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Jonathan K. Pritchard

TitlePROFESSOR
InstitutionUniversity of Chicago
DepartmentHuman Genetics
AddressChicago IL 60637
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    Collapse Bibliographic 
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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    1. Freimer JW, Shaked O, Naqvi S, Sinnott-Armstrong N, Kathiria A, Garrido CM, Chen AF, Cortez JT, Greenleaf WJ, Pritchard JK, Marson A. Systematic discovery and perturbation of regulatory genes in human T cells reveals the architecture of immune networks. Nat Genet. 2022 Aug; 54(8):1133-1144. PMID: 35817986.
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    2. Patel RA, Musharoff SA, Spence JP, Pimentel H, Tcheandjieu C, Mostafavi H, Sinnott-Armstrong N, Clarke SL, Smith CJ. Genetic interactions drive heterogeneity in causal variant effect sizes for gene expression and complex traits. Am J Hum Genet. 2022 Jul 07; 109(7):1286-1297. PMID: 35716666.
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    3. Sasani TA, Ashbrook DG, Beichman AC, Lu L, Palmer AA, Williams RW, Pritchard JK, Harris K. A natural mutator allele shapes mutation spectrum variation in mice. Nature. 2022 05; 605(7910):497-502. PMID: 35545679.
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    4. Wymant C, Bezemer D, Blanquart F, Ferretti L, Gall A, Hall M, Golubchik T, Bakker M, Ong SH, Zhao L, Bonsall D, de Cesare M, MacIntyre-Cockett G, Abeler-Dörner L, Albert J, Bannert N, Fellay J, Grabowski MK, Gunsenheimer-Bartmeyer B, Günthard HF, Kivelä P, Kouyos RD, Laeyendecker O, Meyer L, Porter K, Ristola M, van Sighem A, Berkhout B, Kellam P, Cornelissen M, Reiss P, Fraser C. A highly virulent variant of HIV-1 circulating in the Netherlands. Science. 2022 02 04; 375(6580):540-545. PMID: 35113714.
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    5. Sinnott-Armstrong N, Tanigawa Y, Amar D, Mars N, Benner C, Aguirre M, Venkataraman GR, Wainberg M, Ollila HM, Kiiskinen T, Havulinna AS, Pirruccello JP, Qian J, Shcherbina A. Author Correction: Genetics of 35 blood and urine biomarkers in the UK Biobank. Nat Genet. 2021 Nov; 53(11):1622. PMID: 34608296.
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    6. Võsa U, Claringbould A, Westra HJ, Bonder MJ, Deelen P, Zeng B, Kirsten H, Saha A, Kreuzhuber R, Yazar S, Brugge H, Oelen R, de Vries DH, van der Wijst MGP, Kasela S, Pervjakova N, Alves I, Favé MJ, Agbessi M, Christiansen MW, Jansen R, Seppälä I, Tong L, Teumer A, Schramm K, Hemani G, Verlouw J, Yaghootkar H, Sönmez Flitman R, Brown A, Kukushkina V, Kalnapenkis A, Rüeger S, Porcu E, Kronberg J, Kettunen J, Lee B, Zhang F, Qi T, Hernandez JA, Arindrarto W, Beutner F. Large-scale cis- and trans-eQTL analyses identify thousands of genetic loci and polygenic scores that regulate blood gene expression. Nat Genet. 2021 09; 53(9):1300-1310. PMID: 34475573.
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    7. Naqvi S, Sleyp Y, Hoskens H, Indencleef K, Spence JP, Bruffaerts R, Radwan A, Eller RJ, Richmond S, Shriver MD, Shaffer JR, Weinberg SM, Walsh S, Thompson J, Pritchard JK, Sunaert S, Peeters H, Wysocka J, Claes P. Shared heritability of human face and brain shape. Nat Genet. 2021 06; 53(6):830-839. PMID: 33821002.
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    8. Sinnott-Armstrong N, Naqvi S, Rivas M, Pritchard JK. GWAS of three molecular traits highlights core genes and pathways alongside a highly polygenic background. Elife. 2021 02 15; 10. PMID: 33587031.
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    9. Sinnott-Armstrong N, Sousa IS, Laber S, Rendina-Ruedy E, Nitter Dankel SE, Ferreira T, Mellgren G, Karasik D, Rivas M, Pritchard J, Guntur AR, Cox RD, Lindgren CM, Hauner H, Sallari R, Rosen CJ, Hsu YH, Lander ES, Kiel DP, Claussnitzer M. A regulatory variant at 3q21.1 confers an increased pleiotropic risk for hyperglycemia and altered bone mineral density. Cell Metab. 2021 03 02; 33(3):615-628.e13. PMID: 33513366.
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    10. Sinnott-Armstrong N, Tanigawa Y, Amar D, Mars N, Benner C, Aguirre M, Venkataraman GR, Wainberg M, Ollila HM, Kiiskinen T, Havulinna AS, Pirruccello JP, Qian J, Shcherbina A. Genetics of 35 blood and urine biomarkers in the UK Biobank. Nat Genet. 2021 02; 53(2):185-194. PMID: 33462484.
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    11. Catania S, Dumesic PA, Pimentel H, Nasif A, Stoddard CI, Burke JE, Diedrich JK, Cooke S, Shea T, Gienger E, Lintner R, Yates JR, Hajkova P, Narlikar GJ, Cuomo CA, Pritchard JK, Madhani HD. Evolutionary Persistence of DNA Methylation for Millions of Years after Ancient Loss of a De Novo Methyltransferase. Cell. 2020 Feb 20; 180(4):816. PMID: 32084344.
