Bioengineering (BIOE)

BIOE Class Schedule

Courses

BIOE 100   Bioengineering Freshman Seminar   credit: 0 Hours.

Seminar surveying a broad range of Bioengineering topics. Approved for S/U grading only. Prerequisite: Bioengineering Freshmen Only.

BIOE 120   Introduction to Bioengineering   credit: 1 Hour.

Lectures and discussions of recent trends in bioengineering; topics typically include biological interaction with ultrasound and microwave radiation, modeling, instrumentation, biomaterials, biomechanics, biological heat and mass transfer, and medical imaging techniques.

BIOE 198   Special Topics   credit: 1 to 3 Hours.

Subject offerings related to Bioengineering intended to augment the Bioengineering curriculum. Offerings will be at the freshman level. See class schedule or course information websites for topics and prerequisites. May be repeated if topics vary. Prerequisite: Majors only.

BIOE 201   Conservation Principles Bioeng   credit: 3 Hours.

Material, energy, charge, and momentum balances in biological problems. Steady-state and transient conservation equations for mass, energy, charge, and momentum will be derived and applied to mathematically analyze physiological systems using basic mathematical principles, physical laws, stoichiometry, and thermodynamic properties. Prerequisite: CHEM 104, MCB 150, and PHYS 211.

BIOE 202   Cell & Tissue Engineering Lab   credit: 2 Hours.

Principles of cell biology inherent in tissue engineering design. Lab experience in safely and skillfully manipulating cells of the four tissue types and performing various quantitative analyses on products produced by cells that have differentiated. Prerequisite: MCB 150, and credit or concurrent enrollment in BIOE 206.

BIOE 205   Signals & Systems in Bioengrg   credit: 3 Hours.

Introduction to signals and linear systems with examples from biology and medicine. Linear systems and mathematical models of systems, including differential equations, convolution, Laplace transforms, Fourier series and transforms, and discrete representations. Class examples and coursework apply general techniques to problems in biological signal analysis, including circuits, enzyme kinematics, and physiological system analysis. Use of Matlab and Simulink software to understand more complex systems. Prerequisite: CS 101, MATH 285, and PHYS 212.

BIOE 206   Cellular Bioengineering   credit: 3 Hours.

Molecular and cellular biology focusing on instrumentation and measurement techniques: gene expression, translation, and regulation; cellular energetics and enzyme kinetics; membrane transport and cell signaling; cytoskeleton and the cell cycle; cell biology fundamentals emphasizing modern imaging and measurement systems to quantify cellular function. Credit is not given for both BIOE 206 and MCB 252. Prerequisite: MCB 150.

BIOE 220   Bioenergetics   credit: 4 Hours.

An integrative view of functional organization and energy transfer in biological systems. Emphasis on dynamics and kinetics of quantum, sub-molecular, and molecular interactions for metabolism. Topics include biomolecules of life, laws of thermodynamics, enzyme kinetics, protein-ligand binding, DNA binding, and modeling of molecular systems. Credit is not given for both BIOE 220 and ME 300, PHYS 214, or CHBE 321. Prerequisites: BIOE 201 and BIOE 206.

BIOE 297   Individual Study   credit: 1 to 4 Hours.

Special project or reading activity. May be repeated in the same or separate terms to a maximum of 12 hours. Prerequisite: Approved written application to department as specified by department or instructor.

BIOE 298   Special Topics   credit: 0 to 4 Hours.

Subject offerings of new and developing areas of knowledge in bioengineering intended to augment the existing curriculum. See Class Schedule or departmental course information for topics and prerequisites. May be repeated in the same or separate terms if topics vary to a maximum of 8 hours.

BIOE 301   Introductory Biomechanics   credit: 3 Hours.

Structure and mechanics of biological systems. Statics, dynamics, stress-strain analysis, Newtonian mechanics, and continuum mechanics. Applications to bone, soft tissue, and cells. Prerequisite: PHYS 211.

BIOE 302   Modeling Human Physiology   credit: 3 Hours.

Description, quantification, and modeling of human physiological systems, based on systems fundamentals. Components, relationships, and homeostatic controls of neural, musculoskeletal, respiratory, cardiovascular, endocrine, digestion, and renal-filtration systems. Application of mathematical modeling and MATLAB simulation to further understanding of the systems and relate physiological consequences to changes in environment or component function. Prerequisite: CS 101, BIOE 205, MATH 285, and MCB 252 or BIOE 206.

