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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.
Terms: Aut, Spr | Units: 4 | UG Reqs: WAY-SMA
Instructors: ; Endy, D. (PI); Shih, J. (PI); Smolke, C. (PI); Dabija, D. (TA); Hines, A. (TA); Kim, J. (TA); Xiang, J. (TA)

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 41, BIO 42; or consent of instructor.
Terms: Aut | Units: 4 | UG Reqs: WAY-AQR
Instructors: ; Covert, M. (PI); Mason, J. (TA); McHugh, D. (TA)

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. Lab component reinforces practical skills including genetic design and construction, basic prototyping, and instrumentation. 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
Instructors: ; Camarillo, D. (PI); Lin, M. (PI); Sanchez, G. (PI); Shih, J. (PI); Angulo, B. (TA); Hanna, F. (TA); Yip, M. (TA)

BIOE 191: Bioengineering Problems and Experimental Investigation

Directed study and research for undergraduates on a subject of mutual interest to student and instructor. Prerequisites: consent of instructor and adviser. (Staff)
Terms: Aut, Win, Spr, Sum | Units: 1-5 | Repeatable for credit
Instructors: ; Altman, R. (PI); Andriacchi, T. (PI); Bammer, R. (PI); Barron, A. (PI); Batzoglou, S. (PI); Boahen, K. (PI); Bryant, Z. (PI); Butte, A. (PI); Camarillo, D. (PI); Carter, D. (PI); Cochran, J. (PI); Covert, M. (PI); Deisseroth, K. (PI); Delp, S. (PI); Endy, D. (PI); Fahrig, R. (PI); Feinstein, J. (PI); Fisher, D. (PI); Gambhir, S. (PI); Gold, G. (PI); Goodman, S. (PI); Graves, E. (PI); Hargreaves, B. (PI); Heilshorn, S. (PI); Huang, K. (PI); Jacobs, C. (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); Moore, T. (PI); Pauly, K. (PI); Pelc, N. (PI); Plevritis, S. (PI); Prakash, M. (PI); Quake, S. (PI); Riedel-Kruse, I. (PI); Sanger, T. (PI); Sapolsky, R. (PI); Schnitzer, M. (PI); Scott, M. (PI); Shenoy, K. (PI); Smolke, C. (PI); Spielman, D. (PI); Swartz, J. (PI); Taylor, C. (PI); Wu, J. (PI); Yang, F. (PI); Yock, P. (PI); Zenios, S. (PI); Negrette, J. (GP); Woo, Y. (GP)

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 15 times (up to 60 units total)
Instructors: ; Barres, B. (PI); Blau, H. (PI); Diehn, M. (PI); Elias, J. (PI); Hanawalt, P. (PI); Okamura, A. (PI); Weissman, I. (PI); Wu, J. (PI); Yang, Y. (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 41, BIO 42; or consent of instructor.
Terms: Aut | Units: 4
Instructors: ; Covert, M. (PI); Mason, J. (TA); McHugh, D. (TA)

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, Gibbs Sampling, 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. Prerequisites: programming skills; consent of instructor for 3 units.
Terms: Aut | Units: 3-4
Instructors: ; Altman, R. (PI); Poznik, D. (GP); Szabo, L. (GP)

BIOE 222A: Multimodality Molecular Imaging in Living Subjects I (RAD 222A)

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, and Optics. Covers basics of instrumentation physics, and the origin and properties of the signal generation.
Terms: Aut | Units: 4
Instructors: ; Levin, C. (PI); Moseley, M. (PI); Chang, C. (TA)

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: Aut | Units: 3
Instructors: ; Fahrig, R. (PI); Pelc, N. (PI); Yao, Y. (TA)

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: Aut | Units: 4
Instructors: ; Endy, D. (PI); Smolke, C. (PI); Galanie, S. (TA)

BIOE 273: BIODESIGN FOR MOBILE HEALTH (MED 273)

