Hulin Wu

Summary

Affiliation: University of Rochester
Country: USA

Publications

  1. pmc Numerical discretization-based estimation methods for ordinary differential equation models via penalized spline smoothing with applications in biomedical research
    Hulin Wu
    Department of Biostatistics and Computational Biology, University of Rochester, 601 Elmwood Avenue, Box 630, Rochester, New York 14642, USA
    Biometrics 68:344-52. 2012
  2. ncbi request reprint Statistical methods for HIV dynamic studies in AIDS clinical trials
    Hulin Wu
    Department of Biostatistics and Computational Biology, University of Rochester, School of Medicine and Dentistry, Rochester, NY 14642, USA
    Stat Methods Med Res 14:171-92. 2005
  3. ncbi request reprint Pharmacodynamics of antiretroviral agents in HIV-1 infected patients: using viral dynamic models that incorporate drug susceptibility and adherence
    Hulin Wu
    Department of Biostatistics and Computational Biology, University of Rochester School of Medicine and Dentistry, NY 14642, USA
    J Pharmacokinet Pharmacodyn 33:399-419. 2006
  4. ncbi request reprint Modeling long-term HIV dynamics and antiretroviral response: effects of drug potency, pharmacokinetics, adherence, and drug resistance
    Hulin Wu
    Department of Biostatistics and Computational Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
    J Acquir Immune Defic Syndr 39:272-83. 2005
  5. ncbi request reprint Relationship of plasma HIV-1 RNA dynamics to baseline factors and virological responses to highly active antiretroviral therapy in adolescents (aged 12-22 years) infected through high-risk behavior
    Hulin Wu
    Department of Biostatistics and Computational Biology, University of Rochester School of Medicine and Dentistry, 601 Elmwood Avenue, Rochester, NY 14642, USA
    J Infect Dis 189:593-601. 2004
  6. pmc Modeling and estimation of replication fitness of human immunodeficiency virus type 1 in vitro experiments by using a growth competition assay
    Hulin Wu
    Department of Biostatistics and Computational Biology, University of Rochester School of Medicine and Dentistry, New York 14642, USA
    J Virol 80:2380-9. 2006
  7. doi request reprint Parameter identifiability and estimation of HIV/AIDS dynamic models
    Hulin Wu
    Department of Biostatistics and Computational Biology, University of Rochester School of Medicine and Dentistry, 601 Elmwood Avenue, Box 630, Rochester, NY 14642, USA
    Bull Math Biol 70:785-99. 2008
  8. pmc Modeling and estimation of kinetic parameters and replicative fitness of HIV-1 from flow-cytometry-based growth competition experiments
    Hongyu Miao
    Department of Biostatistics and Computational Biology, University of Rochester School of Medicine and Dentistry, 601 Elmwood Avenue, Box 630, Rochester, NY, 14642, USA
    Bull Math Biol 70:1749-71. 2008
  9. pmc Statistical estimation & inference of cell counts from ELISPOT limiting dilution assays
    Hongmei Yang
    Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, NY 14642, USA
    J Biopharm Stat 23:921-36. 2013
  10. pmc Evaluation of multitype mathematical models for CFSE-labeling experiment data
    Hongyu Miao
    Department of Biostatistics and Computational Biology, University of Rochester School of Medicine and Dentistry, 601 Elmwood Avenue, Box 630, Rochester, NY 14642, USA
    Bull Math Biol 74:300-26. 2012

Detail Information

Publications41

  1. pmc Numerical discretization-based estimation methods for ordinary differential equation models via penalized spline smoothing with applications in biomedical research
    Hulin Wu
    Department of Biostatistics and Computational Biology, University of Rochester, 601 Elmwood Avenue, Box 630, Rochester, New York 14642, USA
    Biometrics 68:344-52. 2012
    ..We apply the proposed methods t an HIV study to further illustrate the usefulness of the proposed approaches...
  2. ncbi request reprint Statistical methods for HIV dynamic studies in AIDS clinical trials
    Hulin Wu
    Department of Biostatistics and Computational Biology, University of Rochester, School of Medicine and Dentistry, Rochester, NY 14642, USA
    Stat Methods Med Res 14:171-92. 2005
    ..We also pose some challenging statistical problems in this area in order to stimulate further study by the statistical research community...
