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Publications

89 papers • 61,917 citations • Sorted by year • Download PDF (PDF by citations)
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1Dissecting tumor transcriptional heterogeneity from single-cell RNA-seq data by generalized binary covariance decomposition
Nature Genetics, 2025, 57, 263-273
16.31Citations (PDF)
2Adjusting for genetic confounders in transcriptome-wide association studies improves discovery of risk genes of complex traits
Nature Genetics, 2024, 56, 336-347
16.317Citations (PDF)
3The Bayesian lens and Bayesian blinkers
Philosophical Transactions Series A, Mathematical, Physical, and Engineering Sciences, 2023, 381,
2.82Citations (PDF)
4A flexible empirical Bayes approach to multivariate multiple regression, and its improved accuracy in predicting multi-tissue gene expression from genotypes
PLoS Genetics, 2023, 19, e1010539
3.31Citations (PDF)
5Fine-mapping studies distinguish genetic risks for childhood- and adult-onset asthma in the HLA region
Genome Medicine, 2022, 14,
9.95Citations (PDF)
6Fine-mapping from summary data with the “Sum of Single Effects” model
PLoS Genetics, 2022, 18, e1010299
3.398Citations (PDF)
7Dispersal syndromes drive the formation of biogeographical regions, illustrated by the case of Wallace’s Line
Global Ecology and Biogeography, 2021, 30, 685-696
5.717Citations (PDF)
8Exploiting the GTEx resources to decipher the mechanisms at GWAS loci
Genome Biology, 2021, 22,
8.4146Citations (PDF)
9Separating measurement and expression models clarifies confusion in single-cell RNA sequencing analysis
Nature Genetics, 2021, 53, 770-777
16.3100Citations (PDF)
10Population-scale tissue transcriptomics maps long non-coding RNAs to complex disease
Cell, 2021, 184, 2633-2648.e19
35.1106Citations (PDF)
11Empirical Bayes shrinkage and false discovery rate estimation, allowing for unwanted variation
Biostatistics, 2020, 21, 15-32
2.111Citations (PDF)
12A Fast Algorithm for Maximum Likelihood Estimation of Mixture Proportions Using Sequential Quadratic Programming
Journal of Computational and Graphical Statistics, 2020, 29, 261-273
2.09Citations (PDF)
13A Simple New Approach to Variable Selection in Regression, with Application to Genetic Fine Mapping
Journal of the Royal Statistical Society Series B: Statistical Methodology, 2020, 82, 1273-1300
2.9366Citations (PDF)
14Cell type–specific genetic regulation of gene expression across human tissues
Science, 2020, 369,
38.2188Citations (PDF)
15The impact of sex on gene expression across human tissues
Science, 2020, 369,
38.2358Citations (PDF)
16A vast resource of allelic expression data spanning human tissues
Genome Biology, 2020, 21,
8.456Citations (PDF)
17Genetic analyses support the contribution of mRNA N6-methyladenosine (m6A) modification to human disease heritability
Nature Genetics, 2020, 52, 939-949
16.3127Citations (PDF)
18Characterizing and inferring quantitative cell cycle phase in single-cell RNA-seq data analysis
Genome Research, 2020, 30, 611-621
4.652Citations (PDF)
19Mendelian randomization accounting for correlated and uncorrelated pleiotropic effects using genome-wide summary statistics
Nature Genetics, 2020, 52, 740-747
16.3316Citations (PDF)
20Author response: Dynamic effects of genetic variation on gene expression revealed following hypoxic stress in cardiomyocytes
2020, ,
0Citations (PDF)
21Detailed modeling of positive selection improves detection of cancer driver genes
Nature Communications, 2019, 10,
14.152Citations (PDF)
22Bayesian multivariate reanalysis of large genetic studies identifies many new associations
PLoS Genetics, 2019, 15, e1008431
3.310Citations (PDF)
23Regional influences on community structure across the tropical-temperate divide
Nature Communications, 2019, 10,
14.139Citations (PDF)
24Discovery and characterization of variance QTLs in human induced pluripotent stem cells
PLoS Genetics, 2019, 15, e1008045
3.343Citations (PDF)
25Estimating recent migration and population-size surfaces
PLoS Genetics, 2019, 15, e1007908
3.352Citations (PDF)
26Inference and visualization of DNA damage patterns using a grade of membership model
Bioinformatics, 2019, 35, 1292-1298
5.06Citations (PDF)
27Creating and sharing reproducible research code the workflowr way
F1000Research, 2019, 8, 1749
0.635Citations (PDF)
28Estimating Time to the Common Ancestor for a Beneficial Allele
Molecular Biology and Evolution, 2018, 35, 1003-1017
4.736Citations (PDF)
