Stanford Biomedical Engineering Research Paper

Courses

BIOE 10N. Form and Function of Animal Skeletons. 3 Units.

Preference to freshmen. The biomechanics and mechanobiology of the musculoskeletal system in human beings and other vertebrates on the level of the whole organism, organ systems, tissues, and cell biology. Field trips to labs.
Same as: ME 10N

BIOE 32Q. Bon Appétit, Marie Curie! The Science Behind Haute Cuisine. 3 Units.

This seminar is for anyone who loves food, cooking or science! We will focus on the science and biology behind the techniques and the taste buds. Not a single lecture will pass by without a delicious opportunity - each weekly meeting will include not only lecture, but also a lab demonstration and a chance to prepare classic dishes that illustrate that day's scientific concepts.

BIOE 36Q. The Biophysics of Innate Immunity. 3 Units.

The innate immune system provides our first line of defense against disease--bothninfections, and cancer. Innate immune effectors such as host defense peptides arendeployed by numerous cell types (for instance neutrophils, macrophages, NK cells,nepithelial cells and keratinocytes) and work by biophysical mechanisms of action. The ourse draws from the primary literature and covers the evolution, structures, mechanisms,and physiological functions of important "innate immune effectors" (components of the innate immune system that can attack pathogens, and infected or host cells, and kill or incapacitate them directly). The course is aimed at students who have an interest in biochemistry, molecular/cellular biology, biophysics, and/or bioengineering.

BIOE 42. Physical Biology. 4 Units.

BIOE 42 is designed to introduce students to general engineering principles that have emerged from theory and experiments in biology. Topics covered will cover the scales from molecules to cells to organisms, including fundamental principles of entropy, diffusion, and continuum mechanics. These topics will link to several biological questions, including DNA organization, ligand binding, cytoskeletal mechanics, and the electromagnetic origin of nerve impulses. In all cases, students will learn to develop toy models that can explain quantitative measurements of the function of biological systems. Prerequisites: MATH 19, 20, 21CHEM 31A, B (or 31X), PHYSICS 41; strongly recommended: CS 106A, CME 100 or MATH 51, and CME 106; or instructor approval.

BIOE 44. Fundamentals for Engineering Biology Lab. 4 Units.

Introduction to next-generation techniques in genetic, molecular, biochemical, and cellular engineering. Lab modules build upon current research including: gene and genome engineering via decoupled design and construction of genetic material; component engineering focusing on molecular design and quantitative analysis of experiments; device and system engineering using abstracted genetically encoded objects; and product development based on useful applications of biological technologies. Concurrent or previous enrollment in BIO 82 or BIO 83.

BIOE 51. Anatomy for Bioengineers. 4 Units.

Fundamental human anatomy, spanning major body systems and tissues including nerve, muscle, bone, cardiovascular, respiratory, gastrointestinal, and renal systems. Explore intricacies of structure and function, and how various body parts come together to form a coherent and adaptable living being. Correlate clinical conditions and therapeutic interventions. Participate in lab sessions with predissected cadaveric material and hands-on learning to gain understanding of the bioengineering human application domain. Encourage anatomical thinking, defining challenges and opportunities for bioengineers.

BIOE 60. Beyond Bitcoin: Applications of Distributed Trust. 1 Unit.

In the past, people have relied on trusted third parties to facilitate the transactions that define our lives: how we store medical records, how we share genomic information with scientists and drug companies, where we get our news, and how we communicate. Advances in distributed systems and cryptography allow us to eschew such parties. Today, we can create a global, irrefutable ledger of transactions, events, and diagnoses, such that rewriting history is computationally infeasible. What can we build on top of such a powerful data structure? What are the consequences of pseudo-legal contracts and promises written in mathematical ink? In this class, we will bring together experts in cryptography, healthcare, and distributed consensus with students across the university. The first weeks present a technical overview of block chain primitives. In the following weeks, the class will focus on discussing applications and policy issues through lectures and guest speakers from various domains across both academia and industry. Limited enrollment, subject to instructor approval.

