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Y Yang, P Carbonetto, D Gerard and M Stephens. Improved methods for empirical Bayes multivariate multiple testing and effect size estimation. arXiv:2406.08784. R package | Simulation code and results

Y Liu, P Carbonetto, J Willwerscheid, S Oakes, K Macleod and M Stephens.
Dissecting tumor transcriptional heterogeneity from single-cell RNA-seq data by generalized binary covariance decomposition.
*bioRxiv* doi:10.1101/2023.08.15.553436 .
R package |
companion code repository

Y Liu, P Carbonetto, M Takahama, A Gruenbaum, D Xie, N Chevrier and M Stephens. A flexible model for correlated count data, with application to analysis of gene expression differences in multi-condition experiments. arXiv:2210.00697. R package

J Willwerscheid, P Carbonetto and M Stephens. ebnm: an R package for solving the empirical Bayes normal means problem using a variety of prior families. arXiv:2110.00152. R package

E Weine, P Carbonetto and M Stephens.
Accelerated dimensionality reduction of single-cell RNA sequencing data with fastglmpca.
*bioRxiv* doi:10.1101/2024.03.23.586420.
R package

Y Zou, P Carbonetto, D Xie, G Wang and M Stephens.
Fast and flexible joint fine-mapping of multiple traits via the Sum of Single Effects model.
*bioRxiv* doi:10.1101/2023.04.14.536893.
R package

Y Kim, W Wang, P Carbonetto and M Stephens.
A flexible empirical Bayes approach to multiple linear regression and connections with penalized regression.
*Journal of Machine Learning Research* 25(185): 1-59, 2024.
R package

S Zhao, W Crouse, S Qian, K Luo, M Stephens and X He.
Adjusting for genetic confounders in transcriptome-wide association studies improves discovery of risk genes of complex traits.
*Nature Genetics* 56: 336–347.
bioRxiv preprint |
R package |
companion code repository

M Takahama, A Patil, G Richey, D Cipurko, K Johnson, P Carbonetto, M Plaster, S Pandey, K Cheronis, T Ueda, A Gruenbaum, T Kawamoto, M Stephens and N Chevrier.
A pairwise cytokine code explains the organism-wide response to sepsis.
*Nature Immunology* 25: 226–239.
Nature Immunology research briefing

J Kang and M Stephens. Empirical Bayes covariance decomposition, and a solution to the multiple tuning Problem in sparse PCA. arXiv:2312.03274.

M Takahama, A Patil, K Johnson, D Cipurko, Y Miki, Y Taketomi, P Carbonetto, M Plaster, G Richey, S Pandey, K Cheronis, T Ueda, A Gruenbaum, S M Dudek, M Stephens, M Murakami and N Chevrier.
Organism-wide analysis of sepsis reveals mechanisms of systemic inflammation.
*bioRxiv* doi:10.1101/2023.01.30.526342.

P Carbonetto, K Luo, A Sarkar, A Hung, K Tayeb, S Pott and M Stephens.
GoM DE: interpreting structure in sequence count data with differential expression analysis allowing for grades of membership.
*Genome Biology* 24: 236.
R package

F Morgante, P Carbonetto, G Wang, Y Zou, A Sarkar and M Stephens.
A flexible empirical Bayes approach to multivariate multiple regression, and its improved accuracy in predicting multi-tissue gene expression from genotypes.
*PLoS Genetics* 19(7): e1010539.
R package |
code and data

M Stephens.
The Bayesian lens and Bayesian blinkers.
*Philosophical Transactions of the Royal Society A* 381: 20220144.

D Xie and M Stephens.
Discussion of 'Confidence intervals for nonparametric empirical Bayes analysis'.
*Journal of the American Statistical Association* 117(539): 1186-1191.

Y Zou, P Carbonetto, G Wang and M Stephens.
Fine-mapping from summary data with the Sum of Single Effects model.
*PLoS Genetics* 18(7): e1010299.
R package |
Simulation code and results

S M Clay, N Schoettler, A M Goldstein, P Carbonetto, M Dapas, M C Altman, M G Rosasco, J E Gern, D J Jackson, H K Im, M Stephens, D L Nicolae and C Ober.
Fine-mapping studies distinguish genetic risks for childhood- and adult-onset asthma in the HLA region.
*Genomic Medicine* 14: 55.

