BME-GSM_Final - Department of Biomedical Engineering ...

Department of 

Biomedical Engineering 

Graduate Studies Manual 

2012–2013

TABLE OF CONTENTS 

Welcome 2 

Biomedical Engineering 4 

Research Programs 5 

About Washington University in St. Louis 6 

Graduate Curriculum 8 

Application and Admissions 10 

Faculty Profi les 12 

Collaborative Research & Educational Programs in BME 31 

Biomaterials and Tissue Engineering 32 

Cardiovascular Engineering 34 

Imaging Technologies 36 

Molecular, Cellular and Systems Engineering 38 

Neural Engineering 40 

Biomedical Engineering 

Washington University in St. Louis 

Campus Box 1097 

One Brookings Drive 

St. Louis, Missouri 63130 

phone: (314) 935-6164 

fax: (314) 935-7448 

bme.wustl.edu 

bme@seas.wustl.edu 

Biomedical Engineering Graduate Advising Manual 2012 | 1

WELCOME 

Greetings from the Department of Biomedical 

Engineering at Washington University in St. Louis. 

Since its founding in 1997, the tireless efforts of our 

faculty, students and staff, along with generous 

support of many friends and colleagues, have 

enabled us to build one of the most highly-ranked 

departments in the U.S. Our department now consists 

of 19.5 core faculty, more than 100 graduate and more 

than 400 undergraduate students. We are housed in 

two fi rst-class research and teaching facilities, the 

Uncas A. Whitaker Hall for Biomedical Engineering 

and the adjoining Stephen F. and Camilla T. Brauer 

Hall. We are eagerly looking to the future with confi - 

dence, optimism and anticipation. We hope that you 

will join us for your further training. 

2 | Washington University School of Engineering & Applied Science | engineering.wustl.edu

Our department builds upon a long tradition of excellence and cooperation 

across the university, especially with our world-class medical school. 

The result is a modern and truly interdisciplinary approach to advancing 

basic science and to enabling us to better understand, diagnose, and treat 

diseases affecting humankind. As described herein, our core faculty's 

research focuses on fi ve cutting-edge areas of biomedical engineering: 

• Biomaterials and tissue engineering 

• Cardiovascular engineering 

• Imaging technologies 

• Molecular, cellular and systems engineering 

• Neural engineering 

Our core and more than 60 affi liated faculty work together in a number 

of interdisciplinary research centers and pathways. This large community 

enables us to cover a diverse and rich spectrum of BME research areas, 

spanning length scales from molecules to the whole organism. This superb 

research training, together with a solid curriculum grounded in biomedical 

engineering, have enabled our graduate alumni to make a meaningful impact 

in many of the premier academic, medical, legal and industrial organizations 

around the world. 

I enjoyed watching the department grow rapidly during the last decade, and 

as we look to the future, even more exciting opportunities lie ahead as we 

continue to build upon our strengths and leverage special opportunities 

to increase our impact. We plan to expand the number of core faculty to 

provide even more depth and breadth to our research areas. Whitaker Hall 

and the adjoining Stephen F. and Camilla T. Brauer Hall provide the physical 

infrastructure necessary for our expanded research and teaching efforts. 

It has been a privilege for me to have participated in helping build this 

endeavor. We greatly appreciate the contributions, encouragement, 

commitment and guidance of a multitude of colleagues, students, friends 

and supporters who have been instrumental in the success of the department. 

To all of them, I and my colleagues express our sincerest and utmost 

appreciation. 

Shelly E. Sakiyama-Elbert, Ph.D. 

Director of Graduate Studies 


BIOMEDICAL ENGINEERING 

Frank C-P Yin 

The Stephen F. and Camilla T. Brauer 

Distinguished Professor of Biomedical 

Engineering and Department Chairman, 

Professor of Medicine 

M.D., University of California- San 

Diego, 1973 

Ph.D., Applied Mechanics (Bioengineering), 

University of California-San 

Diego, 1970 

M.S., Massachusetts Institute of 

Technology, 1967 

B.S., Massachusetts Institute of 


Offi ce: Whitaker Hall, Room 190A 

Phone: (314) 935-6164 

yin@wustl.edu 

Modern biomedical engineers face a far different 

world than those trained even two decades ago. 

Explosive advances in our ability to probe and understand 

molecular and cellular processes and their 

interconnnections now make it imperative that the 

powers of engineering be brought to bear at ever 

smaller as well as at systemwide levels. This will not 

only produce new discoveries at the most fundamental 

levels but also accelerate the translation of these 

discoveries into practical applications. 

Our vision is that future leaders and lasting impact 

will arise from successfully integrating engineering 

concepts and approaches across molecular to 

whole body levels. Moreover, those also trained to 

integrate the analytical, modeling, and systems approaches 

of engineering to the complex and, sometimes 

overwhelming, descriptive details of biology 

will be uniquely positioned to address new and exciting 

opportunities. We are committed to educating 

and training the next generation of biomedical engineers 

with this vision in mind. Consequently, we have 

leveraged our existing strengths to build our department 

around the fi ve research programs representing 

some of the most exciting frontiers. 


RESEARCH PROGRAMS 

r 

We focus on fi ve 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. 

BME Research Programs 


ABOUT WASHINGTON UNIVERSITY IN ST. LOUIS 

BETWEEN CAMPUSES 

The two campuses are three miles 

apart, separated by Forest Park - one of 

the largest (one-third larger than 

Central Park in New York) and most 

beautiful public parks in the country. 

The park has a golf course, an art 

museum, a public zoo, the Missouri History 

Museum and the largest and oldest 

continuously-running municipal outdoor 

theater in the country. Transportation 

between campuses, and the residential 

areas between them, is easy by bicycle 

or University-run 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. 

HOUSING INFORMATION 

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 

or 

Quadrangle Housing Company 

www.offcampushousing.wustl.edu 

THE CAMPUSES 

Founded in 1853, Washington University in St. Louis is an 

independent institution known internationally for its excellence 

in teaching and research. For example, in the 2009 U.S. 

News and World Report rankings of graduate and professional 

programs, 20 programs at the University, including BME, were 

ranked in the top 10. The University offers more than 80 programs 

and nearly 1,600 courses in interdisciplinary as well as 

traditional fi elds leading to bachelor’s, master’s and doctoral 

degrees. The University, including the Danforth and Medical 

Campuses, comprises 2,267 acres and more than 150 buildings. 

The University’s 11,000 undergraduate and graduate students 

come from every state of the union and more than 100 foreign 

countries. The School of Engineering and Applied Sciences 

has fi ve academic departments, many interdepartmental 

programs, and offers undergraduate and graduate degrees in 

both traditional and emerging fi elds. The School of Medicine 

is one of the nation’s largest clinical and biomedical research 

facilities and comprises more than 60 buildings on nearly 230 

acres. 


RESEARCH SUPPORT 

There is ample support for students to pursue their research training. Our core faculty’s annual 

per capita research expenditures currently exceed $800,000, putting us in the top-tier of 

research departments nationwide. Our school of medicine consistently ranks in the top fi ve of 

the 125 U.S. medical schools and third in funding from the National Institutes of Health for research 

and training. In addition to research grants, the department has and participates in NSF 

and NIH-supported training grants dedicated to providing support for graduate students. 

FACILITIES 

In December 2002, the department moved into the new Uncas A. Whitaker Hall for Biomedical 

Engineering. This $42 million, 113,000 sq. ft. building was funded, in part, by a $10 million award 

to the department from The Whitaker Foundation in 1999 in recognition of the extraordinary 

promise of biomedical engineering at Washington University. This building contains more than 

55,000 sq. ft. of state-of-the-art teaching and research facilities, including 15 faculty research 

laboratories, a nanotechnology lab, a microscopy core facility, an imaging core facility, a small 

animal vivarium, three teaching laboratories, a 250-seat auditorium, three large classrooms, 

student and faculty lounges and many conference rooms. The building was designed to enhance 

interactions among the faculty, students and staff by means of a three-story central atrium 

surrounded by corridors leading to distributed offi ces, laboratories and classrooms. 

In 2010, we completed construction on the Stephen F. and Camilla T. Brauer Hall, an approximately 

150,000 sq. ft. building we share with our Department of Energy, Environmental and 

Chemical Engineering. This facility adjoins Whitaker Hall and provides the needed expansion 

space for us over the coming years. 

There are extensive state-of-the-art facilities at the medical school that also support biomedical 

engineering research including: a new world-class imaging center, two of the seven NIH 

Nanotechnology Centers, the major NIH-funded Genome Sequencing Center that was instrumental 

in decoding the human genome and an NIH National Cancer Center that was designated 

in 2001. Several other departments in the School of Engineering also have spaces used for 

BME research. 


GRADUATE CURRICULUM 

DEGREE PROGRAMS AND REQUIREMENTS 

The department offers programs leading to the master of science (M.S.) or doctor of philosophy 

(Ph.D.) in biomedical engineering and combined M.S./M.B.A. and M.D./Ph.D. degrees. The 

latter two degrees are given jointly with the Olin School of Business and the School of Medicine, 

respectively. 

Students pursuing an M.S. degree can do so either with or without a thesis; both options require 

completing a total of 30 credits of graduate work, including the core curriculum (see page 

9). For the thesis option, a minimum of 24 course credits and 6 research credits are required. 

The Ph.D. 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. Generally, students complete the core curriculum and research 

rotations (see page 9) during their fi rst year. Then, upon successfully passing the qualifying 

examination, they advance to candidacy and complete the balance of their requirements. 

Students pursuing the combined degrees must complete the degree requirements for both 

schools. For the three-year M.S./M.B.A., time is saved by allowing selected courses to count 

as electives for the other school’s degree requirement. The M.D./Ph.D. students typically complete 

the fi rst two years of the medical school pre-clinical curriculum while also performing 

one or more research rotations, then the remaining requirements for the Ph.D. degree, and 

fi nally the clinical training years of the medical degree. The department generally gives graduate 

course credits for some of the medical school courses toward fulfi llment of course requirements 

for the Ph.D. degree. This is arranged on an individual basis between the student, his/her 

academic advisor and the director of graduate studies. 


RESEARCH ROTATIONS 

One of the popular and valuable features 

of our doctoral program is the 

research rotation requirement, which 

provides students with an in-depth opportunity 

to sample different research 

areas before selecting their dissertation 

topic. This provides both breadth 

and depth of training in different areas 

of biomedical engineering research 

prior to embarking on the focused training 

needed for dissertation research. 

One of the rotations is the basis for the 

student’s qualifying examination, helping 

to focus the student’s preparation 

for the exam. The extended experience 

in a laboratory enables the student and 

his/her potential dissertation mentor 

an opportunity to ensure compatibility 

prior to both people committing to the 

long-term relationship necessary for 

the successful completion of a dissertation. 

