Tong Tong Wu, PhD

Associate Professor of Biostatistics and Computational Biology

Director, M.A. in Statistics and M.S. in Medical Statistics Programs
Ph.D. (2006) University of California, Los Angeles

Contact Information

University of Rochester
Dept of Biostatistics and Computational Biology
265 Crittenden Boulevard, CU 420630 
Rochester, New York 14642-0630
 
Office: Saunders Research Building 4141
Phone: (585) 276-6858
Fax: (585) 273-1031
E-mail: Tongtong_Wu@urmc.rochester.edu

Research Interests

As a biostatistician, Dr. Tong Tong Wu’s research interests include high-dimensional data analysis, survival analysis, machine learning, computational statistics, and computational biology and statistical genetics. She is also interested in statistical applications and collaborations in various health, medical, and scientific areas, such as cancer, HIV, epidemiology, psychology, and medical engineering.

Selected Publications

(*: joint first or senior authors; $: corresponding author; **: advisee/trainee of Dr. Wu)

Book Chapters

• Gong, H.*, Wu, T.T.*$, and Clarke, E. (2014) (*: joint first authors) Statistical Analysis of High-Dimensional Data for Pancreatic Cancer. In Azmi, A (Ed.), Molecular Diagnostics and Treatment of Pancreatic Cancer: Systems and Network Biology Approaches (Chapter 20). Elsevier Academic Press.

