The Department of Biomedical Engineering Handbook.pdf2 Department of Biomedical Engineering Graduate Studies Handbook 2016-2017 3 Advising Each entering student is guided by the Director

bme.wustl.edu

The Department of Biomedical Engineering

Graduate Student Handbook 2016-2017

Graduate Studies Handbook 2016-2017 1

Table of Contents

PhD in Biomedical Engineering

Admissions Requirements 1

Coursework 1

Advising, Research Rotations 2

Seminars, Journal Clubs 2

Qualifying Exam & Thesis Proposal 2

Teaching, Dissertation Research 2

Master of Science

Admissions Requirements 3

Thesis Option, Non-thesis Option 3

Core Requirements 3

Master of Engineering in Biomedical Innovation

Program Requirements & Timeline 4

Research & Collaboration 5

Admissions Procedures 4

Financial Aid, Housing & Transportation 4

Research 5

Tenured & Tenure-Track Faculty 5

Educational Programs & Research Areas 15

Biomedical Engineering at Washington University is at the very heart of interdisciplinary research and education within the university. With a world-class and research-intensive medical school, there is the broadest commitment in all educational research activities to advancing basic science and research translation that enables us to better understand, diagnose and treat diseases affecting humankind.

As described herein, our Biomedical Engineering faculty’s research focuses on seven cutting-edge areas of biomedical engineering:

» Biomedical and Biological Imaging

» Cancer Technologies

» Cardiovascular Engineering

» Molecular & Cellular Systems Engineering

» Neural Engineering

» Orthopedic Engineering

» Regenerative Engineering in Medicine

Research activities in biomedical engineering are centered in the state-of-the-art Uncas A. Whitaker Hall and Stephen F. and Camilla T. Brauer Halls on the Danforth Campus, with students learning in more than 15 research-dedicated buildings across the Schools of Engineering & Applied Science, Arts & Sciences and Medicine. Our core and more than 70 affiliated faculty participate in a number of interdisciplinary research centers and pathways. This large and collegial community fuels an exciting and committed scientific community that promotes intellectual inquiry, technology transfer, community outreach and student governance. Biomedical Engineering at Washington University provides the highest caliber training through degree-related coursework, unparalleled research seminar series, additional learning opportunities, a broad and rich entrepreneurial culture, and numerous student groups that support social and outreach activities.

We greatly appreciate the contributions, encouragement, commitment and guidance of our many colleagues, students, friends and supporters that have contributed to the success and growth of our department. We hope you will join us to engage in the very best education and preparation for any engineer seeking to improve human health and advance basic science.

Welcome to Biomedical Engineering

Department Facts » 19 tenured/tenure-track faculty

» $10.17 M in research expenditures (FY16)

» 151 Graduate students

» 304 undergraduate students

» No. 14 graduate program in U.S. News ranking (2015)

About the Program Students seeking the PhD in Biomedical Engineering will focus on seven overlapping research programs that represent frontier areas of biomedical engineering and leverage the existing strengths of our current faculty and resources. Our core and more than 70 affiliated faculty participate in a number of interdisciplinary research centers and pathways offering students the opportunity to learn in a diverse and rich spectrum of BME research areas. The MD/PhD in Biomedical Engineering, given jointly with the top-ranked School of Medicine, gives students in-depth training in modern biomedical research and clinical medicine. The typical MD/PhD career combines patient care and biomedical research but leans toward research.

Students pursuing the PhD in Biomedical Engineering must complete a core curriculum; fulfill a distribution requirement; satisfactorily complete two research rotations; pass the qualifying examination; pass the thesis proposal; complete a teaching assistantship; complete one accepted first author publication and submission of second manuscript to a peer-reviewed journal; and complete a research dissertation.

Students pursuing the combined MD/PhD in Biomedical Engineering must complete the degree requirements for both schools. MD/PhD students typically complete the first two years of the medical school pre-clinical curriculum while also performing one or more research rotations, then the remaining requirements for the doctoral degree, and finally the clinical training years of the medical degree. The department generally gives graduate course credits for some of the medical school courses toward fulfillment of course requirements for the PhD degree. This is arranged on an individual basis between the student, his or her academic adviser, and the director of doctoral studies.

Admissions Requirements 1. A baccalaureate degree in engineering or the physical sciences/

mathematics. (A life science degree may be acceptable with evidence of adequate quantitative coursework.)

2. Courses highly recommended:

3. Students seeking financial aid must take the general sections of the Graduate Record Examination. International students must also submit TOEFL scores earned within the past two years.

4. Undergraduate or postgraduate research experience is highly desirable for admission to the PhD program. Letters of recommendation from research mentors are a particularly important part of the graduate application. Descriptions of previous research experience or future research goals in the personal statement portion of the application are also important in the admissions decision.

5. Selected, qualified students residing in the U.S. may be invited to campus to interview with faculty and other students prior to or after being offered admission.

Students wishing to pursue the combined MD/PhD degrees must apply to the Medical Science Training Program of the Washington University School of Medicine. Information about this option can be obtained at: http://mstp.wustl.edu/Pages/index.aspx.

Coursework The doctoral degree requires a minimum of 72 credits beyond the bachelor’s level, with a minimum of 36 being course credits (including the core curriculum) and a minimum of 24 credits of doctoral dissertation research.

The core curriculum that must be satisfied by all PhD students consists of the following:

» One graduate level course in life sciences

» One graduate level course in mathematics

» One graduate level course in computer science or exemption by proficiency

» Four BME courses from the approved list

The core requirements represent 6-7 courses, with a total of 9 graduate courses required for the PhD. Up to 9 units of BME 601C Research Rotation and/or BME 501C Graduate Seminar may be counted towards the 36 units of graduate coursework required for the PhD. Up to two 400-level courses may be counted towards the 9 courses of graduate coursework required for the Ph.D. (not including independent study courses, journal clubs or seminar-based courses).

Lori SettonDirector of Doctoral Studies

Dennis Barbour, MDDirector of Masters Studies

PhD in Biomedical Engineering

» Advanced Calculus and Differential Equations

» Probability and Statistics

» Engineering Mathematics

» Physics

» Introductory Computer Science

» Circuits/ Electrical Networks

» Basic Courses in Molecular and Cell Biology

» General and Organic Chemistry

Graduate Studies Handbook 2016-2017 32 Department of Biomedical Engineering

Advising Each entering student is guided by the Director of Doctoral Studies. The Director will help in the selection of courses and in the selection rotations with the aim of matching each individual’s research interests with those of a research supervisor.

As a student progresses through the doctoral program, the advisor’s role is replaced by the dissertation mentor to reflect the increasing focus on an area of specialization. By the time research is completed, the student will have assembled an advisory group consisting of his/her dissertation committee.

Research Rotations Research rotations serve three important purposes:

1. They provide an opportunity for each student to be exposed to different areas of biomedical engineering research. This broadening experience, prior to the subsequent necessary specialization, should prove to be useful as their careers develop.

2. The rotations serve as an introductions for both students and potential research mentors for the long-term affiliation that is associated with a doctoral dissertation research.

3. The field of research represented in one rotation report serves as the basis for the qualifying examination.

While also enrolled in classes, within the first year of matriculation, students are required to complete one, two or three research rotations, each typically lasting one semester, by the end of their first full year of enrollment. The rotations can be performed under the mentorship of any of the Graduate Group Faculty — core BME faculty and affiliated faculty. A written report, co-signed by the rotation mentor signifying completion of the research, is required at the end of each rotation. A third rotation early in the summer is optional.

SeminarsAll doctoral students are required to attend a weekly research seminar sponsored by the department (or with permission, an affiliated department), which is a pass/fail course carrying 0 units or 1 units. Up to 3 units of BME501C may be counted towards the 36 units course requirement. These seminars provide exposure to state-of-the-art research by scientists both within and outside of Washington University. Regular attendance over the duration of a student’s tenure provides an invaluable educational experience.

