Rxivist logo

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: 65,247 (rank: 557 out of 384,898)
  • Categories:
    • bioinformatics: 12,191 (rank: 404 out of 32,961)
    • evolutionary biology: 1,374 (rank: 3,190 (tie) out of 19,701)
    • genetics: 28,886 (rank: 172 out of 35,569)
    • genomics: 22,796 (rank: 349 out of 40,954)

Downloads per author, site-wide

Preprints

The GTEx Consortium atlas of genetic regulatory effects across human tissues

genetics more details view paper
  • Downloaded 6,420 times
  • Download rankings, all-time:
    • Site-wide: 496 out of 89,886
    • In genetics: 40 out of 4,638
  • Year to date:
    • Site-wide: 427 out of 89,886
  • Since beginning of last month:
    • Site-wide: 538 out of 89,886

Variational Inference of Population Structure in Large SNP Datasets

genetics more details view paper
  • Downloaded 6,315 times
  • Download rankings, all-time:
    • Site-wide: 511 out of 89,886
    • In genetics: 41 out of 4,638
  • Year to date:
    • Site-wide: 12,228 out of 89,886
  • Since beginning of last month:
    • Site-wide: 11,673 out of 89,886

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

genomics more details view paper
  • Downloaded 4,904 times
  • Download rankings, all-time:
    • Site-wide: 786 out of 89,886
    • In genomics: 161 out of 5,717
  • Year to date:
    • Site-wide: 743 out of 89,886
  • Since beginning of last month:
    • Site-wide: 3,124 out of 89,886

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

bioinformatics more details view paper
  • Downloaded 3,958 times
  • Download rankings, all-time:
    • Site-wide: 1,156 out of 89,886
    • In bioinformatics: 196 out of 8,475
  • Year to date:
    • Site-wide: 1,211 out of 89,886
  • Since beginning of last month:
    • Site-wide: 2,136 out of 89,886

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

genetics more details view paper
  • Downloaded 3,356 times
  • Download rankings, all-time:
    • Site-wide: 1,523 out of 89,886
    • In genetics: 111 out of 4,638
  • Year to date:
    • Site-wide: 30,725 out of 89,886
  • Since beginning of last month:
    • Site-wide: 18,725 out of 89,886

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

genetics more details view paper
  • Downloaded 2,953 times
  • Download rankings, all-time:
    • Site-wide: 1,934 out of 89,886
    • In genetics: 152 out of 4,638
  • Year to date:
    • Site-wide: 51,321 out of 89,886
  • Since beginning of last month:
    • Site-wide: 42,430 out of 89,886

False Discovery Rates: A New Deal.

bioinformatics more details view paper
  • Downloaded 2,938 times
  • Download rankings, all-time:
    • Site-wide: 1,946 out of 89,886
    • In bioinformatics: 347 out of 8,475
  • Year to date:
    • Site-wide: 58,115 out of 89,886
  • Since beginning of last month:
    • Site-wide: 60,458 out of 89,886

Visualizing spatial population structure with estimated effective migration surfaces

genetics more details view paper
  • Downloaded 2,627 times
  • Download rankings, all-time:
    • Site-wide: 2,327 out of 89,886
    • In genetics: 180 out of 4,638
  • Year to date:
    • Site-wide: 53,987 out of 89,886
  • Since beginning of last month:
    • Site-wide: 31,717 out of 89,886

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

genomics more details view paper
  • Downloaded 2,580 times
  • Download rankings, all-time:
    • Site-wide: 2,416 out of 89,886
    • In genomics: 459 out of 5,717
  • Year to date:
    • Site-wide: 14,282 out of 89,886
  • Since beginning of last month:
    • Site-wide: 27,917 out of 89,886

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

genomics more details view paper
  • Downloaded 2,552 times
  • Download rankings, all-time:
    • Site-wide: 2,455 out of 89,886
    • In genomics: 464 out of 5,717
  • Year to date:
    • Site-wide: 57,950 out of 89,886
  • Since beginning of last month:
    • Site-wide: 39,057 out of 89,886

