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BIOE 32Q: Bon App├ętit, Marie Curie! The Science Behind Haute Cuisine

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.
Terms: Spr | Units: 3 | Grading: Letter or Credit/No Credit
Instructors: ; Covert, M. (PI)

BIOE 36Q: The Biophysics of Innate Immunity

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.
Terms: not given this year | Units: 3 | Grading: Letter or Credit/No Credit

BIOE 42: Physical Biology

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, 21 CHEM 31A, B (or 31X), PHYSICS 41; strongly recommended: CS 106A, CME 100 or MATH 51, and CME 106; or instructor approval.
Terms: Spr | Units: 4 | UG Reqs: WAY-AQR, WAY-SMA | Grading: Letter (ABCD/NP)

BIOE 44: Fundamentals for Engineering Biology Lab

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.
Terms: Aut, Spr | Units: 4 | UG Reqs: WAY-SMA | Grading: Letter (ABCD/NP)

BIOE 51: Anatomy for Bioengineers

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.
Terms: Spr | Units: 4 | Grading: Letter or Credit/No Credit

BIOE 60: Beyond Bitcoin: Applications of Distributed Trust

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.
Terms: Win | Units: 1 | Grading: Satisfactory/No Credit
Instructors: ; Liphardt, J. (PI)

BIOE 70Q: Medical Device Innovation

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.
Terms: Spr | Units: 3 | UG Reqs: WAY-CE | Grading: Letter (ABCD/NP)

BIOE 80: Introduction to Bioengineering (Engineering Living Matter) (ENGR 80)

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?
Terms: Spr | Units: 4 | UG Reqs: GER:DB-EngrAppSci, WAY-FR | Grading: Letter (ABCD/NP)

BIOE 101: Systems Biology (BIOE 210)

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.
Terms: Aut | Units: 3 | UG Reqs: WAY-AQR | Grading: Letter (ABCD/NP)
Instructors: ; Covert, M. (PI)

BIOE 102: Physical Biology of Macromolecules

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.
Terms: not given this year | Units: 4 | UG Reqs: WAY-AQR, WAY-SMA | Grading: Letter (ABCD/NP)

BIOE 103: Systems Physiology and Design

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.
Terms: Spr | Units: 4 | UG Reqs: WAY-AQR, WAY-SMA | Grading: Letter (ABCD/NP)

BIOE 103B: Systems Physiology and Design

*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
Terms: Spr | Units: 4 | UG Reqs: WAY-AQR, WAY-SMA | Grading: Letter (ABCD/NP)

BIOE 122: Biosecurity and Bioterrorism Response (EMED 122, EMED 222, PUBLPOL 122, PUBLPOL 222)

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.
Terms: Win | Units: 4-5 | UG Reqs: GER: DB-NatSci, GER:EC-GlobalCom, WAY-SI | Grading: Letter or Credit/No Credit
Instructors: ; Trounce, M. (PI)

BIOE 123: Biomedical System Prototyping Lab

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.
Terms: Win | Units: 4 | UG Reqs: WAY-SMA | Grading: Letter (ABCD/NP)

BIOE 131: Ethics in Bioengineering (ETHICSOC 131X)

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.
Terms: Spr | Units: 3 | UG Reqs: GER:EC-EthicReas, WAY-ER | Grading: Letter (ABCD/NP)

BIOE 141A: Senior Capstone Design I

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.
Terms: Aut | Units: 4 | Grading: Letter (ABCD/NP)

BIOE 141B: Senior Capstone Design II

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.
Terms: Win | Units: 4 | Grading: Letter (ABCD/NP)

BIOE 150: Biochemical Engineering (CHEMENG 150)

Systems-level combination of chemical engineering concepts with biological principles. The production of protein pharmaceuticals as a paradigm to explore quantitative biochemistry and cellular physiology, the elemental stoichiometry of metabolism, recombinant DNA technology, synthetic biology and metabolic engineering, fermentation development and control, product isolation and purification, protein folding and formulation, and biobusiness and regulatory issues. Prerequisite: CHEMENG 181 (formerly 188) or BIOSCI 41 or equivalent.
Terms: Win | Units: 3 | Grading: Letter (ABCD/NP)

BIOE 158: Soft Matter in Biomedical Devices, Microelectronics, and Everyday Life (MATSCI 158)

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.
Terms: Win | Units: 4 | UG Reqs: WAY-AQR, WAY-SMA | Grading: Letter or Credit/No Credit

BIOE 191X: Out-of-Department Advanced Research Laboratory in Bioengineering

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.
Terms: Aut, Win, Spr, Sum | Units: 1-15 | Repeatable for credit | Grading: Letter (ABCD/NP)

BIOE 193: Interdisciplinary Approaches to Human Health Research (BIO 193, CHEM 193, CHEMENG 193)

For undergraduate students participating in the Stanford ChEM-H Undergraduate Scholars Program. This course will expose students to interdisciplinary research questions and approaches that span chemistry, engineering, biology, and medicine. Focus is on the development and practice of scientific reading, writing, and presentation skills intended to complement hands-on laboratory research. Students will read scientific articles, write research proposals, make posters, and give presentations.
Terms: Win, Spr | Units: 1 | Repeatable for credit | Grading: Satisfactory/No Credit
Instructors: ; Alfieri, K. (PI)

BIOE 196: INTERACTIVE MEDIA AND GAMES (BIOPHYS 196, CS 544)

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.
Terms: not given this year | Units: 1 | Repeatable for credit | Grading: Satisfactory/No Credit

BIOE 201C: Diagnostic Devices Lab (BIOE 301C)

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.
Terms: Spr | Units: 2 | Grading: Letter (ABCD/NP)
Instructors: ; Lee, J. (PI); Zou, X. (TA)

BIOE 210: Systems Biology (BIOE 101)

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.
Terms: Aut | Units: 3 | Grading: Letter (ABCD/NP)
Instructors: ; Covert, M. (PI)

BIOE 211: Biophysics of Multi-cellular Systems and Amorphous Computing (BIOE 311, BIOPHYS 311, DBIO 211)

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.
Terms: not given this year | Units: 2-3 | Grading: Medical Option (Med-Ltr-CR/NC)

BIOE 212: Introduction to Biomedical Informatics Research Methodology (BIOMEDIN 212, CS 272, GENE 212)

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.
Terms: Spr | Units: 3-5 | Grading: Medical Option (Med-Ltr-CR/NC)

BIOE 213: Stochastic and Nonlinear Dynamics (APPPHYS 223, BIO 223, PHYSICS 223)

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.
Terms: alternate years, given next year | Units: 3 | Grading: Letter or Credit/No Credit

BIOE 214: Representations and Algorithms for Computational Molecular Biology (BIOMEDIN 214, CS 274, GENE 214)

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.
Terms: Aut | Units: 3-4 | Grading: Medical Option (Med-Ltr-CR/NC)

BIOE 215: Physics-Based Simulation of Biological Structure

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.
Terms: not given this year | Units: 3 | Grading: Medical Option (Med-Ltr-CR/NC)

BIOE 217: Translational Bioinformatics (BIOMEDIN 217, CS 275, GENE 217)