Journal ClubsMany laboratories sponsor a journal club, whose purpose is to critically analyze recent journal publications of interest to investigators in that field. Students and postdoctoral fellows

conducting research in that laboratory, as well as those who are rotating through that laboratory, are required to attend these sessions. Generally, a student volunteers to read and present a recent paper of wide interest. Questions from faculty and other students bring out the significance of the paper’s findings and possible weaknesses in its arguments.

Journal Club is an important stepping stone as a student moves into the research phase of their doctoral program. In particular, it provides excellent preparation for the dissertation defense.

Qualifying Exam & Thesis ProposalNo later than the end of the first year of enrollment in the doctoral program, students are required to take and pass both written and oral qualifying examinations. Qualifying exam dates are determined by the number of rotations performed. The written portion consists of one of the rotation reports, while the oral portion covers the fields of research encompassed by the research done in the rotation.

A written and oral thesis proposal normally should be completed within two years of completion of the qualifying exam. The thesis committee must meet annually, however, so the thesis committee must be formed within one year of passing the qualifying exam. The members of the thesis committee may change as the research topic evolves.

TeachingEach doctoral student is required to serve as an unpaid teaching assistant for one semester after they have passed their qualifying examinations. Those desiring an academic career, are strongly encouraged to spend at least one additional semester (with the permission of their thesis mentor) as a teaching assistant in one of the department’s undergraduate or graduate courses.

Dissertation ResearchAfter the thesis proposal is approved, no later than two years after successfully completing the qualifying examination, dissertation research occupies the bulk of the student’s effort. Upon completion of the dissertation, students will defend the dissertation. At the time of the defense, the student will have acceptance of one first-author (or co-first author) paper and submission of a second manuscript in a peer-reviewed journal. After this defense, presentation to and acceptance by the registrar’s office of the final dissertation completes the degree requirements.

About the Program Candidates for the MS must accumulate a total of 30 graduate course credits beyond the bachelor’s degree. Only 6 of the 30 graduate course credits may be transferred from another university. There are two options, thesis and non-thesis.

Admissions Requirements 1. A baccalaureate degree in engineering or the physical sciences/

mathematics. (A life science degree may be acceptable with evidence of adequate quantitative coursework.) Admitted MS students typically have had grade point averages of 3.5 and 3.7 out of 4.0, respectively.

2. Courses highly recommended:

3. Students must take the general sections of the Graduate Record Examination (admitted students have an average score greater than 164 on the quantitative section (new GRE scale) and 4.5 or greater on the analytical section). International students must also submit TOEFL scores earned within the past two years. Scores of 100 or greater are generally required with no less than 20 on each section.

4. Undergraduate or postgraduate research experience is recommended but not mandatory for the MS program. Letters of recommendation from research mentors are a particularly important part of the MS application. Descriptions of previous research experience or future research goals in the personal statement portion of the application are also important in the admissions decision.

Thesis OptionFor this option, a minimum of 24 credits of coursework is required, with the balance being thesis research. The courses must fulfill the core curriculum requirement.

The remainder of the coursework is generally driven by the student’s research interest. Upon completion of the thesis, the candidate must pass an oral defense conducted by his/her thesis committee. This will consist of a public presentation followed by questions from the committee. Candidates must have a cumulative grade point average of 2.7 or better to receive the degree.

Non-thesis Option Candidates must accumulate a total of 30 graduate credits, have a cumulative grade point average of 2.7 or better, and satisfy the core curriculum requirements. The balance of the course credits should be selected with a view toward coherence reflecting a specialization in a research area.

Core Curriculum RequirementsA core curriculum that must be satisfied by all MS students consists of the following:

» Two graduate level courses in life sciences

» One graduate level course in mathematics

» One graduate level course in computer science

» Three BME courses from the approved course list

Graduate level courses given by other departments and schools may be substituted for courses in this list with the permission of the director of masters studies.

Up to two 400-level courses may be counted towards the 9 courses of graduate coursework required for the MS (not including independent study courses, journal clubs or seminar-based courses).

The Master of Science (MS)

» Advanced Calculus and Differential Equations

» Probability and Statistics

» Engineering Mathematics

» Physics

» Introductory Computer Science

» Circuits/ Electrical Networks

» Basic Courses in Molecular and Cell Biology

» General and Organic Chemistry


Admissions Procedures Prospective graduate students should apply online at:

engineering.wustl.edu/gradappinfo.aspx

» PhD deadline for submission: January 15

» MEng-BMI deadline for submission: January 15

» MS (entering Spring) deadline for submission: October 1

» MS (entering Fall) deadline for submission: March 1

Financial Aid In addition to offering you a quality education, the School of Engineering & Applied Science offers students several forms of federal financial assistance.

PhD applicants

All full-time PhD applications are reviewed for full financial support. Most offers of financial support are guaranteed as long as the student is making satisfactory progress toward completion of the degree.

» Chancellor’s Graduate Fellowship (for engineering PhD diversity applicants)

» Olin Fellowship (for engineering women PhD students)

Master’s applicants

Master’s applicants are expected to be self-supporting and are not eligible for teaching or research assistantships. U.S. citizens and permanent residents may be eligible for loans.

Housing The university owns more than 250 apartment complexes available for rent to graduate students. Many of these apartments are connected to the university’s telephone and computer network. For more information:

Parkview Properties: (314) 721-7106

Quadrangle Housing Co.: offcampushousing.wustl.edu

TransportationThe Danforth Campus and the Medical Campus are three miles apart, separated by Forest Park. Transportation between campuses, and the residential areas between them, is easy by bicycle or university shuttle buses. In addition, three stations for Metrolink, the light rail system, serve the university. Free passes for bus and Metrolink service are available to full-time students.

Mark A. AnastasioProfessor of Biomedical Engineering and Associate ChairPhD, Medical Physics, The University of Chicago, 2001

MS, University of Illinois at Chicago, 1995

MSE, University of Pennsylvania, 1993

BS, Illinois Institute of Technology, 1992

Current ResearchThe research activities in my laboratory broadly address the engineering and scientific principles of biomedical imaging. Almost all modern biomedical imaging systems including advanced microscopy methods, X-ray computed tomography, magnetic resonance imaging and photoacoustic computed tomography, to name only a few, utilize computational methods for image formation. The development of image reconstruction methods for novel computed imaging systems is a theme that underlies many of our projects.

Our current research projects include the development of advanced X-ray, optical and acoustical imaging systems that are based on wave physics and can provide important structural and physiological tissue information. These projects can be grouped into the following categories: (1) photoacoustic and thermoacoustic imaging; (2) X-ray phase-contrast imaging; (3) optical and acoustical tomography and holography; and (4) improvement of existing clinical imaging methods.

An image of in-situ mouse lungs obtained by use of an X-ray phase-contrast imager developed in Anastasio’s laboratory.

Research InterestsDevelopment of biomedical imaging

methods; photoacoustic tomography,

X-ray phase-contrast imaging, image

reconstruction and inverse problems in

imaging; theoretical image science

Office: Brauer Hall, Room 2009Phone: (314) 935-3637Email: [email protected]

Master of Engineering in Biomedical InnovationThe MEng-BMI is a 12-month intensive, hands-on program for students seeking to hone their engineering skills and acquire the entrepreneurial skills necessary to convert great ideas into products that benefit people. This professional training program allows students to develop a well-rounded skillset comparable to engineers with multiple years of industry experience.