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

genomics more details view paper
  • Downloaded 2,303 times
  • Download rankings, all-time:
    • Site-wide: 2,930 out of 89,886
    • In genomics: 554 out of 5,717
  • Year to date:
    • Site-wide: 42,570 out of 89,886
  • Since beginning of last month:
    • Site-wide: 27,193 out of 89,886

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

genetics more details view paper
  • Downloaded 2,162 times
  • Download rankings, all-time:
    • Site-wide: 3,236 out of 89,886
    • In genetics: 249 out of 4,638
  • Year to date:
    • Site-wide: 1,899 out of 89,886
  • Since beginning of last month:
    • Site-wide: 3,812 out of 89,886

Exploiting the GTEx resources to decipher the mechanisms at GWAS loci

genetics more details view paper
  • Downloaded 2,118 times
  • Download rankings, all-time:
    • Site-wide: 3,346 out of 89,886
    • In genetics: 254 out of 4,638
  • Year to date:
    • Site-wide: 1,265 out of 89,886
  • Since beginning of last month:
    • Site-wide: 1,104 out of 89,886

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

bioinformatics more details view paper
  • Downloaded 1,906 times
  • Download rankings, all-time:
    • Site-wide: 3,979 out of 89,886
    • In bioinformatics: 716 out of 8,475
  • Year to date:
    • Site-wide: 69,929 out of 89,886
  • Since beginning of last month:
    • Site-wide: 71,529 out of 89,886

Bayesian multivariate reanalysis of large genetic studies identifies many new associations

genomics more details view paper
  • Downloaded 1,811 times
  • Download rankings, all-time:
    • Site-wide: 4,341 out of 89,886
    • In genomics: 736 out of 5,717
  • Year to date:
    • Site-wide: 2,352 out of 89,886
  • Since beginning of last month:
    • Site-wide: 19,694 out of 89,886

Cell type specific genetic regulation of gene expression across human tissues

genomics more details view paper
  • Downloaded 1,805 times
  • Download rankings, all-time:
    • Site-wide: 4,365 out of 89,886
    • In genomics: 741 out of 5,717
  • Year to date:
    • Site-wide: 1,894 out of 89,886
  • Since beginning of last month:
    • Site-wide: 2,006 out of 89,886

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

genomics more details view paper
  • Downloaded 1,590 times
  • Download rankings, all-time:
    • Site-wide: 5,362 out of 89,886
    • In genomics: 891 out of 5,717
  • Year to date:
    • Site-wide: 761 out of 89,886
  • Since beginning of last month:
    • Site-wide: 2,253 out of 89,886

Estimating time to the common ancestor for a beneficial allele

evolutionary biology more details view paper
  • Downloaded 1,374 times
  • Download rankings, all-time:
    • Site-wide: 6,853 out of 89,886
    • In evolutionary biology: 336 out of 5,490
  • Year to date:
    • Site-wide: 78,240 out of 89,886
  • Since beginning of last month:
    • Site-wide: 50,198 out of 89,886

A new sequence logo plot to highlight enrichment and depletion

genetics more details view paper
  • Downloaded 1,333 times
  • Download rankings, all-time:
    • Site-wide: 7,189 out of 89,886
    • In genetics: 514 out of 4,638
  • Year to date:
    • Site-wide: 36,570 out of 89,886
  • Since beginning of last month:
    • Site-wide: 48,208 out of 89,886

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

genomics more details view paper
  • Downloaded 1,139 times
  • Download rankings, all-time:
    • Site-wide: 9,363 out of 89,886
    • In genomics: 1,376 out of 5,717
  • Year to date:
    • Site-wide: 79,983 out of 89,886
  • Since beginning of last month:
    • Site-wide: 69,689 out of 89,886

CorShrink : Empirical Bayes shrinkage estimation of correlations, with applications

genetics more details view paper
  • Downloaded 1,135 times
  • Download rankings, all-time:
    • Site-wide: 9,429 out of 89,886
    • In genetics: 659 out of 4,638
  • Year to date:
    • Site-wide: 22,657 out of 89,886
  • Since beginning of last month:
    • Site-wide: 18,464 out of 89,886