H Shim, Z Xing, E Pantaleo, F Luca, R Pique-Regi and M Stephens. Multi-scale Poisson process approaches for differential expression analysis of high-throughput sequencing data. arXiv:2106.13634. R package | source code implementing the analyses

P Carbonetto, A Sarkar, Z Wang and M Stephens. Non-negative matrix factorization algorithms greatly improve topic model fits. arXiv:2105.13440. R package | companion source code repository

D Gerard and M Stephens.
Unifying and generalizing methods for removing unwanted variation based on negative controls.
*Statistica Sinica* 31: 1145-1166.
arXiv preprint |
R package |
code used to produce results in paper

A Sarkar and M Stephens.
Separating measurement and expression models clarifies confusion in single cell RNA-seq analysis.
*Nature Genetics* 53: 770-777.
bioRxiv preprint |
Python package |
companion website |
companion source code repository

W Wang and M Stephens.
Empirical Bayes matrix factorization.
*Journal of Machine Learning Research* 22(120): 1-40.
arXiv preprint |
R package |
code used to produce results in paper

Z Xing, P Carbonetto and M Stephens.
Flexible signal denoising via flexible empirical Bayes shrinkage.
*Journal of Machine Learning Research* 22(93): 1-28.
arXiv preprint |
R package |
accompanying code and data

A E White, K K Dey, M Stephens and T D Price.
Dispersal syndromes drive the formation of biogeographical regions, illustrated by the case of Wallace’s Line.
*Global Ecology and Biogeography* 30: 685–696.
accompanying code and data

M C Ward, N E Banovich, A Sarkar, M Stephens and Yoav Gilad.
Dynamic effects of genetic variation on gene expression revealed following hypoxic stress in cardiomyocytes.
*eLife* 10: e57345.

D Gerard and M Stephens.
Empirical Bayes shrinkage and false discovery rate estimation, allowing for unwanted variation.
*Biostatistics* 21(1), 15–32.
R package |
code used to produce results in paper

Z Zhang, K Luo, Z Zou, M Qiu, J Tian, L Sieh, H Shi, Y Zou, G Wang, J Morrison, A C Zhu, M Qiao, Z Li, M Stephens, X He and C He.
Genetic analyses support the contribution of mRNA N6-methyladenosine (m6A) modification to human disease heritability.
*Nature Genetics* 52: 939–949.

S Kim-Hellmuth et al.
Cell type–specific genetic regulation of gene expression across human tissues.
*Science* 369(6509): eaaz8528.

J Morrison, N Knoblauch, J Marcus, M Stephens and X He.
Mendelian randomization accounting for correlated and uncorrelated pleiotropic effects using genome-wide summary statistics.
*Nature Genetics* 52: 740–747.
bioRxiv preprint |
code

C J Hsiao, P Tung, J D Blischak, J Burnett, K Barr, K K Dey, M Stephens and Y Gilad.
Characterizing and inferring quantitative cell cycle phase in single-cell RNA-seq data analysis.
*Genome Biology* 30: 611-621.
bioRxiv preprint |
R package

G Wang, A Sarkar, P Carbonetto and M Stephens.
A simple new approach to variable selection in regression, with application to genetic fine mapping.
*Journal of the Royal Statistical Society, Series B* 82: 1273-1300.
R package |
accompanying code and data resources

Y Kim, P Carbonetto, M Stephens and M Anitescu.
A fast algorithm for maximum likelihood estimation of mixture proportions using sequential quadratic programming.
*Journal of Computational and Graphical Statistics* 29: 261-273.
arXiv preprint |
accompanying code resources |
R package

J D Blischak, P Carbonetto and M Stephens.
Creating and sharing reproducible research code the workflowr way.
*F1000Research* 8: 1749 [version 1; peer review: 3 approved].
R package on CRAN |
R package on GitHub

M Lu and M Stephens. Empirical Bayes estimation of normal means, accounting for uncertainty in estimated standard errors. arXiv:1901.10679. accompanying code and data

M C Turchin and M Stephens.
Bayesian multivariate reanalysis of large genetic studies identifies many new associations.
*PLoS Genetics* 15(10): e1008431.
bioRxiv preprint |
R package

S Zhao, J Liu, P Nanga, Y Liu, A E Cicek, N Knoblauch, C He, M Stephens and X He.
Detailed modeling of positive selection improves detection of cancer driver genes.
*Nature Communications* 10: 3399.
bioRxiv preprint |
accompanying code and data resources

A Sarkar, P-Y Tung, J D Blischak, J E Burnett, Y I Li, M Stephens and Y Gilad.
Discovery and characterization of variance QTLs in human induced pluripotent stem cells.
*PLoS Genetics* 15(4): e1008045.
accompanying code and data

