Zhen Yuan Curriculum Vitae - Biomedical Engineering - University ...

Zhen Yuan
Curriculum Vitae
Name: Zhen Yuan (Ph.D.)
Position Title: Research Assistant Professor
Postal Address: Room 289, 1275 Center Drive, JG56 BMS Building, POB
116131, Gainesville, FL 32611
E-mail: yzhen@bme.ufl.edu
Tel: 352-273-9330(O)
Positions, Employment and Education
09/2007- Research Assistant Professor, Biomedical Engineering
Department, University of Florida. Research Field: Biomedical
Imaging and Biomedical Optics.
01/2005-09/2007 Postdoctoral Research Associate, Biomedical Engineering
Department, University of Florida, Gainesville, FL32611. Research
Field: Biomedical Imaging and Signal Processing.
03/2004-01/2005 Postdoctoral Research Fellow, Department of Physics, Clemson
University, SC29634. Research Field: Biomedical Optical Imaging.
03/2002-03/2004 Postdoctoral Research Scientist, Institute of High performance
Computing, National University of Singapore, Singapore 117523.
Research Field: BioMEMS.
06/2002 Ph.D., University of Science and Technology of China (USTC),
Hefei 230026, China. Major: Computational Engineering
(Biomechanics).
Professional Services
Member of SPIE
Senior Member of OSA
Member of IEEE
Member of Biomedical Engineering Society
Reviewers of IEEE Transactions on Biomedical Engineering, IEEE Transactions on
Biomedical Imaging, Applied Optics, Optics Letter, Optics Express,
JOSA A, Medical Physics, Physics in Medicine & Biology, Arthritis &
Rheumatism, Biomedical Optics Express, Journal of Biomedical Optics,
Journal of X-ray Science & Technology
Research Interest
I: Biomedical Imaging and Signal Processing
• Diffuse Optical Imaging & Spectroscopy
• Photoacoustic Imaging & Spectroscopy
• EEG Source Localization and Signal Processing

• X-ray image reconstruction techniques
• Molecular Imaging based on Fluorescent and Bioluminescent Tomography
• Multi-modality Imaging
• Photon Transport in Biological Tissues
II: Neurosciences
• Neurovascular and Neurometabolic Coupling
• Brain Connectivity, Brain (Neuron) Network and Brain Plasticity
• Data Driven and Model Based Neural Signal Analysis Methods
• Neuroinformatics & Computational Informatics
• Epilepsy, Neurocognitive Processing
III: Modeling and Simulation, Computational Engineering
• Inverse Problems, Optimization methods, Numerical Solution of Partial
Differential Equations, Statistical Methods
• Reconstruction Algorithms and Signal Processing Methods
• High Performance Numerical Methods: Meshless Method, Incompatible and
Hybrid Finite Element Methods, Boundary Element methods.
• Modeling and Simulation in Multiphysics
• High Performance Computing: Cluster-based Parallel Computation and CPU-
GPU-based Parallel Computing
• Image Segmentation and Classification, Partial Correlation and Coherence
Analysis, Partial Mutual Information Analysis, Granger Causality Analysis
• Structural, Functional and Effective Connectivity Methods
Programming Skills
Matlab, C++/C, Fortran, ANSYS, Autocad, PATRAN, Abaqus, NASTRAN
Teaching Interests
• High Performance Numerical Methods, High Performance Computing
• Finite Element Method, Biostatistics Methods
• Biomedical Engineering Introduction, Biomedical Optics, Biomedical imaging and
Signal Processing, Applied Optics, Biomedical Instrumentations,
Neuroengineering
• Multivariate Signal Processing Method
Academic Service
• 2007-2010 Served as a member of the Supervisory Committee for 3 Ph. D
candidates in Biomedical Engineering Dept. at the University of Florida
• 2009 Reviewed grant proposals for the National Medical Research Council
(Singapore)
• 2007-2010 Mentored 4 graduate students in Biomedical Engineering Dept. at
University of Florida
• 2006-2010(Summer) Mentored 5 high school students in the Innovation program
at the University of Florida
Editorial board
Editorial board member of Journal of Biosensors and Bioelectronics
Guess Associate Editor of Medical Physics
