UTH

Hulin Wu

Profile

Hulin Wu, Ph.D
The Betty Wheless Trotter Professor & Chair
Department of Biostatistics & Data Science
Director, Center for Big Data in Health Sciences
Professor of Biomedical Informatics

1200 Pressler St. RAS E833
Houston, Texas 77030

713-500-9586 tel
713-500-9525 fax
Email: [email protected]

Biographical Sketch

Education

  • Ph.D., Statistics, 1994, Department of Statistics, Florida State University, Tallahassee, Florida USA
  • M.S., Statistics, 1991, Department of Statistics, Florida State University, Tallahassee, Florida USA
  • M.S., Engineering, 1987, Department of Automatic Control, National University of Defense Technology, P.R. China
  • B.S., Engineering, 1984, Department of Automatic Control, National University of Defense Technology, P.R. China

Positions and Appointments

  • 2017-present. The Betty Wheless Trotter Professor & Chair, Department of Biostatistics & Data Science, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX.
  • 2015-present. Professor, School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, TX.
  • 2015-2017. D.R. Seth Family Professor and Associate Chair, Department of Biostatistics, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX.
  • 2012-2015. Founding Director, Center for Integrative Bioinformatics and Experimental Mathematics, University of Rochester School of Medicine and Dentistry, Rochester, NY
  • 2011-2015. Appointed as Dean’s Professor in recognition of my contribution in helping to shape the life of the institution in a significant way, University of Rochester School of Medicine and Dentistry, Rochester, NY.
  • 2004-2015. Professor, Department of Community & Preventive Medicine (Public Health Sciences), University of Rochester Medical Center, Rochester, NY
  • 2004-2015. Professor, Department of Medicine, University of Rochester Medical Center, Rochester, NY.
  • 2004-2012. Founding Chief, Division of Biomedical Modeling and Informatics, Department of Biostatistics & Computational Biology, University of Rochester Medical Center, Rochester, NY.
  • 2003-2011. Professor of Biostatistics, Department of Biostatistics & Computational Biology, University of Rochester Medical Center, Rochester, NY.
  • 2000-2003. Adjunct Lecturer, Department of Biostatistics, Harvard University, Boston, MA.
  • 2002-2003. Principal Research Scientist, Frontier Science & Technology Research Foundation (non-profit), Chestnut Hill, MA.
  • 1996-2002. Senior Statistical Scientist, Frontier Science & Technology Research Foundation (non-profit), Chestnut Hill, MA.
  • 1994-1996. Visiting Assistant Professor, Department of Mathematical Sciences, the University of Memphis, Memphis, TN.

Awards and Honors

  • Best First-Year Student Award (1990), Department of Statistics, Florida State University
  • First Prize, Student Paper Awards, the 1993 Joint Statistical Meetings, San Francisco, Section on Statistics and the environment, American Statistical Association
  • The ENAR Student Paper Award, the 1994 Spring Meetings, Cleveland, Ohio, the Eastern North American Region of the Biometrics Society (ENAR)
  • Ralph A. Bradley Award (for the most outstanding Ph.D graduate), 1994, Department of Statistics, Florida State University (FSU)
  • The Young Investigator Award, the 1995 Joint Statistical Meetings, Epidemiology Section, American Statistical Association
  • Young Scientist Scholarship Fund Award, 1997, International Workshop on HIV Drug Resistance, Treatment Strategies and Eradication, St. Petersburg, Florida
  • The First Independent Research Support & Transition (FIRST) Awards, 1998-2003, National Institutes of Health (NIH)
  • Young Scientist Scholarship Fund Award, 1998, the 2nd International Workshop on HIV Drug Resistance and Treatment Strategies, Lake Maggiore, Italy
  • Grant proposal review for Developmental Grants Program, Center for AIDS Research (CFAR), University of Washington, 2000
  • Grant proposal review for Dutch AIDS Fund, Amsterdam, Netherlands, 2001
  • Biocomputational Panel of the Information Technology Research Program, the National Science Foundation (NSF), 2003
  • Center Grant Reviewer, National Institute on Drug Abuse, National Institutes of Health (NIH), 2005
  • Grant proposal review for the section of Drug Discovery and Mechanisms of Antimicrobial Resistance, National Institutes of Health (NIH), 2005
  • Fellow, American Statistical Association, 2008
  • The Scientific Advisory Board member, the BMGF-funded (Gate's Foundation) Vaccine Immunology Statistical Center, Fred Hutchinson Cancer Research Center, Seattle, WA, 2009
  • Long-term Visitor, the Statistical and Applied Mathematical Science Institute (SAMSI), Research Triangle Park, North Carolina, Spring, 2011.
  • Standing Committee Member, NIH AIDSRRC Review Section, 2016-2018.

Research Interests

  • Big Health Care Data: EHR/EMR and insurance claim data
  • Biomedical Big Data Analytics: Complex high-dimensional data from high-throughput technologies.
  • Statistical Methods and Theories for Differential Equation Models.
  • Computational Systems Biology and Bioinformatics: Genetic and protein network and multi-scale modeling.
  • Immunological Data Analysis and Modeling: Modeling immune response to influenza and HIV infection.
  • Biomathematical Modeling: Clinical trial modeling and simulations, modeling HIV RNA/cellular dynamics, dynamic prediction of antiviral responses, and modeling AIDS epidemics.
  • Clinical Trials: Clinical trial design, pharmacokinetics and pharmacodynamics (PK/PD) study and Phase I trial design and modeling.
  • Longitudinal Data: Nonparametric regression methods and mixed-effects models.
  • Other Statistical Methodologies: High-dimensional variable selection, Markov chain Monte Carlo (MCMC), Bayesian methods, state-space models, measurement error models, missing data, and spatial statistics.

Teaching Experience

09/2015-present. As Professor at University of Texas School of Public Health, courses developed and taught:

  • Communication, Collaboration and Leadership for Biostatisticians and Data Scientists
  • Big Data in Practice
  • Data Science Analytics Methods (I)
  • Categorical Data Analysis

08/2003–08/2015. As Full Professor at the University of Rochester, courses developed and taught (M.S. and Ph.D. graduate students):

  • Linear Models
  • Seminar in Statistical Literature
  • Topics in Biostatistics: Monte Carlo Methods and Modeling of Biomedical Dynamic Systems
  • Statistical Inference
  • Advanced Topics in Object Data Analysis
  • Advanced Topics in Big Data Issues in Bioinformatics and Computational Biology

08/1994–07/1996. As Assistant Professor at the University of Memphis, courses taught for undergraduate, non-statistics major students, M.S. and Ph.D. graduate students

  • Introduction to Probability Theory
  • Applied Probability and Queueing Theory
  • Multivariate Statistical Methods
  • Experimental Design
  • Inference Theory

09/1989–08/1994. As Teaching Assistant at the Florida State University, assisted in teaching following courses:

  • Fundamental Business Statistics, Statistics through Example, Analysis of Variance and Design of Experiments, Mathematical Statistics, Introductory Probability, Time Series and Forecasting Methods.  

ReGEO

A user-friendly restructured Gene Expression Omnibus (GEO) database for identifying and reuse of gene expression datasets for scientific discoveries.

GETc Research Platform

A user-friendly research platform with analytic tools to efficiently promote use/reuse of time course gene expression data for scientific discoveries.

RegNetwork

RegNetwork is a data repository of five-type transcriptional and post-transcriptional regulatory relationships for human and mouse .

