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Matthew Stephens

TitleProfessor
InstitutionUniversity of Chicago
DepartmentStatistics
AddressChicago IL 60637
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    Collapse Overview 
    Collapse overview
    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.

    Collapse Research 
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    R01MH101825     (STEPHENS, MATTHEW)Aug 1, 2013 - Jun 30, 2018
    NIH
    Statistical analysis of gene expression quantitative trait loci (eQTL)
    Role: Principal Investigator
    U01HL084689     (STEPHENS, MATTHEW)Jun 15, 2006 - May 31, 2010
    NIH
    Multipoint and significance methods for genome-wide association studies
    Role: Principal Investigator
    R01HG002585     (STEPHENS, MATTHEW)Sep 20, 2002 - Jul 31, 2028
    NIH
    Genome analysis: statistical methods and applications
    Role: Principal Investigator
    R56HG002585     (STEPHENS, MATTHEW)Sep 20, 2002 - Aug 31, 2024
    NIH
    Genome analysis: statistical methods and applications
    Role: Principal Investigator

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    Collapse Bibliographic 
    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.
    Newest   |   Oldest   |   Most Cited   |   Most Discussed   |   Timeline   |   Field Summary   |   Plain Text
    PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Denault WRP, Sun H, Carbonetto P, Liu A, De Jager PL, Bennett D, Alzheimer's Disease Functional Genomics Consortium, Wang G, Stephens M. fSuSiE enables fine-mapping of QTLs from genome-scale molecular profiles. bioRxiv. 2025 Aug 17. PMID: 40832254; PMCID: PMC12363973.
      Citations:    
    2. Thompson EE, Zhong X, Carbonetto P, Morin A, Willwerscheid J, Visness CM, Bacharier LB, Kattan M, O'Connor GT, Rivera-Spoljaric K, Wood RA, Gold DR, Khurana Hershey GK, Johnson CC, Miller RL, Seroogy CM, Zoratti EM, Gergen PJ, Levin AM, Altman MC, Hartert T, Stephens M, Jackson DJ, Gern JE, McKennan CG, Ober C. Genetic contributions to epigenetic-defined endotypes of allergic phenotypes in children. Am J Hum Genet. 2025 Jul 03; 112(7):1610-1624. PMID: 40614707; PMCID: PMC12256822.
      Citations:    Fields:    Translation:HumansCells
    3. Yang Y, Tayeb K, Carbonetto P, Zhong X, Ober C, Stephens M. BAYESIAN VARIABLE SELECTION IN A COX PROPORTIONAL HAZARDS MODEL WITH THE "SUM OF SINGLE EFFECTS" PRIOR. ArXiv. 2025 Jun 06. PMID: 40503016; PMCID: PMC12155538.
      Citations:    
    4. Gilad Y, Li M, Allen O, Burnett J, Popp J, Stephens M, Battle A, Lin W, Lin W, Li M, Allen O, Burnett J, Popp JM, Stephens M, Battle A, Gilad Y. Disease-associated loci share properties with response eQTLs under common environmental exposures. Res Sq. 2025 May 14. PMID: 40470191; PMCID: PMC12136233.
      Citations:    
    5. Lin W, Li M, Allen O, Burnett J, Popp JM, Stephens M, Battle A, Gilad Y. Disease-associated loci share properties with response eQTLs under common environmental exposures. bioRxiv. 2025 May 04. PMID: 40654932; PMCID: PMC12247639.
      Citations:    
    6. Nieves KM, Flannigan KL, Hughes E, Stephens M, Thorne AJ, Delanne-Cuménal A, Strayer K, Kola-Ilesanmi D, Wickramasinghe S, Mirzadzar N, Baruta G, McDonald B, Cobo ER, Petri B, Mani S, Hirota SA. Indole-3-propionic acid protects medium-diversity colitic mice via barrier enhancement preferentially over anti-inflammatory effects. Am J Physiol Gastrointest Liver Physiol. 2025 Jun 01; 328(6):G696-G715. PMID: 40257386.
      Citations: 4     Fields:    Translation:Animals
    7. Liu Y, Carbonetto P, Willwerscheid J, Oakes SA, Macleod KF, Stephens M. Dissecting tumor transcriptional heterogeneity from single-cell RNA-seq data by generalized binary covariance decomposition. Nat Genet. 2025 Jan; 57(1):263-273. PMID: 39747597; PMCID: PMC12035913.
      Citations: 5     Fields:    Translation:Humans
    8. Thompson EE, Zhong X, Carbonetto P, Morin A, Willwerscheid J, Visness CM, Bacharier LB, Kattan M, O'Connor GT, Rivera-Spoljaric K, Wood RA, Gold DR, Hershey GKK, Johnson CC, Miller RL, Seroogy CM, Zoratti EM, Gergen PJ, Levin AM, Altman MC, Hartert T, Stephens M, Jackson DJ, Gern JE, McKennan CG, Ober C. Genetic contributions to epigenetic-defined endotypes of allergic phenotypes in children. medRxiv. 2024 Oct 04. PMID: 40034775; PMCID: PMC11875257.