With guidance, students initially identify problems in health care that can be solved through the judicious application of technology. They then spend the remainder of the program learning in groups not only to solve an important problem, but also to learn how to develop and protect intellectual property, to raise money and to construct a business plan to see their solution implemented in society. Graduates will have the tools to start their own companies or take advanced positions in established enterprises dedicated to improving health care.

Program RequirementsThis 12-month professional graduate degree is designed for students interested in entrepreneurship or “intra”preneurship for advanced placement within a medical device company. It is a team-based approach in which students develop the engineering, manufacturing and business skills to solve an unmet clinical need.

The program consists of 30 units that are distributed into five areas:

» Engineering Skills (6 units)

» Master Design (10 units)

» Biomedical Project Development (4 units)

» Biomedical Business Development (4 units)

» Targeted Electives (6 units)

Applicants must be U.S. citizens or permanent U.S. residents.

Program TimelineIdentification of a specific design program for Master Design will take place within two months of the program’s late May-early June start. During this time, students will shadow WashU physicians at either Barnes-Jewish Hospital or St. Louis Children’s Hospital to identify various clinical needs. In July, students will participate in a retreat to brainstorm potential solutions to various clinical needs, and teams will be chosen at the beginning of fall semester and may include team members from other programs in the university.

Research We focus on overlapping research programs that represent frontier areas of biomedical engineering and leverage the existing strengths of our current faculty and resources. These areas provide exciting training opportunities for students with a variety of backgrounds and interests.

Collaborative Research At Washington University, world-class biological, engineering and medical research — along with top-notch, state-of-the-art healthcare — are closely intertwined. For more than 50 years, collaborations between the School of Medicine and the School of Engineering & Applied Science have led to major advances in many areas including: positron emission tomography, medical applications of ultrasound, application of computers to hearing research, bone and ligament healing, nerve regeneration and development of heart valve flow simulators. This atmosphere of collaboration and collegiality between the two schools has been further strengthened and expanded, leading to an exceptional degree of synergy that is one of our hallmarks.

The core faculty, together with affiliated faculty from other departments (listed under the description of each educational program) form a network of mentors dedicated to training the next generation of biomedical engineers. Our goal is to educate students in an interdisciplinary manner so that they can effectively collaborate with physicians, biologists and other life scientists to build their careers. Students can elect to perform their research with any of more than 70 affiliated graduate group mentors. Our graduates are well- equipped to work in multidisciplinary teams tackling cutting-edge and high-impact problems of modern biomedical engineering.

Research SupportResearch pursuits are central to all activities of Washington University. This is reflected in the awarding of more than 6 NIH training grants to support biomedical engineering students, and over $375M in funding from the National Institutes of Health annually. In addition to NIH-sponsored research, the department has and participates in NSF and DOD-sponsored research grants that support doctoral students in the completion of their dissertation research.


Jan BieschkeAssistant Professor of Biomedical EngineeringPhD, Max-Planck-Institute for Biophysical Chemistry, Germany, 2000

Chemistry Diploma, University Goettingen, Germany, 1996

Current ResearchOur research focuses on mechanism of protein misfolding and self-assembly that form cytotoxic fibrillar protein deposits in amyloid diseases such as Alzheimer’s and Parkinson’s disease. My group aims to quantitatively understand the fate of misfolded proteins in the cell. We are tracking the formation and degradation of single particles of misfolded proteins in the cellular environment by single molecule fluorescence and other biophysical techniques. We aim to understand how different proteins influence each other’s misfolding trajectories and to develop strategies to derail protein misfolding processes by small molecules and by conventional and unconventional chaperones.

Research InterestsMechanisms and modulators of age-related protein misfolding processes, amyloid formation, single molecule fluorescence, atomic force microscopy


Mechanism of amyloid self-assembly and possible intervention points (a-e). Unstructured or natively folded monomeric protein assembles into amyloid fibrils in a multistep process that involves an energetic barrier in form of an oligomeric nucleus. Fibrils can replicate in an autocatalytic, prion-like mechanism.

Hong ChenAssistant Professor of Biomedical Engineering, Assistant Professor of Radiation OncologyPhD, Bioengineering, University of Washington-Seattle, 2011

ME, Biomedical Engineering, Xi’an Jiaotong University, 2006

BE, Biomedical Engineering, Xi’an Jiaotong University, 2003

Research InterestsUltrasound imaging; ultrasound therapy; image-guided ultrasound drug delivery (IGUDD)


Current ResearchUltrasound, one of the most widely used medical imaging modalities, is currently being developed as a noninvasive, targeted therapeutic technique that has incredible potential to transform the treatment of a variety of diseases. Combining imaging and therapy, ultrasound provides a platform technology that is applicable for disease diagnosis, targeted therapy delivery, and therapy response monitoring. The mission of the image-guided ultrasound drug delivery (IGUDD) laboratory is to translate basic research advances in ultrasound imaging and therapy into innovative medical devices that can impact cancer patient care. Research in our lab involves two main themes: (1) delivery cancer drugs across biological barriers by ultrasound mechanical effect; (2) controlled cancer drug release by ultrasound thermal effect.

Jianmin CuiProfessor of Biomedical Engineering on the Spencer T. Olin Endowment, Associate Professor of Cell Biology & PhysiologyPhD, Physiology & Biophysics, State University of New York, 1992

MS, Peking University, 1986

BS, Peking University, 1983

Research InterestsMolecular basis of bioelectricity and related diseases in nervous and cardiovascular systems; ion channel function and modulation; discovery of drugs that target ion channels and improve cardiac function; electrophysiology; fluorescence measurements, computer modeling, molecular biology, biophysics

Office: Whitaker Hall, Room 290CPhone: (314) 935-8896Email: [email protected]

Current ResearchIon channels are the molecular units of electrical activity in all cell types, which underlie important physiological functions such as heart contraction and neural activities. Aberrant ion channels are associated with various diseases. My research interests are on ion channel associated diseases and include three aspects: the fundamental mechanisms of ion channel function, the change of these functions by mutation or drugs that lead to diseases, and discovery of new drugs that target ion channels and improve physiological function. We currently use molecular biology, protein biochemistry, electrophysiology, fluorescence techniques, and computer modeling to study two potassium channels: 1) The BK type channels, which are important in the control of blood pressure and neurotransmitter release and are implicated in hypertension and epilepsy; 2) The IKS potassium channels that are important in the rhythmic control of the heart rate. Defects in IKS can cause cardiac arrhythmias that lead to syncope and sudden death.

Ion channels are membrane proteins, formed by different structural domains that sense physiological stimuli (such as the voltage sensing domain, VSD, and the cytosolic Ca2+ sensing domain, CTD) and the pore (the pore-gate domain, PGD). We study how ion channels sense physiological stimulations and how the conformational changes in sensing domains alter the PGD to open the channel pore.

Dennis L. BarbourAssociate Professor of Biomedical Engineering, Associate Professor of Neuroscience and Otolaryngology, Director of Masters StudiesMD, Johns Hopkins School of Medicine, 2003

PhD, Biomedical Engineering, Johns Hopkins University, 2003

BEE, Georgia Institute of Technology, 1995

Current ResearchMy research focuses on the encoding of sound information in the brain and how neural circuits can be modified to improve that encoding under adverse listening conditions, particularly for individuals with hearing loss who use an auditory prosthetic. We design novel software based on advanced machine learning principles that can be used to diagnose auditory processing disorders and then potentially improve listening function through repeated use. Our hearing tests are the most advanced in their class, and the platform we have developed can be applied to other perceptual and cognitive tests to similarly improve the diagnostic power of these tests. Ultimately, these advances will pave the way for more thorough patient evaluations and rational treatment plans to improve patient outcomes.

