Publications
Filters: First Letter Of Keyword is S [Clear All Filters]
Tximeta: Reference sequence checksums for provenance identification in RNA-seq." PLoS Comput Biol 16, no. 2 (2020): e1007664.
"Spatial regression with covariate measurement error: A semiparametric approach." Biometrics 72, no. 3 (2016): 678-86.
"Enrollment Trends and Disparity Among Patients With Lung Cancer in National Clinical Trials, 1990 to 2012." J Clin Oncol 34, no. 33 (2016): 3992-3999.
"Latent class model characterization of neighborhood socioeconomic status." Cancer Causes Control 27, no. 3 (2016): 445-52.
"A general framework for studying genetic effects and gene-environment interactions with missing data." Biostatistics 11, no. 4 (2010): 583-98.
"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.
" "Bayesian methods in clinical trials: a Bayesian analysis of ECOG trials E1684 and E1690." BMC Med Res Methodol 12 (2012): 183.
"A composite likelihood method for bivariate meta-analysis in diagnostic systematic reviews." Stat Methods Med Res 26, no. 2 (2017): 914-930.
"Component-wise gradient boosting and false discovery control in survival analysis with high-dimensional covariates." Bioinformatics 32, no. 1 (2016): 50-7.
"Observation weights unlock bulk RNA-seq tools for zero inflation and single-cell applications." Genome Biol 19, no. 1 (2018): 24.
"SAFE-clustering: Single-cell Aggregated (from Ensemble) clustering for single-cell RNA-seq data." Bioinformatics 35, no. 8 (2019): 1269-1277.
"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.
"SCOPE: A Normalization and Copy-Number Estimation Method for Single-Cell DNA Sequencing." Cell Syst 10, no. 5 (2020): 445-452.e6.
"Age and African-American race impact the validity and reliability of the asthma control test in persistent asthmatics." Respir Res 19, no. 1 (2018): 152.
"Confident difference criterion: a new Bayesian differentially expressed gene selection algorithm with applications." BMC Bioinformatics 16 (2015): 245.
"Regression analysis for secondary response variable in a case-cohort study." Biometrics 74, no. 3 (2018): 1014-1022.
"Block-diagonal discriminant analysis and its bias-corrected rules." Stat Appl Genet Mol Biol 12, no. 3 (2013): 347-59.
"A new Bayesian joint model for longitudinal count data with many zeros, intermittent missingness, and dropout with applications to HIV prevention trials." Stat Med 38, no. 30 (2019): 5565-5586.
"Enrollment Trends and Disparity Among Patients With Lung Cancer in National Clinical Trials, 1990 to 2012." J Clin Oncol 34, no. 33 (2016): 3992-3999.
"Inference on phenotype-specific effects of genes using multivariate kernel machine regression." Genet Epidemiol 42, no. 1 (2018): 64-79.
"Clinical prognostic model for older patients with advanced non-small cell lung cancer." J Geriatr Oncol 10, no. 4 (2019): 555-559.
"Sex differences in grey matter atrophy patterns among AD and aMCI patients: results from ADNI." Neuroimage 56, no. 3 (2011): 890-906.
"FADTTS: functional analysis of diffusion tensor tract statistics." Neuroimage 56, no. 3 (2011): 1412-25.
"Impact of sex and gonadal steroids on neonatal brain structure." Cereb Cortex 24, no. 10 (2014): 2721-31.
"Integrative gene set analysis of multi-platform data with sample heterogeneity." Bioinformatics 30, no. 11 (2014): 1501-7.
"Observation weights unlock bulk RNA-seq tools for zero inflation and single-cell applications." Genome Biol 19, no. 1 (2018): 24.
"SAFE-clustering: Single-cell Aggregated (from Ensemble) clustering for single-cell RNA-seq data." Bioinformatics 35, no. 8 (2019): 1269-1277.
"Heavy-tailed prior distributions for sequence count data: removing the noise and preserving large differences." Bioinformatics 35, no. 12 (2019): 2084-2092.
"Swimming downstream: statistical analysis of differential transcript usage following Salmon quantification." F1000Res 7 (2018): 952.
"Differential damage and repair of DNA-adducts induced by anti-cancer drug cisplatin across mouse organs." Nat Commun 10, no. 1 (2019): 309.
"Alignment and mapping methodology influence transcript abundance estimation." Genome Biol 21, no. 1 (2020): 239.
"A general framework for integrative analysis of incomplete multiomics data." Genet Epidemiol 44, no. 7 (2020): 646-664.
"MASS: meta-analysis of score statistics for sequencing studies." Bioinformatics 29, no. 14 (2013): 1803-5.