Matlab Codes for Non-parametric Regression Methods for Longitudinal Data Analysis: MIxed-Effects Modeling Approaches

Data Set Collections

  1. ACTG 315 Short-Term Viral Dynamic Data for NLME Model Fitting
  2. ACTG 315 Longitudinal Data: Viral Load and CD4+ T Cell Counts for Time-Varying Coefficient Models
  3. ACTG 315 Longitudinal Data for Missing Covariates in Nonlinear Mixed-Effects (NLME) Models
  4. ACTG 315 Long-Term Viral Dynamics for Semiparametric Nonlinear Mixed-Effects Models
  5. ACTG388 Longitudinal Data: CD4+ T Cell Counts in Two Treatment Arms for Nonparametric Mixed-Effects Models
  6. ACTG 398 Longitudinal Viral Load Data for Semiparametric Time-Varying Coefficients Regression Models (Sun and Wu, Scan. J. Statist. 2005)
  7. A5055 Long-Term Viral Dynamic Data (including PK, Adherence, and Drug Resistance): Hierarchical Bayesian (NLME) Models
  8. Dr. Ho's lab: Early Intensive Viral Dynamic Data

Books

Wai-Yuan Tan and Hulin Wu (2005), Deterministic and Stochastic Models of AIDS Epidemics and HIV Infections with Intervention, World Scientific, Singapore.

Hulin Wu and Jin-Ting Zhang (2006), Nonparametric Regression Methods for Longitudinal Data Analysis: Mixed-Effects Modeling Approaches, John Wiley & Sons, Inc., New York.

Hulin Wu , Yamal, J.M., Yaseen, Y., Maroufy, V. (2020), Statistics and Machine Learning Methods for EHR Data: From Data Extraction to Data Analytics (Edited), CRC Press., New York.

Peer-Reviewed Journals

2020

  • Soltanalizadeh, B.+, Rodriguez, E.G., Maroufy, V.+, Zheng, W.J., Wu, H.* (2020), Modeling of Hypoxia gene expression for three different cancer cell lines, International Journal of Computational Biology and Drug Design (IJCBDD), 13(1): 124–143.
  • Derek W. Brown, Stacia M. DeSantis, Thomas J. Greene, Vahed Maroufy, Ashraf Yaseen, Hulin Wu, George Williams, Michael D. Swartz (2020), A Novel Approach for Propensity Score Matching and Stratification for Multiple Treatments: Application to an EHR-Derived Study, Statistics in Medicine, 39(17):2308-2323.
  • George Williams, Vahed Maroufy, Laila Rasmy, Derek Brown, Duo Yu+, Hai Zhu, Yashar Talebi+, Xueying Wang+, Emy Thomas, Gen Zhu+, Ashraf Yaseen, Hongyu Miao, Luis Leon Novelo, Degui Zhi, Stacia DeSantis,  Hongjian Zhu, Jose-Miguel Yamal*, David Aguilar*, Hulin Wu* (2020), Vasopressor Treatment and Mortality Following Non-Traumatic Subarachnoid Hemorrhage: A Nationwide EHR Analysis, Neurosurgical Focus, 48(5):E4, May 2020.
  • G. Patra+, V. Maroufy, B. Soltanalizadeh+, N. Deng+, W. J. Zheng, K. Roberts*, Wu, H.* (2020). A Content-Based Literature Recommendation System for Datasets to Improve Data Reusability - A Case Study on Gene Expression Omnibus (GEO) Datasets. Journal of Biomedical Informatics, Volume 104, April 2020, 103399.
  • Vahed Maroufy, Pankil Shah, Arvand Asghari, Nan Deng, Juan C. Ramirez+, Ashraf Yaseen, Wenjin J. Zheng, Rosemarie N.U. Le, Michihisa Umetani*, Hulin Wu* (2020), Gene expression dynamic analysis reveals co-activation of Sonic Hedgehog and Epidermal Growth Factor followed by dynamic silencing, Oncotarget, 11(15): 1358–1372.
  • Braja Gopal Patra+, Kirk Roberts* and Hulin Wu* (2020), A Content-Based Dataset Recommendation System for Researchers - A Case Study on Gene Expression Omnibus (GEO) Repository, DATABASE-The Journal of Biological Databases and Curation, 2020: baaa064. Published online 2020 Nov 12. doi: 1093/database/baaa064. PMID: 33002137
  • Braja Gopal Patra+, Babak Soltanalizadeh+, Nan Deng+. Leqing Wu, Vahed Maroufy, Canglin Wu, Wenjin Jim Zheng, Kirk Roberts, Hulin Wu*, Ashraf Yaseen* (2020), An Informatics Research Platform to Make Public Gene Expression Time Course Datasets Reusable for More Scientific Discoveries, DATABASE-The Journal of Biological Databases and Curation, 2020: baaa074, doi: 10.1093/database/baaa074. PMID: 33247935.
  • Duo Yu+, George W. Williams, David Aguilar, José-Miguel Yamal, Vahed Maroufy, Xueying Wang+, Chenguang Zhang+, Yuefan Huang+, Yuxuan Gu+, Yashar Talebi+, Hulin Wu* (2020), Machine Learning Prediction of the Adverse Outcome for Nontraumatic Subarachnoid Hemorrhage Patients, Annals of Clinical and Translational Neurology, 7(11), 2178-2185.

2019

  • Wu, L.+, Qiu, X., Yuan, Y.X., Wu, H.* (2019), Parameter Estimation and Variable Selection for Big Systems of Linear Ordinary Differential Equations: A Matrix-Based Approach, Journal of the American Statistical Association, 114 (526), 657-667.    
  • Chen, G., Ramírez, J.C., Deng, N.+, Qiu, X., Wu, C., Zheng, W.J., and Wu, H.* (2019), Restructured GEO: Restructuring Gene Expression Omnibus metadata for genome dynamics analysis, DATABASE-The Journal of Biological Databases and Curation, Volume 2019, 1 January 2019, bay145, https://doi.org/10.1093/database/bay145
  • Wang, Y., Luo, Y., Wu, H. and Miao, H. (2019) Dynamic structural equation models for directed cyclic graphs: the structural identifiability problem, Statistics and Its Interface, 12 (3), 365-375.
  • Deng, N.+, Ramirez, J.C.+, Carey, M., Miao, H., Arias, C.A., Rice, A.P., Wu, H.* (2019), Investigation of temporal and spatial heterogeneities of the immune responses to Bordetella pertussis infection in the lung and spleen of mice via analysis and modeling of dynamic microarray gene expression data, Infectious Disease Modelling, 4: 215-226.
  • Xue, H., Kumar, A.+, Wu, H.* (2019), Parameter Estimation for Semiparametric Ordinary Differential Equation Models, Communications in Statistics-Theory and Methods, 48(24): 5985-6004. https://doi.org/10.1080/03610926.2018.1523433
  • Jia, S., Zhang, C. and Wu, H. (2019), Efficient Semi-parametric Regression for Longitudinal Data with Regularized Estimation of Error Covariance Function, Journal of Nonparametric Statistics, 31 (4), 867-886.

2018

  • Saha, J.M., Liu, H., Hu, P.W., Nikolai, B.C., Wu, H., Miao, H., Rice, A.P. (2018), Proteomic profiling of a primary CD4+ T cell model of HIV-1 latency identifies proteins whose differential expression correlates with reactivation of latent HIV-1, AIDS Research and Human Retroviruses, 34(1):103-110.
  • Carey, M.+, Ramfrez, J.C.+, Wu, S., Wu, H.* (2018), A Big Data Pipeline: Identifying Dynamic Gene Regulatory Networks from Time Course GEO Data with Applications to Influenza Infection, Statistical Methods in Medical Research, 27(7), 1930-1955.
  • Song, J., Carey, M.+, Zhu, H., Miao, H., Ramfrez, J.C.+, and Wu, H.* (2018), Identifying the dynamic gene regulatory network during latent HIV-1 reactivation using high-dimensional ordinary differential equations, International Journal of Computational Biology and Drug Design (IJCBDD), 11(1/2), 135-153.
  • Xue, H., Wu, S., Wu, Y., Wu, H.* (2018), Independence Screening for High Dimensional Nonlinear Additive ODE Models with Applications to Dynamic Gene Regulatory Networks, Statistics in Medicine, 37(17), 2630-2644.
  • Laila Rasmy, Yonghui Wu, Ningtao Wang, Xin Geng, Wenjin Jim Zheng, Fei Wang, Hulin Wu, Hua Xu, Degui Zhi (2018), A Study of Generalizability of Recurrent Neural Network-Based Predictive Models for Heart Failure Onset Risk using a Large and Heterogeneous EHR Data Set, Journal of Biomedical Informatics, 2018 Aug;84:11-16. doi: 10.1016/j.jbi.2018.06.011. Epub 2018 Jun 15.

