X. Wen

发表

A worldwide survey of haplotype variation and linkage disequilibrium in the human genome

D. Conrad, M. Jakobsson, G. Coop, 2006, Nature Genetics.

The Genotype-Tissue Expression (GTEx) project

Ellen T. Gelfand, Bryan M. Gillard, Karna L. Robinson, 2013, Nature Genetics.

The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans

Jun S. Liu, Ellen T. Gelfand, Ayellet V. Segrè, 2015, Science.

A Statistical Framework for Joint eQTL Analysis in Multiple Tissues

M. Stephens, J. Pritchard, X. Wen, 2012, PLoS genetics.

The GTEx Consortium atlas of genetic regulatory effects across human tissues

Christopher D. Brown, Benjamin J. Strober, Stephane E. Castel, 2019, Science.

A Map of Recent Positive Selection in the Human Genome

J. Pritchard, X. Wen, B. Voight, 2006, PLoS biology.

A Quantitative Proteome Map of the Human Body

Christopher D. Brown, Katherine H. Huang, Christopher M. Lee, 2019, Cell.

Which Genetics Variants in DNase-Seq Footprints Are More Likely to Alter Binding?

Cynthia A. Kalita, Gregory A. Moyerbrailean, Chris T. Harvey, 2016, PLoS genetics.

PhenomeXcan: Mapping the genome to the phenome through the transcriptome

X. Wen, H. Im, A. Barbeira, 2020, Science Advances.

Widespread dose-dependent effects of RNA expression and splicing on complex diseases and traits

Christopher D. Brown, Ayellet V. Segrè, M. McCarthy, 2019, bioRxiv.

PhenomeXcan: Mapping the genome to the phenome through the transcriptome

Milton Pividori, Lisa Bastarache, Xiaoquan Wen, 2019, Science Advances.

Using an atlas of gene regulation across 44 human tissues to inform complex disease- and trait-associated variation

Ayellet V. Segrè, M. McCarthy, Manolis Kellis, 2018, Nature Genetics.

Biobank-driven genomic discovery yields new insight into atrial fibrillation biology

Tanya M. Teslovich, Jonathan H. Chung, Ellen M. Schmidt, 2018, Nature Genetics.

Genome-wide association study of 1 million people identifies 111 loci for atrial fibrillation

Tanya M. Teslovich, Jonathan H. Chung, Ellen M. Schmidt, 2018, bioRxiv.

Large scale meta-analysis characterizes genetic architecture for common psoriasis associated variants

James T. Elder, N. Eriksson, G. Abecasis, 2016, Nature Communications.

Local genetic effects on gene expression across 44 human tissues

Eleazar Eskin, Andrew B. Nobel, Fred A. Wright, 2016, bioRxiv.

The genetic regulatory signature of type 2 diabetes in human skeletal muscle

Laura J. Scott, Stephen C. J. Parker, Karen L. Mohlke, 2016, Nature Communications.

Long non-coding RNA gene regulation and trait associations across human tissues

Ellen, Christopher D. Brown, Benjamin J. Strober, 2019, bioRxiv.

Interspecies variation in hominid gut microbiota controls host gene regulation

X. Wen, M. Burns, R. Pique-Regi, 2020, bioRxiv.

High-Resolution Mapping of Crossovers Reveals Extensive Variation in Fine-Scale Recombination Patterns Among Humans

G. Coop, J. Pritchard, X. Wen, 2008, Science.

QuASAR: Quantitative Allele Specific Analysis of Reads

Gregory A. Moyerbrailean, Chris T. Harvey, Gordon O. Davis, 2014, bioRxiv.

Gene, region and pathway level analyses in whole‐genome studies

X. Wen, D. Nicolae, Minsun Song, 2009, Genetic epidemiology.

Integrating molecular QTL data into genome-wide genetic association analysis: Probabilistic assessment of enrichment and colocalization

X. Wen, R. Pique-Regi, F. Luca, 2016, bioRxiv.

False discovery control for penalized variable selections with high-dimensional covariates

Xiaoping Zhou, X. Wen, Yi Li, 2018, Statistical applications in genetics and molecular biology.

