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Matthew Stephens

TitlePROFESSOR
InstitutionUniversity of Chicago
DepartmentStatistics
AddressChicago IL 60637
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    Collapse Overview 
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    My lab works on a wide variety of problems at the interface of Statistics and Genetics. We often tackle problems where novel statistical methods are required, or can learn something new compared with existing approaches. Thus, much of our research involves developing new statistical methodology, many of which have a non-trivial computational component. People in my lab tend to come from a quantitative background (e.g., Statistics, Computer Science), with varying levels of formal or informal Biology training.


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    Collapse selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    1. Sarkar A, Stephens M. Separating measurement and expression models clarifies confusion in single-cell RNA sequencing analysis. Nat Genet. 2021 06; 53(6):770-777. PMID: 34031584.
      View in: PubMed
    2. Ward MC, Banovich NE, Sarkar A, Stephens M, Gilad Y. Dynamic effects of genetic variation on gene expression revealed following hypoxic stress in cardiomyocytes. Elife. 2021 Feb 08; 10. PMID: 33554857.
      View in: PubMed
    3. Barbeira AN, Bonazzola R, Gamazon ER, Liang Y, Park Y, Kim-Hellmuth S, Wang G, Jiang Z, Zhou D, Hormozdiari F, Liu B, Rao A, Hamel AR, Pividori MD, Aguet F. Exploiting the GTEx resources to decipher the mechanisms at GWAS loci. Genome Biol. 2021 01 26; 22(1):49. PMID: 33499903.
      View in: PubMed
    4. White AE, Dey KK, Stephens M, Price TD. Dispersal syndromes drive the formation of biogeographical regions, illustrated by the case of Wallace's Line. Glob Ecol Biogeogr. 2021 Mar; 30(3):685-696. PMID: 33776580.
      View in: PubMed
    5. Oliva M, Muñoz-Aguirre M, Kim-Hellmuth S, Wucher V, Gewirtz ADH, Cotter DJ, Parsana P, Kasela S, Balliu B, Viñuela A, Castel SE, Mohammadi P, Aguet F, Zou Y, Khramtsova EA, Skol AD, Garrido-Martín D, Reverter F, Brown A, Evans P, Gamazon ER, Payne A, Bonazzola R, Barbeira AN, Hamel AR, Martinez-Perez A, Soria JM. The impact of sex on gene expression across human tissues. Science. 2020 09 11; 369(6509). PMID: 32913072.
      View in: PubMed
    6. Kim-Hellmuth S, Aguet F, Oliva M, Muñoz-Aguirre M, Kasela S, Wucher V, Castel SE, Hamel AR, Viñuela A, Roberts AL, Mangul S, Wen X, Wang G, Barbeira AN, Garrido-Martín D, Nadel BB, Zou Y, Bonazzola R, Quan J, Brown A, Martinez-Perez A, Soria JM. Cell type-specific genetic regulation of gene expression across human tissues. Science. 2020 09 11; 369(6509). PMID: 32913075.
      View in: PubMed
    7. Morrison J, Knoblauch N, Marcus JH, Stephens M, He X. Publisher Correction: Mendelian randomization accounting for correlated and uncorrelated pleiotropic effects using genome-wide summary statistics. Nat Genet. 2020 Jul; 52(7):750. PMID: 32472065.
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    8. Zhang Z, Luo K, Zou Z, Qiu M, Tian J, Sieh L, Shi H, Zou Y, Wang G, Morrison J, Zhu AC, Qiao M, Li Z, Stephens M, He X, He C. Genetic analyses support the contribution of mRNA N6-methyladenosine (m6A) modification to human disease heritability. Nat Genet. 2020 09; 52(9):939-949. PMID: 32601472.
      View in: PubMed
    9. Morrison J, Knoblauch N, Marcus JH, Stephens M, He X. Mendelian randomization accounting for correlated and uncorrelated pleiotropic effects using genome-wide summary statistics. Nat Genet. 2020 07; 52(7):740-747. PMID: 32451458.
      View in: PubMed
    10. Hsiao CJ, Tung P, Blischak JD, Burnett JE, Barr KA, Dey KK, Stephens M, Gilad Y. Characterizing and inferring quantitative cell cycle phase in single-cell RNA-seq data analysis. Genome Res. 2020 04; 30(4):611-621. PMID: 32312741.
