Publications

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Presentation
Hung, H M. James. Utilities and challenges of adaptive designs in drug development., 2011.
Bretz, F. Tutorial: Introduction to Multiplicity in Clinical Trials., 2014.
Almirall, D. Tutorial: Getting SMART about Dynamic Treatment Regimes: A Conceptual Introduction., 2014.
Kang, Suhyun. Subgroup Detection and Sample Size Calculation with Proportional Hazards Regression for Survival Data., 2016.
Thall, PF. SMART Design, Conduct, and Analysis in Oncology., 2014.
Laber, Eric B.. Sizing a trial for estimation of an optimal treatment regime., 2014.
Levenson, M. Safety decision-making with multiple sources and different types of studies—recent examples from FDA Advisory Committees., 2011.
Davidian, Marie. A robust method for estimating optimal treatment regimes., 2011.
Bobashev, G. Prediction of the Best Treatment Assignment Using Random Forest with Regression in the Nodes., 2012.
Auman, Todd. Pharmacogenomic interrogation of colorectal cancer using next-generation whole exome sequencing., 2011.
Song, Rui. Penalized Q-Learning for Dynamic Treatment Regimes., 2012.
Heyse, Joseph F.. An Overview of Multiple Testing Procedures for Categorical Data., 2014.
Fine, Jason P.. An overview of competing risks data, with applications in clinical trials., 2011.
Rosenblum, M. Optimal, Two Stage, Adaptive Enrichment Designs for Randomized Trials, using Sparse Linear Programming., 2014.
Ivanova, Anastasia. Oncology Phase II trials with ordinal outcome., 2012.
Ibrahim, Joseph G.. Network Meta-analysis for Ordinal Outcomes: Applications in Comparing Crohn's Disease Treatments., 2016.
Xie, Jichun. Multiple Testing of General Dependence by Quantile-Based Contingency Tables with an Application in Identifying Gene Co-expression Network Change Associated with Cancer Survival., 2016.
Murphy, Susan A.. Micro-Randomized Trials & mHealth., 2014.
Zhao, Luping. Measures of Clinical Benefit in Immuno-Oncology Studies., 2016.
Shortreed, Susan M.. Leveraging Electronic Medical Records to Better Target Suicide Prevention., 2016.
Linn, Kristin A.. IQ-Learning., 2012.
Zhang, Yichi. Interpretable treatment regimes., 2014.
Wong, Kin Yau. Integration of Multiple High-dimensional Genomic Data Types for Survival Prediction., 2016.
Benjamini, Y. In Hochberg’s tradition: Selective Inference for Clinical Trials., 2014.
Sarkar, S. Improving Holm's procedure using pairwise dependencies., 2014.
Nair, Smita. Immune-based therapies., 2016.
Gou, J, and AC Tamhane. Hochberg Multiple Test Procedure Under Negative Dependence., 2014.
Almirall, D, and Susan A. Murphy. Getting SMART about developing individualized sequences of health interventions., 2012.
Chi, Eric. Getting High-throughput Arrays in Order with Convex Biclustering., 2016.
Tzeng, Jung-Ying. A gene-trait similarity regression method for gene-level pharmacogenetics analysis., 2011.
Li, Zhiguo. Fitting Cox models with doubly censored data using spline-based marginal likelihood., 2011.
Madar, V. Faster algorithm to control the Benjamini-Hochberg false discovery rate and its application for analysis of huge genomic data.., 2014.
Wang, L. Evaluation of Viable Dynamic Treatment Regimes in a Sequentially Randomized Trial of Advanced Prostate Cancer., 2014.
Zhao, Yingqi. Estimation of Optimal Dynamic Treatment Regimes., 2014.
Zeng, Donglin. Estimating treatment effects with treatment switching via semi-competing risks models: An application to a colorectal cancer study., 2011.
Zhao, Yingqi. Estimating Individualized Treatment Rules Using Outcome Weighted Learning., 2011.
Boland, Mary Regina. Electronic Health Records and Precision Medicine: Enabling Large-Scale Discoveries Using Phenome-Wide Approaches., 2016.
Madigan, D. Drug safety in spontaneous reports, observational databases, and clinical trials: Can we do better?., 2011.
Simon, R. Development of Predictive Biomarkers for Molecular Targeted Therapy., 2012.
Chen, Liddy M.. Design consideration for complex survival models., 2011.
Carpenter, William R.. Data needs for cancer comparative effectiveness research, and the Integrated Cancer Information and Surveillance System., 2012.
Rom, D. The Closure Principle Revisited., 2014.
Gatsonis, C. Clinical Evaluation of Diagnostic Tests and Biomarkers in CER., 2012.