Students are required to register 

for (without credit) and complete 

two semester-long rotations during 

the fi rst year with a member of the 

Graduate Group Faculty. Students who 

matriculate with a research master’s 

degree in an engineering fi eld need only 

complete one rotation. The specifi c 

rotations are chosen in consultation 

with the student’s academic advisor 

and/or director of graduate studies and 

must be mutually agreeable to both student 

and mentor. At the completion of 

each rotation, the student must submit 

to the department a written report approved 

by the mentor. An optional third 

research rotation may be performed 

during the summer after the fi rst academic 

year. 

CORE CURRICULUM 

A core curriculum must be completed 

by all degree candidates and consists 

of: 

• Two graduate courses in life sciences 

• One graduate course in mathematics 

• One graduate course in computer 

science 

• Biomedical engineering courses as 

specifi ed in the Graduate Policies and 

Regulations booklet. 

The M.S. degree requires at least three 

courses selected from the Educational 

Programs and constituent courses 

listed in the Graduate Policies and 

Regulations Booklet. The Ph.D. degree 

requires at least fi ve courses from the 

list (three of these must be in different 

programs). Other courses may fulfi ll 

this requirement at the discretion of 

the graduate curriculum committee. 

SEMINARS 

The department sponsors a weekly 

seminar series by visitors or Washington 

University faculty or students. 

All full-time graduate students are 

required to enroll in BME 501-Graduate 

Seminar, which is a pass/fail course 

carrying no credit. A passing grade is 

required for each semester for all fulltime 

students and is earned by regular 

attendance at this series, or at equivalent 

seminars. 

QUALIFYING EXAMINATION 

To advance to candidacy, doctoral 

students must pass an oral qualifying 

examination. The oral portion of the 

exam is based on the four scientifi c 

areas related to ones research rotation. 

The student and future dissertation 

mentor select the examination committee 

with approval of the Director 

of Graduate Studies in fi elds pertinent 

to that rotation plus four areas. The 

examination begins with an oral presentation 

to the committee on the rotation 

research, followed by questions addressing 

biomedical engineering topics 

directly related to the written rotation 

report and oral presentation. This portion 

of the examination must take place 

before the start of the second year of 

the doctoral program (at the end of the 

last rotation). 

TEACHING ASSISTANT 

REQUIREMENT 

Doctoral students must serve one semester 

as a teaching assistant (TA) for 

a BME course. The TA duty is in addition 

to the normal coursework and research 

duties for that semester. This usually 

occurs after completing the oral portion 

of the qualifying examination but 

before the thesis proposal. 

THESIS PROPOSAL 

Following successful completion of the 

oral portion of the qualifying examination, 

students will prepare a comprehensive 

written dissertation proposal 

that will be presented orally before the 

student’s dissertation committee. This 

proposal normally should be completed 

within two years of the qualifying exam 

(by the end of the third year), upon 

which the student completes the thesis 

and gives a formal defense. 


APPLICATIONS AND ADMISSIONS 

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 course 

work.) Admitted master’s and doctoral students typically 

have had grade point averages of 3.5 and 3.7 out of 4.0, 

respectively. 

2. Courses highly recommended: 

• 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 

3. Students seeking fi nancial aid must take the general 

sections of the Graduate Record Examination (admitted 

students have averaged a score over 775 on the quantitative 

section or 164 on the new GRE scale and 4.5 or greater on 

the analytical section). International students must also 

submit TOEFL scores earned with the past two years. 

Scores of 100 or greater are generally required with no less 

than 20 of each section 

4. Undergraduate or postgraduate research experience is 

highly desirable for admission to the PhD program, but not 

mandatory for the Master’s 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, qualifi ed 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. 


ADMISSION PROCEDURES 

Prospective students normally apply to 

the department during the fall or winter 

preceding the fall semester in which 

they intend to enroll. Under exceptional 

conditions, applications for enrollment 

in the spring semester will be accepted. 

Applications are only accepted online 

at: http://engineering.wustl.edu/GraduateAdmissions/. 

Deadline to submit 

the application is January 15th for PhD 

applicants. Master’s students are admitted 

on a rolling basis. International 

master’s applicants should apply by 

May 1 for fall admission and November 1 

for spring admission. 

Students wishing to pursue the combined 

M.D./Ph.D. degrees must apply to 

the Medical Science Training Program 

of the Washington University School 

of Medicine and be accepted into both 

the School of Medicine as well as the 

doctoral program of the biomedical 

engineering department. The latter can 

occur before, simultaneously, or after 

acceptance into the School of Medicine. 

Information about this option can be 

obtained at: http://mstp.wustl.edu/ 

Pages/index.aspx 

Students wishing to pursue the 

combined M.S./M.B.A. degrees must 

qualify for, apply to, and be accepted 

into both the M.S. program in BME and 

the M.B.A. program of the Olin School 

of Business. Application can also be 

made during the fi rst year of enrollment 

FINANCIAL AID 

Financial support for doctoral students 

is available on a competitive basis. 

Students desiring such aid must so 

indicate in their application materials. 

Every effort is made to provide fulltime 

doctoral students with full tuition 

support and a stipend competitive with 

other schools. 

Recent graduate degree recipients at spring 2012 commencement. Top row: Paul 

Wanda, Nithya Jesuraj, Prof. Dan Moran, Lin Bai, Yuchen Yuan and Lisa Thompson. 

Bottom row: Prof. Shelly Sakiyama-Elbert, Prof. Frank Yin, Prof. Kurt Thoroughman, 

and Kaitlin Burlingame. 


FACULTY PROFILES 

Mark A. Anastasio 

Professor of Biomedical Engineering 

Ph.D., Medical Physics, The University 

of Chicago, 2001 

M.S., University of Illinois at Chicago, 

1995 

M.S.E., University of Pennsylvania, 1993 

B.S., Illinois Institute of Technology, 

1992 

RESEARCH INTERESTS 

development of biomedical imaging 

methods; photoacoustic tomography, 

X-ray phase-contrast imaging, image 

reconstruction and inverse problems in 

imaging; theoretical image science 

Offi ce: Brauer Hall, Room 2009 

Phone: (314) 935-3637 

Email: anastasio@wustl.edu 

CURRENT RESEARCH 

The research activities in my laboratory broadly address the engineering 

and scientifi c 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. 

SELECTED PUBLICATIONS 

Anastasio MA, Chou CY, Zysk AM, and Brankov JG. 2010. Ideal Observer 

Analysis of Signal Detectability in Phase-Contrast Imaging Employing 

Linear Shift-Invariant Optical Systems. Journal of the Optical Society of 

America A 12: 2648-2659. 

Zysk AM, Schoonover RW, Carney PS and Anastasio MA. 2010. Transport 

of Intensity and Spectrum for Partially Coherent Fields. Optics Letters 

35: 2239-2241. 

Wang K, Ermilov SA, Brecht H-P, Su R, Oraevsky AA and Anastasio MA. 

2011. An Imaging Model Incorporating Ultrasonic Transducer Properties for 

Three-Dimensional Optoacoustic Tomography. IEEE Transactions on Medical 

Imaging 30: 203-214. 

Zhang J, Anastasio MA, Riviere PJ, and Wang LV. 2009. Effects of Imaging 

Model on Image Reconstruction Accuracy in Photoacoustic Tomography. 

IEEE Transactions on Medical Imaging 28:1781-1790. 

Brey EM, Appel A, Chiu Y-C, Zhong Z, and Anastasio MA. 2010. X-Ray Imaging 

of Poly(ethylene glycol) Hydrogels Without Contrast Agents. Tissue 

Engineering 16: 1597-1600. 

Chou C-Y and Anastasio MA. 2009. Noise Texture and Signal Detectability 

in Propagation- Based X-ray Phase-Contrast Tomography. Medical Physics 

37: 270-281. 

Tamhane AA, Anastasio MA, Gui M, Arfanakis K. 2010. Iterative Image 

Reconstruction for PROPELLER-MRI Using the Non-Uniform Fast Fourier 

Transform. Journal of Magnetic Resonance Imaging 32: 211-217. 



Our research focus is split along two main lines of inquiry. The fi rst involves 

reverse-engineering normal brain function. The vertebrate nervous 

system routinely achieves feats of pattern recognition unparalleled by 

modern computers. The natural algorithms underlying this pattern recognition 

and the neuronal circuitry computing them both represent targets 

for research in my lab, predominantly by measuring single and bulk neuron 

activity in awake subjects. We are particularly interested in how complex 

sounds are encoded in the brain when interfering noise is present and how 

language is processed in human brains. A more thorough understanding of 

these issues has the potential to contribute to the engineering of improved 

devices for interfacing with humans, including hearing aids, auditory prostheses 

and linguistic brain-computer interfaces. 

The second line of inquiry involves forward-engineering novel brain function 

by rewiring native cortical brain networks to implement new algorithms. 

Following brain injury such as a stroke, some function is lost and the 

brain network is disrupted. We apply principles of network theory and neuroplasticity 

toward developing brain-computer interfaces that can rewire 

brains and thus recover the lost function. We also develop the technology 

necessary to carry out this type of intervention. Collectively, our research 

represents a combination of neuroscientifi c and neuroengineering endeavors 

that have considerable potential for treating losses of nervous system 

function. 


X Pei, DL Barbour, EC Leuthardt and G Schalk. 2011. Decoding vowels and 

consonants in spoken and imagined words using electrocorticographic 

signals in humans. J Neural Eng 8(4): 046028. 

Katta N, Chen TL, Watkins PV and Barbour DL. 2011. Evaluation of techniques 

used to estimate cortical feature maps. J Neurosci Meth 202(1): 

87-98. 

Watkins PV and Barbour DL. 2011. Rate-level responses in awake marmoset 

auditory cortex. Hear Res 275(1-2): 30-42. 

Watkins PV and Barbour DL. 2011. Level-tuned neurons in primary auditory 

cortex adapt differently to loud versus soft sounds. Cereb Cortex 21(1): 

178-190. 

Walker, EY and Barbour DL. 2010. Designing in vivo concentration gradients 

with discrete controlled release: a computational model. J Neural Eng. 

7(4): 046013. 

Watkins PV and Barbour DL. 2008. Specialized neuronal adaptation for 

preserving input sensitivity. Nature Neurosci. 11: 1259–1261. 