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    11. Kim Y, Carbonetto P, Stephens M, Anitescu M. A Fast Algorithm for Maximum Likelihood Estimation of Mixture Proportions Using Sequential Quadratic Programming. J Comput Graph Stat. 2020; 29(2):261-273. PMID: 33762803.
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    12. Gerard D, Stephens M. Empirical Bayes shrinkage and false discovery rate estimation, allowing for unwanted variation. Biostatistics. 2020 01 01; 21(1):15-32. PMID: 29985984.
      View in: PubMed
    13. Blischak JD, Carbonetto P, Stephens M. Creating and sharing reproducible research code the workflowr way. F1000Res. 2019; 8:1749. PMID: 31723427.
      View in: PubMed
    14. Turchin MC, Stephens M. Bayesian multivariate reanalysis of large genetic studies identifies many new associations. PLoS Genet. 2019 10; 15(10):e1008431. PMID: 31596850.
      View in: PubMed
    15. Zhao S, Liu J, Nanga P, Liu Y, Cicek AE, Knoblauch N, He C, Stephens M, He X. Detailed modeling of positive selection improves detection of cancer driver genes. Nat Commun. 2019 07 30; 10(1):3399. PMID: 31363082.
      View in: PubMed
    16. White AE, Dey KK, Mohan D, Stephens M, Price TD. Regional influences on community structure across the tropical-temperate divide. Nat Commun. 2019 06 14; 10(1):2646. PMID: 31201312.
      View in: PubMed
    17. Sarkar AK, Tung PY, Blischak JD, Burnett JE, Li YI, Stephens M, Gilad Y. Discovery and characterization of variance QTLs in human induced pluripotent stem cells. PLoS Genet. 2019 04; 15(4):e1008045. PMID: 31002671.
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    18. Al-Asadi H, Dey KK, Novembre J, Stephens M. Inference and visualization of DNA damage patterns using a grade of membership model. Bioinformatics. 2019 04 15; 35(8):1292-1298. PMID: 30192911.
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    19. Stephens M. Correction: A Unified Framework for Association Analysis with Multiple Related Phenotypes. PLoS One. 2019; 14(3):e0213951. PMID: 30889189.
      View in: PubMed
    20. Al-Asadi H, Petkova D, Stephens M, Novembre J. Estimating recent migration and population-size surfaces. PLoS Genet. 2019 01; 15(1):e1007908. PMID: 30640906.
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    21. Dey KK, Xie D, Stephens M. A new sequence logo plot to highlight enrichment and depletion. BMC Bioinformatics. 2018 Dec 10; 19(1):473. PMID: 30526486.
      View in: PubMed
    22. Urbut SM, Wang G, Carbonetto P, Stephens M. Flexible statistical methods for estimating and testing effects in genomic studies with multiple conditions. Nat Genet. 2019 01; 51(1):187-195. PMID: 30478440.
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    23. Zhu X, Stephens M. 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. PMID: 30341297.
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    24. Gerard D, Ferrão LFV, Garcia AAF, Stephens M. Genotyping Polyploids from Messy Sequencing Data. Genetics. 2018 11; 210(3):789-807. PMID: 30185430.
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    25. Ferrão LFV, Ferrão RG, Ferrão MAG, Fonseca A, Carbonetto P, Stephens M, Garcia AAF. Accurate genomic prediction of Coffea canephora in multiple environments using whole-genome statistical models. Heredity (Edinb). 2019 03; 122(3):261-275. PMID: 29941997.
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    26. Ward MC, Zhao S, Luo K, Pavlovic BJ, Karimi MM, Stephens M, Gilad Y. Silencing of transposable elements may not be a major driver of regulatory evolution in primate iPSCs. Elife. 2018 04 12; 7. PMID: 29648536.
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    27. Smith J, Coop G, Stephens M, Novembre J. Estimating Time to the Common Ancestor for a Beneficial Allele. Mol Biol Evol. 2018 04 01; 35(4):1003-1017. PMID: 29361025.
      View in: PubMed
    28. Zhu X, Stephens M. BAYESIAN LARGE-SCALE MULTIPLE REGRESSION WITH SUMMARY STATISTICS FROM GENOME-WIDE ASSOCIATION STUDIES. Ann Appl Stat. 2017; 11(3):1561-1592. PMID: 29399241.
