Publications
SynthEx: a synthetic-normal-based DNA sequencing tool for copy number alteration detection and tumor heterogeneity profiling." Genome Biol 18, no. 1 (2017): 66.
""Genome-wide association study identifies five new schizophrenia loci." Nat Genet 43, no. 10 (2011): 969-76.
Joint skeleton estimation of multiple directed acyclic graphs for heterogeneous population." Biometrics 75, no. 1 (2019): 36-47.
"Multicategory reclassification statistics for assessing improvements in diagnostic accuracy." Biostatistics 14, no. 2 (2013): 382-94.
"SAFE-clustering: Single-cell Aggregated (from Ensemble) clustering for single-cell RNA-seq data." Bioinformatics 35, no. 8 (2019): 1269-1277.
"permGPU: Using graphics processing units in RNA microarray association studies." BMC Bioinformatics 11 (2010): 329.
"Rapid and robust resampling-based multiple-testing correction with application in a genome-wide expression quantitative trait loci study." Genetics 190, no. 4 (2012): 1511-20.
"Swimming downstream: statistical analysis of differential transcript usage following Salmon quantification." F1000Res 7 (2018): 952.
"Confident difference criterion: a new Bayesian differentially expressed gene selection algorithm with applications." BMC Bioinformatics 16 (2015): 245.
"Block-diagonal discriminant analysis and its bias-corrected rules." Stat Appl Genet Mol Biol 12, no. 3 (2013): 347-59.
"Purity Independent Subtyping of Tumors (PurIST), A Clinically Robust, Single-sample Classifier for Tumor Subtyping in Pancreatic Cancer." Clin Cancer Res 26, no. 1 (2020): 82-92.
"Biclustering with heterogeneous variance." Proc Natl Acad Sci U S A 110, no. 30 (2013): 12253-8.
"SynthEx: a synthetic-normal-based DNA sequencing tool for copy number alteration detection and tumor heterogeneity profiling." Genome Biol 18, no. 1 (2017): 66.
"I-Boost: an integrative boosting approach for predicting survival time with multiple genomics platforms." Genome Biol 20, no. 1 (2019): 52.
"Multiple testing for gene sets from microarray experiments." BMC Bioinformatics 12 (2011): 209.
"Exploiting expression patterns across multiple tissues to map expression quantitative trait loci." BMC Bioinformatics 17 (2016): 257.
"Partial correlation matrix estimation using ridge penalty followed by thresholding and re-estimation." Biometrics 70, no. 3 (2014): 765-73.
"Alignment and mapping methodology influence transcript abundance estimation." Genome Biol 21, no. 1 (2020): 239.
"Statistical considerations for analysis of microarray experiments." Clin Transl Sci 4, no. 6 (2011): 466-77.
"Robust test method for time-course microarray experiments." BMC Bioinformatics 11 (2010): 391.
"Empirical pathway analysis, without permutation." Biostatistics 14, no. 3 (2013): 573-85.
"Gene selection using iterative feature elimination random forests for survival outcomes." IEEE/ACM Trans Comput Biol Bioinform 9, no. 5 (2012): 1422-31.
"Tximeta: Reference sequence checksums for provenance identification in RNA-seq." PLoS Comput Biol 16, no. 2 (2020): e1007664.
"Observation weights unlock bulk RNA-seq tools for zero inflation and single-cell applications." Genome Biol 19, no. 1 (2018): 24.
"Incorporating higher-order representative features improves prediction in network-based cancer prognosis analysis." BMC Med Genomics 4 (2011): 5.
"Integrative gene set analysis of multi-platform data with sample heterogeneity." Bioinformatics 30, no. 11 (2014): 1501-7.
"Swimming downstream: statistical analysis of differential transcript usage following Salmon quantification." F1000Res 7 (2018): 952.
""Genome-wide association study identifies five new schizophrenia loci." Nat Genet 43, no. 10 (2011): 969-76.
Confident difference criterion: a new Bayesian differentially expressed gene selection algorithm with applications." BMC Bioinformatics 16 (2015): 245.
"Static and Dynamic DNA Loops form AP-1-Bound Activation Hubs during Macrophage Development." Mol Cell 67, no. 6 (2017): 1037-1048.e6.
"Exploiting expression patterns across multiple tissues to map expression quantitative trait loci." BMC Bioinformatics 17 (2016): 257.
"Effective SNP ranking improves the performance of eQTL mapping." Genet Epidemiol 44, no. 6 (2020): 611-619.
"Mapping eQTL by leveraging multiple tissues and DNA methylation." BMC Bioinformatics 18, no. 1 (2017): 455.
