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Bioengineering

Mail Code: 94305-4245
Student Services Phone: Graduate students: (650) 498-2408; Undergraduates: (650) 724-5314
Web Site: http://bioengineering.stanford.edu

Courses offered by the Department of Bioengineering are listed under the subject code BIOE on the Stanford Bulletin's ExploreCourses web site.

Bioengineering is jointly supported by the School of Engineering and the School of Medicine. The facilities and personnel of the Department of Bioengineering are housed in the Shriram Center,  James H. Clark Center, the William F. Durand Building for Space Engineering and Science, the William M. Keck Science Building, the Jerry Yang and Akiko Yamazaki Environment and Energy Building, and the Richard M. Lucas Center for Magnetic Resonance Spectroscopy and Imaging. The departmental headquarters is in the Shriram Center for Bioengineering and Chemical Engineering.

Courses in the teaching program lead to the degrees of Bachelor of Science in Engineering (Bioengineering), Master of Science and Doctor of Philosophy. The department collaborates in research and teaching programs with faculty members in Chemical Engineering, Mechanical Engineering, Electrical Engineering, and departments in the School of Medicine. Quantitative biology is the core science base of the department. The research and educational thrusts are in biomedical computation, biomedical imaging, biomedical devices, regenerative medicine, and cell/molecular engineering. The clinical dimension of the department includes cardiovascular medicine, neuroscience, orthopedics, cancer care, neurology, and environment.

Mission of the Undergraduate Program in Bioengineering

The Stanford Bioengineering (BioE) major enables students to combine engineering and the life sciences in ways that advance scientific discovery, healthcare and medicine, manufacturing, environmental quality, culture, education, and policy. Students who major in BioE earn a fundamental engineering degree for which the raw materials, underlying basic sciences, fundamental toolkit, and future frontiers are all defined by the unique properties of living systems.

The department offers an undergraduate major in Bioengineering (BioE) leading to the B.S. degree in Engineering. An undergraduate major in Biomechanical Engineering and an undergraduate major in Biomedical Computation, both of which lead to the B.S. degree in Engineering, are available through the School of Engineering. For further information, see the Handbook for Undergraduate Engineering Programs at http://ughb.stanford.edu.

Learning Outcomes (Graduate)

The purpose of the master’s program is to provide students with the knowledge and skills necessary for a professional career or doctoral studies. This is done through course work with specialization in an area of the field, including biomedical computation, regenerative medicine and tissue engineering, molecular and cell bioengineering, biomedical imaging, and biomedical devices.

The Ph.D. is conferred upon candidates who have demonstrated substantial scholarship and the ability to conduct independent research. Through course work and guided research, the program prepares students to make original contributions in Bioengineering and related fields.

Graduate Programs in Bioengineering

The University’s requirements for the M.S. and Ph.D. degrees are outlined in the “Graduate Degrees” section of this bulletin.

Admission

Students are expected to enter with a series of core competencies in mathematics, biology, chemistry, physics, computing, and engineering. Students entering the program are assessed by the examination of their undergraduate transcripts and research experiences. Specifically, the department requires that students have completed mathematics through multivariable calculus and differential equations, completed a series of undergraduate biology courses and completed physics, chemistry, and computer sciences courses required of all undergraduate majors in engineering.

Qualified applicants are encouraged to apply for predoctoral national competitive fellowships, especially those from the National Science Foundation. Applicants to the Ph.D. program should consult with their financial aid officers for information and applications.

The deadline for receiving applications is December 2, 2014.

Further information and application forms for all graduate degree programs may be obtained from Graduate Admissions, the Registrar’s Office, http://gradadmissions.stanford.edu.

Bachelor of Science in Engineering (Bioengineering)

The department offers an undergraduate major in Bioengineering (BioE) leading to the B.S. degree in Engineering. For additional information, see the Handbook for Undergraduate Engineering Programs at http://ughb.stanford.edu.


Bioengineering (BioE)

Completion of the undergraduate program in Bioengineering leads to the conferral of the Bachelor of Science in Engineering. The subplan "Bioengineering" appears on the transcript and on the diploma.

Mission of the Undergraduate Program in Bioengineering

The Stanford Bioengineering (BioE) major enables students to combine engineering and the life sciences in ways that advance scientific discovery, healthcare and medicine, manufacturing, environmental quality, culture, education, and policy. Students who major in BioE earn a fundamental engineering degree for which the raw materials, underlying basic sciences, fundamental toolkit, and future frontiers are all defined by the unique properties of living systems.

Students will complete engineering fundamentals courses, including an introduction to BioE and computer programming. A series of core BioE classes beginning in the second year leads to a student-selected depth area and a senior capstone design project. The department also organizes a summer Research Experience for Undergraduates (REU) program. BioE graduates are well prepared to pursue careers and lead projects in research, medicine, business, law, and policy.

Requirements

Units
Mathematics (28-30) 1
28 units minimum required, see Basic Requirement 1)
MATH 41
  & MATH 42
Calculus
   and Calculus (or AP Calculus)
10
Select one of the following:
CME 100Vector Calculus for Engineers (Recommended)5
or MATH 51 Linear Algebra and Differential Calculus of Several Variables
Select one of the following:
CME 102Ordinary Differential Equations for Engineers (Recommended)5
or MATH 53 Ordinary Differential Equations with Linear Algebra
Select one of the following:
CME 104Linear Algebra and Partial Differential Equations for Engineers (Recommended)5
or MATH 52 Integral Calculus of Several Variables
CME 106Introduction to Probability and Statistics for Engineers (Recommended)3-5
or STATS 110 Statistical Methods in Engineering and the Physical Sciences
or STATS 141 Biostatistics
Science (28-33) 2
28 units minimum:
CHEM 31XChemical Principles Accelerated5-10
or CHEM 31A
  & CHEM 31B
Chemical Principles I
   and Chemical Principles II
CHEM 33Structure and Reactivity5
BIO 41Genetics, Biochemistry, and Molecular Biology5
BIO 42Cell Biology and Animal Physiology5
PHYSICS 41Mechanics4
PHYSICS 43Electricity and Magnetism4
Technology in Society (3)
One course required; see Basic Requirement 4
BIOE 131Ethics in Bioengineering (WIM)3
Engineering Fundamentals (12-14)
ENGR 70AProgramming Methodology (same as CS 106A)5
ENGR 80Introduction to Bioengineering4
Fundamentals Elective; see UGHB Fig. 3-4 for approved course list; may not use ENGR 70B or ENGR 70X3-5
Bioengineering Core (36)
BIOE 41Physical Biology of Macromolecules4
BIOE 42Physical Biology of Cells4
BIOE 44Fundamentals for Engineering Biology Lab4
BIOE 51Anatomy for Bioengineers4
BIOE 101Systems Biology4
BIOE 103Systems Physiology and Design4
BIOE 123Optics and Devices Lab4
BIOE 141ASenior Capstone Design I4
BIOE 141BSenior Capstone Design II4
Bioengineering Depth Electives (12)
Four courses, minimum 12 units:12
Computational Modeling of Microbial Communities
Diagnostic Devices Lab
Biophysics of Multi-cellular Systems and Amorphous Computing
Introduction to Biomedical Informatics Research Methodology
Representations and Algorithms for Computational Molecular Biology
Introduction to Imaging and Image-based Human Anatomy
Instrumentation and Applications for Multi-modality Molecular Imaging of Living Subjects
Physics and Engineering of X-Ray Computed Tomography
Probes and Applications for Multi-modality Molecular Imaging of Living Subjects
Functional MRI Methods
Protein Engineering
Advanced Frameworks and Approaches for Engineering Integrated Genetic Systems
Tissue Engineering
Biomechanics of Movement
Introduction to Physiology and Biomechanics of Hearing
Principles and Practice of Optogenetics for Optical Control of Biological Tissues
Total Units119-128
1