Guess Associate Editor of Applied Optics

Honors and Fellowships
“Lixue Pandeng” Scholarship of Chinese Academy of Sciences
Postdoctoral Fellowship of ASTAR (Singapore)
University of Florida: High performance Computing Fellowship (2006)
2008, 2009, 2010 &2011 “Who is Who in America”
2009 ,2010 &2011 “Who is Who in the World”
2010,2011 “Who is Who in Medicine”
2011 “Who is Who in Science and Engineering
Professional Experience
Research Assistant Professor
Dates (July 07 – present)
Dept of Biomedical Engineering, University of Florida, Gainesville, FL 32611
(http://www.bme.ufl.edu)
• Clinically investigated the combined optical and fluorescence
imaging\spectroscopy of breast cancer with enhanced sensitivity and specificity
• Provided a new multi-modality imaging strategy for x-ray guided three-dimensional
diffuse optical tomography\spectroscopy of osteoarthritis with improved resolution
and contrast
• Combined EEG recording and optical tomography/spectroscopy for neurovascular
and neurometabolic coupling
• Granger causality statistical software development for brain connectivity
• Photoacoustic tomography\spectroscopy of epilepsy with high imaging contrast
and resolution
• Research report preparation, NIH research grant applications
• Multi-modality imaging setups development
Postdoctoral Research Fellow
Dates (Jan 05 – July 07)
Dept of Biomedical Engineering, University of Florida, Gainesville, FL 32611
(http://www.bme.ufl.edu)
• Software development for quantitative photoacoustic tomography\spectroscopy
• Diffuse optical imaging software development based on photon transport equation
• Photoacoustic tomography for imaging nanoparticles
• Manages a team of 3 students for photoacoustic imaging system development
Postdoctoral Research Associate
Dates (March 04 – Jan 05)
Dept of Physics, Clemson University, Clemson, SC 29634
(http://www.clemson.edu/ces/departments/physics-astro/)
• Reconstruction algorithm development for diffuse optical imaging of breast cancer
• Software development for diffuse optical spectroscopy of biological tissues
• Reconstruction algorithm development for bioluminescence tomography

Postdoctoral Research Scientist
Dates (March 02 – March 04)
Institute of High Performance Computing, National University of Singapore,
Singapore
(http://www.ihpc.a-star.edu.sg/)
• Model development and numerical simulation in multi-physics
• Biomaterials development and Biomechanics application in BioMEMS.
Teaching Experience
Courses Taught
Spring 2007-2010 Graduate course BME, titled “Advanced Mathematics and High
Performance Numerical Methods” offered through the
Department of Biomedical Engineering at University of Florida
Courses Developed (Collaborate with Dr. Huabei Jiang)
Spring 2007-2010, “Biomedical Imaging,” Graduate course in the Department of
Biomedical Engineering at University of Florida
Patent
• Hybrid Photoacoustic Tomography (PAT) and Diffuse Optical Tomography (DOT):
Methods and Algorithms, International Application No. PCT/US2008/055894.
• METHOD AND APPARATUS FOR TOMOGRAPHIC IMAGING OF ABSOLUTE
OPTICAL ABSORPTION COEFFICIENT IN TURBID MEDIA USING COMBINED
PHOTOACOUSTIC AND DIFFUSING LIGHT MEASUREMENTS
(WO/2009/011934)
Book Chapters
1. Z. Yuan, H. Jiang, “Photoacoustic tomography,” Advances in Optical
Imaging for Clinical Medicine by Dr. N.V. Iftimia, Dr. W. Brugge, and Dr. D.X.
Hammer (John Wiley and Sons Ltd);(http://www.wisepress.com/index.asp-Q-I-E-
9780470619094-advances-in-optical-imaging-for-clinical-medicine,61860).
2. Z. Yuan, H. Jiang, “Photoacoustic tomography for imaging nanoparticles,” in
Cancer Nanotechnology by Drs. Stephen R. Grobmyer and Brij Moudgil.
http://www.springer.com/978-1-60761-608-5.
3. Z. Yuan, H. Jiang, “Diffuse Optical Tomography of osteoarthritis,” in
Handbook of Biophotonics, Volume 2, Photonics for Health Care, Edited by
Jurger Popp, Valery V. Tuchin, Arthur Chiou, and Stefan Heinemann. Published
by Wiley-VCH (2011).

