Matthew Stephens to Humans
This is a "connection" page, showing publications Matthew Stephens has written about Humans.
Connection Strength
0.671
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Separating measurement and expression models clarifies confusion in single-cell RNA sequencing analysis. Nat Genet. 2021 06; 53(6):770-777.
Score: 0.026
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Empirical Bayes shrinkage and false discovery rate estimation, allowing for unwanted variation. Biostatistics. 2020 01 01; 21(1):15-32.
Score: 0.024
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Inference and visualization of DNA damage patterns using a grade of membership model. Bioinformatics. 2019 04 15; 35(8):1292-1298.
Score: 0.023
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A new sequence logo plot to highlight enrichment and depletion. BMC Bioinformatics. 2018 Dec 10; 19(1):473.
Score: 0.022
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Flexible statistical methods for estimating and testing effects in genomic studies with multiple conditions. Nat Genet. 2019 01; 51(1):187-195.
Score: 0.022
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Large-scale genome-wide enrichment analyses identify new trait-associated genes and pathways across 31 human phenotypes. Nat Commun. 2018 10 19; 9(1):4361.
Score: 0.022
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False discovery rates: a new deal. Biostatistics. 2017 04 01; 18(2):275-294.
Score: 0.020
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Visualizing the structure of RNA-seq expression data using grade of membership models. PLoS Genet. 2017 Mar; 13(3):e1006599.
Score: 0.020
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Variance adaptive shrinkage (vash): flexible empirical Bayes estimation of variances. Bioinformatics. 2016 11 15; 32(22):3428-3434.
Score: 0.019
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Visualizing spatial population structure with estimated effective migration surfaces. Nat Genet. 2016 Jan; 48(1):94-100.
Score: 0.018
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A Simple Model-Based Approach to Inferring and Visualizing Cancer Mutation Signatures. PLoS Genet. 2015 Dec; 11(12):e1005657.
Score: 0.018
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msCentipede: Modeling Heterogeneity across Genomic Sites and Replicates Improves Accuracy in the Inference of Transcription Factor Binding. PLoS One. 2015; 10(9):e0138030.
Score: 0.018
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A multivariate genome-wide association analysis of 10 LDL subfractions, and their response to statin treatment, in 1868 Caucasians. PLoS One. 2015; 10(4):e0120758.
Score: 0.017
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Integrated 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 Genet. 2013; 9(10):e1003770.
Score: 0.016
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A unified framework for association analysis with multiple related phenotypes. PLoS One. 2013; 8(7):e65245.
Score: 0.015
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Polygenic modeling with bayesian sparse linear mixed models. PLoS Genet. 2013; 9(2):e1003264.
Score: 0.015
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Genome-wide efficient mixed-model analysis for association studies. Nat Genet. 2012 Jun 17; 44(7):821-4.
Score: 0.014
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Analysis of population structure: a unifying framework and novel methods based on sparse factor analysis. PLoS Genet. 2010 Sep 16; 6(9):e1001117.
Score: 0.013
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Response to Cavalli-Sforza interview [Human Biology 82(3):245-266 (June 2010)]. Hum Biol. 2010 Aug; 82(4):469-70.
Score: 0.013
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Bayesian statistical methods for genetic association studies. Nat Rev Genet. 2009 Oct; 10(10):681-90.
Score: 0.012
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Practical issues in imputation-based association mapping. PLoS Genet. 2008 Dec; 4(12):e1000279.
Score: 0.011
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Linkage disequilibrium-based quality control for large-scale genetic studies. PLoS Genet. 2008 Aug 01; 4(8):e1000147.
Score: 0.011
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Interpreting principal component analyses of spatial population genetic variation. Nat Genet. 2008 May; 40(5):646-9.
Score: 0.011
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Imputation-based analysis of association studies: candidate regions and quantitative traits. PLoS Genet. 2007 Jul; 3(7):e114.
Score: 0.010
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Insights into recombination from population genetic variation. Curr Opin Genet Dev. 2006 Dec; 16(6):565-72.
Score: 0.010
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A fast and flexible statistical model for large-scale population genotype data: applications to inferring missing genotypes and haplotypic phase. Am J Hum Genet. 2006 Apr; 78(4):629-44.
