Publications

[google] [pubmed]

* – denotes equal contribution. Names of Pickrell lab members are bolded.

2017

Mostafavi H, Berisa T, Przeworksi M*, Pickrell JK*. Identifying genetic variants that affect viability in large cohorts. Submitted. [preprint]

Liu JZ, Erlich Y, Pickrell JK. Case-control association mapping by proxy using family history of disease. Nature Genetics. 2017 Jan 16. [preprint] [pubmed]

2016

Pickrell JK, Berisa T, Liu JZ, Segurel L, Tung JY, Hinds D. Detection and interpretation of shared genetic influences on 42 human traits. Nature Genetics. 2016 May 16. [preprint] [pubmed]
Coverage:
[Washington Post]
[The Scientist]

Social Science Genetic Association Consortium. Genome-wide association study identifies 74 loci associated with educational attainment. Nature. 2016 May 11;533(7604):539-42. [pubmed]

Okbay A, Baselmans BM, De Neve JE, Turley P, Nivard MG, Fontana MA, Meddens SF, Linnér RK, Rietveld CA, Derringer J, Gratten J, Lee JJ, Liu JZ, de Vlaming R, Ahluwalia TS, Buchwald J, Cavadino A, Frazier-Wood AC, Furlotte NA, Garfield V, Geisel MH, Gonzalez JR, Haitjema S, Karlsson R, van der Laan SW, Ladwig KH, Lahti J, van der Lee SJ, Lind PA, Liu T, Matteson L, Mihailov E, Miller MB, Minica CC, Nolte IM, Mook-Kanamori D, van der Most PJ, Oldmeadow C, Qian Y, Raitakari O, Rawal R, Realo A, Rueedi R, Schmidt B, Smith AV, Stergiakouli E, Tanaka T, Taylor K, Wedenoja J, Wellmann J, Westra HJ, Willems SM, Zhao W; LifeLines Cohort Study, Amin N, Bakshi A, Boyle PA, Cherney S, Cox SR, Davies G, Davis OS, Ding J, Direk N, Eibich P, Emeny RT, Fatemifar G, Faul JD, Ferrucci L, Forstner A, Gieger C, Gupta R, Harris TB, Harris JM, Holliday EG, Hottenga JJ, De Jager PL, Kaakinen MA, Kajantie E, Karhunen V, Kolcic I, Kumari M, Launer LJ, Franke L, Li-Gao R, Koini M, Loukola A, Marques-Vidal P, Montgomery GW, Mosing MA, Paternoster L, Pattie A, Petrovic KE, Pulkki-Råback L, Quaye L, Räikkönen K, Rudan I, Scott RJ, Smith JA, Sutin AR, Trzaskowski M, Vinkhuyzen AE, Yu L, Zabaneh D, Attia JR, Bennett DA, Berger K, Bertram L, Boomsma DI, Snieder H, Chang SC, Cucca F, Deary IJ, van Duijn CM, Eriksson JG, Bültmann U, de Geus EJ, Groenen PJ, Gudnason V, Hansen T, Hartman CA, Haworth CM, Hayward C, Heath AC, Hinds DA, Hyppönen E, Iacono WG, Järvelin MR, Jöckel KH, Kaprio J, Kardia SL, Keltikangas-Järvinen L, Kraft P, Kubzansky LD, Lehtimäki T, Magnusson PK, Martin NG, McGue M, Metspalu A, Mills M, de Mutsert R, Oldehinkel AJ, Pasterkamp G, Pedersen NL, Plomin R, Polasek O, Power C, Rich SS, Rosendaal FR, den Ruijter HM, Schlessinger D, Schmidt H, Svento R, Schmidt R, Alizadeh BZ, Sørensen TI, Spector TD, Steptoe A, Terracciano A, Thurik AR, Timpson NJ, Tiemeier H, Uitterlinden AG, Vollenweider P, Wagner GG, Weir DR, Yang J, Conley DC, Smith GD, Hofman A, Johannesson M, Laibson DI, Medland SE, Meyer MN, Pickrell JK, Esko T, Krueger RF, Beauchamp JP, Koellinger PD, Benjamin DJ, Bartels M, Cesarini D. Genetic variants associated with subjective well-being, depressive symptoms and neuroticism identified through genome-wide analyses. Nature Genetics. 2016 Apr 18. [preprint] [pubmed]

