Hongyu Miao, PhD

Assistant Professorrecentpic

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) 275-0408
Fax: (585) 273-1031
E-mail: Hongyu_Miao@urmc.rochester.edu

Research Interests

  • parameter estimation of dynamic models, statistical image analysis, complex data mining on manifold
  • systems immunology, structural bioinformatics, multi-scale complex network
  • differential equation model, stochastic process model, probabilistic model
  • 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

  1. Miao, H., Wu, H., Xue, H., “Generalized Ordinary Differential Equation Models”, Journal of the American Statistical Association, in print (2014)
  2. Miao, H., Sangster, M.Y., Livingstone, A.M., Hilchey, S., Zhang, L., Topham, D.J., Mosmann, T.R., Holden-Wiltse, J., Perelson, A.S., Wu, H., Zand, M.S., “Modeling the Dynamics and Migratory Pathways of Virus-Specific Antibody-Secreting Cell Populations in Primary Influenza Infection”, PLOS One, 9(8): e104781. doi: 10.1371/journal.pone.0104781 (2014)
  3. Seckler, J., Leioatts, N., Miao, H., Grossfield, A., “The interplay of structure and dynamics: Insights from a survey of HIV-1 Reverse Transcriptase Crystal Structures”, Proteins: Structure, Function and Bioinformatics 81(10), 1792-1801 (2013)
  4. Xiao, Y., Miao, H., Tang, S., Wu, H., “Modeling Antiretroviral Drug Responses for HIV-1 infected Patients Using Differential Equation Models”, Advanced Drug Delivery Reviews 65(7), 940-953 (2013)
  5. Wang, J., Zhang, L., Jing, C., Ye, G., Wu, H., Miao, H., Wu, Y., Zhou, X., “Multi-scale agent-based modeling on melanoma and its related angiogenesis analysis”, Theoretical Biology and Medical Modeling 10:41, (2013)
  6. 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), 1933-1948 (2013)
  7. Henn, A.D., Laski, M., Yang, H., Qiu, X., Miao, H., Barry, C.T., Wu, H., Zand, M., “Functionally Distinct Subpopulations of CpG-Activated Memory B Cells”, Scientific Reports, 2, ( 2012)
  8. Li, X., Miao, H., Henn, A., Topham, D., Wu, H., Zand, M., Mosmann, T., “Ki-67 expression reveals strong, transient influenza specific CD4 T cell responses after adult vaccination”, Vaccine 30(31), 4581-4584 (2012)
  9. Miao, H., Jin, X., Perelson, A.S., Wu, H., “Evaluation of multitype mathematical models for CFSE-labeling experiment data”, Bulletin of Mathematical Biology, 74(2), 300-326 (2012)
  10. Wu, H., Kumar, A., Miao, H., Holden-Wiltse, J., Mosmann, T.R., Livingstone, A., Belz, G.T., Perelson, A.S., Zand, M., Topham, D.J., “Modeling of Influenza-Specific CD8+ T Cells During the Primary Response Indicates that the Spleen Is a Major Source of Effectors”, Journal of Immunology 187(9), 4474-4482 (2011)
  11. 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), 3-39 (2011).
  12. Xue, H., Miao, H., and Wu, H., “Sieve Estimation of Constant and Time-Varying Coefficients in Nonlinear Ordinary Differential Equation Models by Considering Both Numerical Error and Measurement Error”, Annals of Statistics 38(4), 2351-2387 (2010).
  13. Miao, H., Hollenbaugh, J., Zand, M., Holden-Wiltse, 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), 6687-6698 (2010).
  14. Liang, H., Miao, H., and Wu, H., “Estimation of Constant and Time-Varying Dynamic Parameters of HIV Infection in a Nonlinear Differential Equation Model”, Annals of Applied Statistics 4(1), 460-483 (2010) .
  15. Lee, H. Y., Topham, D. J., Park, S. Y., Hollenbaugh, J., Treanor, J. J., Mosmann, T. R., Jin, X., Ward, B. , Miao, H., Holden-Wiltse, 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).
  16. Miao, H., Dykes, C., Demeter, L.M., and Wu, H., “Differential equation modeling of HIV viral fitness experiments: model identification, model selection, and multi-model inference”, Biometrics 65(1), 292-300 (2009).
  17. Miao, H., Gracewski, S.M., and Dalecki, D., “Ultrasonic excitation of a bubble inside a deformable tube: Implications for ultrasonically-induced hemorrhage,” Journal of the Acoustical Society of America 124(4), 2374-2384 (2008).
  18. 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 HIV-1 from Flow-Cytometry-based growth competition experiments,” Bulletin of Mathematical Biology 70, 1749-1771 (2008).
  19. Miao, H., and Gracewski, S.M., “Coupled FEM and BEM code for simulating acoustically excited bubbles near deformable structures”, Computational Mechanics 42(1), 95-106 (2008).
  20. 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), 785-799 (2008).

 

Data Sharing

  • The real data used in Miao et al., BMB, 74(2), 300-326 (2012): cd4, cd8

 

Dissertations

  1. 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)
  2. Miao, H.,  “Numerical Study of Ultrasound Bioeffects by Solving Gas-Liquid-Solid Interaction Problems with Coupled FEM and BEM”, Ph.D., Dept. of Mechanical Engineering, University of Rochester, Rochester, NY, USA (2007)

Teaching

  1. Computational Statistics (BST 550), Instructor, Spring, 2010
  2. Introduction to Biostatistics (BST 463), Instructor, Fall, 2010
  3. Advanced Topics in Object Data Analysis (BST 550), Invited Lecturer, Fall, 2010
  4. Topics in Immunology (MBI 540), Invited Lecturer, Spring, 2011
  5. Introduction to Biostatistics (BST 463), Instructor, Fall, 2011
  6. Modeling, Computing and Statistical Analysis in Immunology Research, Summer, 2012
    1. Lecture notes (PDF)
    2. Tutorial files (HIV_SBML, SIR_SBML, DEmodel, DEdata)
    3. Lab project files (labproj, VD1.dde, VD2.dde)
  7. Introduction to Biostatistics (BST 463), Instructor, Fall, 2012
  8. Seminar in Statistical Literature (BST 497), Instructor, Fall, 2013

 

Students & Postdocs

  1. Na Lu, PhD in Control Science and Engineering (Xi’an Jiaotong University, China), 2011-2013
  2. Ana Rojas, PhD in Physics and Astronomy (Louisiana State University), 2011-2014
  3. James Seckler, PhD in Physiology and Biophysics (Case Western Reserve University), 2011-2014
  4. Jinyu Hu, PhD in Bioinformatics (Tianjin University), 2013-present

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 web-based 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 agent-based 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 CFSE-labeling experiment data”, Bulletin of Mathematical Biology, 74(2), 300-326 (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, 64-bit 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.
      • DHR-RP 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), 1933-1948 (2013)