4. Z. Yuan, H. Jiang, “Optical Methods and Instrumentation in Brain Imaging and
Therapy,” Invited Book Chapter by Springer.
Selected Peer-Reviewed Articles
Biomedical Imaging and Signal Processing
1. Z. Yuan, HB Jiang, “Quantitative photoacoustic tomography: recovery of optical
absorption coefficient maps of heterogeneous medium,” Applied Physics
Letters 88, 231101APL 1-3 (2006).
2. Z. Yuan, H.Z. Zhao, C.F. Wu, H.B. Jiang, “Imaging of small nanoparticle
containing objects using finite element-based photoacoustic tomography,” Optics
Letters 30, 3054-3056(2005).
3. Z. Yuan, H. Jiang, “Simultaneous recovery of tissue physiological and acoustic
properties and the criteria for wavelength selection in multispectral photoacoustic
tomography,” Optics Letters 34, 1714-1716 (2009).
4. Z. Yuan, Q. Zhang, H.B. Jiang, “3D diffuse optical tomography imaging of
osteoarthritis: initial results in the finger joints,” Journal of Biomedical Optics
12(3), 034001 (2007).
5. Z. Yuan, Q. Zhang, E. Sobel, H. Jiang, “Tomographic x-ray-guided 3D diffuse
optical tomography imaging of osteoarthritis: Initial results in the finger joints,”
Journal of Biomedical Optics 13, 044006 (2008).
6. Z. Yuan, Q. Zhang, E. Sobel, H. Jaign, “Comparison of diffusion approximation
and higher order diffusion equation for optical tomography of osteoarthritis,”
Journal of Biomedical Optics 14, 054013(2009).
7. Z. Yuan, Q. Wang, H. Jiang, “Reconstruction of optical absorption coefficient
maps of heterogeneous medium by photoacoustic tomography coupled with
diffusion equation based regularized Newton Method,” Optics Express 15,
18078-18081(2007).
8. Z. Yuan, Q. Zhang, H. Jiang, “Simultaneous reconstruction optical and acoustic
properties by quantitative photoacoustic tomography,” Optics Express 14, 6749-
6754 (2006).
9. Z. Yuan, H.Z. Zhao, H.B. Jiang, “Finite element-based photoacoustic
tomography: phantom and chicken bone experiments,” Applied Optics 45(13),
3177-3183(2006).
10. Z. Yuan, H.B. Jiang, “An image reconstruction scheme that combines modified
Newton method and efficient initial guess estimation for optical tomography of
finger joints,” Applied Optics 46, 2757-2768 (2007).
11. Z. Yuan, H.B. Jiang, “Three-dimensional finite element-based photoacoustic
tomography: Reconstruction algorithm and simulations,” Medical Physics 34(2),
538-546(2007).
12. Z. Yuan, H. Jiang, “Quantitative photoacoustic tomography,” Philosophical
Transaction of the Royal Society A 367, 3043-3054 (2009).
13. Z. Yuan, X. Hu, H. Jiang, “A higher order diffusion model for three-dimensional
photon migration and image reconstruction in optical tomography,” Physics in
Medicine and Biology 54,65-88(2009).
14. Z. Yuan, H. Jiang. “High resolution x-ray guided three dimensional diffuse optical
tomography of joint tissues in hand osteoarthritis: Morphological and functional
assessments,” Medical Physics, 37 (8), 2010.

15. Z. Yuan, Q. Zhang, E. Sobel, H. Jiang, “Image-guided optical spectroscopy in
diagnosis of osteoarthritis: A clinical study,” Biomedical Optics Express 1, 74-
86(2010).
16. H.B. Jiang, Z. Yuan, X.J. Gu, “Spatially varying optical and acoustic property
reconstruction using finite element-based photoacoustic tomography,” Journal of
the Optical Society of America A 23(4), 878-888 (2006).
17. J. Xiao, Z. Yuan, H. Jiang, “Quantitative multispectral photoacoustic tomography
and wavelength optimization,” Journal of X-Ray Science and Technology, 02
(2010).