BIOE 303   Quantitative Physiology Lab   credit: 2 Hours.

Experiments involving the modeling and measurement of animal and human physiology systems. Use of computer simulations to provide mathematical descriptions of physiology behavior. Calibration and validation of models through hands-on experiments. Focus on quantitative measurement of neural, cardiovascular, respiratory, muscular, and endocrine system functions. Prerequisite: BIOE 302.

BIOE 306   Biofabrication Lab   credit: 3 Hours.

Experiments involving design of bioreactors and microfluidic systems, advanced cell culture, and quantitative analysis techniques such as polmerase chain reaction and atomic force microscopy. Laboratory techniques relating to current literature and state of the art in the field of bioengineering. Prerequisite: BIOE 202. Departmental approval required for non-majors.

BIOE 310   Comp Tools Bio Data   credit: 3 Hours.

Fundamental and applied statistics, including probability distributions, parameter estimation, descriptive statistics, hypothesis testing, and linear regression. Statistical methods in genomics including sequence analysis, gene expression data analysis, human genomic variation, regulatory genomics, and cancer genomics. Credit is not given for both BIOE 310 and IE 300. Prerequisites: BIOE 205 and BIOE 206.

BIOE 360   Transport & Flow in Bioengrg   credit: 3 Hours.

Fundamentals of fluid dynamics and mass transport applied to analysis of biological systems. Quantitative understanding of microscopic to macroscopic phenomena in biological systems related to their sensing by imaging techniques. Molecular phenomena in both healthy tissue and disease using examples from cardiovascular problems and cancer using ultrasound, optical and MRI techniques. Credit is not given for both BIOE 360 and any of CHBE 421, CHBE 451, or TAM 335. Prerequisites: BIOE 201 and BIOE 301.

BIOE 397   Individual Study   credit: 1 to 4 Hours.

Special project or reading activity. May be repeated up to 8 hours in a term to a maximum of 12 total hours. Prerequisite: Approved written application to department as specified by department or instructor.

BIOE 398   Special Topics   credit: 1 to 4 Hours.

Subject offerings of new and developing areas of knowledge in bioengineering intended to augment the existing curriculum. See Class Schedule or departmental course information for topics and prerequisites. May be repeated in the same or separate terms if topics vary to a maximum of 8 hours.

BIOE 410   Computational Cancer Biology   credit: 3 Hours.

Mathematical modeling of the process of carcinogenesis as somatic cell evolution. Focus on current research topics in cancer biology using data from next-generation sequencing technologies. Overview of database resources and algorithmic and modeling methods relating to biological problems. 3 undergraduate hours. No graduate credit. Prerequisite: BIOE 206, CS 101, MATH 285.

BIOE 414   Biomedical Instrumentation   credit: 3 Hours.

Engineering aspects of the detection, acquisition, processing, and display of signals from living systems; biomedical sensors for measurements of biopotentials, ions and gases in aqueous solution, force, displacement, blood pressure, blood flow, heart sounds, respiration, and temperature; therapeutic and prosthetic devices; medical imaging instrumentation. Same as ECE 414. 3 undergraduate hours. 3 graduate hours. Prerequisite: BIOE 205, ECE 205 or ECE 210.

BIOE 415   Biomedical Instrumentation Lab   credit: 2 Hours.

Laboratory to accompany BIOE 414. use of sensors and medical instrumentation for static and dynamic biological inputs. Measurement of biomedical signals. 2 undergraduate hours. 2 graduate hours. Same as ECE 415. Prerequisite: Credit or concurrent registration in BIOE 414.

BIOE 420   Intro Bio Control Systems   credit: 3 Hours.

Systems engineering approach to modeling physiological systems to examine natural biological control systems, homeostasis, and control through eternal medical devices. Introduces open loop and closed loop feedback control; Laplace and Fourier analysis of system behavior; impulse and steady state responses; physiological modeling and system identification; and stability. Includes biological systems for endocrine function, muscle position, neuronal circuits, and cardiovascular function. Mathematical modeling, Matlab and Simulink simulation, and physiological measurements to relate control systems to maintenance of internal environment. 3 undergraduate hours. No graduate credit. Credit is not given for BIOE 420 if credit for AE 353, ECE 486, GE 320, or ME 340 has been earned. Prerequisites: BIOE 205, BIOE 302, BIOE 303, BIOE 414, BIOE 415.