H Al-Asadi, K K Dey, J Novembre and M Stephens.
Inference and visualization of DNA damage patterns using a grade of membership model.
*Bioinformatics* 35(8): 1292-1298.
R package

A E White, K K Dey, D Mohan, M Stephens and T D Price.
Regional influences on community structure across the tropical-temperate divide.
*Nature Communications* 10: 2646.
R package

H Al-Asadi, D Petkova, M Stephens and J Novembre.
Estimating recent migration and population size surfaces.
*PLoS Genetics* 15(1): e1007908.
software

S M Urbut, G Wang, P Carbonetto and M Stephens.
Flexible statistical methods for estimating and testing effects in genomic studies with multiple conditions.
*Nature Genetics* 51(1): 187-195.
bioRxiv preprint |
R package |
accompanying code and data resources

K K Dey and M Stephens. CorShrink: Empirical Bayes shrinkage estimation of correlations, with applications. bioRxiv doi:10.1101/368316. R package | accompanying code and data resources

L Sun and M Stephens. Solving the empirical Bayes normal means problem with correlated noise. arXiv:1812.07488. R package | accompanying code and data resources

L F V Ferrão, R G Ferrão, M A G Ferrão, A Fonseca, P Carbonetto, M Stephens and A A F Garcia.
Accurate genomic prediction of Coffea canephora in multiple environments using whole-genome statistical models.
*Heredity* 122, 261-275.
data

K K Dey, D Xie and M Stephens.
A new sequence logo plot to highlight enrichment and depletion.
*BMC Bioinformatics* 19: 473.
R package |
code used to produce results in paper

X Zhu and M Stephens.
Large-scale genome-wide enrichment analyses identify new trait-associated genes and pathways across 31 human phenotypes.
*Nature Communications* 9: 4361.
software |
online results

M C Ward, S Zhao, K Luo, B J Pavlovic, M M Karimi, M Stephens and Y Gilad.
Silencing of transposable elements may not be a major driver of regulatory evolution in primate iPSCs.
*eLife* 7: e33084.

D Gerard, L F V Ferrão, A A F Garcia and M Stephens.
Genotyping polyploids from messy sequencing data.
*Genetics* 210(3), 789-807.
R package |
code used to produce results in paper

J Smith, G Coop, M Stephens and J Novembre.
Estimating time to the common ancestor for a beneficial allele.
*Molecular Biology and Evolution* 35(4): 1003–1017.

P Carbonetto, X Zhou and, M Stephens. varbvs: fast variable selection for large-scale regression. arXiv:1709.06597. software

X Zhu and M Stephens.
Bayesian large-scale multiple regression with summary statistics from genome-wide association studies.
*Annals of Applied Statistics* 11(3): 1561-1592.
Supplemental materials |
Software |
Preprocessed height data

I E Schor, J F Degner, D Harnett, E Cannavo, F P Casale, H Shim, D A Garfield, E Birney, M Stephens, O Stegle, and E E M Furlong.
Promoter shape varies across populations and affects promoter evolution and expression noise.
*Nature Genetics* 49(4): 550-558.
Supplementary Text and Figures

K Dey, C Hsiao, and M Stephens.
Visualizing the structure of RNA-seq expression data using grade of membership models.
*PLoS Genetics* 13(3): e1006599.
R package on Github |
R package on Bioconductor |
code used to produce results in paper

M Stephens.
False discovery rates: a new deal.
*Biostatistics* 18(2): 275-294.
Supplementary Materials |
R package on CRAN |
R package on Github |
code used to produce results in paper

M Lu and M Stephens.
Variance adaptive shrinkage (vash): Flexible empirical Bayes estimation of variances.
*Bioinformatics* 32(22): 3428-3434.
Supplementary Materials |
Software

A Raj, S Wang, H Shim, A Harpak, Y I Li, B Englemann, M Stephens, Y Gilad, and J K Pritchard.
Thousands of novel translated open reading frames in humans inferred by ribosome footprint profiling.
*eLife* 2016;5:e13328.

D Petkova, J Novembre, and M Stephens.
Visualizing spatial population structure with estimated effective migration surfaces.
*Nature Genetics* 48: 94-100.
Supplementary Text and Figures |
Software

S Mondol, I Moltke, J Hart, M Keigwin, L Brown, M Stephens, and S K Wasser.
New evidence for hybrid zones of forest and savanna elephants in Central and West Africa.
*Mol Ecol* 24(24): 6134-6147, December 2015.