      Citations: 1     
    9. Weine E, Carbonetto P, Stephens M. Accelerated dimensionality reduction of single-cell RNA sequencing data with fastglmpca. Bioinformatics. 2024 08 02; 40(8). PMID: 39110511; PMCID: PMC11322042.
      Citations:    Fields:    Translation:Humans
    10. Weine E, Carbonetto P, Stephens M. Accelerated dimensionality reduction of single-cell RNA sequencing data with fastglmpca. bioRxiv. 2024 Jul 04. PMID: 38585920; PMCID: PMC10996495.
      Citations:    
    11. Zou Y, Xie D, Carbonetto P, Wang G, Stephens M. Fast and flexible joint fine-mapping of multiple traits via the Sum of Single Effects model. bioRxiv. 2024 Jun 18. PMID: 37425935; PMCID: PMC10327118.
      Citations: 1     
    12. Liu Y, Carbonetto P, Willwerscheid J, Oakes SA, Macleod KF, Stephens M. Dissecting tumor transcriptional heterogeneity from single-cell RNA-seq data by generalized binary covariance decomposition. bioRxiv. 2024 May 26. PMID: 37645713; PMCID: PMC10462040.
      Citations:    
    13. Zhao S, Crouse W, Qian S, Luo K, Stephens M, He X. 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. PMID: 38279041; PMCID: PMC10864181.
      Citations: 36     Fields:    Translation:HumansCells
    14. Takahama M, Patil A, Richey G, Cipurko D, Johnson K, Carbonetto P, Plaster M, Pandey S, Cheronis K, Ueda T, Gruenbaum A, Kawamoto T, Stephens M, Chevrier N. A pairwise cytokine code explains the organism-wide response to sepsis. Nat Immunol. 2024 Feb; 25(2):226-239. PMID: 38191855; PMCID: PMC10834370.
      Citations: 20     Fields:    Translation:Animals
    15. Carrillo Diaz de Leon M, Keane K, Roizes S, Liao S, von der Weid PY, Stephens M. Not just fibrotic: endothelial-derived TGFß maintains contractile function and lymphatic muscle phenotype during homeostasis. Am J Physiol Cell Physiol. 2024 01 01; 326(1):C269-C281. PMID: 38047303.
      Citations:    Fields:    Translation:AnimalsCells
    16. Carbonetto P, Luo K, Sarkar A, Hung A, Tayeb K, Pott S, Stephens M. GoM DE: interpreting structure in sequence count data with differential expression analysis allowing for grades of membership. Genome Biol. 2023 10 19; 24(1):236. PMID: 37858253; PMCID: PMC10588049.
      Citations: 8     Fields:    
    17. Carbonetto P, Luo K, Sarkar A, Hung A, Tayeb K, Pott S, Stephens M. GoM DE: interpreting structure in sequence count data with differential expression analysis allowing for grades of membership. bioRxiv. 2023 Sep 14. PMID: 36945441; PMCID: PMC10028846.
      Citations:    
    18. Morgante F, Carbonetto P, Wang G, Zou Y, Sarkar A, Stephens M. A flexible empirical Bayes approach to multivariate multiple regression, and its improved accuracy in predicting multi-tissue gene expression from genotypes. PLoS Genet. 2023 07; 19(7):e1010539. PMID: 37418505; PMCID: PMC10355440.
      Citations: 3     Fields:    
    19. Stephens M. The Bayesian lens and Bayesian blinkers. Philos Trans A Math Phys Eng Sci. 2023 May 15; 381(2247):20220144. PMID: 36970830; PMCID: PMC10041352.
      Citations: 3     Fields:    
    20. Kang Y, Colson-Fearon D, Kim M, Park S, Stephens M, Kim Y, Wetzler E. Socio-economic and psychosocial determinants of violent discipline among parents in Asia Pacific countries during COVID-19: Focus on disadvantaged populations. Child Abuse Negl. 2023 05; 139:106059. PMID: 36805614; PMCID: PMC9933874.
      Citations: 2     Fields:    Translation:HumansPHPublic Health
    21. Takahama M, Patil A, Johnson K, Cipurko D, Miki Y, Taketomi Y, Carbonetto P, Plaster M, Richey G, Pandey S, Cheronis K, Ueda T, Gruenbaum A, Dudek SM, Stephens M, Murakami M, Chevrier N. Organism-Wide Analysis of Sepsis Reveals Mechanisms of Systemic Inflammation. bioRxiv. 2023 Feb 02. PMID: 36778287; PMCID: PMC9915512.
      Citations: 1     
    22. Xie D, Stephens M. Discussion of "Confidence Intervals for Nonparametric Empirical Bayes Analysis". J Am Stat Assoc. 2022; 117(539):1186-1191. PMID: 37275677; PMCID: PMC10237054.
      Citations: 4     
    23. Xue J, Lin Y, Oo D, Zhang J, Zardynezhad A, de Jesus FN, Stephens M, de Almeida LGN, Young D, Dufour A, Liao S. Lymph-derived chemokines direct early neutrophil infiltration in the lymph nodes upon Staphylococcus aureus skin infection. Proc Natl Acad Sci U S A. 2022 08 09; 119(32):e2111726119. PMID: 35914162; PMCID: PMC9371737.