It is strongly recommended that CME 100 Vector Calculus for Engineers, CME 102 Ordinary Differential Equations for Engineers, and CME 104 Linear Algebra and Partial Differential Equations for Engineers) be taken rather than MATH 51 Linear Algebra and Differential Calculus of Several Variables, MATH 52 Integral Calculus of Several Variables, and MATH 53 Ordinary Differential Equations with Linear Algebra. CME 106 Introduction to Probability and Statistics for Engineers utilizes MATLAB, a powerful technical computing program, and should be taken rather than STATS 110 Statistical Methods in Engineering and the Physical Sciences or STATS 141 Biostatistics. If  you are taking the MATH 50 series, it is strongly recommended to take MATH 51M Introduction to MATLAB or CME 192 Introduction to MATLAB.

2

Science must include both Chemistry (CHEM 31A Chemical Principles I and CHEM 31B Chemical Principles II; or CHEM 31X Chemical Principles Accelerated or ENGR 31 Chemical Principles with Application to Nanoscale Science and Technology) and calculus-based Physics, with two quarters of course work in each, in addition to two courses of BIO core. CHEM 31A Chemical Principles I and CHEM 31B Chemical Principles II are considered one course even though given over two quarters. Premeds should take Chemistry, not ENGR 31 Chemical Principles with Application to Nanoscale Science and Technology.

For additional information and sample programs see the Handbook for Undergraduate Engineering Programs (UGHB). Students pursuing a premed program need to take additional courses; see the UGHB, BioE Premed 4-Year Plan.

Honors Program

The School of Engineering offers a program leading to a Bachelor of Science in Engineering: Bioengineering with Honors (ENGR-BSH, BIOE). This program provides the opportunity for qualified BioE majors to conduct independent research at an advanced level with a faculty research adviser and documented in an honors thesis.

In order to receive departmental honors, students admitted to the program must:

  1. Declare the honors program in Axess (ENGR-BSH, Subplan: Bioengineering).
  2. Maintain an overall grade point average (GPA) of at least 3.5 as calculated on the unofficial transcript.
  3. Complete at least two quarters of research with a minimum of nine units of BIOE 191 Bioengineering Problems and Experimental Investigation or BIOE 191X Out-of-Department Advanced Research Laboratory in Bioengineering for a letter grade; up to three units may be used towards the bioengineering depth elective requirements.  
  4. Submit a completed thesis draft to the honors adviser and second reader by the first week of Spring Quarter. Further revisions and final endorsement are to be finished by the second Monday in May, when two signed bound copies plus one PC-compatible CD-ROM are to be submitted to the student services officer.
  5. Attend the Bioengineering Honors Symposium at the end of Spring Quarter and give a poster or oral presentation, or present in another approved suitable forum.  

 For more information and application instructions, see the department's undergraduate site


 

Coterminal B.S./M.S. Program in Bioengineering

This option is available to outstanding Stanford undergraduates who wish to work simultaneously toward a B.S. in another field and an M.S. in Bioengineering. The degrees may be granted simultaneously or at the conclusion of different quarters, though the bachelor’s degree cannot be awarded after the master’s degree has been granted. The University minimum requirements for the coterminal bachelor’s/master’s program are 180 units for the bachelor’s degree plus 45 unduplicated units for the master’s degree. Students may apply for the coterminal B.S. and M.S. program after 120 undergraduate units have been completed, and they must be accepted into our program one quarter before receiving the B.S. degree. Students should apply directly to the Bioengineering Student Service Office by November 3, 2014. Students interested in the coterminal degree must take the Graduate Record Examination (GRE). Prospective applicants should see the department's web site for application form, instructions, and supporting documents.

University requirements for the coterminal M.A. are described in the "Coterminal Bachelor's and Master's Degrees" section of this bulletin. For University coterminal degree program rules and University application forms, see the Stanford Undergrad Coterm Guide.

The application must provide evidence of potential for strong academic performance as a graduate student. The application is evaluated and acted upon by the graduate admissions committee of the department. Students are expected to enter with a series of core competencies in mathematics, biology, chemistry, physics, computing, and engineering. Typically, a GPA of at least 3.5 in engineering, science, and math is expected.

Master of Science in Bioengineering

The Master of Science in Bioengineering requires 45 units of course work. The curriculum consists of core bioengineering courses, technical electives, seminars and unrestricted electives. Core courses focus on quantitative biology and biological systems analysis. Approved technical electives are chosen by the student in consultation with his/her graduate adviser, and can be selected from graduate course offerings in mathematics, statistics, engineering, physical sciences, life sciences, and medicine. Seminars highlight emerging research in bioengineering and provide training in research ethics. Unrestricted electives can be freely chosen by the student in association with his/her adviser.

Requirements

The department’s requirements for the M.S. in Bioengineering are:

1. Core Bioengineering courses (10-11 units)

The following courses are required:

Units
BIOE 300AMolecular and Cellular Bioengineering3
BIOE 300BPhysiology and Tissue Engineering3
Select two of the following:4-5
Molecular and Cellular Engineering Lab
Clinical Needs and Technology
Diagnostic Devices Lab
Total Units10-11

These courses, together with the approved technical electives, should form a cohesive course of study that provides depth and breadth.

2. Approved Technical Electives (26 units)

These units must be selected from graduate courses in mathematics, statistics, engineering, physical science, life science, and medicine. They should be chosen in concert with the bioengineering courses to provide a cohesive degree program in a bioengineering focus area. Students are required to take at least one course in some area of device or instrumentation. Up to 9 units of directed study and research may be used as approved electives.

