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Matthew Stephens - Publications

Affiliations: 
Human Genetics University of Chicago, Chicago, IL 
 University of Washington, Seattle, Seattle, WA 
Area:
genetics, statistics
Website:
http://stephenslab.uchicago.edu/index.html

116 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2021 Sarkar A, Stephens M. Separating measurement and expression models clarifies confusion in single-cell RNA sequencing analysis. Nature Genetics. PMID 34031584 DOI: 10.1038/s41588-021-00873-4  0.44
2021 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. 10. PMID 33554857 DOI: 10.7554/eLife.57345  0.44
2021 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, ... ... Stephens M, et al. Exploiting the GTEx resources to decipher the mechanisms at GWAS loci. Genome Biology. 22: 49. PMID 33499903 DOI: 10.1186/s13059-020-02252-4  1
2020 Kim Y, Carbonetto P, Stephens M, Anitescu M. A Fast Algorithm for Maximum Likelihood Estimation of Mixture Proportions Using Sequential Quadratic Programming. Journal of Computational and Graphical Statistics : a Joint Publication of American Statistical Association, Institute of Mathematical Statistics, Interface Foundation of North America. 29: 261-273. PMID 33762803 DOI: 10.1080/10618600.2019.1689985  0.52
2020 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, ... ... Stephens M, et al. Cell type-specific genetic regulation of gene expression across human tissues. Science (New York, N.Y.). 369. PMID 32913075 DOI: 10.1126/Science.Aaz8528  1
2020 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, ... ... Stephens M, et al. The impact of sex on gene expression across human tissues. Science (New York, N.Y.). 369. PMID 32913072 DOI: 10.1126/Science.Aba3066  0.8
2020 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, et al. Genetic analyses support the contribution of mRNA N-methyladenosine (mA) modification to human disease heritability. Nature Genetics. PMID 32601472 DOI: 10.1038/S41588-020-0644-Z  0.52
2020 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. Nature Genetics. PMID 32472065 DOI: 10.1038/S41588-020-0655-9  0.32
2020 Morrison J, Knoblauch N, Marcus JH, Stephens M, He X. Mendelian randomization accounting for correlated and uncorrelated pleiotropic effects using genome-wide summary statistics. Nature Genetics. PMID 32451458 DOI: 10.1038/S41588-020-0631-4  0.32
2020 Wang G, Sarkar A, Carbonetto P, Stephens M. A simple new approach to variable selection in regression, with application to genetic fine mapping Journal of the Royal Statistical Society Series B-Statistical Methodology. DOI: 10.1111/Rssb.12388  0.52
2019 Blischak JD, Carbonetto P, Stephens M. Creating and sharing reproducible research code the workflowr way. F1000research. 8: 1749. PMID 31723427 DOI: 10.12688/F1000Research.20843.1  0.52
2019 Turchin MC, Stephens M. Bayesian multivariate reanalysis of large genetic studies identifies many new associations. Plos Genetics. 15: e1008431. PMID 31596850 DOI: 10.1371/Journal.Pgen.1008431  0.76
2019 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. Nature Communications. 10: 3399. PMID 31363082 DOI: 10.1038/S41467-019-11284-9  0.32
2019 Urbut SM, Wang G, Carbonetto P, Stephens M. Flexible statistical methods for estimating and testing effects in genomic studies with multiple conditions. Nature Genetics. 51: 187-195. PMID 30478440 DOI: 10.1038/S41588-018-0268-8  0.52
2018 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. PMID 29941997 DOI: 10.1038/S41437-018-0105-Y  0.52
2016 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. 5. PMID 27232982 DOI: 10.7554/Elife.13328  0.36
2016 Raj A, Wang SH, Shim H, Harpak A, Li YI, Engelmann B, Stephens M, Gilad Y, Pritchard JK. Author response: Thousands of novel translated open reading frames in humans inferred by ribosome footprint profiling Elife. DOI: 10.7554/Elife.13328.037  0.36
