#### New Book "Bayesian Designs for Phase I-II Clinial Trials" with my colleagues Professor Peter Thall and Dr. Nguyen

(Chapman & Hall/CRC Biostatistics Series)

#### Selected Publications in Peer-reviewed Journals

(* supervised PhD students or postdocs)

**[Clinical Trial Design]**** [Missing Data] [Mediation Analysis]**

*Clinical Trial Design*

Chu, Y.* and **Yuan, Y.** (2018) BLAST: Bayesian Latent Subgroup Design for Basket Trials Accounting for Patient Heterogeneity. *Journal of the Royal Statistical Society: Series C*, 67, 723-740.

Chu, Y.* and **Yuan, Y.** (2018) A Bayesian Basket Trial Design Using Calibrated Bayesian
Hierarchical Model. *Clinical Trials*, 15, 149-158.

Liu, S., Guo, B. and **Yuan, Y.** (2018) A Bayesian Phase I/II Design for Immunotherapy Trials. *Journal of the American Statistical Association*, to appear.

Riviere, M.K., **Yuan, Y.**, Jourdan, J.H., Dubois, F. and Zohar, S. (2017) Phase I/II Dose-Finding Design for Molecularly Targeted Agent: Plateau Determination using Adaptive Randomization. * Statistical Methods in Medical Research*, to appear.

Murray, T.*, **Yuan, Y**., Thall, P., Elizondo, JH. and Hofstetter, WL. (2017) A Bayesian Utility-Based Stratified Medicine Design for the Effectiveness of Nutritional Prehabilitation in Thoracic Surgery. *Biometrics*, to appear.

Murray, T.*, **Yuan, Y**. and Thall, P. (2017) A Bayesian Machine Learning Method for Optimizing Dynamic Treatment Regimes. *Journal of the American Statistical Association*, to appear.

Yan, F., Mandrekar, SJ. and **Yuan, Y.** (2017) Keyboard: A Novel Bayesian Toxicity Probability Interval Design for Phase I Clinical Trials. * Clinical Cancer Research*, 23, 3994-4003.

Zhou, H.*, Lee, JJ. and **Yuan, Y.** (2017) BOP2: Bayesian Optimal Design for Phase II
Clinical Trials with Simple and Complex Endpoints. *Statistics in Medicine *, 36, 3302-3314.

Pan, H.* and **Yuan, Y.** (2017) A Calibrated Power Prior Approach to Borrow Information from Historical Data with Application to Biosimilar Clinical Trials. *Journal of the Royal Statistical Society: Series C *, 66, 979-996.

Guo, B.* and **Yuan, Y.** (2017) Bayesian Phase I/II Biomarker-based Dose Finding for Precision Medicine with Molecularly Targeted Agents. *Journal of the American Statistical Association*, 112, 508-520.

Murray, T.*, Thall, P., **Yuan, Y**., McAvoy, S. and Gomez, D. (2017) Robust treatment comparison based on utilities of semi-competing risks in non-small-cell lung cancer. *Journal of the American Statistical Association*, 112, 11-23.

Zang, Y.* and **Yuan, Y.** (2017) Optimal Sequential Enrichment Designs for Phase II Clinical Trials. * Statistics in Medicine*, 36, 54-66.

**Yuan, Y.**, Hess, K., Hilsenbeck, S. and Gilbert, M. (2016) Bayesian Optimal Interval Design: A Simple and Well-Performing Design for Phase I Oncology Trials. * Clinical Cancer Research*, 22, 4291-430.

**Yuan, Y.**, Guo, B, Munsell, M., Lu, K. and Jazzari, A. (2016) MIDAS: a practical Bayesian design for platform trials with molecularly targeted agents. *Statistics in Medicine*, 35, 3892-3906.

Zang, Y.*, Liu, S. and **Yuan, Y.** (2016) Optimal Marker-strategy Clinical Trial Design to Detect Predictive Markers for Targeted Therapy. *Biostatistics*, 17, 549-560.

Zhang, L.* and **Yuan, Y.** (2016) A Practical Bayesian Design to Identify the Maximum Tolerated Dose Contour for Drug Combination Trials. * Statistics in Medicine*, 35, 4924-4936.

Riviere, M.K.*,** Yuan, Y.**, Jourdan, J.H., Dubois, F. and Zohar, S. (2016) Phase I/II Dose-Finding Design for Molecularly Targeted Agent: Plateau Determination using Adaptive Randomization. *Statistical Methods in Medical Research*, to appear

Chu, Y.*, Pan, H. and **Yuan, Y.** (2016) Adaptive dose modification for phase I clinical trials. *Statistics in Medicine*, 35, 3497-508.

Iasonos, A. , Wages N., Conaway, M., Cheung, K., **Yuan, Y.** and O’Quigley, J. (2016) Dimension of Model Parameter Space and Operating Characteristics in Adaptive Dose-Finding Studies. *Statistics in Medicine*, 35, 3760-3775.

Pan, H.* and **Yuan, Y. **(2016) A Default Method to Specify Skeletons for Bayesian Model Averaging Continual Reassessment Method for Phase I Clinical Trials. *Statistics in Medicine*, 36, 266-279.