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.
Terms: Win | Units: 4 | Grading: Medical Option (Med-Ltr-CR/NC)

BIOE 219: Special Topics in Development and Cancer: Evolutionary and Quantitative Perspectives (DBIO 219)

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.
Terms: Win | Units: 3 | Grading: Letter (ABCD/NP)

BIOE 220: Introduction to Imaging and Image-based Human Anatomy (RAD 220)

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
Terms: Win | Units: 3 | Grading: Medical Option (Med-Ltr-CR/NC)

BIOE 221: Physics and Engineering of Radionuclide-based Medical Imaging (RAD 221)

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.
Terms: Win | Units: 3 | Grading: Medical Option (Med-Ltr-CR/NC)

BIOE 221G: Gut Microbiota in Health and Disease (GENE 208, MI 221)

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.
Terms: not given this year | Units: 2-3 | Grading: Medical Option (Med-Ltr-CR/NC)

BIOE 222: Physics and Engineering Principles of Multi-modality Molecular Imaging of Living Subjects (RAD 222)

Physics and Engineering Principles of Multi-modality Molecular Imaging of Living Subjects (RAD 222A)nFocuses on instruments, algorithms and other technologies for non-invasive imaging of molecular processes in living subjects. Introduces research and clinical molecular imaging modalities, including 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, signal processing, image reconstruction, image data quantification, applications of machine learning, and applications of molecular imaging in medicine and biology research.
Terms: Aut | Units: 3-4 | Grading: Medical Option (Med-Ltr-CR/NC)
Instructors: ; Levin, C. (PI)

BIOE 223: Physics and Engineering of X-Ray Computed Tomography (RAD 223)

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.
Terms: not given this year | Units: 3 | Grading: Medical Option (Med-Ltr-CR/NC)

BIOE 224: Probes and Applications for Multi-modality Molecular Imaging of Living Subjects (RAD 224)

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.
Terms: Win | Units: 4 | Repeatable for credit | Grading: Medical Option (Med-Ltr-CR/NC)

BIOE 225: Ultrasound Imaging and Therapeutic Applications (RAD 225)

Covers the basic concepts of ultrasound imaging including acoustic properties of biological tissues, transducer hardware, beam formation, and clinical imaging.  Also includes the therapeutic applications of ultrasound including thermal and mechanical effects, visualization of the temperature and radiation force with MRI, tissue assessment with MRI and ultrasound, and ultrasound-enhanced drug delivery. Course website: http://bioe225.stanford.edu
Terms: not given this year | Units: 3 | Grading: Medical Option (Med-Ltr-CR/NC)

BIOE 227: Functional MRI Methods (BIOPHYS 227, RAD 227)

Basics of functional magnetic resonance neuroimaging, including data acquisition, analysis, and experimental design. Journal club sections. Cognitive neuroscience and clinical applications. Prerequisites: basic physics, mathematics; neuroscience recommended.
Terms: Win | Units: 3 | Grading: Medical Option (Med-Ltr-CR/NC)
Instructors: ; Glover, G. (PI)

BIOE 229: Advanced Research Topics in Multi-modality Molecular Imaging of Living Subjects

Covers advanced topics and controversies in molecular imaging in the understanding of biology and disease. Lectures will include discussion on instrumentation, probes and bioassays. Topics will address unmet needs for visualization and quantification of molecular pathways in biology as well as for diagnosis and disease management. Areas of unmet clinical needs include those in oncology, neurology, cardiovascular medicine and musculoskeletal diseases. The aim is to identify important problems and controversies in a field and address them by providing background and relevance through review of the relevant primary literature, and then proposing and evaluating innovative imaging strategies that are designed to address the problem. The organization of lectures is similar to the thought process that is necessary for writing an NIH grant proposal in which aims are proposed and supported by background and relevance. The innovation of proposed approaches will be highlighted. An aim of the course is to inform students on how to creatively think about a problem and propose a solution focusing on the key elements of writing a successful grant proposal. Prerequisites: none.
Terms: not given this year | Units: 3-4 | Grading: Letter or Credit/No Credit

BIOE 231: Protein Engineering (BIOE 331)

The design and engineering of biomolecules emphasizing proteins, antibodies, and enzymes. Combinatorial and rational methodologies, protein structure and function, and biophysical analyses of modified biomolecules. Clinically relevant examples from the literature and biotech industry. Prerequisite: basic biochemistry. Winter, Cochran
Terms: Win | Units: 3 | Grading: Letter (ABCD/NP)
Instructors: ; Lin, M. (PI)

BIOE 236: Biophysical Mechanisms of Innate Immunity

The innate immune system provides our first line of defense against infections of all kinds as well as cancer. Innate immune effectors, e.g. host defense peptides are deployed by numerous cell types (neutrophils, macrophages, NK cells, as well as epithelial cells, keratinocytes, and others) and attack by biophysical mechanisms of action. Disorders of innate immunity are increasingly being implicated in human autoimmune disease. Using primary literature, we will cover the evolution, structures, mechanisms, and functions of innate immune effectors.
Terms: not given this year | Units: 3 | Grading: Letter or Credit/No Credit

BIOE 238: Principles and Tools for Metrology in Biology

A practical introduction to the science of measurement. Emphasis is on the tools used to parse a biological measurement problem. Students will learn to identify and quantitatively address the critical sources of variability and bias using the core concepts of uncertainty, traceability, and validation. Case studies will illustrate use of metrology in current and emergent bioscience and engineering applications.
Terms: not given this year | Units: 2 | Grading: Letter (ABCD/NP)

BIOE 240: The Biology Revolution

Over the last century, engineering advances have brought us incredible marvels of transportation, manufacturing, construction, healthcare, and agriculture; essentially, the modern world as we know it. However, it has been driven in unsustainable means, leading to incredible levels of pollution, global warming, world hunger, and skyrocketing healthcare costs. But we are at a new juncture in our understanding of biology and the technological tools now available to us. Just as chemists used engineering principles to create chemical engineering, a natural means to accelerate re-gaining an alignment with nature would be to engineer biology. In short, this kind of bioengineering research can lead to processes and products where biology itself has been designed through engineering principles: bacteria engineered to produce chemicals; engineered organs to replace faulty ones; novel diagnostic modalities; the ability to engineer cells as if they were machines. What are the impacts if incorporating these new technologies and technological modalities? What is the ultimate impact to our society and planet if we truly begin to engineer biology? And what is the cost of *not* doing so? This course will examine what engineering biology actually means; consider case studies of what kind of products, companies and innovations are already resulting from this new discipline and approach, from street lights made of luciferous trees to creating `clean¿ meat in the lab to engineering the immune system to fight cancer; and discuss what kind of systemic shifts will be required to make this happen in terms of politics, economics, and science.
Terms: Win | Units: 1 | Repeatable for credit | Grading: Letter or Credit/No Credit

BIOE 241: Biological Macromolecules (BIOC 241, BIOPHYS 241, SBIO 241)

