Publications
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.
"Inference on phenotype-specific effects of genes using multivariate kernel machine regression." Genet Epidemiol 42, no. 1 (2018): 64-79.
"Cancer pharmacogenomics: early promise, but concerted effort needed." Science 339, no. 6127 (2013): 1563-6.
"Genome analysis and pleiotropy assessment using causal networks with loss of function mutation and metabolomics." BMC Genomics 20, no. 1 (2019): 395.
"Complete effect-profile assessment in association studies with multiple genetic and multiple environmental factors." Genet Epidemiol 39, no. 2 (2015): 122-33.
""Genome-wide association study identifies five new schizophrenia loci." Nat Genet 43, no. 10 (2011): 969-76.
Rare Variants Association Analysis in Large-Scale Sequencing Studies at the Single Locus Level." PLoS Comput Biol 12, no. 6 (2016): e1004993.
"Identifying individual risk rare variants using protein structure guided local tests (POINT)." PLoS Comput Biol 15, no. 2 (2019): e1006722.
"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.
"Association test using Copy Number Profile Curves (CONCUR) enhances power in rare copy number variant analysis." PLoS Comput Biol 16, no. 5 (2020): e1007797.
"Bayesian analysis on meta-analysis of case-control studies accounting for within-study correlation." Stat Methods Med Res 24, no. 6 (2015): 836-55.
"A New Method for Detecting Associations with Rare Copy-Number Variants." PLoS Genet 11, no. 10 (2015): e1005403.
"Power and sample size calculations for SNP association studies with censored time-to-event outcomes." Genet Epidemiol 36, no. 6 (2012): 538-48.
"Pathway-based identification of SNPs predictive of survival." Eur J Hum Genet 19, no. 6 (2011): 704-9.
"Common variants in psychiatric risk genes predict brain structure at birth." Cereb Cortex 24, no. 5 (2014): 1230-46.
"Exploiting expression patterns across multiple tissues to map expression quantitative trait loci." BMC Bioinformatics 17 (2016): 257.
"Association test using Copy Number Profile Curves (CONCUR) enhances power in rare copy number variant analysis." PLoS Comput Biol 16, no. 5 (2020): e1007797.
"Common variants in psychiatric risk genes predict brain structure at birth." Cereb Cortex 24, no. 5 (2014): 1230-46.
"Identifying individual risk rare variants using protein structure guided local tests (POINT)." PLoS Comput Biol 15, no. 2 (2019): e1006722.
"Meta-analysis for Discovering Rare-Variant Associations: Statistical Methods and Software Programs." Am J Hum Genet 97, no. 1 (2015): 35-53.
"MASS: meta-analysis of score statistics for sequencing studies." Bioinformatics 29, no. 14 (2013): 1803-5.
"Reexamining Dis/Similarity-Based Tests for Rare-Variant Association with Case-Control Samples." Genetics 209, no. 1 (2018): 105-113.
"On the substructure controls in rare variant analysis: Principal components or variance components?" Genet Epidemiol 42, no. 3 (2018): 276-287.
"Analysis of untyped SNPs: maximum likelihood and imputation methods." Genet Epidemiol 34, no. 8 (2010): 803-15.
"A general framework for association tests with multivariate traits in large-scale genomics studies." Genet Epidemiol 37, no. 8 (2013): 759-67.
"A Fast Multiple-Kernel Method With Applications to Detect Gene-Environment Interaction." Genet Epidemiol 39, no. 6 (2015): 456-68.
"PreMeta: a tool to facilitate meta-analysis of rare-variant associations." BMC Genomics 18, no. 1 (2017): 160.
"Meta-analysis of gene-level associations for rare variants based on single-variant statistics." Am J Hum Genet 93, no. 2 (2013): 236-48.
"Genetic analyses of diverse populations improves discovery for complex traits." Nature 570, no. 7762 (2019): 514-518.
"A spatial dirichlet process mixture model for clustering population genetics data." Biometrics 67, no. 2 (2011): 381-90.
"Predicting Alzheimer's Disease Using Combined Imaging-Whole Genome SNP Data." J Alzheimers Dis 46, no. 3 (2015): 695-702.
"Genome analysis and pleiotropy assessment using causal networks with loss of function mutation and metabolomics." BMC Genomics 20, no. 1 (2019): 395.