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    12. Mostafavi H, Harpak A, Agarwal I, Conley D, Pritchard JK, Przeworski M. Variable prediction accuracy of polygenic scores within an ancestry group. Elife. 2020 01 30; 9. PMID: 31999256.
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    13. Trevino AE, Sinnott-Armstrong N, Andersen J, Yoon SJ, Huber N, Pritchard JK, Chang HY, Greenleaf WJ, Pa?ca SP. Chromatin accessibility dynamics in a model of human forebrain development. Science. 2020 01 24; 367(6476). PMID: 31974223.
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    14. Catania S, Dumesic PA, Pimentel H, Nasif A, Stoddard CI, Burke JE, Diedrich JK, Cook S, Shea T, Geinger E, Lintner R, Yates JR, Hajkova P, Narlikar GJ, Cuomo CA, Pritchard JK, Madhani HD. Evolutionary Persistence of DNA Methylation for Millions of Years after Ancient Loss of a De Novo Methyltransferase. Cell. 2020 01 23; 180(2):263-277.e20. PMID: 31955845.
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    15. Antonio ML, Gao Z, Moots HM, Lucci M, Candilio F, Sawyer S, Oberreiter V, Calderon D, Devitofranceschi K, Aikens RC, Aneli S, Bartoli F, Bedini A, Cheronet O, Cotter DJ, Fernandes DM, Gasperetti G, Grifoni R, Guidi A, La Pastina F, Loreti E, Manacorda D, Matullo G, Morretta S, Nava A, Fiocchi Nicolai V, Nomi F, Pavolini C, Pentiricci M, Pergola P, Piranomonte M, Schmidt R, Spinola G, Sperduti A, Rubini M, Bondioli L, Coppa A, Pinhasi R, Pritchard JK. Ancient Rome: A genetic crossroads of Europe and the Mediterranean. Science. 2019 11 08; 366(6466):708-714. PMID: 31699931.
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    16. Calderon D, Nguyen MLT, Mezger A, Kathiria A, Müller F, Nguyen V, Lescano N, Wu B, Trombetta J, Ribado JV, Knowles DA, Gao Z, Blaeschke F, Parent AV, Burt TD, Anderson MS, Criswell LA, Greenleaf WJ, Marson A, Pritchard JK. Landscape of stimulation-responsive chromatin across diverse human immune cells. Nat Genet. 2019 10; 51(10):1494-1505. PMID: 31570894.
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    17. Telis N, Glassberg EC, Pritchard JK, Gunter C. Public Discussion Affects Question Asking at Academic Conferences. Am J Hum Genet. 2019 07 03; 105(1):189-197. PMID: 31256875.
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    18. Liu X, Li YI, Pritchard JK. Trans Effects on Gene Expression Can Drive Omnigenic Inheritance. Cell. 2019 05 02; 177(4):1022-1034.e6. PMID: 31051098.
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    19. Stahlschmidt MC, Collin TC, Fernandes DM, Bar-Oz G, Belfer-Cohen A, Gao Z, Jakeli N, Matskevich Z, Meshveliani T, Pritchard JK, McDermott F, Pinhasi R. Ancient Mammalian and Plant DNA from Late Quaternary Stalagmite Layers at Solkota Cave, Georgia. Sci Rep. 2019 04 29; 9(1):6628. PMID: 31036834.
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    20. Berg JJ, Harpak A, Sinnott-Armstrong N, Joergensen AM, Mostafavi H, Field Y, Boyle EA, Zhang X, Racimo F, Pritchard JK, Coop G. Reduced signal for polygenic adaptation of height in UK Biobank. Elife. 2019 03 21; 8. PMID: 30895923.
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    21. Rosenberg NA, Edge MD, Pritchard JK, Feldman MW. Interpreting polygenic scores, polygenic adaptation, and human phenotypic differences. Evol Med Public Health. 2019; 2019(1):26-34. PMID: 30838127.
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    22. Boyle EA, Pritchard JK, Greenleaf WJ. High-resolution mapping of cancer cell networks using co-functional interactions. Mol Syst Biol. 2018 12 20; 14(12):e8594. PMID: 30573688.
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    23. Glassberg EC, Gao Z, Harpak A, Lan X, Pritchard JK. Evidence for Weak Selective Constraint on Human Gene Expression. Genetics. 2019 02; 211(2):757-772. PMID: 30554168.
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    24. Sharon E, Chen SA, Khosla NM, Smith JD, Pritchard JK, Fraser HB. Functional Genetic Variants Revealed by Massively Parallel Precise Genome Editing. Cell. 2018 10 04; 175(2):544-557.e16. PMID: 30245013.
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    25. Wang SH, Hsiao CJ, Khan Z, Pritchard JK. Post-translational buffering leads to convergent protein expression levels between primates. Genome Biol. 2018 06 27; 19(1):83. PMID: 29950183.
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    26. Knowles DA, Burrows CK, Blischak JD, Patterson KM, Serie DJ, Norton N, Ober C, Pritchard JK, Gilad Y. Determining the genetic basis of anthracycline-cardiotoxicity by molecular response QTL mapping in induced cardiomyocytes. Elife. 2018 05 08; 7. PMID: 29737278.
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    27. Yamamoto R, Wilkinson AC, Ooehara J, Lan X, Lai CY, Nakauchi Y, Pritchard JK, Nakauchi H. Large-Scale Clonal Analysis Resolves Aging of the Mouse Hematopoietic Stem Cell Compartment. Cell Stem Cell. 2018 04 05; 22(4):600-607.e4. PMID: 29625072.