The physical and chemical basis of macromolecular function. Topics include: forces that stabilize macromolecular structure and their complexes; thermodynamics and statistical mechanics of macromolecular folding, binding, and allostery; diffusional processes; kinetics of enzymatic processes; the relationship of these principles to practical application in experimental design and interpretation. The class emphasizes interactive learning, and is divided among lectures, in-class group problem solving, and discussion of current and classical literature. Enrollment limited to 30. Prerequisites: Background in biochemistry and physical chemistry recommended but material available for those with deficiency in these areas; undergraduates with consent of instructor only.
Terms: Spr | Units: 5 | Grading: Medical Option (Med-Ltr-CR/NC)
Instructors: ; Das, R. (PI); Ferrell, J. (PI)

BIOE 242: LAW, TECHNOLOGY, AND LIBERTY (ENGR 243)

New technologies from gene editing to networked computing have already transformed our economic and social structures and are increasingly changing what it means to be human. What role has law played in regulating and shaping these technologies? And what role can and should it play in the future? This seminar will consider these and related questions, focusing on new forms of networked production, the new landscape of security and scarcity, and the meaning of human nature and ecology in an era of rapid technological change. Readings will be drawn from a range of disciplines, including science and engineering, political economy, and law. The course will feature several guest speakers. There are no formal prerequisites in either engineering or law, but students should be committed to pursuing novel questions in an interdisciplinary context. The enrollment goal is to balance the class composition between law and non-law students. Elements used in grading: Attendance, Class Participation, Written Assignments. CONSENT APPLICATION: To apply for this course, students must complete and submit a Consent Application Form available on the SLS website (Click Courses at the bottom of the homepage and then click Consent of Instructor Forms). See Consent Application Form for instructions and submission deadline. This course is cross-listed with the School of Engineering (TBA). May be repeat for credit
Terms: not given this year | Units: 2 | Repeatable for credit | Grading: Letter or Credit/No Credit

BIOE 244: Advanced Frameworks and Approaches for Engineering Integrated Genetic Systems

Concepts and techniques for the design and implementation of engineered genetic systems. Topics covered include the quantitative exploration of tools that support (a) molecular component engineering, (b) abstraction and composition of functional genetic devices, (c) use of control and dynamical systems theory in device and systems design, (d) treatment of molecular "noise", (e) integration of DNA-encoded programs within cellular chassis, (f) designing for evolution, and (g) the use of standards in measurement, genetic layout architecture, and data exchange. Prerequisites: CME104, CME106, CHEM 33, BIO41, BIO42, BIOE41, BIOE42, and BIOE44 (or equivalents), or permission of the instructors.
Terms: Spr | Units: 4 | Grading: Letter or Credit/No Credit

BIOE 248: Neuroengineering Laboratory (NSUR 248)

Laboratory course exploring the basics of neuroelectrophysiology, neuroengineering, and closed-loop neural decoding. Course will use low-cost electrophysiological amplifying equipment and a real-time recording and computational system to measure neural action potentials from invertebrates, record electromyography from people, and create real-time neural decoders for closed-loop human movement control experiments. xFundamental properties of neurons and systems neuroscience will be experimentally verified. Engineering concepts surrounding neural decoders will be explored. Final project in the course will be a student-conceived in-depth experiment. Course information at: http://bioe248.stanford.edu
Terms: not given this year | Units: 3 | Grading: Letter or Credit/No Credit

BIOE 256: Technology Assessment and Regulation of Medical Devices (MS&E 256)

Regulatory approval and reimbursement for new health technologies are critical success factors for product commercialization. This course explores the regulatory and payer environment in the U.S. and abroad, as well as common methods of health technology assessment. Students will learn frameworks to identify factors relevant to the adoption of new health technologies, and the management of those factors in the design and development phases of bringing a product to market through case studies, guest speakers from government (FDA) and industry, and a course project.
Terms: Spr | Units: 3 | Grading: Letter or Credit/No Credit
Instructors: ; Pietzsch, J. (PI)

BIOE 260: Tissue Engineering (ORTHO 260)

Principles of tissue engineering and design strategies for practical applications for tissue repair. Topics include tissue morphogenesis, stem cells, biomaterials, controlled drug and gene delivery, and paper discussions. Students will learn skills for lab research through interactive lectures, paper discussions and research proposal development. Students work in small teams to work on develop research proposal for authentic tissue engineering problems. Lab sessions will teach techniques for culturing cells in 3D, as well as fabricating and characterizing hydrogels as 3D cell niche.
Terms: Spr | Units: 4 | Grading: Letter (ABCD/NP)
Instructors: ; Yang, F. (PI)

BIOE 261: Principles and Practice of Stem Cell Engineering (NSUR 261)

Quantitative models used to characterize incorporation of new cells into existing tissues emphasizing pluripotent cells such as embryonic and neural stem cells. Molecular methods to control stem cell decisions to self-renew, differentiate, die, or become quiescent. Practical, industrial, and ethical aspects of stem cell technology application. Final projects: team-reviewed grants and business proposals.
Terms: not given this year | Units: 3 | Grading: Letter or Credit/No Credit

BIOE 273: Biodesign for Digital Health (MED 273)

Health care is facing significant cross-industry challenges and opportunities created by a number of factors including: the increasing need for improved access to affordable, high-quality care; growing demand from consumers for greater control of their health and health data; the shift in focus from sick care to prevention and health optimization; aging demographics and the increased burden of chronic conditions; and new emphasis on real-world, measurable health outcomes for individuals and populations. Moreover, the delivery of health information and services is no longer tied to traditional brick and mortar hospitals and clinics: it has increasingly become "mobile," enabled by apps, sensors, wearables; simultaneously, it has been augmented and often revolutionized by emerging digital and information technologies, as well as by the data that these technologies generate. This multifactorial transformation presents opportunities for innovation across the entire cycle of care, from wellness, to acute and chronic diseases, to care at the end of life. But how does one approach innovation in digital health to address these health care challenges while ensuring the greatest chance of success? At Stanford Biodesign, we believe that innovation is a process that can be learned, practiced, and perfected; and, it starts with a need. In Biodesign for Digital Health, students will learn about digital health and the Biodesign needs-driven innovation process from over 50 industry experts. Over the course of ten weeks, these speakers join the teaching team in a dynamic classroom environment that includes lectures, panel discussions, and breakout sessions. These experts represent startups, corporations, venture capital firms, accelerators, research labs, health organizations, and more. Student teams will take actual digital and mobile health challenges and learn how to apply Biodesign innovation principles to research and evaluate needs, ideate solutions, and objectively assess them against key criteria for satisfying the needs. Teams take a hands-on approach with the support of need coaches and mentors. On the final day of class, teams present to a panel of digital health experts and compete for project extension funding. Limited enrollment, by application only. Friday section will be used for team projects and for scheduled workshops.
Terms: Aut | Units: 3 | Grading: Letter or Credit/No Credit
Instructors: ; Yock, P. (PI); Zanchi, M. (PI)

BIOE 279: Computational Biology: Structure and Organization of Biomolecules and Cells (BIOMEDIN 279, BIOPHYS 279, CME 279, CS 279)

