Publications
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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.
"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.
"A general framework for detecting disease associations with rare variants in sequencing studies." Am J Hum Genet 89, no. 3 (2011): 354-67.
"A simple and accurate method to determine genomewide significance for association tests in sequencing studies." Genet Epidemiol 43, no. 4 (2019): 365-372.
"Associating somatic mutations to clinical outcomes: a pan-cancer study of survival time." Genome Med 11, no. 1 (2019): 37.
"Joint skeleton estimation of multiple directed acyclic graphs for heterogeneous population." Biometrics 75, no. 1 (2019): 36-47.
"Joint skeleton estimation of multiple directed acyclic graphs for heterogeneous population." Biometrics 75, no. 1 (2019): 36-47.
"Tximeta: Reference sequence checksums for provenance identification in RNA-seq." PLoS Comput Biol 16, no. 2 (2020): e1007664.
"Swimming downstream: statistical analysis of differential transcript usage following Salmon quantification." F1000Res 7 (2018): 952.
"Tximeta: Reference sequence checksums for provenance identification in RNA-seq." PLoS Comput Biol 16, no. 2 (2020): e1007664.
"Swimming downstream: statistical analysis of differential transcript usage following Salmon quantification." F1000Res 7 (2018): 952.
"Bayesian longitudinal low-rank regression models for imaging genetic data from longitudinal studies." Neuroimage 149 (2017): 305-322.
"On the substructure controls in rare variant analysis: Principal components or variance components?" Genet Epidemiol 42, no. 3 (2018): 276-287.
"On the substructure controls in rare variant analysis: Principal components or variance components?" Genet Epidemiol 42, no. 3 (2018): 276-287.
"Incorporating higher-order representative features improves prediction in network-based cancer prognosis analysis." BMC Med Genomics 4 (2011): 5.
"Multivariate phenotype association analysis by marker-set kernel machine regression." Genet Epidemiol 36, no. 7 (2012): 686-95.
"Multivariate phenotype association analysis by marker-set kernel machine regression." Genet Epidemiol 36, no. 7 (2012): 686-95.
"Inference on phenotype-specific effects of genes using multivariate kernel machine regression." Genet Epidemiol 42, no. 1 (2018): 64-79.
"A Fast Multiple-Kernel Method With Applications to Detect Gene-Environment Interaction." Genet Epidemiol 39, no. 6 (2015): 456-68.
"A Fast Multiple-Kernel Method With Applications to Detect Gene-Environment Interaction." Genet Epidemiol 39, no. 6 (2015): 456-68.
"Robust kernel association testing (RobKAT)." Genet Epidemiol 44, no. 3 (2020): 272-282.
"Consistency and overfitting of multi-omics methods on experimental data." Brief Bioinform 21, no. 4 (2020): 1277-1284.
"Cancer pharmacogenomics: early promise, but concerted effort needed." Science 339, no. 6127 (2013): 1563-6.
"Cancer pharmacogenomics: early promise, but concerted effort needed." Science 339, no. 6127 (2013): 1563-6.
"Cancer pharmacogenomics: early promise, but concerted effort needed." Science 339, no. 6127 (2013): 1563-6.
"Data for cancer comparative effectiveness research: past, present, and future potential." Cancer 118, no. 21 (2012): 5186-97.
"SNPpy--database management for SNP data from genome wide association studies." PLoS One 6, no. 10 (2011): e24982.
"A penalized likelihood approach for investigating gene-drug interactions in pharmacogenetic studies." Biometrics 71, no. 2 (2015): 529-37.
"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.
"Power and sample size calculations for SNP association studies with censored time-to-event outcomes." Genet Epidemiol 36, no. 6 (2012): 538-48.
"Statistical considerations for analysis of microarray experiments." Clin Transl Sci 4, no. 6 (2011): 466-77.
"Power and sample size calculations for SNP association studies with censored time-to-event outcomes." Genet Epidemiol 36, no. 6 (2012): 538-48.
"Statistical considerations for analysis of microarray experiments." Clin Transl Sci 4, no. 6 (2011): 466-77.