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    29. Dey KK, Hsiao CJ, Stephens M. Correction: Visualizing the structure of RNA-seq expression data using grade of membership models. PLoS Genet. 2017 May; 13(5):e1006759. PMID: 28549067.
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    30. Stephens M. False discovery rates: a new deal. Biostatistics. 2017 04 01; 18(2):275-294. PMID: 27756721.
      View in: PubMed
    31. Dey KK, Hsiao CJ, Stephens M. Visualizing the structure of RNA-seq expression data using grade of membership models. PLoS Genet. 2017 Mar; 13(3):e1006599. PMID: 28333934.
      View in: PubMed
    32. Schor IE, Degner JF, Harnett D, Cannavò E, Casale FP, Shim H, Garfield DA, Birney E, Stephens M, Stegle O, Furlong EE. Promoter shape varies across populations and affects promoter evolution and expression noise. Nat Genet. 2017 Apr; 49(4):550-558. PMID: 28191888.
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    33. Lu M, Stephens M. Variance adaptive shrinkage (vash): flexible empirical Bayes estimation of variances. Bioinformatics. 2016 11 15; 32(22):3428-3434. PMID: 27436563.
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    34. Raj A, Wang SH, Shim H, Harpak A, Li YI, Engelmann B, Stephens M, Gilad Y, Pritchard JK. Thousands of novel translated open reading frames in humans inferred by ribosome footprint profiling. Elife. 2016 05 27; 5. PMID: 27232982.
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    35. Mondol S, Moltke I, Hart J, Keigwin M, Brown L, Stephens M, Wasser SK. New evidence for hybrid zones of forest and savanna elephants in Central and West Africa. Mol Ecol. 2015 12; 24(24):6134-47. PMID: 26577954.
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    36. Petkova D, Novembre J, Stephens M. Visualizing spatial population structure with estimated effective migration surfaces. Nat Genet. 2016 Jan; 48(1):94-100. PMID: 26642242.
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    37. Shiraishi Y, Tremmel G, Miyano S, Stephens M. A Simple Model-Based Approach to Inferring and Visualizing Cancer Mutation Signatures. PLoS Genet. 2015 Dec; 11(12):e1005657. PMID: 26630308.
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    38. Raj A, Shim H, Gilad Y, Pritchard JK, Stephens M. msCentipede: Modeling Heterogeneity across Genomic Sites and Replicates Improves Accuracy in the Inference of Transcription Factor Binding. PLoS One. 2015; 10(9):e0138030. PMID: 26406244.
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    39. Shim H, Chasman DI, Smith JD, Mora S, Ridker PM, Nickerson DA, Krauss RM, Stephens M. 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. PMID: 25898129.
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    40. Tung J, Zhou X, Alberts SC, Stephens M, Gilad Y. The genetic architecture of gene expression levels in wild baboons. Elife. 2015 Feb 25; 4. PMID: 25714927.
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    41. Gao Z, Waggoner D, Stephens M, Ober C, Przeworski M. An estimate of the average number of recessive lethal mutations carried by humans. Genetics. 2015 Apr; 199(4):1243-54. PMID: 25697177.
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    42. Shim H, Stephens M. WAVELET-BASED GENETIC ASSOCIATION ANALYSIS OF FUNCTIONAL PHENOTYPES ARISING FROM HIGH-THROUGHPUT SEQUENCING ASSAYS. Ann Appl Stat. 2015; 9(2):655-686. PMID: 29399242.
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    43. Mangravite LM, Engelhardt BE, Stephens M, Krauss RM. Mangravite et al. reply. Nature. 2014 Sep 18; 513(7518):E3. PMID: 25230670.
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    44. Raj A, Stephens M, Pritchard JK. fastSTRUCTURE: variational inference of population structure in large SNP data sets. Genetics. 2014 Jun; 197(2):573-89. PMID: 24700103.
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    45. Zhou X, Stephens M. Efficient multivariate linear mixed model algorithms for genome-wide association studies. Nat Methods. 2014 Apr; 11(4):407-9. PMID: 24531419.
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    46. Zhou X, Cain CE, Myrthil M, Lewellen N, Michelini K, Davenport ER, Stephens M, Pritchard JK, Gilad Y. Epigenetic modifications are associated with inter-species gene expression variation in primates. Genome Biol. 2014; 15(12):547. PMID: 25468404.