3. Seminars (4 units)

The seminar units should be fulfilled through:

Units
BIOE 393Bioengineering Departmental Research Colloquium (Students enroll each quarter for 1 unit)3
MED 255The Responsible Conduct of Research1
Total Units4

Other relevant seminar units may also be used with the approval of the faculty adviser. One of the seminar units must be MED 255 The Responsible Conduct of Research.

4. Unrestricted Electives (6 units).

Students are assigned an initial faculty adviser to assist them in designing a plan of study that creates a cohesive degree program with a concentration in a particular bioengineering focus area. These focus areas include, but are not limited to: Biomedical Computation, Regenerative Medicine/Tissue Engineering, Molecular and Cell Bioengineering, Biomedical Imaging, and Biomedical Devices.

To ensure that an appropriate program is pursued by all M.S. candidates, students who first matriculate at Stanford at the graduate level must:

  1. submit an adviser-approved Program Proposal for a Master’s Degree form to the student services office during the first month of the first quarter of enrollment
  2. obtain approval from the M.S. adviser and the Chair of Graduate Studies for any subsequent program change or changes.

It is expected that the requirements for the M.S. in Bioengineering can be completed within approximately one year. There is no thesis requirement for the M.S.

Due to the interdisciplinary nature of Bioengineering, a number of courses are offered directly through the Bioengineering Department but many are available through other departments. See respective ExploreCourses for course descriptions.

Doctor of Philosophy in Bioengineering

A student studying for the Ph.D. degree must complete a master’s degree (45 units) comparable to that of the Stanford M.S. degree in Bioengineering. Up to 45 units of master’s degree residency units may be counted towards the degree. The Ph.D. degree is awarded after the completion of a minimum of 135 units of graduate work as well as satisfactory completion of any additional University requirements. Students admitted to the Ph.D. program with an M.S. degree must complete at least 90 units of work at Stanford. The maximum number of transfer units is 45.

On the basis of the research interests expressed in their application, students are assigned an initial faculty adviser who assists them in choosing courses and identifying research opportunities. The department does not require formal lab rotations, but students are encouraged to explore research activities in two or three labs during their first academic year.

Prior to being formally admitted to candidacy for the Ph.D. degree, the student must demonstrate knowledge of bioengineering fundamentals and a potential for research by passing a qualifying oral examination.

Typically, the exam is taken shortly after the student earns a master’s degree. The student is expected to have a nominal graduate Stanford GPA of 3.25 to be eligible for the exam. Once the student’s faculty sponsor has agreed that the exam is to take place, the student must submit an application folder containing items including a curriculum vitae, research project abstract, and preliminary dissertation proposal to the student services office. Information about the exam may be obtained from the student services office.

In addition to the course requirements of the M.S. degree, doctoral candidates must complete a minimum of 15 additional units of approved formal course work (excluding research, directed study, and seminars).

Dissertation Reading Committee

Each Ph.D. candidate is required to establish a reading committee for the doctoral dissertation within six months after passing the department’s Ph.D. qualifying exams. Thereafter, the student should consult frequently with all members of the committee about the direction and progress of the dissertation research.

A dissertation reading committee consists of the principal dissertation adviser and at least two other readers. Reading committees in Bioengineering may include faculty from another department. It is expected that at least one member of the Bioengineering faculty be on each reading committee. The initial committee, and any subsequent changes, must be officially approved by the department Chair.

University Oral and Dissertation

The Ph.D. candidate is required to take the University oral examination after the dissertation is substantially completed (with the dissertation draft in writing), but before final approval. The examination consists of a public presentation of dissertation research, followed by substantive private questioning on the dissertation and related fields by the University oral committee (four selected faculty members, plus a chair from another department). Once the oral has been passed, the student finalizes the dissertation for reading committee review and final approval. Forms for the University oral scheduling and a one-page dissertation abstract should be submitted to the department student services office at least three weeks prior to the date of the oral for departmental review and approval.

Ph.D. Minor in Bioengineering

Doctoral students pursuing a Ph.D. degree in a major other than Bioengineering may apply for the Ph.D. minor in Bioengineering. A minor is a not a requirement for any degree, but is available when agreed upon by the student and the major and minor department.

Application forms, including the University's general requirements, can be found at http://registrar.stanford.edu/shared/forms.htm.

A student desiring a Ph.D. minor in Bioengineering must have a minor program advisor who is a regular Bioengineering faculty member. This advisor must be a member of the student's reading committee for the doctoral dissertation, and the entire reading committee must meet at least one year prior to the date of the student's dissertation defense.

The Ph.D. minor program must include at least 20 units of course work in Stanford Bioengineering or Bioengineering cognate courses at or above the 200 level. Of these 20 units, no more than 10 can be in cognate courses. All courses listed to fulfill the 20-unit requirement must be taken for a letter grade and the GPA must be at least 3.25. Courses used for a minor may not be used to also meet the requirements for a master's degree.

M.D./Ph.D. Dual Degree Program

Students interested in a career oriented towards bioengineering and medicine can pursue the combined M.D./Ph.D. degree program. Stanford has two ways to do an M.D./Ph.D. U.S. citizens and permanent residents can apply to the Medical Scientist Training Program and can be accepted with funding from both M.D. and Ph.D. programs for stipend and tuition. They can then select a bioengineering laboratory for their Ph.D. Students not admitted to the Medical Scientist Training Program must apply to be admitted separately to the M.D. program and the Ph.D. program of their choice.

The Ph.D. is administered by the Department of Bioengineering. To be formally admitted as a Ph.D. degree candidate in this combined degree program, the student must apply through normal departmental channels and must have earned or have plans to earn an M.S. in bioengineering or other engineering discipline at Stanford or another university. The M.S. requires 45 units of course work which consists of core bioengineering courses, technical electives, seminars, and 6 unrestricted units. Students must also pass the Department of Bioengineering Ph.D. qualifying examination.

For students fulfilling the full M.D. requirements who earned their master’s level engineering degree at Stanford, the Department of Bioengineering waives the normal departmental requirement of 15 units applied towards the Ph.D. degree beyond the master’s degree level through formal course work. Consistent with the University Ph.D. requirements, the department accepts 15 units comprised of courses, research, or seminars approved by the student’s academic adviser and the department chair. Students not completing their M.S. engineering degree at Stanford are required to take 15 units of formal course work in engineering-related areas as determined by their academic adviser.

Joint Degree Programs in Bioengineering and the School of Law

The School of Law and the Department of Bioengineering offer joint programs leading to either a J.D. degree combined with an M.S. degree in Bioengineering or to a J.D. degree combined with a Ph.D. in Bioengineering.

