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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 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 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 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 196: INTERACTIVE MEDIA AND GAMES (BIOPHYS 196)

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: Aut, Win, Spr | Units: 1 | Repeatable for credit | Grading: Satisfactory/No Credit
Instructors: ; Riedel-Kruse, I. (PI)

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 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 222: Instrumentation and Applications for Multi-modality Molecular Imaging of Living Subjects (RAD 222)

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

BIOE 273: Biodesign for Mobile 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, and other mobile devices, 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 mobile 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 Mobile Health, students will learn about mobile 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 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 mobile 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

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.
Terms: Aut | Units: 3 | Grading: Letter or Credit/No Credit
Instructors: ; Chaudhuri, O. (PI)

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 300B: Engineering Concepts Applied to Physiology

This course focuses on engineering approaches to quantifying, modeling and controlling the physiology and pathophysiology of complex systems, from the level of individual cells to tissue, organ and multi-organ systems.
Terms: Aut | 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: Spr | 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 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 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: ; 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); 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); 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, A. (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); Herschlag, D. (PI); Huang, K. (PI); Huang, P. (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); Levenston, M. (PI); Levin, C. (PI); Lin, M. (PI); Liphardt, J. (PI); Longaker, M. (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); 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); 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); Spielman, D. (PI); Sunwoo, J. (PI); Swartz, J. (PI); Taylor, C. (PI); Theriot, J. (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); Xing, L. (PI); Yang, F. (PI); Yock, P. (PI); Zeineh, M. (PI); Zenios, S. (PI)

BIOE 393: Bioengineering Departmental Research Colloquium

Bioengineering department labs at Stanford present recent research projects and results. Guest lecturers. 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. Aut, Win, Spr (Lin, Riedel-Kruse, Barron)
Terms: Aut, Win, Spr | Units: 1 | Repeatable for credit | Grading: Satisfactory/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
Instructors: ; Robertson, C. (PI)

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, A. (PI); Engleman, E. (PI); Etkin, A. (PI); Fahrig, R. (PI); Feinstein, J. (PI); Feng, L. (PI); Fire, A. (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: ; 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, A. (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); Jarosz, D. (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); 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); Spielman, D. (PI); Sunwoo, J. (PI); Swartz, J. (PI); Taylor, C. (PI); Theriot, J. (PI); Wang, B. (PI); Wang, P. (PI); Wang, S. (PI); Weissman, I. (PI); Wernig, M. (PI); Woo, J. (PI); Wu, J. (PI); Xing, L. (PI); Yang, F. (PI); Yock, P. (PI); Zarins, C. (PI); Zenios, S. (PI)
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