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    47. Wen X, Stephens M. BAYESIAN METHODS FOR GENETIC ASSOCIATION ANALYSIS WITH HETEROGENEOUS SUBGROUPS: FROM META-ANALYSES TO GENE-ENVIRONMENT INTERACTIONS. Ann Appl Stat. 2014; 8(1):176-203. PMID: 26413181.
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    48. Carbonetto P, Stephens M. 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. PMID: 24098138.
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    49. Mangravite LM, Engelhardt BE, Medina MW, Smith JD, Brown CD, Chasman DI, Mecham BH, Howie B, Shim H, Naidoo D, Feng Q, Rieder MJ, Chen YD, Rotter JI, Ridker PM, Hopewell JC, Parish S, Armitage J, Collins R, Wilke RA, Nickerson DA, Stephens M, Krauss RM. A statin-dependent QTL for GATM expression is associated with statin-induced myopathy. Nature. 2013 Oct 17; 502(7471):377-80. PMID: 23995691.
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    50. Stephens M. A unified framework for association analysis with multiple related phenotypes. PLoS One. 2013; 8(7):e65245. PMID: 23861737.
      View in: PubMed
    51. Flutre T, Wen X, Pritchard J, Stephens M. A statistical framework for joint eQTL analysis in multiple tissues. PLoS Genet. 2013 May; 9(5):e1003486. PMID: 23671422.
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    52. Luca F, Maranville JC, Richards AL, Witonsky DB, Stephens M, Di Rienzo A. Genetic, functional and molecular features of glucocorticoid receptor binding. PLoS One. 2013; 8(4):e61654. PMID: 23637875.
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    53. Zhou X, Carbonetto P, Stephens M. Polygenic modeling with bayesian sparse linear mixed models. PLoS Genet. 2013; 9(2):e1003264. PMID: 23408905.
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    54. Pai AA, Cain CE, Mizrahi-Man O, De Leon S, Lewellen N, Veyrieras JB, Degner JF, Gaffney DJ, Pickrell JK, Stephens M, Pritchard JK, Gilad Y. The contribution of RNA decay quantitative trait loci to inter-individual variation in steady-state gene expression levels. PLoS Genet. 2012; 8(10):e1003000. PMID: 23071454.
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    55. Hart AB, Engelhardt BE, Wardle MC, Sokoloff G, Stephens M, de Wit H, Palmer AA. Genome-wide association study of d-amphetamine response in healthy volunteers identifies putative associations, including cadherin 13 (CDH13). PLoS One. 2012; 7(8):e42646. PMID: 22952603.
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    56. Howie B, Fuchsberger C, Stephens M, Marchini J, Abecasis GR. Fast and accurate genotype imputation in genome-wide association studies through pre-phasing. Nat Genet. 2012 Jul 22; 44(8):955-9. PMID: 22820512.
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    57. Zhou X, Stephens M. Genome-wide efficient mixed-model analysis for association studies. Nat Genet. 2012 Jun 17; 44(7):821-4. PMID: 22706312.
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    58. Fu AQ, Genereux DP, Stöger R, Burden AF, Laird CD, Stephens M. Statistical inference of in vivo properties of human DNA methyltransferases from double-stranded methylation patterns. PLoS One. 2012; 7(3):e32225. PMID: 22442664.
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    59. Maranville JC, Luca F, Stephens M, Di Rienzo A. Mapping gene-environment interactions at regulatory polymorphisms: insights into mechanisms of phenotypic variation. Transcription. 2012 Mar-Apr; 3(2):56-62. PMID: 22414753.
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    60. Veyrieras JB, Gaffney DJ, Pickrell JK, Gilad Y, Stephens M, Pritchard JK. Exon-specific QTLs skew the inferred distribution of expression QTLs detected using gene expression array data. PLoS One. 2012; 7(2):e30629. PMID: 22359548.
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    61. Degner JF, Pai AA, Pique-Regi R, Veyrieras JB, Gaffney DJ, Pickrell JK, De Leon S, Michelini K, Lewellen N, Crawford GE, Stephens M, Gilad Y, Pritchard JK. DNase?I sensitivity QTLs are a major determinant of human expression variation. Nature. 2012 Feb 05; 482(7385):390-4. PMID: 22307276.
