Publications

$: (joint) lead/senior/corresponding author; #: leader of statistical analyses; **: advisee/trainee

Book Chapters

• Gong, H.$, Wu, T.T.$*, and Clarke, E. (2014) (*: corresponding author) 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/Bioinformatic Papers

• Chang, J., Chen, S., Tang, C.Y., and Wu, T.T. (2020) (alphabetic order) High-Dimensional Empirical Likelihood Inference. Biometrika, accepted.
        R code of a toy example: demo_rev
• Wang, D., Wu, T.T., and Zhao, Y. (2019) Penalized Empirical Likelihood for the Sparse Cox Regression Model. Journal of Statistical Planning and Inference, Volume 201, 71-85.
• Ciminelli, J.T.**, Love, T., and Wu, T.T.$ (2019) Social Network Spatial Model. Spatial Statistics, Volume 29, 129-144.
• 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(6B), 3185-3216.
• 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.
• 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. The 14th International Conference on Mobile Systems, Applications, and Services (MobiSys'16), 235-248.
• Fang, H.-B., Wu, T.T.$, Rapoport, A.P., and Tan, M. (2016) Survival Analysis with Functional Covariates for Partial Follow-up Studies. Statistical Methods in Medical Research, Volume 25(6), 2405-2419.
• Wu, T.T.$ and Lange, K. (2015) Matrix Completion Discriminant Analysis. Computational Statistics and Data Analysis, Volume 92, 115--125.
• Wu, T.T.$, Li, G., and Tang, C.Y. (2015) Empirical Likelihood for Censored Linear Regression and Variable Selection. Scandinavian Journal of Statistics, Volume 42, No 3, 798--812.
        Supplementary File: Proofs of Theorems
• Costello, J. C., ..., NCI DREAM Community, ..., and Stolovitzky, G. (2014) A community effort to assess and improve drug sensitivity prediction algorithms. Nature Biotechnology, Volume 32, 1202--1212.
• Gong, H.$, Wu, T.T.$*, and Clarke, E. (2014) (*: corresponding author) Pathway-Gene Identification for Pancreatic Cancer Survival via Doubly Regularized Cox Regression. BMC Systems Biology, Volume 8 (Suppl 1):S3.
• Chen, S., Grant, E.**, Wu, T.T., and Bowman, F. D. (2014) Some Recent Statistical Learning Methods for Longitudinal High-dimensional Data. WIREs Computational Statistics, Volume 6, No 1, 10-18.
• Tang, C.Y. and Wu, T.T.$ (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.$, Gong, H., and Clarke, E. (2011) A Transcriptome Analysis by Lasso Penalized Cox Regression for Pancreatic Cancer Survival. Journal of Bioinformatics and Computational Biology, Volume 9, Suppl. 1, 1-11.
• Wu, T.T.$ 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
• 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. 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