2015 Petkova D, Novembre J, Stephens M. Visualizing spatial population structure with estimated effective migration surfaces. Nature Genetics. PMID 26642242 DOI: 10.1038/Ng.3464  1
2015 Shiraishi Y, Tremmel G, Miyano S, Stephens M. A Simple Model-Based Approach to Inferring and Visualizing Cancer Mutation Signatures. Plos Genetics. 11: e1005657. PMID 26630308 DOI: 10.1371/Journal.Pgen.1005657  1
2015 Carithers LJ, Ardlie K, Barcus M, Branton PA, Britton A, Buia SA, Compton CC, DeLuca DS, Peter-Demchok J, Gelfand ET, Guan P, Korzeniewski GE, Lockhart NC, Rabiner CA, Rao AK, et al. A Novel Approach to High-Quality Postmortem Tissue Procurement: The GTEx Project. Biopreservation and Biobanking. 13: 311-9. PMID 26484571 DOI: 10.1089/bio.2015.0032  0.44
2015 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. 10: e0138030. PMID 26406244 DOI: 10.1371/Journal.Pone.0138030  1
2015 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. 10: e0120758. PMID 25898129 DOI: 10.1371/Journal.Pone.0120758  1
2015 Tung J, Zhou X, Alberts SC, Stephens M, Gilad Y. The genetic architecture of gene expression levels in wild baboons. Elife. 4. PMID 25714927 DOI: 10.7554/Elife.04729  1
2015 Gao Z, Waggoner D, Stephens M, Ober C, Przeworski M. An estimate of the average number of recessive lethal mutations carried by humans. Genetics. 199: 1243-54. PMID 25697177 DOI: 10.1534/Genetics.114.173351  1
2015 Shim H, Stephens M. Wavelet-based genetic association analysis of functional phenotypes arising from high-throughput sequencing assays Annals of Applied Statistics. 9: 665-686. DOI: 10.1214/14-AOAS776  1
2015 Ardlie KG, DeLuca DS, Segrè AV, Sullivan TJ, Young TR, Gelfand ET, Trowbridge CA, Maller JB, Tukiainen T, Lek M, Ward LD, Kheradpour P, Iriarte B, Meng Y, Palmer CD, ... ... Stephens M, et al. The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans Science. 348: 648-660. DOI: 10.1126/science.1262110  1
2014 Wen X, Stephens M. BAYESIAN METHODS FOR GENETIC ASSOCIATION ANALYSIS WITH HETEROGENEOUS SUBGROUPS: FROM META-ANALYSES TO GENE-ENVIRONMENT INTERACTIONS. The Annals of Applied Statistics. 8: 176-203. PMID 26413181 DOI: 10.1214/13-Aoas695  1
2014 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 Biology. 15: 547. PMID 25468404 DOI: 10.1186/S13059-014-0547-3  1
2014 Mangravite LM, Engelhardt BE, Stephens M, Krauss RM. Mangravite et al. reply. Nature. 513: E3. PMID 25230670 DOI: 10.1038/Nature13630  1
2014 Raj A, Stephens M, Pritchard JK. fastSTRUCTURE: variational inference of population structure in large SNP data sets. Genetics. 197: 573-89. PMID 24700103 DOI: 10.1534/Genetics.114.164350  1
2014 Zhou X, Stephens M. Efficient multivariate linear mixed model algorithms for genome-wide association studies. Nature Methods. 11: 407-9. PMID 24531419 DOI: 10.1038/Nmeth.2848  1
2013 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 Genetics. 9: e1003770. PMID 24098138 DOI: 10.1371/Journal.Pgen.1003770  1
2013 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, ... ... Stephens M, et al. A statin-dependent QTL for GATM expression is associated with statin-induced myopathy. Nature. 502: 377-80. PMID 23995691 DOI: 10.1038/Nature12508  1
2013 Stephens M. A unified framework for association analysis with multiple related phenotypes. Plos One. 8: e65245. PMID 23861737 DOI: 10.1371/Journal.Pone.0065245  1
2013 Flutre T, Wen X, Pritchard J, Stephens M. A statistical framework for joint eQTL analysis in multiple tissues. Plos Genetics. 9: e1003486. PMID 23671422 DOI: 10.1371/Journal.Pgen.1003486  1
2013 Luca F, Maranville JC, Richards AL, Witonsky DB, Stephens M, Di Rienzo A. Genetic, functional and molecular features of glucocorticoid receptor binding. Plos One. 8: e61654. PMID 23637875 DOI: 10.1371/Journal.Pone.0061654  1
2013 Zhou X, Carbonetto P, Stephens M. Polygenic modeling with bayesian sparse linear mixed models. Plos Genetics. 9: e1003264. PMID 23408905 DOI: 10.1371/Journal.Pgen.1003264  1
2012 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 Genetics. 8: e1003000. PMID 23071454 DOI: 10.1371/Journal.Pgen.1003000  1