  3. ncbi request reprint Pharmacodynamics of antiretroviral agents in HIV-1 infected patients: using viral dynamic models that incorporate drug susceptibility and adherence
    Hulin Wu
    Department of Biostatistics and Computational Biology, University of Rochester School of Medicine and Dentistry, NY 14642, USA
    J Pharmacokinet Pharmacodyn 33:399-419. 2006
    ..But their combinations in viral dynamic modeling significantly predicted virologic response. The HIV dynamic modeling can appropriately capture complicated nonlinear relationships and interactions among multiple covariates...
  4. ncbi request reprint Modeling long-term HIV dynamics and antiretroviral response: effects of drug potency, pharmacokinetics, adherence, and drug resistance
    Hulin Wu
    Department of Biostatistics and Computational Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
    J Acquir Immune Defic Syndr 39:272-83. 2005
    ..The proposed mathematic models and statistical techniques may provide a framework to simulate and predict antiviral response for individual patients...
  5. ncbi request reprint Relationship of plasma HIV-1 RNA dynamics to baseline factors and virological responses to highly active antiretroviral therapy in adolescents (aged 12-22 years) infected through high-risk behavior
    Hulin Wu
    Department of Biostatistics and Computational Biology, University of Rochester School of Medicine and Dentistry, 601 Elmwood Avenue, Rochester, NY 14642, USA
    J Infect Dis 189:593-601. 2004
    ....
  6. pmc Modeling and estimation of replication fitness of human immunodeficiency virus type 1 in vitro experiments by using a growth competition assay
    Hulin Wu
    Department of Biostatistics and Computational Biology, University of Rochester School of Medicine and Dentistry, New York 14642, USA
    J Virol 80:2380-9. 2006
    ..A user-friendly computational tool also has been developed and is publicly available on the World Wide Web at http://www.urmc.rochester.edu/bstools/vfitness/virusfitness.htm...
  7. doi request reprint Parameter identifiability and estimation of HIV/AIDS dynamic models
    Hulin Wu
    Department of Biostatistics and Computational Biology, University of Rochester School of Medicine and Dentistry, 601 Elmwood Avenue, Box 630, Rochester, NY 14642, USA
    Bull Math Biol 70:785-99. 2008
    ..Although we have developed the identifiability methods based on an HIV dynamic model, the proposed methodologies are generally applicable to any ordinary differential equation systems...
  8. pmc Modeling and estimation of kinetic parameters and replicative fitness of HIV-1 from flow-cytometry-based growth competition experiments
    Hongyu Miao
    Department of Biostatistics and Computational Biology, University of Rochester School of Medicine and Dentistry, 601 Elmwood Avenue, Box 630, Rochester, NY, 14642, USA
    Bull Math Biol 70:1749-71. 2008
    ..Practical identifiability was investigated via Monte Carlo simulations...
  9. pmc Statistical estimation & inference of cell counts from ELISPOT limiting dilution assays
    Hongmei Yang
    Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, NY 14642, USA
    J Biopharm Stat 23:921-36. 2013
    ..Thus, the t -test or the Wilcoxon Rank Sum test can be applied to detect group differences. These methods are compared through simulations and application to real data. ..
  10. pmc Evaluation of multitype mathematical models for CFSE-labeling experiment data
    Hongyu Miao
    Department of Biostatistics and Computational Biology, University of Rochester School of Medicine and Dentistry, 601 Elmwood Avenue, Box 630, Rochester, NY 14642, USA
    Bull Math Biol 74:300-26. 2012
    ..This model was then employed to understand the proliferation pattern of CD4+ and CD8+ T cells under polyclonal stimulation...
  11. pmc Modeling of influenza-specific CD8+ T cells during the primary response indicates that the spleen is a major source of effectors
    Hulin Wu
    Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, NY 14642, USA
    J Immunol 187:4474-82. 2011
    ..Together, these efforts provide a better understanding of the primary CD8(+) T cell response to influenza infection, changing the view that the spleen plays a minor role in the primary immune response...