BIOE 70Q. Medical Device Innovation. 3 Units.

BIOE 70Q invites students to apply design thinking to the creation of healthcare technologies. Students will learn about the variety of factors that shape healthcare innovation, and through hands-on design projects, invent their own solutions to clinical needs. Guest instructors will include engineers, doctors, entrepreneurs, and others who have helped bring ideas from concept to clinical use.

BIOE 80. Introduction to Bioengineering (Engineering Living Matter). 4 Units.

Students completing BIOE.80 should have a working understanding for how to approach the systematic engineering of living systems to benefit all people and the planet. Our main goals are (1) to help students learn ways of thinking about engineering living matter and (2) to empower students to explore the broader ramifications of engineering life. Specific concepts and skills covered include but are not limited to: capacities of natural life on Earth; scope of the existing human-directed bioeconomy; deconstructing complicated problems; reaction & diffusion systems; microbial human anatomy; conceptualizing the engineering of biology; how atoms can be organized to make molecules; how to print DNA from scratch; programming genetic sensors, logic, & actuators; biology beyond molecules (photons, electrons, etc.); what constraints limit what life can do?; what will be the major health challenges in 2030?; how does what we want shape bioengineering?; who should choose and realize various competing bioengineering futures?.
Same as: ENGR 80

BIOE 101. Systems Biology. 3 Units.

Complex biological behaviors through the integration of computational modeling and molecular biology. Topics: reconstructing biological networks from high-throughput data and knowledge bases. Network properties. Computational modeling of network behaviors at the small and large scale. Using model predictions to guide an experimental program. Robustness, noise, and cellular variation. Prerequisites: CME 102; BIO 82, BIO 84; or consent of instructor.
Same as: BIOE 210

BIOE 103. Systems Physiology and Design. 4 Units.

Physiology of intact human tissues, organs, and organ systems in health and disease, and bioengineering tools used (or needed) to probe and model these physiological systems. Topics: Clinical physiology, network physiology and system design/plasticity, diseases and interventions (major syndromes, simulation, and treatment, instrumentation for intervention, stimulation, diagnosis, and prevention), and new technologies including tissue engineering and optogenetics.  Discussions of pathology of these systems in a clinical-case based format, with a view towards identifying unmet clinical needs.  Learning computational skills that not only enable simulation of these systems but also apply more broadly to biomedical data analysis. Prerequisites: CME 102; PHYSICS 41; BIO 82, BIO 84.

BIOE 103B. Systems Physiology and Design. 4 Units.

*ONLINE Offering of BIOE 103. This pilot class, BIOE103B, is an entirely online offering with the same content, learning goals, and prerequisites as BIOE 103. Students attend class by watching videos and completing assignments remotely. Students may attend recitation and office hours in person, but cannot attend the BIOE103 in-person lecture due to room capacity restraints.* Physiology of intact human tissues, organs, and organ systems in health and disease, and bioengineering tools used (or needed) to probe and model these physiological systems. Topics: Clinical physiology, network physiology and system design/plasticity, diseases and interventions (major syndromes, simulation, and treatment, instrumentation for intervention, stimulation, diagnosis, and prevention), and new technologies including tissue engineering and optogenetics. Discussions of pathology of these systems in a clinical-case based format, with a view towards identifying unmet clinical needs. Learning computational skills that not only enable simulation of these systems but also apply more broadly to biomedical data analysis. Prerequisites: CME 102; PHYSICS 41; BIO 82, BIO 84. strongly recommended PHYSICS 43. Enrollment with Instructor approval.

BIOE 115. Computational Modeling of Microbial Communities. 4 Units.