Y Shiraishi, G Tremmel, S Miyano, and M Stephens.
A simple model-based approach to inferring and visualizing cancer mutation signatures.
*PLoS Genetics* 11(12): e1005657, December 2015.

A Raj, H Shim, Y Gilad, J K Pritchard, and M Stephens.
msCentipede: Modeling heterogeneity across genomic sites improves accuracy in the inference of transcription factor binding.
*PLoS ONE* 10(9): e0138030.
Software

H Shim and M Stephens.
Wavelet-based genetic association analysis of functional phenotypes arising from high-throughput sequencing assays.
*Annals of Applied Statistics* 9(2): 665-686.
Software

K G Ardlie et al.
The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans.
*Science* 348(6235): 648-660, May 2015.

H Shim, D I Chasman, J D Smith, S Mora, P M Ridker, D A Nickerson, R M Krauss, and M Stephens.
A multivariate genome-wide association analysis of 10 LDL subfractions, and their response to statin treatment, in 1868 Caucasians.
*PLoS ONE* 10(4): e0120758.
Software |
Data

Z Gao, D Waggoner, M Stephens, C Ober, and M Przeworski.
An estimate of the average number of recessive lethal mutations carried by humans.
*Genetics* 199(4): 1243-1254.

J Tung, X Zhou, S C Alberts, M Stephens, and Y Gilad.
The genetic architecture of gene expression levels in wild baboons.
*eLife* 2015;4:e04729.

X Zhou, C E Cain, M Myrthil, N Lewellen, K Michelini, E R Davenport, M Stephens, J K Pritchard, and Y Gilad.
Epigenetic modifications are associated with inter-species gene expression variation in primates.
*Genome Biology* 15(12): 547, December 2014.

X Wen and M Stephens.
Bayesian methods for genetic association analysis with heterogeneous subgroups: From meta-analyses to gene-environment interactions.
*Annals of Applied Statistics* 8(1): 176-203.
Supplementary Text

X Zhou and M Stephens.
Efficient multivariate linear mixed model algorithms for genome-wide assocication studies.
*Nature Methods* 11: 407-409.
Software

A Raj, M Stephens, and J K Pritchard.
fastSTRUCTURE: Variational Inference of Population Structure in Large SNP Data Sets.
*Genetics* 197(2): 573-589, June 2014.
Software

L M Mangravite, B E Engelhardt, M W Medina, J D Smith, C D Brown, D I Chasman, B H Mecham, B Howie, H Shim, D Naidoo, Q Feng, M J Rieder, Y D Chen, J I Rotter, P M Ridker, J C Hopewell, S Parish, J Armitage, R Collins, R A Wilke, D A Nickerson, M Stephens, and R M Krauss.
A statin-dependent QTL for GATM expression is associated with statin-induced myopathy.
*Nature* 502: 377-380.

P Carbonetto and M Stephens.
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 Genetics* 9(10): e1003770.
Software

F Luca, J C Maranville, A L Richards, D B Witonsky, M Stephens, and A Di Rienzo.
Genetic, functional and molecular features of glucocorticoid receptor binding.
*PLoS ONE* 8(4): e61654.

M Stephens.
A Unified framework for association analysis with multiple related phenotypes.
*PLoS ONE* 8(7): e65245.

T Flutre, X Wen, J Pritchard, and M Stephens.
A statistical framework for joint eQTL analysis in multiple tissues.
*PLoS Genetics* 9(5): e1003486.
Software

X Zhou, P Carbonetto, and M Stephens.
Polygenic modeling with Bayesian sparse linear mixed models.
*PLoS Genetics* 9(2): e1003264.
Software

Q Li, J K Eng, and M Stephens.
A likelihood-based scoring method for peptide identification using mass spectrometry.
*Annals of Applied Statistics* 6(4): 1775-1794.
arXiv

A A Pai, C E Cain, O Mizrahi-Man, S De Leon, N Lewellen, J-B Veyrieras, J F Degner, D J Gaffney, J K Pickrell, M Stephens, J K Pritchard, and Y Gilad.
The Contribution of RNA Decay Quantitative Trait Loci to Inter-Individual Variation in Steady-State Gene Expression Levels.
*PLoS Genetics* 8(10), e1003000, October 2012.

A B Hart, B E Engelhardt, M C Wardle, G Sokoloff, M Stephens, H de Wit, and A A Palmer.
Genome-Wide Association Study of d-Amphetamine Response in Healthy Volunteers Identifies Putative Associations, Including Cadherin 13 (CDH13).
*PLoS ONE* 7(8): e42646.