Different forms of hearing loss diagnosed by a machine learning algorithm

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Research InterestsAuditory processing, cognitive neuroscience, machine learning and medical diagnostics

Office: Whitaker Hall, Room 200EPhone: (314) 935-7548Email: [email protected]


Vitaly A. Klyachko Associate Professor of Biomedical Engineering, Associate Professor of Cell Biology & PhysiologyPhD, Biophysics. University of Wisconsin-Madison, 2002

MS, BS, Moscow State University, 1998

Research InterestsSynaptic function and plasticity; neural circuits; information analysis; neurological disorders

Office: BJCIH, Room 9610 (Medical School Campus)Phone: (314) 362-5517Email: [email protected]

Current ResearchOur research focuses on synaptic function and plasticity with the goal to understand how neural circuits analyze information in the brain. We are developing novel imaging and electrophysiological techniques to study plasticity at individual synapses and functional circuits. Our lab currently focuses on three main areas of research: (1) Elucidating presynaptic release mechanisms at the level of individual synapses using high-resolution imaging techniques, advanced image analysis and computational approaches; (2) Investigating how presynaptic processes give rise to rapid forms of synaptic plasticity and how this plasticity determines information processing by individual synapses and functional circuits; (3) Relating deregulation in rapid synaptic plasticity with the impairment of information processing observed in neurodegenerative diseases, such as Fragile X syndrome and autism spectrum disorders.

Nanoscale resolution imaging of synaptic vesicle dynamics in central synapses.

Daniel W. MoranProfessor of Biomedical Engineering, Professor of Neuroscience, and Neurological Surgery PhD, Bioengineering, Arizona State University, 1994

BS, Milwaukee School of Engineering, 1989

Research InterestsMotor control; brain-computer interfaces

Office: Whitaker 300FPhone: (314) 747-6291Email: [email protected]

Current ResearchMy lab investigates how various neural substrates control voluntary movement. Our recent findings show that individual cells in primary motor cortex encode both translational and rotational kinematics of arm movement. (i.e. hand position/orientation and their time derivatives) Using novel decoding schemes in our brain-computer interface (BCI) studies, we are able to simultaneously predict movement kinematics from a population of motor cortical neurons allowing our subjects to control computer cursors through thought alone. Furthermore, we have pioneered a new recording modality, electrocorticography or ECoG, that allows us to implant minimally invasive recording electrodes on the surface of the brain for BCI applications. Our subjects have learned to accurately control a 3D computer cursor through neural adaptation of microECoG signals. Future research will involve controlling complex 3D musculoskeletal models with cortical signals with the eventual goal of designing BCI systems for amputees or paralyzed individuals that will allow neuroprosthetic control of a robotic limb or functional electrical stimulation (FES) of a paralyzed limb.

Our lab is interested in the development of novel neuroprosthetics devices capable of interfacing nervous tissue. Neural probes such as the WashU MacroSieve shown here are designed to interface peripheral nerves offering precise motor control of the extremities, accurate recording of sensory stimuli, and bi-directional neural control of integrated prosthetic devices.

Kristen M. NaegleAssistant Professor of Biomedical EngineeringPhD, Biological Engineering, Massachusetts Institute of Technology, 2010

SM, Biological Engineering, Massachusetts Institute of Technology, 2006

MS, Electrical Engineering, University of Washington, 2004

BS, Electrical Engineering, University of Washington, 2001

Research InterestsComputational molecular systems biology, post-translation modifications, signal transduction, proteomics


Current ResearchOur lab is interested in understanding the regulation and function of a wide variety of post-translational modifications (PTMs), in cellular signaling networks. With the advent of new technologies, PTMs are being discovered at unprecedented rates, faster than their role in the cell can be understood. Our lab uses computational techniques, such as data mining and modeling, to make predictions regarding how post-translational modifications are regulated and their subsequent effect on the protein and the networks the protein is involved in regulating. We also use molecular biology techniques to further explore predictions and insights garnered from computational techniques. Our studies are guided by the desire to understand normal and dysregulated signaling events, which can lead to human diseases. Understanding the molecular underpinnings of cellular regulation may improve our ability to design therapeutic interventions for diseases such as cancer, diabetes and neurodegenerative disorders.

Steven C. GeorgeElvera and William Stuckenberg Professor and ChairPhD, University of Washington–Seattle, 1995

MD, University of Missouri–Columbia, 1991

BS, Northwestern University, 1987

Research InterestsTissue engineering; “organ-on-a-chip” technology; vascularizing engineered tissues; cancer microenvironment

Office: Whitaker Hall, Room 190A Phone: (314) 935-6164Email: [email protected]

Current ResearchMy research interests include tissue engineering with a focus on creating in vitro microphysiological systems that mimic specific features of human organs. Of particular interest is the incorporation of a vascular supply to deliver nutrients and remove waste products from both normal (cardiac muscle) and cancerous tissue, which also facilitates investigation of projects related to cancer metastasis, and cardiac muscle repair following infarction. The projects include innovative platform designs, hypothesis-driven (mechanisms of cancer metastasis) investigation, as well as translational projects (high-throughput drug screening). In addition, the research is highly interdisciplinary, involving collaboration from across campus while integrating modern technologies in the areas of induced pluripotent stem cells, genome editing, microfabrication, microfluidics, and optical imaging.

Colon cancer cells (green fluorescence) are combined with endothelial cells (red fluorescence) in a spheroid (250 microns in diameter) and placed in a fibrin gel. 4-7 days later a robust vascular network forms and the cancer cells migrate within the vascular lumens mimicking steps in cancer metastasis


Current ResearchMy research interests are in understanding the design and computing principles of biological sensory systems and translating this knowledge into neuromorphic devices and algorithms. Specifically, we focus on studying the relatively simple invertebrate olfactory system. Combining a variety of electrophysiological recording techniques and computational modeling approaches, we investigate how the multi-dimensional and dynamic odor signals are encoded as neural representations and processed by olfactory circuits in the brain.

Understanding how the nervous system interprets complex sensory stimuli is also important for developing bio-inspired solutions to address parallel engineering problems. We are currently working on developing and using cyborg insects as biorobotic sensing machines. Potential target applications for the electronic nose technology include medical diagnosis, homeland security, environmental monitoring, space explorations, robotics, and human-computer interaction.

Baranidharan RamanAssociate Professor of Biomedical EngineeringPhD, Computer Science, Texas A&M University, 2005

MS, Computer Science, Texas A&M University, 2003

B Eng, Computer Engineering, University of Madras, 2000

Research InterestsComputational and systems neuroscience; neuromorphic engineering; pattern recognition; sensor-based machine olfaction


Research in my laboratory focuses on understanding the design and computing principles of biological sensory systems and translating this knowledge into bio-inspired intelligent systems and machine learning algorithms.

Yoram RudyThe Fred Saigh Distinguished Professor of Engineering, Professor of Cell Biology & Physiology, of Medicine, of Radiology and of Pediatrics, Director, Cardiac Bioelectricity and Arrhythmia CenterPhD, Biomedical Engineering, Case Western Reserve University, 1978

MSc, Technion – Israel Institute of Technology, 1973

BSc, Technion – Israel Institute of Technology, 1971

Research InterestsCardiac electrophysiology and arrhythmias; molecular dynamics of ion channels; computational biology and mathematical modeling; imaging and mapping of cardiac electrical activity in patients

Office: Whitaker Hall, Room 290BPhone: (314) 935-8160Email: [email protected]

Current ResearchRhythm disorders of the heart lead to more than 400,000 cases of sudden death annually in the U.S. alone. Our research aims at understanding the mechanisms that underlie normal and abnormal rhythms of the heart at various levels, from the molecular and cellular to the whole heart. Through development of detailed mathematical models of ion channels biophysics and electrophysiology, and of cardiac cells and tissue, we are investigating arrhythmia mechanisms. We have also developed a novel noninvasive imaging modality (Electrocardiographic Imaging, ECGI) for diagnosis and guided therapy of cardiac arrhythmias. We use ECGI to study mechanisms of clinical arrhythmias (e.g. atrial fibrillation, ventricular tachycardia, heart failure) in patients. Our premise is that an integrated approach to the study of mechanisms at all levels of the cardiac system and the development of novel diagnostic and therapeutic tools will lead to successful strategies for prevention and treatment of cardiac arrhythmias and sudden death.