  12. pmc Quantifying the early immune response and adaptive immune response kinetics in mice infected with influenza A virus
    Hongyu Miao
    Department of Biostatistics and Computational Biology, University of Rochester, Rochester, New York 146421, USA
    J Virol 84:6687-98. 2010
    ..Also, simulation studies were performed to understand the relative contributions of biological parameters to IAV clearance. This study provides a basis to better understand and predict influenza virus immunity...
  13. pmc Hierarchical Bayesian methods for estimation of parameters in a longitudinal HIV dynamic system
    Yangxin Huang
    Department of Biostatistics and Computational Biology, University of Rochester, Rochester, New York 14642, USA
    Biometrics 62:413-23. 2006
    ..The basic concept of the longitudinal HIV dynamic systems and the proposed methodologies are generally applicable to any other biomedical dynamic systems...
  14. pmc Ki-67 expression reveals strong, transient influenza specific CD4 T cell responses after adult vaccination
    Xi Li
    David H Smith Center for Vaccine Biology and Immunology, Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY 14642, USA
    Vaccine 30:4581-4. 2012
    ....
  15. pmc vFitness: a web-based computing tool for improving estimation of in vitro HIV-1 fitness experiments
    Jingming Ma
    Department of Biostatistics and Computational Biology, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA
    BMC Bioinformatics 11:261. 2010
    ..The accurate estimation of viral fitness relies on complicated computations based on statistical methods. This calls for tools that are easy to access and intuitive to use for various experiments of viral fitness...
  16. pmc Nonnucleoside reverse transcriptase inhibitor-resistant HIV is stimulated by efavirenz during early stages of infection
    Jiong Wang
    Department of Medicine, University of Rochester School of Medicine and Dentistry, 601 Elmwood Ave, Rochester, NY 14642, USA
    J Virol 85:10861-73. 2011
    ..Our results indicate that stimulation most likely occurs through a mechanism whereby NNRTIs stimulate priming or elongation of the tRNA...
  17. pmc High-resolution temporal response patterns to influenza vaccine reveal a distinct human plasma cell gene signature
    Alicia D Henn
    Department of Medicine, Division of Nephrology, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
    Sci Rep 3:2327. 2013
    ..With robust statistical methods, time-varying response characteristics of individual subjects were effectively captured along with a shared plasma cell gene signature. ..
  18. pmc Human immunodeficiency virus type 1 protease inhibitor drug-resistant mutants give discordant results when compared in single-cycle and multiple-cycle fitness assays
    Carrie Dykes
    Department of Medicine, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642, USA
    J Clin Microbiol 48:4035-43. 2010
    ..We propose that discordant results in the MCA and SCA are due to alterations in late events in the virus life cycle that are not captured in an SCA, such as burst size, cell-to-cell transmission, or infected-cell life span...
  19. pmc APOBEC3G levels predict rates of progression to AIDS
    Xia Jin
    Departments of Medicine, University of Rochester, Rochester, New York 14642, USA
    Retrovirology 4:20. 2007
    ..These conflicting results indicate that a more comprehensive, conclusive investigation of hA3G expression levels in various patient cohorts is urgently needed...
  20. pmc Differential equation modeling of HIV viral fitness experiments: model identification, model selection, and multimodel inference
    Hongyu Miao
    Department of Biostatistics and Computational Biology, University of Rochester School of Medicine and Dentistry, 601 Elmwood Avenue, Box 630, Rochester, New York 14642, USA
    Biometrics 65:292-300. 2009
    ..We expect that the proposed modeling and inference approaches for the DE models can be widely used for a variety of biomedical studies...
  21. pmc Interpreting CFSE obtained division histories of B cells in vitro with Smith-Martin and cyton type models
    Ha Youn Lee
    Department of Biostatistics and Computational Biology, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA
    Bull Math Biol 71:1649-70. 2009
    ..The most profound effect of the presence of IL-4 was decreased death rates for smaller division classes, which supports a role of IL-4 in the protection of B cells from apoptosis...