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    28. Sparvoli D, Richardson E, Osakada H, Lan X, Iwamoto M, Bowman GR, Kontur C, Bourland WA, Lynn DH, Pritchard JK, Haraguchi T, Dacks JB, Turkewitz AP. Remodeling the Specificity of an Endosomal CORVET Tether Underlies Formation of Regulated Secretory Vesicles in the Ciliate Tetrahymena thermophila. Curr Biol. 2018 03 05; 28(5):697-710.e13. PMID: 29478853.
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    29. Li YI, Knowles DA, Humphrey J, Barbeira AN, Dickinson SP, Im HK, Pritchard JK. Annotation-free quantification of RNA splicing using LeafCutter. Nat Genet. 2018 01; 50(1):151-158. PMID: 29229983.
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    30. Banovich NE, Li YI, Raj A, Ward MC, Greenside P, Calderon D, Tung PY, Burnett JE, Myrthil M, Thomas SM, Burrows CK, Romero IG, Pavlovic BJ, Kundaje A, Pritchard JK, Gilad Y. Impact of regulatory variation across human iPSCs and differentiated cells. Genome Res. 2018 01; 28(1):122-131. PMID: 29208628.
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    31. Harpak A, Lan X, Gao Z, Pritchard JK. Frequent nonallelic gene conversion on the human lineage and its effect on the divergence of gene duplicates. Proc Natl Acad Sci U S A. 2017 11 28; 114(48):12779-12784. PMID: 29138319.
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    32. Calderon D, Bhaskar A, Knowles DA, Golan D, Raj T, Fu AQ, Pritchard JK. Inferring Relevant Cell Types for Complex Traits by Using Single-Cell Gene Expression. Am J Hum Genet. 2017 Nov 02; 101(5):686-699. PMID: 29106824.
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    33. Sharon E, Shi H, Kharbanda S, Koh W, Martin LR, Khush KK, Valantine H, Pritchard JK, De Vlaminck I. Quantification of transplant-derived circulating cell-free DNA in absence of a donor genotype. PLoS Comput Biol. 2017 Aug; 13(8):e1005629. PMID: 28771616.
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    34. Boyle EA, Li YI, Pritchard JK. An Expanded View of Complex Traits: From Polygenic to Omnigenic. Cell. 2017 Jun 15; 169(7):1177-1186. PMID: 28622505.
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    35. Harris K, Pritchard JK. Rapid evolution of the human mutation spectrum. Elife. 2017 04 25; 6. PMID: 28440220.
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    36. Nielsen R, Akey JM, Jakobsson M, Pritchard JK, Tishkoff S, Willerslev E. Tracing the peopling of the world through genomics. Nature. 2017 01 18; 541(7637):302-310. PMID: 28102248.
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    37. Tung PY, Blischak JD, Hsiao CJ, Knowles DA, Burnett JE, Pritchard JK, Gilad Y. Batch effects and the effective design of single-cell gene expression studies. Sci Rep. 2017 01 03; 7:39921. PMID: 28045081.
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    38. Harpak A, Bhaskar A, Pritchard JK. Mutation Rate Variation is a Primary Determinant of the Distribution of Allele Frequencies in Humans. PLoS Genet. 2016 Dec; 12(12):e1006489. PMID: 27977673.
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    39. Telis N, Lehmann BV, Feldman MW, Pritchard JK. A Bibliometric History of the Journal GENETICS. Genetics. 2016 12; 204(4):1337-1342. PMID: 27927899.
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    40. Field Y, Boyle EA, Telis N, Gao Z, Gaulton KJ, Golan D, Yengo L, Rocheleau G, Froguel P, McCarthy MI, Pritchard JK. Detection of human adaptation during the past 2000 years. Science. 2016 11 11; 354(6313):760-764. PMID: 27738015.
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    41. Corces MR, Buenrostro JD, Wu B, Greenside PG, Chan SM, Koenig JL, Snyder MP, Pritchard JK, Kundaje A, Greenleaf WJ, Majeti R, Chang HY. Lineage-specific and single-cell chromatin accessibility charts human hematopoiesis and leukemia evolution. Nat Genet. 2016 10; 48(10):1193-203. PMID: 27526324.
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    42. Kontur C, Kumar S, Lan X, Pritchard JK, Turkewitz AP. Whole Genome Sequencing Identifies a Novel Factor Required for Secretory Granule Maturation in Tetrahymena thermophila. G3 (Bethesda). 2016 08 09; 6(8):2505-16. PMID: 27317773.
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    43. Sharon E, Sibener LV, Battle A, Fraser HB, Garcia KC, Pritchard JK. Genetic variation in MHC proteins is associated with T cell receptor expression biases. Nat Genet. 2016 09; 48(9):995-1002. PMID: 27479906.
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    44. Parker CC, Gopalakrishnan S, Carbonetto P, Gonzales NM, Leung E, Park YJ, Aryee E, Davis J, Blizard DA, Ackert-Bicknell CL, Lionikas A, Pritchard JK, Palmer AA. Genome-wide association study of behavioral, physiological and gene expression traits in outbred CFW mice. Nat Genet. 2016 08; 48(8):919-26. PMID: 27376237.
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    45. Raj A, Wang SH, Shim H, Harpak A, Li YI, Engelmann B, Stephens M, Gilad Y, Pritchard JK. Thousands of novel translated open reading frames in humans inferred by ribosome footprint profiling. Elife. 2016 05 27; 5. PMID: 27232982.
