# Publications

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The optimal discovery procedure for significance analysis of general gene expression studies (2019) bioRxiv

Genome-wide real-time in vivo transcriptional dynamics during Plasmodium falciparum blood-stage development (2018) Nature Communications

Genome-wide real-time in vivo transcriptional dynamics during Plasmodium falciparum blood-stage development (2018) bioRxiv

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Statistical significance of variables driving systematic variation (2013) arXiv

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

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

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

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

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

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

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

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

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

False discovery rate (2011) International Encyclopedia of Statistical Science

A computationally efficient modular optimal discovery procedure (2010) Bioinformatics

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

Supervised normalization of microarrays (2010) Bioinformatics

Cause and express (2009) Nature Biotechnology

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Relaxed significance criteria for linkage analysis (2006) Genetics

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

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

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

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

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

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

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

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)

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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