"Partial correlation matrix estimation using ridge penalty followed by thresholding and re-estimation." Biometrics 70, no. 3 (2014): 765-73.
"Statistical considerations for analysis of microarray experiments." Clin Transl Sci 4, no. 6 (2011): 466-77.
"Purity Independent Subtyping of Tumors (PurIST), A Clinically Robust, Single-sample Classifier for Tumor Subtyping in Pancreatic Cancer." Clin Cancer Res 26, no. 1 (2020): 82-92.
"Statistical considerations for analysis of microarray experiments." Clin Transl Sci 4, no. 6 (2011): 466-77.
"I-Boost: an integrative boosting approach for predicting survival time with multiple genomics platforms." Genome Biol 20, no. 1 (2019): 52.
"PIK3CA mutations enable targeting of a breast tumor dependency through mTOR-mediated MCL-1 translation." Sci Transl Med 8, no. 369 (2016): 369ra175.
"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.
"Whole-Genome and Epigenomic Landscapes of Etiologically Distinct Subtypes of Cholangiocarcinoma." Cancer Discov 7, no. 10 (2017): 1116-1135.
"The association between copy number aberration, DNA methylation and gene expression in tumor samples." Nucleic Acids Res 46, no. 6 (2018): 3009-3018.
"A general framework for detecting disease associations with rare variants in sequencing studies." Am J Hum Genet 89, no. 3 (2011): 354-67.
"Meta-analysis of gene-level associations for rare variants based on single-variant statistics." Am J Hum Genet 93, no. 2 (2013): 236-48.
"Rare Variants Association Analysis in Large-Scale Sequencing Studies at the Single Locus Level." PLoS Comput Biol 12, no. 6 (2016): e1004993.
"Global copy number profiling of cancer genomes." Bioinformatics 32, no. 6 (2016): 926-8.
"Assessing gene-environment interactions for common and rare variants with binary traits using gene-trait similarity regression." Genetics 199, no. 3 (2015): 695-710.
"Efficient estimation of grouped survival models." BMC Bioinformatics 20, no. 1 (2019): 269.
"bcSeq: an R package for fast sequence mapping in high-throughput shRNA and CRISPR screens." Bioinformatics 34, no. 20 (2018): 3581-3583.
"Confident difference criterion: a new Bayesian differentially expressed gene selection algorithm with applications." BMC Bioinformatics 16 (2015): 245.
"Empirical pathway analysis, without permutation." Biostatistics 14, no. 3 (2013): 573-85.
"Block-diagonal discriminant analysis and its bias-corrected rules." Stat Appl Genet Mol Biol 12, no. 3 (2013): 347-59.
"Whole-Genome and Epigenomic Landscapes of Etiologically Distinct Subtypes of Cholangiocarcinoma." Cancer Discov 7, no. 10 (2017): 1116-1135.
"Independence screening for high dimensional nonlinear additive ODE models with applications to dynamic gene regulatory networks." Stat Med 37, no. 17 (2018): 2630-2644.
"Module-based association analysis for omics data with network structure." PLoS One 10, no. 3 (2015): e0122309.
"I-Boost: an integrative boosting approach for predicting survival time with multiple genomics platforms." Genome Biol 20, no. 1 (2019): 52.
"Assessing gene-environment interactions for common and rare variants with binary traits using gene-trait similarity regression." Genetics 199, no. 3 (2015): 695-710.
"A Fast Multiple-Kernel Method With Applications to Detect Gene-Environment Interaction." Genet Epidemiol 39, no. 6 (2015): 456-68.
"Complete effect-profile assessment in association studies with multiple genetic and multiple environmental factors." Genet Epidemiol 39, no. 2 (2015): 122-33.
"Integrative gene set analysis of multi-platform data with sample heterogeneity." Bioinformatics 30, no. 11 (2014): 1501-7.
"A junction coverage compatibility score to quantify the reliability of transcript abundance estimates and annotation catalogs." Life Sci Alliance 2, no. 1 (2019).
"Studying gene and gene-environment effects of uncommon and common variants on continuous traits: a marker-set approach using gene-trait similarity regression." Am J Hum Genet 89, no. 2 (2011): 277-88.
"A penalized likelihood approach for investigating gene-drug interactions in pharmacogenetic studies." Biometrics 71, no. 2 (2015): 529-37.
"Evaluating haplotype effects in case-control studies via penalized-likelihood approaches: prospective or retrospective analysis?" Genet Epidemiol 34, no. 8 (2010): 892-911.
"Joint skeleton estimation of multiple directed acyclic graphs for heterogeneous population." Biometrics 75, no. 1 (2019): 36-47.