2017

  • Chen, I., Kelkar, Y., Gu, Y., Zhou. J., Qiu, X., Wu, H.* (2017), High-Dimensional Linear State Space Models for Dynamic Microbial Interaction Networks, PLOS ONE,12(11): e0187822. https://doi.org/10.1371/journal.pone.0187822.

2016

  • Lu, N.+, Silva, J., Gu, Y., Wu, H., Gelbard, H., Dewhurst, S., Miao, H. (2016), Capillary Extraction by Detecting Polarity in Circular Profiles”, IET Image Processing, 10(5): 339-348.
  • Shen, S. S.,Li, J. J., Hilchey, S. S., Shen, X. X., Tu, C. C., Qiu, X. X., Ng, A. A., Ghaemmaghami, S. S., Wu, H., Zand, M. S., Qu, J. J.* (2016), Ion-Current-Based Temporal Proteomic Profiling of Influenza-A-Virus-Infected Mouse Lungs Revealed Underlying Mechanisms of Altered Integrity of the Lung Microvascular Barrier.  Journal of Proteome Research. 15(2), 540-553. http://dx.doi.org/10.1021/acs.jproteome.5b00927.
  • Yang, H., Baker, S.F., Gonzalez, M.E., Topham, D.J., Martinez-Sobrido, L., Zand, M., Holden-Wiltse, J., Wu, H. (2016), An Improved Method for Estimating Antibody Titers in Microneutralization Assay Using Green Fluorescent Protein, Journal of Biopharmaceutical Statistics, 26(3): 409-420. doi: 10.1080/10543406.2015.1052475.
  • Carey, M.+, Wu, S., Gan, G., Wu, H.* (2016), Correlation-based iterative clustering methods for time course data: the identification of temporal gene response modules for influenza infection in humans, Infectious Disease Modelling, 1(1), 28-39.
  • Sun, X.+, Hu, F.+, Wu, S., Qiu, X., Linel, P.+, Wu, H.* (2016), Controllability and Stability Analysis of Large Transcriptomic Dynamic Systems for Host Response to Influenza Infection in Human, Infectious Disease Modelling, 1(1), 52-70.

2015

  • Qiu, X., Wu, S., Wu, H. (2015), A New Information Criterion Based on Mixture Langevin Distribution for Clustering Circular Data with Application to Time-course Genomic Data, Statistica Sinica, 25, 1459-1476.
  • Wu, H.*, Miao, H., Xue, H., Topham, D.J., Zand, M. (2015), Quantifying Immune Response to Influenza Virus Infection via Multivariate Nonlinear ODE Models with Partially Observed State Variables and Time-Varying Parameters, Statistics in Biosciences, 7(1):147-166.
  • Liu, Z.P.+, Wu, C., Miao, H., Wu, H.* (2015), RegNetwork: an Integrated Database of Transcriptional and Posttranscriptional Regulatory Networks in Human and Mouse, DATABASE-The Journal of Biological Databases and Curation, Vol. 2015: article ID bav095; doi:10.1093/ database/bav095.
  • Qiu, X., Wu, S., Hilchey, S.P., Thakar, J., Liu, Z.P., Welle, S.L., Henn, A.D., Wu, H.*, Zand, M.S.* (2015), Diversity in Compartmental Dynamics of Gene Regulatory Networks: The Immune Response in Primary Influenza A Infection in Mice, PLoS ONE, 10(9): e0138110. DOI: 10.1371/journal.pone.0138110.

2014

  • Gu, W., Wu. H., Miao, H., and Xue, H. (2014), Parameter Estimation for a Type of Nonlinear Stochastic Models Observed with Error, Computational Statistics and Data Analysis, 79, 113-119. Paper | Matlab code & Data
  • 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.* (2014), Modeling the Dynamics and Migratory Pathways of Virus-Specific Antibody-Secreting Cell Populations in Primary Influenza Infection, PLoS ONE, 9(8):e104781. PMID:25171166 | C code & Data
  • Miao, H., Wu, H., and Xue, H. (2014), Generalized Ordinary Differential Equation Models, Journal of the American Statistical Association, 2014 Oct;109(508):1672-1682. PMID:25544787 | C code & Data
  • Wu, S., Liu, Z.P., Qiu, X., and Wu, H.* (2014), Modeling genome-wide dynamic regulatory network in mouse lungs with influenza infection using high-dimensional ordinary differential equations, PLOS ONE, 2014 May 6;9(5):e95276. PMID:24802016 | R Code | Data
  • Wu, H.*, Lu, T., Xue, H., and Liang, H. (2014), Sparse Additive ODEs for Dynamic Gene Regulatory Network Modeling, Journal of the American Statistical Association, 2014 Apr 2;109(506):700-716. PMID:2378633 |  |  | 
  • Wu, S., Xue, H., Wu, Y., Wu, H. (2014), Variable Selection for Sparse High-Dimensional Nonlinear Regression Models by Combining Nonnegative Garrote and Sure Independence Screening, Statistica Sinica, 2014 Jul;24(3):1365-1387. PMID:25170239 |  | Matlab Code
  • Ding, A.A. and Wu, H.* (2014), Estimation of ODE Parameters Using Constrained Local Polynomial Regression, Statistica Sinica, 24, 1613-1631. Paper | R code | Data
  • Linel, P., Wu, S., Deng, N., Wu, H.* (2014), Dynamic transcriptional signatures and network responses for clinical symptoms in influenza-infected human subjects using systems biology approaches, Journal of Pharmacokinetics and Pharmacodynamics, 41, 509-521, PMID:25015847.
  • Amneris E. Luque, Mark Orlando, U-Cheng Leong, Paul D. Allen, Joseph J. Guido, Hongmei Yang and Hulin Wu (2014), Hearing Function in Patients Living with HIV/AIDS, Ear and Hearing, 2014 Nov-Dec;35(6):e282-90. PMID:25127320
  • Liu, Z., Wu, H., Zhu, J., Miao, H. (2014), Systematic Identification of Transcriptional and Post-Transcriptional Regulatory Relationships during Influenza Virus Infection, BMC Bioinformatics,15(1): 336. PMID:25281301 | R code & Data

2013

  • Wang, J., Zhang, L., Jing, C., Ye, G., Wu, H., Miao, H., Wu, Y., Zhou X. (2013), Multi-scale agent-based modelling on melanoma and its related angiogenesis analysis, Theoretical Biology and Medical Modelling, 10:41
  • Yang, H., Topham, D., Holden-Wiltse, J., Wu, H. (2013), Statistical estimation & inference of cell counts from ELISPOT limiting dilution assays , Journal of Biopharmaceutical Statistics,23, 921-926. PMID: 23786336 | 
  • Wu, S, and Wu, H.* (2013), More Powerful Significant Testing for Time Course Gene Expression Data Using Functional Principal Component Analysis Approaches, BMC Bioinformatics, 14:6. PMID: 23323795 |  |  | 
  • Lu, N., Silva, J., Gu, Y., Gerber, S., Wu, H., Gelbard. H., Dewhurst, S., Miao, H. (2013), Directional histogram ratio at random probes: A local thresholding criterion for capillary images, Pattern Recognition, 46(7), 1933-1948. PMID: 23525856 | 
  • Qiu, X., Wu, H. and Hu, R. (2013), The Impact of Quantile and Rank Normalization Procedures on the Testing Power of Gene Differential Expression Analysis, BMC Bioinformatics,14:124. PMID: 23578321
  • Luo, R., Piovoso, M.J., Wu, H., Buzon, M.J., Martinez-Picado, J., Zurakowski, R. (2013), Modeling HIV-1 2-LTR Dynamics Following Raltegravir Intensification, Journal of the Royal Society Interface, 10:20130186. PMID: 23658114
  • Yanni Xiao, Hongyu Miao, Sanyi Tang, Hulin Wu* (2013), Modeling Antiretroviral Drug Responses for HIV-1 infected Patients Using Differential Equation Models, Advanced Drug Delivery Reviews, 65, 940-953. PMID: 23603208
  • Alicia D. Henn, Shuang Wu, Xing Qiu, Melissa Ruda, Michael Stover, Hongmei Yang, Zhiping Liu, Stephen Welle, Jeanne Holden-Wiltse, Hulin Wu*, Martin S. Zand* (2013), High-Resolution Temporal Response Patterns to Influenza Vaccine Reveal a Distinct Human Plasma Cell Gene Signature, Nature Scientific Reports, 3:2327. PMID: 23900141 | Data
  • Jason M Weaver; Hongmei Yang; David Roumanes; Frances Eun-Hyung Lee; Hulin Wu; John J. Treanor; Tim R Mosmann (2013), Increase in IFNγ(-)IL-2(+) cells in recent human CD4 T cell responses to 2009 pandemic H1N1 influenza, PLoS One, 8(3):e57275. PMID: 23526940