      Citations: 3     Fields:    Translation:AnimalsCells
    24. Zou Y, Carbonetto P, Wang G, Stephens M. Fine-mapping from summary data with the "Sum of Single Effects" model. PLoS Genet. 2022 07; 18(7):e1010299. PMID: 35853082; PMCID: PMC9337707.
      Citations: 168     Fields:    
    25. Stephens M, Keane K, Roizes S, Liao S, Weid PV. Mincle-binding DNA aptamer demonstrates therapeutic potential in a model of inflammatory bowel disease. Mol Ther Nucleic Acids. 2022 Jun 14; 28:935-947. PMID: 35782912; PMCID: PMC9207717.
      Citations: 6     
    26. Clay SM, Schoettler N, Goldstein AM, Carbonetto P, Dapas M, Altman MC, Rosasco MG, Gern JE, Jackson DJ, Im HK, Stephens M, Nicolae DL, Ober C. Fine-mapping studies distinguish genetic risks for childhood- and adult-onset asthma in the HLA region. Genome Med. 2022 05 24; 14(1):55. PMID: 35606880; PMCID: PMC9128203.
      Citations: 8     Fields:    Translation:HumansCells
    27. Pulakazhi Venu VK, Alston L, Iftinca M, Tsai YC, Stephens M, Warriyar K V V, Rehal S, Hudson G, Szczepanski H, von der Weid PY, Altier C, Hirota SA. Nr4A1 modulates inflammation-associated intestinal fibrosis and dampens fibrogenic signaling in myofibroblasts. Am J Physiol Gastrointest Liver Physiol. 2021 09 01; 321(3):G280-G297. PMID: 34288735.
      Citations: 27     Fields:    Translation:HumansAnimalsCells
    28. Gerard D, Stephens M. UNIFYING AND GENERALIZING METHODS FOR REMOVING UNWANTED VARIATION BASED ON NEGATIVE CONTROLS. Stat Sin. 2021 Jul; 31(3):1145-1166. PMID: 38148787; PMCID: PMC10751021.
      Citations: 5     
    29. 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; PMCID: PMC8370014.
      Citations: 103     Fields:    Translation:Humans
    30. 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 02 08; 10. PMID: 33554857; PMCID: PMC7906610.
      Citations: 32     Fields:    Translation:HumansCells
    31. 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, GTEx GWAS Working Group, Bastarache L, Jordan DM, Verbanck M, Do R, GTEx Consortium, Stephens M, Ardlie K, McCarthy M, Montgomery SB, Brown CD, Lappalainen T, Wen X, Im HK, Aguet F, Segrè AV. Exploiting the GTEx resources to decipher the mechanisms at GWAS loci. Genome Biol. 2021 01 26; 22(1):49. PMID: 33499903; PMCID: PMC7836161.
      Citations: 159     Fields:    Translation:HumansCells
    32. Stephens M, Liao S, von der Weid PY. Ultra-purification of Lipopolysaccharides reveals species-specific signalling bias of TLR4: importance in macrophage function. Sci Rep. 2021 01 14; 11(1):1335. PMID: 33446670; PMCID: PMC7809447.
      Citations: 9     Fields:    Translation:HumansCells
    33. 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; PMCID: PMC7986858.
      Citations: 8     
    34. Xing Z, Carbonetto P, Stephens M. Flexible Signal Denoising via Flexible Empirical Bayes Shrinkage. J Mach Learn Res. 2021 Jan-Dec; 22. PMID: 38149302; PMCID: PMC10751020.
      Citations: 1     
    35. Wang W, Stephens M. Empirical Bayes Matrix Factorization. J Mach Learn Res. 2021; 22. PMID: 37920532; PMCID: PMC10621241.
      Citations: 14     
    36. Oliva M, Kim-Hellmuth S, Wucher V, Gewirtz ADH, Cotter DJ, Parsana P, Kasela S, Balliu B, Castel SE, Mohammadi P, Zou Y, Khramtsova EA, Skol AD, Reverter F, Brown A, Evans P, Gamazon ER, Payne A, Bonazzola R, Barbeira AN, Hamel AR, Martinez-Perez A, GTEx Consortium, Pierce BL, Stephens M, Eskin E, Dermitzakis ET, Im HK, Engelhardt BE, Ardlie KG, Montgomery SB, Battle AJ, Lappalainen T, Stranger BE, Muñoz-Aguirre M, Viñuela A, Aguet F, Garrido-Martín D, Soria JM, Segrè AV, Guigó R. The impact of sex on gene expression across human tissues. Science. 2020 09 11; 369(6509). PMID: 32913072; PMCID: PMC8136152.
      Citations: 362     Fields:    Translation:HumansCells
    37. Kim-Hellmuth S, Oliva M, Kasela S, Wucher V, Castel SE, Hamel AR, Roberts AL, Mangul S, Wen X, Wang G, Barbeira AN, Nadel BB, Zou Y, Bonazzola R, Quan J, Brown A, GTEx Consortium, Getz G, Dermitzakis ET, Small KS, Stephens M, Xi HS, Im HK, Stranger BE, Ardlie KG, Lappalainen T, Aguet F, Muñoz-Aguirre M, Viñuela A, Garrido-Martín D, Martinez-Perez A, Soria JM, Guigó R, Segrè AV. Cell type-specific genetic regulation of gene expression across human tissues. Science. 2020 09 11; 369(6509). PMID: 32913075; PMCID: PMC8051643.