Statistical Methodology Papers

• Chang, J., Tang, C.Y., and Wu, T.T. (2018) A New Scope of Penalized Empirical Likelihood with High-Dimensional Estimating Equations. Annals of Statistics, Volume 46, 3185–3216.
• Aditya, P., Sen, R., Oh, S.J., Benenson, R., Bhattacharjee, B., Druschel, P., Wu, T.T., Fritz, M., and Schiele, B. (2016) I-Pic: A Platform for Privacy-Compliant Image Capture. ACM MobiSys 2016 TPC, 235-248.
• Wu, T.T.$ and Lange, K. (2015) Matrix Completion Discriminant Analysis. Computational Statistics and Data Analysis, Volume 92, 115-125.
• Wu, T.T.$, Li, G., and Tang, C.Y. (2015) Empirical Likelihood for Censored Linear Regression and Variable Selection. Scandinavian Journal of Statistics, Volume 42, No 3, 798–812.
        Supplementary File: Proofs of Theorems
• Costello, J. C., ..., NCI DREAM Community, ..., and Stolovitzky, G. (2014) A community effort to assess and improve drug sensitivity prediction algorithms. Nature Biotechnology, Volume 32, 1202-1212.
• Fang, H.-B., Wu, T.T.$, Rapoport, A.P., and Tan, M. (2014) Survival Analysis with Functional Covariates for Partial Follow-up Studies. Statistical Methods in Medical Research, Epub.
• Chen, S., Grant, E.**, Wu, T.T., and Bowman, F. D. (2014) Some Recent Statistical Learning Methods for Longitudinal High-dimensional Data. WIREs Computational Statistics, Volume 6, No 1, 10-18.
• Tang, C.Y. and Wu, T.T.$ (2014) Nested Coordinate Descent Algorithms for Empirical Likelihood. Journal of Statistical Computation and Simulation, Volume 84, No 9, 1917-1930.
• Wu, T.T.$ and Wang, S. (2013) Doubly Regularized Cox Regression for High-dimensional Survival Data with Group Structures. Statistics and Its Interface, Volume 6, No 2, 175-186.
• Wu, T.T. (2013) Lasso Penalized Semiparametric Regression on High-Dimensional Recurrent Event Data via Coordinate Descent. Journal of Statistical Computation and Simulation, Volume 83, No 6, 1145-1155.
• Wu, T.T.$ and Wu, Y. (2012) Nonlinear Vertex Discriminant Analysis with Reproducing Kernels. Statistical Analysis and Data Mining, Volume 5, No 2, 167-176.
• Wu, T.T.$ and He, X. (2012) Coordinate Ascent for Penalized Semiparametric Regression on High-Dimensional Panel Count Data. Computational Statistics and Data Analysis, Volume 56, No 1, 25-33.
• Wu, T.T.$ and Lange, K. (2010) The MM Alternative to EM. Statistical Science, Volume 25, No 4, 492-505.
• Wu, T.T.$ and Lange, K. (2010) Multicategory Vertex Discriminant Analysis for High-Dimensional Data. Annals of Applied Statistics, Volume 4, No 4, 1698-1721.
        Supplementary File: Proof of Proposition 1
        R package: VDA
• Li, G.# and Wu, T.T.#$ (2010) (#: alphabetic order) Semiparametric Additive Risks Regression for Two-Stage Design Survival Studies. Statistica Sinica, Volume 20, No 4, 1581-1607.
• Wu, T.T.$, Chen, Y.F., Hastie, T., Sobel, E., and Lange, K. (2009) Genomewide Association Analysis by Lasso Penalized Logistic Regression. Bioinformatics, Volume 25, No 6, 714-721.
        Supplementary Data
        R package: CDLasso
• Wu, T.T.*, Sun, W.*, Yuan, S., Chen, C.-H., and Li, K.-C. (2008) (*: joint first authors) A Method for Analyzing Censored Survival Phenotype with Gene Expression Data. BMC Bioinformatics, Volume 9, 417.
• Wu, T.T.$ and Lange, K. (2008) Coordinate Descent Algorithms for Lasso Penalized Regression. Annals of Applied Statistics, Volume 2, No 1, 224-244.
        Supplementary Appendix: Weak Consistency of Lasso Penalized l1 Regression
        R package: CDLasso
• Lange, K. and Wu, T.T.$ (2008) An MM Algorithm for Multicategory Vertex Discriminant Analysis. Journal of Computational and Graphical Statistics, Volume 17, No 3, 527-544.
        Fortran 90 program and example
        R package: VDA
• Liu, H. and Wu, T.T. (2008) Sample Size Calculation and Power Analysis of Changes in Mean Response over Time. Communications in Statistics – Simulation and Computation, Volume 37, No 9, 1785-1798.
• Liu, H. and Wu, T.T. (2005) Sample Size Calculation and Power Analysis of Time-Averaged Difference. Journal of Modern Applied Statistical Methods, Volume 4, No 2, 434-445.
• Liu, H., Li, G., Cumberland, W.G., and Wu, T.T. (2005) Testing Statistical Significance of the Area under A Receiving Operating Characteristics Curve for Repeated Measures Design with Bootstrapping. Journal of Data Science, Volume 3, No 3, 257-278.
• Liu, H. and Wu, T.T. (2003) Estimating the Area under A Receiver Operating Characteristic (ROC) Curve for Repeated Measures Design. Journal of Statistical Software, Volume 8, Issue 12, 1-18.

