Publications
Block-diagonal discriminant analysis and its bias-corrected rules." Stat Appl Genet Mol Biol 12, no. 3 (2013): 347-59.
"Analysing breast cancer microarrays from African Americans using shrinkage-based discriminant analysis." Hum Genomics 5, no. 1 (2010): 5-16.
"A general framework for studying genetic effects and gene-environment interactions with missing data." Biostatistics 11, no. 4 (2010): 583-98.
"Improving the efficiency of estimation in the additive hazards model for stratified case-cohort design with multiple diseases." Stat Med 35, no. 2 (2016): 282-93.
"Biclustering via sparse clustering." Biometrics 76, no. 1 (2020): 348-358.
"Application of a sequential multiple assignment randomized trial (SMART) design in older patients with chronic lymphocytic leukemia." Ann Oncol 30, no. 4 (2019): 542-550.
"Multiple kernel learning with random effects for predicting longitudinal outcomes and data integration." Biometrics 71, no. 4 (2015): 918-28.
"Celecoxib With Neoadjuvant Chemotherapy for Breast Cancer Might Worsen Outcomes Differentially by COX-2 Expression and ER Status: Exploratory Analysis of the REMAGUS02 Trial." J Clin Oncol 37, no. 8 (2019): 624-635.
"Bayesian gamma frailty models for survival data with semi-competing risks and treatment switching." Lifetime Data Anal 20, no. 1 (2014): 76-105.
"Assessing temporal agreement between central and local progression-free survival times." Stat Med 34, no. 5 (2015): 844-58.
"Penalized nonlinear mixed effects model to identify biomarkers that predict disease progression." Biometrics 73, no. 4 (2017): 1343-1354.
"Phase II, randomized, placebo-controlled study of dovitinib in combination with fulvestrant in postmenopausal patients with HR, HER2 breast cancer that had progressed during or after prior endocrine therapy." Breast Cancer Res 19, no. 1 (2017): 18.
"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.
"Sex differences in grey matter atrophy patterns among AD and aMCI patients: results from ADNI." Neuroimage 56, no. 3 (2011): 890-906.
"Additive mixed effect model for clustered failure time data." Biometrics 67, no. 4 (2011): 1340-51.
"Bayesian influence measures for joint models for longitudinal and survival data." Biometrics 68, no. 3 (2012): 954-64.
"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.
"Bayesian methods in clinical trials: a Bayesian analysis of ECOG trials E1684 and E1690." BMC Med Res Methodol 12 (2012): 183.
"Empirical pathway analysis, without permutation." Biostatistics 14, no. 3 (2013): 573-85.
"Multitrial Evaluation of Progression-Free Survival as a Surrogate End Point for Overall Survival in First-Line Extensive-Stage Small-Cell Lung Cancer." J Thorac Oncol 10, no. 7 (2015): 1099-106.
"Assessing temporal agreement between central and local progression-free survival times." Stat Med 34, no. 5 (2015): 844-58.
"Bayesian design of a survival trial with a cured fraction using historical data." Stat Med 37, no. 26 (2018): 3814-3831.
"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.
"Phase II clinical trials with time-to-event endpoints: optimal two-stage designs with one-sample log-rank test." Stat Med 33, no. 12 (2014): 2004-16.
"Static and Dynamic DNA Loops form AP-1-Bound Activation Hubs during Macrophage Development." Mol Cell 67, no. 6 (2017): 1037-1048.e6.
"Improved detection of epigenomic marks with mixed-effects hidden Markov models." Biometrics 75, no. 4 (2019): 1401-1413.
"Biclustering with heterogeneous variance." Proc Natl Acad Sci U S A 110, no. 30 (2013): 12253-8.
"Differential damage and repair of DNA-adducts induced by anti-cancer drug cisplatin across mouse organs." Nat Commun 10, no. 1 (2019): 309.
"SynthEx: a synthetic-normal-based DNA sequencing tool for copy number alteration detection and tumor heterogeneity profiling." Genome Biol 18, no. 1 (2017): 66.
"SCOPE: A Normalization and Copy-Number Estimation Method for Single-Cell DNA Sequencing." Cell Syst 10, no. 5 (2020): 445-452.e6.
"CODEX2: full-spectrum copy number variation detection by high-throughput DNA sequencing." Genome Biol 19, no. 1 (2018): 202.
"The association between copy number aberration, DNA methylation and gene expression in tumor samples." Nucleic Acids Res 46, no. 6 (2018): 3009-3018.
"Integrative pipeline for profiling DNA copy number and inferring tumor phylogeny." Bioinformatics 34, no. 12 (2018): 2126-2128.
"DiNAMIC: a method to identify recurrent DNA copy number aberrations in tumors." Bioinformatics 27, no. 5 (2011): 678-85.