2012 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. 7: e42646. PMID 22952603 DOI: 10.1371/Journal.Pone.0042646  1
2012 Howie B, Fuchsberger C, Stephens M, Marchini J, Abecasis GR. Fast and accurate genotype imputation in genome-wide association studies through pre-phasing. Nature Genetics. 44: 955-9. PMID 22820512 DOI: 10.1038/Ng.2354  1
2012 Zhou X, Stephens M. Genome-wide efficient mixed-model analysis for association studies. Nature Genetics. 44: 821-4. PMID 22706312 DOI: 10.1038/Ng.2310  1
2012 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. 7: e32225. PMID 22442664 DOI: 10.1371/Journal.Pone.0032225  1
2012 Maranville JC, Luca F, Stephens M, Di Rienzo A. Mapping gene-environment interactions at regulatory polymorphisms: insights into mechanisms of phenotypic variation. Transcription. 3: 56-62. PMID 22414753 DOI: 10.4161/trns.19497  1
2012 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. 7: e30629. PMID 22359548 DOI: 10.1371/Journal.Pone.0030629  1
2012 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. 482: 390-4. PMID 22307276 DOI: 10.1038/Nature10808  1
2012 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 Biology. 13: R7. PMID 22293038 DOI: 10.1186/Gb-2012-13-1-R7  1
2012 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 Research. 22: 602-10. PMID 22207615 DOI: 10.1101/Gr.130468.111  1
2012 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, ... ... Stephens M, et al. Next generation analytic tools for large scale genetic epidemiology studies of complex diseases. Genetic Epidemiology. 36: 22-35. PMID 22147673 DOI: 10.1002/Gepi.20652  1
2012 Carbonetto P, Stephens M. Scalable variational inference for bayesian variable selection in regression, and its accuracy in genetic association studies Bayesian Analysis. 7: 73-108. DOI: 10.1214/12-Ba703  1
2012 Li Q, Eng JK, Stephens M. A likelihood-based scoring method for peptide identification using mass spectrometry Annals of Applied Statistics. 6: 1775-1794. DOI: 10.1214/12-Aoas568  1
2011 Howie B, Marchini J, Stephens M. Genotype imputation with thousands of genomes. G3 (Bethesda, Md.). 1: 457-70. PMID 22384356 DOI: 10.1534/G3.111.001198  1
2011 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 Genetics. 7: e1002162. PMID 21750684 DOI: 10.1371/Journal.Pgen.1002162  1
2011 Fledel-Alon A, Leffler EM, Guan Y, Stephens M, Coop G, Przeworski M. Variation in human recombination rates and its genetic determinants. Plos One. 6: e20321. PMID 21698098 DOI: 10.1371/Journal.Pone.0020321  1
2011 Guan Y, Stephens M. Bayesian variable selection regression for genome-wide association studies and other large-scale problems Annals of Applied Statistics. 5: 1780-1815. DOI: 10.1214/11-Aoas455  1
2010 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. The Annals of Applied Statistics. 4: 871-892. PMID 21625348 DOI: 10.1214/09-Aoas297Suppa  1
2010 Wen X, Stephens M. USING LINEAR PREDICTORS TO IMPUTE ALLELE FREQUENCIES FROM SUMMARY OR POOLED GENOTYPE DATA. The Annals of Applied Statistics. 4: 1158-1182. PMID 21479081 DOI: 10.1214/10-Aoas338  1
2010 Barreiro LB, Marioni JC, Blekhman R, Stephens M, Gilad Y. Functional comparison of innate immune signaling pathways in primates. Plos Genetics. 6: e1001249. PMID 21187902 DOI: 10.1371/Journal.Pgen.1001249  1
2010 Novembre J, Stephens M. Response to Cavalli-Sforza interview [Human Biology 82(3):245-266 (June 2010)] Human Biology. 82: 469-470. PMID 21082913 DOI: 10.3378/027.082.0408  1
2010 Engelhardt BE, Stephens M. Analysis of population structure: a unifying framework and novel methods based on sparse factor analysis. Plos Genetics. 6: e1001117. PMID 20862358 DOI: 10.1371/Journal.Pgen.1001117  1
2010 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, et al. Genome-wide association of lipid-lowering response to statins in combined study populations. Plos One. 5: e9763. PMID 20339536 DOI: 10.1371/Journal.Pone.0009763  1
