Publications

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The functional false discovery rate with applications to genomics (2017) bioRxiv

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Extending tests of Hardy-Weinberg equilibrium to structured populations (2017) bioRxiv

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A nonparametric estimator of population structure unifying admixture models and principal components analysis (2017) bioRxiv

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Mixed membership martial arts: Data-driven analysis of winning martial arts styles (2017) MIT Sloan Sports Analytics Conference

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Scaling probabilistic models of genetic variation to millions of humans (2016) Nature Genetics

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Systems-level analysis of mechanisms regulating yeast metabolic flux (2016) Science

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$F_{ST}$ and kinship for arbitrary population structures II: Method of moments estimators (2016) bioRxiv

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$F_{ST}$ and kinship for arbitrary population structures I: Generalized definitions (2016) bioRxiv

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Beyond the E-Value: Stratified statistics for protein domain prediction (2015) PLOS Computational Biology

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Probabilistic models of genetic variation in structured populations applied to global human studies (2015) Bioinformatics

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Consistent estimation of low-dimensional latent structure in high-dimensional data (2015) arXiv

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A nested parallel experiment demonstrates differences in intensity-dependence between RNA-seq and microarrays (2015) Nucleic Acids Research

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Scaling probabilistic models of genetic variation to millions of humans (2015) bioRxiv

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Testing for genetic associations in arbitrarily structured populations (2015) Nature Genetics

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Testing for genetic associations in arbitrarily structured populations (2015) bioRxiv

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A nested parallel experiment demonstrates differences in intensity-dependence between RNA-seq and microarrays (2014) bioRxiv

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Statistical significance of variables driving systematic variation in high-dimensional data (2014) Bioinformatics

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Beyond the E-value: Stratified statistics for protein domain prediction (2014) arXiv

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subSeq: Determining appropriate sequencing depth through efficient read subsampling (2014) Bioinformatics

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Gene expression profiles associated with acute myocardial infarction and risk of cardiovascular death (2014) Genome Medicine

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Identifying and mapping cell-type-specific chromatin programming of gene expression (2014) Proceedings of the National Academy of Sciences

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Gene set bagging for estimating the probability a statistically significant result will replicate (2013) BMC Bioinformatics

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Probabilistic models of genetic variation in structured populations applied to global human studies (2013) arXiv

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Design and analysis of bar-seq experiments (2013) G3: Genes | Genomes | Genetics

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Statistical significance of variables driving systematic variation (2013) arXiv

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Gene set bagging for estimating replicability of gene set analyses (2013) arXiv

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Cross-dimensional inference of dependent high-dimensional data (2012) Journal of the American Statistical Association

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The sva package for removing batch effects and other unwanted variation in high-throughput experiments (2012) Bioinformatics

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Identifying and mapping cell-type specific chromatin programming of gene expression (2011) arXiv

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A genomic storm in critically injured humans (2011) The Journal of Experimental Medicine

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A computational statistics approach for estimating the spatial range of morphogen gradients (2011) Development

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Dissecting inflammatory complications in critically injured patients by within-patient gene expression changes: A longitudinal clinical genomics study (2011) PLoS Medicine

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The joint null criterion for multiple hypothesis tests (2011) Statistical Applications in Genetics and Molecular Biology

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Human transcriptome array for high-throughput clinical studies (2011) Proceedings of the National Academy of Sciences

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False discovery rate (2011) International Encyclopedia of Statistical Science

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A computationally efficient modular optimal discovery procedure (2010) Bioinformatics

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System-level analysis of genes and functions affecting survival during nutrient starvation in Saccharomyces cerevisiae (2010) Genetics

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Supervised normalization of microarrays (2010) Bioinformatics

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Cause and express (2009) Nature Biotechnology

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QVALITY: Non-parametric estimation of q-values and posterior error probabilities (2009) Bioinformatics

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A general framework for multiple testing dependence (2008) Proceedings of the National Academy of Sciences

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Eigen-$R^2$ for dissecting variation in high-dimensional studies (2008) Bioinformatics

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Non-parametric estimation of posterior error probabilities associated with peptides identified by tandem mass spectrometry (2008) Bioinformatics