Dennis L. Barbour 

Associate Professor of Biomedical 

Engineering, Associate Professor of 

Anatomy & Neurobiology, 

Otolarygology 

M.D., Johns Hopkins School of Medicine, 

2003 

Ph.D., Biomedical Engineering, Johns 

Hopkins University, 2003 

B.E.E., Georgia Institute of Technology, 

1995 


sensory neurophysiology; 

computational neuroscience; braincomputer 

interfaces; brain repair 

Offi ce: Whitaker Hall, Room 200E 

Phone: (314) 935-7548 

Email: dbarbour@wustl.edu 



Jan Bieschke 

Assistant Professor of Biomedical 

Engineering 

Ph.D., Max-Planck-Institute for Biophysical 

Chemistry, Germany, 2000 

Chemistry Diploma, University Goettingen, 

Germany, 1996 


mechanisms and modulators of agerelated 

protein misfolding processes, 

amyloid formation, single molecule 

fl uorescence, atomic force microscopy 


Phone: (314) 935-7038 

Email: bieschke@wustl.edu 


Our research involves the misfolding of endogenous protein or peptide 

fragments to form cytotoxic fi brillar protein deposits characterizes amyloid 

diseases. These misfolded polypeptides, which are believed to be the 

root cause of the pathologies, are specifi c for each disease, such as amyloid 

(A-beta) in Alzheimer’s disease (AD), but the mechanisms of protein 

misfolding and amyloid formation seem to be largely generic. 

However, it is yet unknown by which mechanisms misfolded proteins confer 

their toxicity. My group aims to quantitatively understand the biophysical 

basis generation and fate of misfolded proteins in the cell. We are tracking 

the formation and degradation of single particles of misfolded proteins by 

single molecule fl uorescence and other biophysical techniques. Our further 

aim is to develop strategies to derail protein misfolding processes and to 

engineer new approaches for detoxifying these disease-related protein 

assemblies. 


Bieschke J, et al. 2011. An orcein-related small molecule promotes the conversion 

of toxic oligomers to non-toxic, (beta)-sheet-rich amyloid fi brils. 

Nat Chem Biol. Nov 20;8(1):93-101. 

Bieschke J, Russ J, Friedrich RP, Ehrnhoefer DE, Wobst H, Neugebauer K, 

and Wanker EE. 2010. EGCG remodels mature alpha-synuclein and amyloid-beta 

fi brils and reduces cellular toxicity. Proc. Natl. Acad. Sci. USA. 

107: 7710-7715. 

Ehrnhoefer DE*, Bieschke J*, Boeddrich A, Herbst M, Masino L, Lurz R, 

Engemann S, Pastore A, and Wanker EE. 2008. EGCG redirects amyloidogenic 

polypeptides into unstructured, off-pathway oligomers. Nature 

Struct. Mol. Biol. 15: 558-566. 

Bieschke J, Zhang Q, Bosco DA, Lerner RA, Powers ET, Wentworth P Jr, and 

Kelly JW. 2006. Small molecule oxidation products trigger disease-associated 

protein misfolding. Acc. Chem. Res. 39: 611-619. 

Cohen E*, Bieschke J*, Perciavalle RM, Kelly JW, and Dillin A. 2006. Opposing 

activities protect against age-onset proteotoxicity. Science. 313: 

1604-1610. 

Bieschke J, Weber P, Sarafoff N, Beekes M, Giese A, and Kretzschmar H. 

2004. Autocatalytic self-propagation of misfolded prion protein. Proc. 

Natl. Acad. Sci. USA. 101: 12207-12211. 

Bieschke J, Giese A, Schulz-Schaeffer W, Zerr I, Poser S, Eigen M, and 

Kretzschmar H. 2000. Ultrasensitive detection of pathological prion protein 

aggregates by dual-color scanning for intensely fl uorescent targets. 

Proc Natl Acad Sci U S A. May 9;97(10):5468-73. 

* denotes two authors that contributed equally 



Ion channels are the molecular units of electrical activity in all cell types, 

which underlie important physiological functions such as heart contraction 

and neural activities. My research interests focus on the mechanisms 

of conformational changes during channel opening and closing and on the 

interaction of ion channels with other molecules in the cell. Currently, we 

use a combination of molecular biology, protein biochemistry, patch clamp 

techniques, and kinetic modeling to study two potassium channels: 1) The 

BK type calcium-activated potassium channels, which are important in the 

control of blood pressure and neurotransmitter release. They are implicated 

in hypertension and epilepsy; 2) The IKS potassium channels that 

play a key role in the rhythmic control of the heart rate. Defects in the IKS 

channel protein have been shown to cause severe inherited cardiac arrhythmias 

that often lead to syncope and sudden death. We are interested 

in how these channels sense cellular signals such as the membrane voltage 

and intracellular calcium to open, how disease-associated mutations alter 

channel function, and searching for reagents such as small molecules and 

peptides that modulate these channels and may lead to drugs for the treatment 

of human diseases associated with these channels. 


Wu D, Delaloye K, Zaydman MA, Nekouzadeh A, Rudy Y and Cui J. 2010. 

State-dependent electrostatic interactions of S4 arginines with E1 in S2 

during Kv7.1 activation. J. Gen. Physiol. 135: 575-581. 

Yang J, Krishnamoorthy G, Saxena A, Zhang G, Shi J, Yang H, Delaloye K, 

Sept D and Cui J. 2010. An epilepsy-dyskinesia-associated mutation enhances 

BK channel activation by potentiating Ca2+ sensing. Neuron, 

66: 871-883. 

Lee US and Cui J. 2009. {beta} subunit-specifi c modulations of a mutant 

BK channel associated with epilepsy and dyskinesia. J. Physiol. (London). 

587: 1481-1498. 

Yang H, Shi J, Zhang G, Yang J, Delaloye K and Cui J. 2008. Activation of 

Slo1 BK channels by Mg2+ coordinated between the voltage sensor and the 

RCK1 domains. Nature Structure and Molecular Biology 15: 1152-1159. 

Yang H, Hu L, Shi J, Delaloye K, Horrigan F, and Cui J. 2007. Mg2+ Mediates 

Interaction between the Voltage Sensor and Cytosolic Domain to Activate 

BK channels. Proc. Natl. Acad. Sci., U.S.A. 104: 18270- 18275. 

Shi J, Krishnamoorthy G, Yang Y, Hu L, Chaturvedi N, Harilal D, Qin J, Cui J. 

2002. Mechanism of magnesium activation of calcium-activated potassium 

channels. Nature 418:876-880. 

Jianmin Cui 

Professor of Biomedical Engineering on 

the Spencer T. Olin Endowment, 

Associate Professor of Cell Biology & 

Physiology 

Ph.D., Physiology & Biophysics, State 

University of New York, 1992 

M.S., Peking University, 1986 

B.S., Peking University, 1983 


molecular basis of bioelectricity and 

related diseases in nervous and cardiovascular 

systems; ion channel function 

and modulation; discovery of drugs that 

target ion channels; electrophysiology; 

molecular biology, biophysics 

Offi ce: Whitaker Hall, Room 290C 

Phone: (314) 935-8896 

Email: jcui@wustl.edu 



John P. Cunningham 



Ph.D., Electrical Engineering, Stanford 

University, 2009 

M.S., Stanford University, 2006 

B.A., Dartmouth College, 2002 


computational and systems neuroscience; 

machine learning; signal processing; 

pattern recognition 


Email: cunningham@wustl.edu 


At a high level, we study how complicated systems do interesting things. 

For example, we use our brain in everything that we do, but we understand 

relatively little about how it works. How do populations of neurons control 

complex, sophisticated movement? What new mathematical and computational 

techniques are required to investigate that, and how else can those 

methods be applied? How might these advances help researchers solve 

important problems in medicine and engineering? 

At a technical level, our research involves engineering, computer science, 

and applied statistics, and their application to neural systems. Specifi - 

cally, we design machine learning techniques, statistical methods, and 

optimization algorithms for analysis of neural data, primarily in the motor 

cortex. The purpose of these algorithms is fi rstly to advance scientifi c 

understanding of the neural basis of movement, and secondly, to advance 

computational learning methods in their own right. We commonly study and 

use dynamical systems, dimensionality reduction methods, nonparametric 

Bayesian statistics, approximate inference, optimization techniques, and 

numerical linear algebra. Many of these computational efforts require 

experimental validation; we collaborate closely with experimental systems 

neuroscientists and with brain-machine interface researchers. Overall, our 

research aims to advance understanding of learning and pattern generation 

in computational and biological systems, which has many applications 

across biomedicine and engineering. 


Churchland MM*, Cunningham JP* (contributing equally), Kaufman MT, Foster 

JD, Nuyujukian P, Ryu SI, Shenoy KV. 2012. Neural population dynamics 

during reaching. Nature Jul 5;487(7405): 51-6. 

Cunningham JP, Rasmussen CE, Ghahramani Z. 2012. Gaussian Processes 

for time-marked time-series data. JMLR W&CP. 22: 255-263. 

Cunningham JP, Nuyujukian P, Gilja V, Chestek CA, Ryu SI, and Shenoy KV. 

2011. A closed-loop human simulator for investigating the role of feedback- 

control in brain-machine interfaces. J. Neurophysiology 105: 1932- 

1949. 

Churchland MM, Cunningham JP, Kaufman MT, Ryu SI, and Shenoy KV. 2010. 

Cortical preparatory activity: Representation of movement or fi rst cog in a 

dynamical machine? Neuron 68: 387-400. 

Churchland MM, Yu BM, Cunningham JP, Sugrue LP, Cohen MR, Corrado GS, 

Newsome WT, Clark AM, Hosseini P, Scott BB, Bradley DC, Smith MA, Kohn 

A, Movshon JA, Armstrong KM, Moore T, Chang SW, Snyder LH, Lisberger 

SG, Priebe NJ, Finn IM, Ferster D, Ryu SI, Santhanam G, Sahani M, and 

Shenoy KV. 2010. Stimulus onset quashes neural variability: a widespread 

cortical phenomenon. Nature Neurosci. 13: 369-378. 



Our laboratory investigates basic mechanisms of cardiac arrhythmias 

and cardiac conduction in order to improve antiarrhythmic therapies. We 

employ several state-of-the-art methodologies, including, fast fl uorescent 

imaging of electrical activity with voltage- and calcium-sensitive molecular 

probes and fast imaging techniques; confocal microscopy of immunolabeled 

human myocardium; optical coherence tomography; electrostimulation, 

and electroporation. Through application of these experimental 

methods we study fundamental mechanisms of bioelectric therapy, aiming 

to develop novel pain-free implantable defi brillators. Using optical imaging 

we investigate propagation of action potentials in the human heart 

during normal conduction and during arrhythmias. Using molecular biology 

techniques we investigate pathological remodeling processes, which alter 

gene expression during chronic disease, leading to life-threatening cardiac 

arrhythmias. We hope to learn how to reverse remodeling processes and 

repair damaged heart. 


Efi mov IR, Kroll MW, and Tchou PJ, Eds. 2008. Cardiac Bioelectric Therapy: 

Mechanisms and Practical Implications. Springer. ISBN 978-0-387- 

79402-0. 

