BIOE 212. Introduction to Biomedical Informatics Research Methodology—(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 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.
3 units, Spr (Altman, R; Delp, S; Mitiguy, P.)

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. Recommended: basic biology, physics.
3 units, Win (Gold, G; Butts-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.
4 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.) 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.) Continuation of ME 284A. Integrative cardiovascular physiology, blood fluid mechanics, and transport in the micro circulation. 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—(Formerly 200A.) The molecular and cellular bases of life from an engineering perspective. Quantitative analysis and engineering of biomolecular structure and dynamics, enzyme function, molecular interactions, metabolic pathways, signal transduction, and cellular mechanics. Required: course work in biochemistry and thermodynamics.
3 units, Win (Bryant, Z)

 BIOE 300B. Quantitative Mammalian Physiology and Tissue Engineering—(Formerly 200B.) The interaction, communication, and disorders of major organ systems and relevant developmental biology and tissue engineering from cells to complex organs.
3 units, Spr (Deisseroth, K; Covert, M)

BIOE 301A. Molecular and Cellular Bioengineering Lab—(Formerly 201A.) 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, Win (Cochran, J)

BIOE 301B. Clinical Needs and Technology—(Formerly 201B.) Diagnostic and therapeutic methods employed in medicine. Each student paired with a physician. Labs include a pathology/histology session, pulmonary function testing, and the Goodman Simulation Center. Clinical experience, chosen from 12 specialties, includes observation of an operation or procedure. Final paper. Limited enrollment. Corequisite: 300B.
1 unit, Spr (Feinstein, J)

BIOE 310. Dynamic Models in Biology—How to use the power of computational modeling in biological research. Biological problems including population dynamics, membrane currents, cellular dynamics, the spread of infectious disease, and spatial pattern formation. Key modeling approaches such as linear systems of differential equations, stochastic models, network models, and agent-based models. Matlab tutorial.
3 units, not given this year (Covert, M)

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, alternate years, not given this year (Cochran, J)

BIOE 332A,B. 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, A: Win, B: Spr (Boahen, K)

BIOE 355. Advanced Biochemical Engineering—(Same as CHEMENG 355.) Combining new 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 paradigm for the application of chemical engineering principles to advanced process development within the framework of current business and regulatory requirements. Prerequisite: HEMENG 181 (formerly 188) or BIOSCI 41, or equivalent.
3 units, Spr (Swartz, J)

BIOE 361. Biomaterials in Regenerative Medicine—(Same as MATSCI 381.) 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, Win (Heilshorn, S; Cochran, J)

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; Gomez-Sjoberg, R), Spr (Quake, S)

BIOE 374A. Biodesign Innovation: Needs Finding and Concept Creation—(Same as OIT 384, ME 374A, MED 272A.) Two quarter sequence. Strategies for interpreting clinical needs, researching literature, and searching patents. Clinical and scientific literature review, techniques of intellectual property analysis and feasibility, basic prototyping, and market assessment. Student entrepreneurial teams create, analyze, and screen medical technology ideas, and select projects for development.
3-4 units, Win (Yock, P; Brinton, T; Zenios, S; Milroy, C)

BIOE 374B. Biodesign Innovation: Concept Development and Implementation—(Same as OIT 385, ME 374B, MED 272B.) Two quarter sequence. Concept development and implementation. Early factors for success; how to prototype inventions and refine intellectual property. Lectures, guest medical pioneers, and entrepreneurs about strategic planning, ethical considerations, new venture management, and financing and licensing strategies. Cash requirements; regulatory (FDA), reimbursement, clinical, and legal strategies, and business or research plans.
3-4 units, Spr (Yock, P; Brinton, T; Zenios, S; Milroy, C)

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 (Delp, S)

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, 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, Win, Spr, 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 (Block, S), Spr, Sum (Staff)

BIOE 393. Bioengineering and Biodesign Forum—(Same as ME 389) Guest speakers present research topics at the interfaces of biology, medicine, physics, and engineering. May be repeated for credit.
1 unit, Aut, Win, 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—(Crosslisted in departments in the schools of H&S, Engineering, and Medicine; 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://www.stanford.edu/group/biox/courses/459.html. Recommended: basic mathematics, biology, chemistry, and physics.
1 unit, Aut, Win, 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, alternate years, not given this year  (Taylor, 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, Win, Spr, Sum (Staff)

COGNATE COURSES
See respective department listings for course descriptions and General Education Requirements (GER) information. See degree requirements above or the program’s student services office for applicability of these courses to a major or minor program.

BIOC 218. Computational Molecular Biology—(Same as BIOMEDIN 231.)
3 units, Aut (Staff), Win, Spr (Brutlag, D)

BIOMEDIN 210. Introduction to Biomedical Informatics: Fundamental Methods—(Same as CS 270.)
3 units, Aut (Musen, M)

 BIOMEDIN 217. Translational Bioinformatics—(Same as CS 275.)
4 units, Win (Butte, A; Hillenmeyer, M; Southworth, L)

CHEMENG 450. Advances in Biotechnology
3 units, Spr (Hwang, L; Swartz, J)

EE 369A. Medical Imaging Systems I
3 units, not given this year

EE 369B. Medical Imaging Systems II
3 units, Spr (Nishimura, D)

EE 369C. Medical Image Reconstruction
3 units, Aut (Pauly, J)

ME 280. Skeletal Development and Evolution
3 units, Spr (Carter, D)

ME 287. Soft Tissue Mechanics
3 units, Aut (Levenston, M)

ME 381. Orthopaedic Bioengineering
3 units, Aut (Carter, D)

ME 382A. Medical Device Design
4 units, Win (Andriacchi, T)

ME 382B. Medical Device Design
4 units, Spr (Andriacchi, T)

ME 385. Tissue Engineering Lab
1-2 units, Win (Jacobs, C)

RAD 226. In Vivo Magnetic Resonance Spectroscopy and Imaging
3 units, Win (Spielman, D)

 

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