Pritchard Lab Publications

The names of Pritchard lab members at the time of the project are underlined.
[Most recent papers from PubMed]
[Google Scholar summary]

2022

Learning causal representations of single cells via sparse mechanism shift modeling. Lopez R, Tagasovska N, Ra S, Cho K, Pritchard JK, Regev A. arXiv. 2022.2211.03553 [PDF]

On the number of genealogical ancestors tracing to the source groups of an admixed population. Mooney JA, Agranat-Tamir L, Pritchard JK, Rosenberg NA. arXiv. 2022.2210.12306 [PDF]

Integrative analysis of metabolite GWAS illuminates the molecular basis of pleiotropy and genetic correlation. Smith CJ, Sinnott-Armstrong N, Cichońska A, Julkunen H, Fauman E, Würtz P, Pritchard JK Elife. 2022 Sep;11:e79348 [PDF]

RNA editing underlies genetic risk of common inflammatory diseases. Li Q, Gloudemans MJ, Geisinger JM, Fan B, Aguet F, Sun T, Ramaswami G, Li YI, Ma, J, Pritchard JK, Montgomery SB, Li JB Nature. 2022 Aug;608(7923):569-577 [PDF]

Systematic discovery and perturbation of regulatory genes in human T cells reveals the architecture of immune networks. Freimer JW, Shaked O, Naqvi S, Sinnott-Armstrong N, Kathiria A, Garrido CM, Chen AF, Cortez JT, Greenleaf WJ, Pritchard JK, Marson A. Nat Genet. 2022 Aug;54(8):1133-1144 [PDF]

Genetic interactions drive heterogeneity in causal variant effect sizes for gene expression and complex traits. Patel RA, Musharoff SA, Spence JP, Pimentel H, Tcheandjieu C, Mostafavi H, Sinnott-Armstrong, N, Clarke SL, Smith CJ, Pritchard JK Am J Hum Genet. 2022 Jul;109(7):1286-1297 [PDF]

Large-scale differentiable causal discovery of factor graphs. Lopez R, Hütter JC, Pritchard JK, Regev A. arXiv. 2022.2206.07824 [PDF]

Simple scaling laws control the genetic architectures of human complex traits. Simons YB, Mostafavi H, Smith CJ, Pritchard JK, Stella G. bioRxiv, 2022.10.04.509926 [PDF]

Ancient trans-species polymorphism at the major histocompatibility complex in primates. Fortier AL, Pritchard JK bioRxiv, 2022.06.28.497781 [PDF]

Precise modulation of transcription factor levels reveals drivers of dosage sensitivity. Naqvi S, Kim S, Hoskens H, Matthews HS, Spritz RA, Klein OD, Hallgrimsson B, Swigut T, Claes P, Pritchard JK, Wysocka J. bioRxiv, 2022.06.13.495964 [PDF]

Stable population structure in Europe since the Iron Age, despite high mobility. Antonio ML, Weiß CL, Gao Z, Sawyer S, Oberreiter V, Moots HM, Spence JP, [92 others], Pritchard JK bioRxiv, 2022.05.15.491973 [PDF]

Limited overlap of eQTLs and GWAS hits due to systematic differences in discovery. Mostafavi H, Spence JP, Naqvi S, Pritchard JK. bioRxiv, 2022.05.07.491045 [PDF]

Subfunctionalized expression drives evolutionary retention of ribosomal protein paralogs in vertebrates. Xu A, Molinuevo R, Fazzari E, Tom H, Zhang Z, Menedez J, Casey KM, Ruggero D, Hinck L, Pritchard JK, Barna M. bioRxiv, 2022.05.03.490441 [PDF]

Private and sub-family specific mutations of founder haplotypes in the BXD family reveal phenotypic consequences relevant to health and disease. Ashbrook DG, Sasani T, Maksimov M, Grunturkun MH, Ma N, Villani F, Ren Y, Rothschild D, Chen H, Lu L, Colonna V, Dumont B, Harris K, Gymrek M, Pritchard JK, Palmer AA, Williams RW. bioRxiv, 2022.04.21.489063 [PDF]