Owzar, Kouros. Challenges in genome-wide association analysis of drug-induced toxicity data from clinical trials., 2012.
Sargent, Daniel J.. Biomarker-based clinical trials., 2012.
Korn, E. Biomarker-adaptive clinical trial designs., 2011.
Wang, Ting. Biomarker Stratified Design Enriched by Auxiliary Biomarker., 2016.
Wang, Xiaofei. Biased sampling and its applications in biomarker validation., 2011.
Chow, Shein-Chung. Benefits, Challenges and Obstacles of Adaptive Clinical Trial Designs., 2012.
Wahed, AS. Baseline Covariate Adjustment in SMART Studies via Artificial Randomization., 2014.
Murphy, Susan A.. Assessing Time-Varying Causal Interactions and Treatment Effects with Applications to Mobile Health., 2016.
Kidwell, KM. Addressing the Challenges and Reaping the Benefits of SMARTs., 2014.
Parmigiani, G. Adaptive randomized trial design for patients with recurrent glioblastom., 2011.
Laber, Eric B.. Adaptive inference after model selection., 2011.
Journal Article
He, Qianchuan, and Dan-Yu Lin. "A variable selection method for genome-wide association studies." Bioinformatics 27, no. 1 (2011): 1-8.
Yuan, Shuai, Hao Helen Zhang, and Marie Davidian. "Variable selection for covariate-adjusted semiparametric inference in randomized clinical trials." Stat Med 31, no. 29 (2012): 3789-804.
Yuan, Shuai, Hao Helen Zhang, and Marie Davidian. "Variable selection for covariate-adjusted semiparametric inference in randomized clinical trials." Stat Med 31, no. 29 (2012): 3789-804.
Wang, Xiaofei, Xiaoyi Wang, Lydia Hodgson, Stephen L. George, Daniel J. Sargent, Nate R. Foster, Apar Kishor Ganti, Thomas E. Stinchcombe, Jeffrey Crawford, Robert Kratzke et al. "Validation of Progression-Free Survival as a Surrogate Endpoint for Overall Survival in Malignant Mesothelioma: Analysis of Cancer and Leukemia Group B and North Central Cancer Treatment Group (Alliance) Trials." Oncologist 22, no. 2 (2017): 189-198.
Laber, Eric B., Ying-Qi Zhao, Todd Regh, Marie Davidian, Anastasios Tsiatis, Joseph B. Stanford, Donglin Zeng, Rui Song, and Michael R. Kosorok. "Using pilot data to size a two-arm randomized trial to find a nearly optimal personalized treatment strategy." Stat Med 35, no. 8 (2016): 1245-56.
Viele, Kert, Scott Berry, Beat Neuenschwander, Billy Amzal, Fang Chen, Nathan Enas, Brian Hobbs, Joseph G. Ibrahim, Nelson Kinnersley, Stacy Lindborg et al. "Use of historical control data for assessing treatment effects in clinical trials." Pharm Stat 13, no. 1 (2014): 41-54.
Barry, William T., Charles M. Perou, Kelly P Marcom, Lisa A. Carey, and Joseph G. Ibrahim. "The use of Bayesian hierarchical models for adaptive randomization in biomarker-driven phase II studies." J Biopharm Stat 25, no. 1 (2015): 66-88.
Love, Michael I., Charlotte Soneson, Peter F. Hickey, Lisa K. Johnson, Tessa N Pierce, Lori Shepherd, Martin Morgan, and Rob Patro. "Tximeta: Reference sequence checksums for provenance identification in RNA-seq." PLoS Comput Biol 16, no. 2 (2020): e1007664.
Diéras, Véronique, David Miles, Sunil Verma, Mark Pegram, Manfred Welslau, José Baselga, Ian E. Krop, Kim Blackwell, Silke Hoersch, Jin Xu et al. "Trastuzumab emtansine versus capecitabine plus lapatinib in patients with previously treated HER2-positive advanced breast cancer (EMILIA): a descriptive analysis of final overall survival results from a randomised, open-label, phase 3 trial." Lancet Oncol 18, no. 6 (2017): 732-742.
Olby, Natasha J., Ji-Hey Lim, Nikki Wagner, Natalia Zidan, Peter J. Early, Christopher L. Mariani, Karen R. Muñana, and Eric Laber. "Time course and prognostic value of serum GFAP, pNFH, and S100β concentrations in dogs with complete spinal cord injury because of intervertebral disc extrusion." J Vet Intern Med 33, no. 2 (2019): 726-734.
Olby, Natasha J., Ji-Hey Lim, Nikki Wagner, Natalia Zidan, Peter J. Early, Christopher L. Mariani, Karen R. Muñana, and Eric Laber. "Time course and prognostic value of serum GFAP, pNFH, and S100β concentrations in dogs with complete spinal cord injury because of intervertebral disc extrusion." J Vet Intern Med 33, no. 2 (2019): 726-734.