We study the heart at multiple scales, from the molecular structure of ion channels (left panel) to whole-heart function in patients (right panel).

Lori A. SettonLucy and Stanley Lopata Distinguished Professor of Biomedical Engineering, Director of Doctoral StudiesPhD, Mechanical Engineering/Biomechanics, Columbia University, 1988

MS, Mechanical Engineering/Biomechanics, Columbia University, 1988

BSE, Mechanical and Aerospace Engineering, Princeton University, 1984

Research InterestsMechanobiology of osteoarthritis and intervertebral disc disorders, tissue regeneration and drug delivery in musculoskeletal disease

Office: Whitaker Hall, Room 390E

Phone: (314) 935-8612Email: [email protected]

Current ResearchMechanical loading and inflammation interact and contribute to progressive tissue degeneration in intervertebral disc disorders and osteoarthritis. Translational research in my laboratory includes our development of local drug depots for sustained release of small molecule and protein inflammatory antagonists that can interfere with progressive pathology in these conditions. Our current work focuses on the development of imaging and fluid-based biomarkers of disease to characterize therapy benefits for pain and dysfunction. We are also studying a role for mechanics and protein presentation in regulating tissue regeneration and cellular responses to inflammation, and advancing use of genomic editing for attenuation of inflammation and pain in neuropathy. Members of my laboratory use experimental cellular systems, polymer design, mathematical modeling and animal models to advance our research goals.

Polymers are engineered with precise control of stiffness and peptide presentation for injectable delivery of materials that regulate cell phenotype and biosynthesis in the intervertebral disc

Rohit V. PappuEdwin H. Murty Professor of Engineering, Director, Center for Biological Systems EngineeringPhD, Theoretical and Biological Physics, Tufts University, 1996

MS, Tufts University, 1993

BSc, Bangalore University, 1990

Research InterestsProtein aggregation and its effects on neurodegeneration; biophysics of intrinsically disordered proteins; polymer physics and phase transitions in cell biology

Office: Brauer Hall, Room 2015APhone: (314) 935-7958Email: [email protected]

Current ResearchIntrinsically disordered proteins (IDPs) are the main focus of the Pappu lab. Eukaryotic proteomes are enriched in IDPs. These proteins exhibit conformational heterogeneity as autonomous units and yet they play central roles in cellular functions and disease. We adapt and develop a combination of polymer physics principles, advanced multiscale simulations, and a range of experimental methods to understand the conformational properties, phase behavior, and functions of IDPs. These studies have direct relevance for understanding the driving forces for and mechanisms of phase separation that gives rise to intracellular compartments and the organization of signaling networks. We are also focused on protein aggregation mechanisms and their connection to processes and pathways that lead to neurodegeneration in Huntington’s and Alzheimer’s diseases. Our emphasis on basic science understanding of IDPs has yielded insights that are being translated into practical advances in neurodegenerative disorders and in de novo design of protein-based materials.

Modeling provides a physical basis for spatially organized nucleoli


Jonathan R. SilvaAssistant Professor of Biomedical EngineeringPhD, Biomedical Engineering, Washington University in St. Louis, 2008

MSc, Case Western Reserve University, 2004

BSc, The Johns Hopkins University, 2000

Research InterestsVirtual and Augmented Reality; Electrophysiology; Molecular spectroscopy; Mathematical modeling; Cardiac arrhythmia

Office: Whitaker Hall, Room 290GPhone: (314) 935-8837Email: [email protected]

Current ResearchOur laboratory applies computational and biophysical methods to improve arrhythmia therapies. Current projects include using holograms to guide ablation procedures and creating multi-scale models that connect nano-scale molecular movements to the chaos theory of arrhythmias.

Larry A. TaberThe Dennis and Barbara Kessler Professor of Biomedical EngineeringPhD, Aeronautics and Astronautics, Stanford University, 1979

MS, Stanford University, 1975

BS, Georgia Institute of Technology, 1974

Research InterestsBiomechanics of cardiovascular and nervous system development


Current ResearchOur research deals with the mechanics of embryonic morphogenesis. Using a combination of experimental and theoretical techniques, we study problems including cardiac looping, folding of the cerebral cortex and retinal morphogenesis. A long-term goal of our work is to determine the fundamental biomechanical laws that govern morphogenesis (if such laws exist).

Both the heart and brain are initially tubular structures, with the eyes being spherical protrusions from the brain. During development, the heart loops into a curved tube that divides into a four-chambered pump, the brain folds into a highly convoluted form, and the eye folds and differentiates to create the retina and lens. These processes are driven by mechanical forces.

Understanding how nature manufactures tissues and organs should benefit researchers seeking to prevent and treat congenital malformations, as well as tissue engineers striving to create replacement tissues and organs in vitro.

Computational model and images of optic cup invagination in the chick embryo. From undeformed state (a), light blue region in the model folds inward to create the retina (b,d), similar to in vivo observations (c,e).

Kurt A. ThoroughmanAssociate Professor of Biomedical Engineering, Associate Professor of Neuroscience and of Physical TherapyPhD, Johns Hopkins University, 1999

BA, University of Chicago, 1993

Research InterestsScience and engineering education; human motor control and learning; computational neuroscience

Office: Whitaker Hall, Room 200FEmail: [email protected]

Current ResearchProfessor Thoroughman researches learning in many environments. Emergent research studies improvement in STEM education, on local, regional, national, and global scales. He specializes in holistic education, improving connection across courses and toward broader understanding and life-long meaning. This work connects local projects to national resources, projects, and consortia. He also studies human learning and motor control. Research projects include how experience changes not just what is learned but the learning process itself; learning via observation of others; ability of people to learn with explicit reward feedback; and computational neuroscience. A: Schematic of human subject learning forces

generated by robot, either by moving (bulb on) or by watching video of other’s movement (bulb off). B: Still from training video. From Wanda, Li, and Thoroughman 2013.

Using holograms to guide cardiac arrhythmia ablations.

Jin-Yu ShaoAssociate Professor of Biomedical Engineering, Associate Professor of Biochemistry & Molecular BiophysicsPhD, Mechanical Engineering and Materials Science, Duke University, 1997

MS, Peking University, 1991

BS, Peking University, 1988

Research InterestsCellular and molecular biomechanics; protein-protein interactions, mathematical modeling of biological processes


Current ResearchCombining numerical simulation and biophysical techniques such as the optical trap and the micropipette aspiration technique, my laboratory seeks to understand how human leukocytes or cancer cells roll stably on the endothelium and migrate out of blood vessels. Cell rolling, which is recognized as the first key step for cellular migration into infected tissues, lymph nodes, aortic tissues and cancer metastatic sites is a complicated dynamic process mediated cooperatively by shear stress due to the blood flow, adhesion molecules expressed on rolling cells, as well as cellular mechanical properties. My laboratory also seeks to understand the role of von Willebrand factor (VWF) in hemostasis and thrombosis, as well as the role of Notch receptor in tissue development and cancer. VWF and Notch function depends on enzymatic cleavage, which is mediated by force and other factors like genetic mutation.

On the left is a protein-coated bead trapped by laser. On the right is a human endothelial cell held by a micropipette, which is driven by a piezo stage with nanometer resolution. The mechanics of the cell or its surface proteins can be studied by pressing the cell against the bead then pulling away.