"A simple and accurate method to determine genomewide significance for association tests in sequencing studies." Genet Epidemiol 43, no. 4 (2019): 365-372.
""Genome-wide association study identifies five new schizophrenia loci." Nat Genet 43, no. 10 (2011): 969-76.
Analysis of untyped SNPs: maximum likelihood and imputation methods." Genet Epidemiol 34, no. 8 (2010): 803-15.
"Cancer pharmacogenomics: early promise, but concerted effort needed." Science 339, no. 6127 (2013): 1563-6.
"A general framework for association tests with multivariate traits in large-scale genomics studies." Genet Epidemiol 37, no. 8 (2013): 759-67.
"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.
"A junction coverage compatibility score to quantify the reliability of transcript abundance estimates and annotation catalogs." Life Sci Alliance 2, no. 1 (2019).
"SCOPE: A Normalization and Copy-Number Estimation Method for Single-Cell DNA Sequencing." Cell Syst 10, no. 5 (2020): 445-452.e6.
"TEAM: efficient two-locus epistasis tests in human genome-wide association study." Bioinformatics 26, no. 12 (2010): i217-27.
"Global copy number profiling of cancer genomes." Bioinformatics 32, no. 6 (2016): 926-8.
"Association test using Copy Number Profile Curves (CONCUR) enhances power in rare copy number variant analysis." PLoS Comput Biol 16, no. 5 (2020): e1007797.
"Analysis of untyped SNPs: maximum likelihood and imputation methods." Genet Epidemiol 34, no. 8 (2010): 803-15.
"Effective SNP ranking improves the performance of eQTL mapping." Genet Epidemiol 44, no. 6 (2020): 611-619.
"A general framework for detecting disease associations with rare variants in sequencing studies." Am J Hum Genet 89, no. 3 (2011): 354-67.
"Combining an evolution-guided clustering algorithm and haplotype-based LRT in family association studies." BMC Genet 12 (2011): 48.
"Meta-analysis of gene-level associations for rare variants based on single-variant statistics." Am J Hum Genet 93, no. 2 (2013): 236-48.
"Exploiting expression patterns across multiple tissues to map expression quantitative trait loci." BMC Bioinformatics 17 (2016): 257.
"A framework for transcriptome-wide association studies in breast cancer in diverse study populations." Genome Biol 21, no. 1 (2020): 42.
"Sample size considerations of prediction-validation methods in high-dimensional data for survival outcomes." Genet Epidemiol 37, no. 3 (2013): 276-82.
"Efficient estimation of grouped survival models." BMC Bioinformatics 20, no. 1 (2019): 269.
"fastJT: An R package for robust and efficient feature selection for machine learning and genome-wide association studies." BMC Bioinformatics 20, no. 1 (2019): 333.
""Genome-wide association study identifies five new schizophrenia loci." Nat Genet 43, no. 10 (2011): 969-76.
Genetic analyses of diverse populations improves discovery for complex traits." Nature 570, no. 7762 (2019): 514-518.
"Power and sample size calculations for SNP association studies with censored time-to-event outcomes." Genet Epidemiol 36, no. 6 (2012): 538-48.
"Complete effect-profile assessment in association studies with multiple genetic and multiple environmental factors." Genet Epidemiol 39, no. 2 (2015): 122-33.
"Meta-analysis of genome-wide association studies: no efficiency gain in using individual participant data." Genet Epidemiol 34, no. 1 (2010): 60-6.
"Whole-Genome and Epigenomic Landscapes of Etiologically Distinct Subtypes of Cholangiocarcinoma." Cancer Discov 7, no. 10 (2017): 1116-1135.
"TEAM: efficient two-locus epistasis tests in human genome-wide association study." Bioinformatics 26, no. 12 (2010): i217-27.
"A New Method for Detecting Associations with Rare Copy-Number Variants." PLoS Genet 11, no. 10 (2015): e1005403.
"Sparse meta-analysis with high-dimensional data." Biostatistics 17, no. 2 (2016): 205-20.
"SNPpy--database management for SNP data from genome wide association studies." PLoS One 6, no. 10 (2011): e24982.
"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.
"A general framework for association tests with multivariate traits in large-scale genomics studies." Genet Epidemiol 37, no. 8 (2013): 759-67.
"Multivariate phenotype association analysis by marker-set kernel machine regression." Genet Epidemiol 36, no. 7 (2012): 686-95.