2012

  • Wu, H.*, Xue, H., Kumar A. (2012), Numerical Discretization-Based Estimation Methods for Ordinary Differential Equation Models via Penalized Spline Smoothing with Applications in Biomedical Research., Biometrics, 68(2):344-52 .PMID:22376200 | | Technical Proof | | Patient 1 Data | Patient 2 Data
  • Cao, J., Huang, J.Z., Wu, H. (2012), Penalized Nonlinear Least Squares Estimation of Time-Varying Parameters in Ordinary Differential Equations, Journal of Computational and Graphical Statistics (JCGS), 21:1, 42-56.PMID: 23155351
  • Lee, Y. and Wu, H.* (2012), MARS Approach for Global Sensitivity Analysis of Differential Equation Models with Applications to Dynamics of Influenza Infection, Bulletin of Mathematical Biology, 74(1):73-90.PMID: 21656089
  • Miao, H., Jin, X., Perelson, A.S., Wu, H. (2012), Evaluation of Multitype Mathematical Models for CFSE-Labeling Experiment Data, Bulletin of Mathematical Biology, 74(2):300-26. PMID: 21681605 |  | 
  • Zhou, J., Liu, S.Y., Zhou, F., Wu, H. (2012), Statistical Diagnosis of HIV Model (in Chinese). Chin Sci Bull (Chin Ver). 2012, 57: 666–672, doi: 10.1360/972011-1978.
  • Henn, A.D., Laski, M., Yang, H., Qiu, X., Miao, H., Barry, C.T., Welle, S., Wu, H., Zand, M.S. (2012), Functionally Distinct Subpopulations of CpG-Activated Memory B Cells, Nature Scientific Reports, 2012;2:345. PMID: 22468229 | Data
  • Li, X., Miao, H., Henn, A.D., Topham, D.J.,  Wu, H.,  Zand, M.S., and Mosmann, T.R. (2012), Ki-67 Expression Reveals Strong, Transient Influenza Specific CD4 T Cell Responses After Adult Vaccination, Vaccine, 30, 4581-4584. .PMID: 22554464
  • Tang, S., Xiao, Y., Wang, N., and Wu, H. (2012), Piecewise HIV virus dynamic model with CD4+ T cell count-guided therapy: I, Journal of Theoretical Biology, 308, 123-234. PMID: 22659043

2011

  • Wang, J., Zhang, G.,  Bambara, R.,  Li, D., Liang, H.,  Wu, H.,  Smith, H.,  Lowe, N.,  Demeter, L., and Dykes, C. (2011), Nonnucleoside Reverse Transcriptase Inhibitor (NNRTI)-resistant Virus is Stimulated by Efavirenz (EFV) During Early Stages of Infection, Journal of Virology, 85(20):10861-73. PMID:21835788
  • Wu, H., Kumar, A., Miao, H., Holden-Wiltse, J., Mosmann, T.R., Livingstone, A.M., Belz, G.T., Perelson, A.S., Zand, M., Topham, D.J. (2011), 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, 4474-4482. PMID:21948988 |  |  | 
  • Lu, T., Liang, H., Li, H., Wu, H. (2011), High Dimensional ODEs Coupled with Mixed-Effects Modeling Techniques for Dynamic Gene Regulatory Network Identification, Journal of the American Statistical Association, JASA, 106:496 1242-1258. PMID: 21681605 | Appendix | R Code | 
  • Liu, D., Lu, T., Niu, X.F., and Wu, H.* (2011), Mixed-Effects State Space Models for Analysis of Longitudinal Dynamic Systems, Biometrics, 67, 476-485.PMID:20825393
  • Fang, Y., Wu, H., Zhu, L. (2011), A Two-Stage Estimation Method for Random Coefficient Differential Equation Models with Application to Longitudinal HIV Dynamic Data, Statistica Sinica, 21, 1145-1170. PMID:22171150
  • Miao, H., Xia, X., Perelson, A.S., Wu, H. (2011), On Identifiability of Nonlinear ODE Models and Applications in Viral Dynamics, SIAM Review, 53, 3-39.PMID:21785515
  • Huang, Y., Wu, H., Holden-Wiltse, J., Acosta, P. (2011), A Dynamic Bayesian Nonlinear Mixed-Effects Model of HIV Response Incorporating Medication Adherence, Drug Resistance and Covariates, The Annals of Applied Statistics, 5(1), 551-577,.PMID: 22171150
  • Lartey, M., Sagoe, K.W., Yang, H., Kenu, E., Xexemeku, F., Oliver-Commey, J., Bioma, V., Seshie, M., Sagoe, A., Mingle, J., Flanigan, T.P., Wu, H., Kwara, A. (2011), Viral Decay Rates Are Similar in HIV-Infected Patients with and without TB Coinfection Treated with Efavirenz-containing Antiretroviral Therapy, Clinical Infectious Diseases, 52(4), 547-550. PMID:21252140

2010

  • Zhang, J.T., Wu, H. (2010), Modeling HIV Dynamics Using Unified Mixed-effects Models, American Journal of Mathematical and Management Sciences, 30 (1-2), 83-109. Paper
  • Liang, H., Wu, H.*, (2010), Correction on “Parameter Estimation for Differential Equation Models Using a Framework of Measurement Error in Regression Models (JASA, 103, 1570-1583),” Journal of the American Statistical Association, 105, 1636.
  • Baer, J., Santiago, F., Yang, H., Wu, H., Holden-Wiltse, J., Treanor, J., Topham, D.J. (2010), B Cell Responses to H5 Influenza HA in Human Subjects Vaccinated with Drifted Variants,  Vaccine, 28, 907-915. PMID: 19932673
  • Liang, H., Miao, H., and Wu, H. (2010), Estimation of constant and time-varying dynamic parameters of HIV infection in a nonlinear differential equation model, Annals of Applied Statistics, 4, 460-483. PMID: 20556240 | PMCID: PMC2885820 | Patient 1 Data | Patient 2 Data
  • Wood, R., Liang, H., Wu, H., Middelkoop, K., Oni, T., Rangaka, M.X., Wilkinson, R.J., Bekker, L.G., Lawn, S. D. (2010), Changing prevalence of Tuberculosis infection with increasing age in high-burden townships in South Africa, the International Journal of Tuberculosis and Lung Disease, 14, 406-412. PMID: 20202297
  • Ma, J., Dykes, C., Wu, T., Huang, Y., Demeter, L., Wu, H. (2010), vFitness: a web-based computing tool for improving estimation of in vitro HIV-1 fitness experiments, BMC Bioinformatics, 11:261. PMID: 20482791 | PMCID: PMC2882933
  • Xue, H., Miao, H., Wu, H. (2010), 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, 2351-87. PMID:21132064
  • Miao, H., Hollenbaugh, J.A., Zand, M., Holden-Wiltse, J., Mosmann, T.R., Perelson, A.S., Wu, H., Topham, D.J. (2010), Quantifying the Early Immune Response and Adaptive Immune Response Kinetics in Mice Infected with Influenza A Virus, Journal of Virology, 84, 6687-6698. PMID: 20410284 |  | 
  • Wang, J., Liang, H., Bacheler, L., Wu, H., Deriziotis, K., Demeter, L.M., Dykes, C. (2010), The Non-nucleoside Reverse Transcriptase Inhibitor Efavirenz Stimulates Replication of Human Immunodeficiency Virus Type 1 Harboring Certain Non-nucleoside Resistance Mutations, Virology, 402, 228-237. PMID: 20399480
  • Dykes, C., Wu, H., Sims, M., Holden-Wiltse, J., Demeter, L. (2010), Human immunodeficiency virus type 1 protease inhibitor drug-resistant mutants give discordant results when compared in single-cycle and multiple-cycle fitness assays, Journal of Clinical Microbiology, 48, 4035-4043. PMID: 20826651
  • Huang, Y., Wu, H., Acosta, P. (2010), Hierarchical Bayesian Inference for HIV Dynamic Differential Equation Models Incorporating Multiple Treatment Factors, Biometrical Journal, 52(4), 470-486. PMID: 20661953