Computational techniques for investigating and designing the three-dimensional structure and dynamics of biomolecules and cells. These computational methods play an increasingly important role in drug discovery, medicine, bioengineering, and molecular biology. Course topics include protein structure prediction, protein design, drug screening, molecular simulation, cellular-level simulation, image analysis for microscopy, and methods for solving structures from crystallography and electron microscopy data. Prerequisites: elementary programming background (CS 106A or equivalent) and an introductory course in biology or biochemistry.
Terms: Aut | Units: 3 | Grading: Letter or Credit/No Credit
Instructors: ; Dror, R. (PI); Huang, P. (PI)

BIOE 281: Biomechanics of Movement (ME 281)

Experimental techniques to study human and animal movement including motion capture systems, EMG, force plates, medical imaging, and animation. The mechanical properties of muscle and tendon, and quantitative analysis of musculoskeletal geometry. Projects and demonstrations emphasize applications of mechanics in sports, orthopedics, and rehabilitation.
Terms: Win | Units: 3 | Grading: Letter (ABCD/NP)
Instructors: ; Delp, S. (PI)

BIOE 282: Performance, Development, and Adaptation of Skeletal Muscle

Fundamentals of skeletal muscle by study of classical and recent research articles. Emphasis on the interactions between mechanics, biology, and electrophysiology in skeletal muscle performance, development, adaptation, control, and disease. Lab activities explore research methods discussed in class. Limited Enrollment. Applications due Friday, September 16th by 5pm. Applications available at http://bioe282.stanford.edu/. Prerequisites: engineering or biology core coursework. Fall (Cromie, Liske, Steele, Delp)
Terms: alternate years, given next year | Units: 3 | Grading: Letter (ABCD/NP)

BIOE 283: Mechanotransduction in Cells and Tissues (BIOPHYS 244, ME 244)

Mechanical cues play a critical role in development, normal functioning of cells and tissues, and various diseases. This course will cover what is known about cellular mechanotransduction, or the processes by which living cells sense and respond to physical cues such as physiological forces or mechanical properties of the tissue microenvironment. Experimental techniques and current areas of active investigation will be highlighted. This class is for graduate students only.
Terms: Aut | Units: 3 | Grading: Letter (ABCD/NP)
Instructors: ; Chaudhuri, O. (PI)

BIOE 285: Computational Modeling in the Cardiovascular System (CME 285, ME 285)

This course introduces computational modeling methods for cardiovascular blood flow and physiology. Topics in this course include analytical and computational methods for solutions of flow in deformable vessels, one-dimensional equations of blood flow, cardiovascular anatomy, lumped parameter models, vascular trees, scaling laws, biomechanics of the circulatory system, and 3D patient specific modeling with finite elements; course will provide an overview of the diagnosis and treatment of adult and congenital cardiovascular diseases and review recent research in the literature in a journal club format. Students will use SimVascular software to do clinically-oriented projects in patient specific blood flow simulations.
Terms: alternate years, given next year | Units: 3 | Grading: Letter or Credit/No Credit

BIOE 291: Principles and Practice of Optogenetics for Optical Control of Biological Tissues

Principles and practice of optical control of biological processes (optogenetics), emphasizing bioengineering approaches. Theoretical, historical, and current practice of the field. Requisite molecular-genetic, optoelectronic, behavioral, clinical, and ethical concepts, and mentored analysis and presentation of relevant papers. Final projects of research proposals and a laboratory component in BioX to provide hands-on training. Contact instructor before registering.
Terms: Aut | Units: 3 | Grading: Letter or Credit/No Credit
Instructors: ; Deisseroth, K. (PI)

BIOE 299B: Practical Training

Educational opportunities in high technology research and development labs in industry. Students engage in internship work and integrate that work into their academic program. Following internship work, students complete a research report outlining work activity, problems investigated, key results, and follow-up projects they expect to perform. Meets the requirements for curricular practical training for students on F-1 visas. Student is responsible for arranging own internship/employment and faculty sponsorship. Register under faculty sponsor's section number. All paperwork must be completed by student and faculty sponsor, as the student services office does not sponsor CPT. Students are allowed only two quarters of CPT per degree program. Course may be repeated twice.
Terms: Sum | Units: 1 | Repeatable for credit | Grading: Satisfactory/No Credit

BIOE 300A: Molecular and Cellular Bioengineering

The molecular and cellular bases of life from an engineering perspective. Analysis and engineering of biomolecular structure and dynamics, enzyme function, molecular interactions, metabolic pathways, signal transduction, and cellular mechanics. Quantitative primary literature. Prerequisites: CHEM 171 and BIO 41 or equivalents; MATLAB or an equivalent programming language.
Terms: Win | Units: 3 | Grading: Letter (ABCD/NP)
Instructors: ; Bintu, L. (PI)

BIOE 300B: Quantitative Physiology

An engineering approach to understanding physiological phenomenon.nCourse introduces weekly topics in biology and human physiology paired with a mathematical approach to modeling and understanding that week's topic. No strict prerequisites. No prior background in biology is required or assumed. Familiarity with linear algebra, statistics, and programming is recommended. Course information at: http://bioe300b.stanford.edu
Terms: Aut | Units: 3 | Grading: Letter (ABCD/NP)
Instructors: ; Nuyujukian, P. (PI)

BIOE 300C: Medical Devices, Diagnostics, and Pharmaceuticals: Technologies, Regulation, and Applications

Preference to Bioengineering graduate students. Major classes of technologies including imaging techniques, chemical diagnostics, drug design and delivery. Topics include pacemakers, fMRI, PCR, stents, and biomaterials. Principles, practical limitations, and feature trade-offs in clinical settings.
Terms: not given this year | Units: 3 | Grading: Letter (ABCD/NP)

BIOE 301A: Molecular and Cellular Engineering Lab

Preference to Bioengineering graduate students. Practical applications of biotechnology and molecular bioengineering including recombinant DNA techniques, molecular cloning, microbial cell growth and manipulation, and library screening. Emphasis is on experimental design and data analysis. Limited enrollment. Fall
Terms: Aut | Units: 2 | Grading: Letter (ABCD/NP)
Instructors: ; Bintu, L. (PI); Huang, P. (PI)

BIOE 301B: Clinical Needs and Technology

The goal of this course is to introduce bioengineering students to medical technology as it is used in current clinical practice, in the modern tertiary care, subspecialty hospital. Half of the course will be devoted to labs, in which small groups of students participate in hands-on experiences using advanced clinical technology in areas such as medical imaging, robotic surgery, and minimally invasive diagnosis and treatment. The second half of the course brings pairs of students and clinical faculty mentors together for a more in-depth, focused exposure to clinical care in one specific area. Final grades will be based on attendance, and presentations made by each pair of student to the class about their mentoring experience.
Terms: Win | Units: 2 | Grading: Satisfactory/No Credit
Instructors: ; Daniel, B. (PI)

BIOE 301C: Diagnostic Devices Lab (BIOE 201C)

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.
Terms: Spr | Units: 2 | Grading: Letter (ABCD/NP)
Instructors: ; Lee, J. (PI); Zou, X. (TA)

BIOE 301D: Microfluidic Device Laboratory (GENE 207)