A flexible modeling and inference framework for estimating variant effect sizes from GWAS summary statistics. Spence JP, Sinnott-Armstrong N, Assimes TL, Pritchard JK. bioRxiv, 2022.04.18.488696 [PDF]

Is competition for cellular resources a driver of complex trait heritability? Simons Y, Naret O, Fellay J, Pritchard JK. bioRxiv, 2022.03.25.485854 [PDF]

A Genetic History of Continuity and Mobility in the Iron Age Central Mediterranean. Moots HM, Antonio M, Sawyer S, Spence JP, [20 others], Pritchard JK, Pinhasi R. bioRxiv, 2022.03.13.483276 [PDF]

A natural mutator allele shapes mutation spectrum variation in mice. Sasani TA, Ashbrook DG, Beichman AC, Lu L, Palmer AA, Williams RW, Pritchard JK, Harris K Nature. 2022 May;605(7910):497-502 [PDF]

2021

Shared heritability of human face and brain shape. Naqvi S, Sleyp Y, Hoskens H, Indencleef K, Spence JP, [9 others], Jonathan K Pritchard, S Sunaert, H Peeters, J Wysocka, and P Claes. Nat Genet. 2021 53(6):830-839 [PDF]

GWAS of three molecular traits highlights core genes and pathways alongside a highly polygenic background. Sinnott-Armstrong N, Naqvi S, Rivas M, Pritchard JK Elife. 2021 10:e58615 [PDF]

A regulatory variant at 3.q21.1 confers an increased pleiotropic risk for hyperglycemia and altered bone mineral density. Sinnott-Armstrong N, Sousa IS, Laber S, Rendina-Ruedy E, Nitter Dankel SE, Ferreira T, Mellgren G, Karasik D, Rivas M, Pritchard JK, [9 others], and Melina Claussnitzer. Cell Metab. 2021 33(3):615-628 [PDF]

Genetics of 35 blood and urine biomarkers in the UK Biobank. Sinnott-Armstrong N, Tanigawa Y, Amar D, Mars N, Benner C, Aguirre M, Venkataraman GR, Wainberg M, Ollila HM, Kiiskinen T, [11 others], JK Pritchard, MJ Daly, and MA Rivas. Nat Genet. 2021 53(2):185-197 [PDF]

2020

Evolutionary Persistence of DNA Methylation for Millions of Years after Ancient Loss of a De Novo Methyltransferase. Catania S, Dumesic PA. Pimentel H, Nasif A, Stoddard C, [9 others], Pritchard JK, and Madhani HD. Cell. 2020 180(2):263-277 [PDF]

Variable prediction accuracy of polygenic scores within an ancestry group. Mostafavi H, Harpak A, Agarwal I, Conley D, Pritchard JK, Przeworski M Elife. 2020 9:e48376. [PDF]

Chromatin accessibility dynamics in a model of human forebrain development. Trevino AE, Sinnott-Armstrong, N., Andersen J, Yoon S, Huber N, Pritchard JK, Chang HY, Greenleaf WJ, Pasca SP Science. 2020 367(6476) [PDF]

2019

Ancient Rome: A genetic crossroads of Europe and the Mediterranean. Antonio ML, Gao Z, Moots HM, Lucci M, Candilio F, Sawyer S, Oberreiter V, Calderon D, Devitofranceschi K, Aikens RC, [26 others], A Coppa A, Pinhasi R, and JK. Pritchard Science. 2019 366(6466):708-714. [PDF]

Landscape of stimulation-responsive chromatin across diverse human immune cells. Calderon D, Nguyen MLT, Mezger A, Kathiria A, Müller F, Nguyen V, Lescano N, Wu, B, Tombetta J, Ribado JV, Knowles DA, Gao Z, Blaeschke F, Parent AV, Burt TD, Anderson MS, Criswell LA, Greenleaf WJ, Marson a, and Pritchard JK . Nat Genet. 2019 51(10):1494-1505 [PDF]

