R packages and related source code are at github.com/sdzhao.

Preprints (* denotes PhD student):

1. Barbehenn*, A. and Zhao, S.D.
   A nonparametric regression approach to asymptotically optimal estimation of normal means.
   arxiv:2205.00336
2. Barbehenn*, A. and Zhao, S.D.
   Nonparametric empirical Bayes biomarker imputation and estimation.
   arxiv:2306.07239
3. Wang*, Y. and Zhao, S.D.
   Linear shrinkage for predicting responses in large-scale multivariate linear regression.
   arxiv:2104.08970

Published (* denotes PhD student):

1. Rong, Y., Zhao, S.D., Zheng, S., and Li, Y. (2023).
   Kernel Cox partially linear regression: building predictive models for cancer patients' survival.
   Statistics in Medicine, in press.
2. Traniello, I.M., Bukhari, S.A., Dibaeinia, P., Serrano, G., Avalos, A., Cash Ahmed, A., Sankey, A.L., Hernaez, M., Sinha, S., Zhao, S.D., Catchen, J., and Robinson, G.E. (2023).
   Single-cell dissection of aggression in honeybee colonies.
   Nature Ecology & Evolution, 7, 1232–1244.
3. Zhou*, R., Zucker, D.M., and Zhao, S.D. (2023).
   Power of testing for exposure effects under incomplete mediation.
   International Journal of Biostatistics, in press.
4. Blatti, C., de la Fuente Cedeño, J., Gao, H., Marín-Goñi, I., Chen, Z., Zhao, S.D., Tan, W., Weinshilboum, R., Kalari, K.R., Wang, L., and Hernaez, M. (2023).
   Bayesian machine learning enables identification of transcriptional network disruptions associated with drug-resistant prostate cancer.
   Cancer Research, 83, 1361–1380.
5. Xin*, H. and Zhao, S.D. (2023).
   A nonparametric empirical Bayes approach to covariance matrix estimation.
   Biometrics, 79, 1201–1212.
6. Taylor, A.J., Cardenas-Torres*, E., Miller, M.J., Zhao, S.D., and Engeseth, N.J. (2022).
   Microbes associated with spontaneous cacao fermentations -- a systematic review and meta-analysis.
   Current Research in Food Science, 5, 1452–1464.
7. Zhu, H., Zhao, S.D., Ray, A., Zhang, Y., and Li, X. (2022).
   A comprehensive temporal patterning gene network in Drosophila medulla neuroblasts revealed by single-cell RNA sequencing.
   Nature Communications, 13, 1247.
8. Zhou*, R., Zhao, S.D., and Parast, L. (2022).
   Estimation of the proportion of treatment effect explained by a high-dimensional surrogate.
   Statistics in Medicine, 41, 2227–2246.
9. Yin, W., Zhao, S.D., and Liang, F. (2022).
   Bayesian penalized Buckley-James method for high dimensional bivariate censored regression models.
   Lifetime Data Analysis, 28, 282–318.
10. Taneja, I., Damhorst, G., Lopez-Espina, C., Zhao, S.D., Zhu, R., Khan, S., White, K., Kumar, J., Vincent, A., Yeh, L, Majdizadeh, S., Weir, W., Isbell, S., Skinner, J., Devanand, M., Azharuddin, S., Meenakshisundaram, R., Upadhyay, R., Syed, A., Bauman, T., Devito, J., Heinzmann, C., Podolej, G., Shen, L., Timilsina, S., Quinlan, L., Manafirasi, S., Valera, E., Reddy Jr., B., and Bashir, R. (2021).
    Diagnostic and prognostic capabilities of a biomarker and EMR-based machine learning algorithm for sepsis.
    Clinical and Translational Science 14, 1578–1589.
11. Zhao, S. D. and Biscarri*, W. (2021).
    A regression modeling approach to structured shrinkage estimation.
    Journal of the American Statistical Association, 117, 1684–1694.
12. Wang*, Y. and Zhao, S. D. (2021).
    A nonparametric empirical Bayes approach to large-scale multivariate regression.
    Computational Statistics and Data Analysis 156, 107130.
13. Zhao, S. D. (2021).
    Simultaneous estimation of normal means with side information.