Samsky, Marc D., Chetan B. Patel, Ashleigh Owen, Phillip J. Schulte, Jacob Jentzer, Paul B. Rosenberg, Michael G Felker, Carmelo A. Milano, Adrian F. Hernandez, and Joseph G. Rogers. "Ten-year experience with extended criteria cardiac transplantation." Circ Heart Fail 6, no. 6 (2013): 1230-8.
Zhang, Xiang, Shunping Huang, Fei Zou, and Wei Wang. "TEAM: efficient two-locus epistasis tests in human genome-wide association study." Bioinformatics 26, no. 12 (2010): i217-27.
Wilson, Florence R., Abhishek Varu, Debanjali Mitra, Chris Cameron, and Shrividya Iyer. "Systematic review and network meta-analysis comparing palbociclib with chemotherapy agents for the treatment of postmenopausal women with HR-positive and HER2-negative advanced/metastatic breast cancer." Breast Cancer Res Treat 166, no. 1 (2017): 167-177.
Silva, Grace O., Marni B. Siegel, Lisle E. Mose, Joel S. Parker, Wei Sun, Charles M. Perou, and Mengjie Chen. "SynthEx: a synthetic-normal-based DNA sequencing tool for copy number alteration detection and tumor heterogeneity profiling." Genome Biol 18, no. 1 (2017): 66.
Silva, Grace O., Marni B. Siegel, Lisle E. Mose, Joel S. Parker, Wei Sun, Charles M. Perou, and Mengjie Chen. "SynthEx: a synthetic-normal-based DNA sequencing tool for copy number alteration detection and tumor heterogeneity profiling." Genome Biol 18, no. 1 (2017): 66.
Love, Michael I., Charlotte Soneson, and Rob Patro. "Swimming downstream: statistical analysis of differential transcript usage following Salmon quantification." F1000Res 7 (2018): 952.
Love, Michael I., Charlotte Soneson, and Rob Patro. "Swimming downstream: statistical analysis of differential transcript usage following Salmon quantification." F1000Res 7 (2018): 952.
Vock, David M., Michael T. Durheim, Wayne M. Tsuang, Ashley Finlen C Copeland, Anastasios A. Tsiatis, Marie Davidian, Megan L. Neely, David J. Lederer, and Scott M. Palmer. "Survival Benefit of Lung Transplantation in the Modern Era of Lung Allocation." Ann Am Thorac Soc 14, no. 2 (2017): 172-181.
Kang, Suhyun, Wenbin Lu, and Rui Song. "Subgroup detection and sample size calculation with proportional hazards regression for survival data." Stat Med 36, no. 29 (2017): 4646-4659.
Kang, Suhyun, Wenbin Lu, and Rui Song. "Subgroup detection and sample size calculation with proportional hazards regression for survival data." Stat Med 36, no. 29 (2017): 4646-4659.
Kang, Suhyun, Wenbin Lu, and Rui Song. "Subgroup detection and sample size calculation with proportional hazards regression for survival data." Stat Med 36, no. 29 (2017): 4646-4659.
Jung, Sin-Ho. "Stratified Fisher's exact test and its sample size calculation." Biom J 56, no. 1 (2014): 129-40.
Ma, Xiaoye, Lei Nie, Stephen R. Cole, and Haitao Chu. "Statistical methods for multivariate meta-analysis of diagnostic tests: An overview and tutorial." Stat Methods Med Res 25, no. 4 (2016): 1596-619.
Jung, Sin-Ho, Ho Yun Lee, and Shein-Chung Chow. "Statistical Methods for Conditional Survival Analysis." J Biopharm Stat 28, no. 5 (2018): 927-938.
Jung, Sin-Ho. "Statistical issues for design and analysis of single-arm multi-stage phase II cancer clinical trials." Contemp Clin Trials 42 (2015): 9-17.
Lu, Tsui-Shan, Matthew P. Longnecker, and Haibo Zhou. "Statistical inferences for data from studies conducted with an aggregated multivariate outcome-dependent sample design." Stat Med 36, no. 6 (2017): 985-997.
Diao, Guoqing, Donglin Zeng, Joseph G. Ibrahim, Alan Rong, Oliver Lee, Kathy Zhang, and Qingxia Chen. "Statistical design of noninferiority multiple region clinical trials to assess global and consistent treatment effects." J Biopharm Stat 27, no. 6 (2017): 933-944.
Owzar, Kouros, William T. Barry, and Sin-Ho Jung. "Statistical considerations for analysis of microarray experiments." Clin Transl Sci 4, no. 6 (2011): 466-77.