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    46. Lan X, Pritchard JK. Coregulation of tandem duplicate genes slows evolution of subfunctionalization in mammals. Science. 2016 May 20; 352(6288):1009-13. PMID: 27199432.
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    47. Li YI, van de Geijn B, Raj A, Knowles DA, Petti AA, Golan D, Gilad Y, Pritchard JK. RNA splicing is a primary link between genetic variation and disease. Science. 2016 Apr 29; 352(6285):600-4. PMID: 27126046.
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    48. Burrows CK, Banovich NE, Pavlovic BJ, Patterson K, Gallego Romero I, Pritchard JK, Gilad Y. Genetic Variation, Not Cell Type of Origin, Underlies the Majority of Identifiable Regulatory Differences in iPSCs. PLoS Genet. 2016 Jan; 12(1):e1005793. PMID: 26812582.
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    49. Gymrek M, Willems T, Guilmatre A, Zeng H, Markus B, Georgiev S, Daly MJ, Price AL, Pritchard JK, Sharp AJ, Erlich Y. Abundant contribution of short tandem repeats to gene expression variation in humans. Nat Genet. 2016 Jan; 48(1):22-9. PMID: 26642241.
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    50. Raj A, Shim H, Gilad Y, Pritchard JK, Stephens M. msCentipede: Modeling Heterogeneity across Genomic Sites and Replicates Improves Accuracy in the Inference of Transcription Factor Binding. PLoS One. 2015; 10(9):e0138030. PMID: 26406244.
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    51. van de Geijn B, McVicker G, Gilad Y, Pritchard JK. WASP: allele-specific software for robust molecular quantitative trait locus discovery. Nat Methods. 2015 Nov; 12(11):1061-3. PMID: 26366987.
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    52. Grubert F, Zaugg JB, Kasowski M, Ursu O, Spacek DV, Martin AR, Greenside P, Srivas R, Phanstiel DH, Pekowska A, Heidari N, Euskirchen G, Huber W, Pritchard JK, Bustamante CD, Steinmetz LM, Kundaje A, Snyder M. Genetic Control of Chromatin States in Humans Involves Local and Distal Chromosomal Interactions. Cell. 2015 Aug 27; 162(5):1051-65. PMID: 26300125.
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    53. Thomas SM, Kagan C, Pavlovic BJ, Burnett J, Patterson K, Pritchard JK, Gilad Y. Reprogramming LCLs to iPSCs Results in Recovery of Donor-Specific Gene Expression Signature. PLoS Genet. 2015 May; 11(5):e1005216. PMID: 25950834.
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    54. Pai AA, Pritchard JK, Gilad Y. The genetic and mechanistic basis for variation in gene regulation. PLoS Genet. 2015 Jan; 11(1):e1004857. PMID: 25569255.
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    55. Battle A, Khan Z, Wang SH, Mitrano A, Ford MJ, Pritchard JK, Gilad Y. Genomic variation. Impact of regulatory variation from RNA to protein. Science. 2015 Feb 06; 347(6222):664-7. PMID: 25657249.
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    56. Banovich NE, Lan X, McVicker G, van de Geijn B, Degner JF, Blischak JD, Roux J, Pritchard JK, Gilad Y. Methylation QTLs are associated with coordinated changes in transcription factor binding, histone modifications, and gene expression levels. PLoS Genet. 2014 Sep; 10(9):e1004663. PMID: 25233095.
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    57. Çaliskan M, Pritchard JK, Ober C, Gilad Y. The effect of freeze-thaw cycles on gene expression levels in lymphoblastoid cell lines. PLoS One. 2014; 9(9):e107166. PMID: 25192014.
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    58. Raj A, Stephens M, Pritchard JK. fastSTRUCTURE: variational inference of population structure in large SNP data sets. Genetics. 2014 Jun; 197(2):573-89. PMID: 24700103.
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    59. Cusanovich DA, Pavlovic B, Pritchard JK, Gilad Y. The functional consequences of variation in transcription factor binding. PLoS Genet. 2014 Mar; 10(3):e1004226. PMID: 24603674.
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    60. Simons YB, Turchin MC, Pritchard JK, Sella G. The deleterious mutation load is insensitive to recent population history. Nat Genet. 2014 Mar; 46(3):220-4. PMID: 24509481.
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    61. Nalabothula N, McVicker G, Maiorano J, Martin R, Pritchard JK, Fondufe-Mittendorf YN. The chromatin architectural proteins HMGD1 and H1 bind reciprocally and have opposite effects on chromatin structure and gene regulation. BMC Genomics. 2014 Feb 01; 15:92. PMID: 24484546.
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    62. Zhou X, Cain CE, Myrthil M, Lewellen N, Michelini K, Davenport ER, Stephens M, Pritchard JK, Gilad Y. Epigenetic modifications are associated with inter-species gene expression variation in primates. Genome Biol. 2014; 15(12):547. PMID: 25468404.
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    63. Jeong C, Alkorta-Aranburu G, Basnyat B, Neupane M, Witonsky DB, Pritchard JK, Beall CM, Di Rienzo A. Admixture facilitates genetic adaptations to high altitude in Tibet. Nat Commun. 2014; 5:3281. PMID: 24513612.
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    64. Birney E, Pritchard JK. Archaic humans: Four makes a party. Nature. 2014 Jan 02; 505(7481):32-4. PMID: 24352230.