"Quantitative trait analysis in sequencing studies under trait-dependent sampling." Proc Natl Acad Sci U S A 110, no. 30 (2013): 12247-52.
"DiNAMIC: a method to identify recurrent DNA copy number aberrations in tumors." Bioinformatics 27, no. 5 (2011): 678-85.
"Meta-analysis of sequencing studies with heterogeneous genetic associations." Genet Epidemiol 38, no. 5 (2014): 389-401.
"Global copy number profiling of cancer genomes." Bioinformatics 32, no. 6 (2016): 926-8.
"SynthEx: a synthetic-normal-based DNA sequencing tool for copy number alteration detection and tumor heterogeneity profiling." Genome Biol 18, no. 1 (2017): 66.
"Integrative pipeline for profiling DNA copy number and inferring tumor phylogeny." Bioinformatics 34, no. 12 (2018): 2126-2128.
"Allele-specific copy-number discovery from whole-genome and whole-exome sequencing." Nucleic Acids Res 43, no. 14 (2015): e90.
"Single-nucleotide resolution analysis of nucleotide excision repair of ribosomal DNA in humans and mice." J Biol Chem 294, no. 1 (2019): 210-217.
"Identifying individual risk rare variants using protein structure guided local tests (POINT)." PLoS Comput Biol 15, no. 2 (2019): e1006722.
"Improved detection of epigenomic marks with mixed-effects hidden Markov models." Biometrics 75, no. 4 (2019): 1401-1413.
"A general framework for integrative analysis of incomplete multiomics data." Genet Epidemiol 44, no. 7 (2020): 646-664.
"SCOPE: A Normalization and Copy-Number Estimation Method for Single-Cell DNA Sequencing." Cell Syst 10, no. 5 (2020): 445-452.e6.
"Alignment and mapping methodology influence transcript abundance estimation." Genome Biol 21, no. 1 (2020): 239.
"A genome-wide association study identifies novel loci for paclitaxel-induced sensory peripheral neuropathy in CALGB 40101." Clin Cancer Res 18, no. 18 (2012): 5099-109.
"Performance of rapid influenza H1N1 diagnostic tests: a meta-analysis." Influenza Other Respir Viruses 6, no. 2 (2012): 80-6.
"Assessing the dependence of sensitivity and specificity on prevalence in meta-analysis." Biostatistics 12, no. 4 (2011): 710-22.
"Doubly-robust estimators of treatment-specific survival distributions in observational studies with stratified sampling." Biometrics 69, no. 4 (2013): 830-9.
"A global sensitivity test for evaluating statistical hypotheses with nonidentifiable models." Biometrics 66, no. 2 (2010): 558-66.
"Multivariate network-level approach to detect interactions between large-scale functional systems." Med Image Comput Comput Assist Interv 13, no. Pt 2 (2010): 298-305.
"Statistical methods for multivariate meta-analysis of diagnostic tests: An overview and tutorial." Stat Methods Med Res 25, no. 4 (2016): 1596-619.
"A moment-adjusted imputation method for measurement error models." Biometrics 67, no. 4 (2011): 1461-70.
"Multivariate varying coefficient models for DTI tract statistics." Med Image Comput Comput Assist Interv 13, no. Pt 1 (2010): 690-7.
"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.
"Accelerated intensity frailty model for recurrent events data." Biometrics 70, no. 3 (2014): 579-87.
"A hybrid Bayesian hierarchical model combining cohort and case-control studies for meta-analysis of diagnostic tests: Accounting for partial verification bias." Stat Methods Med Res 25, no. 6 (2016): 3015-3037.
"Diseased region detection of longitudinal knee MRI data." Inf Process Med Imaging 23 (2013): 632-43.
"Multiscale adaptive marginal analysis of longitudinal neuroimaging data with time-varying covariates." Biometrics 68, no. 4 (2012): 1083-92.
"A longitudinal functional analysis framework for analysis of white matter tract statistics." Inf Process Med Imaging 23 (2013): 220-31.
"Bayesian design of superiority clinical trials for recurrent events data with applications to bleeding and transfusion events in myelodyplastic syndrome." Biometrics 70, no. 4 (2014): 1003-13.
"A composite likelihood method for bivariate meta-analysis in diagnostic systematic reviews." Stat Methods Med Res 26, no. 2 (2017): 914-930.
"Efficient semiparametric estimation of short-term and long-term hazard ratios with right-censored data." Biometrics 69, no. 4 (2013): 840-9.
"Basic concepts and methods for joint models of longitudinal and survival data." J Clin Oncol 28, no. 16 (2010): 2796-801.
"Comparison of operational characteristics for binary tests with clustered data." Stat Med 34, no. 15 (2015): 2325-33.