Quing ZhuProfessor of Biomedical EngineeringPhD, University of Pennsylvania, 1992

MS, Chinese Academy of Medical Science, 1987

BSE, Northern Jiaotong University, 1983

Research InterestsCancer Detection and Diagnosis and Cancer Treatment Assessment and prediction utilizing Diffused Optical Tomography, Phoacoustic Tomography, Optical Coherence Tomography and Ultrasound

Office: Whitaker Hall, Room 300DPhone: (314) 935-7519Email: [email protected]

Current ResearchProfessor Zhu is a pioneer of combining ultrasound and near infrared (NIR) imaging modalities for clinical diagnosis of cancers and for treatment assessment and prediction of cancers. This combined approach overcomes the localization uncertainty of optical reconstruction and improves the ultrasound diagnosis. She and her team have explored the theory and modeling behind this novel technique and have conducted clinical studies. Initial results have shown great success in early diagnosis of malignant and benign breast lesions and in predicting and monitoring breast cancer treatment response using this technique. Her pioneering research has now been heralded by the imaging and radiology community as an important advance in society’s ability to distinguish benign and malignant lesions in the breast. In addition, Zhu and her team have pioneered co-registered ultrasound and photoacoustic imaging techniques for ovarian cancer detection and diagnosis and have obtained initial premising results.

Frank YinStephen F. and Camilla T. Brauer Distinguished Professor of Biomedical Engineering (Department Chair, 1997-2013)MD, University of California-San Diego, 1973

PhD, University of California-San Diego, 1970

MS, Massachusetts Institute of Technology, 1967

BS, Massachusetts Institute of Technology, 1965

Research InterestsTissue and cell biomechanics, hemodynamics

Office: Whitaker Hall, Room 3003Phone: (314) 935-7177Email: [email protected]

Current ResearchOur research has covered a variety of areas in both solid and fluid biomechanics. Among the former are studies elucidating the constitutive properties of myocardium, pericardium and heart valves; determining the mechanical effects of cardiac contraction on the coronary circulation; determining the morphological, functional, and genetic responses of cultured cells to various mechanical stimuli; and examining the mechanical properties of subcellular constituents such as actin stress fibers. Biaxial stretching and indentation with custom-made macro-devices and an atomic force microscope have been mainstay experimental tools which have been complemented with theoretical and computational approaches. We have also studied the effects of hypertension and several classes of antihypertensive drugs on arterial hemodynamics. Our research has implications for cancer, tissue healing and remodeling, and treatment of hypertension. I am now semi-retired and no longer have an active laboratory.

Merged fluorescent images (f-actin in red, zyxin in green) of unstretched (left) and stretched (10%, 3 hrs, right) endothelial cells. Zyxin localizes at ends of f-actin fibers without stretch (white arrow) whereas it translocates onto actin fibers after stretching.

Advancing breast cancer diagnosis with high optical contrast

Biomedical and Biological ImagingImaging activities at WashU are interdisciplinary, involving the Departments of Biomedical Engineering, Electrical & Systems Engineering and Computer Science & Engineering. In addition, strong and long-standing collaborative interaction with the School of Medicine gives our students ample opportunities to participate in biomedical and biological science projects that involve imaging.

Opportunities to learn the principles and applications of imaging technologies are available through the Imaging Science and Engineering Graduate Certificate Program, which is a coordinated program of courses, seminars and laboratory experiences jointly offered by the participating departments. Imaging activities also have a wide span from the microscopic, such as the imaging of tissues and cells, to the macroscopic imaging of the whole body, and from basic research to clinical application. Research includes the study and development of technology for acquiring, processing, transmitting, and storing image data.

Samuel Achilefu Molecular optical and multimodal imaging

Hongyu An MRI, MR physicis, sequence design, image reconstruction, PET/MR imaging, PET attenuation correction, motion correction

Beau Ances fmri, Alzheimer’s disease, HIV

Martha Bagnall Vestibular and spinal neural circuits in zebrafish

Deanna Barch Cognitive neuroscience, development, psychopathology, functional connectivity, structural connectivity, multi modal imaging

Philip Bayly Biomechanics, mechanobiology, cell motility, flagella, cilia, imaging

Paul Bridgman Axon guidances growth cones, substrate patterning, microfluidics, light and electron microscopy

Michael Bruchas Neural Circuits in affective behaviors, Optogenetics,Neural device an bio-tool development, In vivo imaging (neuron level), affective behavior, G-protein signaling in circuits

Shantanu Chakrabartty Self-powered sensors, wireless telemetry, energy harvesting, neuromorphic systems

Delphine Chen, MD Positron emission tomography, lung imaging, immune cell imaging

Joseph Culver Diffuse optical tomography, non-invasive optical imaging

Guy Genin Interfaces and adhesion in physiology and nature; optical strain analysis; continuum mechanics; viscoelasticity

Michael Greenberg Heart failure, molecular motors, single molecule, optical trapping, stem cells, tissue engineering

Timothy Holy Novel optical microscopy to record large neuronal populations

Daniel Kerschensteiner, MD Neural circuits, vision, 2-photon imaging, electrophysiology, retina, visual processing

Sándor Kovács, MD Mathematical physiology, kinematic modeling, cardiovascular biophysics, echocardiography, cardiac cathaterization, cardiac MRI, hemodynamics, human physiology

Albert Lai Bioinformatics

Gregory Lanza, MD Targeted drug delivery. Molecular imaging, Nanomedicine, Vascular disease, Liquid and Solid Cancer Technologiess, Contrast Agent Development

Eric Leuthardt, MD Brain Computer Interfaces, Neuroprosthetics, Advanced Imaging, Resting State fMRI

Matthew Lew in-vivo imaging, 3D super-resolution microscopy, single-molecule fluorescence, computational optics

Harold Li Radiation therapy dosimetry, Dose imaging device, Image-guided radiation therapy

Ilya Monosov Neuronal mechanisms of voluntary behavior

Arye Nehorai Forward models, inverse models, statistical analysis, quantitative methods, modeling

Joseph A. O’Sullivan Computational imaging; imaging science; computed tomography; positron emission tomography; x-ray imaging

Parag Parikh, MD MRI, PET, tracking, radiation, pancreas, intestine, liver, radioembolization, fluoroscopy

Zachary Pincus Systems Biology of Aging; Biology of Individuality

David Piston Signal transduction

Vijay Sharma Molecular Imaging, PET and SPECT Agents, Myocardial Perfusion, Alzheimer`s Disease, Multidrug Resistance

Kooresh Isaac Shoghi Computational biology at the interface with in-vivo imaging in animal models, in particular as it relates to metabolic regulation and obesity, diabetes

Monica Shokeen Development and evaluation of small- and macro-molecular agents for multi-modal molecular imaging of cancer and cardiovascular diseases

Sheng-Kwei Song Diffusion basis spectrum imaging, diffusion fMRI, inflammation, Cancer Technologies, axonal injury and loss, demyelination

S. Joshua Swamidass, MD Machine learning, computational biology, chemical informatics, bioinformatics, neural networks, pharmacology, drug toxicity, drug design

Yuan-Chuan Tai PET, molecular imaging, theranostic, radiotracer, plant imaging, phenotyping

Simon Tang Disc Degeneration; Low back pain; osteoporosis and fragility

David Van Essen Functional brain-mapping

Yong Wang Inverse problem and imaging in electrophysiology; Magnetic resonacne imaging

Samuel Wickline, MD Physical acoustics, cardiac and vascular material properties and mechanical function

Pamela Woodard, MD PET, MRI, Molecular Imaging, Cardiac Imaging, Translational Research, PET tracers, Atherosclerosis

Tiezhi Zhang Novel CT system, multi-pixel x-ray source, and radiation detector

Jie Zheng Cardiac MRI and PET, cardiovascular imaging, myocardial ischemia and heart failure, skeletal muscle exercise, diabetic foot

Affiliated Faculty

Primary FacultyMark Anastasio

Hong Chen

Vitaly Klyachko

Yoram Rudy

Jonathan Silva

Quing Zhu


Cancer TechnologiesCancer Technologies seeks to enhance our understanding and treatment options for cancer using the latest methods and approaches in engineering. The broad goals of Cancer Technologies are to apply the latest engineering methods and techniques (imaging, microfluidics, optogenetics) to enhance understanding and therapy for cancer. Faculty working in this area seek to understand how cancer metastasizes by examining how cells migrate through tissue, enter the circulation, and exit at distant sites (lung, brain, liver, bone). In addition, faculty seek to develop novel imaging methods (ultrasound, photoacoustic) that can detect cancer at earlier stages, as well as provide information on the functional or metabolic state of the cancer.