2009

  • Miao, H., Dykes, C., Demeter, L., Wu, H. (2009), Differential Equation Modeling of HIV Viral Fitness Experiments: Model Identification, Model Selection, and Multi-Model Inference, Biometrics, 65, 292-300. PMID: 18510656 | 
  • Eron, J.J., Park, J.G., Haubrich, R.,  Aweeka, F., Bastow, B., Pakes, G.E., Yu, S., Wu, H., and Richman, D.D. for the ACTG5126 Study Team (2009), Predictive Value of Pharmacokinetic-Adjusted Phenotypic Susceptibility on Response to Ritonavir-Enhanced Protease Inhibitors (PI) in Human Immunodeficiency Virus-Infected Subjects Failing Prior PI Therapy, Antimicrobial Agents and Chemotherapy, 53, 2335-2341. PMID: 19307363
  • Lee, H.Y., Topham, D.J., Park, S.Y., Hollenbaugh, J., Treanor, J., Mosmann, T.R., Jin, X., Ward, B., Miao, H., Holden-Wiltse, J.,  Perelson, A.S.,  Zand, M.,  Wu, H. (2009), Simulation and Prediction of the Adaptive Immune Response to Influenza A Virus Infection, Journal of Virology, 83, 7151-7165. PMID: 19439465 | PMCID: PMC2704765 |  | 
  • Lee, H.Y., Hawkins, E., Zand, M.S., Mosmann, T., Wu, H., Hodgkin, P.D., Perelson, A.S. (2009), Interpreting CFSE Obtained Division Histories of B Cells in Vitro with Smith-Martin and Cyton Type Models, Bulletin of Mathematical Biology, 71, 1649-1670. PMID: 19381725

2008

  • Huang, Y. and Wu, H. (2008), Bayesian Experimental Design for Long-Term Longitudinal HIV Dynamic Studies, Journal of Statistical Planning and Inference, 138, 105-113. PMCID: PMC3225901 | Data | Fortran Code
  • Wu, L., Hu, J.X., and Wu, H. (2008), Joint Inference for Nonlinear Mixed-Effects Models and Time to Event at the Presence of Missing Data, Biostatistics, 9(2), 308-320. PMID: 17728318
  • Chen, J. and Wu, H. (2008), Efficient Local Estimation for Time-varying Coefficients in Deterministic Dynamic Models with Applications to HIV-1 Dynamics, Journal of the American Statistical Association, 103, 369-384. Paper | Data | VDM_main.c
  • Wu, H., Zhu, H., Miao, H., and Perelson, A.S. (2008), Parameter Identifiability and Estimation of HIV/AIDS Dynamic Models, Bulletin of Mathematical Biology, 70(3), 785-799. PMID: 18247096
  • Miao, H., Dykes, C., Demeter, L.M., Cavenaugh, J., Park, S.Y., Perelson, A.S., and Wu, H. (2008), Modeling and Estimation of Kinetic Parameters and Replicative Fitness of HIV-1 from Flow-Cytometry-Based Growth Competition Experiments, Bulletin of Mathematical Biology, 70, 1749-1771. PMID: 18648886 | 
  • Chen, J. and Wu, H. (2008), Estimation of time-varying parameters in deterministic dynamic models, Statistica Sinica, 18, 987-1006. Paper | Data
  • Liang, H., Wu, H., Zou, G. (2008), A Note on Conditional AIC for Linear Mixed-Effects Models, Biometrika, 95, 773-778. PMID: 19122890 | PMCID: PMC2572765
  • Huang, Y., Liang, H., and Wu, H. (2008), Identifying significant covariates for anti-HIV treatment response: mechanism-based differential equation models and empirical semiparametric regression models, Statistics in Medicine, 27, 4722-4739. PMID: 18407583 | PMCID: PMC2574674
  • Liang, H., Wu, H., (2008), Parameter Estimation for Differential Equation Models Using a Framework of Measurement Error in Regression Models, Journal of the American Statistical Association, 103, 1570-1583. PMID: 19956350 | PMCID: PMC2631937

2007

  • Jin, X., Wu, H. and Smith, H. (2007), APOBEC3G Levels Predict Rates of Progression to AIDS, Retrovirology, 4:20. Paper | PMID: 17374143 | PMCID: PMC1832211
  • Flanigan, R.M., Nawoczenski, D.A., Chen, L., Wu, H., and DiGiovanni, B.F. (2007), The Influence of Foot Position on Stretching of the Plantar Fascia, Foot & Ankle, 28, 815-822. PMID: 17666175
  • Palumbo, P., Wu, H., Chadwick E. et al. (2007), Virologic Response to Potent Antiretroviral Therapy and Modeling of HIV Dynamics in Early Pediatric Infection, The Journal of Infectious Diseases, 196, 23-29. PMID: 17538879
  • Wu, H. (2007). Discussion of “Parameter Estimation for Differential Equations: A Generalized Smoothing Approach,” by J. O. Ramsay, G. Hooker, D. Campbell and J. Cao. Journal of the Royal Statistical Society, Ser. B. 69, 789. Paper
  • Zhu, H. and Wu, H. (2007), Estimation of Smoothing Time-Varying Parameters in State Space Models, Journal of Computational and Graphical Statistics (JCGS), 16(4), 813-832. 

2006

  • Huang, Y. and Wu, H. (2006), “A Bayesian Approach for Estimating Antiviral Efficacy in HIV Dynamic Models," Journal of Applied Statistics, 33, 155-174. Paper | Data | Fortran Code
  • Wu, H., Huang, Y., Dykes, C., Liu, D., Ma, J., Perelson, A.S., Demeter, L. (2006), Modeling and Estimation of Replication Fitness of Human Immunodeficiency Virus type 1 in Vitro Experiments Using a Growth Competition Assay, Journal of Virology, 80, 2380-2389. PMID: 16474144 | PMCID: PMC1395363
  • Park, J.G. and Wu, H. (2006), “Backfitting and Local Likelihood Methods for Nonparametric Mixed-Effects Models with Longitudinal Data," Journal of Statistical Planning and Inference, 136, 3760-3782. Paper | Data
  • Huang, Y., Liu, D. and Wu, H. (2006), Hierarchical Bayesian Methods for Estimation of Parameters in a Longitudinal HIV Dynamic System, Biometrics, 62, 413-423. PMID: 16918905 | PMCID: PMC2435289 | Data | Fortran Code | Technical Report
  • Wu, H., Huang, Y. and Acosta, E.P. et al. (2006), Pharmacodynamics of Antiretroviral Agents in HIV-1 Infected Patients Using Viral Dynamic Models That Incorporate Drug Susceptibility and Adherence, Journal of Pharmacokinetics and Pharmacodynamics, 33, 399-419. PMID: 16583266 | Data
  • Liu, D., Yu, J., Reichman, R., Chang, X., Wu, H., Jin, X. (2006), Statistical Determination of Threshold for Cellular Division in the CFSE-Labeling Assay, Journal of Immunological Methods, 312, 126-136. PMID: 16712866
  • Dykes, C., Wang, J., Jin, X., Planelles, V., An, D.S., Tallo, A., Huang, Y., Wu, H., Demeter, L.M. (2006), 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, Journal of Clinical Microbiology, 44, 1930-1943. PMID: 16757582 | PMCID: PMC1489405
  • Treanor, J., Wu, H., Liang, H., and Topham, D.J. (2006), Immune responses to vaccinia and influenza elicited during primary versus recent or distant secondary smallpox vaccination of adults, Vaccine, 24, 6913-6923.PMCID:17014939