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    65. Khan Z, Ford MJ, Cusanovich DA, Mitrano A, Pritchard JK, Gilad Y. Primate transcript and protein expression levels evolve under compensatory selection pressures. Science. 2013 Nov 29; 342(6162):1100-4. PMID: 24136357.
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    66. McVicker G, van de Geijn B, Degner JF, Cain CE, Banovich NE, Raj A, Lewellen N, Myrthil M, Gilad Y, Pritchard JK. Identification of genetic variants that affect histone modifications in human cells. Science. 2013 Nov 08; 342(6159):747-9. PMID: 24136359.
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    67. Flutre T, Wen X, Pritchard J, Stephens M. A statistical framework for joint eQTL analysis in multiple tissues. PLoS Genet. 2013 May; 9(5):e1003486. PMID: 23671422.
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    68. Alkorta-Aranburu G, Beall CM, Witonsky DB, Gebremedhin A, Pritchard JK, Di Rienzo A. The genetic architecture of adaptations to high altitude in Ethiopia. PLoS Genet. 2012; 8(12):e1003110. PMID: 23236293.
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    69. Pickrell JK, Pritchard JK. Inference of population splits and mixtures from genome-wide allele frequency data. PLoS Genet. 2012; 8(11):e1002967. PMID: 23166502.
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    70. Gaffney DJ, McVicker G, Pai AA, Fondufe-Mittendorf YN, Lewellen N, Michelini K, Widom J, Gilad Y, Pritchard JK. Controls of nucleosome positioning in the human genome. PLoS Genet. 2012; 8(11):e1003036. PMID: 23166509.
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    71. Pai AA, Cain CE, Mizrahi-Man O, De Leon S, Lewellen N, Veyrieras JB, Degner JF, Gaffney DJ, Pickrell JK, Stephens M, Pritchard JK, Gilad Y. The contribution of RNA decay quantitative trait loci to inter-individual variation in steady-state gene expression levels. PLoS Genet. 2012; 8(10):e1003000. PMID: 23071454.
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    72. Ecker JR, Bickmore WA, Barroso I, Pritchard JK, Gilad Y, Segal E. Genomics: ENCODE explained. Nature. 2012 Sep 06; 489(7414):52-5. PMID: 22955614.
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    73. Zullo JM, Demarco IA, Piqué-Regi R, Gaffney DJ, Epstein CB, Spooner CJ, Luperchio TR, Bernstein BE, Pritchard JK, Reddy KL, Singh H. DNA sequence-dependent compartmentalization and silencing of chromatin at the nuclear lamina. Cell. 2012 Jun 22; 149(7):1474-87. PMID: 22726435.
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    74. Pickrell JK, Gilad Y, Pritchard JK. Comment on "Widespread RNA and DNA sequence differences in the human transcriptome". Science. 2012 Mar 16; 335(6074):1302; author reply 1302. PMID: 22422963.
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    75. 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. A systematic survey of loss-of-function variants in human protein-coding genes. Science. 2012 Feb 17; 335(6070):823-8. PMID: 22344438.
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    76. Veyrieras JB, Gaffney DJ, Pickrell JK, Gilad Y, Stephens M, Pritchard JK. Exon-specific QTLs skew the inferred distribution of expression QTLs detected using gene expression array data. PLoS One. 2012; 7(2):e30629. PMID: 22359548.
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    77. Degner JF, Pai AA, Pique-Regi R, Veyrieras JB, Gaffney DJ, Pickrell JK, De Leon S, Michelini K, Lewellen N, Crawford GE, Stephens M, Gilad Y, Pritchard JK. DNase?I sensitivity QTLs are a major determinant of human expression variation. Nature. 2012 Feb 05; 482(7385):390-4. PMID: 22307276.
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    78. 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.
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    79. Perry GH, Melsted P, Marioni JC, Wang Y, Bainer R, Pickrell JK, Michelini K, Zehr S, Yoder AD, Stephens M, Pritchard JK, Gilad Y. Comparative RNA sequencing reveals substantial genetic variation in endangered primates. Genome Res. 2012 Apr; 22(4):602-10. PMID: 22207615.
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    80. Perry GH, Reeves D, Melsted P, Ratan A, Miller W, Michelini K, Louis EE, Pritchard JK, Mason CE, Gilad Y. A genome sequence resource for the aye-aye (Daubentonia madagascariensis), a nocturnal lemur from Madagascar. Genome Biol Evol. 2012; 4(2):126-35. PMID: 22155688.
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    81. Huang L, Jakobsson M, Pemberton TJ, Ibrahim M, Nyambo T, Omar S, Pritchard JK, Tishkoff SA, Rosenberg NA. Haplotype variation and genotype imputation in African populations. Genet Epidemiol. 2011 Dec; 35(8):766-80. PMID: 22125220.
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    82. Pritchard JK. Whole-genome sequencing data offer insights into human demography. Nat Genet. 2011 Sep 28; 43(10):923-5. PMID: 21956387.
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    83. Melsted P, Pritchard JK. Efficient counting of k-mers in DNA sequences using a bloom filter. BMC Bioinformatics. 2011 Aug 10; 12:333. PMID: 21831268.
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    84. 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 01; 27(15):2144-6. PMID: 21690102.
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    85. Hancock AM, Witonsky DB, Alkorta-Aranburu G, Beall CM, Gebremedhin A, Sukernik R, Utermann G, Pritchard JK, Coop G, Di Rienzo A. Adaptations to climate-mediated selective pressures in humans. PLoS Genet. 2011 Apr; 7(4):e1001375. PMID: 21533023.