This course exposes students to the design, fabrication, and testing of microfluidic devices for biological applications through combination of lectures and hands-on lab sessions. In teams of two, students will produce a working prototype devices designed to address specific design challenges within the biological community using photolithography, soft lithography, and imaging techniques.
Terms: Win | Units: 3-4 | Grading: Letter or Credit/No Credit
Instructors: ; Fordyce, P. (PI)

BIOE 311: Biophysics of Multi-cellular Systems and Amorphous Computing (BIOE 211, BIOPHYS 311, DBIO 211)

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.
Terms: not given this year | Units: 2-3 | Grading: Medical Option (Med-Ltr-CR/NC)

BIOE 313: Neuromorphics: Brains in Silicon (EE 207)

(Formerly EE 304) Neuromorphic systems run perceptual, cognitive and motor tasks in real-time on a network of highly interconnected nonlinear units. To maximize density and minimize energy, these units--like the brain's neurons--are heterogeneous and stochastic. The first half of the course covers learning algorithms that automatically synthesize network configurations to perform a desired computation on a given heterogeneous neural substrate. The second half of the course surveys system-on-a-chip architectures that efficiently realize highly interconnected networks and mixed analog-digital circuit designs that implement area and energy-efficient nonlinear units. Prerequisites: EE102A is required.
Terms: Spr | Units: 3 | Grading: Letter (ABCD/NP)

BIOE 326A: In Vivo MR: SpinPhysics and Spectroscopy (RAD 226A)

Collections of independent identical nuclear spins are well described by the classical vector model of magnetic resonance imaging, however, interaction among spins, as occur in many in vivo processes, require a more complete description. This course develops the basic physics and engineering principles of these interactions with emphasis on current research questions and clinical spectroscopy applications. Prerequisite: EE396b; familiarity with MRI, linear algebra recommended.
Terms: Win | Units: 3 | Repeatable for credit | Grading: Medical Option (Med-Ltr-CR/NC)
Instructors: ; Spielman, D. (PI)

BIOE 326B: In Vivo MR: Relaxation Theory and Contrast Mechanisms (RAD 226B)

Principles of nuclear magnetic resonance relaxation theory as applicable to in vivo processes with an emphasis on medical imaging. Topics: physics and mathematics of relaxation, relaxation times in normal and diseased tissues, magnetization transfer contrast, chemical exchange saturation transfer, MRI contrast agents, and hyperpolarized 13C. Prerequisites: BIOE 22A
Terms: Spr | Units: 3 | Grading: Medical Option (Med-Ltr-CR/NC)

BIOE 331: Protein Engineering (BIOE 231)

The design and engineering of biomolecules emphasizing proteins, antibodies, and enzymes. Combinatorial and rational methodologies, protein structure and function, and biophysical analyses of modified biomolecules. Clinically relevant examples from the literature and biotech industry. Prerequisite: basic biochemistry. Winter, Cochran
Terms: Win | Units: 3 | Grading: Letter (ABCD/NP)
Instructors: ; Lin, M. (PI)

BIOE 333: Interfacial Phenomena and Bionanotechnology

Control over and understanding of interfacial phenomena and colloidal science are the essential foundation of bionanotechnology. Key mathematical relationships derived by Laplace, Gibbs, Kelvin and Young are derived and explained, along with the thermodynamics of systems of large interfacial area. Forces controlling surface and interfacial phenomena and surfactant and biomacromolecule self-assembly are discussed. Protein folding/unfolding and aggregation, and nano- and microfluidics are elucidated in these terms. Students will gain insight into the interplay between physical and chemical properties of biomolecules. Spring, (Barron, A.)
Terms: not given this year | Units: 3 | Grading: Letter (ABCD/NP)

BIOE 334: Engineering Principles in Molecular Biology

The achievements and difficulties that exemplify the interface of theory and quantitative experiment. Topics include: bistability, cooperativity, robust adaptation, kinetic proofreading, analysis of fluctuations, sequence analysis, clustering, phylogenetics, maximum likelihood methods, and information theory. Sources include classic papers.
Terms: not given this year | Units: 3 | Grading: Letter (ABCD/NP)

BIOE 335: Molecular Motors I

Physical mechanisms of mechanochemical coupling in biological molecular motors, using F1 ATPase as the major model system. Applications of biochemistry, structure determination, single molecule tracking and manipulation, protein engineering, and computational techniques to the study of molecular motors.
Terms: not given this year | Units: 3 | Grading: Letter (ABCD/NP)

BIOE 337: Organismic Biophysics and Living Soft-matter

Integrated physical biology; from molecules to organisms. Tree of life, diversity of life forms. Multi-scale/hierarchical systems in biophysics, Hierarchical self-organization. Basic theory of squishy materials, colloidal physics. Phase transitions in living soft-matter. Experimental techniques in soft-matter physics. Active fluid models for living matter. Design of self-assembling and self-organizing, biomimetic supramolecular systems.
Terms: not given this year | Units: 3 | Grading: Letter (ABCD/NP)

BIOE 342A: Mechanobiology and Biofabrication Methods (BIOPHYS 342A, ME 342A)

Cell mechanobiology topics including cell structure, mechanical models, and chemo-mechanical signaling. Review and apply methods for controlling and analyzing the biomechanics of cells using traction force microscopy, AFM, micropatterning and cell stimulation. Practice and theory for the design and application of methods for quantitative cell mechanobiology.
Terms: not given this year | Units: 3 | Grading: Letter or Credit/No Credit

BIOE 355: Advanced Biochemical Engineering (CHEMENG 355)

Combines biological knowledge and methods with quantitative engineering principles. Quantitative review of biochemistry and metabolism; recombinant DNA technology and synthetic biology (metabolic engineering). The production of protein pharaceuticals as a paradigm for the application of chemical engineering principles to advanced process development within the framework of current business and regulatory requirements. Prerequisite: CHEMENG 181 (formerly 188) or BIOSCI 41, or equivalent.
Terms: Spr | Units: 3 | Grading: Letter or Credit/No Credit
Instructors: ; Swartz, J. (PI)

BIOE 361: Biomaterials in Regenerative Medicine (MATSCI 381)

Materials design and engineering for regenerative medicine. How materials interact with cells through their micro- and nanostructure, mechanical properties, degradation characteristics, surface chemistry, and biochemistry. Examples include novel materials for drug and gene delivery, materials for stem cell proliferation and differentiation, and tissue engineering scaffolds. Prerequisites: undergraduate chemistry, and cell/molecular biology or biochemistry.
Terms: Spr | Units: 3 | Grading: Letter (ABCD/NP)

BIOE 370: Microfluidic Device Laboratory

Fabrication of microfluidic devices for biological applications. Photolithography, soft lithography, and micromechanical valves and pumps. Emphasis is on device design, fabrication, and testing.
Terms: alternate years, given next year | Units: 2 | Grading: Letter or Credit/No Credit

BIOE 371: Global Biodesign: Medical Technology in an International Context (MED 271)