      Citations: 205     Fields:    Translation:HumansCells
    38. Wang G, Sarkar A, Carbonetto P, Stephens M. A simple new approach to variable selection in regression, with application to genetic fine mapping. J R Stat Soc Series B Stat Methodol. 2020 Dec; 82(5):1273-1300. PMID: 37220626; PMCID: PMC10201948.
      Citations: 460     
    39. 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.
      Citations: 6     Fields:    
    40. 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; PMCID: PMC7483307.
      Citations: 109     Fields:    Translation:HumansCells
    41. 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; PMCID: PMC7343608.
      Citations: 333     Fields:    
    42. 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; PMCID: PMC7197478.
      Citations: 53     Fields:    Translation:HumansCells
    43. 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; PMCID: PMC7986967.
      Citations: 5     
    44. 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; PMCID: PMC8204175.
      Citations: 7     Fields:    Translation:Humans
    45. Blischak JD, Carbonetto P, Stephens M. Creating and sharing reproducible research code the workflowr way. F1000Res. 2019; 8:1749. PMID: 31723427; PMCID: PMC6833990.
      Citations: 28     Fields:    
    46. Turchin MC, Stephens M. Bayesian multivariate reanalysis of large genetic studies identifies many new associations. PLoS Genet. 2019 10; 15(10):e1008431. PMID: 31596850; PMCID: PMC6802844.
      Citations: 10     Fields:    
    47. 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; PMCID: PMC6667447.
      Citations: 48     Fields:    Translation:Humans
    48. 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; PMCID: PMC6570764.
      Citations: 13     Fields:    Translation:Animals
    49. 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; PMCID: PMC6474585.
      Citations: 41     Fields:    Translation:HumansCells
    50. 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; PMCID: PMC6821257.
      Citations: 3     Fields:    Translation:Humans
    51. Stephens M. Correction: A Unified Framework for Association Analysis with Multiple Related Phenotypes. PLoS One. 2019; 14(3):e0213951. PMID: 30889189; PMCID: PMC6424389.
      Citations: 2     Fields:    
    52. 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; PMCID: PMC6347299.
      Citations: 51     Fields:    Translation:Humans
    53. 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; PMCID: PMC6288878.
      Citations: 29     Fields:    Translation:HumansCells
    54. 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; PMCID: PMC6309609.
      Citations: 230     Fields:    Translation:Humans
    55. 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; PMCID: PMC6195536.
      Citations: 47     Fields:    Translation:Humans
    56. Gerard D, Stephens M, Ferrão LFV, Garcia AAF. Genotyping Polyploids from Messy Sequencing Data. Genetics. 2018 11; 210(3):789-807. PMID: 30185430; PMCID: PMC6218231.
      Citations: 88     Fields:    Translation:Animals
    57. Cottagiri M, Nyandjo M, Stephens M, Mantilla JJ, Saito H, Mackay IR, Rose NR, Njoku DB. In drug-induced, immune-mediated hepatitis, interleukin-33 reduces hepatitis and improves survival independently and as a consequence of FoxP3+ T-cell activity. Cell Mol Immunol. 2019 08; 16(8):706-717. PMID: 30030493; PMCID: PMC6804902.
      Citations: 5     Fields:    Translation:HumansAnimalsCells
    58. Carbonetto P, Stephens M, Ferrão LFV, Ferrão RG, Ferrão MAG, Fonseca A, 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; PMCID: PMC6460747.
      Citations: 18     Fields:    Translation:Animals
    59. 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; PMCID: PMC5943035.
      Citations: 17     Fields:    Translation:HumansAnimalsCells
    60. 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; PMCID: PMC5888984.
      Citations: 36     Fields:    Translation:Humans
    61. 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; PMCID: PMC5796536.
      Citations: 89     
    62. 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; PMCID: PMC5446108.
      Citations:    Fields:    
    63. Stephens M. False discovery rates: a new deal. Biostatistics. 2017 04 01; 18(2):275-294. PMID: 27756721; PMCID: PMC5379932.
      Citations: 577     Fields:    Translation:Humans
    64. 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; PMCID: PMC5363805.
      Citations: 88     Fields:    Translation:HumansAnimalsCells
    65. Schor IE, Degner JF, Harnett D, Casale FP, Shim H, Garfield DA, Birney E, Stephens M, Stegle O, Furlong EE, Cannavò E. Promoter shape varies across populations and affects promoter evolution and expression noise. Nat Genet. 2017 Apr; 49(4):550-558. PMID: 28191888.
      Citations: 47     Fields:    Translation:AnimalsCellsPHPublic Health
    66. Lu M, Stephens M. Variance adaptive shrinkage (vash): flexible empirical Bayes estimation of variances. Bioinformatics. 2016 11 15; 32(22):3428-3434. PMID: 27436563; PMCID: PMC5181563.