Lou Q, Fedorov VV, Glukhov AV, Fast VG, Moazami N, and Efi mov IR. 2011. 

Heterogeneity and Remodeling of Transmural Ventricular Excitation-Contraction 

Coupling in Human Heart Failure. Circulation 123(17): 1881-1890. 

Glukhov AV, Fedorov VV, Lou Q, Ravikumar VK, Kalish PW, Schuessler RB, 

Moazami N, and Efi mov IR. 2010. Transmural Dispersion Of Repolarization 

In Failing And Non Failing Human Ventricle. Circ Res. 106(5): 981-991. 

Fedorov VV, Schuessler RB, Hemphill M, Ambrosi CM, Chang R, Voloshina 

AS, Brown K, Hucker WJ, and Efi mov IR. 2009. Structural and Functional 

Evidence for Discrete Exit Pathways that Connect the Canine Sino-Atrial 

Node and Atria. Circ. Res. 104(7): 915-923. 

Igor R. Efimov 

The Lucy and Stanley Lopata 

Distinguished Professor of Biomedical 

Engineering, Professor of Cell Biology 

& Physiology, Medicine, and Radiology 

Ph.D., Biophysics & Biomedical Engineering, 

Moscow Institute of Physics & 


M.Sc., Moscow Institute of Physics & 


B.Sc., Moscow Institute of Physics & 



cardiac bioelectricity; biophotonic 

imaging; cardiovascular tissue 

engineering; implantable devices 

Offi ce: Whitaker Hall, Room 390F 

Phone: (314) 935-8612 

Email: igor@wustl.edu 



Donald L. Elbert 



Ph.D., Chemical Engineering, University 

of Texas-Austin, 1997 

B.S., University of Notre Dame, 1990 


biomaterials; cell and tissue 

engineering 

Offi ce: Whitaker Hall, Room 300D 

Phone: (314) 935-7519 

Email: elbert@wustl.edu 


Our laboratory is developing new hydrogel scaffolds that self-assemble in 

the presence of living cells, applying ‘bottom-up’ design principles. The materials 

are bioactive and designed to resist protein adsorption. “Modules’” 

are formed by a phase separation process, and are designed to carry out 

unique functions, for example, to deliver proteins or drugs, or to degrade 

to form pores. Assembly of the modules around the cells allows for the 

formation of multiple compartments that contain different cell types. 

We believe that these strategies hold great promise to produce synthetic 

scaffolds that are better mimics of natural extracellular matrix. 


Elbert DL. 2011. Bottom-up Tissue Engineering. Curr Opin Biotechnol. 

Oct;22(5): 674-80. Epub 2011 Apr 27. 

Elbert DL. 2011. Liquid-liquid two-phase systems for the production of 

porous hydrogels and hydrogel microspheres for biomedical applications: 

A tutorial review. Acta Biomaterialia 7: 31-56. 

Flake MM, Nguyen PK, Scott RA, Vandiver LR, Willits RK, and Elbert DL. 

2011. Poly(ethylene glycol) microparticles produced by precipitation polymerization 

in aqueous solution. Biomacromolecules 12: 844-850. 

Roam JL, Xu H, Nguyen PK, and Elbert DL. 2010. The Formation of Protein 

Concentration Gradients Mediated by Density Differences of 

Poly(ethylene glycol) Microspheres. Biomaterials 31: 8642-8650. 

Scott EA, Nichols MA, Willits RK, and Elbert DL. 2010. Modular scaffolds 

assembled around living cells using poly(ethylene glycol) microspheres 

with macroporation via a non-cytotoxic porogen. Acta Biomaterialia 

6: 29-38. 

Alford SK, Wang Y, Feng Y, Longmore GD, and Elbert DL. 2010. Prediction 

of sphingosine 1-phosphate stimulated endothelial cell migration rates 

using biochemical measurements. Annals of Biomedical Engineering 38: 

2775-2790. 

Nichols MA, Scott EA, and Elbert DL. 2009. Factors affecting size and 

swelling of poly(ethylene glycol) microspheres formed in aqueous sodium 

sulfate solutions without surfactants. Biomaterials 30: 5283-5291. 



Our 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 Alzheimer’s, mental 

retardation and autism spectrum disorders. 


Deng PY, Sojka D, and Klyachko VA. 2011. Abnormal presynaptic shortterm 

plasticity and information processing in a mouse model of Fragile X 

Syndrome. J Neurosci. Jul 27;31(30): 10971-82. 

Kandaswamy U, Deng PY, Stevens CF, and Klyachko VA. 2010. The role of 

presynaptic dynamics in processing of natural spike trains in hippocampal 

synapses. J. Neurosci. 30: 15904-15914. 

Klyachko VA and Stevens CF. 2006. Temperature-dependent shift of 

balance among the components of short-term plasticity in hippocampal 

synapses. J. Neurosci. 26: 6945-6957. 

Klyachko VA and Stevens CF. 2006. Excitatory and feed-forward inhibitory 

hippocampal synapses work synergistically as an adaptive fi lter of natural 

spike trains. PLoS Biology 4: e207. 

Klyachko VA and Stevens CF. 2003. Connectivity optimization and the 

positioning of cortical areas. Proc. Natl. Acad. Sci. USA 100: 7937-41. 

Klyachko VA and Jackson MB. 2002. Capacitance steps and fusion pores of 

small and large-dense-core vesicles in nerve terminals. Nature 418: 89-92. 

Klyachko VA, Ahern GP and Jackson MB. 2001. cGMP-mediated facilitation 

in nerve terminals by enhancement of the spike after-hyperpolarization. 

Neuron 31: 1015-1025. 

Vitaly A. Klyachko 


Engineering, Assistant Professor of 

Cell Biology & Physiology 

Ph.D., Biophysics. University of Wisconsin-Madison, 

2002 

M.S., B.S., Moscow State University, 

1998 


synaptic function and plasticity; neural 

circuits; information analysis; neurological 

disorders 

Offi ce: BJCIH, Room 9610 (Medical 

School Campus) 

Phone: (314) 362-5517 

Email: klyachko@wustl.edu 



Daniel W. Moran 



Anatomy & Neurobiology, and 

Physical Therapy 

Ph.D., Bioengineering, Arizona State 


B.S., Milwaukee School of Engineering, 

1989 


motor control; brain-computer 

interfaces 


Phone: (314) 935-8836 

Email: dmoran@wustl.edu 


My primary research interest is in the area of motor control. My lab investigates 

how various neural substrates control voluntary movement. Specifi - 

cally, I am interested in motor cortical representation of arm movements. 

Our recent fi ndings 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 or dura matter for BCI applications. 

Our recent results in non-human primates shows that epidural 

ECoG spectral power in the 60-200 Hz range is well correlated with ensemble 

single unit activity. Over a period of one week, the subjects learned 

to accurately control a 2D computer cursor through neural adaptation of 

microECoG signals over “cortical control columns” having diameters on the 

order of a few mm. These results suggest that the mildly-invasive epidural 

microECoG is a pragmatic and possibly optimal modality for controlling 

neuroprosthetic devices. 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. 


Pearce TM and Moran DM. 2012. Strategy-dependent encoding of planned 

arm movements in dorsal premotor cortex. Science PMID: 22821987 [Epub 

ahead of print]. 

Wang W, Chan SS, Heldman DA and Moran DW. 2010. Motor cortical representation 

of hand position and rotation during reaching. Journal of Neuroscience 

30: 958-962. 



Our lab is interested in understanding the regulation and function of a 

wide variety of post-translational modifi cations (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 

modifi cations 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. 


Naegle KM, White FM, Lauffenburger DA, Yaffe MB. 2012. Robust co-regulation 

of tyrosine phosphorylation sites on proteins reveals novel protein 

interactions. Mol BioSys DOI: 10.1039/C2MB25200G 

Naegle KM, Welsch RE, Yaffe MB, White FM, and Lauffenburger DA. 2011. 

MCAM: Multiple clustering analysis methodology for deriving hypotheses 

and insights from high-throughput proteomic datasets. PLoS Comput Biol. 

Jul;7(7): e1002119. Epub 2011 Jul 21. 

Naegle KM, Gymrek M, Joughin BA, Wagner JP, Welsch RE, Yaffe MB, 

Lauffenburger DA, and White FM. 2010. PTMScout: A web resource for 

analysis of high-throughput post-translational proteomic studies. Molecular 

and Cellular Proteomics 9(11): 2558-2570. 

Joughin BA, Naegle KM, Huang PH, Yaffe MB, Lauffenburger DA, and White 

FM. 2009. An integrated comparative phosphoproteomic and bioinformatic 

approach reveals a novel class of MPM-2 motifs upregulated in 

EGFRvIII-expressing Glioblastoma cells. Molecular BioSystems 5(1): 59-67. 

Kristen M. Naegle 



Ph.D., Biological Engineering, 

Massachusetts Institute of Technology, 

2010 

M.S., Massachusetts Institute of 


M.S., University of Washington, 2004 

B.S., University of Washington, 2001 


computational molecular systems 

biology, post-translation modifi cations, 

signal transduction, proteomics 


Phone: (314) 935-7665 

Email: knaegle@wustl.edu 



Rohit V. Pappu 

Professor of Biomedical Engineering, 

Professor of Biochemistry & Molecular 

Biophysics, Director of the Center for 

Biological Systems Engineering, 

Ph.D., Theoretical and Biological 

Physics, Tufts University, 1996 

M.S., Tufts University, 1993 

B.Sc., Bangalore University, 1990 


protein aggregation and its effects on 

neurodegeneration; protein-nucleic 

acid interactions and modeling of transcriptional 

regulation; macrocolecular 

self-assembly and protein folding 


Phone: (314) 935-7958 

Email: pappu@wustl.edu 


Research in our lab is focused on intrinsically disordered proteomes. 

Eukaryotic proteomes are enriched in intrinsically disordered proteins 

(IDPs) that function despite being unable to fold autonomously into well 

defi ned three-dimensional structures. In specifi c projects, we are working 

on the mechanisms of IDP aggregation, specifi cally the mechanisms 

of aggregation of proteins with expanded polyglutamine tracts because it 

is directly relevant to Huntington’s disease. Recent efforts have focused 

on the cis-regulation of polyglutamine aggregation by fl anking sequences 

derived from huntingtin and the interplay between aggregation and heterotypic 

interactions as determinants of neurodegeneration. Investigations 

of sequence-to-ensemble relationships of IDPs are being leveraged to 

understand how conformational heterogeneity is used to achieve specifi city 

in molecular recognition. The systems of active investigation include 

transcription factors, single-stranded DNA binding proteins, the Notch 

intracellular domain, proteins of the nuclear transport system, microtubule 

associated proteins that regulate axonal transport, and RNA binding proteins. 