Score: 0.009
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The effects of genotype-dependent recombination, and transmission asymmetry, on linkage disequilibrium. Genetics. 2006 Mar; 172(3):2001-5.
Score: 0.009
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Accounting for decay of linkage disequilibrium in haplotype inference and missing-data imputation. Am J Hum Genet. 2005 Mar; 76(3):449-62.
Score: 0.009
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Evidence for substantial fine-scale variation in recombination rates across the human genome. Nat Genet. 2004 Jul; 36(7):700-6.
Score: 0.008
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Adjusting for genetic confounders in transcriptome-wide association studies improves discovery of risk genes of complex traits. Nat Genet. 2024 Feb; 56(2):336-347.
Score: 0.008
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Modeling linkage disequilibrium and identifying recombination hotspots using single-nucleotide polymorphism data. Genetics. 2003 Dec; 165(4):2213-33.
Score: 0.008
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A comparison of bayesian methods for haplotype reconstruction from population genotype data. Am J Hum Genet. 2003 Nov; 73(5):1162-9.
Score: 0.008
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Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics. 2003 Aug; 164(4):1567-87.
Score: 0.008
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Fine-mapping studies distinguish genetic risks for childhood- and adult-onset asthma in the HLA region. Genome Med. 2022 05 24; 14(1):55.
Score: 0.007
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Dynamic effects of genetic variation on gene expression revealed following hypoxic stress in cardiomyocytes. Elife. 2021 02 08; 10.
Score: 0.006
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Exploiting the GTEx resources to decipher the mechanisms at GWAS loci. Genome Biol. 2021 01 26; 22(1):49.
Score: 0.006
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The impact of sex on gene expression across human tissues. Science. 2020 09 11; 369(6509).
Score: 0.006
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Cell type-specific genetic regulation of gene expression across human tissues. Science. 2020 09 11; 369(6509).
Score: 0.006
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Genetic analyses support the contribution of mRNA N6-methyladenosine (m6A) modification to human disease heritability. Nat Genet. 2020 09; 52(9):939-949.
Score: 0.006
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Characterizing and inferring quantitative cell cycle phase in single-cell RNA-seq data analysis. Genome Res. 2020 04; 30(4):611-621.
Score: 0.006
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Detailed modeling of positive selection improves detection of cancer driver genes. Nat Commun. 2019 07 30; 10(1):3399.
Score: 0.006
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Discovery and characterization of variance QTLs in human induced pluripotent stem cells. PLoS Genet. 2019 04; 15(4):e1008045.
Score: 0.006
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Estimating recent migration and population-size surfaces. PLoS Genet. 2019 01; 15(1):e1007908.
Score: 0.006
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Silencing of transposable elements may not be a major driver of regulatory evolution in primate iPSCs. Elife. 2018 04 12; 7.
Score: 0.005
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Estimating Time to the Common Ancestor for a Beneficial Allele. Mol Biol Evol. 2018 04 01; 35(4):1003-1017.
Score: 0.005
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Thousands of novel translated open reading frames in humans inferred by ribosome footprint profiling. Elife. 2016 05 27; 5.
Score: 0.005
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An estimate of the average number of recessive lethal mutations carried by humans. Genetics. 2015 Apr; 199(4):1243-54.
Score: 0.004
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Mangravite et al. reply. Nature. 2014 Sep 18; 513(7518):E3.
Score: 0.004
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fastSTRUCTURE: variational inference of population structure in large SNP data sets. Genetics. 2014 Jun; 197(2):573-89.
Score: 0.004
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Epigenetic modifications are associated with inter-species gene expression variation in primates. Genome Biol. 2014; 15(12):547.
Score: 0.004
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A statin-dependent QTL for GATM expression is associated with statin-induced myopathy. Nature. 2013 Oct 17; 502(7471):377-80.
Score: 0.004
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Genetic, functional and molecular features of glucocorticoid receptor binding. PLoS One. 2013; 8(4):e61654.
Score: 0.004
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The contribution of RNA decay quantitative trait loci to inter-individual variation in steady-state gene expression levels. PLoS Genet. 2012; 8(10):e1003000.