Provides biologists with basic computational tools and knowledge to confront large datasets in a quantitative manner. Students learn basic programming skills focused on Matlab, but also are introduced to Perl and Python. Topics include: image analysis, bioinformatics algorithms, reaction diffusion modeling, Monte Carlo algorithms, and population dynamics. Students apply computational skills to a miniature research project studying the human gut microbiota.
Same as: MI 245

BIOE 122. Biosecurity and Bioterrorism Response. 4-5 Units.

Overview of the most pressing biosecurity issues facing the world today. Guest lecturers have included former Secretary of State Condoleezza Rice, former Special Assistant on BioSecurity to Presidents Clinton and Bush Jr. Dr. Ken Bernard, Chief Medical Officer of the Homeland Security Department Dr. Alex Garza, eminent scientists, innovators and physicians in the field, and leaders of relevant technology companies. How well the US and global healthcare systems are prepared to withstand a pandemic or a bioterrorism attack, how the medical/healthcare field, government, and the technology sectors are involved in biosecurity and pandemic or bioterrorism response and how they interface, the rise of synthetic biology with its promises and threats, global bio-surveillance, making the medical diagnosis, isolation, containment, hospital surge capacity, stockpiling and distribution of countermeasures, food and agriculture biosecurity, new promising technologies for detection of bio-threats and countermeasures. Open to medical, graduate, and undergraduate students. No prior background in biology necessary. 4 units for twice weekly attendance (Mon. and Wed.); additional 1 unit for writing a research paper for 5 units total maximum.
Same as: EMED 122, EMED 222, PUBLPOL 122, PUBLPOL 222

BIOE 123. Biomedical System Prototyping Lab. 4 Units.

The Bioengineering System Prototyping Laboratory is a fast-paced, team-based system engineering experience, in which teams of 2-3 students design and build a fermenter that meets a set of common requirements along with a set of unique team-determined requirements. Students learn-by-doing hands-on skills in electronics and mechanical design and fabrication. Teams also develop process skills and an engineering mindset by aligning specifications with requirements, developing output metrics and measuring performance, and creating project proposals and plans. The course culminates in demonstration of a fully functioning fermenter that meets the teams' self-determined metrics. n nLearning goals: 1) Design, fabricate, integrate, and characterize practical electronic and mechanical hardware systems that meet clear requirements in the context of Bioengineering (i.e., build something that works). 2) Use prototyping tools, techniques, and instruments, including: CAD, 3D printing, laser cutting, microcontrollers, and oscilloscopes. 3) Create quantitative system specifications and test measurement plans to demonstrate that a design meets user requirements. 4) Communicate design elements, choices, specifications, and performance through design reviews and written reports. 5) Collaborate as a team member on a complex system design project (e.g., a fermenter). n nLimited enrollment, with priority for Bioengineering undergraduates. Prerequisites: PHYSICS 43, or equivalent. Experience with Matlab and/or Python is recommended.

BIOE 131. Ethics in Bioengineering. 3 Units.

Bioengineering focuses on the development and application of new technologies in the biology and medicine. These technologies often have powerful effects on living systems at the microscopic and macroscopic level. They can provide great benefit to society, but they also can be used in dangerous or damaging ways. These effects may be positive or negative, and so it is critical that bioengineers understand the basic principles of ethics when thinking about how the technologies they develop can and should be applied. On a personal level, every bioengineer should understand the basic principles of ethical behavior in the professional setting. This course will involve substantial writing, and will use case-study methodology to introduce both societal and personal ethical principles, with a focus on practical applications.
Same as: ETHICSOC 131X

BIOE 140. Physical Biology of Macromolecules. 4 Units.

Principles of statistical physics, thermodynamics, and kinetics with applications to molecular biology. Topics include entropy, temperature, chemical forces, enzyme kinetics, free energy and its uses, self assembly, cooperative transitions in macromolecules, molecular machines, feedback, and accurate replication. Prerequisites: MATH 19, 20, 21; CHEM 31A, B (or 31X); strongly recommended: PHYSICS 41, CME 100 or MATH 51, and CME 106; or instructor approval.