This course ( BIOE371, MED271) exposes students to the challenges and opportunities of developing and implementing innovative health technologies to help patients around the world. Non-communicable diseases, such as metabolic and chronic respiratory disease, now account for 7 in 10 deaths worldwide, creating the need for innovative health technologies that work across diverse global markets. At the beginning of the quarter, the course will provide an overview of the dynamic global health technology industry. Next, faculty members, guest experts, and students will discuss key differences and similarities when commercializing new products in the for-profit health technology sector across six important regions: the US and Europe, China and Japan, and India and Brazil. Finally, the course will explore critical ¿global health¿ issues that transcend international borders and how technology can be leveraged to address them. This section will culminate with an interactive debate focused on whether for-profit, nonprofit, or hybrid models are best for implementing sustainable global health solutions. The last class will be devoted to synthesis, reflection, and a discussion of career opportunities in the global health technology field.
Terms: Aut | Units: 1 | Grading: Medical Option (Med-Ltr-CR/NC)

BIOE 374A: Biodesign Innovation: Needs Finding and Concept Creation (ME 368A, MED 272A)

In this two-quarter course series ( BIOE 374A/B, MED 272A/B, ME 368A/B, OIT 384/5), multidisciplinary student teams identify real-world unmet healthcare needs, invent new health technologies to address them, and plan for their implementation into patient care. During the first quarter (winter), students select and characterize an important unmet healthcare problem, validate it through primary interviews and secondary research, and then brainstorm and screen initial technology-based solutions. In the second quarter (spring), teams select a lead solution and move it toward the market through prototyping, technical re-risking, strategies to address healthcare-specific requirements (regulation, reimbursement), and business planning. Final presentations in winter and spring are made to a panel of prominent health technology experts and/or investors. Class sessions include faculty-led instruction and case studies, coaching sessions by industry specialists, expert guest lecturers, and interactive team meetings. Enrollment is by application only, and students are expected to participate in both quarters of the course. Visit http://biodesign.stanford.edu/programs/stanford-courses/biodesign-innovation.html to access the application, examples of past projects, and student testimonials. More information about Stanford Biodesign, which has led to the creation of nearly 50 venture-backed healthcare companies and has helped hundreds of student launch health technology careers, can be found at http://biodesign.stanford.edu/.
Terms: Win | Units: 4 | Grading: Medical Option (Med-Ltr-CR/NC)

BIOE 374B: Biodesign Innovation: Concept Development and Implementation (ME 368B, MED 272B)

In this two-quarter course series ( BIOE 374A/B, MED 272A/B, ME 368A/B, OIT 384/5), multidisciplinary student teams identify real-world unmet healthcare needs, invent new health technologies to address them, and plan for their implementation into patient care. During the first quarter (winter), students select and characterize an important unmet healthcare problem, validate it through primary interviews and secondary research, and then brainstorm and screen initial technology-based solutions. In the second quarter (spring), teams select a lead solution and move it toward the market through prototyping, technical re-risking, strategies to address healthcare-specific requirements (regulation, reimbursement), and business planning. Final presentations in winter and spring are made to a panel of prominent health technology experts and/or investors. Class sessions include faculty-led instruction and case studies, coaching sessions by industry specialists, expert guest lecturers, and interactive team meetings. Enrollment is by application only, and students are expected to participate in both quarters of the course. Visit http://biodesign.stanford.edu/programs/stanford-courses/biodesign-innovation.html to access the application, examples of past projects, and student testimonials. More information about Stanford Biodesign, which has led to the creation of nearly 50 venture-backed healthcare companies and has helped hundreds of student launch health technology careers, can be found at http://biodesign.stanford.edu/.
Terms: Spr | Units: 4 | Grading: Medical Option (Med-Ltr-CR/NC)

BIOE 375A: Biodesign Innovation: Needs Finding and Concept Creation

Enrollment limited to SCPD students. Two quarter sequence. Inventing new medical devices and instrumentation, including: methods of validating medical needs; techniques for analyzing intellectual property; basics of regulatory (FDA) and reimbursement planning; brainstorming and early prototyping. Guest lecturers and practical demonstrations.
Terms: not given this year | Units: 2 | Grading: Letter (ABCD/NP)

BIOE 375B: Biodesign Innovation: Concept Development and Implementation

Enrollment limited to SCPD students. Two quarter sequence. How to take a medical device invention forward from early concept to technology translation and development. Topics include prototyping; patent strategies; advanced planning for reimbursement and FDA approval; choosing translation route (licensing versus start-up); ethical issues including conflict of interest; fundraising approaches and cash requirements; essentials of writing a business or research plan; strategies for assembling a development team. Prerequisite: BIOE 375A
Terms: not given this year | Units: 2 | Grading: Letter (ABCD/NP)

BIOE 376: Startup Garage: Design

A hands-on, project-based course, in which teams identify and work with users, domain experts, and industry participants to identify an unmet customer need, design new products or services that meet that need, and develop business models to support the creation and launch of startup products or services. This course integrates methods from human-centered design, lean startup, and business model planning. Each team will conceive, design, build, and field-test critical aspects of both the product or service and the business model.
Terms: Aut | Units: 4 | Grading: Letter or Credit/No Credit

BIOE 377: Startup Garage: Testing and Launch

STRAMGT 356/BIOE 376 teams that concluded at the end of fall quarter that their preliminary product or service and business model suggest a path to viability, may continue with STRAMGT 366/BIOE 377 in winter quarter. Teams develop more elaborate versions of their product/service and business model, perform a series of experiments to test key hypotheses about their product and business model, and prepare and present an investor pitch for a seed round of financing to a panel of seasoned investors and entrepreneurs.
Terms: Win | Units: 4 | Grading: Letter or Credit/No Credit

BIOE 381: Orthopaedic Bioengineering (ME 381)

Engineering approaches applied to the musculoskeletal system in the context of surgical and medical care. Fundamental anatomy and physiology. Material and structural characteristics of hard and soft connective tissues and organ systems, and the role of mechanics in normal development and pathogenesis. Engineering methods used in the evaluation and planning of orthopaedic procedures, surgery, and devices.
Terms: Aut | Units: 3 | Grading: Letter (ABCD/NP)
Instructors: ; Levenston, M. (PI)

BIOE 390: Introduction to Bioengineering Research (MED 289)

Preference to medical and bioengineering graduate students with first preference given to Bioengineering Scholarly Concentration medical students. Bioengineering is an interdisciplinary field that leverages the disciplines of biology, medicine, and engineering to understand living systems, and engineer biological systems and improve engineering designs and human and environmental health. Students and faculty make presentations during the course. Students expected to make presentations, complete a short paper, read selected articles, and take quizzes on the material.
Terms: Aut | Units: 1-2 | Repeatable for credit | Grading: Medical Satisfactory/No Credit

BIOE 391: Directed Study

May be used to prepare for research during a later quarter in 392. Faculty sponsor required. May be repeated for credit.
Terms: Aut, Win, Spr, Sum | Units: 1-6 | Repeatable for credit | Grading: Satisfactory/No Credit