BIOE 430   Intro Synthetic Biology   credit: 3 or 4 Hours.

Introduction to the field of synthetic biology. Engineering applications of biomolecular systems and cellular capabilities for a variety of application biological background of gene regulation, experimental methods for circuit engineering, and mathematical basis for circuit modeling. Examples in biofuels, biomedicine, and other areas will be discussed. 3 undergraduate hours. 4 graduate hours. Prerequisite: BIOE 206 or MCB 252; and MATH 285.

BIOE 435   Senior Design I   credit: 2 Hours.

Capstone bioengineering design activity to develop solutions to projects provided by academia, industry, or clinical settings, utilizing principles of design, engineering analysis, and functional operation of engineering systems. Concept-design, safety, human-factors, quality, and Six-Sigma considerations. Initial solution proposals meeting professional technical-writing and communication standards. Concluded in BIOE 436. 2 undergraduate hours. No graduate credit. Prerequisite: BIOE 301, BIOE 414, and BIOE 415.

BIOE 436   Senior Design II   credit: 2 Hours.

Continuation of BIOE 435. Design teams finalize concepts, evaluate alternatives, model and analyze solutions, build and test a final product, and present the results professionally to project sponsors. 2 undergraduate hours. No graduate credit. Prerequisite: BIOE 435.

BIOE 476   Tissue Engineering   credit: 3 Hours.

Tissue engineering therapies for cell-based, material-based, and therapeutic-based solutions. Stem cells, immunology, and clinical applications. 3 undergraduate hours. 3 graduate hours. Prerequisite: BIOE 301.

BIOE 479   Cancer Nanotechnology   credit: 3 Hours.

Applications in Cancer and Mechanobiology will provide an introduction to basic concepts in applications of nanotechnology in mechanobiology and in cancer. This is a highly interdisciplinary field of research where knowledge from various discipline need to be presented and integrated. The course will be a team taught course by faculty from Engineering and LAS. There will be 4 main sections of the course; (i) biological concepts and cancer biology, (ii) introduction to bottom nanotechnology and nanomedicine, (iii) Microfluidics, Lab on Chip, and Top Down Nanotechnology, and (iv) applications in cellular mechanics, i.e. mechanobiology and nanotechnology. The course will be targeted for first year graduate students and senior undergraduate students. 3 undergraduate hours. 3 graduate hours. Approved for letter and S/U grading. Prerequisite: BIOE 206, CHEM 232.

BIOE 497   Individual Study   credit: 1 to 4 Hours.

Special project or reading activity. 1 to 4 undergraduate hours. 1 to 4 graduate hours. May be repeated up to 8 hours in a term to a maximum of 12 total hours. Prerequisite: Approved written application to department as specified by department or instructor.

BIOE 498   Special Topics   credit: 1 to 4 Hours.

Subject offerings of new and developing areas of knowledge in bioengineering intended to augment the existing curriculum. See Class Schedule or departmental course information for topics and prerequisites. 1 to 4 undergraduate hours. 1 to 4 graduate hours. May be repeated in the same or separate terms if topics vary to a maximum of 12 hours, but no more than 8 in any one term.

BIOE 499   Senior Thesis   credit: 1 to 5 Hours.

Limited in general to seniors in the curriculum in bioengineering. Any others must have the consent of the head of the department. Each student taking the course must register in a minimum of 5 hours either in one term or divided over two terms. A maximum registration of 10 hours in two terms is permitted. 1 to 5 undergraduate hours. No graduate credit. May be repeated, if topics vary. Prerequisite: Majors only, senior standing.

BIOE 500   Graduate Seminar   credit: 0 or 1 Hours.

Lecture surveying a broad range of Bioengineering topics. 0 or 1 graduate hours. No professional credit. Approved for S/U grading only. May be repeated to a maximum of 2 hours.

BIOE 501   Seminar Discussion   credit: 1 Hour.

Familiarization with reading and discussing academic journals in Bioengineering. Approved for S/U grading only.