Corrigendum: Synchronized age-related gene expression changes across multiple tissues in human and the link to complex diseases

Ellen T. Gelfand, Ayellet V. Segrè, Casandra A. Trowbridge, 2016, Scientific Reports.

Correction: A Map of Recent Positive Selection in the Human Genome

Xiaoquan Wen, J. Pritchard, X. Wen, 2006, PLoS Biology.

Fine‐mapping and QTL tissue‐sharing information improves the reliability of causal gene identification

K. Ardlie, X. Wen, H. Im, 2020, Genetic epidemiology.

Fine-mapping and QTL tissue-sharing information improve causal gene identification and transcriptome prediction performance

K. Ardlie, X. Wen, H. Im, 2020, bioRxiv.

Impact of admixture and ancestry on eQTL analysis and GWAS colocalization in GTEx

Christopher D. Brown, Margaret L. Antonio, Alicia R. Martin, 2020, Genome biology.

Impact of admixture and ancestry on eQTL analysis and GWAS colocalization in GTEx

Christopher D. Brown, Margaret L. Antonio, Nathan S. Abell, 2019, Genome Biology.

Genome-wide Association Analysis of Psoriatic Arthritis and Cutaneous Psoriasis Reveals Differences in Their Genetic Architecture.

James T. Elder, C. Gieger, G. Abecasis, 2015, American journal of human genetics.

Integrating comprehensive functional annotations to boost power and accuracy in gene-based association analysis

G. Abecasis, H. Kang, M. Boehnke, 2019, bioRxiv.

Integrating comprehensive functional annotations to boost power and accuracy in gene-based association analysis

G. Abecasis, H. Kang, M. Boehnke, 2019, bioRxiv.

Genetic signature to provide robust risk assessment of psoriatic arthritis development in psoriasis patients

Matthew T. Patrick, James T. Elder, G. Abecasis, 2018, Nature Communications.

An eQTL landscape of kidney tissue in human nephrotic syndrome

Paul J. Hoover, Shuqiang Li, N. Hacohen, 2018, bioRxiv.

Documentation for structure software : Version 2 . 3

J. Pritchard, D. Falush, X. Wen, 2009 .

Analyzing and reconciling colocalization and transcriptome-wide association studies from the perspective of inferential reproducibility.

X. Wen, R. Pique-Regi, F. Luca, 2022, American journal of human genetics.

The Role of Environmental Heterogeneity in Meta‐Analysis of Gene–Environment Interactions With Quantitative Traits

Jeremy MG Taylor, M. Boehnke, J. M. Taylor, 2014, Genetic epidemiology.

PTWAS: investigating tissue-relevant causal molecular mechanisms of complex traits using probabilistic TWAS analysis

X. Wen, R. Pique-Regi, A. Barbeira, 2020, Genome Biology.

Cell type–specific genetic regulation of gene expression across human tissues

R. Guigó, G. Getz, M. Stephens, 2020, Science.

A Unified View of False Discovery Rate Control: Reconciliation of Bayesian and Frequentist Approaches

X. Wen, 2018, 1803.05284.

Which genetic variants in DNase I sensitive regions are functional?

Cynthia A. Kalita, Gregory A. Moyerbrailean, Chris T. Harvey, 2014, bioRxiv.

Probabilistic Colocalization of Genetic Variants from Complex and Molecular Traits: Promise and Limitations

X. Wen, H. Im, R. Pique-Regi, 2020, bioRxiv.

Probabilistic colocalization of genetic variants from complex and molecular traits: promise and limitations.