      Citations: 3     Fields:    Translation:HumansAnimals
    67. 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; PMCID: PMC4940163.
      Citations: 92     Fields:    Translation:HumansCells
    68. Moltke I, Hart J, Stephens M, Mondol S, Keigwin M, Brown L, 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.
      Citations: 15     Fields:    Translation:AnimalsCells
    69. 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; PMCID: PMC4696895.
      Citations: 225     Fields:    Translation:HumansAnimalsCells
    70. 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; PMCID: PMC4667891.
      Citations: 66     Fields:    Translation:HumansCells
    71. Stephens MD, Hubble VB, Ernst RK, van Hoek ML, Melander RJ, Cavanagh J, Melander C. Potentiation of Francisella Resistance to Conventional Antibiotics through Small Molecule Adjuvants. Medchemcomm. 2016 Jan 01; 7(1):128-131. PMID: 26877862; PMCID: PMC4749165.
      Citations: 9     
    72. 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; PMCID: PMC4583425.
      Citations: 20     Fields:    Translation:HumansCells
    73. 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; PMCID: PMC4405269.
      Citations: 286     Fields:    Translation:Humans
    74. 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; PMCID: PMC4383332.
      Citations: 58     Fields:    Translation:Animals
    75. 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; PMCID: PMC4391560.
      Citations: 38     Fields:    Translation:Humans
    76. 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; PMCID: PMC5795621.
      Citations: 13     
    77. Mangravite LM, Engelhardt BE, Stephens M, Krauss RM. Mangravite et al. reply. Nature. 2014 Sep 18; 513(7518):E3. PMID: 25230670.
      Citations: 2     Fields:    Translation:Humans
    78. 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; PMCID: PMC4063916.
      Citations: 747     Fields:    Translation:Humans
    79. 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; PMCID: PMC4211878.
      Citations: 433     Fields:    
    80. 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; PMCID: PMC4290387.
      Citations: 41     Fields:    Translation:HumansAnimalsCells
    81. 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; PMCID: PMC4583155.
      Citations: 27     
    82. 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; PMCID: PMC3789883.
      Citations: 41     Fields:    Translation:HumansCells
    83. 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; PMCID: PMC3933266.
      Citations: 117     Fields:    Translation:HumansCells
    84. Stephens M. A unified framework for association analysis with multiple related phenotypes. PLoS One. 2013; 8(7):e65245. PMID: 23861737; PMCID: PMC3702528.
      Citations: 152     Fields:    Translation:Humans
    85. Wen X, Pritchard J, Stephens M, Flutre T. A statistical framework for joint eQTL analysis in multiple tissues. PLoS Genet. 2013 May; 9(5):e1003486. PMID: 23671422; PMCID: PMC3649995.
      Citations: 141     Fields:    
    86. 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; PMCID: PMC3640037.
      Citations: 13     Fields:    Translation:HumansCells
    87. Zhou X, Carbonetto P, Stephens M. Polygenic modeling with bayesian sparse linear mixed models. PLoS Genet. 2013; 9(2):e1003264. PMID: 23408905; PMCID: PMC3567190.
      Citations: 427     Fields:    Translation:Humans
    88. 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; PMCID: PMC3469421.
      Citations: 68     Fields:    Translation:HumansCells
    89. 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; PMCID: PMC3429486.
      Citations: 55     Fields:    Translation:Humans
    90. 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; PMCID: PMC3696580.
      Citations: 1137     Fields:    Translation:Humans
    91. Zhou X, Stephens M. Genome-wide efficient mixed-model analysis for association studies. Nat Genet. 2012 Jun 17; 44(7):821-4. PMID: 22706312; PMCID: PMC3386377.
      Citations: 1808     Fields:    Translation:Humans
    92. Fu AQ, Genereux DP, Burden AF, Laird CD, Stephens M, Stöger R. Statistical inference of in vivo properties of human DNA methyltransferases from double-stranded methylation patterns. PLoS One. 2012; 7(3):e32225. PMID: 22442664; PMCID: PMC3307717.
      Citations: 10     Fields:    Translation:HumansAnimalsCells
    93. 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.
      Citations: 7     Fields:    Translation:HumansAnimals
    94. 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; PMCID: PMC3281037.
      Citations: 16     Fields:    Translation:HumansCells
    95. 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; PMCID: PMC3501342.
      Citations: 412     Fields:    Translation:HumansCells
    96. 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; PMCID: PMC3334587.
      Citations: 132     Fields:    Translation:HumansCells
    97. Perry GH, Marioni JC, Wang Y, Bainer R, Pickrell JK, Michelini K, Zehr S, Yoder AD, Stephens M, Pritchard JK, Gilad Y, Melsted P. Comparative RNA sequencing reveals substantial genetic variation in endangered primates. Genome Res. 2012 Apr; 22(4):602-10. PMID: 22207615; PMCID: PMC3317143.
      Citations: 83     Fields:    Translation:HumansAnimalsCells
    98. 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, Feuer EJ, Gillanders EM, Zöllner S. Next generation analytic tools for large scale genetic epidemiology studies of complex diseases. Genet Epidemiol. 2012 Jan; 36(1):22-35. PMID: 22147673; PMCID: PMC3368075.