"Integrative gene set analysis of multi-platform data with sample heterogeneity." Bioinformatics 30, no. 11 (2014): 1501-7.
"A New Method for Detecting Associations with Rare Copy-Number Variants." PLoS Genet 11, no. 10 (2015): e1005403.
"Association test using Copy Number Profile Curves (CONCUR) enhances power in rare copy number variant analysis." PLoS Comput Biol 16, no. 5 (2020): e1007797.
"Global copy number profiling of cancer genomes." Bioinformatics 32, no. 6 (2016): 926-8.
"Allele-specific copy-number discovery from whole-genome and whole-exome sequencing." Nucleic Acids Res 43, no. 14 (2015): e90.
"Differential damage and repair of DNA-adducts induced by anti-cancer drug cisplatin across mouse organs." Nat Commun 10, no. 1 (2019): 309.
"Integrative gene set analysis of multi-platform data with sample heterogeneity." Bioinformatics 30, no. 11 (2014): 1501-7.
"Whole-Genome and Epigenomic Landscapes of Etiologically Distinct Subtypes of Cholangiocarcinoma." Cancer Discov 7, no. 10 (2017): 1116-1135.
"Mapping eQTL by leveraging multiple tissues and DNA methylation." BMC Bioinformatics 18, no. 1 (2017): 455.
"Across-Platform Imputation of DNA Methylation Levels Incorporating Nonlocal Information Using Penalized Functional Regression." Genet Epidemiol 40, no. 4 (2016): 333-40.
"Intergenerational response to the endocrine disruptor vinclozolin is influenced by maternal genotype and crossing scheme." Reprod Toxicol 78 (2018): 9-19.
"The association between copy number aberration, DNA methylation and gene expression in tumor samples." Nucleic Acids Res 46, no. 6 (2018): 3009-3018.
"Integrative analysis of sequencing and array genotype data for discovering disease associations with rare mutations." Proc Natl Acad Sci U S A 112, no. 4 (2015): 1019-24.
"PIK3CA mutations enable targeting of a breast tumor dependency through mTOR-mediated MCL-1 translation." Sci Transl Med 8, no. 369 (2016): 369ra175.
"Differential damage and repair of DNA-adducts induced by anti-cancer drug cisplatin across mouse organs." Nat Commun 10, no. 1 (2019): 309.
"Single-nucleotide resolution analysis of nucleotide excision repair of ribosomal DNA in humans and mice." J Biol Chem 294, no. 1 (2019): 210-217.
"Nucleotide excision repair capacity increases during differentiation of human embryonic carcinoma cells into neurons and muscle cells." J Biol Chem 294, no. 15 (2019): 5914-5922.
"Incorporating higher-order representative features improves prediction in network-based cancer prognosis analysis." BMC Med Genomics 4 (2011): 5.
"DiNAMIC: a method to identify recurrent DNA copy number aberrations in tumors." Bioinformatics 27, no. 5 (2011): 678-85.
"Associating somatic mutations to clinical outcomes: a pan-cancer study of survival time." Genome Med 11, no. 1 (2019): 37.
"Single-nucleotide resolution analysis of nucleotide excision repair of ribosomal DNA in humans and mice." J Biol Chem 294, no. 1 (2019): 210-217.
"Improved detection of epigenomic marks with mixed-effects hidden Markov models." Biometrics 75, no. 4 (2019): 1401-1413.
"Nucleotide excision repair capacity increases during differentiation of human embryonic carcinoma cells into neurons and muscle cells." J Biol Chem 294, no. 15 (2019): 5914-5922.
" "Pharmacogenetics, enzyme probes and therapeutic drug monitoring as potential tools for individualizing taxane therapy." Pharmacogenomics 14, no. 5 (2013): 555-74.
"Quantifying center of pressure variability in chondrodystrophoid dogs." Vet J 226 (2017): 26-31.
"Quantifying center of pressure variability in chondrodystrophoid dogs." Vet J 226 (2017): 26-31.
"Translational studies of phenotypic probes for the mononuclear phagocyte system and liposomal pharmacology." J Pharmacol Exp Ther 347, no. 3 (2013): 599-606.
"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.
"Superiority of combining two independent trials in interim futility analysis." Stat Methods Med Res 29, no. 2 (2020): 522-540.
"Continual reassessment method with regularization in phase I clinical trials." J Biopharm Stat 30, no. 6 (2020): 964-978.
"Practical designs for Phase I combination studies in oncology." J Biopharm Stat 26, no. 1 (2016): 150-66.
"Dose-finding designs for trials of molecularly targeted agents and immunotherapies." J Biopharm Stat 27, no. 3 (2017): 477-494.