Efforts are underway to extract common principles from the study 

of specifi c IDP systems in order to converge on a framework that enables 

the prediction and remodeling of cellular phenotypes that are the result of 

integrative responses of nested hierarchies of biomolecular networks. 


Das RK, Mao AH, Pappu RV. 2012. Unmasking functional motifs within 

disordered regions of proteins. Science Signaling 5: pe17,1-3. 

Das RK, Crick SL, Pappu RV. 2012. N-terminal segments modulate the 

alpha-helical propensities of the intrinsically disordered basic regions of 

bZIP proteins. Journal of Molecular Biology 416: 287-299. 

Halfmann R, Alberti S, Krishnan R, Lyle N, O’Donnell CW, King OD, Berger B, 

Pappu RV, Lindquist S. 2011. Opposing effects of glutamine and asparagine 

govern prion formation by intrinsically disordered proteins. Molecular Cell 

43: 72-84. 

Mao AH, Crick SL, Vitalis A, Chicoine CL, Pappu RV. 2010. Net charge per 

residue modulates conformational ensembles of intrinsically disordered 

proteins. Proceedings of the National Academy of Sciences USA 107: 8183- 

8188. 

Williamson TE, Vitalis A, Crick SL, Pappu RV. 2010. Modulation of polyglutamine 

conformations and dimer formation by the N-terminus of huntingtin. 

Journal of Molecular Biology 396: 1295-1309. 



My research interests are in understanding the design and computing principles 

of biological sensory systems and translating this knowledge into 

neuromorphic devices and algorithms. Specifi cally, 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. In collaboration with the National Institute of Standards 

and Technology, we are currently developing a neuromorphic ‘electronic 

nose’ based on MEMS microsensor arrays for non-invasive chemical 

sensing. Potential target applications for the electronic nose technology 

include medical diagnosis, homeland security, environmental monitoring, 

space explorations, robotics, and human-computer interaction. 


Raman B, Stopfer M and Semancik S. 2011. Mimicking biological design 

and computing principles in artifi cial olfaction. ACS Chem Neurosci. May 

27;2(9): 487-499. 

Raman B, Joseph J, Tang J and Stopfer M. 2010. Temporally diverse fi ring 

patterns in olfactory receptor neurons underlie spatio-temporal neural 

codes for odors. J. Neurosci. 30(6): 1994-2006. 

Benkstein K, Raman B, Montgomery CB, Martinez CJ and Semancik S. 2010. 

Microsensors in Dynamic Backgrounds: Towards real-time breath monitoring 

with temperature programmed microsensors. IEEE Sensors, Special 

Issue on Sensors for Breath Analysis 10: 137-144. 

Ito I, Bazhenov M, Ong CR, Raman B and Stopfer M. 2009. Frequency transitions 

in odor-evoked neural oscillations. Neuron 64: 692-706. 

Raman B, Meier DC, Evju JK and Semancik S. 2009. Designing and Optimizing 

Microsensor Arrays for Recognizing Chemical Hazards in Complex 

Environments. Sensors & Actuators B. 137(2): 617-629. 

Raman B, Hertz J, Benkstein K and Semancik S. 2008. A bio-inspired methodology 

for artifi cial olfaction. Analytical Chemistry 80(22): 8364-8471. 

Ito I, Ong CR, Raman B and Stopfer M. 2008. Sparse odor representation 

and olfactory learning. Nature Neuroscience. 11(10): 1177-1184. 

Raman B, Kotseroglou T, Clark L, Lebl M and Gutierrez-Osuna R. 2007. 

Neuromorphic processing for optical microbead arrays: dimensionality 

reduction and contrast enhancement. IEEE Sensors 7(4): 506-514. 

Baranidharan Raman 



Ph.D., Computer Science, Texas A&M 

Engineering, 2005 

M.S., Texas A&M Engineering, 2003 

B. Eng., University of Madras, 2000 


computational and systems neuroscience; 

neuromorphic engineering; pattern 

recognition; sensor-based machine 

olfaction 


Phone: (314) 935-8538 

Email: barani@wustl.edu 



Yoram Rudy 

The Fred Saigh Distinguished Professor 

of Engineering, Professor of Cell 

Biology & Physiology, Medicine, 

Radiology and Pediatrics 

Ph.D., Biomedical Engineering, Case 

Western Reserve University, 1978 

M.Sc., Technion – Israel Institute of 


B.Sc., Technion – Israel Institute of 



cardiac electrophysiology and 

arrhythmias; molecular dynamics of ion 

channels; computational biology and 

mathematical modeling; imaging and 

mapping of cardiac electrical activity 

Offi ce: Whitaker Hall, Room 290B 

Phone: (314) 935-8160 

Email: rudy@wustl.edu 


Our research aims at understanding the mechanisms that underlie normal 

and abnormal rhythms of the heart at various levels, from the molecular 

(ion channel) and cellular to the whole heart. We are also developing a novel 

noninvasive imaging modality (Electrocardiographic Imaging, ECGI) for the 

diagnosis and guided therapy of cardiac arrhythmias. Rhythm disorders of 

the heart lead to over 400,000 cases of sudden death annually in the U.S. 

alone. Through the development of detailed mathematical models of ion 

channels biophysics and electrophysiology, and of cardiac cells and tissue, 

we are investigating the mechanisms and consequences of geneticallyinherited 

cardiac arrhythmias, impaired cell-to-cell communication, and 

abnormal spread of the cardiac impulse in the diseased heart (e.g. myocardial 

infarction). ECGI imaging has been tested and evaluated extensively 

with excellent results in experimental setups and in patients with various 

heart conditions, including comparisons to catheter mapping and multielectrode 

mapping directly from the heart during open-heart surgery. 

ECGI is currently used to study mechanisms of various cardiac arrhythmias 

(e.g. atrial fi brillation, ventricular tachycardia, heart failure) in patients 

and to guide therapeutic interventions. 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. 


OHara TJ, Virág L, Varró A, Rudy Y. 2011. Simulation of the undiseased 

human cardiac ventricular action potential: Model formulation and experimental 

validation. PLoS Computational Biology 7(5): e1002061.doi:10.1371/ 

journal.pcbi.1002061 

Wang Y, Cuculich PS, Zhang J, Desouza KA, Vijayakumar R, Chen J, Faddis 

MN, Lindsay BD, Smith TW, Rudy Y. 2011. Noninvasive Electroanatomic 

Mapping of Human Ventricular Arrhythmias Using ECG Imaging (ECGI). 

Science Translational Medicine 3(98): 191-200 

Clancy CE and Rudy Y. 1999. Linking a genetic defect to its cellular phenotype 

in a cardiac arrhythmia. Nature 400: 566-569. 

Silva JR, H. Pan H, Wu D, Nekouzadeh A, Decker K, Cui J, Baker NA, Sept D 

and Rudy Y. 2009. A multiscale model linking ion-channel molecular dynamics 

and electrostatics to the cardiac action potential. Proc. Natl. Acad. 

Sci. USA. 106: 11102-11106. 

Ramanathan C, Ghanem RN, Jia P, Ryu K and Rudy Y. 2004. Electrocardiographic 

imaging (ECGI): a noninvasive imaging modality for cardiac electrophysiology 

and arrhythmia. Nature Medicine 10: 422-428. 



My lab is interested in developing new bioactive scaffolds for tissue 

engineering. These scaffolds contain bioactive signals that include signals 

for cell-type specifi c adhesion and migration, growth factors to promote 

cell proliferation and differentiation. Our goal is to make materials that 

can sense cell-derived signals during regeneration and respond by providing 

biological signals to enhance tissue regeneration. 

Growth factors are potent protein drugs that are powerful regulators of 

biological function. Their presence in tissues is highly regulated in both 

time and space. The ability to tightly regulate the release of growth factors 

is essential in the development of tissue engineering scaffolds. My 

laboratory is using combinatorial methods to design novel materials for 

affi nity-based protein delivery. We are currently testing the ability of 

these bioactive drug delivery systems to promote nerve regeneration in 

both peripheral nerve and spinal cord injury models in collaboration with 

clinical faculty. 


McCreedy,DA, Silverman C, Gottleib DI, and Sakiyama-Elbert SE. 2012. 

Transgenic Enrichment of Mouse Embryonic Stem Cell-derived Progenitor 

Motor Neurons. Stem Cell Research 8: 368-378. 

Johnson PJ, Tatara A, McCreedy DA, Shiu A, and Sakiyama-Elbert SE. 2010. 

Tissue-engineered fi brin scaffolds containing neural progenitors enhance 

functional recovery in a subacute model of SCI. Soft Matter 6: 5127-5137. 

Wood MD, MacEwan MR, French AR, Moore AM, Hunter, Mackinnon SE, Moran 

DW, Borschel GH and Sakiyama-Elbert SE. 2010. Fibrin Matrices with 

Affi nity-based Delivery Systems and Neurotrophic Factors Promote Functional 

Nerve Regeneration. Biotechnology and Bioengineering 106:970-9. 

Johnson PJ, Tatara A, Shiu A and Sakiyama-Elbert SE. 2010. Controlled 

release of neurotrophin-3 and platelet derived growth factor from fi brin 

scaffolds containing neural progenitor cells enhances survival and differentiation 

into neurons in a subacute model of SCI. Cell Transplantation 19: 

89-101. 

Willerth SM, Rader A and Sakiyama-Elbert SE. 2008. The Effect of Controlled 

Growth Factor Delivery on Embryonic Stem Cell Differentiation 

Inside of Fibrin Scaffolds. Stem Cell Research 1: 205-218. 

Shelly E. 

Sakiyama-Elbert 

Professor of Biomedical 

Engineering on the Joseph and Florence 

Farrow Endowment, Associate 

Department Chair and Director of 

Graduate Studies, Professor 

of Energy, Environmental & Chemical 

Engineering, and Surgery 

Ph.D., Chemical Engineering, California 

Institute of Technology, 2000 

M.S., California Institute of Technology, 

1998 

B.S., Massachusetts Institute of 



biomaterials; drug delivery; tissue 

engineering; stem cells 

Offi ce: Whitaker Hall, Room 390B 

Phone: (314) 935-7556 

Email: sakiyama@wustl.edu 



Jin-Yu Shao 



Energy, Environmental & Chemical 


Biochemistry & Molecular Biophysics 

Ph.D., Mechanical Engineering and Materials 

Science, Duke University, 1997 

M.S., Peking University, 1991 

B.S., Peking University, 1988 


cellular and molecular biomechanics; 

protein-protein interactions, 

mathematical modeling of biological 

processes 


Phone: (314) 935-7467 

Email: shao@biomed.wustl.edu 


Combining 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 fi rst 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 fl ow, adhesion molecules expressed on rolling cells, leukocytes, 

and endothelial cells, as well as mechanical properties of these cells. This 

process has been implicated in infl ammatory, infectious, cardiovascular, 

and cancerous diseases. 