Collaborative Papers

• Young, D.R., Cohen, D., Koebnick, C., Mohan, Y., Saksvig, B.I., Sidell, M., and Wu, T.T. Longitudinal Associations of Physical Activity Among Females from Adolescence to Young Adulthood. Journal of Adolescent Health, accepted.
• Chen, W., Anokhina, V., Miller, B., Dieudonne, G., Abramowitz, M.K., Kashyap, R., Yan, C., Wu, T.T., Bentley, K., and Bushinsky, D.A. (2018) Patients with Advanced Chronic Kidney Disease and Vascular Calcification Have a Large Hydrodynamic Radius of Secondary Calciprotein Particles. Nephrology Dialysis Transplantation, 1-9.
• Groth, S.W., LaLonde, A.**, Wu, T.T., and Fernandez, I.D. (2018) Obesity candidate genes, gestational weight gain and body weight changes in pregnant women. Nutrition, Volume 48, 61-66.
• Xiao, J., Huang, X., Alkhers, N., Alzamil, H., Alzoubi, S., Wu, T.T., Castillo, D., Campbell, F., Harokopakis-Hajishengallis, E., Koo, H. (2018) Candida albicans and Early Childhood Caries: A Systematic Review and Meta-analysis. Caries Research, Volume 52(1-2), 102-112.
• Wang, B., Wang, H.-W., Guo, H., Anderson, E., Tang, Q., Wu, T.T., Falola, R., Smith, T., Andrews, P.M., and Chen, Y. (2017) Optical Coherence Tomography (OCT) and Computer-Aided Diagnosis (CAD) of a Murine Model of Chronic Kidney Disease (CKD). Journal of Biomedical Optics, Volume 22(12), 1-11.
• Meng, Y.**, Groth, S.W., Quinn, J., Bisognano, J.D., and Wu, T.T. (2017) An Exploration of Gene-Gene Interactions and Their Effects on Hypertension. International Journal of Genomics, Volume 2017, Article ID 7208318..
• Jaworski, J.P., Bryk, P., Brower, Z., Zheng, B., Hessell, A.J., Rosenberg, A.F., Wu, T.T., Sanz, I., Keefer, M.C., Haigwood, N.L., and Kobie, J.J. (2017) Pre-Existing Neutralizing Antibody Mitigates B cell Dysregulation and Enhances the Env-Specific Antibody Response  in SHIV-Infected Rhesus Macaques. PLoS One, 12(2):e0172524.
• Abu-Farsakh, S., Wu, T.T., Lalonde, A.**, Sun, J., and Zhou, Z. (2017) High expression of the Claudin-2 in esophageal carcinoma and precancerous lesions is significantly associated with the bile salt receptors VDR and TGR5. BMC Gastroenterology, 17:33.
• Pang, C., Lalonde, A.**, Godfrey, T.E., Que, J., Da, J., Sun, J., Wu, T.T., and Zhou, Z. (2017) Bile salt receptor TGR5 is highly expressed in esophageal adenocarcinoma and precancerous lesions with significantly worse overall survival and gender differences. Clinical and Experimental Gastroenterology, Volume 10, 29-37.
• Tang, Q., Wang, J., Frank, A., Lin, J., Li, Z., Chen, C.W., Jin, L., Wu, T.T., Greenwald, B.D., Mashimo, H., and Chen, Y. (2016) Depth-resolved imaging of colon tumor using optical coherence tomography and fluorescence laminar optical tomography. Biomedical Optics Express, Volume 7, 5218-5232.
• Ramirez, G., Proctor, A.R., Jung, K.W., Wu, T.T., Han, S., Adams, R.R., Ren, J., Byun, D.K., Madden, K.S., Brown, E.B., Foster, T.H., Farzam, P., Durduran, T., and Choe, R. (2016) Chemotherapeutic drug-specific alteration of microvascular blood flow in murine breast cancer xenografts as measured by diffuse correlation spectroscopy. Biomedical Optics Express, Volume 7, Issue 9, 3610-3630.
• Choy, B., Lalonde, A.**, Taboada, S., Wu, T.T., and Zhou, Z. (2016) MCM4 and MCM7, Potential Novel Proliferation Markers, Significantly Correlated with Ki67, Bmi1, and Cyclin E Expression in Esophageal Adenocarcinoma, Squamous Cell Carcinoma, and Precancerous Lesions. Human Pathology, Volume 57, 126-135.