"CRM2DIM: A SAS macro for implementing the dual-agent Bayesian continual reassessment method." Comput Methods Programs Biomed 176 (2019): 211-223.
"Rapid enrollment design for finding the optimal dose in immunotherapy trials with ordered groups." J Biopharm Stat 29, no. 4 (2019): 625-634.
"The rapid enrollment design for Phase I clinical trials." Stat Med 35, no. 15 (2016): 2516-24.
"Selection of the initial design for the two-stage continual reassessment method." J Biopharm Stat 27, no. 3 (2017): 495-506.
"Seamless Phase IIa/IIb and enhanced dose-finding adaptive design." J Biopharm Stat 26, no. 5 (2016): 912-23.
"Generation of a Transcriptional Radiation Exposure Signature in Human Blood Using Long-Read Nanopore Sequencing." Radiat Res 193, no. 2 (2020): 143-154.
"Multivariate recurrent events in the presence of multivariate informative censoring with applications to bleeding and transfusion events in myelodysplastic syndrome." J Biopharm Stat 24, no. 2 (2014): 429-42.
"Localized differences in caudate and hippocampal shape are associated with schizophrenia but not antipsychotic type." Psychiatry Res 211, no. 1 (2013): 1-10.
"Predictive Blood-Based Biomarkers in Patients with Epithelial Ovarian Cancer Treated with Carboplatin and Paclitaxel with or without Bevacizumab: Results from GOG-0218." Clin Cancer Res 26, no. 6 (2020): 1288-1296.
"Randomized, double-blind study comparing proposed biosimilar LA-EP2006 with reference pegfilgrastim in breast cancer." Future Oncol 12, no. 11 (2016): 1359-67.
" "Tximeta: Reference sequence checksums for provenance identification in RNA-seq." PLoS Comput Biol 16, no. 2 (2020): e1007664.
"CRM2DIM: A SAS macro for implementing the dual-agent Bayesian continual reassessment method." Comput Methods Programs Biomed 176 (2019): 211-223.
"Statistical design of noninferiority multiple region clinical trials to assess global and consistent treatment effects." J Biopharm Stat 27, no. 6 (2017): 933-944.
"Translational studies of phenotypic probes for the mononuclear phagocyte system and liposomal pharmacology." J Pharmacol Exp Ther 347, no. 3 (2013): 599-606.
"Rare Variants Association Analysis in Large-Scale Sequencing Studies at the Single Locus Level." PLoS Comput Biol 12, no. 6 (2016): e1004993.
"Seamless Phase IIa/IIb and enhanced dose-finding adaptive design." J Biopharm Stat 26, no. 5 (2016): 912-23.
"Cancer pharmacogenomics: early promise, but concerted effort needed." Science 339, no. 6127 (2013): 1563-6.
"Joint modeling of survival and longitudinal non-survival data: current methods and issues. Report of the DIA Bayesian joint modeling working group." Stat Med 34, no. 14 (2015): 2181-95.
"A counterfactual p-value approach for benefit-risk assessment in clinical trials." J Biopharm Stat 25, no. 3 (2015): 508-24.
"Identifying optimal dosage regimes under safety constraints: An application to long term opioid treatment of chronic pain." Stat Med 37, no. 9 (2018): 1407-1418.
"Pharmacogenetics, enzyme probes and therapeutic drug monitoring as potential tools for individualizing taxane therapy." Pharmacogenomics 14, no. 5 (2013): 555-74.
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Meta-analysis methods and models with applications in evaluation of cholesterol-lowering drugs." Stat Med 31, no. 28 (2012): 3597-616.
"Bayesian multivariate skew meta-regression models for individual patient data." Stat Methods Med Res 28, no. 10-11 (2019): 3415-3436.
" "Reinforcement learning strategies for clinical trials in nonsmall cell lung cancer." Biometrics 67, no. 4 (2011): 1422-33.
"Efficient methods for signal detection from correlated adverse events in clinical trials." Biometrics 75, no. 3 (2019): 1000-1008.
"Phase II cancer clinical trials with heterogeneous patient populations." J Biopharm Stat 22, no. 2 (2012): 312-28.
"Onset of persistent pseudomonas aeruginosa infection in children with cystic fibrosis with interval censored data." BMC Med Res Methodol 16, no. 1 (2016): 122.
"Enrollment and Stopping Rules for Managing Toxicity Requiring Long Follow-Up in Phase II Oncology Trials." J Biopharm Stat 25, no. 6 (2015): 1206-14.
"Nucleotide excision repair capacity increases during differentiation of human embryonic carcinoma cells into neurons and muscle cells." J Biol Chem 294, no. 15 (2019): 5914-5922.
"Intergenerational response to the endocrine disruptor vinclozolin is influenced by maternal genotype and crossing scheme." Reprod Toxicol 78 (2018): 9-19.
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