2015

Mathieson I, Lazaridis I, Rohland N, Mallick S, Patterson N, Roodenberg SA, Harney E, Stewardson K, Fernandes D, Novak M, Sirak K, Gamba C, Jones ER, Llamas B, Dryomov S, Pickrell J, Arsuaga JL, de Castro JM, Carbonell E, Gerritsen F, Khokhlov A, Kuznetsov P, Lozano M, Meller H, Mochalov O, Moiseyev V, Guerra MA, Roodenberg J, Vergès JM, Krause J, Cooper A, Alt KW, Brown D, Anthony D, Lalueza-Fox C, Haak W, Pinhasi R, Reich D. Genome-wide patterns of selection in 230 ancient Eurasians. Nature. 2015 Nov 23. [preprint] [pubmed]

Berisa T, Pickrell JK. Approximately independent linkage disequilibrium blocks in human populations. Bioinformatics. 2015 Sep 22. [preprint] [pubmed] [data]

Pickrell JK. Fulfilling the promise of Mendelian randomization. submitted. [preprint]

2014

Pickrell JK, Reich D. Toward a new history and geography of human genes informed by ancient DNA. Trends in Genetics. 2014 Sep;30(9):377-89. [pubmed] [preprint]
Coverage:
[Pacific Standard]
[Razib Khan]
[Wall Street Journal]

Hodgson JA, Pickrell JK, Pearson LN, Quillen EE, Prista A, Rocha J, Soodyall H, Shriver MD, Perry GH. Natural selection for the Duffy-null allele in the recently admixed people of Madagascar. Proceedings of the Royal Society B: Biological Sciences. 2014 Aug 22;281(1789). [pubmed]

Pasaniuc B, Zaitlen N, Shi H, Bhatia G, Gusev A, Pickrell J, Hirschhorn J, Strachan DP, Patterson N, Price AL. Fast and accurate imputation of summary statistics enhances evidence of functional enrichment. Bioinformatics. 2014. [pubmed] [preprint]

Pickrell JK. Joint analysis of functional genomic data and genome-wide association studies of 18 human traits. The American Journal of Human Genetics. 2014 Apr 3;94(4):559-73. [pubmed] [preprint] [blog post] [data]

Pickrell JK, Patterson N, Loh PR, Lipson M, Berger B, Stoneking M, Pakendorf B, Reich D. Ancient west Eurasian ancestry in southern and eastern Africa. PNAS. 2014 Feb 18;111(7):2632-7. [pubmed] [preprint]
Coverage:
[New Scientist]
[Nature]
[GenomeWeb]
[Razib Khan]
[John Hawks]

Prüfer K, Racimo F, Patterson N, Jay F, Sankararaman S, Sawyer S, Heinze A, Renaud G, Sudmant PH, de Filippo C, Li H, Mallick S, Dannemann M, Fu Q, Kircher M, Kuhlwilm M, Lachmann M, Meyer M, Ongyerth M, Siebauer M, Theunert C, Tandon A, Moorjani P, Pickrell J, Mullikin JC, Vohr SH, Green RE, Hellmann I, Johnson PL, Blanche H, Cann H, Kitzman JO, Shendure J, Eichler EE, Lein ES, Bakken TE, Golovanova LV, Doronichev VB, Shunkov MV, Derevianko AP, Viola B, Slatkin M, Reich D, Kelso J, Pääbo S. The complete genome sequence of a Neanderthal from the Altai Mountains. Nature. 2014 Jan 2;505(7481):43-9. [pubmed]

