Bioengineering
BIOE 212: Introduction to Biomedical Informatics Research Methodology (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: BIOMEDIN 210, 211, 214, 217 or consent of instructor.
Terms: Aut | Units: 3
Instructors: Altman, R.; Cheng, B.; Klein, T.
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: Spr | Units: 3-4
BIOE 220: Imaging Anatomy (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.
Terms: Win | Units: 3
Instructors: Gold, G.; Pauly, K.
BIOE 222A: Multimodality Molecular Imaging in Living Subjects (RAD 222A)
Focus on instruments and chemistries for imaging of cellular and molecular processes in vivo. Basics of instrumentation physics, chemistry of molecular imaging probes, and an introduction to preclinical and clinical molecular imaging modalities.
Terms: Aut | Units: 4
Instructors: Contag, C.; Rao, J.; Xing, L.
BIOE 222B: Multimodality Molecular Imaging in Living Subjects II (RAD 222B)
In vivo imaging techniques and applications to preclinical models and clinical disease management. Focus on cancer research, neurobiology, cardiovascular and musculoskeletal diseases.
Terms: Win | Units: 4
Instructors: Contag, C.; Rao, J.; Xing, L.
BIOE 222C: Topics in Multimodality Imaging in Living Subjects (RAD 222C)
Focuses on emerging chemistries and instruments that address unmet needs for improved diagnosis and disease management in cancer, neurological disease, cardiovascular medicine and musculoskeletal disorders. Objective is to identify problems or controversies in the field, and to resolve them through understanding the relevant primary literature.
Terms: Spr | Units: 4
Instructors: Contag, C.; Rao, J.; Xing, L.
BIOE 261: Principles and Practice of Stem Cell Engineering
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: alternate years, given next year | Units: 3
BIOE 280: Skeletal Development and Evolution (ME 280)
The mechanobiology of skeletal growth, adaptation, regeneration, and aging is considered from developmental and evolutionary perspectives. Emphasis is on the interactions between mechanical and chemical factors in the regulation of connective tissue biology. Prerequisites: 80, or Human Biology core, or Biological Sciences core.
Terms: Spr | Units: 3
Instructors: Carter, D.
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
Instructors: Delp, S.
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. Prerequisites: engineering or biology core coursework.
Terms: Aut | Units: 3
Instructors: Delp, S.
BIOE 284A: Cardiovascular Bioengineering (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.
Terms: Aut | Units: 3
Instructors: Taylor, C.
BIOE 284B: Cardiovascular Bioengineering
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.
Terms: Win | Units: 3
Instructors: Taylor, C.
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.
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: Aut | Units: 3
Instructors: 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.
Terms: Win | Units: 3
Instructors: Covert, M.; Deisseroth, K.
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.
Terms: Aut | Units: 2
Instructors: 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.
Terms: Win | Units: 1
Instructors: Feinstein, J.
BIOE 301C: Diagnostic Imaging Lab
Biomedical instruments and diagnostic devices. Emphasis is on comparing measurements with theoretical predictions. Labs include ECG, MRI, microfluidics, CT, and EEG. Prerequisites: 300B and 301B.
Terms: Spr | Units: 2
Instructors: Boahen, K.
BIOE 310: Systems Biology (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.
Terms: not given this year | Units: 3
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.
Terms: alternate years, given next year | Units: 3
BIOE 332: Large-Scale Neural Modeling
Emphasis is on modeling neural systems at the circuit level, ranging from feature maps in neocortex to episodic memory in hippocampus. Simulation exercises to explore the roles of cellular properties, synaptic plasticity, spike synchrony, rhythmic activity, recurrent connectivity, and noise and heterogeneity; quantitative techniques to analyze and predict network behavior. Work in teams of two; run simulations in real-time on neuromorphic hardware developed for this purpose.
Terms: Win | Units: 3
Instructors: Boahen, K.
BIOE 333: Interfacial Phenomena and Bionanotechnology
Fundamental and applied study of interfacial phenomena and effects of surface-active molecules on behavior of important biological, biochemical, environmental, and bioengineering systems. Discussion of central mathematical equations in surface science attributed to Laplace, Gibbs, Kelvin, and Young. Self-assembly of surfactants and biomolecules. Relevance of interfacial phenomena to protein folding/unfolding and microfluidics. Applications to recent research advances in bionano- and biomicrotechnology, using scientific literature.
Terms: Spr | Units: 3
Instructors: 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.
Terms: not given this year | Units: 3
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: alternate years, given next year | Units: 3
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.
Terms: not given this year | Units: 3
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: Win | Units: 3
Instructors: Swartz, J.
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: Win, alternate years, not given next year | Units: 3
Instructors: Cochran, J.; Heilshorn, S.
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: Win | Units: 2
Instructors: Melin, J.; Quake, S.
BIOE 374A: Biodesign Innovation Core: Needs Finding and Concept Creation (ME 368A, MED 272A)
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. May be taken alone (2 units) or in combination with the project component (4 units).
Terms: Win | Units: 2-4
Instructors: Brinton, T.; Milroy, J.; Yock, P.; Zenios, S.
BIOE 374B: Biodesign Innovation Core: Concept Development and Implementation (ME 368B, MED 272B)
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. May be taken alone (2 units) or in combination with the project component (4 units). Prerequisite: MED 272A, ME368A, or BIOE 374A.
Terms: Spr | Units: 2-4
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: Carter, D.
BIOE 386: Neuromuscular Biomechanics
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.
Terms: not given this year | Units: 3
BIOE 390: Introduction to Bioengineering Research (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.
Terms: Aut, Win | Units: 1-2
Instructors: 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.
Terms: Aut, Win, Spr, Sum | Units: 1-6
Instructors: Altman, R.; Boahen, K.; Bryant, Z.; Carter, D.; Cochran, J.; Covert, M.; Deisseroth, K.; Delp, S.; Fahrig, R.; Gambhir, S.; Jacobs, C.; Kovacs, G.; Levin, C.; Longaker, M.; Pauly, K.; Pelc, N.; Quake, S.; Scott, M.; Smolke, C.; Spielman, D.; Swartz, J.; Taylor, C.; Yock, P.
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
Instructors: Altman, R.; Barron, A.; Boahen, K.; Bryant, Z.; Carter, D.; Cochran, J.; Covert, M.; Deisseroth, K.; Delp, S.; Endy, A.; Fahrig, R.; Gambhir, S.; Gold, G.; Goodman, S.; Heilshorn, S.; Huang, K.; Jacobs, C.; Kovacs, G.; Levenston, M.; Pauly, K.; Pelc, N.; Quake, S.; Scott, M.; Smolke, C.; Spielman, D.; Swartz, J.; Taylor, C.; Yock, P.
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.
Terms: Aut, Win, Spr | Units: 1
Instructors: Altman, R.
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: Spr | Units: 3
Instructors: Swartz, J.
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
Instructors: Robertson, C.
BIOE 484: Computational Methods in Cardiovascular Bioengineering (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.
Terms: Spr | Units: 3
Instructors: Figueroa Alvarez, C.
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: not given this year | Units: 3