"Statistical considerations for analysis of microarray experiments." Clin Transl Sci 4, no. 6 (2011): 466-77.
"Statistical considerations for analysis of microarray experiments." Clin Transl Sci 4, no. 6 (2011): 466-77.
"Pathway-based identification of SNPs predictive of survival." Eur J Hum Genet 19, no. 6 (2011): 704-9.
"Block-diagonal discriminant analysis and its bias-corrected rules." Stat Appl Genet Mol Biol 12, no. 3 (2013): 347-59.
"Sample size considerations of prediction-validation methods in high-dimensional data for survival outcomes." Genet Epidemiol 37, no. 3 (2013): 276-82.
"Gene selection using iterative feature elimination random forests for survival outcomes." IEEE/ACM Trans Comput Biol Bioinform 9, no. 5 (2012): 1422-31.
"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.
"Pathway-based identification of SNPs predictive of survival." Eur J Hum Genet 19, no. 6 (2011): 704-9.
"Static and Dynamic DNA Loops form AP-1-Bound Activation Hubs during Macrophage Development." Mol Cell 67, no. 6 (2017): 1037-1048.e6.
"Intergenerational response to the endocrine disruptor vinclozolin is influenced by maternal genotype and crossing scheme." Reprod Toxicol 78 (2018): 9-19.
"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.
"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.
"A spatial dirichlet process mixture model for clustering population genetics data." Biometrics 67, no. 2 (2011): 381-90.
""Genome-wide association study identifies five new schizophrenia loci." Nat Genet 43, no. 10 (2011): 969-76.
"Genome-wide association study identifies five new schizophrenia loci." Nat Genet 43, no. 10 (2011): 969-76.
"Genome-wide association study identifies five new schizophrenia loci." Nat Genet 43, no. 10 (2011): 969-76.
"Genome-wide association study identifies five new schizophrenia loci." Nat Genet 43, no. 10 (2011): 969-76.
"Genome-wide association study identifies five new schizophrenia loci." Nat Genet 43, no. 10 (2011): 969-76.
"Genome-wide association study identifies five new schizophrenia loci." Nat Genet 43, no. 10 (2011): 969-76.
permGPU: Using graphics processing units in RNA microarray association studies." BMC Bioinformatics 11 (2010): 329.
"permGPU: Using graphics processing units in RNA microarray association studies." BMC Bioinformatics 11 (2010): 329.
"SynthEx: a synthetic-normal-based DNA sequencing tool for copy number alteration detection and tumor heterogeneity profiling." Genome Biol 18, no. 1 (2017): 66.
"SynthEx: a synthetic-normal-based DNA sequencing tool for copy number alteration detection and tumor heterogeneity profiling." Genome Biol 18, no. 1 (2017): 66.
"SynthEx: a synthetic-normal-based DNA sequencing tool for copy number alteration detection and tumor heterogeneity profiling." Genome Biol 18, no. 1 (2017): 66.
"Multiple testing for gene sets from microarray experiments." BMC Bioinformatics 12 (2011): 209.
"Robust test method for time-course microarray experiments." BMC Bioinformatics 11 (2010): 391.
"Multiple testing for gene sets from microarray experiments." BMC Bioinformatics 12 (2011): 209.
"A junction coverage compatibility score to quantify the reliability of transcript abundance estimates and annotation catalogs." Life Sci Alliance 2, no. 1 (2019).
"A junction coverage compatibility score to quantify the reliability of transcript abundance estimates and annotation catalogs." Life Sci Alliance 2, no. 1 (2019).
"A junction coverage compatibility score to quantify the reliability of transcript abundance estimates and annotation catalogs." Life Sci Alliance 2, no. 1 (2019).
"Alignment and mapping methodology influence transcript abundance estimation." Genome Biol 21, no. 1 (2020): 239.
"The association between copy number aberration, DNA methylation and gene expression in tumor samples." Nucleic Acids Res 46, no. 6 (2018): 3009-3018.
"The association between copy number aberration, DNA methylation and gene expression in tumor samples." Nucleic Acids Res 46, no. 6 (2018): 3009-3018.