2013

Brandt G, Haak W, Adler CJ, Roth C, Szécsényi-Nagy A, Karimnia S, Möller-Rieker S, Meller H, Ganslmeier R, Friederich S, Dresely V, Nicklisch N, Pickrell JK, Sirocko F, Reich D, Cooper A, Alt KW; Genographic Consortium. Ancient DNA reveals key stages in the formation of central European mitochondrial genetic diversity. Science. 2013 Oct 11;342(6155):257-61. [pubmed]

Loh PR, Lipson M, Patterson N, Moorjani P, Pickrell JK, Reich D, Berger B. Inferring Admixture Histories of Human Populations Using Linkage Disequilibrium. Genetics. 2013 Apr;193(4):1233-54.[preprint] [pubmed]

2012

Pickrell JK, Pritchard JK. Inference of population splits and mixtures from genome-wide allele frequency data. PLoS Genetics. 2012 Nov;8(11):e1002967. [pubmed] [preprint] [TreeMix software] [blog post]
Coverage:
[Nature Genetics]

Pickrell JK, Patterson N, Barbieri C, Berthold F, Gerlach L, Güldemann T, Kure B, Mpoloka SW, Nakagawa H, Naumann C, Lipson M, Loh PR, Lachance J, Mountain J, Bustamante CD, Berger B, Tishkoff SA, Henn BM, Stoneking M, Reich D, Pakendorf B. The genetic prehistory of southern Africa. Nature Communications 2012 Oct 16;3:1143. [pubmed] [preprint] [blog post]
Coverage:
[Nature]
[ScienceNews]
[Razib Khan]

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. 2012 Oct;8(10):e1003000. [pubmed]

Jostins L, Pickrell JK, Macarthur DG, Barrett JC. Misuse of hierarchical linear models overstates the significance of a reported association between OXTR and prosociality [Letter to the editor]. Proc Natl Acad Sci U S A. 2012 Apr 12. [pubmed]

Pickrell JK, Gilad Y, Pritchard JK. Comment on “Widespread RNA and DNA sequence differences in the human transcriptome” [Technical Comment on Li et al. (2011)]. Science. 2012 Mar 16;335(6074):1302. [pubmed] [blog post]
See also: Technical Comments by Kleinman and Majewski and Lin et al., and a response from Li et al.
Coverage:
[Nature]

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. [pubmed]

MacArthur DG, Balasubramanian S, Frankish A, Huang N, Morris J, Walter K, Jostins L, Habegger L, Pickrell JK, Montgomery SB, Albers CA, Zhang ZD, Conrad DF, Lunter G, Zheng H, Ayub Q, DePristo MA, Banks E, Hu M, Handsaker RE, Rosenfeld JA, Fromer M, Jin M, Mu XJ, Khurana E, Ye K, Kay M, Saunders GI, Suner MM, Hunt T, Barnes IH, Amid C, Carvalho-Silva DR, Bignell AH, Snow C, Yngvadottir B, Bumpstead S, Cooper DN, Xue Y, Romero IG, 1000 Genomes Project Consortium, Wang J, Li Y, Gibbs RA, McCarroll SA, Dermitzakis ET, Pritchard JK, Barrett JC, Harrow J, Hurles ME, Gerstein MB, Tyler-Smith C. A systematic survey of loss-of-function variants in human protein-coding genes. Science. 2012 Feb 17;335(6070):823-8. [pubmed]

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 5;482(7385):390-4. [pubmed]

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. 2012 Apr;22(4):602-10. [pubmed]

2011 and prior

Pickrell JK*, Gaffney DJ*, Gilad Y, Pritchard JK. False positive peaks in ChIP-seq and other sequencing-based functional assays caused by unannotated high copy number regions. Bioinformatics. 2011 Aug 1;27(15):2144-6. [pubmed] [data]

Bell JT, Pai AA, Pickrell JK, Gaffney DJ, Pique-Regi R, Degner JF, Gilad Y, Pritchard JK. DNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines. Genome Biology. 2011 Jan 20;12(1):R10. [pubmed]