2010 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. 464: 768-72. PMID 20220758 DOI: 10.1038/Nature08872  1
2010 Blekhman R, Marioni JC, Zumbo P, Stephens M, Gilad Y. Sex-specific and lineage-specific alternative splicing in primates. Genome Research. 20: 180-9. PMID 20009012 DOI: 10.1101/Gr.099226.109  1
2010 Basu S, Stephens M, Pankow JS, Thompson EA. A likelihood-based trait-model-free approach for linkage detection of binary trait Biometrics. 66: 205-213. PMID 19459835 DOI: 10.1111/J.1541-0420.2009.01270.X  1
2010 Li Q, MacCoss MJ, Stephens M. A nested mixture model for protein identification using mass spectrometry Annals of Applied Statistics. 4: 962-987. DOI: 10.1214/09-Aoas316  1
2009 Hubisz MJ, Falush D, Stephens M, Pritchard JK. Inferring weak population structure with the assistance of sample group information. Molecular Ecology Resources. 9: 1322-32. PMID 21564903 DOI: 10.1111/J.1755-0998.2009.02591.X  1
2009 Stephens M, Balding DJ. Bayesian statistical methods for genetic association studies. Nature Reviews. Genetics. 10: 681-90. PMID 19763151 DOI: 10.1038/Nrg2615  1
2008 Guan Y, Stephens M. Practical issues in imputation-based association mapping. Plos Genetics. 4: e1000279. PMID 19057666 DOI: 10.1371/Journal.Pgen.1000279  1
2008 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 Genetics. 4: e1000214. PMID 18846210 DOI: 10.1371/Journal.Pgen.1000214  1
2008 Wasser SK, Joseph Clark W, Drori O, Stephen Kisamo E, Mailand C, Mutayoba B, Stephens M. Combating the illegal trade in African elephant ivory with DNA forensics. Conservation Biology : the Journal of the Society For Conservation Biology. 22: 1065-71. PMID 18786100 DOI: 10.1111/J.1523-1739.2008.01012.X  1
2008 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. 456: 98-101. PMID 18758442 DOI: 10.1038/Nature07331  1
2008 Scheet P, Stephens M. Linkage disequilibrium-based quality control for large-scale genetic studies. Plos Genetics. 4: e1000147. PMID 18670630 DOI: 10.1371/Journal.Pgen.1000147  1
2008 Marioni JC, Mason CE, Mane SM, Stephens M, Gilad Y. RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Research. 18: 1509-17. PMID 18550803 DOI: 10.1101/Gr.079558.108  1
2008 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, et al. Polymorphisms of the HNF1A gene encoding hepatocyte nuclear factor-1 alpha are associated with C-reactive protein. American Journal of Human Genetics. 82: 1193-201. PMID 18439552 DOI: 10.1016/J.Ajhg.2008.03.017  1
2008 Novembre J, Stephens M. Interpreting principal component analyses of spatial population genetic variation Nature Genetics. 40: 646-649. PMID 18425127 DOI: 10.1038/Ng.139  1
2008 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) 456, (98-101)) Nature. 456: 274. DOI: 10.1038/Nature07566  1
2008 Stephens M. Inference Under the Coalescent Handbook of Statistical Genetics: Third Edition. 2: 878-908. DOI: 10.1002/9780470061619.ch26  1
2007 Falush D, Stephens M, Pritchard JK. Inference of population structure using multilocus genotype data: dominant markers and null alleles. Molecular Ecology Notes. 7: 574-578. PMID 18784791 DOI: 10.1111/J.1471-8286.2007.01758.X  1
2007 Sabeti PC, Varilly P, Fry B, Lohmueller J, Hostetter E, Cotsapas C, Xie X, Byrne EH, McCarroll SA, Gaudet R, Schaffner SF, Lander ES, Frazer KA, Ballinger DG, ... ... Stephens M, et al. Genome-wide detection and characterization of positive selection in human populations. Nature. 449: 913-8. PMID 17943131 DOI: 10.1038/Nature06250  0.88
2007 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, ... ... Stephens M, et al. A second generation human haplotype map of over 3.1 million SNPs. Nature. 449: 851-61. PMID 17943122 DOI: 10.1038/Nature06258  0.88
2007 Servin B, Stephens M. Imputation-based analysis of association studies: candidate regions and quantitative traits. Plos Genetics. 3: e114. PMID 17676998 DOI: 10.1371/Journal.Pgen.0030114  1