The J.D./M.S. and J.D./Ph.D. degree programs are designed for students who wish to prepare themselves intensively for careers in areas relating to both law and bioengineering. Students interested in either joint degree program must apply and gain entrance separately to the School of Law and the Department of Bioengineering and, as an additional step, must secure permission from both academic units to pursue degrees in those units as part of a joint degree program. Interest in either joint degree program should be noted on the student's admission applications and may be considered by the admission committee of each program. Alternatively, an enrolled student in either the Law School or the Bioengineering Department may apply for admission to the other program and for joint degree status in both academic units after commencing study in either program.

Joint degree students may elect to begin their course of study in either the School of Law or the Department of Bioengineering. Faculty advisers from each academic unit will participate in the planning and supervising of the student's joint program. Students must be enrolled full time in the Law School for the first year of law school, and, at some point during the joint program, may be required to devote one or more quarters largely or exclusively to studies in the Bioengineering program regardless of whether enrollment at that time is in the Law School or in the Department of Bioengineering. At all other times, enrollment may be in the graduate school or the Law School, and students may choose courses from either program regardless of where enrolled. Students must satisfy the requirements for both the J.D. and the M.S. or Ph.D. degrees as specified in the Stanford Bulletin or elsewhere.

The Law School shall approve courses from the Bioengineering Department that may count toward the J.D. degree, and the Bioengineering Department shall approve courses from the Law School that may count toward the M.S. or Ph.D. degree in Bioengineering. In either case, approval may consist of a list applicable to all joint degree students or may be tailored to each individual student's program. The lists may differ depending on whether the student is pursuing an M.S. or a Ph.D. in Bioengineering.

In the case of a J.D./M.S. program, no more than 45 units of approved courses may be counted toward both degrees. In the case of a J.D./Ph.D. program, no more than 54 units of approved courses may be counted toward both degrees. In either case, no more than 36 units of courses that originate outside the Law School may count toward the law degree. To the extent that courses under this joint degree program originate outside of the Law School but count toward the law degree, the law school credits permitted under Section 17(1) of the Law School Regulations shall be reduced on a unit-per-unit basis, but not below zero. The maximum number of law school credits that may be counted toward the M.S. or Ph.D. in Bioengineering is the greater of: (i) 15 units; or (ii) the maximum number of units from courses outside of the department that M.S. or Ph.D. candidates in Bioengineering are permitted to count toward the applicable degree under general departmental guidelines or in the case of a particular student's individual program. Tuition and financial aid arrangements will normally be through the school in which the student is then enrolled.

Chair: Norbert J. Pelc

Professors: Russ B. Altman, Annelise E. Barron, Kwabena Boahen, Dennis R. Carter, Karl Deisseroth, Scott L. Delp, Norbert J. Pelc, Stephen R. Quake, Matthew Scott, James R. Swartz, Paul Yock

Associate Professors: Jennifer R. Cochran, Markus Willard Covert, Andrew Endy, Jan T. Liphardt, Christina D. Smolke

Assistant Professors: Zev David Bryant, David B. Camarillo, Kerwyn C. Huang, Jin Hyung Lee, Michael Lin, Manu Prakash, Stanley Qi (effective October 2014), Ingmar Riedel-Kruse, Bo Wang (effective May 2015), Fan Yang

Courtesy Professors: Bruce Daniel, Daniel S. Fisher, Sanjiv Sam Gambhir, Garry Gold, Stuart B. Goodman, Thomas Krummel, Craig Levin, Michael T. Longaker, David Magnus, Lloyd B. Minor, Paul J. Wang, Joseph Woo

Courtesy Associate Professors: Rebecca Fahrig, Jeffrey A. Feinstein, Garry E. Gold, Brian Hargreaves, Sarah Heilshorn, Ellen Kuhl, Kim Butts Pauly, Marc E. Levenston, Sakti Srivastava

Courtesy Assistant Professors: James Wall

Consulting Faculty: Todd Brinton, Stephen Fodor, Uday Kumar, John Linehan, Gordon Saul, Charles Taylor

Graduate Related Courses

Units
BIOMEDIN 210Modeling Biomedical Systems: Ontology, Terminology, Problem Solving3
BIOMEDIN 217Translational Bioinformatics4
CHEMENG 450Advances in Biotechnology3
EE 369AMedical Imaging Systems I3
EE 369BMedical Imaging Systems II3
ME 280Skeletal Development and Evolution3
ME 287Mechanics of Biological Tissues3
ME 381Orthopaedic Bioengineering3
RAD 226In Vivo Magnetic Resonance Spectroscopy and Imaging3

Courses

BIOE 10N. Form and Function of Animal Skeletons. 3 Units.

Preference to freshmen. The biomechanics and mechanobiology of the musculoskeletal system in human beings and other vertebrates on the level of the whole organism, organ systems, tissues, and cell biology. Field trips to labs.
Same as: ME 10N.

BIOE 32Q. Bon Appètit, Marie Curie! The Science Behind Haute Cuisine. 3 Units.

This seminar is for anyone who loves food, cooking or science! We will focus on the science and biology behind the techniques and the taste buds. Not a single lecture will pass by without a delicious opportunity - each weekly meeting will include not only lecture, but also a lab demonstration and a chance to prepare classic dishes that illustrate that day's scientific concepts.

BIOE 36Q. The Biophysics of Innate Immunity. 3 Units.

The innate immune system provides our first line of defense against disease--bothninfections, and cancer. Innate immune effectors such as host defense peptides arendeployed by numerous cell types (for instance neutrophils, macrophages, NK cells,nepithelial cells and keratinocytes) and work by biophysical mechanisms of action. The ourse draws from the primary literature and covers the evolution, structures, mechanisms,and physiological functions of important "innate immune effectors" (components of the innate immune system that can attack pathogens, and infected or host cells, and kill or incapacitate them directly). The course is aimed at students who have an interest in biochemistry, molecular/cellular biology, biophysics, and/or bioengineering.

BIOE 41. Physical Biology of Macromolecules. 4 Units.

Principles of statistical physics, thermodynamics, and kinetics with applications to molecular biology. Topics include entropy, temperature, chemical forces, enzyme kinetics, free energy and its uses, self assembly, cooperative transitions in macromolecules, molecular machines, feedback, and accurate replication. Prerequisites: MATH 41, 42; CHEM 31A, B (or 31X); strongly recommended: PHYSICS 41, CME 100 or MATH 51, and CME 106; or instructor approval.

BIOE 42. Physical Biology of Cells. 4 Units.