18. Q. Zhang, L. Yin, Y. Tan, Z. Yuan, H. Jiang, “Quantitative bioluminescence
tomography guided by diffuse optical tomography,” Optics Express 16, 1481-
1483 (2008).
19. Z. Yuan, “Recent advances in Nano imaging using photoacoustic
measurements” Nano express 2011 (invited paper).
20. Q. Zhang, Z. Liu, P. Camey, Z. Yuan, H. Jiang, “Noninvasive imaging of epileptic
seizure in vivo using photoacoustic tomography,” Physics in Medicine and
Biology 53(7),1921-1931(2008).
21. J. Zhang, Z. Wang, Z. Yuan and H. Jiang, “Computer aided classification of
optical images for diagnosis of osteoarthritis in the finger joints,” Journal of X-
Ray Science and Technology, 2011 (accepted).
22. Z. Yuan, H. Jiang, “A more vigorous quantitative photoacoustic tomography
reconstruction method,” Journal of Biomedical Optics Letters, 2011 (in review).
23. Z. Yuan, Q. Zhang, H. Jiang. “X-ray guided three-dimensional diffuse optical
imaging of the finger joints in osteoarthritis and psoriatic arthritis: A comparable
study,” Journal of Biomedical Optics (in review).
Computational Bioengineering and Computational Engineering
24. H. Li, Z. Yuan, K.Y. Lam et al., “Model development and numerical simulation of
electric-stimulus-responsive hydrogels subject to external electric field,”
Biosensors and Bioelectronics19 (9), 1097-1107 (2004).
25. H. Li, Z. Yuan, T.Y. Ng, K.Y. Lam, “Constitutive model development and
microstructural topology optimization for Nafion hydrogel membrane with ionic
clustering,” Journal of Biomaterials Science-Polymer Edition.14, 1181-1196
(2003).
26. L. Yin, Z. Yuan, L.H. He, “Model development and numerical simulation of
temperature-sensitive hydrogels,” Computational Materials Sciences 31, 299-
308 (2004).
27. Z. Yuan, C.C. Wu, Hua Li, “Homogenized-based topology design for pure torsion
of composite shafts,” ACTA MECHANICA SINICA 19(3), 241-246(2003).
28. L. Yin, Z. Yuan et al., “Model development and numerical simulation of
biohydrogels in aqueous salt solutions,” ACTA MECHANICA SINICA 37(3), 363-
367(2005).
29. Z. Yuan, C.C. Wu, “Topology optimization for microstructures of cross-section of
composite torsional shafts,” ACTA MECHANICA SINICA, 35(1): 39-42(2003).
30. Z. Yuan, C.C. Wu, “Topology optimization of continuum structures using
incompatible finite elements,” ACTA MECHANICA SINICA 35(2), 176-180(2003).
31. Z. Yuan, C.C. Wu, “Topology optimization for periodic linear elastic
microstructures of composite materials,” ACTA MECHANICA SOLIDA SINICA
24(1), 40-45(2003).

32. Z. Yuan, C.C. Wu, “Numerical simulation of mechanical properties of prestress
concrete members due to creep and shrinkage,” ACTA MECHANICA SOLIDA
SINICA 24, 298-303(2001).
33. Z. Yuan, Z.R. Li, C.C. Wu, “Simulation of Mixed-mode Fatigue Crack Growth by
Element Free Galerkin Method,” Engineering Mechanics 19(1), 25-28(2002).
34. Z. Yuan, Y. Liu, “Effective method for dynamic analysis of interaction of fluid and
structure of mechanical equipment,” Journal of Mechanical Strength (1), 16-
17(2000).
35. Z. Yuan, C.C. Wu, “Analytical respond sensitivity computation using incompatible
elements,” Journal of Mechanical Strength 24(1), 59-61(2002).
36. Z. Yuan, C.C. Wu, “Topology optimization of continuum structure using hybrid
elements and artificial material model,” Journal of China University of Science
and Technology 31 (6), 694-699(2001). (In Chinese with English Abstract)
37. S. Zhuang, C.C. Wu, Z. Yuan, “Microscopic investigation of cellular materials
mechanical properties based on homogenization theory,” Materials Science and
Engineering 19(4), 9-13(2001). (In Chinese with English Abstract)
Neuroimaging and Neuroinformatics
38. J. Zhang, T. Guo and Z. Yuan, “Analysis of fMRI Data Using an Integrated
Principal Component Analysis and Supervised Affinity Propagation Clustering
Approach,” IEEE Transaction on Biomedical Engineering,2011(8),PMID:
21859596.