      Citations: 42     Fields:    Translation:Humans
    99. Howie B, Marchini J, Stephens M. Genotype imputation with thousands of genomes. G3 (Bethesda). 2011 Nov; 1(6):457-70. PMID: 22384356; PMCID: PMC3276165.
      Citations: 619     Fields:    
    100. 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; PMCID: PMC3131293.
      Citations: 72     Fields:    Translation:HumansCells
    101. 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; PMCID: PMC3117798.
      Citations: 74     Fields:    Translation:Humans
    102. 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; PMCID: PMC3002988.
      Citations: 62     Fields:    Translation:HumansAnimalsCells
    103. 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; PMCID: PMC2940725.
      Citations: 73     Fields:    Translation:Humans
    104. 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; PMCID: PMC3072818.
      Citations: 41     
    105. 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.
      Citations: 4     Fields:    Translation:Humans
    106. 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; PMCID: PMC2842298.
      Citations: 125     Fields:    Translation:HumansCTClinical Trials
    107. 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; PMCID: PMC3089435.
      Citations: 803     Fields:    Translation:HumansCells
    108. Fu AQ, Genereux DP, Laird CD, Stephens M, Stöger R. 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; PMCID: PMC3103139.
      Citations: 13     
    109. 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; PMCID: PMC2813474.
      Citations: 170     Fields:    Translation:HumansAnimalsCells
    110. Stephens M, Balding DJ. Bayesian statistical methods for genetic association studies. Nat Rev Genet. 2009 Oct; 10(10):681-90. PMID: 19763151.
      Citations: 221     Fields:    Translation:Humans
    111. 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; PMCID: PMC3518025.
      Citations: 1089     Fields:    
    112. Guan Y, Stephens M. Practical issues in imputation-based association mapping. PLoS Genet. 2008 Dec; 4(12):e1000279. PMID: 19057666; PMCID: PMC2585794.
      Citations: 116     Fields:    Translation:Humans
    113. 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; PMCID: PMC2556086.
      Citations: 364     Fields:    Translation:HumansCells
    114. 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; PMCID: PMC2682747.
      Citations: 3     
    115. Novembre J, Johnson T, Bryc K, Boyko AR, Auton A, Indap A, King KS, Bergmann S, Nelson MR, Stephens M, Bustamante CD, Kutalik Z. Genes mirror geography within Europe. Nature. 2008 Nov 06; 456(7218):98-101. PMID: 18758442; PMCID: PMC2735096.
      Citations: 674     Fields:    Translation:Humans
    116. Scheet P, Stephens M. Linkage disequilibrium-based quality control for large-scale genetic studies. PLoS Genet. 2008 Aug 01; 4(8):e1000147. PMID: 18670630; PMCID: PMC2475504.
      Citations: 8     Fields:    Translation:HumansCells
    117. 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; PMCID: PMC2527709.
      Citations: 1471     Fields:    Translation:Humans
    118. 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; PMCID: PMC2427318.
      Citations: 100     Fields:    Translation:Humans
    119. Novembre J, Stephens M. Interpreting principal component analyses of spatial population genetic variation. Nat Genet. 2008 May; 40(5):646-9. PMID: 18425127; PMCID: PMC3989108.
      Citations: 263     Fields:    Translation:Humans
    120. International HapMap Consortium, Frazer KA, Ballinger DG, Cox DR, Hinds DA, Stuve LL, Gibbs RA, Belmont JW, Boudreau A, Hardenbol P, Leal SM, Pasternak S, Wheeler DA, Willis TD, Yu F, Yang H, Zeng C, Gao Y, Hu H, Hu W, Li C, Lin W, Liu S, Pan H, Tang X, Wang J, Wang W, Yu J, Zhang B, Zhang Q, Zhao H, Zhao H, Zhou J, Gabriel SB, Barry R, Blumenstiel B, Camargo A, Defelice M, Faggart M, Goyette M, Gupta S, Moore J, Nguyen H, Onofrio RC, Parkin M, Roy J, Stahl E, Winchester E, Ziaugra L, Altshuler D, Shen Y, Yao Z, Huang W, Chu X, He Y, Jin L, Liu Y, Shen Y, Sun W, Wang H, Wang Y, Wang Y, Xiong X, Xu L, Waye MM, Tsui SK, Xue H, Wong JT, Galver LM, Fan JB, Gunderson K, Murray SS, Oliphant AR, Chee MS, Montpetit A, Chagnon F, Ferretti V, Leboeuf M, Phillips MS, Verner A, Hudson TJ, Kwok PY, Cai D, Koboldt DC, Miller RD, Pawlikowska L, Taillon-Miller P, Xiao M, Tsui LC, Mak W, Song YQ, Tam PK, Nakamura Y, Kawaguchi T, Kitamoto T, Morizono