Author: Matthew Stephens

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Preprints

The GTEx Consortium atlas of genetic regulatory effects across human tissues

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Variational Inference of Population Structure in Large SNP Datasets

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Characterizing and inferring quantitative cell cycle phase in single-cell RNA-seq data analysis

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A simple new approach to variable selection in regression, with application to genetic fine-mapping

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Visualizing the Structure of RNA-seq Expression Data using Grade of Membership Models

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Bayesian large-scale multiple regression with summary statistics from genome-wide association studies

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False Discovery Rates: A New Deal.

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Visualizing spatial population structure with estimated effective migration surfaces

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Flexible statistical methods for estimating and testing effects in genomic studies with multiple conditions

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Thousands of novel translated open reading frames in humans inferred by ribosome footprint profiling

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Exploiting the GTEx resources to decipher the mechanisms at GWAS loci

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A large-scale genome-wide enrichment analysis identifies new trait-associated genes, pathways and tissues across 31 human phenotypes

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Mendelian randomization accounting for correlated and uncorrelated pleiotropic effects using genome-wide summary statistics

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Cell type specific genetic regulation of gene expression across human tissues

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A simple model-based approach to inferring and visualizing cancer mutation signatures

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Bayesian multivariate reanalysis of large genetic studies identifies many new associations

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Separating measurement and expression models clarifies confusion in single cell RNA-seq analysis

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Estimating time to the common ancestor for a beneficial allele

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A new sequence logo plot to highlight enrichment and depletion

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CorShrink : Empirical Bayes shrinkage estimation of correlations, with applications

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msCentipede: Modeling heterogeneity across genomic sites improves accuracy in the inference of transcription factor binding

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Inference and visualization of DNA damage patterns using a grade of membership model

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Model-based analysis of positive selection significantly expands the list of cancer driver genes, including RNA methyltransferases

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Estimating recent migration and population size surfaces

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Genotyping Polyploids from Messy Sequencing Data

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Discovery and characterization of variance QTLs in human induced pluripotent stem cells

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Silencing Of Transposable Elements May Not Be A Major Driver Of Regulatory Evolution In Primate Induced Pluripotent Stem Cells

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Epigenetic Modifications are Associated with Inter-species Gene Expression Variation in Primates

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Variance Adaptive Shrinkage (vash): Flexible Empirical Bayes estimation of variances

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The Genetic Architecture of Gene Expression Levels in Wild Baboons

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A multivariate genome-wide association analysis of 10 LDL subfractions, and their response to statin treatment, in 1868 Caucasians

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Dynamic effects of genetic variation on gene expression revealed following hypoxic stress in cardiomyocytes

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