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    62. Gaffney DJ, Veyrieras JB, Degner JF, Pique-Regi R, Pai AA, Crawford GE, Stephens M, Gilad Y, Pritchard JK. Dissecting the regulatory architecture of gene expression QTLs. Genome Biol. 2012 Jan 31; 13(1):R7. PMID: 22293038.
      View in: PubMed
    63. Perry GH, Melsted P, Marioni JC, Wang Y, Bainer R, Pickrell JK, Michelini K, Zehr S, Yoder AD, Stephens M, Pritchard JK, Gilad Y. Comparative RNA sequencing reveals substantial genetic variation in endangered primates. Genome Res. 2012 Apr; 22(4):602-10. PMID: 22207615.
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    64. Mechanic LE, Chen HS, Amos CI, Chatterjee N, Cox NJ, Divi RL, Fan R, Harris EL, Jacobs K, Kraft P, Leal SM, McAllister K, Moore JH, Paltoo DN, Province MA, Ramos EM, Ritchie MD, Roeder K, Schaid DJ, Stephens M, Thomas DC, Weinberg CR, Witte JS, Zhang S, Zöllner S, Feuer EJ, Gillanders EM. Next generation analytic tools for large scale genetic epidemiology studies of complex diseases. Genet Epidemiol. 2012 Jan; 36(1):22-35. PMID: 22147673.
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    65. Howie B, Marchini J, Stephens M. Genotype imputation with thousands of genomes. G3 (Bethesda). 2011 Nov; 1(6):457-70. PMID: 22384356.
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    66. Maranville JC, Luca F, Richards AL, Wen X, Witonsky DB, Baxter S, Stephens M, Di Rienzo A. Interactions between glucocorticoid treatment and cis-regulatory polymorphisms contribute to cellular response phenotypes. PLoS Genet. 2011 Jul; 7(7):e1002162. PMID: 21750684.
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    67. Fledel-Alon A, Leffler EM, Guan Y, Stephens M, Coop G, Przeworski M. Variation in human recombination rates and its genetic determinants. PLoS One. 2011; 6(6):e20321. PMID: 21698098.
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    68. Barreiro LB, Marioni JC, Blekhman R, Stephens M, Gilad Y. Functional comparison of innate immune signaling pathways in primates. PLoS Genet. 2010 Dec 16; 6(12):e1001249. PMID: 21187902.
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    69. Engelhardt BE, Stephens M. Analysis of population structure: a unifying framework and novel methods based on sparse factor analysis. PLoS Genet. 2010 Sep 16; 6(9):e1001117. PMID: 20862358.
      View in: PubMed
    70. Wen X, Stephens M. USING LINEAR PREDICTORS TO IMPUTE ALLELE FREQUENCIES FROM SUMMARY OR POOLED GENOTYPE DATA. Ann Appl Stat. 2010 Sep; 4(3):1158-1182. PMID: 21479081.
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    71. Novembre J, Stephens M. Response to Cavalli-Sforza interview [Human Biology 82(3):245-266 (June 2010)]. Hum Biol. 2010 Aug; 82(4):469-70. PMID: 21082913.
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    72. Barber MJ, Mangravite LM, Hyde CL, Chasman DI, Smith JD, McCarty CA, Li X, Wilke RA, Rieder MJ, Williams PT, Ridker PM, Chatterjee A, Rotter JI, Nickerson DA, Stephens M, Krauss RM. Genome-wide association of lipid-lowering response to statins in combined study populations. PLoS One. 2010 Mar 22; 5(3):e9763. PMID: 20339536.
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    73. Pickrell JK, Marioni JC, Pai AA, Degner JF, Engelhardt BE, Nkadori E, Veyrieras JB, Stephens M, Gilad Y, Pritchard JK. Understanding mechanisms underlying human gene expression variation with RNA sequencing. Nature. 2010 Apr 01; 464(7289):768-72. PMID: 20220758.
      View in: PubMed
    74. Fu AQ, Genereux DP, Stöger R, Laird CD, Stephens M. STATISTICAL INFERENCE OF TRANSMISSION FIDELITY OF DNA METHYLATION PATTERNS OVER SOMATIC CELL DIVISIONS IN MAMMALS. Ann Appl Stat. 2010; 4(2):871-892. PMID: 21625348.
