletal tissues, such as bone, cartilage, and skeletal muscle, and nervous tissues (central and peripheral nervous system). Design considerations and concepts in market analysis examined.

BMEN E4530 DRUG AND GENE DELIVERY. 3.00 points.

Prerequisites: BMEN E3010
Application of polymers and other materials in drug and gene delivery, with focus on recent advances in field. Basic polymer science, pharmacokinetics, and biomaterials, cell-substrate interactions, drug delivery system fabrication from nanoparticles to microparticles and electrospun fibrous membranes. Applications include cancer therapy, immunotherapy, gene therapy, tissue engineering, and regenerative medicine. Course readings include textbook chapters and journal papers. Homework assignments take format of assay responding to open-ended question. Term paper and 30-minute PowerPoint presentation required at end of semester

BMEN E4535 Immunoengineering with Biomaterials and Nanotechnology. 3.00 points.

Introduction to fundamental aspects of immunology and engineering strategies to modulate the immune system to improve human health. We will cover the innate and adaptive immune system and current methods to characterize the immune response. Applications focus on cancer, vaccines, and autoimmune disorders

BMEN E4545 Multimodal Neuroimaging. 0.00-3.00 points.

Prerequisites: MATLAB and/or Python
Practical implementation of neuroimaging techniques, data types, processing methods and clinical findings on independent datasets across a variety of neurological and psychiatric conditions. Basics from anatomy to digital image analysis will be explored culminating in a final project

BMEN E4550 MICRO/NANO STRUCT CELL ENG. 3.00 points.

Lect: 3.

Prerequisites: (BIOL UN2005) and (BIOL UN2006) or BIOL C2005 AND BIOL C2006; or equivalent.

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.

BMEN E4580 FOUND OF NANOBIOSCI/NANOBIOTECH. 3.00 points.

Lect: 3.

Prerequisites: (BIOL UN2005) and (BIOL UN2006) and (BMEN E4001) and (BMEN E4002) or instructor's permission.

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.

BMEN E4590 BIOMEMS:CELL/MOLECULAR APPLIC. 3.00 points.

Lect: 3.

Prerequisites: or equivalent. Chemistry.

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.

BMEN E4750 SOUND AND HEARING. 3.00 points.

Lect: 3.

Prerequisites: (PHYS UN1401) and (MATH UN1201)

Introductory acoustics, basics of waves and discrete mechanical systems. The mechanics of hearing - how sound is transmitted through the external and middle ear to the inner ear, and the mechanical processing of sound within the inner ear.

BMEN E4899 Research Training. 0.00 points.

Prerequisites: Instructor's permission.
Research training course. Recommended in preparation for laboratory related research

BMEN E4999 FIELDWORK. 1.00-2.00 points.

Prerequisites: Obtained internship and approval from faculty advisor. BMEN graduate students only.
Only for BMEN graduate students who need relevant work experience as part of their program of study. Final reports required. May not be taken for pass/fail credit or audited

BMEN E6000 Graduate Special Topic. 3 points.

Lect: 3.

Prerequisites: Instructors may impose prerequisites depending on the topic.

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

BMEN E6001 TOPICS IN BIOMED NANOTECHNOLOGY. 3.00 points.

Prerequisites: Targeted toward graduate students; undergraduate student may participate with instructor's permission.
Review and critical discussion of recent literature in nanobiotechnology and synthetic biology. Experimental and theoretical techniques, critical advances. Quality judgments of scientific impact and technical accuracy. Styles of written and graphical communication, the peer review process

BMEN E6003 COMP MODELING-PHYSIOL SYSTEMS. 3.00 points.

Lect: 3.

Prerequisites: (APMA E4200) and (BMEN E4001) and (BMEN E4002) or equivalent.

Advanced computational modeling and quantitative analysis of selected physiological systems from molecules to organs. Selected systems are analyzed in depth with an emphasis on modeling methods and quantitative analysis. Topics may include cell signaling, molecular transport, excitable membranes, respiratory physiology, nerve transmission, circulatory control, auditory signal processing, muscle physiology, data collection and analysis.

BMEN E6005 Biomedical Innovation I. 3 points.

Lect: 3.

Prerequisites: Master's students only.

Project-based design experience for graduate students. Elements of design process, including need identification, concept generation, concept selection, and implementation. Development of design prototype and introduction to entrepreneurship and implementation strategies. Real-world training in biomedical design and innovation.

BMEN E6006 BIOMEDICAL DESIGN II. 3.00 points.

Lect. 3.

Second semester of project-based design experience for graduate students. Elements of design process, with focus on skills development, prototype development and testing, and business planning. Real-world training in biomedical design, innovation, and entrepreneurship

BMEN E6007 LAB-TO-MARKET. 3.00 points.