39. Q. Zhang, Z. Liu, P. Camey, Z. Yuan, H. Jiang, “Noninvasive imaging of epileptic
seizure in vivo using photoacoustic tomography,” Physics in Medicine and
Biology 53(7),1921-1931(2008).
40. Z. Yuan, H. Jiang, “A nonlinear reconstruction method for EEG source locations,”
IEEE Transactions on Biomedical Imaging, 2011 (in review).
41. Z. Yuan, H. Jiang, “Investigation of brain effective connectivity in epilepsy using
diffuse optical measurement, “ASE 2011 Conference.
42. R. Jiang, Z. Yuan, H. Jiang. “Imaging the blood flow and cellular morphology in
epilepsy with diffuse optical tomography,” 2010 Technical Digest of OSA
Biomedical Optics Topical Meeting, Miami, Florida, USA. April.
Invited International Conference Presentations
1. Z. Yuan, H. Jiang. Three-dimensional finite element-based PAT: initial results,
Proc. SPIE 6437, 64371A, 2007.
2. Z. Yuan, L. Yin, H. Jiang. Numerical simulation of transient nonlinear behaviors
of electric-sensitive hydrogel membrane under an external electric field, Proc.
SPIE 6465, 64650W, 2007.
3. Z. Yuan, Q. Zhang, Y. Sun, H. Jiang. Simultaneous reconstruction of acoustic
and optical properties of in-vivo tissues by PAT, Proc. SPIE 6437, 64371V,
2007.
4. Z. Yuan, Q. Zhang, H.B. Jiang. Diagnosis of osteoarthritis in the finger joints by
three-dimensional diffuse optical tomography: Pilot clinical results. 2006
Technical Digest of OSA Biomedical Optics Topical Meeting, Fort Lauderdale,
Florida, USA, March 19–23, 2006.

5. Z. Yuan, Q. Zhang, Y. Sun, H. Jiang. Simultaneous reconstruction of acoustic
and optical properties of in-vivo tissues by PAT, Proc. SPIE 6437, 64371V,
2007.
6. Z. Yuan, H. Jiang. Simultaneous recovery of chromophore concentrations and
ultrasound velocity by PAT. Proc. SPIE BO203, 63, 2009.
7. Z. Yuan, H. Jiang. X-ray guided 3D DOT imaging of OA finger joints: a clinical
study. Proc. SPIE BO110, 11, 2009.
8. Z. Yuan, H. Jiang. Diffuse optical imaging of OA finger joints by higher-order
diffuse equations. Proc. SPIE BO118, 68, 2009.
9. H, Jiang, Z. Yuan. Quantitative photoacoustic tomography: recover of optical
absorption coefficient maps of heterogeneous media, Proc. SPIE 6437, 64371S,
2007.
10. Q. Zhang, Z. Yuan, H. Jiang, X-ray guided 3D diffuse optical tomography: in
vivo study of osteoarthritis in the finger joints, Proc. SPIE 6431, 643112, 2007.
11. Z. Yuan, H. Li, Ng T. Y. and J. Chen. A coupled multi-field formulation for
stimuli-responsive hydrogel subject to electric field, Proceeding of the
International Conference on Scientific & Engineering Computation (IC-
SEC):884-887, Singapore, 2002.
12. Z. Yuan, L. Yin, C.C. Wu et al. Topology optimization of continuum structures
using high performance finite elements, Proceeding of the 4th International
Conference on Nonlinear Mechanics: 717-720, Shanghai, China, 2002.
13. Z. Yuan et al. “Image-guided photoacoustic spectroscopy in diagnosis of
osteoarthritis,” 2011 Photonics West, SPIE, California.
14. Z. Yuan et al., “ The diffuse optical imaging of epilepsy network in small
animal,” ASE 2010, Texas.