Principles of transport, continuum mechanics, and fluids, with applications to cell biology. Topics include random walks, diffusion, Langevin dynamics, transport theory, low Reynolds number flow, and beam theory, with applications including quantitative models of protein trafficking in the cell, mechanics of the cell cytoskeleton, the effects of molecular noise in development, the electromagnetics of nerve impulses, and an introduction to cardiovascular fluid flow. Prerequisites: MATH 41, 42; CHEM 31A, B (or 31X); strongly recommended: CS 106A, PHYSICS 41, CME 100 or MATH 51, and CME 106; or instructor approval. 4 units, Spr (Huang, K).

BIOE 44. Fundamentals for Engineering Biology Lab. 4 Units.

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 41.

BIOE 51. Anatomy for Bioengineers. 4 Units.

Fundamental human anatomy, spanning major body systems and tissues including nerve, muscle, bone, cardiovascular, respiratory, gastrointestinal, and renal systems. Explore intricacies of structure and function, and how various body parts come together to form a coherent and adaptable living being. Correlate clinical conditions and therapeutic interventions. Participate in lab sessions with predissected cadaveric material and hands-on learning to gain understanding of the bioengineering human application domain. Encourage anatomical thinking, defining challenges and opportunities for bioengineers.

BIOE 70Q. Medical Device Innovation. 3 Units.

BIOE 70Q introduces students to the design of medical technologies and the non-technical factors that impact their clinical adoption and market success. Guest speakers include engineers, doctors, and other professionals who have helped bring ideas from concept to clinical use. Hands-on design projects will challenge students to invent their own solutions to clinical needs. No previous engineering training is required.

BIOE 80. Introduction to Bioengineering. 4 Units.

Broad but rigorous overview of the field of bioengineering, centered around the common theme of engineering analysis and design of biological systems. Topics include biomechanics, systems and synthetic biology, physical biology, biomolecular engineering, tissue engineering, and devices. Emphasis on critical thinking and problem solving approaches, and quantitative methods applied to biology. 4 units, Spr (Cochran)
Same as: ENGR 80.

BIOE 101. Systems Biology. 4 Units.

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.
Same as: BIOE 210.

BIOE 103. Systems Physiology and Design. 4 Units.

Physiology of intact human tissues, organs, and organ systems in health and disease, and bioengineering tools used (or needed) to probe and model these physiological systems. Topics: Clinical physiology, network physiology and system design/plasticity, diseases and interventions (major syndromes, simulation, and treatment, instrumentation for intervention, stimulation, diagnosis, and prevention), and new technologies including tissue engineering and optogenetics. Discussions of pathology of these systems in a clinical-case based format, with a view towards identifying unmet clinical needs. Learning computational skills that not only enable simulation of these systems but also apply more broadly to biomedical data analysis. Prerequisites: MATH 41, 42; CME 102; PHY 41; BIO 41, 42; strongly recommended PHY 43; or instructor approval.

BIOE 115. Computational Modeling of Microbial Communities. 4 Units.

Provides biologists with basic computational tools and knowledge to confront large datasets in a quantitative manner. Students learn basic programming skills focused on Matlab, but also are introduced to Perl and Python. Topics include: image analysis, bioinformatics algorithms, reaction diffusion modeling, Monte Carlo algorithms, and population dynamics. Students apply computational skills to a miniature research project studying the human gut microbiota.
Same as: MI 245.

BIOE 123. Optics and Devices Lab. 4 Units.

This course provides a hands-on introduction to designing, and building devices for controlling experiments in the field of bioengineering. This course focuses on the tools and concepts related to optics and electronics, but also touches on other valuable techniques such as rapid prototyping and micro-fluidics. The first part of the course consists of guided modules, while the second half of the course is project based where students design and develop their own biotic game. Prerequisites: BIOE 41 and Matlab recommended.

BIOE 131. Ethics in Bioengineering. 3 Units.

Bioengineering focuses on the development and application of new technologies in the biology and medicine. These technologies often have powerful effects on living systems at the microscopic and macroscopic level. They can provide great benefit to society, but they also can be used in dangerous or damaging ways. These effects may be positive or negative, and so it is critical that bioengineers understand the basic principles of ethics when thinking about how the technologies they develop can and should be applied. On a personal level, every bioengineer should understand the basic principles of ethical behavior in the professional setting. This course will involve substantial writing, and will use case-study methodology to introduce both societal and personal ethical principles, with a focus on practical applications.

BIOE 141A. Senior Capstone Design I. 4 Units.

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.

BIOE 141B. Senior Capstone Design II. 4 Units.

Lecture/Lab. Second course of two-quarter capstone sequence. Team based project introduces students to the process of designing new biological technologies to address societal needs. Emphasis is on implementing and testing the design from the first quarter with the at least one round of prototype iteration. Guest lectures and practical demonstrations are incorporated. Prerequisites: BIOE123 and BIOE44. This course is open only to seniors in the undergraduate Bioengineering program.

BIOE 191. Bioengineering Problems and Experimental Investigation. 1-5 Unit.

Directed study and research for undergraduates on a subject of mutual interest to student and instructor. Prerequisites: consent of instructor and adviser. (Staff).

BIOE 191X. Out-of-Department Advanced Research Laboratory in Bioengineering. 1-15 Unit.

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.

BIOE 201C. Diagnostic Devices Lab. 3 Units.

This course exposes students to the engineering principles and clinical application of medical devices through lectures and hands-on labs, performed in teams of two. Teams take measurements with these devices and fit their data to theory presented in the lecture. Devices covered include X-ray, CT, MRI, EEG, ECG, Ultrasound and BMI (Brain-machine interface). Prerequisites: BIOE 103 or BIOE 300B or EE 122B.
Same as: BIOE 301C.

BIOE 210. Systems Biology. 4 Units.

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.
Same as: BIOE 101.

BIOE 211. Biophysics of Multi-cellular Systems and Amorphous Computing. 2-3 Units.

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 discuss relevant literature and introduced to and apply pertinent mathematical and biophysical modeling approaches to various aspect multi-cellular systems, furthermore carry out real biology experiments over the web. Specific topics include: (Morphogen) gradients; reaction-diffusion systems (Turing patterns); visco-elastic aspects and forces in tissues; morphogenesis; coordinated gene expression, genetic oscillators and synchrony; genetic networks; self-organization, noise, robustness, and evolvability; game theory; emergent behavior; criticality; symmetries; scaling; fractals; agent based modeling. The course is geared towards a broadly interested graduate and advanced undergraduates audience such as from bio / applied physics, computer science, developmental and systems biology, and bio / tissue / mechanical / electrical engineering. Prerequisites: Previous knowledge in one programming language - ideally Matlab - is recommended; undergraduate students benefit from BIOE 41, BIOE 42, or equivalent.
Same as: BIOE 311, BIOPHYS 311, DBIO 211.