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. Excessive VWF cleavage results in von Willebrand disease, 

a potentially-fatal bleeding disorder, whereas insuffi cient VWF cleavage 

results in thrombotic thrombocytopenic purpura, a disease characterized 

by microvascular thrombosis. Either excessive or insuffi cient Notch cleavage 

alters downstream signaling that may lead to diseases like T-cell acute 

lymphoblastic leukemia and breast carcinoma. 


Chen Y, Yao DK and Shao JY. 2010. The constitutive equation for membrane 

nanotube formation. Ann. Biomed. Eng. 38: 3756-3765. 

Ying J, Ling Y, Westfi eld LA, Sadler JE and Shao JY. 2010. Unfolding the A2 

domain of von Willebrand factor with the optical trap. Biophysical Journal. 

98: 1685-1693. 

Shao JY. 2009. Biomechanics of leukocyte and endothelial cell surface. In 

Current Topics in Membranes, ed. Klaus Ley, Elsevier Inc. 25-45. 

Chen Y, Liu B, Xu G and Shao JY. 2009. Validation, in-depth analysis, and 

modifi cation of the micropipette aspiration technique. Cell. Mol. Bioeng. 

2: 351-365. 

Liu B, Yu Y, Yao DK and Shao JY. 2009. A direct micropipette-based calibration 

method for AFM cantilevers. Rev. Sci. Instrum. 80: 065109. 

Xu G and Shao JY. 2008. Human neutrophil surface protrusion: viscoelasticity 

and cytoskeletal involvement. Am. J. Physiol. Cell Physiol. 295: 

C1434-C1444. 

Yao DK and Shao JY. 2008. A novel technique of quantifying fl exural stiffness 

of rod-like structures. Cell. Mol. Bioeng. 1:75-83. 



The heart beat is controlled by an organized electrical rhythm that triggers 

the mechanical contraction. Electrical disruption leads to arrhythmias that 

cause sudden death. In the membranes of the heart cells, it is the opening 

and closing of specialized ion channel proteins that generates the electric 

signal- an action potential. As charges move across the membrane, they alter 

the voltage across it. Linking the molecular basis of the action potential 

and the diseases that affect it to the whole cell, tissue and organ physiology 

poses a daunting multi-scale challenge because protein motions occur 

in tiny fractions of a millisecond, but arrhythmias occur on a timeframe of 

minutes. Space is also at issue; individual ion channels occupy nanometers 

of space, while the whole heart fi lls many centimeters. One method to address 

this dilemma is computational modeling, where we begin by describing 

the behavior of one ion channel alteration that is known to cause disease 

in great detail. Then, we can place the altered channel behavior into a 

larger model that contains broad strokes representing the cell, a piece of 

tissue, or even the whole heart. 

Because the time and spatial scales involved are so small, obtaining molecular-level 

information is particularly diffi cult. Recent techniques combine 

electrical measurements with fl uorescent indicators of molecular events 

for this purpose. When the cell voltage changes, the channel moves along 

with fl uors attached to key locations. The environmental change alters 

the fl uorescence, which is observed by a sensitive detector. These kinds of 

experiments are only recently being applied to cardiac proteins. 

My research involves fi rst conducting experiments to defi ne how cardiac 

ion channels open and close. After understanding how channels work at 

this level, we then measure how quickly each movement takes place in a 

cardiac myocyte. This experimental data linking molecular and native cell 

physiology can then be incorporated into a model that recapitulates the 

cellular electrophysiology so that the functional consequences of altered 

molecular movements can be understood. 


Silva JR, H. Pan H, Wu D, Nekouzadeh A, Decker K, Cui J, Baker NA, Sept D 

and Rudy Y. 2009. A multiscale model linking ion-channel molecular dynamics 

and electrostatics to the cardiac action potential. Proc. Natl. Acad. Sci. 

USA. 106:11102-11106. 

Silva JR and Rudy Y. Multi-scale electrophysiology modeling: from atom to 

organ. J. Gen. Physiol. 135:575-581 

Jonathan R. Silva 



Ph.D., Biomedical Engineering, Washington 

University in St. Louis, 2008 

M.Sc., Case Western Reserve University, 

2004 

B.Sc., The Johns Hopkins University, 

2000 


cardiac electrophysiology and arrhythmias; 

molecular spectroscopy; ion channel 

biophysics; mathematical modeling 

of ion channels and action potentials 

Offi ce: Whitaker Hall, Room 290G 

Phone: (314) 935-8837 

Email: jonsilva@wustl.edu 



Larry A. Taber 

The Dennis and Barbara Kessler 

Professor of Biomedical Engineering 

Ph.D., Aeronautics and Astronautics, 

Stanford University, 1979 

M.S., Stanford University, 1975 

B.S., Georgia Institute of Technology, 

1974 


biomechanics of cardiovascular and 

nervous system development 


Phone: (314) 935-8544 

Email: lat@biomed.wustl.edu 


Our research deals primarily with the mechanics of embryonic morphogenesis. 

Currently, we are studying the role that mechanical forces play in 

heart, brain, and eye development. Although the structure and function of 

these organs differ greatly, many similarities exist among the biophysical 

processes that create them. A long-term goal of our work is to determine 

the fundamental biomechanical laws that govern morphogenesis (if such 

laws exist). 

In the early embryo, both the heart and brain are tubular structures, with 

the eyes being spherical membranes protruding from the brain. As the 

embryo grows, these organs undergo dramatic changes in shape. The heart 

tube loops into a curved tube and divides into a four-chambered pump, 

the brain expands and folds into its characteristic highly convoluted form, 

and the eye folds and differentiates to create the retina and lens. These 

processes involve a dynamic interaction of genetic and epigenetic (including 

mechanical) factors. Any abnormalities in morphogenesis can lead to 

severe congenital defects. We investigate these problems by integrating 

computational models with laboratory experiments on embryos. 

We believe that much can be gained by studying how nature manufactures 

tissues and organs. A fundamental understanding of these processes 

should benefi t researches seeking to prevent and treat congenital malformations, 

as well as tissue engineers striving to create replacement tissues 

and organs in vitro. 


Varner VD, Voronov DA, Taber LA. 2010. Mechanics of head fold formation: 

investigating tissue-level forces during early development. Development. 

137:3801-3811. 

Xu G, Knutsen AK, Dikranian K, Kroenke CD, Bayly PV and Taber LA. 2010. 

Axons pull on the brain, but tension does not drive cortical folding. J Biomech 

Eng. Jul;132(7):071013. 

Filas BA, Bayly PV, Taber LA. 2010. Mechanical stress as a regulator of 

cytoskeletal contractility and nuclear shape in embryonic epithelia. Ann 

Biomed Eng 39: 443-454. 

Taber LA. 2009. Towards a unifi ed theory for morphomechanics. Phil Trans 

Roy Soc A 367: 3555-3583. 

Taber LA. 2006. Biophysical mechanisms of cardiac looping. Int J Dev Biol 

50: 323-332. 



Our laboratory studies the computational basis of human motor performance. 

Characterizing motor control and motor learning processes in 

healthy human adults will identify the specifi c signals used to plan movements 

and build motor predictions, which will in turn predict the neuronal 

activities required for motor learning. Comparing these predictions to 

physiological recordings from non-human primates will indicate the brain 

areas that likely underlie these computations. Understanding normal motor 

behavior and its neuronal basis will make possible the measurement of 

these processes in disease, further the development of insightful clinical 

tests in movement neurology, facilitate the early detection of symptoms, 

and make possible treatments of motor diseases at the earliest and least 

problematic stages. Emerging research projects include motor control 

and learning in children; cognitive components to motor behavior; motor 

dysfunction and recovery of function in Parkinson’s disease; and theories 

of movement, biomechanics, refl ex and brain. 

We also study innovations in undergraduate education in science, technology, 

engineering and mathematics (STEM). Our work aims to improve motivation, 

achievement, and understanding across courses and semesters, 

especially for underclassmen. 


Schaefer SY, Shelly IL, Thoroughman KA. 2012. Beside the point: motor 

adaptation without feedback-based error correction in task-irrelevant 

conditions. J Neurophysiol. Feb;107(4): 1247-56. 

Semrau JA, Daitch AL, Thoroughman KA. 2012. Environmental experience 

within and across testing days determines the strength of human visuomotor 

adaptation. Exp Brain Res. Feb;216(3): 409-18. 

Taylor JA and Thoroughman KA. 2008. Motor adaptation scaled by the diffi 

culty of a secondary cognitive task. PLoS One 2008 Jun 18;3(6): e2485. 

Fine MS and Thoroughman KA. 2007. The trial-by-trial transformation of 

error into sensorimotor adaptation changes with environmental dynamics. 

Journal of Neurophysiology 98: 1392-404. 

Taylor JA and Thoroughman KA. 2007. Divided attention impairs human 

motor adaptation but not feedback control. Journal of Neurophysiology 98: 

317-326. 

Fine MS and Thoroughman KA. 2006. Motor Adaptation to Single Force 

Pulses: Sensitive to Direction but Insensitive to Within-Movement Pulse 

Placement and Magnitude. Journal of Neurophysiology 96: 710-720. 

Thoroughman KA and Taylor JA. 2005. Rapid reshaping of human motor 

generalization. Journal of Neuroscience 25: 8948-8953. 

Kurt A. Thoroughman 


Engineering, Associate Chair for 

Undergraduate Studies, Associate 

Professor of Anatomy & Neurobiology, 

Physical Therapy 

Director, Undergraduate Studies, SEAS 

Ph.D., Biomedical Engineering, 

Johns Hopkins University, 1999 

B.A., University of Chicago, 1993 


human motor control and learning; 

neural computation; undergraduate 

engineering education 


Email: thoroughman@biomed.wustl.edu 



Lihong Wang 

The Gene K. Beare Distinguished 

Professor of Biomedical Engineering, 

Professor of Radiology 

Ph.D., Electrical Engineering, Rice 


M.S., Huazhong University of Science 

& Technology, 1987 

B.S., Huazhong University of Science 

& Technology, 1984 


biophotonic imaging 

Offi ce: Whitaker Hall, Room 190D 

Phone: (314) 935-6152 

Email: lhwang@biomed.wustl.edu 


Our research focuses on non-ionizing biophotonic imaging. Our laboratory 

invented or discovered functional photoacoustic tomography, photoacoustic 

microscopy (PAM), photoacoustic Doppler effect, photoacoustic 

reporter gene imaging, focused scanning microwave-induced thermoacoustic 

tomography, the universal photoacoustic or thermoacoustic 

reconstruction algorithm, frequency-swept ultrasound-modulated optical 

tomography, time-reversed ultrasonically encoded (TRUE) optical focusing, 

sonoluminescence tomography, Mueller-matrix optical coherence 

tomography, optical coherence computed tomography, and oblique-incidence 

refl ectometry. Our photoacoustic or thermoacoustic imaging modalities 

provide speckle-free images with high electromagnetic contrast 

and high ultrasonic resolution at large penetration depths. In particular, 

PAM broke through the long-standing penetration limit of conventional 

optical microscopy and reached super-depths for noninvasive biochemical, 

functional, and molecular imaging in living tissue at high resolution. 