2005

  • Wu, H. (2005), “Statistical Methods for HIV Dynamic Studies in AIDS Clinical Trials," Statistical Methods in Medical Research, 14, 171-192. Paper
  • Sun, Y. and Wu, H. (2005), “Semiparametric Time-Varying Coefficients Regression Model for Longitudinal Data," Scan. J. Statist., 32, 21-47. Paper | Data
  • Wu, H., Huang, Y. and Acosta, E.P. et al. (2005), Modeling Long-Term HIV Dynamics and Antiretroviral Response: Effects of Drug Potency, Pharmacokinetics, Adherence, and Drug Resistance, JAIDS, 39, 272-283. PMID: 15980686 | Data | 

2004

  • Wu, H. and Liang, H. (2004), “Backfitting Random Varying-Coefficient Models with Time-Dependent Smoothing Covariates," Scan. J. Statist., 31, 3-19. Paper | Data | 
  • Wu, H., Lathey, J., Ruan, P., et al. (2004), “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," Journal of Infectious Diseases, 189, 593-601. PMID: 14767811
  • Wu, H., Zhao, C. and Liang, H. (2004), “ Comparison of Linear, Nonlinear and Semiparametric Models for Estimating HIV Dynamic Parameters," Biometrical Journal, 46, 233-245. Paper
  • Acosta, E.P., Wu, H., Hammer, S.M. et al. (2004), “Comparison of Two Indinavir/Ritonavir Regimens in the Treatment of HIV-Infected Individuals," JAIDS, 37, 1358-1366. PMID: 15483465

2003

  • Liang, H., Wu, H., and Carroll, R.J. (2003), “The Relationship Between Virologic and Immunologic Responses in AIDS Clinical Research Using Mixed-Effects Varying-Coefficient Semiparametric Models with Measurement Error," Biostatistics, 4, 297-312. Paper | Data
  • Hamzeh, F.M., Benson, C., Gerber, J., Currier, J., McCrea, J., Deutsch, P., Ruan, P., Wu, H., Lee, J., Flexner, C. (2003), "Steady-State Pharmacokinetic Interaction of Modified-Dose Indinavir and Rifabutin," Clinical Pharmacology and Therapeutics, 73, 159-169. PMID: 12621381
  • DiCenzo, R., Forrest, A., Squires, K.E., Hammer, S.M., Fischl, M.A., Wu, H., Cha, R., Morese, G.D. and the Adult AIDS Clinical Trials Group Protocol 368/886 Study Team (2003), “Indinavir, Efavirenz and Abacavir Pharmacokinetics in Human Immunodeficiency Virus-Infected Subjects," Antimicrobial Agents and Chemotherapy, 47, 1929-1935. PMID: 12760869 | PMCID: PMC155818
  • Sun, Y. and Wu, H. (2003), “AUC-Based Tests for Nonparametric Functions with Longitudinal Data," Statistica Sinica, 13, 593-612. Paper
  • Huang, Y., Rosenkranz, S., Wu, H. (2003), “Modeling HIV Dynamics and Antiviral Responses with Consideration of Time-Varying Drug Exposures, Adherence and Phenotypic Sensitivity," Mathematical Biosciences, 184, 165-186. PMID: 12832146 | 
  • Wu, H., Mellors, J., Ruan, P. et al. (2003), “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," JAIDS, 32, 557-564. PMID: 12902798
  • Hass, D.W., Wu, H., Li, H. et al. (2003), “MDR1 Gene Polymorphisms and Phase 1 Viral Decay during HIV-1 Infection: An Adult AIDS Clinical Trials Group Study," JAIDS, 34, 295-298. Paper
  • Zhang, Y., Liu, W., and Wu, H. (2003), “ A simple nonparametric two-sample test for the distribution function of event time with interval censored data," Journal of Nonparametric Statistics, 15, 643-652.Paper | Data

2002

  • Wu, H. and Wu, L. (2002), “Identification of Significant Host Factors for HIV Dynamics Modeled by Nonlinear Mixed-Effect Models," Statistics in Medicine, 21, 753-771. PMID: 11870815 | Data
  • Wu, H. and Ding, A.A. (2002), “Design of Viral Dynamic Studies for Efficiently Assessing Potency of Anti-HIV Therapies in AIDS Clinical Trials," Biometrical Journal, 2, 175-196. Paper
  • Wu, H. and Zhang, J.T. (2002), “Local Polynomial Mixed-Effects Models for Longitudinal Data," Journal of the American Statistical Association, 97, 883-897. Paper | Data
  • Wu, L. and Wu, H. (2002), “ Missing time-dependent covariates in human immunodeficiency virus dynamic models," Journal of the Royal Statistical Society, Series C (Applied Statistics), 51, 297-318. Paper | Data
  • Wu, H. and Zhang, J.T. (2002), “The Study of Long-Term HIV Dynamics Using Semiparametric Nonlinear Mixed-Effects Models," Statistics in Medicine, 21, 3655-3675. PMID: 12436462 | Data

2001

  • Ding, A.A. and Wu, H. (2001), “Assessing Antiviral Potency of Anti-HIV Therapies in Vivo by Comparing Viral Decay Rates in Viral Dynamic Models," Biostatistics, 2, 13-29 Paper
  • Wu, H. and Wu, L. (2001), “A Multiple Imputation Method for Missing Covariates in Non-linear Mixed-effects Models with Application to HIV Dynamics," Statistics in Medicine, 20 (12), 1755-1769. PMID: 11406839 | Data
  • Wu, H., Connick E., Kuritzkes, D.R. et al. (2001), “Multiple CD4+ Cell Kinetic Patterns and Their Relationships with Baseline Factors and Virologic Responses in HIV-1 Type 1 Patients Receiving Highly Active Antiretroviral Therapy," AIDS Research and Human Retroviruses, 17(13), 1237-1246. PMID: 11559422

2000

  • Ding, A.A. and Wu, H. (2000), “A Comparison Study of Models and Fitting Procedures for Biphasic Viral Dynamics in HIV-1 Infected Patients Treated with Antiviral Therapies," Biometrics, 56, 293-300. PMID: 10783809 | Data
  • Kuritzkes, D., Sevin A., Young, B., Bakhtiari, M., Wu, H., Clair, M.S., Connick, E., Landay, A.L., Spritzler, J., Kessler, H., and Lederman, M.M. (2000), “Effect of zidovudine resistance mutations on virologic response to treatment with zidovudine-lamivudine-ritonavir: genotypic analysis of human immunodeficiency virus type 1 isolates from AIDS clinical trials group protocol 315. ACTG Protocol 315 Team.," Journal of Infectious Diseases, 181, 491-497. PMID: 10669331
  • Wu, H. and Tan, W.Y. (2000), “Modelling the HIV Epidemic: A State-Space Approach," Mathematical and Computer Modelling, 32, 197-215. (Epidemiology Young Investigator Award). 