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    86. Pai AA, Bell JT, Marioni JC, Pritchard JK, Gilad Y. A genome-wide study of DNA methylation patterns and gene expression levels in multiple human and chimpanzee tissues. PLoS Genet. 2011 Feb; 7(2):e1001316. PMID: 21383968.
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    87. 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 Biol. 2011; 12(1):R10. PMID: 21251332.
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    88. Pritchard J, Loeb A. Cosmology: Hydrogen was not ionized abruptly. Nature. 2010 Dec 09; 468(7325):772-3. PMID: 21150988.
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    89. Pickrell JK, Pai AA, Gilad Y, Pritchard JK. Noisy splicing drives mRNA isoform diversity in human cells. PLoS Genet. 2010 Dec 09; 6(12):e1001236. PMID: 21151575.
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    90. Pique-Regi R, Degner JF, Pai AA, Gaffney DJ, Gilad Y, Pritchard JK. Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data. Genome Res. 2011 Mar; 21(3):447-55. PMID: 21106904.
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    91. Pritchard JK. How we are evolving. Sci Am. 2010 Oct; 303(4):40-7. PMID: 20923127.
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    92. Pritchard JK, Di Rienzo A. Adaptation - not by sweeps alone. Nat Rev Genet. 2010 Oct; 11(10):665-7. PMID: 20838407.
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    93. Coop G, Witonsky D, Di Rienzo A, Pritchard JK. Using environmental correlations to identify loci underlying local adaptation. Genetics. 2010 Aug; 185(4):1411-23. PMID: 20516501.
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    94. Hancock AM, Witonsky DB, Ehler E, Alkorta-Aranburu G, Beall C, Gebremedhin A, Sukernik R, Utermann G, Pritchard J, Coop G, Di Rienzo A. Colloquium paper: human adaptations to diet, subsistence, and ecoregion are due to subtle shifts in allele frequency. Proc Natl Acad Sci U S A. 2010 May 11; 107 Suppl 2:8924-30. PMID: 20445095.
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    95. 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.
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    96. Pritchard JK, Pickrell JK, Coop G. The genetics of human adaptation: hard sweeps, soft sweeps, and polygenic adaptation. Curr Biol. 2010 Feb 23; 20(4):R208-15. PMID: 20178769.
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    97. 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. PMID: 19808877.
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    98. Gilad Y, Pritchard JK, Thornton K. Characterizing natural variation using next-generation sequencing technologies. Trends Genet. 2009 Oct; 25(10):463-71. PMID: 19801172.
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    99. 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 Genet. 2009 Jun; 5(6):e1000500. PMID: 19503611.
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    100. Davison D, Pritchard JK, Coop G. An approximate likelihood for genetic data under a model with recombination and population splitting. Theor Popul Biol. 2009 Jun; 75(4):331-45. PMID: 19362099.
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    101. Hubisz MJ, Falush D, Stephens M, Pritchard JK. Inferring weak population structure with the assistance of sample group information. Mol Ecol Resour. 2009 Sep; 9(5):1322-32. PMID: 21564903.
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    102. 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 Res. 2009 May; 19(5):826-37. PMID: 19307593.
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    103. Schroeder KB, Jakobsson M, Crawford MH, Schurr TG, Boca SM, Conrad DF, Tito RY, Osipova LP, Tarskaia LA, Zhadanov SI, Wall JD, Pritchard JK, Malhi RS, Smith DG, Rosenberg NA. Haplotypic background of a private allele at high frequency in the Americas. Mol Biol Evol. 2009 May; 26(5):995-1016. PMID: 19221006.
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    104. Kudaravalli S, Veyrieras JB, Stranger BE, Dermitzakis ET, Pritchard JK. Gene expression levels are a target of recent natural selection in the human genome. Mol Biol Evol. 2009 Mar; 26(3):649-58. PMID: 19091723.
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    105. Veyrieras JB, Kudaravalli S, Kim SY, Dermitzakis ET, Gilad Y, Stephens M, Pritchard JK. High-resolution mapping of expression-QTLs yields insight into human gene regulation. PLoS Genet. 2008 Oct; 4(10):e1000214. PMID: 18846210.
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    106. Gilad Y, Rifkin SA, Pritchard JK. Revealing the architecture of gene regulation: the promise of eQTL studies. Trends Genet. 2008 Aug; 24(8):408-15. PMID: 18597885.
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    107. Hancock AM, Witonsky DB, Gordon AS, Eshel G, Pritchard JK, Coop G, Di Rienzo A. Adaptations to climate in candidate genes for common metabolic disorders. PLoS Genet. 2008 Feb; 4(2):e32. PMID: 18282109.
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    108. Coop G, Wen X, Ober C, Pritchard JK, Przeworski M. High-resolution mapping of crossovers reveals extensive variation in fine-scale recombination patterns among humans. Science. 2008 Mar 07; 319(5868):1395-8. PMID: 18239090.
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    109. Novembre J, Pritchard JK, Coop G. Adaptive drool in the gene pool. Nat Genet. 2007 Oct; 39(10):1188-90. PMID: 17898775.
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    110. Kim SY, Pritchard JK. Adaptive evolution of conserved noncoding elements in mammals. PLoS Genet. 2007 Sep; 3(9):1572-86. PMID: 17845075.
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    111. Falush D, Stephens M, Pritchard JK. Inference of population structure using multilocus genotype data: dominant markers and null alleles. Mol Ecol Notes. 2007 Jul 01; 7(4):574-578. PMID: 18784791.