"Empirical pathway analysis, without permutation." Biostatistics 14, no. 3 (2013): 573-85.
"Quantifying the average of the time-varying hazard ratio via a class of transformations." Lifetime Data Anal 21, no. 2 (2015): 259-79.
"Evaluating haplotype effects in case-control studies via penalized-likelihood approaches: prospective or retrospective analysis?" Genet Epidemiol 34, no. 8 (2010): 892-911.
"Reexamining Dis/Similarity-Based Tests for Rare-Variant Association with Case-Control Samples." Genetics 209, no. 1 (2018): 105-113.
"Robust kernel association testing (RobKAT)." Genet Epidemiol 44, no. 3 (2020): 272-282.
"Pharmacogenomics as a risk mitigation strategy for chemotherapeutic cardiotoxicity." Pharmacogenomics 14, no. 2 (2013): 205-13.
"PreMeta: a tool to facilitate meta-analysis of rare-variant associations." BMC Genomics 18, no. 1 (2017): 160.
"Predicting Alzheimer's Disease Using Combined Imaging-Whole Genome SNP Data." J Alzheimers Dis 46, no. 3 (2015): 695-702.
"Analysis of secondary phenotypes in multigroup association studies." Biometrics 76, no. 2 (2020): 606-618.
"Across-Platform Imputation of DNA Methylation Levels Incorporating Nonlocal Information Using Penalized Functional Regression." Genet Epidemiol 40, no. 4 (2016): 333-40.
"Testing and estimation in marker-set association study using semiparametric quantile regression kernel machine." Biometrics 72, no. 2 (2016): 364-71.
"A simple and accurate method to determine genomewide significance for association tests in sequencing studies." Genet Epidemiol 43, no. 4 (2019): 365-372.
"Multiple testing for gene sets from microarray experiments." BMC Bioinformatics 12 (2011): 209.
"A general framework for studying genetic effects and gene-environment interactions with missing data." Biostatistics 11, no. 4 (2010): 583-98.
"Meta-analysis of sequencing studies with heterogeneous genetic associations." Genet Epidemiol 38, no. 5 (2014): 389-401.
"Identifying individual risk rare variants using protein structure guided local tests (POINT)." PLoS Comput Biol 15, no. 2 (2019): e1006722.
"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.
"Secondary analysis of case-control association studies: Insights on weighting-based inference motivate a new specification test." Stat Med 39, no. 22 (2020): 2869-2882.
"Meta-analysis for Discovering Rare-Variant Associations: Statistical Methods and Software Programs." Am J Hum Genet 97, no. 1 (2015): 35-53.
"On the substructure controls in rare variant analysis: Principal components or variance components?" Genet Epidemiol 42, no. 3 (2018): 276-287.
"Rare Variants Association Analysis in Large-Scale Sequencing Studies at the Single Locus Level." PLoS Comput Biol 12, no. 6 (2016): e1004993.
"permGPU: Using graphics processing units in RNA microarray association studies." BMC Bioinformatics 11 (2010): 329.
"Incorporating Functional Information in Tests of Excess De Novo Mutational Load." Am J Hum Genet 97, no. 2 (2015): 272-83.
"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.
"A general framework for detecting disease associations with rare variants in sequencing studies." Am J Hum Genet 89, no. 3 (2011): 354-67.
"SynthEx: a synthetic-normal-based DNA sequencing tool for copy number alteration detection and tumor heterogeneity profiling." Genome Biol 18, no. 1 (2017): 66.
"Associating somatic mutations to clinical outcomes: a pan-cancer study of survival time." Genome Med 11, no. 1 (2019): 37.
"A New Method for Detecting Associations with Rare Copy-Number Variants." PLoS Genet 11, no. 10 (2015): e1005403.
""Genome-wide association study identifies five new schizophrenia loci." Nat Genet 43, no. 10 (2011): 969-76.
A general framework for association tests with multivariate traits in large-scale genomics studies." Genet Epidemiol 37, no. 8 (2013): 759-67.
"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.
"Statistical considerations for analysis of microarray experiments." Clin Transl Sci 4, no. 6 (2011): 466-77.
"Multivariate phenotype association analysis by marker-set kernel machine regression." Genet Epidemiol 36, no. 7 (2012): 686-95.
"Functional-mixed effects models for candidate genetic mapping in imaging genetic studies." Genet Epidemiol 38, no. 8 (2014): 680-91.
"Bayesian longitudinal low-rank regression models for imaging genetic data from longitudinal studies." Neuroimage 149 (2017): 305-322.
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