BIOE 212. Introduction to Biomedical Informatics Research Methodology. 3 Units.

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. Because the team projects start in the first week of class, attendance that week is strongly recommended. Prerequisites: BIOMEDIN 210, 211, 214, 217 or consent of instructor.
Same as: BIOMEDIN 212, CS 272, GENE 212.

BIOE 214. Representations and Algorithms for Computational Molecular Biology. 3-4 Units.

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.
Same as: BIOMEDIN 214, CS 274, GENE 214.

BIOE 220. Introduction to Imaging and Image-based Human Anatomy. 3 Units.

Focus on learning the fundamentals of each imaging modality including X-ray Imaging, Ultrasound, CT, and MRI, to learn normal human anatomy and how it appears on medical images, to learn the relative strengths of the modalities, and to answer, "What am I looking at?" Course website: http://rad220.stanford.edu
Same as: RAD 220.

BIOE 221. Physics and Engineering of Radionuclide Imaging. 3 Units.

Physics, instrumentation, and algorithms for positron emission tomography (PET) and single photon emission computed tomography (SPECT). Topics include basic physics of photon emission and detection, electronics, system design, strategies for tomographic image reconstruction, data correction algorithms, methods of image quantification, and image quality assessment, and current developments in the field. Prerequisites: Completion of university level mathematics and physics.
Same as: RAD 221.

BIOE 222. Instrumentation and Applications for Multi-modality Molecular Imaging of Living Subjects. 4 Units.

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. Covers basics of instrumentation physics, the origin and properties of the signal generation, and image data quantification.
Same as: RAD 222A.

BIOE 223. Physics and Engineering of X-Ray Computed Tomography. 3 Units.

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.
Same as: RAD 223.

BIOE 224. Probes and Applications for Multi-modality Molecular Imaging of Living Subjects. 4 Units.

Focuses on molecular contrast agents (a.k.a. "probes") that interrogate and target specific cellular and molecular disease mechanisms. Covers the ideal characteristics of molecular probes and how to optimize their design for use as effective imaging reagents that enables readout of specific steps in biological pathways and reveal the nature of disease through noninvasive imaging assays. Prerequisites: none.
Same as: RAD 222B.

BIOE 225. Ultrasound Imaging and Therapeutic Applications. 3 Units.

Covers the basic concepts of ultrasound imaging including acoustic properties of biological tissues, transducer hardware, beam formation, and clinical imaging. Also includes the therapeutic applications of ultrasound including thermal and mechanical effects, visualization of the temperature and radiation force with MRI, tissue assessment with MRI and ultrasound, and ultrasound-enhanced drug delivery. Course website: http://bioe325.stanford.edu
Same as: RAD 225.

BIOE 226. In Vivo Magnetic Resonance Spectroscopy and Imaging. 3 Units.

Collections of identical independent nuclear spins are described by the classical vector model of magnetic resonance imaging (MRI); however, interactions among spins, as occur in many in vivo processes, require a more complete description. Physics and engineering principles of these in vivo magnetic resonance phenomena with emphasis on current research questions and clinical applications. Topics: quantum mechanical description of magnetic resonance, density matrix theory, product operator formalism, relaxation theory and contrast mechanisms, spectroscopic imaging, spectral editing, and multinuclear studies. Prerequisites: EE 369B or familiarity with magnetic resonance, working knowledge of linear algebra.
Same as: RAD 226.

BIOE 227. Functional MRI Methods. 3 Units.

(Same as RAD 227, BIOPHYS 227) Basics of functional magnetic resonance neuroimaging, including data acquisition, analysis, and experimental design. Journal club sections. Cognitive neuroscience and clinical applications. Prerequisites: basic physics, mathematics; neuroscience recommended.

BIOE 229. Advanced Research Topics in Multi-modality Molecular Imaging of Living Subjects. 4 Units.

Covers advanced topics and controversies in molecular imaging in the understanding of biology and disease. Lectures will include discussion on instrumentation, probes and bioassays. Topics will address unmet needs for visualization and quantification of molecular pathways in biology as well as for diagnosis and disease management. Areas of unmet clinical needs include those in oncology, neurology, cardiovascular medicine and musculoskeletal diseases. The aim is to identify important problems and controversies in a field and address them by providing background and relevance through review of the relevant primary literature, and then proposing and evaluating innovative imaging strategies that are designed to address the problem. The organization of lectures is similar to the thought process that is necessary for writing an NIH grant proposal in which aims are proposed and supported by background and relevance. The innovation of proposed approaches will be highlighted. An aim of the course is to inform students on how to creatively think about a problem and propose a solution focusing on the key elements of writing a successful grant proposal. Prerequisites: none.
Same as: RAD 222C.

BIOE 231. Protein Engineering. 3 Units.

The design and engineering of biomolecules emphasizing proteins, antibodies, and enzymes. Combinatorial and rational methodologies, protein structure and function, and biophysical analyses of modified biomolecules. Clinically relevant examples from the literature and biotech industry. Prerequisite: basic biochemistry. Winter, Cochran
Same as: BIOE 331.

BIOE 236. Biophysical Mechanisms of Innate Immunity. 3 Units.

The innate immune system provides our first line of defense against infections of all kinds as well as cancer. Innate immune effectors, e.g. host defense peptides are deployed by numerous cell types (neutrophils, macrophages, NK cells, as well as epithelial cells, keratinocytes, and others) and attack by biophysical mechanisms of action. Disorders of innate immunity are increasingly being implicated in human autoimmune disease. Using primary literature, we will cover the evolution, structures, mechanisms, and functions of innate immune effectors.

BIOE 244. Advanced Frameworks and Approaches for Engineering Integrated Genetic Systems. 4 Units.

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.

BIOE 260. Tissue Engineering. 3 Units.

Principles of tissue engineering and design strategies for practical applications for tissue repair. Topics include tissue components and dynamics, morphogenesis, stem cells, cellular fate processes, cell and tissue characterization, controlled drug and gene delivery, bioreactors, cell-materials interactions, and host integration. Present research proposal to solve a real life tissue engineering problem.
Same as: ORTHO 260.

BIOE 261. Principles and Practice of Stem Cell Engineering. 3 Units.

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.
Same as: NSUR 261.

BIOE 273. BIODESIGN FOR MOBILE HEALTH. 1-2 Unit.

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.
Same as: MED 273.

BIOE 280. Skeletal Development and Evolution. 3 Units.

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: BIO 42, and ME 80 or BIOE 42.
Same as: ME 280.