  22. ncbi request reprint Statistical determination of threshold for cellular division in the CFSE-labeling assay
    Dacheng Liu
    Department of Biostatistics and Computational Biology, University of Rochester School of Medicine and Dentistry, Rochester, New York, NY 14642, USA
    J Immunol Methods 312:126-36. 2006
    ..071% (95% confidence) and 0.114% (99% confidence) of total CFSE-labeled cells under our laboratory conditions. We offer our methods presented here for other investigators to calculate a threshold in their own CFSE-labeling experiments...
  23. pmc Evaluation of a multiple-cycle, recombinant virus, growth competition assay that uses flow cytometry to measure replication efficiency of human immunodeficiency virus type 1 in cell culture
    Carrie Dykes
    Department of Medicine, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
    J Clin Microbiol 44:1930-43. 2006
    ..This flow cytometry-based growth competition assay offers advantages over current assays for HIV replication efficiency and should prove useful for the evaluation of patient samples in clinical trials...
  24. pmc B cell responses to H5 influenza HA in human subjects vaccinated with a drifted variant
    Jane Baer
    David H Smith Center for Vaccine Biology and Immunology, Aab Institute for Biomedical Sciences, Department of Microbiology and Immunology, Rochester, NY, USA
    Vaccine 28:907-15. 2010
    ..These observations suggest prior vaccination against H5 influenza HA induces cellular immune responses that cross-react among drifted variants, without precluding a response to new, or existing HA strains...
  25. pmc Simulation and prediction of the adaptive immune response to influenza A virus infection
    Ha Youn Lee
    Department of Biostatistics and Computational Biology, University of Rochester, Rochester, New York 14642, USA
    J Virol 83:7151-65. 2009
    ..We further compared alternative model structures, for example, B-cell activation directly by the virus versus that through professional antigen-presenting cells or dendritic cell licensing of CD8 T cells...
  26. pmc Modeling genome-wide dynamic regulatory network in mouse lungs with influenza infection using high-dimensional ordinary differential equations
    Shuang Wu
    Department of Biostatistics and Computational Biology, University of Rochester, Rochester, New York, United States of America
    PLoS ONE 9:e95276. 2014
    ..The application to the influenza infection data elucidates the potentials of our pipeline in providing valuable insights into systematic modeling of complicated biological processes. ..
  27. pmc More powerful significant testing for time course gene expression data using functional principal component analysis approaches
    Shuang Wu
    Department of Biostatistics and Computational Biology, University of Rochester, 601 Elmwood Avenue, Rochester, NY 14642, USA
    BMC Bioinformatics 14:6. 2013
    ..Most of the existing methods for this problem are designed for data with longitudinal replicates. But in reality, many time course gene experiments have no replicates or only have a small number of independent replicates...
  28. pmc Mars approach for global sensitivity analysis of differential equation models with applications to dynamics of influenza infection
    Yeonok Lee
    Department of Biostatistics and Computational Biology, The University of Rochester, Rochester, NY 14642, USA
    Bull Math Biol 74:73-90. 2012
    ..We present an application example of sensitivity analysis of ODE models for influenza infection to further illustrate the usefulness of the proposed method...
  29. pmc The impact of quantile and rank normalization procedures on the testing power of gene differential expression analysis
    Xing Qiu
    Department of Biostatistics and Computational Biology, University of Rochester, 601 Elmwood Avenue, Box 630, Rochester, New York 14642, USA
    BMC Bioinformatics 14:124. 2013
    ..In this study, we find that these normalization procedures can have a profound impact on differential expression analysis, especially in terms of testing power...
  30. ncbi request reprint The study of long-term HIV dynamics using semi-parametric non-linear mixed-effects models
    Hulin Wu
    Frontier Science and Technology Research Foundation, 1244 Boylston Street, Suite 303, Chestnut Hill, MA 02467, USA
    Stat Med 21:3655-75. 2002
    ..Small-scale simulation and bootstrap studies show that our bootstrap procedures work well. The proposed approach and procedures are applied to long-term HIV dynamic data from an AIDS clinical study...
  31. ncbi request reprint Viral dynamics and their relations to baseline factors and longer term virologic responses in treatment-naive HIV-1-infected patients receiving abacavir in combination with HIV-1 protease inhibitors
    Hulin Wu
    Frontier Science and Technology Research Foundation, Chestnut Hill, Massachusetts 02467, USA
    J Acquir Immune Defic Syndr 33:557-63. 2003
    ..These data suggest that the potency of the 5 treatment regimens was similar and was not predictive of long-term virologic failure...