2007 Roychoudhury A, Stephens M. Fast and accurate estimation of the population-scaled mutation rate, theta, from microsatellite genotype data. Genetics. 176: 1363-6. PMID 17579241 DOI: 10.1534/Genetics.105.049080  1
2007 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. Proceedings of the National Academy of Sciences of the United States of America. 104: 4228-33. PMID 17360505 DOI: 10.1073/Pnas.0609714104  1
2007 Hellenthal G, Stephens M. msHOT: modifying Hudson's ms simulator to incorporate crossover and gene conversion hotspots. Bioinformatics (Oxford, England). 23: 520-1. PMID 17150995 DOI: 10.1093/Bioinformatics/Btl622  1
2006 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. Nature Genetics. 38: 1419-23. PMID 17115058 DOI: 10.1038/Ng1920  1
2006 Bhangale TR, Stephens M, Nickerson DA. Automating resequencing-based detection of insertion-deletion polymorphisms. Nature Genetics. 38: 1457-62. PMID 17115056 DOI: 10.1038/Ng1925  1
2006 Hellenthal G, Stephens M. Insights into recombination from population genetic variation. Current Opinion in Genetics & Development. 16: 565-72. PMID 17049225 DOI: 10.1016/J.Gde.2006.10.001  1
2006 Scheet P, Stephens M. A fast and flexible statistical model for large-scale population genotype data: applications to inferring missing genotypes and haplotypic phase. American Journal of Human Genetics. 78: 629-44. PMID 16532393 DOI: 10.1086/502802  1
2006 Stephens M, Sloan JS, Robertson PD, Scheet P, Nickerson DA. Automating sequence-based detection and genotyping of SNPs from diploid samples. Nature Genetics. 38: 375-81. PMID 16493422 DOI: 10.1038/Ng1746  1
2006 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. American Journal of Human Genetics. 78: 437-50. PMID 16465620 DOI: 10.1086/500808  1
2006 Hellenthal G, Pritchard JK, Stephens M. The effects of genotype-dependent recombination, and transmission asymmetry, on linkage disequilibrium. Genetics. 172: 2001-5. PMID 16387890 DOI: 10.1534/Genetics.104.039271  1
2006 Gottardo R, Besag J, Stephens M, Murua A. Probabilistic segmentation and intensity estimation for microarray images. Biostatistics (Oxford, England). 7: 85-99. PMID 16049139 DOI: 10.1093/Biostatistics/Kxi042  1
2005 Stephens M, Scheet P. Accounting for decay of linkage disequilibrium in haplotype inference and missing-data imputation. American Journal of Human Genetics. 76: 449-62. PMID 15700229 DOI: 10.1086/428594  1
2004 Ptak SE, Roeder AD, Stephens M, Gilad Y, Pääbo S, Przeworski M. Absence of the TAP2 human recombination hotspot in chimpanzees. Plos Biology. 2: e155. PMID 15208713 DOI: 10.1371/Journal.Pbio.0020155  1
2004 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. Nature Genetics. 36: 700-6. PMID 15184900 DOI: 10.1038/Ng1376  1
2004 Williams NM, Preece A, Morris DW, Spurlock G, Bray NJ, Stephens M, Norton N, Williams H, Clement M, Dwyer S, Curran C, Wilkinson J, Moskvina V, Waddington JL, Gill M, et al. Identification in 2 independent samples of a novel schizophrenia risk haplotype of the dystrobrevin binding protein gene (DTNBP1). Archives of General Psychiatry. 61: 336-44. PMID 15066891 DOI: 10.1001/Archpsyc.61.4.336  1
2004 Plomin R, Turic DM, Hill L, Turic DE, Stephens M, Williams J, Owen MJ, O'Donovan MC. A functional polymorphism in the succinate-semialdehyde dehydrogenase (aldehyde dehydrogenase 5 family, member A1) gene is associated with cognitive ability. Molecular Psychiatry. 9: 582-6. PMID 14981524 DOI: 10.1038/Sj.Mp.4001441  1
2004 Turic D, Langley K, Mills S, Stephens M, Lawson D, Govan C, Williams N, Van Den Bree M, Craddock N, Kent L, Owen M, O'Donovan M, Thapar A. Follow-up of genetic linkage findings on chromosome 16p13: evidence of association of N-methyl-D aspartate glutamate receptor 2A gene polymorphism with ADHD. Molecular Psychiatry. 9: 169-73. PMID 14966475 DOI: 10.1038/Sj.Mp.4001387  1
2004 Stephens M. Haplotypes, hotspots, and a multilocus model for linkage disequilibrium Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 2983: 147.  1