BIOE 392: Directed Investigation

For Bioengineering graduate students. Previous work in 391 may be required for background; faculty sponsor required. May be repeated for credit.
Terms: Aut, Win, Spr, Sum | Units: 1-10 | Repeatable for credit | Grading: Satisfactory/No Credit
Instructors: ; Airan, R. (PI); Alizadeh, A. (PI); Altman, R. (PI); Andriacchi, T. (PI); Annes, J. (PI); Appel, E. (PI); Baker, J. (PI); Bammer, R. (PI); Bao, Z. (PI); Barron, A. (PI); Batzoglou, S. (PI); Bertozzi, C. (PI); Bintu, L. (PI); Boahen, K. (PI); Bowden, A. (PI); Bryant, Z. (PI); Butte, A. (PI); Camarillo, D. (PI); Carter, D. (PI); Chang, H. (PI); Chaudhuri, O. (PI); Chen, X. (PI); Cheng, C. (PI); Chichilnisky, E. (PI); Chiu, W. (PI); Cochran, J. (PI); Contag, C. (PI); Covert, M. (PI); Criddle, C. (PI); Curtis, C. (PI); Dabiri, J. (PI); Dahl, J. (PI); Das, R. (PI); De Leo, G. (PI); Deisseroth, K. (PI); Delp, S. (PI); Demirci, U. (PI); Dionne, J. (PI); Elias, J. (PI); Endy, D. (PI); Engleman, E. (PI); Ennis, D. (PI); Etkin, A. (PI); Fahrig, R. (PI); Feinstein, J. (PI); Feng, L. (PI); Fire, A. (PI); Fischbach, M. (PI); Fordyce, P. (PI); Gambhir, S. (PI); Ganguli, S. (PI); Garcia, C. (PI); Giaccia, A. (PI); Glenn, J. (PI); Glover, G. (PI); Gold, G. (PI); Goodman, S. (PI); Graves, E. (PI); Greenleaf, W. (PI); Hargreaves, B. (PI); Heilshorn, S. (PI); Heller, S. (PI); Herschlag, D. (PI); Huang, K. (PI); Huang, P. (PI); Idoyaga, J. (PI); Ingelsson, E. (PI); Jarosz, D. (PI); Jonikas, M. (PI); Khuri-Yakub, B. (PI); Kim, P. (PI); Kovacs, G. (PI); Krasnow, M. (PI); Krummel, T. (PI); Kuhl, E. (PI); Kuo, C. (PI); Lee, J. (PI); Leskovec, J. (PI); Levenston, M. (PI); Levin, C. (PI); Lin, M. (PI); Liphardt, J. (PI); Longaker, M. (PI); Malenka, R. (PI); Marsden, A. (PI); Monje-Deisseroth, M. (PI); Montgomery, S. (PI); Moore, T. (PI); Nishimura, D. (PI); Nolan, G. (PI); Nuyujukian, P. (PI); O'Brien, L. (PI); Okamura, A. (PI); Pauly, J. (PI); Pauly, K. (PI); Pelc, N. (PI); Petrov, D. (PI); Plevritis, S. (PI); Prakash, M. (PI); Pruitt, B. (PI); Qi, S. (PI); Quake, S. (PI); Rando, T. (PI); Raymond, J. (PI); Red-Horse, K. (PI); Reddy, S. (PI); Reijo Pera, R. (PI); Relman, D. (PI); Riedel-Kruse, I. (PI); Rose, J. (PI); Rutt, B. (PI); Saggar, M. (PI); Sanger, T. (PI); Santa Maria, P. (PI); Sapolsky, R. (PI); Sattely, E. (PI); Schnitzer, M. (PI); Scott, M. (PI); Shenoy, K. (PI); Smolke, C. (PI); Soh, H. (PI); Soltesz, I. (PI); Sonnenburg, J. (PI); Spielman, D. (PI); Sunwoo, J. (PI); Swartz, J. (PI); Taylor, C. (PI); Theriot, J. (PI); Wall, D. (PI); Wang, B. (PI); Wang, P. (PI); Wang, S. (PI); Weissman, I. (PI); Wernig, M. (PI); Woo, J. (PI); Wu, J. (PI); Wu, S. (PI); Wyss-Coray, T. (PI); Xing, L. (PI); Yang, F. (PI); Yang, Y. (PI); Yock, P. (PI); Zeineh, M. (PI); Zenios, S. (PI)

BIOE 393: Bioengineering Departmental Research Colloquium

Required Bioengineering department colloquium for first year Ph.D. and M.S. students. Topics include applications of engineering to biology, medicine, biotechnology, and medical technology, including biodesign and devices, molecular and cellular engineering, regenerative medicine and tissue engineering, biomedical imaging, and biomedical computation.
Terms: Aut, Win, Spr | Units: 1 | Repeatable for credit | Grading: Satisfactory/No Credit
Instructors: ; Endy, D. (PI)

BIOE 395: Problem choice and decision trees in science and engineering

Science and engineering researchers often spend days choosing a problem and years solving it. However, the problem initially chosen and subsequent course adjustments made along the project's decision tree, have an outsize influence on its likelihood of success and ultimate impact. This course will establish a framework for choosing problems and navigating a project's decision tree, emphasizing the role of intuition-building exercises and a stepwise analysis of assumptions. No prior knowledge is required.
Terms: Spr | Units: 2 | Grading: Letter (ABCD/NP)

BIOE 450: Advances in Biotechnology (CHEMENG 450)

Overview of cutting edge advances in biotechnology with a focus on therapeutic and health-related topics. Academic and industrial speakers from a range of areas including protein engineering, immuno-oncology, DNA sequencing, the microbiome, phamacogenomics, industrial enzymes, synthetic biology, and more. Course is designed for students interested in pursuing a career in the biotech industry
Terms: Spr | Units: 3 | Grading: Letter or Credit/No Credit

BIOE 454: Synthetic Biology and Metabolic Engineering (CHEMENG 454)

Principles for the design and optimization of new biological systems. Development of new enzymes, metabolic pathways, other metabolic systems, and communication systems among organisms. Example applications include the production of central metabolites, amino acids, pharmaceutical proteins, and isoprenoids. Economic challenges and quantitative assessment of metabolic performance. Pre- or corequisite: CHEMENG 355 or equivalent.
Terms: not given this year | Units: 3 | Grading: Letter or Credit/No Credit

BIOE 459: Frontiers in Interdisciplinary Biosciences (BIO 459, BIOC 459, CHEM 459, CHEMENG 459, PSYCH 459)

Students register through their affiliated department; otherwise register for CHEMENG 459. For specialists and non-specialists. Sponsored by the Stanford BioX Program. Three seminars per quarter address scientific and technical themes related to interdisciplinary approaches in bioengineering, medicine, and the chemical, physical, and biological sciences. Leading investigators from Stanford and the world present breakthroughs and endeavors that cut across core disciplines. Pre-seminars introduce basic concepts and background for non-experts. Registered students attend all pre-seminars; others welcome. See http://biox.stanford.edu/courses/459.html. Recommended: basic mathematics, biology, chemistry, and physics.
Terms: Aut, Win, Spr | Units: 1 | Repeatable for credit | Grading: Medical Satisfactory/No Credit

BIOE 485: Modeling and Simulation of Human Movement (ME 485)

Direct experience with the computational tools used to create simulations of human movement. Lecture/labs on animation of movement; kinematic models of joints; forward dynamic simulation; computational models of muscles, tendons, and ligaments; creation of models from medical images; control of dynamic simulations; collision detection and contact models. Prerequisite: 281, 331A,B, or equivalent.
Terms: Spr | Units: 3 | Grading: Letter or Credit/No Credit

BIOE 500: Thesis (Ph.D.)