BIOE 281. Biomechanics of Movement. 3 Units.

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.
Same as: ME 281.

BIOE 283. Mechanotransduction in Cells and Tissues. 3 Units.

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.
Same as: ME 244.

BIOE 284B. Cardiovascular Bioengineering. 3 Units.

Continuation of ME/BIOE 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.

BIOE 287. Introduction to Physiology and Biomechanics of Hearing. 3 Units.

Hearing is fundamental to our ability to communicate, yet in the US alone over 30 million people suffer some form of hearing impairment. As engineers and scientists, it is important for us to understand the underlying principles of the auditory system if we are to devise better ways of helping those with hearing loss. The goal of this course is to introduce undergraduate and graduate students to the anatomy, physiology, and biomechanics of hearing. Principles from acoustics, mechanics, and hydrodynamics will be used to build a foundational understanding of one of the most complex, interdisciplinary, and fascinating areas of biology. Topics include the evolution of hearing, computational modeling approaches, fluid-structure interactions, ion-channel transduction, psychoacoustics, diagnostic tools, and micrometer to millimeter scale imaging methods. We will also study current technologies for mitigating hearing loss via passive and active prostheses, as well as future regenerative therapies.
Same as: ME 166, ME 266.

BIOE 291. Principles and Practice of Optogenetics for Optical Control of Biological Tissues. 3 Units.

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.

BIOE 300A. Molecular and Cellular Bioengineering. 3 Units.

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.

BIOE 300B. Physiology and Tissue Engineering. 3 Units.

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.

BIOE 301A. Molecular and Cellular Engineering Lab. 2 Units.

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. Corequisite: 300A. Fall (Cochran).

BIOE 301B. Clinical Needs and Technology. 2 Units.

The goal of this course is to introduce bioengineering students to medical technology as it is used in current clinical practice, in the modern tertiary care, subspecialty hospital. Half of the course will be devoted to labs, in which small groups of students participate in hands-on experiences using advanced clinical technology in areas such as medical imaging, robotic surgery, and minimally invasive diagnosis and treatment. The second half of the course brings pairs of students and clinical faculty mentors together for a more in-depth, focused exposure to clinical care in one specific area. Final grades will be based on attendance, and presentations made by each pair of student to the class about their mentoring experience.

BIOE 301C. Diagnostic Devices Lab. 3 Units.

This course exposes students to the engineering principles and clinical application of medical devices through lectures and hands-on labs, performed in teams of two. Teams take measurements with these devices and fit their data to theory presented in the lecture. Devices covered include X-ray, CT, MRI, EEG, ECG, Ultrasound and BMI (Brain-machine interface). Prerequisites: BIOE 103 or BIOE 300B or EE 122B.
Same as: BIOE 201C.

BIOE 311. Biophysics of Multi-cellular Systems and Amorphous Computing. 2-3 Units.

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 discuss relevant literature and introduced to and apply pertinent mathematical and biophysical modeling approaches to various aspect multi-cellular systems, furthermore carry out real biology experiments over the web. Specific topics include: (Morphogen) gradients; reaction-diffusion systems (Turing patterns); visco-elastic aspects and forces in tissues; morphogenesis; coordinated gene expression, genetic oscillators and synchrony; genetic networks; self-organization, noise, robustness, and evolvability; game theory; emergent behavior; criticality; symmetries; scaling; fractals; agent based modeling. The course is geared towards a broadly interested graduate and advanced undergraduates audience such as from bio / applied physics, computer science, developmental and systems biology, and bio / tissue / mechanical / electrical engineering. Prerequisites: Previous knowledge in one programming language - ideally Matlab - is recommended; undergraduate students benefit from BIOE 41, BIOE 42, or equivalent.
Same as: BIOE 211, BIOPHYS 311, DBIO 211.

BIOE 313. Neuromorphics: Brains in Silicon. 3 Units.

This course introduces neuromorphic system design, starting at the device level, going through the circuit level, and ending up at the system level. At the device level, it covers MOS transistor operation in the subthreshold region. At the circuit level, it covers silicon neuron and synapse design. And at the system level, it covers to reroutable interconnection. At the end of the course, you will understand how various neuromorphic architectures¿ area and energy use scale with network size. Prerequisites: EE114 & EE108A.
Same as: EE 304.

BIOE 331. Protein Engineering. 3 Units.

The design and engineering of biomolecules emphasizing proteins, antibodies, and enzymes. Combinatorial and rational methodologies, protein structure and function, and biophysical analyses of modified biomolecules. Clinically relevant examples from the literature and biotech industry. Prerequisite: basic biochemistry. Winter, Cochran
Same as: BIOE 231.

BIOE 332. Large-Scale Neural Modeling. 3 Units.

This course examines the dynamics of large networks of spiking neurons (several thousand), with particular focus on how these networks achieve cognitive behaviors such as working memory, selective attention, and decision making. The course will feature lectures and labs using two Python-based simulators: Brian, a software platform, and Neurogrid, a hardware platform that simulates up to a million spiking neurons in real time. Most of the course will be project-based, allowing students to explore their individual interests.

BIOE 333. Interfacial Phenomena and Bionanotechnology. 3 Units.

Control over and understanding of interfacial phenomena and colloidal science are the essential foundation of bionanotechnology. Key mathematical relationships derived by Laplace, Gibbs, Kelvin and Young are derived and explained, along with the thermodynamics of systems of large interfacial area. Forces controlling surface and interfacial phenomena and surfactant and biomacromolecule self-assembly are discussed. Protein folding/unfolding and aggregation, and nano- and microfluidics are elucidated in these terms. Students will gain insight into the interplay between physical and chemical properties of biomolecules. Spring, (Barron, A.).

BIOE 334. Engineering Principles in Molecular Biology. 3 Units.

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.

BIOE 335. Molecular Motors I. 3 Units.

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.

BIOE 337. Organismic Biophysics and Living Soft-matter. 3 Units.

Integrated physical biology; from molecules to organisms. Tree of life, diversity of life forms. Multi-scale/hierarchical systems in biophysics, Hierarchical self-organization. Basic theory of squishy materials, colloidal physics. Phase transitions in living soft-matter. Experimental techniques in soft-matter physics. Active fluid models for living matter. Design of self-assembling and self-organizing, biomimetic supramolecular systems.

BIOE 355. Advanced Biochemical Engineering. 3 Units.

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.
Same as: CHEMENG 355.

BIOE 361. Biomaterials in Regenerative Medicine. 3 Units.

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.
Same as: MATSCI 381.

BIOE 370. Microfluidic Device Laboratory. 2 Units.