Hongyu An MRI, MR physicis, sequence design, image reconstruction, PET/MR imaging, PET attenuation correction, motion correction

Gregory Lanza, MD Targeted drug delivery. Molecular imaging, Nanomedicine, Vascular disease, Liquid and Solid Cancer Technologiess, Contrast Agent Development

Christopher Maher Genomics, Transcriptomics, Bioinformatics, Cancer Technologies, Computational Biology, non-coding RNA, Systems Biology

Garland Marshall Molecular modeling, drug design, medicinal chemistry, organic synthesis

Parag Parikh, MD MRI, PET, tracking, radiation, pancreas, intestine, liver, radioembolization, fluoroscopy

Amit Pathak Cellular mechanics, mechanobiology of the cell

Philip Payne Complex Systems, Artificial Intelligence, Knowledge Engineering, Visualization

Sheng-Kwei Song Diffusion basis spectrum imaging, diffusion fMRI, inflammation, Cancer Technologies, axonal injury and loss, demyelination


Yuan-Chuan Tai PET, molecular imaging, theranostic, radiotracer, plant imaging, phenotyping

Affiliated Faculty

Cardiovascular EngineeringCardiovascular disease is the number one cause of death and disability in developed countries. Cardiovascular Engineering encompasses a multi-disciplinary effort to improve our understanding of cardiovascular disease and develop better therapies. Our research topics range from nano-scale molecular experiments to clinical trials that evaluate therapeutic efficacy. The unifying theme is using engineering principles to improve cardiovascular health and address this leading cause of death.An important feature of this program is its multidisciplinary approach, which allows researchers in our program to uniquely address cardiovascular challenges. Topics currently under investigation include: the dynamics of electrical and mechanical activity of the heart; characterizing the electro-mechanical properties of cells and tissue comprising the heart wall; studying interactions of blood cells with receptors on the endothelium; computational modeling of the developing and adult heart during health and disease; structural bases of function and pharmacological modulation of normal and disease-associated mutant cardiac ion channels; multiscale modeling of cardiac ion channel structure and function; developing methods for targeted imaging of the anatomy and function of heart and vessels; understanding the biochemical and mechanical factors underlying angiogenesis; and describing function at the cellular and organ level with novel imaging methods, including noninvasive functional imaging in patients that were developed by our faculty.



Sándor Kovács, MD Mathematical physiology, kinematic modeling, cardiovascular biophysics, echocardiography, cardiac cathaterization, cardiac MRI, hemodynamics, human physiology

Gregory Lanza, MD Targeted drug delivery, Molecular imaging, Nanomedicine, Vascular disease, Liquid and Solid Cancer Technologiess, Contrast Agent Development

Robert Mecham Extracellular matrix, vascular development, vascular disease, cell-matrix interactions, tissue mechanics and development

Jeanne Nerbonne Regulation of membrane excitability, structure and function of ion channels

Colin Nichols Molecular aspects of potassium channels

Stacey Rentschler, MD Programming and reprogramming cardiac conduction, arrhythmias, optical mapping, gene therapy

Kooresh Isaac Shoghi Computational biology at the interface with in-vivo imaging in animal models, in particular as it relates to metabolic regulation and obesity, diabetes

Jessica Wagenseil Vascular mechanics, vascular development, extracellular matrix, elastin, elastic fibers, vascular modeling

Samuel Wickline, MD Physical acoustics, cardiac and vascular material properties and mechanical function


Affiliated Faculty

Primary FacultyHong Chen

Steve George, MD

Kristen Naegle

Quing Zhu

Primary FacultyJianmin Cui

Steven George, MD

Yoram Rudy

Jin-Yu Shao

Jonathan Silva

Larry Taber


Molecular & Cellular Systems EngineeringThe molecular and cellular networks that compose cells and tissues fundamentally determine the emergent properties that shape the physiology of healthy organs and pathological tissues that cause diseases, like neurodegeneration and cancer. Their complexity requires novel and integrated approaches that span scales, ideas, and techniques. Pushing the boundary of knowledge in the direction of understanding molecular, cellular, and tissue systems will allow us to gain the insight required to build better therapies. The MCSE group is composed of diverse faculty, collaborating across many departments and schools at Washington University in St. Louis, which are tackling such problems as: the basic understanding of systems composed of proteins, genes, and metabolites; the networks of protein aggregation; and the networks of electrically excitable cells such as the heart, nervous system and the brain. The MCSE group employs a myriad of techniques, including biophysics, advanced imaging methods, multiscale computational methods, and systems-approaches to measurement to gain knowledge in the basic operations of these systems or their involvement in neurodegenerative disorders, cancer, and cardiovascular disease.

Maxim Artyomov Systems Immunology


Greg Bowman Biophysics, Biochemistry, Molecular Simulation, Drug Development, Protein Engineering

Michael Brent Bioinformatics and systems biology


Michael Bruchas Behavior, G protein coupled receptors, neurobiology, pain, psychiatry, signal transductio

Barak Cohen Evolution of complex traits; synthetic biology for engineering gene expression

Gautam Dantas Anibiotic resistance, synthetic biol-ogy, bioenergy, human microbiome, metagenomics, microbial ecology and biodiversity, probiotic engineer-ing, pathogenomics

Aaron DiAntonio, MD Molecular mechanisms of axonal degeneration and regeneration in neuronal repair

Anthony French, MD Human Immunology, Innate Immunity, Autoimmunity, Viral Immunity, NK cells, mathematical modeling, mouse models


Jeffrey Gordon, MD Microbiome; systems biology; metabolic regulation; food webs; postnatal development; gnotobiotic animal models, gut mucosal immunit


Farshid Guilak Biomechanics, tissue engineering, regenerative medicine, osteoarthritis, synthetic biology, stem cells, mechanobiology, mechanotransduction, cell mechanics

James Havranek Computational protein design, protein DNA interactions

James Huettner Glutamate receptors, chimeric subunits, in vitro differentiation, neural differentiation from stem cells

Albert LaiBioinformatics

Jin-Moo Lee, MD Stroke, Brain injury, Alzheimer’s disease, Brain repair

Chris Lingle ion channel biophysics, modeling of channel gating and cell excitability, methods of analysis

Christopher Maher Genomics, Transcriptomics, Bioinformatics, Cancer Technologies, Computational Biology, non-coding RNA, Systems Biology

Garland Marshall Molecular modeling, drug design, medicinal chemistry, organic synthesis

Audrey McAlinden Cartilage engineering, chondrocytes, stem cells, osteoarthritis, microRNAs, long non-coding RNAs, growth factors

Gretchen Meyer Skeletal Muscle Physiology, Adipose Signaling, Regeneration, Injury

Jeffrey Milbrandt, MD Functional genomics, metabolic pathway, mitochondria, nerve regeneration, neurodegeneration, transcriptional networks

Jeffrey Millman Pluripotent stem cells, diabetes, iPS cells, embryonic stem cells, differentiation, tissue engineering, metabolism, biomaterials

Rob Mitra Genomics. Genome Engineering. Computational Biology. Transcription Factors.