    Statistica Sinica, 31, 1571–1592.
14. Avalos, A., Fang, M., Pan, H., Lluch, A. R., Lipka, A. E., Zhao, S. D., Giray, T., Robinson, G. E., Zhang, G., and Hudson, M. E. (2020).
    Genomic regions influencing aggressive behavior in honey bees are defined by colony allele frequencies.
    Proceedings of the National Academy of Sciences 117, 17135–17141.
15. Zhao, S. D. and Nguyen, Y. T. (2020).
    Nonparametric false discovery rate control for identifying simultaneous signals.
    Electronic Journal of Statistics 14, 110–142.
16. Zhou*, R. R., Wang, L., and Zhao, S. D. (2020).
    Estimation and inference for the indirect effect in high-dimensional linear mediation models.
    Biometrika 107, 573–589.
    (An earlier version of this paper was a winner of a 2018 American Statistical Association Section of Statistics in Genomics and Genetics distinguished student paper award.)
17. Xiang, D., Zhao, S. D., and Cai, T. T. (2019).
    Signal classification for the integrative analysis of multiple sequences of multiple tests.
    Journal of the Royal Statistical Society, Series B 81, 707–734.
18. Saul, M.C., Blatti, C., Yang, W., Bukhari, S.A., Shpigler, H.Y., Troy, J.M., Seward, C.H., Sloofman, L., Chandrasekaran, S., Bell, A.M., Stubbs, L., Robinson, G.E., Zhao, S.D.†, and Sinha, S.† (2019).
    (†Co-corresponding authors)
    Cross‐species systems analysis of evolutionary toolkits of neurogenomic response to social challenge.
    Genes, Brain and Behavior 18, e12502.
19. Tabe-Bordbar, S., Emad, A., Zhao, S.D., and Sinha, S. (2018)
    A closer look at cross-validation for assessing the accuracy of gene regulatory networks and models.
    Scientific Reports 8, 6620.
20. Rong, Y., Zhao, S.D., Zhu, J., Yuan, W., Cheng, W., and Li, Y. (2018)
    More accurate semiparametric regression in pharmacogenomics.
    Statistics and its Interface 11, 573–580.
21. Hu, R., Morley, M.P., Brandimarto, J., Tucker, N.R., Parsons, V.A., Zhao, S.D., Meder, B., Katus, H.A., Rühle, F., Stoll, M., Villard, E., Cambien, F., Lin, H., Smith, N.L., Felix, J.F., Vasan, R.S., van der Harst, P., Newton-Cheh, C., Li, J., Kim, C. E., Hakonarson, H., Hannenhalli, S., Ashley, E.A., Moravec, C. S., Tang, W.H.W., Maillet, M., Molkentin, J.D., Ellinor, P.T., Margulies, K.B., and Cappola, T.P. (2018)
    Genetic reduction in left ventricular protein kinase C-α and adverse ventricular remodeling in human subjects.
    Circulation: Genomics and Precision Medicine 11, e001901.
22. Biscarri*, W., Zhao, S.D., and Brunner, R.J. (2018).
    A simple and fast method for computing the Poisson binomial distribution function.
    Computational Statistics and Data Analysis 122, 92–100.
23. Taneja, I., Reddy, B., Damhorst, G., Zhao, S.D., Hassan, U., Price, Z., Jensen, T., Ghonge, T., Patel, M., Wachspress, S., Winter, J., Rappleye, M., Smith, G., Healey, R., Ajmal, M., Anwaruddin, S., Khan, M., Patel, J., Rawal, H., Sarwar, R., Soni, S., Anwarudding, S., Davis, B., Kumar, J., White, K., Bashir, R., and Zhu, R. (2017).
    Combining biomarkers with EMR data to improve sepsis identification.
    Scientific Reports 7, 10800.
24. Zhao, S.D., Cai, T.T., and Li, H. (2017).
    Optimal detection of weak positive dependence between two sequences of multiple tests.
    Journal of Multivariate Analysis 160, 169–184.
25. Bukhari, S.A., Saul, M., Seward, C., Zhang, H., Bensky, M., James, N., Zhao, S.D., Chandrasekaran, S., Stubbs, L., and Bell, A. (2017).