This seminar examines the emerging Mobile Health industry. Mobile Health is the provision of health services and information via mobile technologies such as mobile phones and wearable sensors. Faculty from Stanford University and other Academic Institutions and guest lecturers from the Mobile Health industry discuss the driving needs, opportunities and challenges that characterize the emerging Mobile Health innovation landscape, and present an overview of the technologies, initiatives and companies that are transforming the way we access health care today.
Terms: Aut | Units: 1-2
Instructors: ; Wang, P. (PI); Yock, P. (PI); Zanchi, M. (PI); Daniel, A. (GP)

BIOE 283: Mechanotransduction in Cells and Tissues (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
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
Instructors: ; Deisseroth, K. (PI); Ferenczi, E. (TA)

BIOE 300B: Physiology and Tissue Engineering

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. (Covert)
Terms: Aut | Units: 3
Instructors: ; Covert, M. (PI); Madl, C. (TA); Ye, A. (TA)

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 (Cochran)
Terms: Aut | Units: 2
Instructors: ; Cochran, V. (PI); Cherf, G. (TA); Mitchell, A. (TA); Wang, T. (TA)

BIOE 311: Biophysics of Multi-cellular Systems and Amorphous Computing

This course 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 will discuss relevant literature and will be introduced to and apply pertinent mathematical and biophysical modeling approaches to various aspect of multi-cellular systems.
Terms: Aut | Units: 2-3
Instructors: ; Riedel-Kruse, I. (PI); Jin, X. (TA)

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
Instructors: ; Zenios, S. (PI); Gur, S. (SI); Lin, R. (SI); Siegelman, R. (SI); Price, R. (GP); Woo, Y. (GP)

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
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 5 times (up to 10 units total)
Instructors: ; Gold, G. (PI); Wang, P. (PI)

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
Instructors: ; Altman, R. (PI); Bammer, R. (PI); Barron, A. (PI); Batzoglou, S. (PI); Boahen, K. (PI); Bryant, Z. (PI); Butte, A. (PI); Camarillo, D. (PI); Carter, D. (PI); Cochran, J. (PI); Covert, M. (PI); Deisseroth, K. (PI); Delp, S. (PI); Endy, D. (PI); Fahrig, R. (PI); Feinstein, J. (PI); Gambhir, S. (PI); Gold, G. (PI); Goodman, S. (PI); Graves, E. (PI); Hargreaves, B. (PI); Heilshorn, S. (PI); Huang, K. (PI); Jacobs, C. (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); Moore, T. (PI); Pauly, K. (PI); Pelc, N. (PI); Plevritis, S. (PI); Prakash, M. (PI); Quake, S. (PI); Riedel-Kruse, I. (PI); Sapolsky, R. (PI); Schnitzer, M. (PI); Scott, M. (PI); Shenoy, K. (PI); Smolke, C. (PI); Spielman, D. (PI); Swartz, J. (PI); Taylor, C. (PI); Wu, J. (PI); Yang, F. (PI); Yock, P. (PI); Zenios, S. (PI); Negrette, J. (GP); Woo, Y. (GP)

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
Instructors: ; Alizadeh, A. (PI); Altman, R. (PI); Andriacchi, T. (PI); Bammer, R. (PI); Barron, A. (PI); Batzoglou, S. (PI); Boahen, K. (PI); Bryant, Z. (PI); Butte, A. (PI); Camarillo, D. (PI); Carter, D. (PI); Cochran, J. (PI); Covert, M. (PI); Deisseroth, K. (PI); Delp, S. (PI); Endy, D. (PI); Etkin, A. (PI); Fahrig, R. (PI); Feinstein, J. (PI); Feng, L. (PI); Fire, A. (PI); Gambhir, S. (PI); Garcia, C. (PI); Gold, G. (PI); Goodman, S. (PI); Graves, E. (PI); Hargreaves, B. (PI); Heilshorn, S. (PI); Huang, K. (PI); Jacobs, C. (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); Moore, T. (PI); Pauly, J. (PI); Pauly, K. (PI); Pelc, N. (PI); Plevritis, S. (PI); Prakash, M. (PI); Pruitt, B. (PI); Quake, S. (PI); Reijo Pera, R. (PI); Relman, D. (PI); Riedel-Kruse, I. (PI); Sapolsky, R. (PI); Schnitzer, M. (PI); Scott, M. (PI); Shenoy, K. (PI); Smolke, C. (PI); Spielman, D. (PI); Swartz, J. (PI); Taylor, C. (PI); Wu, J. (PI); Yang, F. (PI); Yock, P. (PI); Zenios, S. (PI); Negrette, J. (GP); Woo, Y. (GP)

