Graduate courses in Bioengineering

(Same as BIOMEDIN 212, CS 272, GENE 212.) 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. Guest lectures from professional biomedical informatics systems builders on issues related to the process of project management. Software engineering basics. Prerequisites: 210, 211 or 214, or consent of instructor.

3 units, Aut (Altman, R; Cheng, B; Klein, T)

BIOE 214. Representations and Algorithms for Computational Molecular Biology

(Same as BIOMEDIN 214, CS 274, GENE 214.) Topics: algorithms for alignment of biological sequences and structures, computing with strings, phylogenetic tree construction, hidden Markov models, computing with networks of genes, 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, graphical display of biological data, machine learning (clustering and classification), and natural language text processing. Prerequisites: programming skills; consent of instructor for 3 units.

3-4 units, Spr (Altman, R)

BIOE 220. Imaging Anatomy

(Same as RAD 220.) The physics of medical imaging and human anatomy through medical images. Emphasis is on normal anatomy, contrast mechanisms, and the relative strengths of each imaging modality. Labs reinforce imaging techniques and anatomy. Prerequisites: basic biology, physics.

3 units, Win (Gold, G; Pauly, K)

BIOE 222A. Multimodality Molecular Imaging in Living Subjects I

(Same as RAD 222A.) Instruments for imaging molecular and cellular events in animals and human beings using novel assays. Instrumentation physics, chemistry of molecular imaging probes, and applications to preclinical models and clinical disease management.

4 units, Aut (Gambhir, S; Rao, J)

BIOE 222B. Multimodality Molecular Imaging in Living Subjects II

(Same as RAD 222B.) In vivo imaging techniques and applications to preclinical models and clinical disease management. Focus on cancer research, neurobiology, cardiovascular and musculoskeletal diseases.

2 units, Win (Gambhir, S; Rao, J)

BIOE 261. Principles and Practice of Stem Cell Engineering

(Same as 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.

3 units, Aut (Deisseroth, K; Palmer, T)

BIOE 281. Biomechanics of Movement

(Same as 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.

3 units, Aut (Delp, S)

BIOE 284A. Cardiovascular Bioengineering

(Same as ME 284A.) Via Internet. Bioengineering principles applied to the cardiovascular system. Anatomy of human cardiovascular system, comparative anatomy, and allometric scaling principles. Cardiovascular molecular and cell biology. Overview of continuum mechanics. Form and function of blood, blood vessels, and the heart from an engineering perspective. Normal, diseased, and engineered replacement tissues.

3 units, Aut (Taylor, C)

BIOE 284B. Cardiovascular Bioengineering

(Same as ME 284B.) Via Internet. Continuation of ME 284A. Integrative cardiovascular physiology, blood fluid mechanics, and transport in the microcirculation. Sensing, feedback, and control of the circulation. Overview of congenital and adult cardiovascular disease, diagnostic methods, and treatment strategies. Engineering principles to evaluate the performance of cardiovascular devices and the efficacy of treatment strategies.

3 units, Win (Taylor, C)

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 a equivalent programming language.

3 units, Aut (Bryant, Z)

BIOE 300B. Physiology and Tissue Engineering

The interaction, communication, and disorders of major organ systems and relevant developmental biology and tissue engineering from cells to complex organs.

3 units, Win (Deisseroth, K; Covert, M)

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, library screening, and microarrays. Emphasis is on experimental design and data analysis. Limited enrollment. Corequisite: 300A.

2 units, Aut (Cochran, J)

BIOE 301B. Clinical Needs and Technology

Diagnostic and therapeutic methods in medicine. Labs include a pathology/histology session, pulmonary function testing, and the Goodman Simulation Center. Each student paired with a physician for observation of an operation or procedure. Limited enrollment. Corequisite: 300B.

1 unit, Win (Feinstein, J)

BIOE 310. Systems Biology

(Same as BIOC 278, CS 278, CSB 278.) 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: background in biology and mathematical analysis.

3 units, Aut (Covert, M; Dill, D; Brutlag, D; Ferrell, J)

BIOE 331. Protein Engineering

The design and engineering of biomolecules emphasizing proteins, antibodies, and enzymes. Combinatorial methodologies, rational design, protein structure and function, and biophysical analyses of modified biomolecules. Clinically relevant examples from the literature and biotech industry. Prerequisite: basic biochemistry.

3 units, Win (Cochran, J), alternate years, not given next year

BIOE 332A. Large-Scale Neural Modeling

Emphasis is on cortical computation, from feature maps in the neocortex to episodic memory in the hippocampus, with attention to the roles of recurrent connectivity, rhythmic activity, spike synchrony, synaptic plasticity, and noise and heterogeneity. Large-scale models run in real-time on neuromorphic hardware developed for this purpose. Techniques to analyze and predict network behavior; applications to data recorded from models in laboratory. Techniques introduced are used to develop projects in second half of two-quarter sequence.

3 units, Win (Boahen, K)

BIOE 332B. Large-Scale Neural Modeling

Emphasis is on cortical computation, from feature maps in the neocortex to episodic memory in the hippocampus, with attention to the roles of recurrent connectivity, rhythmic activity, spike synchrony, synaptic plasticity, and noise and heterogeneity. Simulation exercises to model neural phenomena; quantitative techniques to analyze and predict network behavior; modeling projects to study neural systems of interest. Student teams of two run large-scale models in real-time on neuromorphic hardware developed for this purpose. Prerequisite: 332A.