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

bioinformatics more details view paper
  • Downloaded 994 times
  • Download rankings, all-time:
    • Site-wide: 11,701 out of 89,886
    • In bioinformatics: 1,882 out of 8,475
  • Year to date:
    • Site-wide: 70,671 out of 89,886
  • Since beginning of last month:
    • Site-wide: 84,490 out of 89,886

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

genomics more details view paper
  • Downloaded 944 times
  • Download rankings, all-time:
    • Site-wide: 12,693 out of 89,886
    • In genomics: 1,731 out of 5,717
  • Year to date:
    • Site-wide: 42,061 out of 89,886
  • Since beginning of last month:
    • Site-wide: 45,241 out of 89,886

Estimating recent migration and population size surfaces

bioinformatics more details view paper
  • Downloaded 884 times
  • Download rankings, all-time:
    • Site-wide: 14,078 out of 89,886
    • In bioinformatics: 2,197 out of 8,475
  • Year to date:
    • Site-wide: 63,464 out of 89,886
  • Since beginning of last month:
    • Site-wide: 64,013 out of 89,886

Genotyping Polyploids from Messy Sequencing Data

bioinformatics more details view paper
  • Downloaded 837 times
  • Download rankings, all-time:
    • Site-wide: 15,320 out of 89,886
    • In bioinformatics: 2,355 out of 8,475
  • Year to date:
    • Site-wide: 63,384 out of 89,886
  • Since beginning of last month:
    • Site-wide: 82,220 out of 89,886

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

genomics more details view paper
  • Downloaded 808 times
  • Download rankings, all-time:
    • Site-wide: 16,150 out of 89,886
    • In genomics: 2,057 out of 5,717
  • Year to date:
    • Site-wide: 73,366 out of 89,886
  • Since beginning of last month:
    • Site-wide: 64,302 out of 89,886

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

genomics more details view paper
  • Downloaded 721 times
  • Download rankings, all-time:
    • Site-wide: 19,203 out of 89,886
    • In genomics: 2,296 out of 5,717
  • Year to date:
    • Site-wide: 83,077 out of 89,886
  • Since beginning of last month:
    • Site-wide: 74,110 out of 89,886

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

genomics more details view paper
  • Downloaded 681 times
  • Download rankings, all-time:
    • Site-wide: 20,887 out of 89,886
    • In genomics: 2,420 out of 5,717
  • Year to date:
    • Site-wide: 86,843 out of 89,886
  • Since beginning of last month:
    • Site-wide: 85,811 out of 89,886

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

bioinformatics more details view paper
  • Downloaded 674 times
  • Download rankings, all-time:
    • Site-wide: 21,247 out of 89,886
    • In bioinformatics: 3,055 out of 8,475
  • Year to date:
    • Site-wide: 84,829 out of 89,886
  • Since beginning of last month:
    • Site-wide: 76,258 out of 89,886

The Genetic Architecture of Gene Expression Levels in Wild Baboons

genomics more details view paper
  • Downloaded 628 times
  • Download rankings, all-time:
    • Site-wide: 23,488 out of 89,886
    • In genomics: 2,609 out of 5,717
  • Year to date:
    • Site-wide: 79,991 out of 89,886
  • Since beginning of last month:
    • Site-wide: 51,399 out of 89,886

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

genetics more details view paper
  • Downloaded 467 times
  • Download rankings, all-time:
    • Site-wide: 34,341 out of 89,886
    • In genetics: 2,035 out of 4,638
  • Year to date:
    • Site-wide: 84,205 out of 89,886
  • Since beginning of last month:
    • Site-wide: 81,627 out of 89,886

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

genomics more details view paper
  • Downloaded 330 times
  • Download rankings, all-time:
    • Site-wide: 49,433 out of 89,886
    • In genomics: 4,172 out of 5,717
  • Year to date:
    • Site-wide: 7,976 out of 89,886
  • Since beginning of last month:
    • Site-wide: 19,100 out of 89,886

PanLingua

Sign up for the Rxivist weekly newsletter! (Click here for more details.)


News