J Maranville, F Luca, M Stephens, and A Di Rienzo.
Mapping gene-environment interactions at regulatory polymorphisms: insights into mechanisms of phenotypic variation.
*Transcription* 3(2): 56-62.

B Howie, C Fuchsberger, M Stephens, J Marchini, and GR Abecasis.
Fast and accurate genotype imputation in genome-wide association studies through pre-phasing.
*Nature Genetics* 44(8): 955-959.

X Zhou and M Stephens.
Genome-wide efficient mixed model analysis for association studies.
*Nature Genetics* 44(7): 821-824.
Supplementary Text |
Software

A Q Fu, D P Genereux, R Stoger, A F Burden, C D Laird, and M Stephens.
Statistical inference of in vivo properties of human DNA methyltransferases from double-stranded methylation patterns.
*PLoS ONE* 7(3): e32225.
Software

G H Perry, P Melsted, J C Marioni, Y Wang, R Bainer, J K Pickrell, K Michelini, S Zehr, A D Yoder, M Stephens, J K Pritchard, and Y Gilad.
Comparative RNA sequencing reveals substantial genetic variation in endangered primates.
*Genome Biology* 22: 602-610, 2011.

P Carbonetto and M Stephens.
Scalable variational inference for Bayesian variable selection in regression, and its accuracy in genetic association studies.
*Bayesian Analysis* 7(1): 73-108, March 2012.
Software

J-B Veyrieras, D J Gaffney, J K Pickrell, Y Gilad, M Stephens, and J K Pritchard.
Exon-specific QTLs skew the inferred distribution of expression QTLs detected using gene expression array data.
*PLoS One* 7(2), e30629, February 2012.

J F Degner, A A Pai, R Pique-Regi, J-B Veyrieras, D J Gaffney, J K Pickrell, S De Leon, K Michelini, N Lewellen, G E Crawford, M Stephens, Y Gilad, and J K Pritchard.
DNase I sensitivity QTLs are a major determinant of human expression variation.
*Nature* 482: 390-394, February 2012.

D J Gaffney, J-B Veyrieras, J F Degner, R Pique-Regi, A A Pai, G E Crawford, M Stephens, Y Gilad, and J K Pritchard.
Dissecting the regulatory architecture of gene expression QTLs.
*Genome Biology* 13:R7, January 2012.

L E Mechanic, H-S Chen, C I Amos, N Chatterjee, N J Cox, R L Divi, R Fan, E L Harris, K Jacobs, P Kraft, S M Leal, K McAllister, J H Moore, D N Paltoo, M A Province, E M Ramos, M D Ritchie, K Roeder, D J Schaid, M Stephens, D C Thomas, C R Weinberg, J S Witte, S Zhang, S Zollner, E J Feuer, and E M Gillanders.
Next generation analytic tools for large scale genetic epidemiology studies of complex diseases.
*Genetic Epidemiology* 36(1): 22-35, December 2011.

B Howie, J Marchini, and M Stephens.
Genotype imputation with thousands of genomes.
*G3: Genes, Genomics, Genetics* 1(6): 457-470, November 2011.

Y Guan and M Stephens.
Bayesian Variable Selection Regression for Genome-wide Association Studies, and other Large-Scale Problems.
*Annals of Applied Statistics* 5(3): 1780-1815, September 2011.

J C Maranville, F Luca, A L Richards, X Wen, D B Witonsky, S Baxter, M Stephens, and A Di Rienzo.
Interactions between Glucocorticoid Treatment and Cis-Regulatory Polymorphisms Contribute to Cellular Response Phenotypes.
*PLoS Genetics* 7(7): e1002162, July 2011.

A Fledel-Alon, E M Leffler, Y Guan, M Stephens, G Coop, and M Przeworski.
Variation in Human Recombination Rates and Its Genetic Determinants.
*PLoS ONE* 6(6): e20321, June 2011.

A Q Fu, D P Genereux, R Stoger, C D Laird, and M Stephens.
Statistical inference of transmission fidelity of DNA methylation patterns over somatic cell divisions in mammals.
*Annals of Applied Statistics* 4(2): 871-892, June 2010.

Q Li, M MacCoss, and M Stephens.
A nested mixture model for protein identification using mass spectrometry.
*Annals of Applied Statistics* 4(2): 962-987, June 2010.

X Wen and M Stephens.
Using linear predictors to impute allele frequencies from summary or pooled genotype data.
*Annals of Applied Statistics* 4(3): 1158-1182, September 2010.
Software

J Novembre and M Stephens.
Response to Cavalli-Sforza interview.
*Human Biology* 82(4): 469-470, August 2010.

