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Author: Matthew Stephens

  • ORCiD: http://orcid.org/0000-0001-5397-9257
  • Most recently observed institution: Department of Human Genetics, University of Chicago; Department of Statistics , University of Chicago

Rankings

  • All-time downloads: 69,825 (rank: 582 out of 427,351)
  • Categories:
    • bioinformatics: 12,921 (rank: 407 out of 36,237)
    • evolutionary biology: 1,384 (rank: 3,505 (tie) out of 21,826)
    • genetics: 31,295 (rank: 160 out of 38,054)
    • genomics: 24,225 (rank: 342 out of 44,718)

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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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    • In genetics: 43 out of 5,034
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Characterizing and inferring quantitative cell cycle phase in single-cell RNA-seq data analysis

genomics more details view paper
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A simple new approach to variable selection in regression, with application to genetic fine-mapping

bioinformatics more details view paper
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Visualizing the Structure of RNA-seq Expression Data using Grade of Membership Models

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    • In genetics: 118 out of 5,034
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Bayesian large-scale multiple regression with summary statistics from genome-wide association studies

genetics more details view paper
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False Discovery Rates: A New Deal.

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Exploiting the GTEx resources to decipher the mechanisms at GWAS loci

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

genomics more details view paper
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Visualizing spatial population structure with estimated effective migration surfaces

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    • In genetics: 195 out of 5,034
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Thousands of novel translated open reading frames in humans inferred by ribosome footprint profiling

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    • In genomics: 507 out of 6,271
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Mendelian randomization accounting for correlated and uncorrelated pleiotropic effects using genome-wide summary statistics

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    • In genetics: 220 out of 5,034
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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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Cell type specific genetic regulation of gene expression across human tissues

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    • In genomics: 617 out of 6,271
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A simple model-based approach to inferring and visualizing cancer mutation signatures

bioinformatics more details view paper
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    • In bioinformatics: 799 out of 9,286
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    • Site-wide: 48,900 out of 101,171

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

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Bayesian multivariate reanalysis of large genetic studies identifies many new associations

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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

genetics more details view paper
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    • In genetics: 548 out of 5,034
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CorShrink : Empirical Bayes shrinkage estimation of correlations, with applications

genetics more details view paper
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    • In genetics: 666 out of 5,034
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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

genomics more details view paper
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Estimating recent migration and population size surfaces

bioinformatics more details view paper
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Genotyping Polyploids from Messy Sequencing Data

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    • In bioinformatics: 2,558 out of 9,286
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Discovery and characterization of variance QTLs in human induced pluripotent stem cells

genomics more details view paper
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Silencing Of Transposable Elements May Not Be A Major Driver Of Regulatory Evolution In Primate Induced Pluripotent Stem Cells

genomics more details view paper
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Epigenetic Modifications are Associated with Inter-species Gene Expression Variation in Primates

genomics more details view paper
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Variance Adaptive Shrinkage (vash): Flexible Empirical Bayes estimation of variances

bioinformatics more details view paper
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The Genetic Architecture of Gene Expression Levels in Wild Baboons

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

genetics more details view paper
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    • In genetics: 2,203 out of 5,034
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Dynamic effects of genetic variation on gene expression revealed following hypoxic stress in cardiomyocytes

genomics more details view paper
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    • In genomics: 3,995 out of 6,271
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