29A new sequence logo plot to highlight enrichment and depletion
BMC Bioinformatics, 2018, 19,
3.333Citations (PDF)
30Genotyping Polyploids from Messy Sequencing Data
Genetics, 2018, 210, 789-807
4.2117Citations (PDF)
31Large-scale genome-wide enrichment analyses identify new trait-associated genes and pathways across 31 human phenotypes
Nature Communications, 2018, 9,
14.157Citations (PDF)
32Accurate genomic prediction of Coffea canephora in multiple environments using whole-genome statistical models
Heredity, 2018, 122, 261-275
3.130Citations (PDF)
33Flexible statistical methods for estimating and testing effects in genomic studies with multiple conditions
Nature Genetics, 2018, 51, 187-195
16.3192Citations (PDF)
34Promoter shape varies across populations and affects promoter evolution and expression noise
Nature Genetics, 2017, 49, 550-558
16.352Citations (PDF)
35Bayesian large-scale multiple regression with summary statistics from genome-wide association studies
Annals of Applied Statistics, 2017, 11,
1.283Citations (PDF)
36Visualizing the structure of RNA-seq expression data using grade of membership models
PLoS Genetics, 2017, 13, e1006599
3.390Citations (PDF)
37Variance adaptive shrinkage (<i>vash</i>): flexible empirical Bayes estimation of variances
Bioinformatics, 2016, 32, 3428-3434
5.07Citations (PDF)
38Author response: Thousands of novel translated open reading frames in humans inferred by ribosome footprint profiling
2016, ,
0Citations (PDF)
39Wavelet-based genetic association analysis of functional phenotypes arising from high-throughput sequencing assays
Annals of Applied Statistics, 2015, 9,
1.219Citations (PDF)
40New evidence for hybrid zones of forest and savanna elephants in Central and West Africa
Molecular Ecology, 2015, 24, 6134-6147
3.942Citations (PDF)
41An Estimate of the Average Number of Recessive Lethal Mutations Carried by Humans
Genetics, 2015, 199, 1243-1254
4.253Citations (PDF)
42The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans
Science, 2015, 348, 648-660
38.23,698Citations (PDF)
43Visualizing spatial population structure with estimated effective migration surfaces
Nature Genetics, 2015, 48, 94-100
16.3402Citations (PDF)
44A Simple Model-Based Approach to Inferring and Visualizing Cancer Mutation Signatures
PLoS Genetics, 2015, 11, e1005657
3.391Citations (PDF)
45A Multivariate Genome-Wide Association Analysis of 10 LDL Subfractions, and Their Response to Statin Treatment, in 1868 Caucasians
PLoS ONE, 2015, 10, e0120758
2.5334Citations (PDF)
46msCentipede: Modeling Heterogeneity across Genomic Sites and Replicates Improves Accuracy in the Inference of Transcription Factor Binding
PLoS ONE, 2015, 10, e0138030
2.527Citations (PDF)
47fastSTRUCTURE: Variational Inference of Population Structure in Large SNP Data Sets
Genetics, 2014, 197, 573-589
4.21,169Citations (PDF)
48Bayesian methods for genetic association analysis with heterogeneous subgroups: From meta-analyses to gene–environment interactions
Annals of Applied Statistics, 2014, 8,
1.235Citations (PDF)
49Mangravite et al. reply
Nature, 2014, 513, E3-E3
40.14Citations (PDF)
50Epigenetic modifications are associated with inter-species gene expression variation in primates
Genome Biology, 2014, 15,
8.452Citations (PDF)
51Efficient multivariate linear mixed model algorithms for genome-wide association studies
Nature Methods, 2014, 11, 407-409
14.5550Citations (PDF)
52A statin-dependent QTL for GATM expression is associated with statin-induced myopathy
Nature, 2013, 502, 377-380
40.1181Citations (PDF)
53Integrated Enrichment Analysis of Variants and Pathways in Genome-Wide Association Studies Indicates Central Role for IL-2 Signaling Genes in Type 1 Diabetes, and Cytokine Signaling Genes in Crohn's Disease
PLoS Genetics, 2013, 9, e1003770
3.349Citations (PDF)
54Polygenic Modeling with Bayesian Sparse Linear Mixed Models
PLoS Genetics, 2013, 9, e1003264
3.3530Citations (PDF)
55A Statistical Framework for Joint eQTL Analysis in Multiple Tissues
PLoS Genetics, 2013, 9, e1003486
3.3168Citations (PDF)
56Genetic, Functional and Molecular Features of Glucocorticoid Receptor Binding
PLoS ONE, 2013, 8, e61654
2.519Citations (PDF)
57A Unified Framework for Association Analysis with Multiple Related Phenotypes
PLoS ONE, 2013, 8, e65245
2.5169Citations (PDF)
58The Contribution of RNA Decay Quantitative Trait Loci to Inter-Individual Variation in Steady-State Gene Expression Levels
PLoS Genetics, 2012, 8, e1003000
3.380Citations (PDF)