Introduction to and application of commercialization of biomedical innovations. Topics include needs clarification, stakeholder analysis, market analysis, value proposition, business models, intellectual property, regulatory, and reimbursement. Development of path-to-market strategy and pitch techniques

BMEN E6505 Advanced Biomaterials for Tissue Engineering. 3.00 points.

Prerequisites: (BMEN E4501) or equivalent.
Corequisites: BMEN E4002,BMEN E4001

Advanced biomaterial selection and biomimetic scaffold design for tissue engineering and regenerative medicine. Formulation of bio-inspired design criteria, scaffold characterization and testing, and applications on forming complex tissues or organogenesis. Laboratory component includes basic scaffold fabrication, characterization and in vitro evaluation of biocompatibility. Group projects target the design of scaffolds for select tissue engineering applications.

BMEN E6510 STEM CELL, GENOME ENG ＆ REGEN MED. 3.00 points.

Lect: 3.

Prerequisites: (BMEN E4001) or (BMEN E4002) and Biology, Cell Biology.

General lectures on stem cell biology followed by student presentations and discussion of the primary literature. Themes presented include: basic stem cell concepts; basic cell and molecular biological characterization of endogenous stem cell populations; concepts related to reprogramming; directed differentiation of stem cell populations; use of stem cells in disease modeling or tissue replacement/repair; clinical translation of stem cell research.

BMEN E6520 Instructive Biomaterials. 3.00 points.

Covers biomaterials that are instructive or have been designed or engineered to be instructive; structure-function-property relationships in natural and synthetic biomaterials. Advances in understanding of material properties emphasized; including electroactivity, chemical, mechanical, geometry/architecture, and the modification of material surfaces and context of their effect on biological function. Evolving field of smart biomaterials discussed. Exercises/demonstrations using materials characterization equipment conducted.

BMEN E9100 MASTERS RESEARCH. 1.00-6.00 points.

Candidates for the M.S. degree may conduct an investigation of some problem in biomedical engineering. No more than 6 points in this course may be counted for graduate credit

BMEN E9200 Master's Thesis in BME. 0.00 points.

This is a Pass/Fail zero credit course, “BME Master's Thesis” for MS students who are in the process of doing a thesis (BMEN E9100). It would be registered for before/during the final semester, the semester when the student will be defending the thesis. It must be approved by the faculty mentor

BMEN E9500 DOCTORAL RESEARCH. 1.00-6.00 points.

Doctoral candidates are required to make an original investigation of a problem in biomedical engineering, the results of which are presented in the dissertation

BMEN E9700 BIOMEDICAL ENGINEERING SEMINAR. 0.00 points.

0 pts. Sem: 1.

All matriculated graduate students are required to attend the seminar as long as they are in residence. No degree credit is granted. The seminar is the principal medium of communication among those with biomedical engineering interests within the University. Guest speakers from other institutions, Columbia faculty, and students within the Department who are advanced in their studies frequently offer sessions

BMEN E9800 DOCTORAL RESEARCH INSTRUCTION. 3.00-12.00 points.

A candidate for the Eng.Sc.D. degree in biomedical engineering must register for 12 points of doctoral research instruction. Registration may not be used to satisfy the minimum residence requirement for the degree

BMEN E9900 DOCTORAL DISSERTATION. 0.00 points.

0 pts.

A candidate for the doctorate in biomedical engineering or applied biology may be required to register for this course in every term after the students course work has been completed and until the dissertation has been accepted

CBMF W4761 COMPUTATIONAL GENOMICS. 3.00 points.

Lect: 3.

Prerequisites: Working knowledge of at least one programming language, and some background in probability and statistics.
Computational techniques for analyzing genomic data including DNA, RNA, protein and gene expression data. Basic concepts in molecular biology relevant to these analyses. Emphasis on techniques from artificial intelligence and machine learning. String-matching algorithms, dynamic programming, hidden Markov models, expectation-maximization, neural networks, clustering algorithms, support vector machines. Students with life sciences backgrounds who satisfy the prerequisites are encouraged to enroll

ECBM E4040 NEURAL NETWRKS ＆ DEEP LEARNING. 3.00 points.

Lect: 3.

Prerequisites: (BMEB W4020) or (BMEE E4030) or (ECBM E4090) or (EECS E4750) or (COMS W4771) or BMEB W4020 OR BMEE E4030 OR ECBM E4090 OR EECS E4750 OR COMS W4771; or equivalent.
Developing features - internal representations of the world, artificial neural networks, classifying handwritten digits with logistics regression, feedforward deep networks, back propagation in multilayer perceptrons, regularization of deep or distributed models, optimization for training deep models, convolutional neural networks, recurrent and recursive neural networks, deep learning in speech and object recognition

ECBM E4060 INTRO-GENOMIC INFO SCI ＆ TECH. 3.00 points.

