Hongyu Miao, PhD
Assistant Professor
Core Director of Center for Biodefense Immune Modeling
Associate Core Director of Center for AIDS Research
PhD in Mechanical Engineering (2007), University of Rochester
MS in Statistics (2011), University of Rochester
C.V. (with complete publications)
Contact Information:

Saunders Research Building 4134
Department of Biostatistics and Computational Biology
University of Rochester
265 Crittenden Blvd, Rochester, NY 14642
Phone: (585) 2750408
Fax: (585) 2731031
Email: Hongyu_Miao@urmc.rochester.edu
Research Interests
 Computational Biology: systems immunology, structural bioinformatics, multiscale complex network
 Statistics: parameter estimation, image analysis, data mining on manifold
 Mathematical Modeling: differential equation, stochastic process, probabilistic model
 Application: HIV, influenza, drug/vaccine intervention
Awards and Honors
 David P. Byar Young Investigator Travel Award, ASA Biometrics, 2008
 Provost’s Multidisciplinary Award, University of Rochester, 2008
Selected Publications
 Seckler, J., Leioatts, N., Miao, H., Grossfield, A., “The interplay of structure and dynamics: Insights from a survey of HIV1 Reverse Transcriptase Crystal Structures”, Proteins: Structure, Function and Bioinformatics 81(10), 17921801 (2013)
 Xiao, Y., Miao, H., Tang, S., Wu, H., “Modeling Antiretroviral Drug Responses for HIV1 infected Patients Using Differential Equation Models”, Advanced Drug Delivery Reviews 65(7), 940953 (2013)
 Wang, J., Zhang, L., Jing, C., Ye, G., Wu, H., Miao, H., Wu, Y., Zhou, X., “Multiscale agentbased modeling on melanoma and its related angiogenesis analysis”, Theoretical Biology and Medical Modeling 10:41, (2013)
 Lu, N., Silva, J., Gu, Y., Gerber, S., Wu, H., Lord, E., Gelbard, H., Dewhurst, S., Miao, H., “Directional Histogram Ratio at Random Probes: A Local Thresholding Criterion for Capillary Images”, Pattern Recognition , 46(7), 19331948 (2013)
 Henn, A.D., Laski, M., Yang, H., Qiu, X., Miao, H., Barry, C.T., Wu, H., Zand, M., “Functionally Distinct Subpopulations of CpGActivated Memory B Cells”, Scientific Reports, 2, ( 2012)
 Li, X., Miao, H., Henn, A., Topham, D., Wu, H., Zand, M., Mosmann, T., “Ki67 expression reveals strong, transient influenza specific CD4 T cell responses after adult vaccination”, Vaccine 30(31), 45814584 (2012)
 Miao, H., Jin, X., Perelson, A.S., Wu, H., “Evaluation of multitype mathematical models for CFSElabeling experiment data”, Bulletin of Mathematical Biology, 74(2), 300326 (2012)
 Wu, H., Kumar, A., Miao, H., HoldenWiltse, J., Mosmann, T.R., Livingstone, A., Belz, G.T., Perelson, A.S., Zand, M., Topham, D.J., “Modeling of InfluenzaSpecific CD8+ T Cells During the Primary Response Indicates that the Spleen Is a Major Source of Effectors”, Journal of Immunology 187(9), 44744482 (2011)
 Miao, H., Xia, X., Perelson, A.S., and Wu H., “On Identifiability of Nonlinear ODE Models with Applications in Viral Dynamics”, SIAM Review 53(1), 339 (2011).
 Xue, H., Miao, H., and Wu, H., “Sieve Estimation of Constant and TimeVarying Coefficients in Nonlinear Ordinary Differential Equation Models by Considering Both Numerical Error and Measurement Error”, Annals of Statistics 38(4), 23512387 (2010).
 Miao, H., Hollenbaugh, J., Zand, M., HoldenWiltse, J., Mosmann, T.R., Perelson, A.S., Wu, H., Topham, D.J., “Quantifying the early immune response and adaptive immune response kinetics in mice infected by influenza A virus”, Journal of Virology 84(13), 66876698 (2010).
 Liang, H., Miao, H., and Wu, H., “Estimation of Constant and TimeVarying Dynamic Parameters of HIV Infection in a Nonlinear Differential Equation Model”, Annals of Applied Statistics 4(1), 460483 (2010) .
 Lee, H. Y., Topham, D. J., Park, S. Y., Hollenbaugh, J., Treanor, J. J., Mosmann, T. R., Jin, X., Ward, B. , Miao, H., HoldenWiltse, J., Perelson, A. S., Zand, M. S., Wu, H., “Simulation and prediction of the adaptive immune response to influenza A virus infection”, Journal of Virology 83(14), (2009).
 Miao, H., Dykes, C., Demeter, L.M., and Wu, H., “Differential equation modeling of HIV viral fitness experiments: model identification, model selection, and multimodel inference”, Biometrics 65(1), 292300 (2009).
 Miao, H., Gracewski, S.M., and Dalecki, D., “Ultrasonic excitation of a bubble inside a deformable tube: Implications for ultrasonicallyinduced hemorrhage,” Journal of the Acoustical Society of America 124(4), 23742384 (2008).
 Miao, H., Dykes, C., Demeter, L.M., Cavenaugha, J., Parka, S.Y., Perelson, A.S., and Wu H., “Modeling and estimation of kinetic parameters and replication fitness of HIV1 from FlowCytometrybased growth competition experiments,” Bulletin of Mathematical Biology 70, 17491771 (2008).