X. Wen, H. Im, R. Pique-Regi, 2020, American journal of human genetics.

Mapping genomic regulation of kidney disease and traits through high-resolution and interpretable eQTLs

X. Wen, M. Sampson, B. Humphreys, 2022, bioRxiv.

Probabilistic integration of transcriptome-wide association studies and colocalization analysis prioritizes molecular pathways of complex traits

X. Wen, H. Im, R. Pique-Regi, 2022, bioRxiv.

Web Supplementary Material for “ Bayesian Model Selection in Complex Linear Systems , as Illustrated in Genetic Association Studies ”

X. Wen, 2013 .

Environmental perturbations lead to extensive directional shifts in RNA processing

X. Wen, R. Pique-Regi, A. Pai, 2017, bioRxiv.

Integrating transcriptomics, metabolomics, and GWAS helps reveal molecular mechanisms for metabolite levels and disease risk

M. Laakso, F. Collins, M. Boehnke, 2022, American journal of human genetics.

Cell type–specific genetic regulation of gene expression across human tissues

Stephane E. Castel, R. Guigó, G. Getz, 2019, Science.

Genetic control of the dynamic transcriptional response to immune stimuli and glucocorticoids at single cell resolution

R. Slatcher, X. Wen, Julong Wei, 2021, bioRxiv.

The GTEx Consortium atlas of genetic regulatory effects across human tissues

Christopher D. Brown, Katherine H. Huang, Jared L. Nedzel, 2019, Science.

Analysis of transcriptional changes in the immune system associated with pubertal development in a longitudinal cohort of children with asthma

R. Slatcher, X. Wen, Julong Wei, 2022, bioRxiv.

Supplemental Material for : Which genetic variants in DNase-seq footprints are more likely to alter binding ?

X. Wen, F. Luca, G. Moyerbrailean, 2016 .

Characterization of caffeine response regulatory variants in vascular endothelial cells

Cynthia A. Kalita, X. Wen, Julong Wei, 2024, bioRxiv.

High-throughput allele-specific expression across 250 environmental conditions

Xiang Zhou, Xiaoquan Wen, Cynthia A. Kalita, 2016, Genome research.

Genetic effects on gene expression across human tissues

Nicola J. Rinaldi, Ian C. McDowell, Christopher D. Brown, 2017, Nature.

Perinatal Lead Exposure Alters Gut Microbiota Composition and Results in Sex-specific Bodyweight Increases in Adult Mice.

X. Wen, K. Boehnke, D. Dolinoy, 2016, Toxicological sciences : an official journal of the Society of Toxicology.

The impact of rare variation on gene expression across tissues

Gao Wang, Mary Goldman, Brian Craft, 2016, Nature.

Evidence for extensive transmission distortion in the human genome.

J. Pritchard, X. Wen, C. Ober, 2004, American journal of human genetics.

Broad-Scale Recombination Patterns Underlying Proper Disjunction in Humans

Daniel J. Wilson, G. Coop, X. Wen, 2009, PLoS genetics.

Population-scale tissue transcriptomics maps long non-coding RNAs to complex disease

Christopher D. Brown, Katherine H. Huang, Christopher M. Lee, 2021, Cell.

High-throughput characterization of genetic effects on DNA–protein binding and gene transcription

Christopher D. Brown, Cynthia A. Kalita, X. Wen, 2018, bioRxiv.

USING LINEAR PREDICTORS TO IMPUTE ALLELE FREQUENCIES FROM SUMMARY OR POOLED GENOTYPE DATA.

Matthew Stephens, Xiaoquan Wen, M. Stephens, 2010, The annals of applied statistics.

Using an atlas of gene regulation across 44 human tissues to inform complex disease- and trait-associated variation

M. McCarthy, Manolis Kellis, G. Getz, 2018, Nature Genetics.

BAYESIAN METHODS FOR GENETIC ASSOCIATION ANALYSIS WITH HETEROGENEOUS SUBGROUPS: FROM META-ANALYSES TO GENE-ENVIRONMENT INTERACTIONS.

Matthew Stephens, Xiaoquan Wen, M. Stephens, 2011, The annals of applied statistics.

Synchronized age-related gene expression changes across multiple tissues in human and the link to complex diseases

Andrew B. Nobel, Fred A. Wright, Ivan Rusyn, 2015, Scientific Reports.

Effects of MYBPC3 loss of function mutations preceding hypertrophic cardiomyopathy.

Lap Man Lee, X. Wen, J. Shavit, 2019, JCI insight.