L B Barreiro, J C Marioni, R Blekham, M Stephens, and Y Gilad.
Functional comparison of innate immune signaling pathways in primates.
*PLoS Genetics* 6(12): e1001249, December 2010.

B E Engelhardt and M Stephens.
Analysis of population structure: a unifying framework and novel methods based on sparse factor analysis.
*PLoS Genetics* 6(9): e1001117.
Software

J K Pickrell, J C Marioni, A A Pai, J F Degner, B E Engelhardt, E Nkadori, J B Veyrieras, M Stephens, Y Gilad, and J K Pritchard.
Understanding mechanisms underlying human gene expression variation with RNA sequencing.
*Nature* 464(7289):768-72, Mar 2010.

M J Barber, L M Mangravite, C L Hyde, D I Chasman, J D Smith, C A McCarty, X Li, R A Wilke, M J Rieder, P T Williams, P M Ridker, A Chatterjee, J I Rotter, D A Nickerson, M Stephens, and R M Krauss.
Genome-wide association of lipid-lowering response to statins in combined study populations.
*PLoS ONE* Mar 2010.
Supplementary Results Data Page

R Blekhman, J C Marioni, P Zumbo, M Stephens, and Y Gilad.
Sex-specific and lineage-specific alternative splicing in primates.
*Genome Res* 20(2):180-9, Feb 2010.

S Basu, M Stephens, J S Pankow, and E A Thompson.
A Likelihood-Based Trait-Model-Free Approach for Linkage Detection of Binary Trait.
*Biometrics* 66(1):205-13, Mar 2009.

M J Hubisz, D Falush, M Stephens, and J K Pritchard.
Inferring weak population structure with the assistance of sample group information.
*Molecular Ecology Resources* 9:1322-1332, 2009.

M Stephens and D J Balding.
Bayesian statistical methods for genetic association studies.
*Nat Rev Genet* 10(10):681-90, Oct 2009.

Y Guan and M Stephens.
Practical issues in imputation-based association mapping.
*PLoS Genet* 4(12), Dec 2008.

J Novembre, T Johnson, K Bryc, Z Kutalik, A R Boyko, A Auton, A Indap, K S King, S Bergmann, M R Nelson, M Stephens, and C D Bustamante.
Genes mirror geography within Europe.
*Nature* 456(7218):98-101, Nov 2008.

J B Veyrieras, S Kudaravalli, S Y Kim, E T Dermitzakis, Y Gilad, M Stephens, and J K Pritchard.
High-resolution mapping of expression-QTLs yields insight into human gene regulation.
*PLoS Genet* 4(10), Oct 2008.

S K Wasser, W J Clark, O Drori, E S Kisamo, C Mailand, B Mutayoba, and M Stephens.
Combating the illegal trade in African elephat ivory with DNA forensics.
*Conserv Biol* 22(4):1065-1071, Aug 2008.

J C Marioni, C E Mason, S M Mane, M Stephens, and Y Gilad.
RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays.
*Genome Res* 18(9):1509-1517, Sep 2008.
Software

P Scheet and M Stephens.
Linkage disequilibrium-based quality control for large-scale genetic studies.
*PLoS Genet* 4(8), 2008.

A P Reiner, M J Barber, Y Guan, P M Ridker, L A Lange, D I Chasman, J D Walston, G M Cooper, N S Jenny, M J Rieder, J P Durda, J D Smith, J Novembre, R P Tracy, J I Rotter, M Stephens, D A Nickerson, and R M Krauss.
Polymorphisms of the HNF1A gene encoding hepatocyte nuclear factor-1 alpha are accosicated with c-reactive protein.
*Am J Hum Genet* 82(5):1193-1201, May 2008.

J Novembre and M Stephens.
Interpreting principal component analyses of spatial population genetic variation.
*Nat Genet* 40(5):646-649, May 2008.
Supplementary Materials

The International HapMap Consortium.
A second generation human haplotype map of over 3.1 million SNPs.
*Nature* 449(7164):851-61, Oct 2007.

B Servin and M Stephens.
Imputation-based analysis of association studies: candidate regions and quantitative traits.
*PLoS Genet* 3(7), Jul 2007.
Supplementary File S1 |
Supplementary File S2

D Falush, M Stephens, and J K Pritchard.
Inference of population structure using multilocus genotype data: dominant markers and null alleles.
*Molecular Ecology Notes* 7:574-578, Jul 2007.