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    75. Blekhman R, Marioni JC, Zumbo P, Stephens M, Gilad Y. Sex-specific and lineage-specific alternative splicing in primates. Genome Res. 2010 Feb; 20(2):180-9. PMID: 20009012.
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    76. Stephens M, Balding DJ. Bayesian statistical methods for genetic association studies. Nat Rev Genet. 2009 Oct; 10(10):681-90. PMID: 19763151.
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    77. Hubisz MJ, Falush D, Stephens M, Pritchard JK. Inferring weak population structure with the assistance of sample group information. Mol Ecol Resour. 2009 Sep; 9(5):1322-32. PMID: 21564903.
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    78. Guan Y, Stephens M. Practical issues in imputation-based association mapping. PLoS Genet. 2008 Dec; 4(12):e1000279. PMID: 19057666.
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    79. Veyrieras JB, Kudaravalli S, Kim SY, Dermitzakis ET, Gilad Y, Stephens M, Pritchard JK. High-resolution mapping of expression-QTLs yields insight into human gene regulation. PLoS Genet. 2008 Oct; 4(10):e1000214. PMID: 18846210.
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    80. Yan R, Yuan G, Stephens MD, He X, Henry CS, Dandy DS, Lear KL. Evanescent field response to immunoassay layer thickness on planar waveguides. Appl Phys Lett. 2008 Sep 08; 93(10):101110. PMID: 19529840.
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    81. Novembre J, Johnson T, Bryc K, Kutalik Z, Boyko AR, Auton A, Indap A, King KS, Bergmann S, Nelson MR, Stephens M, Bustamante CD. Genes mirror geography within Europe. Nature. 2008 Nov 06; 456(7218):98-101. PMID: 18758442.
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    82. Scheet P, Stephens M. Linkage disequilibrium-based quality control for large-scale genetic studies. PLoS Genet. 2008 Aug 01; 4(8):e1000147. PMID: 18670630.
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    83. Marioni JC, Mason CE, Mane SM, Stephens M, Gilad Y. RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Res. 2008 Sep; 18(9):1509-17. PMID: 18550803.
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    84. Reiner AP, Barber MJ, Guan Y, Ridker PM, Lange LA, Chasman DI, Walston JD, Cooper GM, Jenny NS, Rieder MJ, Durda JP, Smith JD, Novembre J, Tracy RP, Rotter JI, Stephens M, Nickerson DA, Krauss RM. 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. PMID: 18439552.
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    85. Novembre J, Stephens M. Interpreting principal component analyses of spatial population genetic variation. Nat Genet. 2008 May; 40(5):646-9. PMID: 18425127.
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    86. A second generation human haplotype map of over 3.1 million SNPs. Nature. 2007 Oct 18; 449(7164):851-61. PMID: 17943122.
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    87. Sabeti PC, Varilly P, Fry B, Lohmueller J, Hostetter E, Cotsapas C, Xie X, Byrne EH, McCarroll SA, Gaudet R, Schaffner SF, Lander ES. Genome-wide detection and characterization of positive selection in human populations. Nature. 2007 Oct 18; 449(7164):913-8. PMID: 17943131.
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    88. Falush D, Stephens M, Pritchard JK. Inference of population structure using multilocus genotype data: dominant markers and null alleles. Mol Ecol Notes. 2007 Jul 01; 7(4):574-578. PMID: 18784791.
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    89. Roychoudhury A, Stephens M. Fast and accurate estimation of the population-scaled mutation rate, theta, from microsatellite genotype data. Genetics. 2007 Jun; 176(2):1363-6. PMID: 17579241.
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    90. Servin B, Stephens M. Imputation-based analysis of association studies: candidate regions and quantitative traits. PLoS Genet. 2007 Jul; 3(7):e114. PMID: 17676998.
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    91. Wasser SK, Mailand C, Booth R, Mutayoba B, Kisamo E, Clark B, Stephens M. Using DNA to track the origin of the largest ivory seizure since the 1989 trade ban. Proc Natl Acad Sci U S A. 2007 Mar 06; 104(10):4228-33. PMID: 17360505.
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    92. Hellenthal G, Stephens M. msHOT: modifying Hudson's ms simulator to incorporate crossover and gene conversion hotspots. Bioinformatics. 2007 Feb 15; 23(4):520-1. PMID: 17150995.