2003 Li N, Stephens M. Modeling linkage disequilibrium and identifying recombination hotspots using single-nucleotide polymorphism data. Genetics. 165: 2213-33. PMID 14704198  1
2003 Stephens M, Donnelly P. A comparison of bayesian methods for haplotype reconstruction from population genotype data. American Journal of Human Genetics. 73: 1162-9. PMID 14574645 DOI: 10.1086/379378  1
2003 Falush D, Stephens M, Pritchard JK. Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics. 164: 1567-87. PMID 12930761  1
2003 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, et al. Traces of human migrations in Helicobacter pylori populations. Science (New York, N.Y.). 299: 1582-5. PMID 12624269 DOI: 10.1126/Science.1080857  1
2003 Stephens M, Donnelly P. Ancestral Inference in Population Genetics Models with Selection (with Discussion) Australian & New Zealand Journal of Statistics. 45: 395-430. DOI: 10.1111/1467-842X.00295  0.96
2003 Stephens M, Donnelly P. Ancestral inference in population genetics models with selection Australian and New Zealand Journal of Statistics. 45: 395-423.  1
2002 Balding DJ, Carothers AD, Marchini JL, Cardon LR, Vetta A, Griffiths B, Weir BS, Hill WG, Goldstein D, Strimmer K, Myers S, Beaumont MA, Glasbey CA, Mayer CD, Richardson S, ... ... Stephens M, et al. Discussion on the meeting on 'statistical modelling and analysis of genetic data' Journal of the Royal Statistical Society. Series B: Statistical Methodology. 64: 737-775. DOI: 10.1111/1467-9868.00359  1
2001 Kirov G, Lowry CA, Stephens M, Oldfield S, O'Donovan MC, Lightman SL, Owen MJ. Screening ABCG1, the human homologue of the Drosophila white gene, for polymorphisms and association with bipolar affective disorder. Molecular Psychiatry. 6: 671-7. PMID 11673795 DOI: 10.1038/Sj.Mp.4000899  1
2001 Zhang S, Pakstis AJ, Kidd KK, Zhao H. Comparisons of two methods for haplotype reconstruction and haplotype frequency estimation from population data. American Journal of Human Genetics. 69: 906-14. PMID 11536083 DOI: 10.1086/323622  1
2001 Stephens M, Smith NJ, Donnelly P. A new statistical method for haplotype reconstruction from population data. American Journal of Human Genetics. 68: 978-89. PMID 11254454 DOI: 10.1086/319501  1
2001 Stephens M, Smith NJ, Donnelly P. Reply to Zhang et al. American Journal of Human Genetics. 69: 912-914. DOI: 10.1086/323623  0.96
2001 Stephens M, Kirov G, Owen MJ. ADARB1, a brain specific member of the RNA-specific adenosine deaminase family and bipolar affective disorder American Journal of Medical Genetics - Neuropsychiatric Genetics. 105: 622.  1
2000 Hoogendoorn B, Norton N, Kirov G, Williams N, Hamshere ML, Spurlock G, Austin J, Stephens MK, Buckland PR, Owen MJ, O'Donovan MC. Cheap, accurate and rapid allele frequency estimation of single nucleotide polymorphisms by primer extension and DHPLC in DNA pools Human Genetics. 107: 488-493. PMID 11140947 DOI: 10.1007/S004390000397  1
2000 Pritchard JK, Stephens M, Rosenberg NA, Donnelly P. Association mapping in structured populations. American Journal of Human Genetics. 67: 170-81. PMID 10827107 DOI: 10.1086/302959  1
2000 Stephens M. Dealing with label switching in mixture models Journal of the Royal Statistical Society. Series B: Statistical Methodology. 62: 795-809. DOI: 10.1111/1467-9868.00265  1
2000 Stephens M, Donnelly P. Inference in molecular population genetics Journal of the Royal Statistical Society. Series B: Statistical Methodology. 62: 605-655. DOI: 10.1111/1467-9868.00254  1
2000 Kirov G, Stephens M, Williams N, O'Donovan M, Owen M. Automated genotyping of single-nucleotide polymorphisms by extension of fluorescently labelled primers: Analysis of individual and pooled DNA samples Balkan Journal of Medical Genetics. 3: 23-28.  1
2000 Kirov G, Stephens M, Owen MJ. Examining the 4p16 region for association with bipolar disorder using DNA pooling American Journal of Medical Genetics - Neuropsychiatric Genetics. 96: 548.  1
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