BIOE 502   Bioengineering Professionalism   credit: 2 Hours.

Ethical questions and conduct, procedures, and professional standards in the practice of bioengineering. Authorship and mentoring, use of animal and human subjects, conflict of interest, ethical behavior in scientific research, intellectual property, and approval processes for drugs and biomedical devices. 2 graduate hours. No professional credit.

BIOE 504   Analytical Methods in Bioeng   credit: 4 Hours.

Mathematical concept relating to modeling of physiological and bio-molecular processes and the instrumentation used to measure those processes. Review of matrix methods, probability, linear systems, and integral transforms. Singular value decomposition, Bayesian decision making, and linear system solutions to ordinary differential equations. Application of concepts to biosensor design and evaluation, tracer kinetic modeling, and filtering and curve-fitting approaches to forward modeling problems. Prerequisite: MATH 285.

BIOE 505   Computational Bioengineering   credit: 4 Hours.

Mathematical and statistical models plus accompanying computational techniques central to many aspects of systems biology and bioengineering research. Theory of supervised and unsupervised learning; linear models; dimension reduction; Monte Carlo computation; analysis of gene expression data and genome sequence data; modeling of gene transcription network signaling pathways. Same as CSE 505. 4 graduate hours. No professional credit. Prerequisite: STAT 400.

BIOE 506   Molecular Biotechniques   credit: 4 Hours.

Introduction to modern biotechnologies for studies on the Central Dogma of Biology (DNA, RNA, and Protein) as well as cellular organelles and cell imaging. In-depth review of traditional established methods and emerging ones, emphasizing high precision, high spatial/temporal resolution, high-throughput, molecular accuracy, sensitivity and real-time imaging. Techniques include single molecule sequencing, super resolution cell imaging, and gene therapeutic methods. Example applications of technology are included through relevant journal articles. 4 graduate hours. No professional credit. Prerequisite: MCB 250.

BIOE 507   Advanced Bioinstrumentation   credit: 4 Hours.

Instrumentation and underlying theory employed in bioengineering. Concepts in the design and operation of sensors, fundamentals of optics, basic control theory and systems, digital components, and fundamental principles of medical imaging techniques. Specific knowledge of one biomedical instrument or system will be emphasized including detailed mathematical analysis. Prerequisite: BIOE 504.

BIOE 510   Computational Cancer Biology   credit: 4 Hours.

Mathematical modeling of the process of carcinogenesis as somatic cell evolution. Focus on current research topics in cancer biology using data from next-generation sequencing technologies. Overview of database resources and algorithmic and modeling methods relating to biological problems. 4 graduate hours. No professional credit. Prerequisite: BIOE 206, CS 101, MATH 285.

BIOE 540   Algorithmic Genomic Biology   credit: 4 Hours.

The purpose of the course is to give each student enough background and training in the area of algorithmic genomic biology so that each will be able to do research in this area, and publish papers. The main focus of the course is phylogeny (evolutionary tree) estimation, multiple sequence alignment, and genome-scale phylogenetics, which are problems that present very interesting challenges from a computational and statistical standpoint. Time permitting, we will also discuss computational problems in microbiome analysis, protein function and structure prediction, genome assembly, and even historical linguistics. Students will learn the mathematical and computational foundations in these areas, read the current literature, and do a team research project. The course is designed for doctoral students in computer science, computer engineering, bioengineering, mathematics, and statistics, and does not depend on any prior background in biology. The technical material will depend on discrete algorithms, graph theory, simulations, and probabilistic analysis of algorithms. Same as CS 581. 4 graduate hours. No professional credit. Prerequisite: CS 374 and CS 361/STAT 361, or consent of instructor.

BIOE 570   Seminar Series   credit: 1 Hour.

Guest topics will vary, but will typically cover topics of current interest relevant to the bioengineering field. Lecture and discussion on topics relevant to the development, regulatory approval, marketing, and application of systems used in the fields of biomedical imaging, life science research, and pharmaceutical discovery. Emphasis upon case studies on topics that will include regulatory approval, intellectual property, strategy, and technology innovation. 1 graduate hour. No professional credit. Approved for S/U grading only. May be repeated up to 2 hours in separate terms. Prerequisite: For students enrolled in the M.Eng. in Bioengineering degree program.