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Calibrating the performance of SNP arrays for whole-genome association studies (2008) PLoS Genetics

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Mapping gene expression quantitative trait loci by singular value decomposition and independent component analysis (2008) BMC Bioinformatics

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Mapping the genetic architecture of gene expression in human liver (2008) PLoS Biology

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A genome-wide gene expression signature of environmental geography in leukocytes of Moroccan Amazighs (2008) PLoS Genetics

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Posterior error probabilities and false discovery rates: two sides of the same coin (2008) Journal of Proteome Research

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Assigning significance to peptides identified by tandem mass spectrometry using decoy databases (2008) Journal of Proteome Research

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Harnessing naturally randomized transcription to infer regulatory relationships among genes (2007) Genome Biology

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Optimality driven nearest centroid classification from genomic data (2007) PLoS ONE

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Capturing heterogeneity in gene expression studies by surrogate variable analysis (2007) PLoS Genetics

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On the design and analysis of gene expression studies in human populations (2007) Nature Genetics

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The optimal discovery procedure: a new approach to simultaneous significance testing (2007) Journal of the Royal Statistical Society: Series B (Statistical Methodology)

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Normalization of two-channel microarrays accounting for experimental design and intensity-dependent relationships (2007) Genome Biology

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Gene-Expression Variation Within and Among Human Populations (2007) The American Journal of Human Genetics

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The optimal discovery procedure for large-scale significance testing, with applications to comparative microarray experiments (2006) Biostatistics

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Relaxed significance criteria for linkage analysis (2006) Genetics

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A new approach to intensity-dependent normalization of two-channel microarrays (2006) Biostatistics

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A reanalysis of a published Affymetrix GeneChip control dataset (2006) Genome Biology

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Significance analysis of time course microarray experiments (2005) Proceedings of the National Academy of Sciences

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Genetic interactions between polymorphisms that affect gene expression in yeast (2005) Nature

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Multiple locus linkage analysis of genomewide expression in yeast (2005) PLoS Biology

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Edge: extraction and analysis of differential gene expression (2005) Bioinformatics

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Longitudinal transcriptional analysis of developing neointimal vascular occlusion and pulmonary hypertension in rats (2004) Physiological Genomics

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Strong control, conservative point estimation and simultaneous conservative consistency of false discovery rates: A unified approach (2004) Journal of the Royal Statistical Society: Series B (Statistical Methodology)

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The positive false discovery rate: A Bayesian interpretation and the q-value (2003) Annals of Statistics

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Statistical significance for genomewide studies (2003) Proceedings of the National Academy of Sciences

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SAM thresholding and false discovery rates for detecting differential gene expression in DNA microarrays (2003) The Analysis of Gene Expression Data: Methods and Software

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Genome-wide analysis of mRNA translation profiles in Saccharomyces cerevisiae (2003) Proceedings of the National Academy of Sciences

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Statistical methods for identifying differentially expressed genes in DNA microarrays (2003) Functional Genomics: Methods and Protocols

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A direct approach to false discovery rates (2002) Journal of the Royal Statistical Society: Series B (Statistical Methodology)

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False discovery rates: Theory and applications to DNA microarrays (2002) Stanford University PhD Dissertation

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Precision and functional specificity in mRNA decay (2002) Proceedings of the National Academy of Sciences

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In vivo regulation of human skeletal muscle gene expression by thyroid hormone (2002) Genome Research

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Empirical Bayes analysis of a microarray experiment (2001) Journal of the American Statistical Association

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Estimating the positive false discovery rate under dependence, with applications to DNA microarrays (2001) Stanford Statistics Technical Report

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Approximate p-values for local sequence alignments: Numerical studies (2001) Journal of Computational Biology

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Microarrays, empirical Bayes methods, and false discovery rates (2001) Stanford Statistics Technical Report

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A new approach to false discovery rates and multiple hypothesis testing (2001) Stanford Statistics Technical Report

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The false discovery rate: A Bayesian interpretation and the q-value (2001) Stanford Statistics Technical Report

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Empirical Bayes analysis of a microarray experiment (2001) Stanford Statistics Technical Report

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Function digraphs of quadratic maps modulo p (2001) Fibonacci Quarterly

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