Our Monte Carlo model of photon transport in biological tissues has been 

used worldwide. We are currently investigating these noninvasive imaging 

techniques for their utility in cancer diagnostics and neurosciences. 


Xu X, Liu H, and Wang LV. 2011. Time-reversed ultrasonically encoded optical 

focusing into scattering media. Photonics 5: 154–157. 

Wang LV. 2009. Multiscale photoacoustic microscopy and computed 

tomography. Nature Photonics 3: 503–509. 

Wang LV and Wu HI. 2007. Biomedical Optics: Principles and Imaging. 

Hoboken (NJ): Wiley. Joseph Goodman Book Award. 

Zhang HF, Maslov K, Stoica G and Wang LV. 2006. Functional photoacoustic 

microscopy for high-resolution and noninvasive in vivo imaging. Nature 

Biotechnology 24: 848-851. 

Wang X, Pang Y, Ku G, Xie X, Stoica G and Wang LV. 2003. Non-invasive 

laser-induced photoacoustic tomography for structural and functional 

imaging of the brain in vivo. Nature Biotechnology 21:803–806. 


COLLABORATIVE RESEARCH & EDUCATIONAL PROGRAMS IN BME 

At Washington University, world-class biological, engineering and medical research — along 

with topnotch, state-of-the-art healthcare — are closely intertwined. For more than 50 years, 

collaborations between the School of Medicine and the School of Engineering have led to 

major advances in many areas including: positron emission tomography, medical applications 

of ultrasound, application of computers to hearing research, and development of heart valve 

fl ow simulators. Since the establishment of the Department of Biomedical Engineering in 1997, 

this atmosphere of collaboration and collegiality between the two schools has been further 

strengthened and expanded, leading to an exceptional degree of synergism that is one of our 

hallmarks. All of our core faculty have been hired since 1997 and comprise a young, dynamic 

and still-expanding group that will eventually number more than 28. 

The core faculty, together with affi liated faculty from other departments (listed in the description 

of each educational program on the following pages) 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 member of the network. The commitment and diverse talent of these 

faculty provide a vast array of choices to enable students to refi ne their unique quantitative 

and analytical engineering skills and apply them to relevant biomedical problems. As a result, 

our graduates are well-equipped to work in multidisciplinary teams tackling cutting-edge and 

high-impact problems of modern biomedical engineering. 

Our network of mentors is grouped into the fi ve educational programs detailed on the following 

pages. These educational programs refl ect the major research programs of our department. 


EDUCATIONAL PROGRAMS IN BME 

Biomaterials & Tissue Engineering 

• biocompatible engineered 

materials 

• engineered materials for 

regenerative medicine 

• materials for drug and gene 

delivery 

• cell and tissue biomechanics 

in development, injury and 

healing 

Biomaterials & Tissue Engineering, a truly interdisciplinary 

program, 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. 

Faculty in this program 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 to create 

replacements for tissues damaged by disease or trauma; and 

to understand the processes that drive cellular and tissue 

responses in development and in pathological states. 

In addition to the outstanding experimental competence of 

program faculty, several of the participating researchers 

provide broad expertise in the theoretical and mathematical 

aspects of cell and tissue engineering. 


PROGRAM OF STUDY 

Students in this program follow a 

course of study in accordance with 

the general regulations of the Department 

of Biomedical Engineering. 

Courses available to satisfy 

degree requirements include the 

following: 

BME 511 Biotechnology Techniques 

for Engineers 

BME 521 Kinetics of Receptormediated 

Processes 

BME 523 Biomaterials Science 

BME 524 Tissue Engineering 

BME 525 Engineering Aspects of 

Biotechnology 

BME 527 Design of Artifi cial 

Organs 

BME 558 Biological Transport 

BME 563 Orthopedic 

Biomechanics: Bones and Joints 

BME 564 Orthopedic 

Biomechanics: Cartilage/Tendon 

PROGRAM FACULTY 

Phil Bayly, Ph.D. 

Quantitative characterization 

and modeling of brain trauma and 

development 

Paul Bridgman, Ph.D. 

Basic cellular properties of developing 

nerve and muscle 

Donald Elbert, Ph.D. 

Biomaterials, drug delivery, scaffolds 

for tissue engineering 

Anthony French, M.D., Ph.D. 

Viral immunology, modeling pathogenetic 

mechanisms 

Spencer Lake, Ph.D. 

Tissue biomechanics of tendon and 

ligament, multi-scale modeling, 

microstructural structure-function 

relationships of tissues 

Joshua Maurer, Ph.D. 

Click chemistry, biomaterials for 

neuroscience 

Robert Mecham, Ph.D. 

Extracellular matrix and its infl uence 

on the phenotype of cells 

Shelly Sakiyama-Elbert, Ph.D. 

Biomaterials, drug delivery 

Linda Sandell, Ph.D. 

Chondrogenesis; skeletal development 

Jin-Yu Shao, Ph.D. 

Cell mechanics, receptor and ligand 

interactions 

Matthew Silva, Ph.D. 

Bone mechanics, tendon mechanics 

and repair 

Larry Taber, Ph.D. 

Mechanics of brain and heart development 

Steve Thomopoulos, Ph.D. 

Orthopedic mechanics, mechanics 

of tendinous cells and tissue 



Cardiovascular Engineering 

• cardiac bioelectricity 

• vascular cell mechanics 

• new paradigms for 

defi brillation 

• mechanisms of cardiac 

arrhythmias 

• electrocardiographic 

imaging 

Cardiovascular Engineering integrates physiology, cell and 

molecular biology, bioelectricity and biomechanics to describe, 

understand, and re-engineer the cardiovascular systems. 

The goal is to develop, test, and validate a quantitative 

and predictive understanding of the systems from an engineering 

standpoint and to apply that understanding toward 

the solution of biomedically-relevant problems. 

An important feature of this program is its multidisciplinary 

approach to the study of these systems. Research interests 

range from the study of ion channels and their protein structure, 

blood, cardiac, and vascular cells to the human cardiovascular 

systems in vivo. Topics currently under investigation 

include: the relationship between the electrical and mechanical 

activity of the heart; characterizing the electro-mechanical 

properties of cells and tissue comprising the heart wall; 

studying the properties and interactions of blood cell surface 

structures with receptors on endothelial cells, computational 

modeling of the developing and adult heart during health and 

disease, developing methods for targeted imaging of heart 

and vessels, understanding the biochemical and mechanical 

factors underlying angiogenesis, and describing function 

at the cellular and organ level with various imaging methods 

including acoustic, biophotonic, magnetic resonance, and electrocardiographic 

imaging. 


PROGRAM OF STUDY PROGRAM FACULTY 

Program students are expected to 

take four to six courses in the fi rst 

year in accordance with the general 

regulations of the department. The 

following courses are among those 

from which students in this 

program can select: 

BME 471 Bioelectrical Phenomena 

BME 556 Experimental Methods in 

Biomechanics 

BME 557 Cell and Subcellular 

Biomechanics 

BME 559 Intermediate 

Biomechanics 

BME 562 Mechanics of Growth and 

Development 

BME 567 Cardiac Mechanics 

BME 568 Cardiovascular Dynamics 

BME 573 Applied Bioelectricity 

BME 574 Quantitative Bioelectricity 

and Cardiac Excitation 

BME 575 Molecular Basis of 

Bioelectrical Excitation 

BME 5909 Physiology of the Heart 

ESE 482 Digital Signal Processing 

MAE 533, 534 Fluid Dynamics I & II 

MAE 546 Finite Element Analysis 

MAE 547 Advanced Finite Element 

Analysis 

Philip Bayly, Ph.D. 

Nonlinear dynamics; quantitative 

characterization and modeling of 

brain trauma and development 

Jianmin Cui, Ph.D. 

Ion channels in physiology and 

disease 

Igor Efi mov, Ph.D. 

Mechanisms and therapy of arrhythmia, 

implantable devices, 

antiarrhythmic therapy, biophotonic 

imaging 

Sandor Kovacs, M.D., Ph.D. 

Cardiovascular biophysics, mathematical 

modeling of diastolic 

function 

Gregory Lanza, Ph.D. 

Targeted contrast agents, molecular 

imaging 

James Miller, Ph.D. 

Physical acoustics, cardiac material 

properties and mechanics, 

cardiac biophysics 

Jeanne Nerbonne, Ph.D. 

Regulation of membrane excitability, 

structure and function of ion 

channels 

Colin Nichols, Ph.D. 

Molecular aspects of potassium 

channels 

Yoram Rudy, Ph.D. 

Cardiac electrophysiology, modeling 

of the cardiac system, cellular 

electrophysiology and communication 

in the heart 


Mechanical properties of white 

blood cell microvilli, receptorligand 

mechanics 

Kooresh I. Shoghi, Ph.D. 

Computational biology at the interface 

with in-vivo imaging in animal 

models, in particular as it relates to 

metabolic regulation and obesity, 

diabetes 

Jonathan Silva, Ph.D. 

Cardiac electrophysiology and 

arrhythmias; molecular spectroscopy; 

ion channel biophysics; mathematical 

modeling of ion channels 

and action potentials 

Larry Taber, Ph.D. 

Mechanics of cardiovascular and 

brain development 

Samuel Wickline, M.D. 

Physical acoustics, cardiac and 

vascular material properties and 

mechanical function 

Pamela Woodard, M.D. 

CT/ MR cardiac imaging 



Imaging Technologies 

• photoacoustic tomography 

• thermoacoustic 

tomography 

• phase-contrast x-ray 

imaging 

• electrocardiographic 

imaging 

• optical bioelectric imaging 

• nanoparticle imaging 

agents 

• diffuse optical tomography 

• optical coherence computed 

tomography 

• ultrasound-modulated 

optical tomography 

• neural imaging 

• time-reversed ultrasonically 

encoded (TRUE) optical 

focusing 

• multimodality imaging 

Imaging activities at Washington University are interdisciplinary, 

involving the Departments of Biomedical Engineering, 

Electrical and Systems Engineering, and Computer Science 

and Engineering in the School of Engineering and Applied 

Science. In addition, strong and long-standing collaborative 

interaction with departments in the School of Medicine give 

engineering students at Washington University ample opportunities 

to participate in biomedical and biological science 

projects that involve imaging. 