59Scalable Variational Inference for Bayesian Variable Selection in Regression, and Its Accuracy in Genetic Association Studies
Bayesian Analysis, 2012, 7,
1.6159Citations (PDF)
60Dissecting the regulatory architecture of gene expression QTLs
Genome Biology, 2012, 13,
8.4151Citations (PDF)
61DNase I sensitivity QTLs are a major determinant of human expression variation
Nature, 2012, 482, 390-394
40.1478Citations (PDF)
62Fast and accurate genotype imputation in genome-wide association studies through pre-phasing
Nature Genetics, 2012, 44, 955-959
16.31,351Citations (PDF)
63Exon-Specific QTLs Skew the Inferred Distribution of Expression QTLs Detected Using Gene Expression Array Data
PLoS ONE, 2012, 7, e30629
2.516Citations (PDF)
64Genome-Wide Association Study of d-Amphetamine Response in Healthy Volunteers Identifies Putative Associations, Including Cadherin 13 (CDH13)
PLoS ONE, 2012, 7, e42646
2.563Citations (PDF)
65Genome-wide efficient mixed-model analysis for association studies
Nature Genetics, 2012, 44, 821-824
16.32,156Citations (PDF)
66Bayesian variable selection regression for genome-wide association studies and other large-scale problems
Annals of Applied Statistics, 2011, 5,
1.2240Citations (PDF)
67Interactions between Glucocorticoid Treatment and Cis-Regulatory Polymorphisms Contribute to Cellular Response Phenotypes
PLoS Genetics, 2011, 7, e1002162
3.386Citations (PDF)
68Genotype Imputation with Thousands of Genomes
G3: Genes, Genomes, Genetics, 2011, 1, 457-470
2.0750Citations (PDF)
69Using linear predictors to impute allele frequencies from summary or pooled genotype data
Annals of Applied Statistics, 2010, 4,
1.252Citations (PDF)
70Understanding mechanisms underlying human gene expression variation with RNA sequencing
Nature, 2010, 464, 768-772
40.1996Citations (PDF)
71Analysis of Population Structure: A Unifying Framework and Novel Methods Based on Sparse Factor Analysis
PLoS Genetics, 2010, 6, e1001117
3.399Citations (PDF)
72Genome-Wide Association of Lipid-Lowering Response to Statins in Combined Study Populations
PLoS ONE, 2010, 5, e9763
2.5195Citations (PDF)
73Bayesian statistical methods for genetic association studies
Nature Reviews Genetics, 2009, 10, 681-690
19.1337Citations (PDF)
74Interpreting principal component analyses of spatial population genetic variation
Nature Genetics, 2008, 40, 646-649
16.3431Citations (PDF)
75RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays
Genome Research, 2008, 18, 1509-1517
4.62,147Citations (PDF)
76High-Resolution Mapping of Expression-QTLs Yields Insight into Human Gene Regulation
PLoS Genetics, 2008, 4, e1000214
3.3442Citations (PDF)
77Practical Issues in Imputation-Based Association Mapping
PLoS Genetics, 2008, 4, e1000279
3.3136Citations (PDF)
78Imputation-Based Analysis of Association Studies: Candidate Regions and Quantitative Traits
PLoS Genetics, 2007, 3, e114
3.3389Citations (PDF)
79A second generation human haplotype map of over 3.1 million SNPs
Nature, 2007, 449, 851-861
40.13,633Citations (PDF)
80A Fast and Flexible Statistical Model for Large-Scale Population Genotype Data: Applications to Inferring Missing Genotypes and Haplotypic Phase
American Journal of Human Genetics, 2006, 78, 629-644
6.81,527Citations (PDF)
81Inference of Population Structure Using Multilocus Genotype Data: Linked Loci and Correlated Allele Frequencies
Genetics, 2003, 164, 1567-1587
4.26,490Citations (PDF)
82Modeling Linkage Disequilibrium and Identifying Recombination Hotspots Using Single-Nucleotide Polymorphism Data
Genetics, 2003, 165, 2213-2233
4.2716Citations (PDF)
83Dealing with label switching in mixture models
Journal of the Royal Statistical Society Series B: Statistical Methodology, 2000, 62, 795-809
2.9721Citations (PDF)
84Inference of Population Structure Using Multilocus Genotype Data
Genetics, 2000, 155, 945-959
4.226,688Citations (PDF)
85False discovery rates: a new deal
Biostatistics, 0, , kxw041
2.1361Citations (PDF)
86Silencing of transposable elements may not be a major driver of regulatory evolution in primate iPSCs
ELife, 0, 7,
1.619Citations (PDF)
87Dynamic effects of genetic variation on gene expression revealed following hypoxic stress in cardiomyocytes
ELife, 0, 10,
1.631Citations (PDF)
88The genetic architecture of gene expression levels in wild baboons
ELife, 0, 4,
1.671Citations (PDF)
89Thousands of novel translated open reading frames in humans inferred by ribosome footprint profiling
ELife, 0, 5,
1.6101Citations (PDF)