Lect: 3.

Introduction to computational biology with emphasis on genomic data science tools and methodologies for analyzing data, such as genomic sequences, gene expression measurements and the presence of mutations. Applications of machine learning and exploratory data analysis for predicting drug response and disease progression. Latest technologies related to genomic information, such as single-cell sequencing and CRISPR, and the contributions of genomic data science to the drug development process

ECBM E4070 Computing with Brain Circuits of Model Organisms. 3.00 points.

Prerequisites: BIOL W3004 AND ELEN E3801; and Python programming experience, or instructor's permission.
Building the functional map of the fruit fly brain. Molecular transduction and spatio-temporal encoding in the early visual system. Predictive coding in the Drosophila retina. Canonical circuits in motion detection. Canonical navigation circuits in the central complex. Molecular transduction and combinatorial encoding in the early olfactory system. Predictive coding in the antennal lobe. The functional role of the mushroom body and the lateral horn. Canonical circuits for associative learning and innate memory. Projects in Python

ECBM E4090 BRAIN COMPUTER INTERFACES LAB. 3.00 points.

Lect: 2. Lab: 3.

Prerequisites: (ELEN E3801) ELEN E3801
Hands-on experience with basic neural interface technologies. Recording EEG (electroencephalogram) signals using data acquisition systems (non-invasive, scalp recordings). Real-time analysis and monitoring of brain responses. Analysis of intention and perception of external visual and audio signals

ECBM E6070 TPC NEUROSCI ＆ DEEP LEARN. 3.00 points.

Lect: 2.

Prerequisites: Instructor's permission.

Selected advanced topics in neuroscience and deep learning. Content varies from year to year, and different topics rotate through the course numbers 6070 to 6079.

EEBM E6090 TPCS:COMPUT NEUROSCI/NEUROENGI. 3.00 points.

Lect: 2.

Prerequisites: Instructor's permission.
Selected advanced topics in computational neuroscience and neuroengineering. Content varies from year to year, and different topics rotate through the course numbers 6090-6099

EEBM E6091 TPCS IN COMP NEUROSCI/ENGINEERING. 3.00 points.

Lect: 2.

Prerequisites: Instructor's permission.
Selected advanced topics in computational neuroscience and neuroengineering. Content varies from year to year, and different topics rotate through the course numbers 6090-6099. Topic: Devices and Analysis for Neural Circuits

EEBM E6095 TOPICS IN COMP NEUROSI ＆ ENG. 3.00 points.

Prerequisites: Instructor's permission.
Selected advanced topics in computational neuroscience and neuroengineering. Content varies from year to year, and different topics rotate through the course numbers 6090 to 6099

EEBM E6099 TPCS:COMPUT NEUROSCI/NEUROENGI. 3.00 points.

Lect: 2.

Prerequisites: Instructor's permission.
Selected advanced topics in computational neurscience and neuroengineering. Content varies from year to year, and different topics rotate through the course numbers 6090-6099

MEBM E4439 MODELING ＆ ID OF DYNAMIC SYST. 3.00 points.

Prerequisites: (APMA E2101) and (ELEN E3801) or APMA E2101 AND ELEN E3801; EEME E3601; APMA E2101, ELEN E3801, or corequisite EEME E3601, or permission of instructor.
Corequisites: EEME E3601
Generalized dynamic system modeling and simulation. Fluid, thermal, mechanical, diffusive, electrical, and hybrid systems are considered. Nonlinear and high order systems. System identification problem and Linear Least Squares method. State-space and noise representation. Kalman filter. Parameter estimation via prediction-error and subspace approaches. Iterative and bootstrap methods. Fit criteria. Wide applicability: medical, energy, others. MATLAB and Simulink environments

MEBM E4710 MORPHOGENESIS:BIOL MAT SHP/STR. 3.00 points.

Prerequisites: Courses in mechanics, thermodynamics, and ordinary differential equations at the undergraduate level or instructor's permission.
Introduction to how shape and structure are generated in biological materials using engineering approach emphasizing application of fundamental physical concepts to a diverse set of problems. Mechanisms of pattern formation, self-assembly, and self-organization in biological materials, including intracellular structures, cells, tissues, and developing embryos. Structure, mechanical properties, and dynamic behavior of these materials. Discussion of experimental approaches and modeling. Course uses textbook materials as well as collection of research papers