A Roychoudhury and M Stephens.
Fast and accurate estimation of the population-scaled mutation rate, theta, from microsatellite genotype data.
*Genetics* 176(2):1363-1366, Jun 2007.

G Hellenthal and M Stephens.
msHOT: modifying Hudson's ms simulator to incorporate crossover and gene conversion hotspots.
*Bioinformatics* 23(4):520-521, 2007.

S K Wasser, C Mailand, R Booth, B Mutayoba, E Kisamo, B Clark, and M Stephens.
Using DNA to track the origin of the largest ivory seizure since the 1989 trade ban.
*Proc Natl Acad Sci U S A* 104(10):4228-4233, Mar 2007.

T Du Raedt, M Stephens, I Heyns, H Brems, D Thijs, L Messiaen, K Stephens, C Lazaro, K Wimmer, H Kehrer-Sawatzki, D Vidaud, L Kluwe, P Marynen, and E Legius.
Conservation of hotspots for recombination in low-copy repeats associated with the NF1 microdeletion.
*Nat Genet* 38(12):1419-1423, 2006.

T R Bhangale, M Stephens, and D A Nickerson.
Automating resequencing-based detection of insertion-deletion polymorphisms.
*Nat Genet* 38(12):1457-1462, 2006.

G Hellenthal and M Stephens.
Insights into recombination from population genetic variation.
*Curr Opin Genet Dev* 16(6):565-572, 2006.

R Gottardo, J Besag, M Stephens, and A Murua.
Probabilistic segmentation and intensity estimation for microarray images.
*Biostatistics* 7(1):85-99, 2006.

G Hellenthal, J K Pritchard, and M Stephens.
The effects of genotype-dependent recombination, and transmission asymmetry, on linkage disequilibrium.
*Genetics* 172(3):2001-2005, 2006.

M Stephens, J S Sloan, P D Robertson, P Scheet, and D A Nickerson.
Automating sequence-based detection and genotyping of SNPs from diploid samples.
*Nat Genet* 38(3):375-381, 2006.

P Scheet and M Stephens.
A fast and flexible method for large-scale population genotype data: applications to inferring missing genotypes and haplotypic phase.
*Am J Hum Genet* 78(4):629-644, 2006.

J Marchini, D Cutler, N Patterson, M Stephens, E Eskin, E Halperin, S Lin, Z S Qin, H M Munro, G R Abecasis, and P Donnelly.
A comparison of phasing algorithms for trios and unrelated individuals.
*Am J Hum Genet* 78(3):437-450, 2006.

The International HapMap Consortium.
A haplotype map of the human genome.
*Nature* 237(7063):1299-1320, 2005.

M Stephens and P Scheet.
Accounting for decay of linkage disequilibrium in haplotype inference and missing-data imputation.
*Am J Hum Genet* 76(3):449-462, 2005.

D C Crawford, T Bhangale, N Li, G Hellenthal, M J Rieder, D A Nickerson, and M Stephens.
Evidence for substantial fine-scale variation in recombination rates across the human genome.
*Nat Genet* 36(7):700-706, 2004.

S E Ptak, A D Roeder, M Stephens, Y Gilad, S Paabo, and M Przeworski.
Absence of the TAP2 human recombination hotspot in chimpanzees.
*PLoS Biology* 2(6):849-855, 2004.

S K Wasser, A M Shedlock, K Comstock, E A Ostrander, B Mutayoba, and M Stephens.
Assigning African elephant DNA to geographic region of origin: applications to the ivory trade.
*Proc Natl Acad Sci U S A* 41:14844-14852, 2004.
Software

N Li and M Stephens.
Modeling linkage disequilibrium and identifying recombination hotspots using single-nucleotide polymorphism data.
*Genetics* 165(4)2213-2233, 2003.

M Stephens and P Donnelly.
A comparison of Bayesian methods for haplotype reconstruction from population genotype data.
*Am J Hum Genet* 73(5):1162-1169, 2003.

D Falush, M Stephens, and J K Pritchard.
Inference of population structure from multilocus genotype data: linked loci and correlated allele frequencies.
*Genetics* 164:1567-1587. 2003.

D Falush, T Wirth, D Linz, J K Pritchard, M Stephens, M Kidd, M J Blaser, D Y Graham, S Vacher, G I Perez-Perez, Y Yamoka, F Megraud, K Otto, U Reichard, E Katzowitsch, X Wang, M Achtman, and S Suerbaum.
Traces of human migrations in Heliobacter pylori populations.
*Science* 299(5612):1582-1585, 2003.