Zang, Y.*, J. Lee and **Yuan, Y.** (2016) Two-stage marker-stratified clinical trial design in the presence of biomarker misclassification. *Journal of the Royal Statistical Society: Series C*, 65, 585-601.

Guo, B., Li, Y. and **Yuan, Y.** (2016) A dose-schedule-finding design for phase I/II clinical trials. *Journal of the Royal Statistical Society: Series C*, 65, 259-272.

Chen, Z., **Yuan, Y.**, Li, Z., Kutner, M., Owonikoko, T., Curran, W, Khuri, F. and Kowalski, J. (2015) Dose escalation with over-dose and under-dose controls in phase I/II clinical trials.* Contemporary Clinical Trials*, 43, 133-141.

Shen, W.*, Ning, J. and **Yuan, Y**. (2015) Bayesian sequential monitoring design for clinical trials with non-compliance *Statistics in Medicine*, 34, 2104-2115.

Zang, Y.*, Liu, S. and **Yuan, Y.** (2015) Optimal Marker-Adaptive Designs for Targeted Therapy Based on Imperfectly Measured Biomarkers. *Journal of the Royal Statistical Society: Series C*, 64, 635-650.

Liu, S. and **Yuan, Y.** (2015) Bayesian Optimal Interval Designs for Phase I Clinical Trials. *Journal of the Royal Statistical Society: Series C*, 64, 507-523.

Guo, B. and **Yuan, Y.** (2015) A Bayesian Design for Phase I/II Clinical Trials with Nonignorable Dropout.* Statistics in Medicine*, 34, 1721-1732.

Shen, W.*, Ning, J. and **Yuan, Y**. (2015) A Direct Method to Evaluate the Time-dependent Predictive Accuracy for Biomarkers.* Biometrics*, 71, 439-449.

Liu, S., Pan, H., Huang Q., Xia, J. and **Yuan, Y.** (2015) Bridging Continual Reassessment Method for Phase I Clinical Trials in Different Ethnic Populations. *Statistics in Medicine*, 10, 1681-1694.

Riviere, M.K.*, **Yuan, Y.**, Dubois, F. and Zohar, S. (2015) A Bayesian Dose-finding Design for Clinical Trials Combining a Cytotoxic Agent with a Molecularly Targeted Agent. *Journal of the Royal Statistical Society: Series C*, 64, 215-229.

Jin, I.H.*, Liu, S., Thall, P. and **Yuan, Y.** (2014) Using Data Augmentation to Facilitate Conduct of Phase I/II Clinical Trials with Delayed Outcomes. *Journal of the American Statistical Association*, 109, 525-536.

Riviere M.K., ** Yuan Y. **, Dubois F. and Zohar S. (2014) A Bayesian dose-finding design for drug combination clinical trials based on the logistic model. * Pharmaceutial Statistics*, 13, 247-257.

Zang, Y.*, Lee J. and **Yuan, Y.** (2014) Adaptive designs for identifying optimal biological dose for molecularly targeted agents. *Clinical Trials*,
11, 319-327.

Cai, C.*, Liu, S. and **Yuan, Y.** (2014) A Bayesian Design for Phase II Clinical Trials with Delayed Responses Based on Multiple Imputation. *Statistics in Medicine*, 33, 4017-4028.

Liu, S., **Yuan, Y.** , Castillo, R., Guerrero, T. and Johnson, V.E. (2014) Evaluation of Deformable Image Registration Spatial Accuracy Using a Bayesian Hierarchical Model. *Biometrics*, 70, 366-377.

Cai, C.*, **Yuan, Y.** and Ji, Y. (2014) A Bayesian Phase I/II Design for Oncology Clinical Trials of Combining Biological Agents. *Journal of the Royal Statistical Society: Series C*, 63, 159-173.

Liu, S., Yin, G. and **Yuan, Y.** (2013) Bayesian Data Augmentation Dose Finding with Continual Reassessment Method and Delayed Toxicity. *Annals of Applied Statistics*, 4, 2138-2156.

Ahn, J.*, **Yuan, Y.**, Parmigiani, G., Suraokar, M. B., Diao, L., Wistuba, I. and Wang W. (2013) DeMix: Deconvolution for mixed cancer transcriptomes using raw measured data. *Bioinformatics*, 29, 1865-1871.

Cai, C.*, **Yuan, Y.** and Johnson, V.E. (2013) Bayesian adaptive phase II screening design for combination trials. *Clinical Trials*, 10, 353-362.

Jin, I.H.*, **Yuan, Y.** and Liang, F. (2013) Bayesian analysis for exponential random graph models using the adaptive exchange sampler. *Statistics and Its Interface*, 6, 559-576.

Zang, Y*. and **Yuan, Y.** (2013) A Shrinkage Method for Testing the Hardy-Weinberg Equilibrium in Case-Control Studies. *Genetic Epidemiology*, 37, 743-750.

**Yuan, Y.**, Thall, P. andWolf, J. (2012) Estimating Progression-free Survival When the Progression Status of Some Subjects is Unknown. *Journal of the Royal Statistical Society: Series C*, 61, 135-149.