International Conference Papers
1. Z. Yuan, Q.Z. Zhang, H.B. Jiang. 3D diffuse optical tomography of finger joints
based on globally convergent methods and enhanced initial values optimization
scheme. 2006 Technical Digest of OSA Biomedical Optics Topical Meeting, Fort
Lauderdale, Florida, USA, March 19–23, 2006.
2. Z. Yuan, Q. Wang, H.B. Jiang. Recovery of Absolute Absorption Coefficient
Maps of Heterogeneous Media by Photoacoustic Tomography Coupled with
Diffusion Optical Reconstruction Algorithm. 2008 Technical Digest of OSA
Biomedical Optics Topical Meeting, Florida, USA, March 16–20.
3. Z. Yuan, X. Hu, H. Jiang. A Simplified Spherical Harmonics Approximated
Radiation Transport Model for Three Dimensional (3-D) Photon Migration in
Small Volume Tissues. 2008 Technical Digest of OSA Biomedical Optics
Topical Meeting, Florida, USA, March 16–20.
4. Z. Yuan, Q.Z. Zhang, H.B. Jiang. A clinical investigation on x-ray guided
three-dimensional diffuse optical imaging of osteoarthritis in the finger
joints. 2010 Technical Digest of OSA Biomedical Optics Topical Meeting, Miami,
Florida, USA. April.
5. Z. Yuan, H.B. Jiang. Diffusion approximation and higher-order diffusion
equations for optical tomography of osteoarthritis: A comparable study. 2010
Technical Digest of OSA Biomedical Optics Topical Meeting, Miami, Florida,
USA. April.
6. Z. Yuan, Q. Zhang, E. Sobel, H. Jiang. Imaging molecular signatures for
detection of osteoarthritis by combining spectral and spatial a-priori information.

2010 Technical Digest of OSA Biomedical Optics Topical Meeting, Miami,
Florida, USA. April.
7. Z. Yuan, Q. Zhang, E. Sobel, H. Jiang. X-ray guided three-dimensional diffuse
optical tomography of osteoarthritis and psoriatic arthritis in finger joints: A
comparable study. 2010 Technical Digest of OSA Biomedical Optics Topical
Meeting, Miami, Florida, USA. April.
8. Z. Yuan, H.B. Jiang. Simultaneous recovery of tissue physiological and acoustic
properties and uniqueness in multi-spectral photoacoustic tomography. 2010
Technical Digest of OSA Biomedical Optics Topical Meeting, Miami, Florida,
USA. April.
9. H, Jiang, Z. Yuan. Quantitative photoacoustic tomography: recover of optical
absorption coefficient maps of heterogeneous media, Proc. SPIE 6437, 64371S,
2007.
10. Q. Zhang, Z. Yuan, H. Jiang, X-ray guided 3D diffuse optical tomography: in
vivo study of osteoarthritis in the finger joints, Proc. SPIE 6431, 643112, 2007.
11. Qizhi Zhang, Lu Yin, Yiyong Tan, Z. Yuan. Three-Dimensional Bioluminescence
Tomography Assisted by Diffuse Optical Tomography. 2008 Technical Digest of
OSA Biomedical Optics Topical Meeting, Florida, USA, March 16–20.
12. Z. Yuan, C. Wu. Numerical problem study on structural topology optimization,
Proceedings of the 11 th National Computational Mechanics Conference,
Guangzhou, China, 2001.
13. Q. Zhang, Z. Yuan. “In vivo x-ray guided optical tomography of osteoarthritis in
the knee joints,” 2010 Technical Digest of OSA Biomedical Optics Topical
Meeting, Miami, Florida, USA. April.
14. R. Jiang, Z. Yuan, H. Jiang. “Imaging the blood flow and cellular morphology in
epilepsy with diffuse optical tomography,” 2010 Technical Digest of OSA
Biomedical Optics Topical Meeting, Miami, Florida, USA. April.
15. Q. Zhang, Z. Yuan, H. Jiang. “Diffuse Optical Tomography of large joints: a
phantom study,” 2010 Technical Digest of OSA Biomedical Optics Topical
Meeting, Miami, Florida, USA. April.
16. Q. Zhang, Z. Yuan, H. Jiang. “Imaging osteoarthritis in the knee joints using x-
ray guided diffuse optical tomography,” SPIE 7548, 2010.