 Miao, H., and Gracewski, S.M., “Coupled FEM and BEM code for simulating acoustically excited bubbles near deformable structures”, Computational Mechanics 42(1), 95106 (2008).
 Wu, H., Zhu, H., Miao, H., and Perelson, A.S., “Parameter Identifiability and Estimation of HIV/AIDS Dynamic Models,” Bulletin of Mathematical Biology 70(3), 785799 (2008).
Data Sharing
Dissertations
 Miao, H., “Understanding B Cell Kinetics in Humans via Heavy Water Labeling Using Nonlinear Mixed Effects Models and Stochastic Approximation EM algorithms”, M.S., Dept. of Biostatistics and Computational Biology, University of Rochester, Rochester, NY, USA (Nov., 2010)
 Miao, H., “Numerical Study of Ultrasound Bioeffects by Solving GasLiquidSolid Interaction Problems with Coupled FEM and BEM”, Ph.D., Dept. of Mechanical Engineering, University of Rochester, Rochester, NY, USA (2007)
Teaching
 Computational Statistics (BST 550), Instructor, Spring, 2010
 Introduction to Biostatistics (BST 463), Instructor, Fall, 2010
 Advanced Topics in Object Data Analysis (BST 550), Invited Lecturer, Fall, 2010
 Topics in Immunology (MBI 540), Invited Lecturer, Spring, 2011
 Introduction to Biostatistics (BST 463), Instructor, Fall, 2011
 Modeling, Computing and Statistical Analysis in Immunology Research, Summer, 2012
 Introduction to Biostatistics (BST 463), Instructor, Fall, 2012
 Seminar in Statistical Literature (BST 497), Instructor, Fall, 2013
Students & Postdocs
 Na Lu, PhD in Control Science and Engineering (Xi’an Jiaotong University, China), 20112013
 Ana Rojas, PhD in Physics and Astronomy (Louisiana State University), 20112014
 James Seckler, PhD in Physiology and Biophysics (Case Western Reserve University), 20112014
 Jinyu Hu, PhD in Bioinformatics (Tianjin University), 2013present
Computing Packages
 DynaBubble by Miao, H., Department of Mechanical Engineering, University of Rochester, 2004~2006.
 A simulator of dynamic interactions between microbubbles, deformable cells and vessels under ultrasounic excitation based on finite element and boundary element methods;
 DEDiscover by Wu, H., Gregory, R.W., Miao, H., Wu, C., LeBlanc, A., Department of Biostatistics and Computational Biology, University of Rochester, 2006~present.
 A general tool for ordinary differential equation modeling, simulation, sensitivity analysis, and data fitting;
 Support delay differential equations;
 Local/global/hybrid optimization algorithms available.
 HIVFit by Miao, H., Ji, R., Department of Biostatistics and Computational Biology, University of Rochester, 2008~2009
 A webbased calculator for HIV viral fitness based on dynamic models;
 Available upon request (UR campus computers have direct access).
 MathStat by Miao, H., Department of Biostatistics and Computational Biology, University of Rochester, 2006~present
 A general and comprehensive computing packages for dealing with important mathematical and statistical problems;
 Flexible structures based on Boost C++ (ublas), LAPACK, ARPACK, SuperLU etc.
 Heterogeneous data table, linear algebra, random number generator, statistical distributions, special functions, interpolation, quadrature, ODE solver, local/global/memetic optimization, MCMC, clustering, data smoothing, nonlinear regression, mixed model (more to come);
 ABCFSE by Miao, H., Department of Biostatistics and Computational Biology, University of Rochester, 2010~present
 An agentbased modeling (ABM) based simulation tool for understanding cell cycles with considering proliferation, death and silence in CFSE experiments. An activation stage is explicitly added to account for the activation delay for the 1st generation cells to start to act.
 You need Boost C++ together with MathStat to compiler the code. For MathStat, see the link above.
 If you find this code useful to your work, please cite the following paper:
Miao, H., Jin, X., Perelson, A.S., Wu, H., “Evaluation of multitype mathematical models for CFSElabeling experiment data”, Bulletin of Mathematical Biology, 74(2), 300326 (2012)
 Image Gadgets by Miao, H., Lu, N., and Gu, Y., Department of Biostatistics and Computational Biology, University of Rochester, 2010~present
 Stack Splitter. An ImageJ macro that splits a batch of hyperstack image files in the format of (x,y,c,z,t). To use it, install the LOCI plugin first, then simply select a folder and all image files under this folder will be automatically split and the extracted stacks will be saved under the same folder. For large stacks, 64bit of ImageJ as well as >3GB memory might be necessary.
 Matched Filtering. A MATLAB implementation of the matched filtering algorithm for vessel extraction from a 2D image. An example file is included to illustrated how to use the code.
 DHRRP Thresholding Algorithm. A MATLAB implementation of the directional histogram ratio (DHR) with random probes (RP) method for capillary image thresholding. Please cite the paper below if the codes are useful to you:
 Lu, N., Silva, J., Gu, Y., Gerber, S., Wu, H., Lord, E., Gelbard, H., Dewhurst, S., Miao, H., “Directional Histogram Ratio at Random Probes: A Local Thresholding Criterion for Capillary Images”, Pattern Recognition , 46(7), 19331948 (2013)