A Quantitative Proteome Map of the Human Body

Christopher D. Brown, Katherine H. Huang, Christopher M. Lee, 2019, Cell.

Genome-wide association studies of metabolites in Finnish men identify disease-relevant loci

Emily C. Hector, N. Freimer, M. Laakso, 2022, Nature Communications.

Widespread dose-dependent effects of RNA expression and splicing on complex diseases and traits

Christopher D. Brown, M. McCarthy, M. Stephens, 2019, bioRxiv.

Interactions between Glucocorticoid Treatment and Cis-Regulatory Polymorphisms Contribute to Cellular Response Phenotypes

Matthew Stephens, Xiaoquan Wen, Francesca Luca, 2011, PLoS genetics.

Analyzing and Reconciling Colocalization and Transcriptome-wide Association Studies from the Perspective of Inferential Reproducibility

X. Wen, R. Pique-Regi, F. Luca, 2021, bioRxiv.

Molecular QTL discovery incorporating genomic annotations using Bayesian false discovery rate control

Xiaoquan Wen, X. Wen, 2016 .

Efficient Integrative Multi-SNP Association Analysis using Deterministic Approximation of Posteriors

Xiaoquan Wen, Yeji Lee, Francesca Luca, 2015, bioRxiv.

QuASAR: quantitative allele-specific analysis of reads

Xiaoquan Wen, Roger Pique-Regi, Gregory A. Moyerbrailean, 2015, Bioinform..

Quantify and control reproducibility in high-throughput experiments

Yi Zhao, Matthew Sampson, Xiaoquan Wen, 2020, Nature Methods.

Cross-Population Joint Analysis of eQTLs: Fine Mapping and Functional Annotation

Xiaoquan Wen, Francesca Luca, Roger Pique-Regi, 2014, bioRxiv.

Documentation for structure software : Version 2 . 3

J. Pritchard, D. Falush, X. Wen, 2009 .

PTWAS: investigating tissue-relevant causal molecular mechanisms of complex traits using probabilistic TWAS analysis

Xiaoquan Wen, Yuhua Zhang, Hae Kyung Im, 2019, Genome Biology.

Coverage and Characteristics of the Affymetrix GeneChip Human Mapping 100K SNP Set

Xiaoquan Wen, Dan L Nicolae, Nancy J Cox, 2006, PLoS genetics.

Probabilistic integration of transcriptome-wide association studies and colocalization analysis identifies key molecular pathways of complex traits

X. Wen, H. Im, R. Pique-Regi, 2023, American journal of human genetics.

QuASAR‐MPRA: accurate allele‐specific analysis for massively parallel reporter assays

Christopher D. Brown, Xiaoquan Wen, Christopher Brown, 2018, Bioinform..

Revisiting the genome-wide significance threshold for common variant GWAS

M. Boehnke, X. Wen, B. Mukherjee, 2021, G3.

Functional dynamic genetic effects on gene regulation are specific to particular cell types and environmental conditions

Cynthia A. Kalita, Y. Gilad, X. Wen, 2021, bioRxiv.

Exploring the phenotypic consequences of tissue specific gene expression variation inferred from GWAS summary statistics

Nicola J. Rinaldi, Ian C. McDowell, Christopher D. Brown, 2018, Nature Communications.

Interpreting Coronary Artery Disease Risk Through Gene–Environment Interactions in Gene Regulation

G. O. Davis, X. Wen, R. Pique-Regi, 2019, Genetics.

Interpreting Coronary Artery Disease Risk Through Gene–Environment Interactions in Gene Regulation

Gordon O. Davis, X. Wen, R. Pique-Regi, 2018, Genetics.

Bayesian model comparison in genetic association analysis: linear mixed modeling and SNP set testing.

Xiaoquan Wen, X. Wen, Xiaoquan Wen, 2014, Biostatistics.

Functional dynamic genetic effects on gene regulation are specific to particular cell types and environmental conditions.

Cynthia A. Kalita, Y. Gilad, X. Wen, 2021, eLife.