Opportunities for educational experience to learn the principles 

and applications of imaging technologies are available 

through the Imaging Science and Engineering Graduate Certifi 

cate 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. 



Biomedical engineering students 

in this program follow a course 

of study in accordance with the 

general requirements of the BME 

Department. The following courses 

are available to students in this 

program: 

BME 494 Medical Imaging 

BME 502 Cardiovascular Magnetic 

Resonance Imaging 

BME 504 Optical Bioelectric 

Imaging 

BME 505 Advanced MRI and 

Molecular Imaging 

BME 533 Biomedical Image 

Processing 

BME 591 Biomedical Optics I: 

Principles 

BME 592 Biomedical Optics II: 

Imaging 

BME 5907 Advanced Concepts in 

Image Science 

ESE 523 Information Theory 

ESE 524 Detection and Estimation 

Theory 

ESE 578 Digital Representation of 

Signals 

ESE 587 Ultrasonic Imaging 

ESE 588 Quantitative Image 

Processing 

CSE 509A Digital Image Processing 

CSE 546T Computational Geometry 

CSE 552A Advanced Computer 

Graphics 

Samuel Achilefu, Ph.D. 

Molecular optical and multimodal 

imaging 

Mark Anastasio, Ph.D. 

Image reconstruction, photoacoustic 

imaging, phase contrast x-ray 

imaging 

Dennis Barbour, M.D., Ph.D. 

Neuronal imaging 

Joseph Culver, Ph.D. 

Diffuse optical tomography, noninvasive 

optical imaging 

Igor Efi mov, Ph.D. 

Cardiac and optical imaging, optical 

coherence tomography 

Timothy Holy, Ph.D. 

Optical methods for neural imaging 

Yanle Hu, Ph.D. 

MRI techniques to guide radiation 

therapy 

Suzanne Lapi, Ph.D. 

Development of positron emitting 

radiotracers, novel radioisotopes 

to imaging animals for the biodistribution 

of labeled compounds of 

biological interest 

H. Harold Li, Ph.D. 

Dose imaging for radiation therapy 

Gregory Lanza, Ph.D. 

Targeted contrast agents, molecular 

imaging 

James Miller, Ph.D. 

Ultrasonic imaging 

Joseph O’Sullivan, Ph.D. 

Tomographic imaging 

Paragh Parikh, M.D. 

Technology development for 

radiation therapy, real-time tumor 

tracking 

Marcus Raichle, M.D. 

Functional brain imaging 

Yoram Rudy, Ph.D. 

Noninvasive imaging of cardiac 

activation 

Kooresh I. Shoghi, Ph.D. 

Computational biology at the interface 

with in-vivo imaging in animal 

models, in particular as it relates to 

metabolic regulation and obesity, 

diabetes 

Yuan-Chuan Tai, Ph.D. 

High resolution PET and multimodal 

imaging, functional plant 

imaging 

David Van Essen, Ph.D. 

Functional brain-mapping 

Lihong Wang, Ph.D. 

Photoacoustic tomography, thermoacoustic 

tomography, optical 

imaging 

Samuel Wickline, M.D. 

Cardiac magnetic resonance 

imaging, molecular imaging 

Pamela Woodard, M.D. 

CT/MR cardiac imaging 

Jie Zheng, Ph.D. 

Cardiovascular imaging applications 

using magnetic resonance 

imaging (MRI), quantifi cation of 

myocardial oxygen extraction ratio 

and oxygen consumption 



Molecular, Cellular & Systems Engineering 

• sequence-structure-function 

relationships of cell 

surface receptors and ion 

channels 

• mechanisms of proteinprotein 

and protein-DNA 

interactions 

• protein aggregation, selfassembly 

and protein homeostasis 

• engineering approaches to 

model and manipulate biomolecular 

systems and networks 

Biological systems are complex and are built on interactive 

hierarchical structures, which are encoded by genetic information 

and respond to cues through an intricate network of 

regulatory and signaling networks. These networks display 

emergent properties through non-linear control and dynamical 

responses that span multiple length and time scales. Complex 

diseases such as aging-related disorders, cardiovascular diseases, 

and cancers are associated with aging-related degradation 

or catastrophic failures of protein-protein and proteinnucleic 

acid interaction networks. The development of modern 

therapeutics requires an integrated approach that builds on 

structure-function relationships at the molecular and cellular 

levels, and predicting/anticipating emergent properties / 

responses at the tissue/system level. 

The Molecular Cellular & Systems Engineering (MCSE) thrust 

within Biomedical Engineering brings together a group of 

individuals within and beyond the department who study interactions 

and dynamics at the molecular and cellular level to 

enable phenotyping, manipulation, and engineering of complex 

biological systems. The approaches include a combination of 

biophysical studies that focus on molecular & cellular interactions, 

self assembly, high throughput genomic and proteomic 

methods, advanced imaging methods, and multiscale computational 

methods. 


PROGRAM OF STUDY 

Students in the program must satisfy 

general Biomedical Engineering 

Department degree requirements. 

Recommended electives can be 

selected from the following list: 

BME 521 Kinetics of Receptormediated 

Processes 

BME 537 Computational Molecular 

Biology 

BME 559 Intermediate 

Biomechanics 

BME 5610 Protein Structures 

and Dynamics 

BME 572 Biological Neural 

Computation 

PROGRAM FACULTY 

Jan Bieschke, Ph.D. 

Mechanisms of neurodegeneration, 

macromolecular self-assembly and 

proteostasis networks 

Michael Brent, Ph.D. 

Bioinformatics and systems 

biology 

Barak Cohen, Ph.D. 

Evolution of complex traits; 

synthetic biology for engineering 

gene expression 


Ion channel structure-function relationship, 

biophysics of ion channels 

John Cunningham, Ph.D. 

Machine learning for neural systems; 

network models for motor 

cortex computation 

Gautam Dantas, Ph.D. 

Anibiotic resistance, synthetic biology, 

human microbiome, metagenomics; 

James Havranek, Ph.D. 

DNA-binding specifi city; computational 

design of novel proteinnucleic 

acid interfaces 

Jin-Moo Lee, M.D./Ph.D. 

Plaque formation and processing 

in Alzheimer’s disease and cerebral 

familial angiopathy 

Timothy Lohman, Ph.D. 

Helicase-catalyzed DNA unwinding 

and ssDNA translocation, ssDNAprotein 

interactions 

Garland Marshall, Ph.D. 

Molecular design, protein structure 

and function 

Robi Mitra, Ph.D. 

High throughput diagnostics and 

DNA sequencing 

Kristen Naegle, Ph.D. 

Control of signaling networks by 

post-translational modifi cations, 

machine learning methods 



channels 

Rohit Pappu, Ph.D. 

Protein aggregation in neurodegeneration, 

biophysics of intrinsically 

disordered proteomes 

Jay Ponder, Ph.D. 

Computational chemistry and algorithm 

development 

Barani Raman, Ph.D. 

Receptor-mediated processing of 

complex sensory signals, neuromorphic 

engineering 


Blood coagulation, cell and tissue 

mechanics, infl ammation, molecular 

biomechanics 

Jonathan Silva, Ph.D. 

Cardiac electrophysiology and 

arrhythmias; molecular spectroscopy; 

ion channel biophysics; mathematical 

modeling of ion channels 

and action potentials 

Joseph Henry Steinbach, Ph.D. 

Function of transmitter-gated 

membrane channels, pharmacology, 

synapse biology 

Gary Stormo, Ph.D. 

Protein–DNA interactions, RNA 

structure, mathematical modeling 

S. Joshua Swamidass, M.D., Ph.D. 

High throughput screening, machine 

learning, cheminformatics 

Xiaowei Wang, Ph.D. 

Gene targeting by miRNAs, role of 

miRNA in cancer development 



Neural Engineering 

• brain-computer interfaces 

• computational neuroscience 

• visual/auditory signal 

processing 

• neural plasticity 

• neuroprostheses 

Neural 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. 



Program students are expected to 

take courses in accordance with 

the regulations of the BME Department 

and in consultation with their 

academic advisor. Relevant Biology 

and BME courses include: 

BME 471 Bioelectrical Phenomena 

BME 533 Biomedical Signal Processing 

BME 572 Biological Neural 

Computation 

BME 573 Applied Bioelectricity 

BME 575 Molecular Basis of Bioelectrical 

Excitation 

BIOL 5571 Cellular Neurobiology 

BIOL 5651 Neural Systems 

Beau Ances, M.D.,Ph.D. 

Brain imaging of neurocognitive 

disorders associated with HIV and 

dementia 

Dennis Barbour, M.D.,Ph.D. 

Sensory neurophysiology and cortical 

circuitry, neurocomputation 

Paul Bridgman, Ph.D. 

Basic cellular properties of developing 

nerve and muscle 

Andreas Burkhalter, Ph.D. 

Synaptic mechanisms and organization 

of forward and feedback 

circuits in visual cortex 


Molecular biology and physiology 

of ion channels 

John Cunningham, Ph.D. 

Neuroengineering, machine learning, 

and brain-computer interfaces 

Timothy Holy, Ph.D. 

Neural mechanisms underlying 

olfaction 

James Huettner, Ph.D. 

Physiology of glutamate receptormediated 

signaling in the nervous 

system 

Vitaly Klyachko, Ph.D. 

Synaptic basis for neural plasticity 

Eric Leuthardt, M.D. 

Brain-computer interfaces, 

neuroprostheses 

Daniel Moran, Ph.D. 

Motor control, neuroprostheses 



channels 

Camillo Padoa-Schioppa, Ph.D. 

Cognitive and neuronal mechanisms 

of decision-making 

Steven Petersen, Ph.D. 

Human functional neuro-imaging 

of vision, attention, memory, and 

language 

Marcus Raichle, M.D. 

Central nervous system function of 

humans and nonhuman primates 

Barani Raman, Ph.D. 

Systems neuroscience of olfaction, 

biosensors on chips 

Larry Snyder, Ph.D. 

Processing of sensory information 

for goal-directed eye and arm 

movements in primates 

Kurt Thoroughman, Ph.D. 

Psychophysics of motor behavior, 

neural computation 

David Van Essen, Ph.D. 

Information processing in the 

primate visual system using physiological, 

anatomical and computational 

approaches 

Robert Wilkinson, Ph.D. 

Synaptic structure and function, 

particularly vesicle processing 

pathways 


notes

notes

DEPARTMENT OF 

BIOMEDICAL ENGINEERING 

School of Engineering & Applied Science 

Washington University in St. Louis 

One Brookings Drive 

Campus Box 1097 

St. Louis, MO 63130 

(314) 935-6164 

bme.wustl.edu 

bme@seas.wustl.edu

BME-GSM_Final - Department of Biomedical Engineering ...

You also want an ePaper? Increase the reach of your titles

Delete template?

Save as template?