"Detection of gene-gene interactions using multistage sparse and low-rank regression." Biometrics 72, no. 1 (2016): 85-94.
"Bayesian path specific frailty models for multi-state survival data with applications." Biometrics 71, no. 3 (2015): 760-71.
"Estimation of treatment effect for the sequential parallel design." Stat Med 30, no. 30 (2011): 3496-506.
"Robust kernel association testing (RobKAT)." Genet Epidemiol 44, no. 3 (2020): 272-282.
"Variable selection for covariate-adjusted semiparametric inference in randomized clinical trials." Stat Med 31, no. 29 (2012): 3789-804.
"Optimal estimation for regression models on τ-year survival probability." J Biopharm Stat 25, no. 3 (2015): 539-47.
"Comparative effectiveness of oxaliplatin vs non-oxaliplatin-containing adjuvant chemotherapy for stage III colon cancer." J Natl Cancer Inst 104, no. 3 (2012): 211-27.
"Racial Differences in Diffusion of Intensity-Modulated Radiation Therapy for Localized Prostate Cancer." Am J Mens Health 10, no. 5 (2016): 399-407.
"Provider-based research networks and diffusion of surgical technologies among patients with early-stage kidney cancer." Cancer 121, no. 6 (2015): 836-43.
"Enrollment Trends and Disparity Among Patients With Lung Cancer in National Clinical Trials, 1990 to 2012." J Clin Oncol 34, no. 33 (2016): 3992-3999.
""Genome-wide association study identifies five new schizophrenia loci." Nat Genet 43, no. 10 (2011): 969-76.
Multivariate phenotype association analysis by marker-set kernel machine regression." Genet Epidemiol 36, no. 7 (2012): 686-95.
"Set-valued dynamic treatment regimes for competing outcomes." Biometrics 70, no. 1 (2014): 53-61.
"Localized differences in caudate and hippocampal shape are associated with schizophrenia but not antipsychotic type." Psychiatry Res 211, no. 1 (2013): 1-10.
"A multiple imputation strategy for sequential multiple assignment randomized trials." Stat Med 33, no. 24 (2014): 4202-14.
"A New Method for Detecting Associations with Rare Copy-Number Variants." PLoS Genet 11, no. 10 (2015): e1005403.
"Comparison of adaptive treatment strategies based on longitudinal outcomes in sequential multiple assignment randomized trials." Stat Med 36, no. 3 (2017): 403-415.
"Incorporating Patient Preferences into Estimation of Optimal Individualized Treatment Rules." Biometrics 74, no. 1 (2018): 18-26.
"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.
"The Long Noncoding RNA Promotes Sarcoma Metastasis by Regulating RNA Splicing Pathways." Mol Cancer Res 18, no. 10 (2020): 1534-1544.
"Genetic association analysis under complex survey sampling: the Hispanic Community Health Study/Study of Latinos." Am J Hum Genet 95, no. 6 (2014): 675-88.
"Statistical inferences for data from studies conducted with an aggregated multivariate outcome-dependent sample design." Stat Med 36, no. 6 (2017): 985-997.
"Secondary outcome analysis for data from an outcome-dependent sampling design." Stat Med 37, no. 15 (2018): 2321-2337.
"Accelerated failure time model for data from outcome-dependent sampling." Lifetime Data Anal 27, no. 1 (2021): 15-37.
"Sample size and power determination in joint modeling of longitudinal and survival data." Stat Med 30, no. 18 (2011): 2295-309.
"Bayesian meta-experimental design: evaluating cardiovascular risk in new antidiabetic therapies to treat type 2 diabetes." Biometrics 68, no. 2 (2012): 578-86.
"Phase II cancer clinical trials with heterogeneous patient populations." J Biopharm Stat 22, no. 2 (2012): 312-28.
"On sample size calculation for comparing survival curves under general hypothesis testing." J Biopharm Stat 22, no. 3 (2012): 485-95.
"Power and sample size calculations for SNP association studies with censored time-to-event outcomes." Genet Epidemiol 36, no. 6 (2012): 538-48.
"Sample size estimation in educational intervention trials with subgroup heterogeneity in only one arm." Stat Med 32, no. 12 (2013): 2140-54.
"Sample size considerations of prediction-validation methods in high-dimensional data for survival outcomes." Genet Epidemiol 37, no. 3 (2013): 276-82.
"On random sample size, ignorability, ancillarity, completeness, separability, and degeneracy: sequential trials, random sample sizes, and missing data." Stat Methods Med Res 23, no. 1 (2014): 11-41.
"Power and sample size calculation for microarray studies." J Biopharm Stat 22, no. 1 (2012): 30-42.
"