3 units, Spr (Boahen, K)

BIOE 333. Interfacial Phenomena and Bionanotechnology

How biological, biochemical, environmental, and bioengineering problems require understanding of the properties of systems of large interfacial area and surface-active molecules. Concepts used by Laplace, Gibbs, Kelvin, and Young to describe these systems. Self-assembling aspects of surface-active molecules including biological molecules. The relevance of interfacial phenomena to protein folding/unfolding and microfluidic devices. Applications to recent research advances in bionano- and biomicrotechnology, drawing from the scientific literature.

3 units, Spr (Barron, A)

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.

3 units, Aut (Staff)

BIOE 335. Molecular Motors I: F1 ATPase

Physical mechanisms of mechanochemical coupling in biological molecular motors, using F1 ATPase as the principal model system. Applications of biochemistry, structure determination, single molecule tracking and manipulation, protein engineering, and computational techniques to the study of molecular motors.

3 units, Spr (Bryant, Z)

BIOE 341. Computational Neural Networks

Distributed neural network implementations of algorithms for signal processing, function approximation, and control. Representation of information in networks of spiking neurons. Supervised and unsupervised learning algorithms. Radial basis functions, principal and independent components analysis, reinforcement learning, support-vector machines, self-organizing maps, auto-associative learning, hidden Markov models. Related methods from information theory, signal processing, bayesian estimation, and stochastic systems. Final project in software or programmable hardware. Prerequisites: linear algebra, dynamic systems, and probability theory as in MATH 103, EE 102A, and EE 178 or equivalent, and programming experience in C++ or Matlab.

3 units, Aut (Sanger, T)

BIOE 355. Advanced Biochemical Engineering

(Same as 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 BIO 41, or equivalent.

3 units, Spr (Swartz, J)

BIOE 361. Biomaterials in Regenerative Medicine

(Same as 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.

3 units, alternate years, not given this year

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.

2 units, Win (Quake, S)

BIOE 374A. Biodesign Innovation: Needs Finding and Concept Creation

(Same as ME 368A, MED 272A, OIT 581.) 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.

2 units, Win (Yock, P; Zenios, S; Brinton, T; Milroy, C)

BIOE 374B. Biodesign Innovation: Concept Development and Implementation

(Same as ME 368B, MED 272B, OIT 583.) 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.

2 units, Spr (Yock, P; Zenios, S; Brinton, T; Milroy, C)

BIOE 375A. Biodesign Innovation, Project A

(Same as ME 369A, MED 273A, OIT 582.) Interdisciplinary student teams select a medical need, characterize it fully, develop a needs statement, invent potential conceptual approaches to solving the need, and pursue initial prototyping and planning for regulatory and reimbursement pathways. Guest experts. Corequisite: MED 272A/BIOE 374A/ME 368A/OIT 581.

2 units, Win (Yock, P; Zenios, S; Milroy, C; Brinton, T)

BIOE 375B. Biodesign Innovation, Project B

(Same as ME 369B, MED 273B, OIT 584.) Interdisciplinary teams select the most promising invention from BIOE 375A and move into prototyping and project planning. Teams develop strategies for patenting, FDA submission, third-party reimbursement, licensing agreement or launching a start-up, including cash forecasting and business plan. Prerequisites: MED 375A/ME 369A/BIOE 375A/OIT 582. Corequisite: MED 272B/ME 368B/BIOE 374B/OIT 583.

2 units, Spr (Yock, P; Milroy, C; Brinton, T; Zenios, S)

BIOE 386. Neuromuscular Biomechanics

(Same as ME 386.) The interplay between mechanics and neural control of movement. State of the art assessment through a review of classic and recent journal articles. Emphasis is on the application of dynamics and control to the design of assistive technology for persons with movement disorders.

3 units, not given this year

BIOE 390. Introduction to Bioengineering Research

(Same as MED 289.) Preference to medical and bioengineering graduate 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. Topics include: imaging; molecular, cell, and tissue engineering; biomechanics; biomedical computation; biochemical engineering; biosensors; and medical devices. Limited enrollment.

1-2 units, Aut (Taylor, C), Win (Taylor, C)

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.

1-6 units, Aut (Staff), Win (Staff), Spr (Staff), Sum (Staff)

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.

1-10 units, Aut (Staff), Win (Staff), Spr (Staff), Sum (Staff)

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.

1 unit, Aut (Altman, R), Win (Altman, R), Spr (Altman, R)

BIOE 454. Synthetic Biology and Metabolic Engineering

(Same as 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.

3 units, alternate years, not given this year

BIOE 459. Frontiers in Interdisciplinary Biosciences

(Same as BIO 459, BIOC 459, CHEMENG 459, CHEM 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.

1 unit, Aut (Robertson, C), Win (Robertson, C), Spr (Robertson, C)

BIOE 484. Computational Methods in Cardiovascular Bioengineering

(Same as ME 484.) Lumped parameter, one-dimensional nonlinear and linear wave propagation, and three-dimensional modeling techniques applied to simulate blood flow in the cardiovascular system and evaluate the performance of cardiovascular devices. Construction of anatomic models and extraction of physiologic quantities from medical imaging data. Problems in blood flow within the context of disease research, device design, and surgical planning.

3 units, Spr (Figueroa Alvarez, C)

BIOE 485. Modeling and Simulation of Human Movement

(Same as 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.

3 units, Spr (Delp, S)

BIOE 500. Thesis (Ph.D.)

1-15 units, Aut (Staff), Win (Staff), Spr (Staff), Sum (Staff)

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Stanford Bulletin, Archive 2008-09

Stanford Bulletin, Archive 2008-09

Alphabetical Index

Bulletin Archive

Graduate courses in Bioengineering