1999

  • Wu, H. and Ding, A. (1999), “Population HIV-1 Dynamics in Vivo: Applicable Models and Inferential Tools for Virological Data from AIDS Clinical Trials," Biometrics, 55, 410-418. PMID: 11318194 | Data
  • Wu, H., Kuritzkes, D.R., and McClernon, D.R. et al. (1999), “Characterization of Viral Dynamics in Human Immunodeficiency Virus Type 1-Infected Patients Treated with Combination Antiretroviral Therapy: Relationships to Host Factors, Cellular Restoration and Virological Endpoints," Journal of Infectious Diseases, 179(4):799-807. PMID: 10068574 | Data
  • Luzuriaga, K., Wu, H., and McManus, M. et al. (1999), “Dynamics of Human Immunodeficiency Virus Type-1 Replication in Vertically-Infected Infants," Journal of Virology, 73, 362-367. PMID: 9847340 | PMCID: PMC103841
  • Wu, H., Ding, A. and DeGruttola, V. (1999), “Why are the decay rates in plasma HIV-1 different for different treatments and in different patient populations?" AIDS, 13 (3): 429-430. PMID: 10199240
  • Wu, H. (1999), “How Frequently Should Viral Load be Monitored to Evaluate Antiretroviral Therapies in AIDS Clinical Trials?" Journal of Acquired Immune Deficiency Syndromes and Human Retrovirology, 20, 97-99. PMID: 9928739
  • Ding, A.A. and Wu, H. (1999), “Relationships between Antiviral Treatment Effects and Biphasic Viral Decay Rates in Modeling HIV Dynamics," Mathematical Biosciences, 160, 63-82. PMID: 10465932 | Data
  • Wu, H., Ruan, P., Ding, A.A., Sullivan, J.L. and Luzuriaga, K. (1999), “Inappropriate Model-Fitting Methods May Lead To Significant Underestimates of Viral Decay Rates in HIV Dynamic Studies," Journal of Acquired Immune Deficiency Syndromes and Human Retrovirology, 21, 426-428. PMID: 10458627
  • Spear, GT, Olinger G, Sullivan B, Landay AL, Kessler, H, Connick E, Kuritzkes D, St. Clair M, Spritzler J, Wu H, Lederman MM (1999) “Alteration of complement protein levels after antiretroviral therapy in HIV-infected persons," AIDS Research and Human Retroviruses, 15, 1713-15. PMID: 10606095

1998

  • Huffer, F.W. and Wu, H. (1998), “Markov Chain Monte Carlo for Autologistic Regression Models with Application to the Distribution of Plant Species," Biometrics, 54, 509-524. Paper
  • Tan, W.Y. and Wu, H. (1998),“Stochastic Modeling of the Dynamics of CD4+ T Cell Infection by HIV and some Monte Carlo Studies," Mathematical Biosciences, 147, 173-205. PMID: 9433062
  • Wu, H., Ding, A. and DeGruttola. V. (1998), “Estimation of HIV Dynamic Parameters," Statistics in Medicine, 17, 2463-2485. PMID: 9819839

1997

  • Wu, H. and Huffer, F.W. (1997), “Modelling the Distribution of Plant Species Using the Autologistic Regression Model," Environmental and Ecological Statistics, Vol. 4, No.1, 49-64. (First Prize, Student Paper Awards by Section on Statistics and the Environment of ASA) 
  • George, E.O. and Wu, H. (1997), “Testing for Treatment Related Trend with Partially Exchangeable Clustered Data," Biometrics, 53, 479-487. PMID: 9192447

Thesis, Proceedings, and Book Chapters

Wu, H. (1994), “Regression Models for Spatial Binary Data with Application to the Distribution of Plant Species," Ph.D. dissertation, Department of Statistics, Florida State University.

Wu, H. and Tan, W.Y (1996),“Modeling and Monitoring the Progression of HIV Infection Using Nonlinear Kalman Filter," ASA 1996 Proceedings of the Biometrics Section, 372-377.

Tan, W.Y. and Wu, H. (1997), “A Stochastic Model of the Pathogenesis of HIV at the Cellular Level and Some Monte Carlo Studies," Simulation in the Medical Sciences, Edited by Anderson, J.G. and Katzper, M., The Society for Computer Simulation International, the 1997 SCS Western Multiconference, 78-86.

Ding, A. and Wu, H. (1997), “Modeling HIV Dynamics with Treatment of Reverse Transcriptase Inhibitor Drugs," ASA 1997 Proceedings of the Epidemiology Section, 52-57.

Wu, H. and Ding A.A. (1999), “Assessing Anti-HIV Therapies Using Viral Dynamics: An Overview," Concepts and Applications of Systemics, Cybernetics and Informatics, Edited by Torres, M., Sanchez, B., and Wills, E., Proceedings of 3rd World Multi-conference on Systemics, Cybernetics and Informatics, Vol. 8, 490-497.

Wu, H., Zhang, B., and Spritzler, J. (1999), “Modeling and Analyzing Cellular Kinetics for HIV-infected Patients Treated with Potent Antiviral Therapies in AIDS Clinical Trials," ASA 1999 Proceedings of the Biometrics Section, 123-128.

Ding, A. and Wu, H. (1999), “Statistical Tests in Nonlinear Mixed-Effect Models with Application to Potency Comparison of Anti-HIV Therapies," ASA 1999 Proceedings of Biopharmaceutical Statistics Section, 58-63.

Wu, H. and Zhao, S. (2002), “Chapter 17. Models for Infectious Diseases,"Advanced Medical Statistics, Fang, J.Q. and Lu, Y. (editors). World Sciences Publisher, Singapore.

Huang, Y. and Wu, H. (2004), “Mechanistic PK/PD Modeling of Antiretroviral Therapies in AIDS Clinical Trials," Advanced Methods of Pharmacokinetic & Pharmacodynamic Systems Analysis, Volume III, edited by David Z. D’Argenio. New York: Kluwer Academical Publishers, Page 221-237.

Huang, Y. and Wu, H. (2005), “Bayesian Estimation of Individual Parameters in an HIV Dynamic Model Using Long-Term Viral Load Data," Deterministic and Stochastic Models of AIDS Epidemics and HIV Infections with Intervention, edited by W.Y. Tan and H. Wu. Singapore: World Scientific.

Huang, Y. and Wu, H. (2008), “HIV Dynamics Modeling and Prediction of Clinical Outcomes in AIDS Clinical Research,” Statistical Advances in the Biomedical Sciences: Clinical Trials, Epidemiology, Survival Analysis, and Bioinformatics, edited by Atanu Biswas, Sujay Datta, Jason P. Fine, and Mark R. Segal.  New York, Wiley InterScience.

Wu, H., Miao, H., Warnes, G.R., Wu, C., LeBlanc, A., Dykes, C., Demeter, L.M. (2008), “DEDiscover: A Computation and Simulation Tool for HIV Viral Fitness Research,” 2008 International Conference on BioMedical Engineering and Informatics proceeding, http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=4548758&userType=inst&tag=1.

Wu, S., Liu, Z.P., Qiu, X., Wu, H. (2013), High-Dimensional Ordinary Differential Equation Models for Reconstructing Genome-Wide Dynamic Regulatory Networks, Topics in Applied Statistics, Proceeding of 2012 Symposium of the International Chinese Statistical Association. Page 173-191.

Wu, H., (2017), Book review on “Exposure-Response Modeling: Methods and Practical Implementation” by Jixian Wang, Journal of the American Statistical Association, 112(517), 458.

Patra, B.G.+, Kar, R., Roberts, K., and Wu, H. (2020), Mental Health Severity Detection from Psychological Forum Data using Domain-Specific Unlabelled Data. In AMIA 2020 Infromatics Summit, Houston, TX, USA, pp. 487-496. (Best CRI Paper).