Fabrication of microfluidic devices for biological applications. Photolithography, soft lithography, and micromechanical valves and pumps. Emphasis is on device design, fabrication, and testing.

BIOE 371. Global Biodesign: Medical Technology in an International Context. 1-3 Unit.

(Same as OIT 587) Seminar examines the development and commercialization of medical technologies in the global setting focusing primarily on Europe, India and China. Faculty and guest speakers from industry and government discuss the status of the industry, as well as opportunities in and challenges to medical technology innovation unique to each geography. Topics related to development of technologies for bottom of the pyramid markets are also addressed. Students enrolling for 3 units are required to write and deliver a final paper.
Same as: MED 271.

BIOE 372. Design for Service Innovation. 4 Units.

(Same as OIT 343/01) Open to graduate students from all schools and departments. An experiential project course in which students work in multidisciplinary teams to design new services to address the needs of medically patients. Project teams partner with "safety net" hospitals and clinics to find better ways to deliver care to the low income and uninsured patients these institutions serve. Students learn proven innovation processes from experienced GSB, d. school, and SoM faculty, interface with students from across the university, and have the opportunity to see their ideas translated into improvements in the quality and efficiency of healthcare in the real world. Prerequisite: admission to the course is by application only. Applications available at http://DesignForService.stanford.edu. Applications must be submitted by November 16, 2011.
Same as: HRP 274, MED 274.

BIOE 374A. Biodesign Innovation: Needs Finding and Concept Creation. 4 Units.

This is the first quarter of a two-quarter course series (OIT 384/OIT 385). In this course, students learn how to develop comprehensive solutions (most commonly medical devices) to some of the most significant medical problems. The first quarter includes an introduction to needs finding methods, brainstorming and concept creation. Students learn strategies for understanding and interpreting clinical needs, researching literature and searching patents. Working in small entrepreneurial multidisciplinary teams, students gain exposure to clinical and scientific literature review, techniques of intellectual property analysis and feasibility, basic prototyping and market assessment. Students create, analyze and screen medical technology ideas, and select projects for future development. Final presentations at the end of the winter quarter to a panel of prominent inventors and investors in medical technology provide the impetus for further work in the spring quarter. Course format includes expert guest lecturers (Thu: 4:15 to 6:05 pm), faculty-led practical demonstrations and coaching sessions and interactive team meetings under the mentorship of Biodesign fellows (Tues: 4:15 to 6:05 pm). Projects from previous years included: prevention of hip fractures in the elderly; methods to accelerate healing after surgery; less invasive techniques for bariatric surgery; point of care diagnostics to improve emergency room efficiency; novel devices to bring specialty-type of care to primary care community doctors. More than 4,000 patients have been treated to date with technologies developed as part of this program and more than ten venture-backed companies were started by alums of the program. Students must apply and be accepted into the course. The application is available online at http://biodesign.stanford.edu/bdn/courses/bioe374.jsp.
Same as: ME 368A, MED 272A.

BIOE 374B. Biodesign Innovation: Concept Development and Implementation. 4 Units.

Two quarter sequence (continuation of OIT385 - see OIT384 for complete description of the sequence). The second quarter focuses on how to take a conceptual solution to an important medical need forward from early concept to technology translation, development and possible commercialization. Students expand on the topics they learned in OIT384 to learn about prototyping; patent strategies; advanced planning for reimbursement and FDA approval; choosing translation and commercialization route (licensing vs. start-up); marketing, sales and distribution strategies; ethical issues including conflict of interest; fundraising approaches and cash requirements; financial modeling; essentials of writing a business or research plan; strategies for assembling a development team. Students continue to work in multidisciplinary teams to select a final concept and develop a business plan. Final presentations are made to a panel of prominent venture investors and serve the role of a VC pitch. nnNew students (i.e. students who did not take OIT384 in the winter quarter) will need to submit an application at http://www.stanford.edu/group/biodesign/courseapplication11.html. Students who took OIT384 in the winter quarter are automatically accepted into the spring quarter.
Same as: ME 368B, MED 272B.

BIOE 375A. Biodesign Innovation: Needs Finding and Concept Creation. 2 Units.

Enrollment limited to SCPD students. 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.

BIOE 375B. Biodesign Innovation: Concept Development and Implementation. 2 Units.

Enrollment limited to SCPD students. 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. Prerequisite: BIOE 375A.

BIOE 376. Startup Garage: Design. 4 Units.

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.

BIOE 377. Startup Garage: Testing and Launch. 4 Units.

STRAMGT 356/BIOE 376 teams that concluded at the end of fall quarter that their preliminary product or service and business model suggest a path to viability, may continue with STRAMGT 366/BIOE 377 in winter quarter. Teams develop more elaborate versions of their product/service and business model, perform a series of experiments to test key hypotheses about their product and business model, and prepare and present an investor pitch for a seed round of financing to a panel of seasoned investors and entrepreneurs.

BIOE 381. Orthopaedic Bioengineering. 3 Units.

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.
Same as: ME 381.

BIOE 386. Neuromuscular Biomechanics. 3 Units.

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.

BIOE 390. Introduction to Bioengineering Research. 1-2 Unit.

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.
Same as: MED 289.

BIOE 391. Directed Study. 1-6 Unit.

May be used to prepare for research during a later quarter in 392. Faculty sponsor required. May be repeated for credit.

BIOE 392. Directed Investigation. 1-10 Unit.

For Bioengineering graduate students. Previous work in 391 may be required for background; faculty sponsor required. May be repeated for credit.

BIOE 393. Bioengineering Departmental Research Colloquium. 1 Unit.

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).

BIOE 450. Advances in Biotechnology. 3 Units.

Guest academic and industrial speakers. Latest developments in fields such as bioenergy, green process technology, production of industrial chemicals from renewable resources, protein pharmaceutical production, industrial enzyme production, stem cell applications, medical diagnostics, and medical imaging. Biotechnology ethics, business and patenting issues, and entrepreneurship in biotechnology.
Same as: CHEMENG 450.

BIOE 454. Synthetic Biology and Metabolic Engineering. 3 Units.

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.
Same as: CHEMENG 454.

BIOE 459. Frontiers in Interdisciplinary Biosciences. 1 Unit.

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.
Same as: BIO 459, BIOC 459, CHEM 459, CHEMENG 459, PSYCH 459.

BIOE 484. Computational Methods in Cardiovascular Bioengineering. 3 Units.

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.
Same as: ME 484.

BIOE 485. Modeling and Simulation of Human Movement. 3 Units.

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.
Same as: ME 485.

BIOE 500. Thesis. 1-15 Unit.

(Staff)
Same as: Ph.D.

BIOE 802. TGR Dissertation. 0 Units.

(Staff).