  32. pmc Indinavir, efavirenz, and abacavir pharmacokinetics in human immunodeficiency virus-infected subjects
    Robert Dicenzo
    University at Buffalo, Buffalo, New York, USA
    Antimicrob Agents Chemother 47:1929-35. 2003
    ..Abacavir did not influence the pharmacokinetics or exposure parameters of either indinavir or efavirenz. The levels of efavirenz exposure were similar in subjects receiving efavirenz q12h or q24h...
  33. ncbi request reprint Modeling HIV dynamics and antiviral response with consideration of time-varying drug exposures, adherence and phenotypic sensitivity
    Yangxin Huang
    Frontier Science and Technology Research Foundation, Inc, 1244 Boylston Street, Suite 303, Chestnut Hill, MA 02467, USA
    Math Biosci 184:165-86. 2003
    ..The proposed models and methods may be useful in AIDS clinical trial simulations...
  34. ncbi request reprint The relationship between virologic and immunologic responses in AIDS clinical research using mixed-effects varying-coefficient models with measurement error
    Hua Liang
    Department of Biostatistics, St Jude Children s Research Hospital, 332 North Lauderdale St, Memphis, TN 38105, USA
    Biostatistics 4:297-312. 2003
    ..From this study, we find an interesting relationship between viral load and CD4+ cell counts during antiviral treatments. Biological interpretations and clinical implications are discussed...
  35. ncbi request reprint MDR1 gene polymorphisms and phase 1 viral decay during HIV-1 infection: an adult AIDS Clinical Trials Group study
    David W Haas
    Division of Infectious Diseases, Vanderbilt University School of Medicine, 345 24th Avenue, North, Suite 105, Nashville, TN 37212, USA
    J Acquir Immune Defic Syndr 34:295-8. 2003
    ..It is concluded with 95% confidence that phase 1 viral decay differences between exon 26 TT and CC groups are unlikely to exceed 18%...
  36. ncbi request reprint Comparison of two indinavir/ritonavir regimens in the treatment of HIV-infected individuals
    Edward P Acosta
    Division of Clinical Pharmacology, University of Alabama at Birmingham School of Medicine, Birmingham, AL 35294 0019, USA
    J Acquir Immune Defic Syndr 37:1358-66. 2004
    ....
  37. ncbi request reprint Identification of significant host factors for HIV dynamics modelled by non-linear mixed-effects models
    Hulin Wu
    Frontier Science and Technology Research Foundation Inc, 1244 Boylston Street, Suite 303, Chestnut Hill, Massachusetts 02467, U S A
    Stat Med 21:753-71. 2002
    ..We recommend a multiple imputation method to handle missing covariates. A real data set from an AIDS clinical trial is analysed based on various covariate selection methods and missing data methods...
  38. pmc Pharmacokinetics of nelfinavir and efavirenz in antiretroviral-naive, human immunodeficiency virus-infected subjects when administered alone or in combination with nucleoside analog reverse transcriptase inhibitors
    Patrick F Smith
    Adult ACTG Pharmacology Support Laboratory, Laboratory for Antiviral Research, Department of Pharmacy Practice, School of Pharmacy and Pharmaceutical Sciences, University at Buffalo, Buffalo, NY 12460, USA
    Antimicrob Agents Chemother 49:3558-61. 2005
    ..There were no significant differences in efavirenz pharmacokinetics...
  39. ncbi request reprint Virologic response to potent antiretroviral therapy and modeling of HIV dynamics in early pediatric infection
    Paul Palumbo
    Department of Pediatrics, University of Medicine and Dentistry New Jersey Medical School, Newark, NJ, USA
    J Infect Dis 196:23-9. 2007
    ..Similar studies are needed in pediatric populations, in whom differing dynamics might translate into age-specific treatment approaches...