M Stephens and P Donnelly.
Ancestral inference in population genetics models with selection.
*Australian and New Zealand Journal of Statistics* 45:901-931, 2003.

M Stephens, N J Smith, and P Donnelly.
A new statistical method for haplotype reconstruction from population data.
*Am J Hum Genet* 68(4):978-989, 2001.

J K Pritchard, M Stephens, and P Donnelly.
Inference of population structure using multilocus genotype data.
*Genetics* 155(2):945-959, 2000.

J K Pritchard, M Stephens, N A Rosenberg, and P Donnelly.
Association mapping in structured populations.
*Am J Hum Genet* 67:170-181, 2000.

M Stephens and P Donnelly.
Inference in molecular population genetics.
*J R Stat Soc, Ser B* 62:605-655, 2000.

M Stephens.
Dealing with label-switching in mixture models.
*J R Stat Soc, Ser B* 62:795-809, 2000.

M Stephens.
Bayesian analysis of mixtures with an unknown number of components - an alternative to reversible jump methods.
*Annals of Statistics* 28(1), 2000.

M Stephens.
Times on trees and the age of an allele.
*Theoretical Population Biology* 57:109-119, 2000.

M Stephens.
Problems with computational methods in population genetics.
*Bulletin of the International Statistical Institute* 52nd session, 1999.

M Stephens. Bayesian Methods for Mixtures of Normal Distributions. DPhil thesis - University of Oxford.

M Stephens. The Results of Gregor Mendel - An analysis and comparison with the results of other researchers. Dip Stat thesis - University of Cambridge.

H Al-Asadi. Statistical methods for genetic data. PhD thesis - University of Chicago, 2018.

K Dey. Model-based visualization of structure in biological data. PhD thesis - University of Chicago, 2018.

A Fu. Models and Inference of Transmission of DNA Methylation Patterns in Mammalian Somatic Cells. PhD thesis - University of Washington, 2008.

A Goldstein. A variational Bayesian approach for combining weak learners into a strong learner in regression problems. PhD thesis - University of Chicago, 2022.

G Hellenthal. Exploring Rates and Patterns of Variability in Gene Conversion and Crossover in the Human Genome. PhD thesis - University of Washington, 2006.

J Kang. Learning meaningful representations of data with empirical Bayes methods. PhD thesis - University of Chicago, 2024.

Y Kim. Bayesian shrinkage methods for high-dimensional regression. PhD thesis - University of Chicago, 2020.

M Li. Trajectory exploration and inference for scRNA-seq data on whole versus leaf ends only trajectories. Masters thesis - University of Chicago, 2022.

Q Li. Statistical Methods for Peptide and Protein Identification using Mass Spectrometry. PhD thesis - University of Washington, 2008.

M Lu. Generalized adaptive shrinkage methods and applications in genomics studies. PhD thesis - University of Chicago, 2018.

D Petkova. Inferring Effective Migration from Geographically Indexed Genetic Data. PhD thesis - University of Chicago, 2013.

P Scheet. A Flexible and Computationally Tractable Model for Patterns of Population Genetic Variation. PhD thesis - University of Washington, 2006.

L Sun. Topics on empirical Bayes normal means. PhD thesis - University of Chicago, 2020.

M Turchin. Beyond the low-hanging fruit: leveraging summary data in human population and statistical genetics. PhD thesis - University of Chicago, 2017.

S Urbut. Flexible statistical methods for jointly modeling effects. PhD thesis - University of Chicago, 2017.

D Xie. Empirical Bayes methods for count data. PhD thesis - University of Chicago, 2023.

Z Xing. Poisson Multiscale Methods for High-throughput Sequencing Data. PhD thesis - University of Chicago, 2016.

K Xu. EbayesThresh with Heterogeneous Variance. Masters paper - University of Chicago, 2017.

L Wang. Comparison of multiple regression methods on data sets with varying degrees of correlation. B.Sc. thesis - University of Chicago, 2021.

W Wang. Applications of adaptive shrinkage in multiple statistical problems. PhD thesis - University of Chicago, 2017.

X Wen. Bayesian Analysis of Genetic Association Data, Accounting for Heterogeneity. PhD thesis - University of Chicago, 2011.

J Willwerscheid. Empirical Bayes matrix factorization: methods and applications. PhD thesis - University of Chicago, 2021.

X Zhu. A Bayesian large-scale multiple regression model for genome-wide association summary statistics. PhD thesis - University of Chicago, 2017.

Y Zou. Bayesian variable selection from summary data, with application to joint fine-mapping of multiple traits. PhD thesis - University of Chicago, 2021.