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    112. Pemberton TJ, Jakobsson M, Conrad DF, Coop G, Wall JD, Pritchard JK, Patel PI, Rosenberg NA. Using population mixtures to optimize the utility of genomic databases: linkage disequilibrium and association study design in India. Ann Hum Genet. 2008 Jul; 72(Pt 4):535-46. PMID: 18513279.
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    113. Completing the map of human genetic variation. Nature. 2007 May 10; 447(7141):161-5. PMID: 17495918.
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    114. Zollner S, Pritchard JK. Overcoming the winner's curse: estimating penetrance parameters from case-control data. Am J Hum Genet. 2007 Apr; 80(4):605-15. PMID: 17357068.
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    115. Tishkoff SA, Reed FA, Ranciaro A, Voight BF, Babbitt CC, Silverman JS, Powell K, Mortensen HM, Hirbo JB, Osman M, Ibrahim M, Omar SA, Lema G, Nyambo TB, Ghori J, Bumpstead S, Pritchard JK, Wray GA, Deloukas P. Convergent adaptation of human lactase persistence in Africa and Europe. Nat Genet. 2007 Jan; 39(1):31-40. PMID: 17159977.
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    116. Noonan JP, Coop G, Kudaravalli S, Smith D, Krause J, Alessi J, Chen F, Platt D, Pääbo S, Pritchard JK, Rubin EM. Sequencing and analysis of Neanderthal genomic DNA. Science. 2006 Nov 17; 314(5802):1113-8. PMID: 17110569.
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    117. Conrad DF, Jakobsson M, Coop G, Wen X, Wall JD, Rosenberg NA, Pritchard JK. A worldwide survey of haplotype variation and linkage disequilibrium in the human genome. Nat Genet. 2006 Nov; 38(11):1251-60. PMID: 17057719.
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    118. Nanduri VR, Pritchard J, Levitt G, Glaser AW. Long term morbidity and health related quality of life after multi-system Langerhans cell histiocytosis. Eur J Cancer. 2006 Oct; 42(15):2563-9. PMID: 16959486.
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    119. Murgia C, Pritchard JK, Kim SY, Fassati A, Weiss RA. Clonal origin and evolution of a transmissible cancer. Cell. 2006 Aug 11; 126(3):477-87. PMID: 16901782.
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    120. Voight BF, Kudaravalli S, Wen X, Pritchard JK. A map of recent positive selection in the human genome. PLoS Biol. 2006 Mar; 4(3):e72. PMID: 16494531.
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    121. Hellenthal G, Pritchard JK, Stephens M. The effects of genotype-dependent recombination, and transmission asymmetry, on linkage disequilibrium. Genetics. 2006 Mar; 172(3):2001-5. PMID: 16387890.
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    122. Rosenberg NA, Mahajan S, Ramachandran S, Zhao C, Pritchard JK, Feldman MW. Clines, clusters, and the effect of study design on the inference of human population structure. PLoS Genet. 2005 Dec; 1(6):e70. PMID: 16355252.
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    123. Conrad DF, Andrews TD, Carter NP, Hurles ME, Pritchard JK. A high-resolution survey of deletion polymorphism in the human genome. Nat Genet. 2006 Jan; 38(1):75-81. PMID: 16327808.
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    124. Voight BF, Pritchard JK. Confounding from cryptic relatedness in case-control association studies. PLoS Genet. 2005 Sep; 1(3):e32. PMID: 16151517.
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    125. Zöllner S, Wen X, Pritchard JK. Association mapping and fine mapping with TreeLD. Bioinformatics. 2005 Jul 15; 21(14):3168-70. PMID: 15855250.
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    126. Zöllner S, Pritchard JK. Coalescent-based association mapping and fine mapping of complex trait loci. Genetics. 2005 Feb; 169(2):1071-92. PMID: 15489534.
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    127. Montana G, Pritchard JK. Statistical tests for admixture mapping with case-control and cases-only data. Am J Hum Genet. 2004 Nov; 75(5):771-89. PMID: 15386213.
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    128. Horton R, Rosenberg NA, Pritchard JK, Weber JL, Cann HM, Kidd KK, Zhivotovsky LA, Feldman MW. Read all about it: The Lancet's Paper of the Year, 2003. Lancet. 2003 Dec 20; 362(9401):2101-3. PMID: 14697815.
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    129. Zöllner S, Wen X, Hanchard NA, Herbert MA, Ober C, Pritchard JK. Evidence for extensive transmission distortion in the human genome. Am J Hum Genet. 2004 Jan; 74(1):62-72. PMID: 14681832.
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    130. Rosenberg NA, Li LM, Ward R, Pritchard JK. Informativeness of genetic markers for inference of ancestry. Am J Hum Genet. 2003 Dec; 73(6):1402-22. PMID: 14631557.
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    131. Wall JD, Pritchard JK. Assessing the performance of the haplotype block model of linkage disequilibrium. Am J Hum Genet. 2003 Sep; 73(3):502-15. PMID: 12916017.
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    132. Wall JD, Pritchard JK. Haplotype blocks and linkage disequilibrium in the human genome. Nat Rev Genet. 2003 Aug; 4(8):587-97. PMID: 12897771.
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    133. Falush D, Stephens M, Pritchard JK. Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics. 2003 Aug; 164(4):1567-87. PMID: 12930761.