**Yuan, Y.** and Johnson, V.E. (2012) Goodness-of-Fit Diagnostics for Bayesian Hierarchical Models. *Biometrics* 68, 156-164.

Huo, L.*, **Yuan, Y.** and Yin, G. (2012) Dose Finding in Drug Combinations with Discrete and Continuous Doses. *Bayesian Analysis*, 7, 235-252.

**Yuan, Y.** and Yin, G. (2011) Robust EM Continual Reassessment Method in Oncology Dose Finding.* Journal of the American Statistical Association* 106, 818-831. (**featured article**)

Lei, X., **Yuan, Y.** and Yin, G. (2011) Bayesian phase II adaptive randomization by jointly modeling time-to-event efficacy and binary toxicity. *Lifetime Data Analysis* 17, 156-174.

**Yuan, Y.** and Yin, G. (2011) Bayesian phase I/II drug-combination trial design in oncology. *Annals of Applied Statistics*, 5, 924-942.

**Yuan, Y.** and Yin, G. (2011) Bayesian Hybrid Design in Phase I Oncology Clinical Trials. *Statistics in Medicine*, 30, 2098-2108.

**Yuan, Y.**, Huang, X. and Liu, S. (2011) A Bayesian response-adaptive covariate-balanced
randomization design for clinical trials. *Statistics in Medicine*, 30, 1218-1229.

**Yuan, Y.** and Yin, G. (2011) On adaptive randomization: is it useful? *Journal of Clinical Oncology*, 29, e390-e392

Yin, G., Ma, Y., Liang, F. and **Yuan, Y.** (2011) Stochastic generalized method of moments. *Journal of Computational and Graphical Statistics* 20, 714-727.

**Yuan, Y.** and Yin, G. (2011) Dose-response curve estimation: A semiparametric mixture approach. *Biometrics* 67, 1543-1554.

Yin, G. and **Yuan, Y.** (2009) Bayesian Model Averaging Continual Reassessment Method
in Phase I Clinical Trials.* Journal of the American Statistical Association* 104, 954-968.

Song P.X., Li, M. and **Yuan, Y.** (2009) Joint Regression Analysis of Correlated Data Using Gaussian Copulas. *Biometrics* 65, 60-68.

Yin, G. and **Yuan, Y.** (2009) A latent contingency table approach to dose-finding for combinations of two agents. *Biometrics* 65, 866-875.

Yin, G. and **Yuan, Y.** (2009) Bayesian Dose-finding in Oncology for Drug Combinations by Copula Regression. *Journal of the Royal Statistical Society: Series C* 58, 211-224.

**Yuan, Y.** and Yin, G. (2009) Bayesian Dose-finding by Jointly Modeling Toxicity and Efficacy
as Time-to-Event Outcomes. *Journal of the Royal Statistical Society: Series C* 58, 719-736.

**Yuan, Y.** and Johnson, V.E. (2008) Bayesian Hypothesis Tests Using Nonparametric Statistics. *Statistica Sinica* 18, 1185-1200

**Yuan, Y.** and Yin, G. (2008) Sequential Continual Reassessment Method for Two-dimensional Dose Finding. *Statistics in Medicine* 27, 5664-5678.

*Missing Data Analysis*

Ahn, J.*, Liu, S., Wang W. and **Yuan, Y.** (2013) Bayesian Latent-class Mixed-effect Hybrid Models for Dyadic Longitudinal Data with Non-ignorable Dropouts. *Biometrics*, 69, 914-924.

Zhang G. and **Yuan, Y.** (2012) Modeling Longitudinal Dyadic Data with Nonignorable Dropout with Application to a Breast Cancer Study. *Annals of Applied Statistics*, 6, 753-771.

**Yuan, Y.** and Yin, G. (2010). Quantile regression for longitudinal studies with nonignorable missing data. *Biometrics*, 66, 105-114.

**Yuan, Y.** and Little, R.J.A. (2009) Meta-analysis of studies with missing data. *Biometrics* 65, 487-496.

**Yuan, Y.** and Little, R.J.A. (2009) Mixed-effect hybrid models for longitudinal data with nonignorable dropout. *Biometrics* 65, 478-486.
**Yuan, Y.**, and Little, R.J.A. (2007) Model-Based Estimates of the Finite Population Mean for
Two-Stage Cluster Samples with Unit Non-response. *Journal of the Royal Statistical Society: Series C* 56, 79-97.

**Yuan, Y.**, and Little, R.J.A. (2007) Parametric and Semiparametric Model-based Estimates of the Finite Population Mean for Two-Stage Cluster Samples with Item Nonresponse. *Biometrics* 63, 1172-1180.

*Mediation Analysis*

Huang, J.* and **Yuan, Y.** (2016) Bayesian Dynamic Mediation Analysis, *Psychological Methods*, to appear.

**Yuan, Y.** and MacKinnon D. (2014) Robust mediation analysis based on mediation regression. *Psychological Methods*, 19, 1-20.

**Yuan, Y.** and MacKinnon D. (2009) Bayesian mediation analysis. *Psychological Methods*, 14, 301-322.