BIOE 141A. Senior Capstone Design I. 4 Units.

Lecture/Lab. First course of two-quarter capstone sequence. Team based project introduces students to the process of designing new biological technologies to address societal needs. Topics include methods for validating societal needs, brainstorming, concept selection, and the engineering design process. First quarter deliverable is a design for the top concept. Second quarter involves implementation and testing. Guest lectures and practical demonstrations are incorporated. Prerequisites: BIOE 123 and BIOE 44. This course is open only to seniors in the undergraduate Bioengineering program.

BIOE 141B. Senior Capstone Design II. 4 Units.

Lecture/Lab. Second course of two-quarter capstone sequence. Team based project introduces students to the process of designing new biological technologies to address societal needs. Emphasis is on implementing and testing the design from the first quarter with the at least one round of prototype iteration. Guest lectures and practical demonstrations are incorporated. Prerequisites: BIOE123 and BIOE44. This course is open only to seniors in the undergraduate Bioengineering program. IMPORTANT NOTE: class meets in Shriram 112.

BIOE 158. Soft Matter in Biomedical Devices, Microelectronics, and Everyday Life. 4 Units.

The relationships between molecular structure, morphology, and the unique physical, chemical, and mechanical behavior of polymers and other types of soft matter are discussed. Topics include methods for preparing synthetic polymers and examination of how enthalpy and entropy determine conformation, solubility, mechanical behavior, microphase separation, crystallinity, glass transitions, elasticity, and linear viscoelasticity. Case studies covering polymers in biomedical devices and microelectronics will be covered. Recommended: ENGR 50 and CHEM 31A or equivalent.
Same as: CHEMENG 160, MATSCI 158

BIOE 191. Bioengineering Problems and Experimental Investigation. 1-5 Unit.

Directed study and research for undergraduates on a subject of mutual interest to student and instructor. Prerequisites: consent of instructor and adviser. (Staff).

BIOE 191X. Out-of-Department Advanced Research Laboratory in Bioengineering. 1-15 Unit.

Individual research by arrangement with out-of-department instructors. Credit for 191X is restricted to declared Bioengineering majors pursuing honors and requires department approval. See http://bioengineering.stanford.edu/education/undergraduate.html for additional information. May be repeated for credit.

BIOE 196. INTERACTIVE MEDIA AND GAMES. 1 Unit.

Interactive media and games increasingly pervade and shape our society. In addition to their dominant roles in entertainment, video games play growing roles in education, arts, and science. This seminar series brings together a diverse set of experts to provide interdisciplinary perspectives on these media regarding their history, technologies, scholarly research, industry, artistic value, and potential future.
Same as: BIOPHYS 196

BIOE 201C. Diagnostic Devices Lab. 2 Units.

This course exposes students to the engineering principles and clinical application of medical devices through lectures and hands-on labs, performed in teams of two. Teams take measurements with these devices and fit their data to theory presented in the lecture. Devices covered include X-ray, CT, MRI, EEG, ECG, Ultrasound and BMI (Brain-machine interface). Prerequisites: BIOE 103 or BIOE 300B.
Same as: BIOE 301C

BIOE 210. Systems Biology. 3 Units.

Complex biological behaviors through the integration of computational modeling and molecular biology. Topics: reconstructing biological networks from high-throughput data and knowledge bases. Network properties. Computational modeling of network behaviors at the small and large scale. Using model predictions to guide an experimental program. Robustness, noise, and cellular variation. Prerequisites: CME 102; BIO 82, BIO 84; or consent of instructor.
Same as: BIOE 101

BIOE 211. Biophysics of Multi-cellular Systems and Amorphous Computing. 2-3 Units.