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    93. Bhangale TR, Stephens M, Nickerson DA. Automating resequencing-based detection of insertion-deletion polymorphisms. Nat Genet. 2006 Dec; 38(12):1457-62. PMID: 17115056.
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    94. Raedt TD, Stephens M, Heyns I, Brems H, Thijs D, Messiaen L, Stephens K, Lazaro C, Wimmer K, Kehrer-Sawatzki H, Vidaud D, Kluwe L, Marynen P, Legius E. Conservation of hotspots for recombination in low-copy repeats associated with the NF1 microdeletion. Nat Genet. 2006 Dec; 38(12):1419-23. PMID: 17115058.
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    95. Hellenthal G, Stephens M. Insights into recombination from population genetic variation. Curr Opin Genet Dev. 2006 Dec; 16(6):565-72. PMID: 17049225.
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    96. Sanda C, Weitzel P, Tsukahara T, Schaley J, Edenberg HJ, Stephens MA, McClintick JN, Blatt LM, Li L, Brodsky L, Taylor MW. Differential gene induction by type I and type II interferons and their combination. J Interferon Cytokine Res. 2006 Jul; 26(7):462-72. PMID: 16800785.
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    97. Stephens M, Sloan JS, Robertson PD, Scheet P, Nickerson DA. Automating sequence-based detection and genotyping of SNPs from diploid samples. Nat Genet. 2006 Mar; 38(3):375-81. PMID: 16493422.
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    98. Scheet P, Stephens M. 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. PMID: 16532393.
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    99. Marchini J, Cutler D, Patterson N, Stephens M, Eskin E, Halperin E, Lin S, Qin ZS, Munro HM, Abecasis GR, Donnelly P. A comparison of phasing algorithms for trios and unrelated individuals. Am J Hum Genet. 2006 Mar; 78(3):437-50. PMID: 16465620.
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    100. Hellenthal G, Pritchard JK, Stephens M. The effects of genotype-dependent recombination, and transmission asymmetry, on linkage disequilibrium. Genetics. 2006 Mar; 172(3):2001-5. PMID: 16387890.
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    101. Gottardo R, Besag J, Stephens M, Murua A. Probabilistic segmentation and intensity estimation for microarray images. Biostatistics. 2006 Jan; 7(1):85-99. PMID: 16049139.
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    102. Stephens M, Scheet P. Accounting for decay of linkage disequilibrium in haplotype inference and missing-data imputation. Am J Hum Genet. 2005 Mar; 76(3):449-62. PMID: 15700229.
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    103. Wasser SK, Shedlock AM, Comstock K, Ostrander EA, Mutayoba B, Stephens M. Assigning African elephant DNA to geographic region of origin: applications to the ivory trade. Proc Natl Acad Sci U S A. 2004 Oct 12; 101(41):14847-52. PMID: 15459317.
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    104. Ptak SE, Roeder AD, Stephens M, Gilad Y, Pääbo S, Przeworski M. Absence of the TAP2 human recombination hotspot in chimpanzees. PLoS Biol. 2004 Jun; 2(6):e155. PMID: 15208713.
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    105. Crawford DC, Bhangale T, Li N, Hellenthal G, Rieder MJ, Nickerson DA, Stephens M. Evidence for substantial fine-scale variation in recombination rates across the human genome. Nat Genet. 2004 Jul; 36(7):700-6. PMID: 15184900.
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    106. Li N, Stephens M. Modeling linkage disequilibrium and identifying recombination hotspots using single-nucleotide polymorphism data. Genetics. 2003 Dec; 165(4):2213-33. PMID: 14704198.
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    107. Stephens M, Donnelly P. A comparison of bayesian methods for haplotype reconstruction from population genotype data. Am J Hum Genet. 2003 Nov; 73(5):1162-9. PMID: 14574645.
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    108. Falush D, Stephens M, Pritchard JK. Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics. 2003 Aug; 164(4):1567-87. PMID: 12930761.
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    109. Falush D, Wirth T, Linz B, Pritchard JK, Stephens M, Kidd M, Blaser MJ, Graham DY, Vacher S, Perez-Perez GI, Yamaoka Y, Mégraud F, Otto K, Reichard U, Katzowitsch E, Wang X, Achtman M, Suerbaum S. Traces of human migrations in Helicobacter pylori populations. Science. 2003 Mar 07; 299(5612):1582-5. PMID: 12624269.
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