• Huber, A.R., Tan, D., Sun, J., Dean, D., Wu, T.T., and Zhou, Z. (2015) High expression of carbonic anhydrase IX is significantly associated with glandular lesions in gastroesophageal junction and with tumorigenesis markers BMI1, MCM4 and MCM7. BMC Gastroenterology, 15:80.
• Grant, E.**, Young, D.R.*, and Wu, T.T.* (2015) (*: joint senior authors) Predictors for Physical Activity in Adolescent Girls Using Statistical Shrinkage Techniques for Hierarchical Longitudinal Mixed Effects Models. PLOS ONE, 10(4): e0125431.
• Zook, K.R., Saksvig, B.I.,Wu, T.T., and Young, D.R. (2014) Physical Activity Trajectories and Multi-Level Factors among Adolescent Girls. Journal of Adolescent Health, Volume 54, No 1, 74-80.
• Young, D.R., Saksvig, B.I., Wu, T.T., Zook, K., Li, X.**, Champaloux, S., Grieser, M., Lee, S., and Treuth, M. (2014) Multilevel Correlates of Physical Activity For Early, Mid, and Late Adolescent Girls. Journal of Physical Activity & Health, Volume 11, No 5, 950-960.
• Gong, H.*, Wu, T.T.*$, and Clarke, E. (2014) (*: joint first authors) Pathway-Gene Identification for Pancreatic Cancer Survival via Doubly Regularized Cox Regression. BMC Systems Biology, Volume 8 (Suppl 1):S3.
• Morrison, S., Shenassa, E., Mendola, P., Wu, T.T., and Schoendorf, K. (2013) Allostatic load may not be associated with chronic stress in pregnant women, NHANES 1999-2006. Annals of Epidemiology, Volume 23, 294-297.
• Young, D.R., Camhi, S., Wu, T.T., Hagberg, J., and Stefanick, M.L. (2013) Relationships Among Changes in C-Reactive Protein and Cardiovascular Disease Risk Factors With Lifestyle Interventions. Nutrition, Metabolism & Cardiovascular Diseases, Volume 23, 857-
  863.
• Wu, T.T., Gong, H., and Clarke, E. (2011) A Transcriptome Analysis by Lasso Penalized Cox Regression for Pancreatic Cancer Survival. Journal of Bioinformatics and Computational Biology, Volume 9, Suppl. 1, 1-11.
• Hamza, M., Wang, X.M., Wu, T.T., Jaber, L., Brahim, J.S., Rowan, J.S., and Dionne, R.A. (2010) Nitric Oxide is Negatively Correlated to Pain During Acute Inflammation. Molecular Pain, Volume 6, No 55.
• Saligan, L.N., Levy-Clarke, G., Wu, T.T., Faia, L.J., Wroblewski, K., Yeh, S., Nussenblatt, R.B., and Sen, H.N. (2010) Quality of Life in Sarcoidosis: Comparing the Impact of Ocular and Non-Ocular Involvement of the Disease. Ophthalmic Epidemiology, Volume 17, No 4, 217-224.
• Park, C.C., Ahn, S., Bloom, J.S., Lin, A., Wang, R.T., Wu, T.T., Sekar, A., Khan, A.H., Farr, C.J., Lusis, A.J., Leahy, R.M., Lange, K., and Smith, D. (2008) Fine mapping of regulatory loci for mammalian gene expression using radiation hybrids. Nature Genetics, Volume 40, No 4, 421-429.
        Supplementary information
• Liu, H., Miller, L.G., Golin, C.E., Hays, R.D., Wu, T.T., Wenger, N.S., and Kaplan, A.H. (2007) Repeated Measures Analyses of Dose Timing of Antiretroviral Medication and its Relationship to HIV Virologic Outcomes. Statistics in Medicine, Volume 26, No 5, 991-1007.
• Liu, H., Miller, L.G., Hays, R.D., Golin, C.E., Wu, T.T., Wenger, N.S., and Kaplan, A.H. (2006) Repeated Measures Longitudinal Analyses of HIV Virologic Response as A Function of Percent Adherence, Dose Timing, Genotypic Sensitivity, and Other Factors. Journal of Acquired Immune Deficiency Syndromes, Volume 41, No 3, 315-322.