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    134. Falush D, Wirth T, Linz B, Pritchard JK, Stephens M, Kidd M, Blaser MJ, Graham DY, Vacher S, Perez-Perez GI, Yamaoka Y, Mégraud F, Otto K, Reichard U, Katzowitsch E, Wang X, Achtman M, Suerbaum S. Traces of human migrations in Helicobacter pylori populations. Science. 2003 Mar 07; 299(5612):1582-5. PMID: 12624269.
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    135. Rosenberg NA, Pritchard JK, Weber JL, Cann HM, Kidd KK, Zhivotovsky LA, Feldman MW. Genetic structure of human populations. Science. 2002 Dec 20; 298(5602):2381-5. PMID: 12493913.
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    136. Pritchard JK, Cox NJ. The allelic architecture of human disease genes: common disease-common variant...or not? Hum Mol Genet. 2002 Oct 01; 11(20):2417-23. PMID: 12351577.
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    137. Pritchard JK, Donnelly P. Case-control studies of association in structured or admixed populations. Theor Popul Biol. 2001 Nov; 60(3):227-37. PMID: 11855957.
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    138. Pritchard JK. Deconstructing maize population structure. Nat Genet. 2001 Jul; 28(3):203-4. PMID: 11431683.
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    139. Pritchard JK, Przeworski M. Linkage disequilibrium in humans: models and data. Am J Hum Genet. 2001 Jul; 69(1):1-14. PMID: 11410837.
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    140. Pritchard JK. Are rare variants responsible for susceptibility to complex diseases? Am J Hum Genet. 2001 Jul; 69(1):124-37. PMID: 11404818.
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    141. Beaumont M, Barratt EM, Gottelli D, Kitchener AC, Daniels MJ, Pritchard JK, Bruford MW. Genetic diversity and introgression in the Scottish wildcat. Mol Ecol. 2001 Feb; 10(2):319-36. PMID: 11298948.
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    142. Rosenberg NA, Woolf E, Pritchard JK, Schaap T, Gefel D, Shpirer I, Lavi U, Bonne-Tamir B, Hillel J, Feldman MW. Distinctive genetic signatures in the Libyan Jews. Proc Natl Acad Sci U S A. 2001 Jan 30; 98(3):858-63. PMID: 11158561.
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    143. Thomson R, Pritchard JK, Shen P, Oefner PJ, Feldman MW. Recent common ancestry of human Y chromosomes: evidence from DNA sequence data. Proc Natl Acad Sci U S A. 2000 Jun 20; 97(13):7360-5. PMID: 10861004.
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    144. Pritchard JK, Stephens M, Donnelly P. Inference of population structure using multilocus genotype data. Genetics. 2000 Jun; 155(2):945-59. PMID: 10835412.
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    145. Pritchard JK, Stephens M, Rosenberg NA, Donnelly P. Association mapping in structured populations. Am J Hum Genet. 2000 Jul; 67(1):170-81. PMID: 10827107.
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    146. Allen RW, Traver M, Pritchard JK. DNA analysis in a paternity case involving a triploid fetus. Transfusion. 2000 Feb; 40(2):240-4. PMID: 10686009.
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    147. Pritchard JK, Seielstad MT, Perez-Lezaun A, Feldman MW. Population growth of human Y chromosomes: a study of Y chromosome microsatellites. Mol Biol Evol. 1999 Dec; 16(12):1791-8. PMID: 10605120.
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    148. Pritchard JK, Rosenberg NA. Use of unlinked genetic markers to detect population stratification in association studies. Am J Hum Genet. 1999 Jul; 65(1):220-8. PMID: 10364535.
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    149. Robson AJ, Bergstrom CT, Pritchard JK. Risky business: sexual and asexual reproduction in variable environments. J Theor Biol. 1999 Apr 21; 197(4):541-56. PMID: 10196096.
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    150. Bergstrom CT, Pritchard J. Germline bottlenecks and the evolutionary maintenance of mitochondrial genomes. Genetics. 1998 Aug; 149(4):2135-46. PMID: 9691064.
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    151. Pritchard JK, Schaeffer SW. Polymorphism and divergence at a Drosophila pseudogene locus. Genetics. 1997 Sep; 147(1):199-208. PMID: 9286680.
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    152. Pritchard JK, Feldman MW. Statistics for microsatellite variation based on coalescence. Theor Popul Biol. 1996 Dec; 50(3):325-44. PMID: 9000493.
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    153. Pritchard JK, Feldman MW. Genetic data and the african origin of humans. Science. 1996 Nov 29; 274(5292):1548a. PMID: 17816997.
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    154. Pritchard JK, Feldman MW. Genetic data and the African origin of humans. Science. 1996 Nov 29; 274(5292):1548-9. PMID: 8966621.
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    155. Yu RC, Morris JF, Pritchard J, Chu TC. Defective alloantigen-presenting capacity of 'Langerhans cell histiocytosis cells'. Arch Dis Child. 1992 Nov; 67(11):1370-2. PMID: 1471889.
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    156. Purtilo DT, Sakamoto K, Saemundsen AK, Sullivan JL, Synnerholm AC, Anvret M, Pritchard J, Sloper C, Sieff C, Pincott J, Pachman L, Rich K, Cruzi F, Cornet JA, Collins R, Barnes N, Knight J, Sandstedt B, Klein G. Documentation of Epstein-Barr virus infection in immunodeficient patients with life-threatening lymphoproliferative diseases by clinical, virological, and immunopathological studies. Cancer Res. 1981 Nov; 41(11 Pt 1):4226-36. PMID: 6272967.
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