"Genomewide Meta-Analysis Validates a Role for S1PR1 in Microtubule Targeting Agent-Induced Sensory Peripheral Neuropathy." Clin Pharmacol Ther 108, no. 3 (2020): 625-634.
"A variable selection method for genome-wide association studies." Bioinformatics 27, no. 1 (2011): 1-8.
"Prediction of a time-to-event trait using genome wide SNP data." BMC Bioinformatics 14 (2013): 58.
"Association test using Copy Number Profile Curves (CONCUR) enhances power in rare copy number variant analysis." PLoS Comput Biol 16, no. 5 (2020): e1007797.
"A junction coverage compatibility score to quantify the reliability of transcript abundance estimates and annotation catalogs." Life Sci Alliance 2, no. 1 (2019).
"SCOPE: A Normalization and Copy-Number Estimation Method for Single-Cell DNA Sequencing." Cell Syst 10, no. 5 (2020): 445-452.e6.
"Consistency and overfitting of multi-omics methods on experimental data." Brief Bioinform 21, no. 4 (2020): 1277-1284.
"Integrative pipeline for profiling DNA copy number and inferring tumor phylogeny." Bioinformatics 34, no. 12 (2018): 2126-2128.
"A general framework for association tests with multivariate traits in large-scale genomics studies." Genet Epidemiol 37, no. 8 (2013): 759-67.
"Generation of a Transcriptional Radiation Exposure Signature in Human Blood Using Long-Read Nanopore Sequencing." Radiat Res 193, no. 2 (2020): 143-154.
"I-Boost: an integrative boosting approach for predicting survival time with multiple genomics platforms." Genome Biol 20, no. 1 (2019): 52.
"TEAM: efficient two-locus epistasis tests in human genome-wide association study." Bioinformatics 26, no. 12 (2010): i217-27.
"Tximeta: Reference sequence checksums for provenance identification in RNA-seq." PLoS Comput Biol 16, no. 2 (2020): e1007664.
"Sparse meta-analysis with high-dimensional data." Biostatistics 17, no. 2 (2016): 205-20.
"Statistical significance for hierarchical clustering." Biometrics 73, no. 3 (2017): 811-821.
"Allele-specific copy-number discovery from whole-genome and whole-exome sequencing." Nucleic Acids Res 43, no. 14 (2015): e90.
"Prediction of a time-to-event trait using genome wide SNP data." BMC Bioinformatics 14 (2013): 58.
"Rare Variants Association Analysis in Large-Scale Sequencing Studies at the Single Locus Level." PLoS Comput Biol 12, no. 6 (2016): e1004993.
"Integrative gene set analysis of multi-platform data with sample heterogeneity." Bioinformatics 30, no. 11 (2014): 1501-7.
"Association test using Copy Number Profile Curves (CONCUR) enhances power in rare copy number variant analysis." PLoS Comput Biol 16, no. 5 (2020): e1007797.
"A general framework for integrative analysis of incomplete multiomics data." Genet Epidemiol 44, no. 7 (2020): 646-664.
"CODEX2: full-spectrum copy number variation detection by high-throughput DNA sequencing." Genome Biol 19, no. 1 (2018): 202.
"Analysing breast cancer microarrays from African Americans using shrinkage-based discriminant analysis." Hum Genomics 5, no. 1 (2010): 5-16.
"Intergenerational response to the endocrine disruptor vinclozolin is influenced by maternal genotype and crossing scheme." Reprod Toxicol 78 (2018): 9-19.
"Pathway-based identification of SNPs predictive of survival." Eur J Hum Genet 19, no. 6 (2011): 704-9.
"Common variants in psychiatric risk genes predict brain structure at birth." Cereb Cortex 24, no. 5 (2014): 1230-46.
"Analysis of gene-gene interactions using gene-trait similarity regression." Hum Hered 78, no. 1 (2014): 17-26.
"A general framework for studying genetic effects and gene-environment interactions with missing data." Biostatistics 11, no. 4 (2010): 583-98.
"Analysis of untyped SNPs: maximum likelihood and imputation methods." Genet Epidemiol 34, no. 8 (2010): 803-15.
"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.
"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.
"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.
"Nomenclature for alleles of the thiopurine methyltransferase gene." Pharmacogenet Genomics 23, no. 4 (2013): 242-8.
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