Score: 0.004
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Genome-wide association study of d-amphetamine response in healthy volunteers identifies putative associations, including cadherin 13 (CDH13). PLoS One. 2012; 7(8):e42646.
Score: 0.004
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Fast and accurate genotype imputation in genome-wide association studies through pre-phasing. Nat Genet. 2012 Jul 22; 44(8):955-9.
Score: 0.004
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Statistical inference of in vivo properties of human DNA methyltransferases from double-stranded methylation patterns. PLoS One. 2012; 7(3):e32225.
Score: 0.004
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Mapping gene-environment interactions at regulatory polymorphisms: insights into mechanisms of phenotypic variation. Transcription. 2012 Mar-Apr; 3(2):56-62.
Score: 0.003
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Exon-specific QTLs skew the inferred distribution of expression QTLs detected using gene expression array data. PLoS One. 2012; 7(2):e30629.
Score: 0.003
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DNase?I sensitivity QTLs are a major determinant of human expression variation. Nature. 2012 Feb 05; 482(7385):390-4.
Score: 0.003
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Dissecting the regulatory architecture of gene expression QTLs. Genome Biol. 2012 Jan 31; 13(1):R7.
Score: 0.003
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Comparative RNA sequencing reveals substantial genetic variation in endangered primates. Genome Res. 2012 Apr; 22(4):602-10.
Score: 0.003
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Next generation analytic tools for large scale genetic epidemiology studies of complex diseases. Genet Epidemiol. 2012 Jan; 36(1):22-35.
Score: 0.003
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Interactions between glucocorticoid treatment and cis-regulatory polymorphisms contribute to cellular response phenotypes. PLoS Genet. 2011 Jul; 7(7):e1002162.
Score: 0.003
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Variation in human recombination rates and its genetic determinants. PLoS One. 2011; 6(6):e20321.
Score: 0.003
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Functional comparison of innate immune signaling pathways in primates. PLoS Genet. 2010 Dec 16; 6(12):e1001249.
Score: 0.003
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Genome-wide association of lipid-lowering response to statins in combined study populations. PLoS One. 2010 Mar 22; 5(3):e9763.
Score: 0.003
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Understanding mechanisms underlying human gene expression variation with RNA sequencing. Nature. 2010 Apr 01; 464(7289):768-72.
Score: 0.003
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Sex-specific and lineage-specific alternative splicing in primates. Genome Res. 2010 Feb; 20(2):180-9.
Score: 0.003
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High-resolution mapping of expression-QTLs yields insight into human gene regulation. PLoS Genet. 2008 Oct; 4(10):e1000214.
Score: 0.003
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Genes mirror geography within Europe. Nature. 2008 Nov 06; 456(7218):98-101.
Score: 0.003
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RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Res. 2008 Sep; 18(9):1509-17.
Score: 0.003
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Polymorphisms of the HNF1A gene encoding hepatocyte nuclear factor-1 alpha are associated with C-reactive protein. Am J Hum Genet. 2008 May; 82(5):1193-201.
Score: 0.003
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A second generation human haplotype map of over 3.1 million SNPs. Nature. 2007 Oct 18; 449(7164):851-61.
Score: 0.003
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Genome-wide detection and characterization of positive selection in human populations. Nature. 2007 Oct 18; 449(7164):913-8.
Score: 0.003
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Automating resequencing-based detection of insertion-deletion polymorphisms. Nat Genet. 2006 Dec; 38(12):1457-62.
Score: 0.002
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Conservation of hotspots for recombination in low-copy repeats associated with the NF1 microdeletion. Nat Genet. 2006 Dec; 38(12):1419-23.
Score: 0.002
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Differential gene induction by type I and type II interferons and their combination. J Interferon Cytokine Res. 2006 Jul; 26(7):462-72.
Score: 0.002
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A comparison of phasing algorithms for trios and unrelated individuals. Am J Hum Genet. 2006 Mar; 78(3):437-50.
Score: 0.002
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Absence of the TAP2 human recombination hotspot in chimpanzees. PLoS Biol. 2004 Jun; 2(6):e155.
Score: 0.002
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Traces of human migrations in Helicobacter pylori populations. Science. 2003 Mar 07; 299(5612):1582-5.
Score: 0.002