Provides an interdisciplinary perspective on the design, emergent behavior, and functionality of multi-cellular biological systems such as embryos, biofilms, and artificial tissues and their conceptual relationship to amorphous computers. Students discuss relevant literature and introduced to and apply pertinent mathematical and biophysical modeling approaches to various aspect multi-cellular systems, furthermore carry out real biology experiments over the web. Specific topics include: (Morphogen) gradients; reaction-diffusion systems (Turing patterns); visco-elastic aspects and forces in tissues; morphogenesis; coordinated gene expression, genetic oscillators and synchrony; genetic networks; self-organization, noise, robustness, and evolvability; game theory; emergent behavior; criticality; symmetries; scaling; fractals; agent based modeling. The course is geared towards a broadly interested graduate and advanced undergraduates audience such as from bio / applied physics, computer science, developmental and systems biology, and bio / tissue / mechanical / electrical engineering. Prerequisites: Previous knowledge in one programming language - ideally Matlab - is recommended; undergraduate students benefit from BIOE 42, or equivalent.
Same as: BIOE 311, BIOPHYS 311, DBIO 211

BIOE 212. Introduction to Biomedical Informatics Research Methodology. 3-5 Units.

Capstone Biomedical Informatics (BMI) experience. Hands-on software building. Student teams conceive, design, specify, implement, evaluate, and report on a software project in the domain of biomedicine. Creating written proposals, peer review, providing status reports, and preparing final reports. Issues related to research reproducibility. Guest lectures from professional biomedical informatics systems builders on issues related to the process of project management. Software engineering basics. Because the team projects start in the first week of class, attendance that week is strongly recommended. Prerequisites: BIOMEDIN 210 or 214 or 215 or 217 or 260. Preference to BMI graduate students. Consent of instructor required.
Same as: BIOMEDIN 212, CS 272, GENE 212

BIOE 213. Stochastic and Nonlinear Dynamics. 3 Units.

Theoretical analysis of dynamical processes: dynamical systems, stochastic processes, and spatiotemporal dynamics. Motivations and applications from biology and physics. Emphasis is on methods including qualitative approaches, asymptotics, and multiple scale analysis. Prerequisites: ordinary and partial differential equations, complex analysis, and probability or statistical physics.
Same as: APPPHYS 223, BIO 223

BIOE 214. Representations and Algorithms for Computational Molecular Biology. 3-4 Units.

Topics: introduction to bioinformatics and computational biology, algorithms for alignment of biological sequences and structures, computing with strings, phylogenetic tree construction, hidden Markov models, basic structural computations on proteins, protein structure prediction, protein threading techniques, homology modeling, molecular dynamics and energy minimization, statistical analysis of 3D biological data, integration of data sources, knowledge representation and controlled terminologies for molecular biology, microarray analysis, machine learning (clustering and classification), and natural language text processing. Prerequisite: CS 106B; recommended: CS161; consent of instructor for 3 units.
Same as: BIOMEDIN 214, CS 274, GENE 214

BIOE 215. Physics-Based Simulation of Biological Structure. 3 Units.

Modeling, simulation, analysis, and measurement of biological systems. Computational tools for determining the behavior of biological structures- from molecules to organisms. Numerical solutions of algebraic and differential equations governing biological processes. Simulation laboratory examples in biology, engineering, and computer science. Limited enrollment. Prerequisites: basic biology, mechanics (F=ma), ODEs, and proficiency in C or C++ programming.

BIOE 217. Translational Bioinformatics. 4 Units.

Computational methods for the translation of biomedical data into diagnostic, prognostic, and therapeutic applications in medicine. Topics: multi-scale omics data generation and analysis, utility and limitations of public biomedical resources, machine learning and data mining, issues and opportunities in drug discovery, and mobile/digital health solutions. Case studies and course project. Prerequisites: programming ability at the level of CS 106A and familiarity with biology and statistics.
Same as: BIOMEDIN 217, CS 275, GENE 217

BIOE 219. Special Topics in Development and Cancer: Evolutionary and Quantitative Perspectives. 3 Units.