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
Instructors: ; Boahen, K. (PI); Lee, J. (PI); Liphardt, J. (PI); Quake, S. (PI); Yang, F. (PI)

BIOE 500: Thesis (Ph.D.)

(Staff)
Terms: Aut, Win, Spr, Sum | Units: 1-15 | Repeatable for credit
Instructors: ; Altman, R. (PI); Bammer, R. (PI); Barron, A. (PI); Batzoglou, S. (PI); Boahen, K. (PI); Bryant, Z. (PI); Butte, A. (PI); Camarillo, D. (PI); Carter, D. (PI); Cochran, J. (PI); Covert, M. (PI); Deisseroth, K. (PI); Delp, S. (PI); Endy, D. (PI); Fahrig, R. (PI); Feinstein, J. (PI); Gambhir, S. (PI); Garcia, C. (PI); Gold, G. (PI); Goodman, S. (PI); Graves, E. (PI); Hargreaves, B. (PI); Heilshorn, S. (PI); Huang, K. (PI); Jacobs, C. (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); Moore, T. (PI); Pauly, J. (PI); Pauly, K. (PI); Pelc, N. (PI); Plevritis, S. (PI); Prakash, M. (PI); Pruitt, B. (PI); Quake, S. (PI); Relman, D. (PI); Riedel-Kruse, I. (PI); Rose, J. (PI); Sanger, T. (PI); Sapolsky, R. (PI); Schnitzer, M. (PI); Scott, M. (PI); Shenoy, K. (PI); Smolke, C. (PI); Spielman, D. (PI); Swartz, J. (PI); Taylor, C. (PI); Wu, J. (PI); Yang, F. (PI); Yock, P. (PI); Zenios, S. (PI); Negrette, J. (GP); Woo, Y. (GP)

BIOE 802: TGR Dissertation

(Staff)
Terms: Aut, Win, Spr, Sum | Units: 0 | Repeatable for credit
Instructors: ; Altman, R. (PI); Baker, J. (PI); Bammer, R. (PI); Barron, A. (PI); Batzoglou, S. (PI); Boahen, K. (PI); Bryant, Z. (PI); Butte, A. (PI); Camarillo, D. (PI); Carter, D. (PI); Chang, H. (PI); Cochran, J. (PI); Contag, C. (PI); Covert, M. (PI); Deisseroth, K. (PI); Delp, S. (PI); Endy, D. (PI); Etkin, A. (PI); Fahrig, R. (PI); Feinstein, J. (PI); Gambhir, S. (PI); Ganguli, S. (PI); Garcia, C. (PI); Glover, G. (PI); Gold, G. (PI); Goodman, S. (PI); Graves, E. (PI); Hargreaves, B. (PI); Heilshorn, S. (PI); Huang, K. (PI); Jacobs, C. (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); Moore, T. (PI); Pauly, K. (PI); Pelc, N. (PI); Plevritis, S. (PI); Prakash, M. (PI); Quake, S. (PI); Reijo Pera, R. (PI); Riedel-Kruse, I. (PI); Rose, J. (PI); Sanger, T. (PI); Sapolsky, R. (PI); Schnitzer, M. (PI); Scott, M. (PI); Shenoy, K. (PI); Smolke, C. (PI); Spielman, D. (PI); Swartz, J. (PI); Taylor, C. (PI); Wernig, M. (PI); Wu, J. (PI); Yang, F. (PI); Yock, P. (PI); Zarins, C. (PI); Zenios, S. (PI); Negrette, J. (GP); Woo, Y. (GP)
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