(Staff)
Terms: Aut, Win, Spr, Sum | Units: 1-15 | Repeatable for credit | Grading: Satisfactory/No Credit
Instructors: ; Alizadeh, A. (PI); Altman, R. (PI); Andriacchi, T. (PI); Appel, E. (PI); Baker, J. (PI); Bammer, R. (PI); Bao, Z. (PI); Barron, A. (PI); Batzoglou, S. (PI); Bertozzi, C. (PI); Bintu, L. (PI); Boahen, K. (PI); Bryant, Z. (PI); Butte, A. (PI); Camarillo, D. (PI); Carter, D. (PI); Chang, H. (PI); Chaudhuri, O. (PI); Cheng, C. (PI); Chichilnisky, E. (PI); Cochran, J. (PI); Contag, C. (PI); Covert, M. (PI); Dabiri, J. (PI); Dahl, J. (PI); Deisseroth, K. (PI); Delp, S. (PI); Demirci, U. (PI); Elias, J. (PI); Endy, D. (PI); Engleman, E. (PI); Etkin, A. (PI); Fahrig, R. (PI); Feinstein, J. (PI); Feng, L. (PI); Fire, A. (PI); Fischbach, M. (PI); Fordyce, P. (PI); Gambhir, S. (PI); Ganguli, S. (PI); Garcia, C. (PI); Glenn, J. (PI); Glover, G. (PI); Gold, G. (PI); Goodman, S. (PI); Graves, E. (PI); Greenleaf, W. (PI); Hargreaves, B. (PI); Heilshorn, S. (PI); Huang, K. (PI); Huang, P. (PI); Khuri-Yakub, B. (PI); Kim, P. (PI); Kovacs, G. (PI); Krummel, T. (PI); Kuhl, E. (PI); Lee, J. (PI); Levenston, M. (PI); Levin, C. (PI); Lin, M. (PI); Liphardt, J. (PI); Longaker, M. (PI); Montgomery, S. (PI); Moore, T. (PI); Nishimura, D. (PI); Nuyujukian, P. (PI); Okamura, A. (PI); Pauly, J. (PI); Pauly, K. (PI); Pelc, N. (PI); Plevritis, S. (PI); Prakash, M. (PI); Pruitt, B. (PI); Qi, S. (PI); Quake, S. (PI); Rando, T. (PI); Raymond, J. (PI); Reijo Pera, R. (PI); Relman, D. (PI); Riedel-Kruse, I. (PI); Rose, J. (PI); Sanger, T. (PI); Sapolsky, R. (PI); Sattely, E. (PI); Schnitzer, M. (PI); Scott, M. (PI); Shenoy, K. (PI); Smolke, C. (PI); Soh, H. (PI); Spielman, D. (PI); Swartz, J. (PI); Taylor, C. (PI); Theriot, J. (PI); Wang, B. (PI); Wang, P. (PI); Weissman, I. (PI); Wernig, M. (PI); Woo, J. (PI); Wu, J. (PI); Xing, L. (PI); Yang, F. (PI); Yock, P. (PI); Zenios, S. (PI)

BIOE 802: TGR Dissertation

(Staff)
Terms: Aut, Win, Spr, Sum | Units: 0 | Repeatable for credit | Grading: TGR
Instructors: ; Airan, R. (PI); Alizadeh, A. (PI); Altman, R. (PI); Andriacchi, T. (PI); Appel, E. (PI); Baker, J. (PI); Bammer, R. (PI); Bao, Z. (PI); Barron, A. (PI); Batzoglou, S. (PI); Bertozzi, C. (PI); Bintu, L. (PI); Boahen, K. (PI); Bowden, A. (PI); Bryant, Z. (PI); Butte, A. (PI); Camarillo, D. (PI); Carter, D. (PI); Chang, H. (PI); Chaudhuri, O. (PI); Cheng, C. (PI); Chichilnisky, E. (PI); Chiu, W. (PI); Cochran, J. (PI); Contag, C. (PI); Covert, M. (PI); Curtis, C. (PI); Dabiri, J. (PI); Dahl, J. (PI); Deisseroth, K. (PI); Delp, S. (PI); Demirci, U. (PI); Elias, J. (PI); Endy, D. (PI); Engleman, E. (PI); Etkin, A. (PI); Fahrig, R. (PI); Feinstein, J. (PI); Feng, L. (PI); Fire, A. (PI); Fischbach, M. (PI); Fordyce, P. (PI); Gambhir, S. (PI); Ganguli, S. (PI); Garcia, C. (PI); Glenn, J. (PI); Glover, G. (PI); Gold, G. (PI); Goodman, S. (PI); Graves, E. (PI); Greenleaf, W. (PI); Hargreaves, B. (PI); Heilshorn, S. (PI); Huang, K. (PI); Huang, P. (PI); Ingelsson, E. (PI); Jarosz, D. (PI); Khuri-Yakub, B. (PI); Kim, P. (PI); Kovacs, G. (PI); Krummel, T. (PI); Kuhl, E. (PI); Lee, J. (PI); Leskovec, J. (PI); Levenston, M. (PI); Levin, C. (PI); Lin, M. (PI); Liphardt, J. (PI); Longaker, M. (PI); Marsden, A. (PI); Montgomery, S. (PI); Moore, T. (PI); Nishimura, D. (PI); Nolan, G. (PI); Nuyujukian, P. (PI); Okamura, A. (PI); Pauly, J. (PI); Pauly, K. (PI); Pelc, N. (PI); Plevritis, S. (PI); Prakash, M. (PI); Pruitt, B. (PI); Qi, S. (PI); Quake, S. (PI); Rando, T. (PI); Raymond, J. (PI); Reijo Pera, R. (PI); Relman, D. (PI); Riedel-Kruse, I. (PI); Rose, J. (PI); Sanger, T. (PI); Sapolsky, R. (PI); Sattely, E. (PI); Schnitzer, M. (PI); Scott, M. (PI); Shenoy, K. (PI); Smolke, C. (PI); Soh, H. (PI); Soltesz, I. (PI); Sonnenburg, J. (PI); Spielman, D. (PI); Sunwoo, J. (PI); Swartz, J. (PI); Taylor, C. (PI); Theriot, J. (PI); Wall, D. (PI); Wang, B. (PI); Wang, P. (PI); Wang, S. (PI); Weissman, I. (PI); Wernig, M. (PI); Woo, J. (PI); Wu, J. (PI); Wyss-Coray, T. (PI); Xing, L. (PI); Yang, F. (PI); Yock, P. (PI); Zarins, C. (PI); Zeineh, M. (PI); Zenios, S. (PI)
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