Camillo Padoa-Schioppa Decision Making, Neurophysiology, Modeling, Primates

Amit Pathak Cellular mechanics, mechanobiology of the cell

Philip Payne Complex Systems, Artificial Intelligence, Knowledge Engineering, Visualization

Zachary Pincus Systems Biology of Aging; Biology of Individuality

David Piston Signal transduction

Jay Ponder Molecular modeling, biomolecular structure, computational protein engineering, ligand/drug design

Linda Sandell Synovial joint, cartilage, synovium, meniscus, genetics of cartilage repair, human joint studies

Vijay Sharma Molecular Imaging, PET and SPECT Agents, Myocardial Perfusion, Alzheimer`s Disease, Multidrug Resistance

Monica Shokeen Development and evaluation of small- and macro-molecular agents for multi-modal molecular imaging of cancer and cardiovascular diseases


Xiaowei Wang Bioinformatics, computational biology, microRNA, Cancer Technologies


Hani Zaher Ribosome, Translation, Quality Control, mRNA modifications, Aptamers, RNA biology

Affiliated Faculty

Neural EngineeringNeural Engineering research involves fundamental and applied studies related to neurons, neural systems, behavior and neurological disease. This program encompasses a broad spectrum of activities including explicit mathematical modeling; exploring novel approaches to sensory (vision, hearing, smell and touch) and motor processing; exploring fundamentals of neural plasticity; and designing neuroprosthetics. The approaches involve a wide range of physical scales, including information processing at the molecular, cellular, systems and behavioral levels. Common to all of these efforts is the use of mathematical tools and an engineering perspective to generate novel insights into basic and applied neuroscience.

Martha Bagnall Vestibular and spinal neural circuits in zebrafish


David Brody, MD Traumatic brain injury, Alzheimer’s disease, Diffusion MRI, Axonal injury, Human studies, Experimental animal studies, Amyloid-beta oligomers, Radiological pathological correlations

Michael Bruchas Neural Circuits in affective behaviors, Optogenetics, Neural device an bio-tool development, In vivo imaging (neuron level), affective behavior, G-protein signaling in circuits

Andreas Burkhalter Synaptic mechanisms and organization of forward and feedback circuits in visual cortex

Shantanu Chakrabartty Self-powered sensors, wireless telemetry, energy harvesting, neuromorphic systems

ShiNung Ching Neural Dynamics and Control Theory, Brain Network Analysis, Theoretical Neuroscience

Maurizio Corbetta, MD Cognition, imaging, attention, recovery, vision

Timothy Holy Novel optical microscopy to record large neuronal populations

James Huettner glutamate receptors, chimeric subunits, in vitro differentiation, neural differentiation from stem cells

Daniel Kerschensteiner, MD Neural circuits, vision, 2-photon imaging, electrophysiology, retina, visual processing

Jin-Moo Lee, MD Stroke, Brain injury, Alzheimer’s disease, Brain repair


Chris Lingle ion channel biophysics, modeling of channel gating and cell excitability, methods of analysis

Rob Mitra Genomics. Genome Engineering. Computational Biology. Transcription Factors.

Ilya Monosov Neuronal mechanisms of voluntary behavior

Arye Nehorai Forward models, inverse models, statistical analysis, quantitative methods, modeling


Camillo Padoa-Schioppa Decision Making, Neurophysiology, Modeling, Primates

Steven Petersen Human functional neuroimaging of vision, attention, memory, and language

W. Zachary Ray, MD neuroprosthetics, resorbable electronics, nerve regeneration, spinal cord injury

Lawrence Snyder, MD Primate sensory-motor and cognitive neurophysiology; electrophysiological bases and correlates of resting state functional connectivity (rs-fcMRI).

David Van Essen Functional brain-mapping

Affiliated Faculty

Primary FacultyDennis Barbour, MD

Jianmin Cui

Vitaly Klyachko

Daniel Moran

Barani Raman

Jonathan Silva

Larry Taber

Kurt Thoroughman

Primary FacultyJan Bieschke

Jianmin Cui

Vitaly Klyachko

Kristen Naegle

Rohit Pappu

Barani Raman

Yoram Rudy

Jonathan Silva


Regenerative Engineering in MedicineRegenerative Engineering in Medicine combines cell and molecular biology, cell biophysics and engineering methods to understand and control the organization and function of tissues. One practical goal is to supply tissues that can function normally when implanted in humans who lack, either due to disease or accident, the corresponding endogenous tissue function. Another goal is to design methods to control cell/tissue development and wound healing. Faculty in this program also seek to develop new biomaterials to resist rejection and induce the regeneration of tissues; to discover new ways to deliver genes, drugs and other biologicals; to reconstitute tissues from cells of various types. Additionally, theoretical and mathematical aspects of cell and tissue engineering are explored to understand the processes that drive cellular and tissue responses in development and in pathological states.




James Huettner glutamate receptors, chimeric subunits, in vitro differentiation, neural differentiation from stem cells

Spencer Lake Orthopedic, soft tissues, tendon/ligament, biomechanics, structure-function



Robert Mecham Extracellular matrix, vascular development, vascular disease, cell-matrix interactions, tissue mechanics and development


Jeffrey Millman Pluripotent stem cells, diabetes, iPS cells, embryonic stem cells, differentiation, tissue engineering, metabolism, biomaterials

W. Zachary Ray, MD Neuroprosthetics, resorbable electronics, nerve regeneration, spinal cord injury

Stacey Rentschler, MD Programming and reprogramming cardiac conduction, arrhythmias, optical mapping, gene therapy

Matthew Silva Skeletal biomechanics and mechanobiology; bone strength; osteoporosis; skeletal imaging


Jessica Wagenseil vascular mechanics, vascular development, extracellular matrix, elastin, elastic fibers, vascular modeling

Affiliated Faculty

Orthopedic EngineeringPrimary FacultySteven George, MD

Lori Setton

Larry Taber

Frank Yin, MD

Primary FacultyLori Setton

Orthopedic Engineering combines principles of tissue engineering, cell biology, and biomechanics to generate new knowledge of bone and soft tissue biology and develop novel therapies to treat musculoskeletal disease.

The broad goals of orthopedic engineering are to apply engineering methods and techniques (biomechanics, tissue engineering, imaging) to uniquely understand the musculoskeletal system and to develop novel therapies. Faculty working in this area seek to understand the mechanical and material properties of bone and soft tissues (muscle, cartilage) and to exploit biomaterial and cellular processes to mediate injury responses and promote regeneration. Computational models play a significant role in the design of and development of new experimental methods and protocols.



Michael Harris Biomechanics, orthopedics, musculoskeletal modeling, human subject research, subject-specific modeling, motion analysis

Spencer Lake Orthopedic, soft tissues, tendon/ligament, biomechanics, structure-function



W. Zachary Ray, MD Neuroprosthetics, resorbable electronics, nerve regeneration, spinal cord injury

Linda Sandell Synovial joint, cartilage, synovium, meniscus, genetics of cartilage repair, human joint studies

Matthew Silva Skeletal biomechanics and mechanobiology; bone strength; osteoporosis; skeletal imaging


Affiliated Faculty

bme.wustl.edu

Department of Biomedical Engineering CB 1097 • 1 Brookings Drive • St. Louis, MO 63130Phone: (314) 935-6164 • Fax: (314) 935-7448Email: [email protected]

Documents

The Department of Biomedical Engineering Handbook.pdf2 Department of Biomedical Engineering Graduate Studies Handbook 2016-2017 3 Advising Each entering student is guided by the Director