The course will serve as a literature-based introductory guide for synthesis of ideas in developmental biology and cancer, with an emphasis on evolutionary analysis and quantitative thinking. The goal for this course is for students to understand how we know what we know about fundamental questions in the field of developmental biology and cancer, and how we ask good questions for the future. We will discuss how studying model organisms has provided the critical breakthroughs that have helped us understand developmental and disease mechanisms in higher organisms. The students are expected to be able to read the primary literature and think critically about experiments to understand what is actually known and what questions still remain unanswered. Students will develop skills in the educated guesswork to apply order-of-magnitude methodology to questions in development and cancer.
Same as: DBIO 219

BIOE 220. Introduction to Imaging and Image-based Human Anatomy. 3 Units.

Focus on learning the fundamentals of each imaging modality including X-ray Imaging, Ultrasound, CT, and MRI, to learn normal human anatomy and how it appears on medical images, to learn the relative strengths of the modalities, and to answer, "What am I looking at?" Course website: http://bioe220.stanford.edu.
Same as: RAD 220

BIOE 221. Physics and Engineering of Radionuclide-based Medical Imaging. 3 Units.

Physics, instrumentation, and algorithms for radionuclide-based medical imaging, with a focus on positron emission tomography (PET) and single photon emission computed tomography (SPECT). Topics include basic physics of photon emission from the body and detection, sensors, readout and data acquisition electronics, system design, strategies for tomographic image reconstruction, system calibration and data correction algorithms, methods of image quantification, and image quality assessment, and current developments in the field. Prerequisites: A year of university-level mathematics and physics.
Same as: RAD 221

BIOE 221G. Gut Microbiota in Health and Disease. 2-3 Units.

Preference to graduate students. Focus is on the human gut microbiota. Students enrolling for 3 units receive instruction on computational approaches to analyze microbiome data and must complete a related project.
Same as: GENE 208, MI 221

BIOE 222. Instrumentation and Applications for Multi-modality Molecular Imaging of Living Subjects. 3-4 Units.

Focuses on instruments, algorithms and other technologies for imaging of cellular and molecular processes in living subjects. Introduces preclinical and clinical molecular imaging modalities, including strategies for molecular imaging using PET, SPECT, MRI, Ultrasound, Optics, and Photoacoustics. For each modality, lectures cover the basics of the origin and properties of imaging signal generation, instrumentation physics and engineering of signal detection, image signal processing, image reconstruction, and image data quantification.
Same as: RAD 222

BIOE 223. Physics and Engineering of X-Ray Computed Tomography. 3 Units.

CT scanning geometries, production of x-rays, interactions of x-rays with matter, 2D and 3D CT reconstruction, image presentation, image quality performance parameters, system components, image artirfacts, radiation dose. Prerequisites: differential and integral calculus. Knowledge of Fourier transforms (EE261) recommended.
Same as: RAD 223

BIOE 224. Probes and Applications for Multi-modality Molecular Imaging of Living Subjects. 4 Units.

Focuses on molecular contrast agents (a.k.a. "probes") that interrogate and target specific cellular and molecular disease mechanisms. Covers the ideal characteristics of molecular probes and how to optimize their design for use as effective imaging reagents that enables readout of specific steps in biological pathways and reveal the nature of disease through noninvasive imaging assays. Prerequisites: none.
Same as: RAD 224

Research - Biomedical Devices

Researchers working in biomedical design invent new technologies for life sciences research and clinical applications. Bioengineers are helping to translate advances in the life sciences into devices that directly impact human welfare and the future of scientific research.

Research projects at Stanford include:

  • Cardiovascular Devices (VIBE Lab) - Dr. Chris Cheng
  • Neural prosthetic systems
  • Development of cellular-microelectrode hybrid biosensors
  • Synthetic bone materials for fracture fixation
  • Micro-Electrical-Mechanical (MEMS) devices
  • Microfluidic devices
  • Computer-assisted surgical navigation
  • Novel drug delivery systems

Bioengineering faculty members working in this area:

Consulting faculty members working in this area are:

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