  40. ncbi request reprint Joint inference for nonlinear mixed-effects models and time to event at the presence of missing data
    Lang Wu
    Department of Statistics, 333 6356 Agricultural Road, University of British Columbia, Vancouver, British Columbia V6T 1Z2, Canada
    Biostatistics 9:308-20. 2008
    ..We provide a method for simultaneous likelihood inference on the 2 models and allow for nonignorable data missing. The approach is illustrated with a recent AIDS study by jointly modeling HIV viral dynamics and time to viral rebound...
  41. ncbi request reprint Steady-state pharmacokinetic interaction of modified-dose indinavir and rifabutin
    Fayez M Hamzeh
    Johns Hopkins Hospital, Johns Hopkins University, Osler 527, 600 N Wolfe Street, Baltimore, MD 21287 5554, USA
    Clin Pharmacol Ther 73:159-69. 2003
    ..Therefore this study was designed to evaluate alternative dosing regimens...

Research Grants17

  1. AIDS Clinical Trail Modeling and Stimulatinos
    Hulin Wu; Fiscal Year: 2007
    ..The developed systems will be a useful tool for AIDS clinicians to develop individualized treatments for their patients. ..
  2. AIDS Clinical Trail Modeling and Stimulatinos
    Hulin Wu; Fiscal Year: 2006
    ..The developed systems will be a useful tool for AIDS clinicians to develop individualized treatments for their patients. ..
  3. Nonparametric Modeling of Long-term HIV/Cell Dynamics
    Hulin Wu; Fiscal Year: 2005
    ..We expect that the results from this project can be used to assess the long-term effectiveness of antiretroviral therapies and provide information for long-term care and treatment management for HIV-I-infected patients. ..
  4. AIDS Clinical Trail Modeling and Stimulatinos
    Hulin Wu; Fiscal Year: 2005
    ..The developed systems will be a useful tool for AIDS clinicians to develop individualized treatments for their patients. ..
  5. Nonparametric Modeling of Long-term HIV/Cell Dynamics
    Hulin Wu; Fiscal Year: 2003
    ..We expect that the results from this project can be used to assess the long-term effectiveness of antiretroviral therapies and provide information for long-term care and treatment management for HIV-I-infected patients. ..
  6. AIDS Clinical Trail Modeling and Stimulatinos
    Hulin Wu; Fiscal Year: 2003
    ..The developed systems will be a useful tool for AIDS clinicians to develop individualized treatments for their patients. ..
  7. Nonparametric Modeling of Long-term HIV/Cell Dynamics
    Hulin Wu; Fiscal Year: 2004
    ..We expect that the results from this project can be used to assess the long-term effectiveness of antiretroviral therapies and provide information for long-term care and treatment management for HIV-I-infected patients. ..
  8. AIDS Clinical Trail Modeling and Stimulatinos
    Hulin Wu; Fiscal Year: 2004
    ..The developed systems will be a useful tool for AIDS clinicians to develop individualized treatments for their patients. ..
  9. AIDS Clinical Trail Modeling and Stimulatinos
    Hulin Wu; Fiscal Year: 2003
    ..The developed systems will be a useful tool for AIDS clinicians to develop individualized treatments for their patients. ..
  10. Nonparametric Modeling of Long-term HIV/Cell Dynamics
    Hulin Wu; Fiscal Year: 2003
    ..We expect that the results from this project can be used to assess the long-term effectiveness of antiretroviral therapies and provide information for long-term care and treatment management for HIV-I-infected patients. ..
  11. Nonparametric Modeling of Long-term HIV/Cell Dynamics
    Hulin Wu; Fiscal Year: 2002
    ..We expect that the results from this project can be used to assess the long-term effectiveness of antiretroviral therapies and provide information for long-term care and treatment management for HIV-I-infected patients. ..
  12. MODELS AND INFERENTIAL TOOLS FOR HIV1 DYNAMICS IN VIVO
    Hulin Wu; Fiscal Year: 2002
    ..Thus, the proposed HIV-1 dynamic models in vivo and statistical inferential methodology will provide a powerful tool to understand the pathogenesis of HIV and to search for a cure for AIDS. ..
  13. Estimation Methods for Nonlinear ODE Models in AIDS Research
    Hulin Wu; Fiscal Year: 2010
    ....