T, Nagashima A, Ohnishi Y, Sekine A, Tanaka T, Tsunoda T, Deloukas P, Bird CP, Delgado M, Dermitzakis ET, Gwilliam R, Hunt S, Morrison J, Powell D, Stranger BE, Whittaker P, Bentley DR, Daly MJ, de Bakker PI, Barrett J, Chretien YR, Maller J, McCarroll S, Patterson N, Pe'er I, Price A, Purcell S, Richter DJ, Sabeti P, Saxena R, Schaffner SF, Sham PC, Varilly P, Stein LD, Krishnan L, Smith AV, Tello-Ruiz MK, Thorisson GA, Chakravarti A, Chen PE, Cutler DJ, Kashuk CS, Lin S, Guan W, Li Y, Munro HM, Qin ZS, Thomas DJ, McVean G, Auton A, Bottolo L, Cardin N, Eyheramendy S, Freeman C, Marchini J, Myers S, Spencer C, Stephens M, Donnelly P, Cardon LR, Clarke G, Evans DM, Morris AP, Weir BS, Mullikin JC, Sherry ST, Feolo M, Skol A, Zhang H, Matsuda I, Fukushima Y, Macer DR, Suda E, Rotimi CN, Adebamowo CA, Ajayi I, Aniagwu T, Marshall PA, Nkwodimmah C, Royal CD, Leppert MF, Dixon M, Peiffer A, Qiu R, Kent A, Kato K, Niikawa N, Adewole IF, Knoppers BM, Foster MW, Clayton EW, Watkin J, Muzny D, Nazareth L, Sodergren E, Weinstock GM, Yakub I, Birren BW, Wilson RK, Fulton LL, Rogers J, Burton J, Carter NP, Clee CM, Griffiths M, Jones MC, McLay K, Plumb RW, Ross MT, Sims SK, Willey DL, Chen Z, Han H, Kang L, Godbout M, Wallenburg JC, Bellemare G, Saeki K, Wang H, An D, Fu H, Li Q, Wang Z, Wang R, Holden AL, Brooks LD, McEwen JE, Guyer MS, Wang VO, Peterson JL, Shi M, Spiegel J, Sung LM, Zacharia LF, Collins FS, Kennedy K, Jamieson R, Stewart J, Olivier JF, Roumy S, Sallée C, Abecasis GR, L'Archevêque P. A second generation human haplotype map of over 3.1 million SNPs. Nature. 2007 Oct 18; 449(7164):851-61. PMID: 17943122; PMCID: PMC2689609.
      Citations: 2381     Fields:    Translation:Humans
    121. Sabeti PC, Varilly P, Fry B, Lohmueller J, Hostetter E, Cotsapas C, Xie X, Byrne EH, McCarroll SA, Gaudet R, Schaffner SF, Lander ES, International HapMap Consortium, Frazer KA, Ballinger DG, Cox DR, Hinds DA, Stuve LL, Gibbs RA, Belmont JW, Boudreau A, Hardenbol P, Leal SM, Pasternak S, Wheeler DA, Willis TD, Yu F, Yang H, Zeng C, Gao Y, Hu H, Hu W, Li C, Lin W, Liu S, Pan H, Tang X, Wang J, Wang W, Yu J, Zhang B, Zhang Q, Zhao H, Zhao H, Zhou J, Gabriel SB, Barry R, Blumenstiel B, Camargo A, Defelice M, Faggart M, Goyette M, Gupta S, Moore J, Nguyen H, Onofrio RC, Parkin M, Roy J, Stahl E, Winchester E, Ziaugra L, Altshuler D, Shen Y, Yao Z, Huang W, Chu X, He Y, Jin L, Liu Y, Shen Y, Sun W, Wang H, Wang Y, Wang Y, Xiong X, Xu L, Waye MM, Tsui SK, Xue H, Wong JT, Galver LM, Fan JB, Gunderson K, Murray SS, Oliphant AR, Chee MS, Montpetit A, Chagnon F, Ferretti V, Leboeuf M, Phillips MS, Verner A, Hudson TJ, Kwok PY, Cai D, Koboldt DC, Miller RD, Pawlikowska L, Taillon-Miller P, Xiao M, Tsui LC, Mak W, Song YQ, Tam PK, Nakamura Y, Kawaguchi T, Kitamoto T, Morizono T, Nagashima A, Ohnishi Y, Sekine A, Tanaka T, Tsunoda T, Deloukas P, Bird CP, Delgado M, Dermitzakis ET, Gwilliam R, Hunt S, Morrison J, Powell D, Stranger BE, Whittaker P, Bentley DR, Daly MJ, de Bakker PI, Barrett J, Chretien YR, Maller J, McCarroll S, Patterson N, Pe'er I, Price A, Purcell S, Richter DJ, Sabeti P, Saxena R, Sham PC, Stein LD, Krishnan L, Smith AV, Tello-Ruiz MK, Thorisson GA, Chakravarti A, Chen PE, Cutler DJ, Kashuk CS, Lin S, Guan W, Li Y, Munro HM, Qin ZS, Thomas DJ, McVean G, Auton A, Bottolo L, Cardin N, Eyheramendy S, Freeman C, Marchini J, Myers S, Spencer C, Stephens M, Donnelly P, Cardon LR, Clarke G, Evans DM, Morris AP, Weir BS, Johnson TA, Mullikin JC, Sherry ST, Feolo M, Skol A, Zhang H, Matsuda I, Fukushima Y, Macer DR, Suda E, Rotimi CN, Adebamowo CA, Ajayi I, Aniagwu T, Marshall PA, Nkwodimmah C, Royal CD, Leppert MF, Dixon M, Peiffer A, Qiu R, Kent A, Kato K, Niikawa N, Adewole IF, Knoppers BM, Foster MW, Clayton EW, Watkin J, Muzny D, Nazareth L, Sodergren E, Weinstock GM, Yakub I, Birren BW, Wilson RK, Fulton LL, Rogers J, Burton J, Carter NP, Clee CM, Griffiths M, Jones MC, McLay K, Plumb RW, Ross MT, Sims SK, Willey DL, Chen Z, Han H, Kang L, Godbout M, Wallenburg JC, Bellemare G, Saeki K, Wang H, An D, Fu H, Li Q, Wang Z, Wang R, Holden AL, Brooks LD, McEwen JE, Guyer MS, Wang VO, Peterson JL, Shi M, Spiegel J, Sung LM, Zacharia LF, Collins FS, Kennedy K, Jamieson R, Stewart J, Olivier JF, Roumy S, Sallée C, Abecasis GR, L'Archevêque P. Genome-wide detection and characterization of positive selection in human populations. Nature. 2007 Oct 18; 449(7164):913-8. PMID: 17943131; PMCID: PMC2687721.