    Temporal dynamics of neurogenomic plasticity in response to social interactions in male threespined sticklebacks.
    PLoS Genetics 13, e1006840.
26. Shpigler, H.Y., Saul, M.C., Corona, F., Block, L., Cash-Ahmed, A., Zhao, S.D., and Robinson, G.E. (2017).
    Deep evolutionary conservation of autism-related genes.
    Proceedings of the National Academy of Sciences 114, 9653–9658.
    (Reported in Science, The Times of London, Scotland's The Herald, IFLScience, and EurekAlert!)
27. Saul, M.C., Seward, C.H., Troy, J.M., Zhang, H., Sloofman, L.G., Lu, X., Weisner, P.A., Caetano-Anolles, D., Sun, H., Zhao, S.D., Chandrasekaran, S., Sinha, S., and Stubbs, L. (2017).
    Transcriptional regulatory dynamics drive coordinated metabolic and neural response to social challenge in mice.
    Genome Research 27, 959–972.
28. Zhao, S.D., Cai T.T., Cappola T.P., Margulies K.B., and Li H. (2017).
    Sparse simultaneous signal detection for identifying genetically controlled disease genes.
    Journal of the American Statistical Association 112, 1032–1046.
29. Zhao, S.D. (2017).
    Integrative genetic risk prediction using nonparametric empirical Bayes classification.
    Biometrics 73, 582–592.
30. Dicker, L.D. and Zhao, S.D. (2016).
    High-dimensional classification via nonparametric empirical Bayes and maximum likelihood.
    Biometrika 103, 21–34.
31. Yan, X., Hu, Z., Feng, Y., Hu, X., Yuan, J., Zhao, S.D., Zhang, Y., Yang, L., Shan, W., He, Q., Fan, L., Kandalaft, L.E., Tanyi, J.L., Li, C., Yuan, C.-X., Zhang, D., Yuan, H., Hua, K., Lu, Y., Katsaros, D., Huang, Q., Montone, K., Fan, Y., Coukos, G., Boyd, J., Sood, A.K., Rebbeck, T., Mills, G.B., Dang, C.V., and Zhang, L. (2015).
    Comprehensive genomic characterization of long non-coding RNAs across human cancers.
    Cancer Cell 28, 529–540.
32. Li, Y.R., Zhao, S.D., Mohebnasab, M., Li, J., Bradfield, J., Steel, L., Abrams, D., Kobie, J., Mentch, F., Glessner, J., Guo, Y., Wei, Z., Cardinale, C., Bakay, M., Connoly, J., Li, D., Maggadottir, S.M., Thomas, K.A., Qiu, H., Chiavacci, R., Kim, C., Wang, F., Snyder, J., Flatø, B., Førre, Ø., Denson, L., Thompson, S.D., Becker, M., Guthery, S.L., Latiano, A., Perez, E., Resnick, E., Strisciuglio, C., Staiano, A., Miele, E., Silverberg, M., Lie, B.A., Punaro, M., Russell, R., Wilson, D., Dubinsky, M.C., Monos, D.S., Annese, V., Munro, J., Wise, C., Chapel, H., Cunningham-Rundles, C., Orange, J., Behrens, E.M., Sullivan, K., Kugathasan, S., Griffiths, A., Satsangi, J., Grant, S., Sleiman, P., Finkel, T., Polychronakos, C., Baldassano, R.N., Luning Prak, E., Ellis, J., Li, H., Keating, B.J., and Hakonarson, H. (2015).
    Genetic sharing and heritability of pediatric age of onset autoimmune diseases.
    Nature Communications 6, 8442.
33. Li, Y.R., Li, J., Zhao, S.D., Bradfield, J.P., Mentch, F.D., Maggadottir, S.M., Hou, C., Abrams, D.J., Chang, D., Gao, F., Guo, D., Wei, Z., Connoly, J.J., Cardinale C., Bakay, M., Glessner, J.and Kao, C., Thomas, K.A., Qiu, H., Chiavacci, R., Kim, C., Wang, F., Snyder, J.and Richie, M.D., Flatø, B., Førre, Ø., Denson, L., Thompson, S.D., Becker, M.L., Guthery, S.L., Latiano, A., Perez, E., Resnick, E., Russell, R.D., Wilson, D., Silverberg, M.S., Annese, V., Lie, B.A., Punaro, M., Dubinsky, M.C., Monos, D.S., Strisciuglio, C., Staiano, A., Miele, E., Kugathasan, S., Ellis, J.A., Munro, J., Sullivan, K., Wise, C., Chapel, H., Cunningham-Rundles, C., Grant, S.F.A., Orange, J., Sleiman, P.M.A., Behrens, E., Griffiths, A., Satsangi, J., Finkel, T., Keinan, A., Luning Prak, E.T., Polychronakos, C., Baldassano, B., Li, H., Keating, B.J., and Hakonarson, H. (2015).