Pickrell JK, Pai AA, Gilad Y, Pritchard JK. Noisy splicing drives mRNA isoform diversity in human cells. PLoS Genetics. 2010 Dec 9;6(12):e1001236. [pubmed] [data]
Coverage:
[F1000]
[Nature Reviews Genetics]

Kosova G, Pickrell JK, Kelley JL, McArdle PF, Shuldiner AR, Abney M, Ober C. The CFTR Met 470 allele is associated with lower birth rates in fertile men from a population isolate. PLoS Genetics. 2010 Jun 3;6(6):e1000974. [pubmed]

Pickrell JK, Marioni JC, Pai AA, Degner JF, Engelhardt BE, Nkadori E, Veyrieras J-B, Stephens M, Gilad Y, Pritchard JK. Understanding mechanisms underlying human gene expression variation with RNA sequencing. Nature. 2010 Apr 1;464(7289):768-72 [pubmed] [slidecast] [data]
Coverage:
[F1000]
[Nature Reviews Genetics]
[GenomeWeb]

Pritchard JK, Pickrell JK, Coop G. The genetics of human adaptation: hard sweeps, soft sweeps, and polygenic adaptation. Current Biology. 2010 Feb 23;20(4):R208-R215. [pubmed]

Perry GH, Pickrell JK. A rod cell marker of nocturnal ancestry [News and Views on Solovei et al. (2009)]. Journal of Human Evolution. 2010 Feb;58(2):207-10. [pubmed]

Degner JF, Marioni JC, Pai AA, Pickrell JK, Nkadori E, Gilad Y, Pritchard JK. Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data. Bioinformatics. 2009 Dec 15;25(24):3207-12. [pubmed]

Barreiro LB, Ben-Ali M, Quach H, Laval G, Patin E, Pickrell JK, Bouchier C, Tichit M, Neyrolles O, Gicquel B, Kidd JR, Kidd KK, Alcaïs A, Ragimbeau J, Pellegrini S, Abel L, Casanova JL, Quintana-Murci L. Evolutionary dynamics of human Toll-like receptors and their different contributions to host defense. PLoS Genetics. 2009 Jul;5(7):e1000562. [pubmed]

Coop G*, Pickrell JK*, Novembre J, Kudaravalli S, Li J, Absher D, Myers RM, Cavalli-Sforza LL, Feldman MW, Pritchard JK. The role of geography in human adaptation. PLoS Genetics. 2009 Jun;5(6):e1000500. [pubmed]
Coverage:
[Nature]
[Nature Genetics]

Faddah DA, Ganko EW, McCoach C, Pickrell JK, Hanlon SE, Mann FG, Mieczkowska JO, Jones CD, Lieb JD, Vision TJ. Systematic identification of balanced transposition polymorphisms in Saccharomyces cerevisiae. PLoS Genetics. 2009 Jun;5(6):e1000502. [pubmed]

Pickrell JK, Coop G, Novembre J, Kudaravalli S, Li JZ, Absher D, Srinivasan BS, Barsh GS, Myers RM, Feldman MW, Pritchard JK. Signals of recent positive selection in a worldwide sample of human populations. Genome Research. 2009 May;19(5):826-37. [pubmed] [HGDP Selection Browser]
Coverage:
[NYTimes]

Dalmasso C, Pickrell J, Tuefferd M, Génin E, Bourgain C, Broët P. A mixture model approach to multiple testing for the genetic analysis of gene expression. BMC Proceedings. 2007;1 Suppl 1:S141. [pubmed]

Pickrell J, Clerget-Darpoux F, Bourgain C. Power of genome-wide association studies in the presence of interacting loci. Genetic Epidemiology. 2007 Nov;31(7):748-62. [pubmed]

Sharp SI, Pickrell JK, Jahn CL. Identification of a novel “chromosome scaffold” protein that associates with Tec elements undergoing en masse elimination in Euplotes crassus. Molecular Biology of the Cell. 2003 Feb;14(2):571-84. [pubmed]