      Citations: 1147     Fields:    Translation:HumansCells
    122. 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; PMCID: PMC1974779.
      Citations: 851     
    123. 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; PMCID: PMC1894599.
      Citations: 12     Fields:    Translation:Cells
    124. Servin B, Stephens M. Imputation-based analysis of association studies: candidate regions and quantitative traits. PLoS Genet. 2007 Jul; 3(7):e114. PMID: 17676998; PMCID: PMC1934390.
      Citations: 310     Fields:    Translation:Humans
    125. 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; PMCID: PMC1805457.
      Citations: 31     Fields:    Translation:Animals
    126. 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.
      Citations: 66     Fields:    
    127. Bhangale TR, Stephens M, Nickerson DA. Automating resequencing-based detection of insertion-deletion polymorphisms. Nat Genet. 2006 Dec; 38(12):1457-62. PMID: 17115056.
      Citations: 41     Fields:    Translation:HumansCells
    128. 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.
      Citations: 35     Fields:    Translation:HumansAnimalsCells
    129. Hellenthal G, Stephens M. Insights into recombination from population genetic variation. Curr Opin Genet Dev. 2006 Dec; 16(6):565-72. PMID: 17049225.
      Citations: 22     Fields:    Translation:HumansAnimals
    130. 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.
      Citations: 67     Fields:    Translation:HumansCells
    131. 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.
      Citations: 75     Fields:    
    132. 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; PMCID: PMC1424677.
      Citations: 974     Fields:    Translation:Humans
    133. Marchini J, Cutler D, Patterson N, Stephens M, Eskin E, Halperin E, Lin S, Qin ZS, Munro HM, Abecasis GR, Donnelly P, International HapMap Consortium. A comparison of phasing algorithms for trios and unrelated individuals. Am J Hum Genet. 2006 Mar; 78(3):437-50. PMID: 16465620; PMCID: PMC1380287.
      Citations: 136     Fields:    Translation:Humans
    134. 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; PMCID: PMC1456301.
      Citations: 7     Fields:    Translation:Humans
    135. 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.
      Citations: 4     Fields:    
    136. 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; PMCID: PMC1196397.
      Citations: 570     Fields:    Translation:HumansCells
    137. 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; PMCID: PMC522003.
      Citations: 74     Fields:    Translation:AnimalsCells
    138. Ptak SE, Roeder AD, Stephens M, Gilad Y, Przeworski M, Pääbo S. Absence of the TAP2 human recombination hotspot in chimpanzees. PLoS Biol. 2004 Jun; 2(6):e155. PMID: 15208713; PMCID: PMC423135.
      Citations: 59     Fields:    Translation:HumansAnimalsCells
    139. 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.
      Citations: 146     Fields:    Translation:Humans
    140. 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; PMCID: PMC1462870.
      Citations: 518     Fields:    Translation:Humans
    141. 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; PMCID: PMC1180495.
      Citations: 1210     Fields:    Translation:Humans
    142. Stephens M, Pritchard JK, Falush D. Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics. 2003 Aug; 164(4):1567-87. PMID: 12930761; PMCID: PMC1462648.
      Citations: 2787     Fields:    Translation:HumansAnimalsCells
    143. Wirth T, Linz B, Pritchard JK, Stephens M, Kidd M, Blaser MJ, Graham DY, Vacher S, Perez-Perez GI, Yamaoka Y, Otto K, Reichard U, Katzowitsch E, Wang X, Achtman M, Suerbaum S, Falush D, Mégraud F. Traces of human migrations in Helicobacter pylori populations. Science. 2003 Mar 07; 299(5612):1582-5. PMID: 12624269.
      Citations: 456     Fields:    Translation:HumansCells
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