• Krieger, N.S., Asplin, J., Granja, I., Chen, L., Spataru, D., Wu, T.T.#, Grynpas, M., and Bushinsky, D.A. (2020) Chlorthalidone with Potassium Citrate Decreases Calcium Oxalate Stones and Increases Bone Quality in Hypercalciuric Stone-Forming Rats. Kidney International, accepted.
• Chen, W.**, Fitzpatrick, J., Sozio, S.M., Jaar, B.G., Estrella, M.M., Riascos-Bernal, D.F., c, Qiu, Y., Kurland, I.J., Dubin, R.F., Chen, Y., Parekh, R.S., Bushinsky, D.A., and Sibinga, N. (2020) Identification of Novel Biomarkers and Pathways for Coronary Artery Calcification in Non-diabetic Patients on Hemodialysis. Kidney360, accepted.
• Ramchandren, S., Wu, T.T.#, Finkel, R., Siskind, C., Feely, S., Burns, J.,  Reilly, M., Estilow, T., Shy, M., Bacon, C., Shy, R., Cornett, K., Muntoni, F., Day, J., Lloyd, T., Sumner, C., Herrmann, D., Kirk, C., Yum, S. (2021) Development and Validation of the Pediatric CMT Quality of Life Outcome Measure. Annals of Neurology, Volume 89, 369-379.
• Koebnick, C., Saksvig, B.I., Li, X., Sidell, M., Wu, T.T.#, and Young, D.R. (2020) The Accuracy of Self-Reported Body Weight Is High but Dependent on Recent Weight Change and Negative Affect in Teenage Girls. International Journal of Environmental Research and Public Health, Volume 17(21), 8203.
• Ren, J., Ramirez, G.A., Proctor, A.R., Wu, T.T.#, Benoit, D., and Choe, R. (2020) Spatial Frequency Domain Imaging for Longitudinal Monitoring of Vascularization during Mouse Femoral Graft Healing. Biomedical Optics Express, Volume 11(10), 5442-5455.
• Xiao, J., Fogarty, C., Wu, T.T.#, Alkhers, N., Zeng, Y., Thomas, M., Youssef, M., Wang, L., Cowens, L., Abdelsalam, H., and Nikitkova, A. (2019) Oral health and Candida carriage in socioeconomically disadvantaged US pregnant women. BMC Pregnancy and Childbirth, Volume 19, Article number: 480.
• Meng, Y., Wu, T.T., Billings, R., Kopycka-Kedzierawski, D.T., and Xiao, J. (2019) Human genes influence the interaction between Streptococcus mutans and host caries susceptibility: a genome-wide association study in children with primary dentition. International Journal of Oral Science, Volume 11(2), Article number: 19.
• Krieger, N.S., Asplin, J., Granja, I., Ramos, F.M., Flotteron, C., Chen, L., Wu, T.T.#, Grynpas, M., and Bushinsky, D.A. (2019) Chlorthalidone Is Superior to Potassium Citrate in Reducing Calcium Phosphate Stones and Increasing Bone Quality in Hypercalciuric Stone-Forming Rats. Journal of the American Society of Nephrology, Volume 30(7), 1163-1173.
• Chen,W.**, Fitzpatrick, J., Monroy-Trujillo, J., Sozio, S., Jaar, B., Estrella, M., Wu, T.T.#, Melamed, M., Parekh, R., and Bushinsky, D.A. (2019) Diabetes Mellitus Modifies the Associations of Serum Magnesium Concentration with Arterial Calcification and Stiffness in Incident Hemodialysis Patients. Kidney International Reports, Volume 4(6), 806-813.
• Konkel, B., Lavin, C., Wu, T.T.#, Anderson, E., Iwamoto, A., Rashid, H., Gaitian, B., Boones, J., Cooper, M., Abrams, P., Gilbert, A., Tang, Q., Levi, M., Fujimoto, J.G., Andrews, P., and Chen, Y. (2019) Fully Automated Analysis of OCT Imaging of Human Kidneys for Prediction of Post-transplant Function. Biomedical Optics Express, Volume 10(4), 1794-1821.
• Young, D.R., Sidell, M., Koebnick, C., Saksvig, B.I., Mohan, Y., Cohen, D., and Wu, T.T.#$ (2019) Longitudinal Sedentary Time among Females from Ages 17 to 23 Years. American Journal of Preventive Medicine, Volume 56(4), 540-547.
• Xiao, J., Alkhers, N., Kopycka-Kedzierawski, D.T., Billings, R., Wu, T.T.#, Castillo, D., Rasubala, L., Malmstrom, H., Ren, Y., and Eliav, E. (2019) Prenatal Oral Health Care and Early Childhood Caries Prevention: A Systematic Review and Meta-analysis. Caries Research, Volume 53(4), 411-421.
• Lee, C.Y., Robinson, D.A., Johnson, C.A., Zhang, Y.**, Wong, J., Joshi, D.J., Wu, T.T.#, and Knight, P.A. (2019) A Randomized Controlled Trial of Liposomal Bupivacaine Parasternal Intercostal Block for Sternotomy. Annals of Thoracic Surgery, Volume 107(1), 128-134.
• Young, D.R., Cohen, D., Koebnick, C., Mohan, Y., Saksvig, B.I., Sidell, M., and Wu, T.T.#$ (2018) Longitudinal Associations of Physical Activity Among Females from Adolescence to Young Adulthood. Journal of Adolescent Health, Volume 63(4), 466-473.
• 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, Volume 34(6), 992-1000.
• 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.
• 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, Issue 9, 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(9), 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.