Psychosocial experiences modulate asthma-associated genes through gene-environment interactions

R. Slatcher, X. Wen, D. Wildman, 2020, bioRxiv.

PSYCHOSOCIAL EXPERIENCES , ASTHMA AND GXE 1 Title : Psychosocial experiences modulate asthma-associated genes through gene-environment interactions

R. Slatcher, X. Wen, D. Wildman, 2020 .

Genetic signature to provide robust risk assessment of psoriatic arthritis development in psoriasis patients

James T. Elder, G. Abecasis, H. Kang, 2018, Nature Communications.

Robust Bayesian FDR Control Using Bayes Factors, with Applications to Multi-tissue eQTL Discovery

X. Wen, 2017, Statistics in Biosciences.

Bayesian Multi-SNP Genetic Association Analysis: Control of FDR and Use of Summary Statistics

Xiaoquan Wen, Yeji Lee, Roger Pique-Regi, 2018, bioRxiv.

Association studies for untyped markers with TUNA

Xiaoquan Wen, Dan L. Nicolae, X. Wen, 2008, Bioinform..

Bayesian Analysis of Multiway Tables in Association Studies: A Model Comparison Approach

Xiaoquan Wen, X. Wen, 2012, 1208.4621.

A high-throughput RNA-seq approach to profile transcriptional responses

Gregory A. Moyerbrailean, R. Pique-Regi, Chris T. Harvey, 2015, Scientific Reports.

Statistical Assessment of Replicability via Bayesian Model Criticism

Xiaoquan Wen, Yi Zhao, X. Wen, 2021, 2105.03993.

QuASAR-MPRA: Accurate allele-specific analysis for massively parallel reporter assays

Christopher D. Brown, Cynthia A. Kalita, Gregory A. Moyerbrailean, 2017, bioRxiv.

Bayesian model selection in complex linear systems, as illustrated in genetic association studies

Xiaoquan Wen, X. Wen, Xiaoquan Wen, 2013, Biometrics.

Extended data: Impact of admixture and ancestry on eQTL analysis and GWAS colocalization in GTEx

Christopher D. Brown, Margaret L. Antonio, Michael J. Gloudemans, 2020 .

MOLECULAR QTL DISCOVERY INCORPORATING GENOMIC ANNOTATIONS USING BAYESIAN FALSE DISCOVERY RATE CONTROL1 BY XIAOQUAN WEN

X. Wen, 2016 .

Exploring the phenotypic consequences of tissue specific gene expression variation inferred from GWAS summary statistics

Mary Goldman, Brian Craft, Jingchun Zhu, 2016, Nature Communications.

Exploring the Phenotypic Consequences of Tissue Specific Gene Exploring the Phenotypic Consequences of Tissue Specific Gene Expression Variation Inferred from GWAS Summary Statistics Expression Variation Inferred from GWAS Summary Statistics

Ian C. McDowell, Christopher D. Brown, Eun Yong Kang, 2021 .

Robust Bayesian FDR Control Using Bayes Factors, with Applications to Multi-tissue eQTL Discovery

Xiaoquan Wen, X. Wen, 2013, 1311.3981.

Effective QTL Discovery Incorporating Genomic Annotations

Xiaoquan Wen, X. Wen, 2015, bioRxiv.

Structural factor equation models for causal network construction via directed acyclic mixed graphs

Yan Zhou, Xiaoquan Wen, Peter X-K Song, 2020, Biometrics.

Genetic control of the dynamic transcriptional response to immune stimuli and glucocorticoids at single-cell resolution

R. Slatcher, X. Wen, Julong Wei, 2023, Genome research.

Imperfect gold standard gene sets yield inaccurate evaluation of causal gene identification methods

X. Wen, J. Morrison, Lijia Wang, 2023, bioRxiv.

Biobank-driven genomic discovery yields new insight into atrial fibrillation biology

Tanya M. Teslovich, Jonathan H. Chung, Ryan D. Crawford, 2018, Nature Genetics.

JUMP: replicability analysis of high-throughput experiments with applications to spatial transcriptomic studies

X. Wen, Yan Li, Pengfei Lyu, 2023, bioRxiv.