Research Grants

(As Principal Investigator or Co-Principal Investigator)

  • Principal Investigator: NIH Grant R29 AI 43220, "Models and Inferential Tools for HIV-1 Dynamics in Vivo," funded (FIRST Award) by the National Institute of Allergy and Infectious Diseases/NIH, 1998-2003.
  • Principal Investigator: NIH Grant R01 AI 45356, "Modeling Cellular Kinetics in Treated HIV Patients," funded by the National Institute of Allergy and Infectious Diseases/NIH, 1999-2003.
  • Principal Investigator: NIH Grant R01 AI 52765, "Nonparametrical Modeling of Long-Term HIV/Cell Dynamics," funded by the National Institute of Allergy and Infectious Diseases/NIH, 2002-2006.
  • Principal Investigator: NIH Grant R01 AI 055290, "AIDS Clinical Trial Modeling and Simulations," funded by the National Institute of Allergy and Infectious Diseases/NIH, 2003-2008.
  • Principal Investigator & Director: NIH Grant Contract NOI-AI 50020,"Center for Biodefense Immune Modeling," Funded by NIAID/NIH, 2005-2015.
  • Co-Principal Investigator & Co-Director: NIH Grant UL1 RR024160, "The Biomedical Informatics (BI) Key Function, the University of Rochester's Clinical and Translational Science Institute," (Co-PIs: Drs. David Krusch and Dongwen Wang), funded by NIH/NCRR, 2006-2011.
  • Co-Principal Investigator: Novel ethodology CTSI grant, "Development of Objective Gating Methods for High-Dimensional Flow Cytometry Data for Translational Research," (Co-PI with Dr. Tim Mosmann), funded by the University of Rochester CTSI, 2008-2009.
  • Principal Investigator: NIH Subcontract, R21 AI078842, "Analysis of Differential Resistance Emergence Risk for Differential Treatment Applications," (PI at University of Delaware: Ryan M. Zurakowski), funded by NIAID/NIH, 2009-2011.
  • Principal Investigator: Multidisciplinary Pilot Award, University of Rochester Developmental Center for AIDS Research (D-CFAR), "Meta-Population Model of HIV/TB Co-Epidemics in a Cape Town Community," funded by NIAID/NIH, 2009-2010.
  • Principal Investigator: NIH Grant RO1 AI087135, "Estimation Methods for Nonlinear ODE Models in AIDS Research," funded by NIAID/NIH 2010-2013.
  • Principal Investigator: Novel Methodology CTSI grant, "Development of Statistical Methods and Bioinformatics Tools for Modeling Dynamic Gene Regulatory Networkds for Translational Research - A Systems Biology Approach," funded by the University of Rochester CTSI, 2010-2012 .
  • Co-Principal Investigator: NIH Institutional Research Training Grant (T32), "Training in Biostatistics for HIV/AIDS," (Co-PI: Dr. Hua Liang), funded by NIAID/NIH 2010-2015.
  • Principal Investigator: Administrative Supplements (for U.S. - China Biomedical Collaborative Research on Cancer, Allergy, Immunology, and Infectious Diseases including HIV/AIDS and its Co-morbidities) to the NIH Grant RO1 AI087135, “Estimation Methods for Nonlinear ODE Models in AIDS Research,” funded by NIAID/NIH, 2011-2012.
  • Co-Principal Investigator (Contact-PI): NIH Grant NO1 AI 50020, “Center for Biodefense Immune Modeling," (Co-PI: Martin Zand, M.D./Ph.D.) funded by the National Institute of Allergy and Infectious Diseases/NIH (5-year renewal), 2010-2015.
  • Principal Investigator: NIH Subcontract, R21 AI110288, “HIV 2LTR Dynamics and Cryptic Viremia,” (PI at University of Delaware: Ryan M. Zurakowski), funded by NIAID/NIH, 2014-2016.
  • Principal Investigator: NIH Grant 2 R01 AI087135-05 (renewed), “Statistical Methods for ODE Models in AIDS Research,” funded by NIAID/NIH, 2015-2021.

(As Core Director, Co-Investigator or Statistician)

  • My Role: Senior Statistician and Section Head, NIH Grant U01 AI38855, “Adult ACTG-Statistical Analysis and Data Management Center,” (PI: Victor De Gruttola and Michael Hughes), a contract project funded by the National Institute of Allergy and Infectious Diseases/NIH, 1996–2003.
  • My Role: Senior Statistician, NIH Grant P01 AI56356, “HSV-1 Amplicon Vectors for HIV Vaccine Delivery,” (PI: Michael C. Keefer), a program project funded by the National Institute of Allergy and Infectious Diseases/NIH, 2003–2008.
  • My Role: Senior Statistician, NIH Grant RO1 HL079511, “Images of a Healthy Worksite,” (PI: Isabel Diana Fernandez), funded by NHLBI/NIH, 2004–2008.
  • My Role: Statistician, ATPM Grant, “Baby-Friendly’s Impact on Duration and Exclusivity,” (PI: Ann Marie Dozier), funded by ATPM, 2004-2005.
  • My Role: Steering Committee Member and Director of the Biomathematics, Biostatistics and Bioinformatics Core, Developmental-Center for AIDS Research (D-CFAR), (Co-PIs: Drs. Stephen Dewhurst and Michael Keefer), funded by the National Institute of Allergy and Infectious Diseases/NIH, 2008–2013.
  • My Role: Director, Biostatistics  and Data Management Core, the New York Influenza Center of Excellence (NYICE), Co-PIs: Drs. John Treanor and David Topham, funded by NIAID/NIH, 2007-2014.
  • My Role: Co-Investigator and Statistician, URMC CTSI Novel Methodology Grant, “Using Heavy Water in vivo Labeling to Measure Human Proliferation and Die-Away Kinetics- Development of the Core Facility at the University of Rochester,” (PI: Frances Eun-Hyung Lee, MD), funded by URMC CTSI, 2007-2008.
  • My Role: Co-Investigator and Senior Statistician, NIH Grant RO1 DC009395, “Hearing Impairment in HIV/AIDS,” (PI: Amneris E. Luque), funded by NIAID/NIH, 2009-2014.
  • My Role: Senior Statistician, CDC Grant 3 U48 DP001910-01S1, “The Rochester Prevention Research Center,” (PI: Tom Pearson), funded by CDC, 2009-2014.
  • My Role: Director, Biostatistics and Modeling Core, NIH Program Grant 3PO1 MH64570, “Novel Adjunctive Therapies for NeuroAIDS,” (PI: Harris A. Gelbard, M.D./Ph.D.), funded by NIH, 2010-2015.
  • My Role: Director, Biostatistics and Data Management Core, NIH Program Grant 1 PO1 AI078907, “B Cells in Health and Disease,” (PI: Ignacio Sanz, MD), funded by NIAID/NIH, 2010-2015.
  • My Role:Director, the Biostatistics, Bioinformatics and Computational Biology Core and the Steering Committee Member, Center for AIDS Research (D-CFAR), (Co-PIs: Drs. Stephen Dewhurst and Michael Keefer), funded by the National Institute of Allergy and Infectious Diseases/NIH, 2013–2018.
  • My Role: Co-Investigator, NIH SBIR grant “An Integrated Biomedical Dataset Discovery System for Immunological Research Databases (BIRD)”, (Co-PI: Canglin Wu and Hua Xu), funded by NIAID/NIH, 2017-2018.
  • Co-Leader, Biostatistics Section, CPRIT PR170668, “Data Science and Informatics Core for Cancer Research”, (PI: Dr. Wenjin J. Zheng), funded by CPRIT, 2017-2022.
  • Co-Director, Clinical and Biostatistics Core, P30AI161943-01, “Texas Developmental Center for AIDS Research (D-CFAR),” (PI: Thomas Peter Giordano), funded by NIH/NIAID, 2021-2026.

Research Projects

Statistics on the Web

Statistical Societies

Biomedical Informatics and Bioengineering Societies

Biomathematical Societies

Markov Chain Monte Carlo

Other Biodefense Immune Modeling Centers

Virology/Immunology Modeling Groups

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