    Meta-analysis of shared genetic architecture in pediatric autoimmune disease.
    Nature Medicine 9, 1018–1027.
34. Hu, X., Feng, Y., Zhang, D., Zhao, S.D., Hu, Z., Greshock, J., Zhang, Y., Yang, L., Zhong, X., Wang, L.-P., Jean, S., Li, C., Huang, Q., Katsaros, D., Montone, K., Tanyi, J.L., Lu, Y., Boyd, J., Nathanson, K.L., Li, H., Mills, G.B., and Zhang, L. (2014).
    A functional genomic approach identifies FAL1 as an oncogenic long noncoding RNA that associates with BMI1 and represses p21 expression in human cancer.
    Cancer Cell 26, 344–357.
35. Zhao, S.D., Parmigiani, G., Huttenhower, C., and Waldron, L. (2014).
    Más-o-menos: a simple sign averaging method for discrimination in genomic data analysis.
    Bioinformatics 30, 3062–3069.
36. Zhao, S.D. and Li, Y. (2014).
    Score test variable screening.
    Biometrics 70, 862–871.
37. Zhao, S.D., Cai, T.T., and Li, H. (2014).
    More powerful genetic association testing via a new statistical framework for integrative genomics.
    Biometrics 70, 881–890.
38. Zhao, S.D., Cai, T.T., and Li, H. (2014).
    Direct estimation of differential networks.
    Biometrika 101, 253–268.
39. Li, Y., Dicker, L., and Zhao, S.D. (2014).
    The Dantzig selector for censored linear regression models.
    Statistica Sinica 24, 251–268.
40. Limaye, S., Riley, S., Zhao, S.D., O'Neill, A., Posner, M., Adkins, D., Jaffa, Z., Clark, J., and Haddad, R. (2013).
    A randomized phase II study of docetaxel with or without vandetanib in recurrent or metastatic squamous cell carcinoma of head and neck (SCCHN).
    Oral Oncology 49, 835–841.
41. Nardi, V., Sadow, P.M., Juric, D., Zhao, S.D., Cosper, A.K., Bergethon, K., Scialabba, V.L., Batten, J.M., Borger, D.R., Iafrate, A.J., Heist, R.S., Lawrence, D.P., Flaherty, K.T., Bendell, J.C., Deschler, D., Li, Y., Wirth, L.J., and Dias-Santagata, D. (2013).
    Detection of novel actionable genetic changes in salivary duct carcinoma helps direct patient treatment.
    Clinical Cancer Research 19, 480–490.
42. Zhao, S.D. and Li, Y. (2012).
    Principled sure independence screening for Cox models with ultra-high-dimensional covariates.
    Journal of Multivariate Analysis 105, 397–411.
43. Stryjewski, T.P., Benadretti, D.B., Zhao, S.D., Rowe, S., and Mitnick, C.D. (2011).
    Preliminary clinical outcomes from the Peruvian National Cataract Elimination Plan.
    Revista Panamericana de Salud Publica 28, 282–288.
44. Goguen, L.A., Chapuy, C.I., Li, Y., Zhao, S.D., and Annino, D.J. (2010).
    Neck dissection after chemoradiation: timing and complications.
    Archives of Otolaryngology - Head and Neck Surgery 136, 1071–1077.
45. Zhao, S.D. and Li, Y. (2009).
    A note on optimal weights and variable selections for multivariate survival data.
    Science in China, Series A 52, 1131–1133.
46. Janket, S.J., Bollu, P., and Zhao, S.D. (2008).
    Questionable performance of a questionnaire.
    Journal of Dental Research 87: e1.