BIOE 571   Biological Measurement I   credit: 4 Hours.

Introduce fundamental concepts related to the detection and analysis of biological analytes, biomedical images, and physiological parameters. Topics include signal-to-noise analysis, noise characterization, data aliasing, analog-to-digital conversion, and common strategies for noise reduction. The fundamental phenomena behind biological measurements such as DNA sequencing, fluorescence microscopy. MRI imaging, OCT imaging, and ultrasound imaging will be discussed along with the factors that influence noise and contrast from the standpoint of fundamental physics, instrumentation/hardware, and post-measurement data/signal processing. Prerequisite: For students enrolled in the M.Eng Bioinstrumentation major.

BIOE 572   Biological Measurement II   credit: 4 Hours.

Advanced techniques relating to state-of the art bioinstrumentation technologies. Topics include fluorescence, genomic and proteomic diagnostics, bioinformatics, biosensors, ultrasound imaging, and microscopy. Prerequisite: BIOE 571. For Bioinstrumentation majors only.

BIOE 573   Managing Business Operations   credit: 4 Hours.

Introduction to fundamental principles of design, management, and improvement of business operations and product innovations. Strategies and techniques for managing processes, projects, process improvement and new product development. 4 graduate hours. No professional credit. Prerequisite: For students enrolled in the M.Eng in Bioengineering degree program.

BIOE 574   Bioinstrument Innovation   credit: 4 Hours.

Innovation and technology management in the Bioinstrumentation field. Tools, concepts, and analytical frameworks that enhance the ability to define and analyze strategic problems stemming from innovation and technological change, and to identify sources of competitive advantage from both an industry and firm-level perspective. Prerequisite: For Bioinstrumentation majors only.

BIOE 575   Bioinstrumentation Project   credit: 6 Hours.

Capstone bioinstrumentation design activity developing project solutions appropriate for academic, industrial, or clinical settings, utilizing principles of design, engineering analysis, and functional operation of engineering systems. Focus on concept-design, safety, human-factors, quality, design for requirements, regulatory strategy, and Six-Sigma considerations. Prerequisite: BIOE 571 and BIOE 572. Students enrolled in the Bioinstrumentation major in the Master of Engineering (M.Eng) degree program.

BIOE 581   MRI Pulse Sequence Design   credit: 3 Hours.

Modular approach to pulse sequence programming in magnetic resonance imaging; descriptions of current pulse sequences; RF pulse design; data sampling considerations; k-space acquisition trajectories. Pulse sequence development simulator usage to program, simulate, and reconstruct images from student-designed acquisitions. Prerequisite: ECE 480.

BIOE 582   Stats & Algo in Genomic Bio   credit: 4 Hours.

This course will provide students with the practical knowledge of statistical analysis and computational modeling techniques relevant for applications in genomics and systems biology. The focus will be on the fundamental concepts and algorithms for gene finding, genome annotation, sequence alignment, phylogenetic reconstruction, gene expression and network analysis, Genome-Wide Association Studies (GWAS), etc. 4 graduate hours. No professional credit. Prerequisite: STAT 100, MCB 250, MATH 220, CS 101, or equivalent. Restricted to MEng Students only.

BIOE 583   HT Genomic Data Analysis   credit: 4 Hours.

The course will provide students with important practical skills for handling genomic big data and analyzing the results of various types of high-throughput sequencing experiments. The focus will be on achieving proficiency in data management and processing based on popular file formats in genomic biology. 4 graduate hours. No professional credit. Prerequisite: STAT 100, MCB 250, CS 101, or equivalent. For students enrolled in the M.Eng in Bioengineering - Computational Genomics concentration.

BIOE 597   Individual Study   credit: 1 to 8 Hours.

Special project or reading activity. May be repeated. Prerequisite: Approved written application to department as specified by department or instructor.

BIOE 598   Special Topics   credit: 1 to 4 Hours.

Subject offerings of new and developing areas of knowledge in bioengineering intended to augment the existing curriculum. See Class Schedule or departmental course information for topics and prerequisites. May be repeated in the same or separate terms if topics vary to a maximum of 12 hours, but no more than 8 in any one term.

BIOE 599   Thesis Research   credit: 0 to 16 Hours.

Bioengineering graduate thesis research. Approved for S/U grading only. May be repeated.