"The association between copy number aberration, DNA methylation and gene expression in tumor samples." Nucleic Acids Res 46, no. 6 (2018): 3009-3018.
"MASS: meta-analysis of score statistics for sequencing studies." Bioinformatics 29, no. 14 (2013): 1803-5.
"Meta-analysis for Discovering Rare-Variant Associations: Statistical Methods and Software Programs." Am J Hum Genet 97, no. 1 (2015): 35-53.
"Meta-analysis of sequencing studies with heterogeneous genetic associations." Genet Epidemiol 38, no. 5 (2014): 389-401.
"PreMeta: a tool to facilitate meta-analysis of rare-variant associations." BMC Genomics 18, no. 1 (2017): 160.
"PreMeta: a tool to facilitate meta-analysis of rare-variant associations." BMC Genomics 18, no. 1 (2017): 160.
"Meta-analysis for Discovering Rare-Variant Associations: Statistical Methods and Software Programs." Am J Hum Genet 97, no. 1 (2015): 35-53.
"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 New Method for Detecting Associations with Rare Copy-Number Variants." PLoS Genet 11, no. 10 (2015): e1005403.
"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 New Method for Detecting Associations with Rare Copy-Number Variants." PLoS Genet 11, no. 10 (2015): e1005403.
"A New Method for Detecting Associations with Rare Copy-Number Variants." PLoS Genet 11, no. 10 (2015): e1005403.
"Integrative pipeline for profiling DNA copy number and inferring tumor phylogeny." Bioinformatics 34, no. 12 (2018): 2126-2128.
"Observation weights unlock bulk RNA-seq tools for zero inflation and single-cell applications." Genome Biol 19, no. 1 (2018): 24.
"Reexamining Dis/Similarity-Based Tests for Rare-Variant Association with Case-Control Samples." Genetics 209, no. 1 (2018): 105-113.
"Pathway-guided identification of gene-gene interactions." Ann Hum Genet 78, no. 6 (2014): 478-91.
"Global copy number profiling of cancer genomes." Bioinformatics 32, no. 6 (2016): 926-8.
"Complete effect-profile assessment in association studies with multiple genetic and multiple environmental factors." Genet Epidemiol 39, no. 2 (2015): 122-33.
"Reexamining Dis/Similarity-Based Tests for Rare-Variant Association with Case-Control Samples." Genetics 209, no. 1 (2018): 105-113.
"Allele-specific copy-number discovery from whole-genome and whole-exome sequencing." Nucleic Acids Res 43, no. 14 (2015): e90.
"Module-based association analysis for omics data with network structure." PLoS One 10, no. 3 (2015): e0122309.
"Global copy number profiling of cancer genomes." Bioinformatics 32, no. 6 (2016): 926-8.
"Complete effect-profile assessment in association studies with multiple genetic and multiple environmental factors." Genet Epidemiol 39, no. 2 (2015): 122-33.
"Analysis of gene-gene interactions using gene-trait similarity regression." Hum Hered 78, no. 1 (2014): 17-26.
"SCOPE: A Normalization and Copy-Number Estimation Method for Single-Cell DNA Sequencing." Cell Syst 10, no. 5 (2020): 445-452.e6.
"Complete effect-profile assessment in association studies with multiple genetic and multiple environmental factors." Genet Epidemiol 39, no. 2 (2015): 122-33.
"SCOPE: A Normalization and Copy-Number Estimation Method for Single-Cell DNA Sequencing." Cell Syst 10, no. 5 (2020): 445-452.e6.
"Identifying individual risk rare variants using protein structure guided local tests (POINT)." PLoS Comput Biol 15, no. 2 (2019): e1006722.
"Identifying individual risk rare variants using protein structure guided local tests (POINT)." PLoS Comput Biol 15, no. 2 (2019): e1006722.
"Identifying individual risk rare variants using protein structure guided local tests (POINT)." PLoS Comput Biol 15, no. 2 (2019): e1006722.
"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.
"Genetic analyses of diverse populations improves discovery for complex traits." Nature 570, no. 7762 (2019): 514-518.
"Genetic analyses of diverse populations improves discovery for complex traits." Nature 570, no. 7762 (2019): 514-518.
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