Huque, Md Hamidul, Howard D. Bondell, Raymond J. Carroll, and Louise M. Ryan. "Spatial regression with covariate measurement error: A semiparametric approach." Biometrics 72, no. 3 (2016): 678-86.
Huque, Md Hamidul, Howard D. Bondell, Raymond J. Carroll, and Louise M. Ryan. "Spatial regression with covariate measurement error: A semiparametric approach." Biometrics 72, no. 3 (2016): 678-86.
Huque, Md Hamidul, Howard D. Bondell, Raymond J. Carroll, and Louise M. Ryan. "Spatial regression with covariate measurement error: A semiparametric approach." Biometrics 72, no. 3 (2016): 678-86.
Mitha, Faheem, Herodotos Herodotou, Nedyalko Borisov, Chen Jiang, Josh Yoder, and Kouros Owzar. "SNPpy--database management for SNP data from genome wide association studies." PLoS One 6, no. 10 (2011): e24982.
Yang, Yanyan, Jinchuan Hu, Christopher P. Selby, Wentao Li, Askar Yimit, Yuchao Jiang, and Aziz Sancar. "Single-nucleotide resolution analysis of nucleotide excision repair of ribosomal DNA in humans and mice." J Biol Chem 294, no. 1 (2019): 210-217.
Wisdom, Amy J., Yvonne M. Mowery, Cierra S. Hong, Jonathon E. Himes, Barzin Y. Nabet, Xiaodi Qin, Dadong Zhang, Lan Chen, Hélène Fradin, Rutulkumar Patel et al. "Single cell analysis reveals distinct immune landscapes in transplant and primary sarcomas that determine response or resistance to immunotherapy." Nat Commun 11, no. 1 (2020): 6410.
Wisdom, Amy J., Yvonne M. Mowery, Cierra S. Hong, Jonathon E. Himes, Barzin Y. Nabet, Xiaodi Qin, Dadong Zhang, Lan Chen, Hélène Fradin, Rutulkumar Patel et al. "Single cell analysis reveals distinct immune landscapes in transplant and primary sarcomas that determine response or resistance to immunotherapy." Nat Commun 11, no. 1 (2020): 6410.
Chen, Yasheng, Songbai Ji, Xunlei Wu, Hongyu An, Hongtu Zhu, Dinggang Shen, and Weili Lin. "Simulation of brain mass effect with an arbitrary Lagrangian and Eulerian FEM." Med Image Comput Comput Assist Interv 13, no. Pt 2 (2010): 274-81.
Hyun, Jung Won, Yimei Li, John H. Gilmore, Zhaohua Lu, Martin Styner, and Hongtu Zhu. "SGPP: spatial Gaussian predictive process models for neuroimaging data." Neuroimage 89 (2014): 70-80.
Skup, Martha, Hongtu Zhu, Yaping Wang, Kelly S. Giovanello, Ja-an Lin, Dinggang Shen, Feng Shi, Wei Gao, Weili Lin, Yong Fan et al. "Sex differences in grey matter atrophy patterns among AD and aMCI patients: results from ADNI." Neuroimage 56, no. 3 (2011): 890-906.
Laber, Eric B., Daniel J. Lizotte, and Bradley Ferguson. "Set-valued dynamic treatment regimes for competing outcomes." Biometrics 70, no. 1 (2014): 53-61.
Liu, Ying, Yuanjia Wang, and Donglin Zeng. "Sequential multiple assignment randomization trials with enrichment design." Biometrics 73, no. 2 (2017): 378-390.
Mao, Lu, and D Y. Lin. "Semiparametric regression for the weighted composite endpoint of recurrent and terminal events." Biostatistics 17, no. 2 (2016): 390-403.
Pan, Yinghao, Jianwen Cai, Matthew P. Longnecker, and Haibo Zhou. "Secondary outcome analysis for data from an outcome-dependent sampling design." Stat Med 37, no. 15 (2018): 2321-2337.
Yuan, Jiacheng, Herbert Pang, Tiejun Tong, Dong Xi, Wenzhao Guo, and Peter Mesenbrink. "Seamless Phase IIa/IIb and enhanced dose-finding adaptive design." J Biopharm Stat 26, no. 5 (2016): 912-23.
Wang, Rujin, Dan-Yu Lin, and Yuchao Jiang. "SCOPE: A Normalization and Copy-Number Estimation Method for Single-Cell DNA Sequencing." Cell Syst 10, no. 5 (2020): 445-452.e6.
Wang, Rujin, Dan-Yu Lin, and Yuchao Jiang. "SCOPE: A Normalization and Copy-Number Estimation Method for Single-Cell DNA Sequencing." Cell Syst 10, no. 5 (2020): 445-452.e6.

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