Public discussion affects questions asking at academic conferences. Telis N, Glassberg EC, Pritchard JK, Gunter C Am J Hum Genet. 2019 105(1):189-197 [PDF]

Trans Effects on Gene Expression Can Drive Omnigenic Inheritance. Liu X, Li YI, Pritchard JK Cell. 2019 177(40):1022-1034 [PDF]

Ancient Mammalian and Plant DNA from Late Quaternary Stalagmite Layers at Solkota Cave, Georgia. Stahlschmidt MC, Collin TC, Fernandes DM, Bar-Oz G, Belfer-Cohen A, Gao Z, Jakeli N, Matskevich Z, Meshveliani T, Pritchard JK, McDermott F, and Pinhasi R. Sci Rep. 2019 9(1):6628 [PDF]

Reduced signal for polygenic adaptation of height in UK Biobank. Berg JJ, Harpak A, Sinnott-Armstrong N, Joergensen AM, Mostafavi H, Field Y, Boyle EA, Zhang X, Racimo F, Pritchard JK, Coop G. Elife. 2019 8:e39725 [PDF]

Interpreting polygenic scores, polygenic adaptation, and human phenotypic differences. Rosenberg NA, Edge MD, Pritchard JK, Feldman MW Evol Med Public Health. 2018 2019(1):26-34. [PDF]

Evidence of weak selective constraint on human gene expression. Glassberg EC, Gao Z, Harpak A, Lan X, Pritchard JK Genetics. 2019 211(2):757-772 [PDF]

2018

High-resolution mapping of cancer cell networks using co-functional interactions Boyle EA, Pritchard JK, Greenleaf WJ Molecular Systems Biology, 14(12), 2018. [PDF]

Narcolepsy risk loci are enriched in immune cells and suggest autoimmune modulation of the T cell receptor repertoire Ollila H, Sharon E, Lin L, Sinnott-Armstrong N, Ambati A, Hillary RP, Jolanki O, Faraco J, Einen M, Luo G, et al. bioRxiv 373555, 2018. [PDF]

SciReader: A Cloud-based Recommender System for Biomedical Literature Desai P, Telis N, Lehmann B, Bettinger K, Pritchard JK bioRxiv 333922, 2018. [PDF]

Functional Genetic Variants Revealed by Massively Parallel Precise Genome Editing. Sharon E, Chen SA, Khosla NM, Smith JD, Pritchard JK, Fraser HB. Cell. 2018 175(2):544-557. [PDF]

Post-translational buffering leads to convergent protein expression levels between primates. Wang SH, Hsiao CJ, Khan Z, Pritchard JK Genome Biol. 2018 19(1):83. [PDF]

Determining the genetic basis of anthracycline-cardiotoxicity by molecular response QTL mapping in induced cardiomyocytes. Knowles DA, Burrows CK, Blischak JD, Patterson KM, Serie DJ, Norton N, Ober C, Pritchard JK, Gilad Y. Elife. 2018 7: e33480. [PDF]

Large-Scale Clonal Analysis Resolves Aging of the Mouse Hematopoietic Stem Cell Compartment. Yamamoto R, Wilkinson AC, Ooehara J, Lan X, Lai CY, Pritchard JK, Nakauchi H Cell Stem Cell. 2018 22(4):600-607.e4. [PDF]

Remodeling the Specificity of an Endosomal CORVET Tether Underlies Formation of Regulated Secretory Vesicles in the Ciliate Tetrahymena thermophila. 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 Curr Biol. 2018 28(5):697-710.e13 [PDF]

Annotation-free quantification of RNA splicing using LeafCutter. Li YI, Knowles, DA, Humphrey J, Barbeira AN, Dickinson SP, Im HK, Pritchard, JK Nat Genet. 2018 50(1):151-158. [PDF]

Impact of regulatory variation across human iPSCs and differentiated cells. 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 Genome Res. 2018 28(1):122-131. [PDF]

2017

Frequent nonallelic gene conversion on the human lineage and its effect on the divergence of gene duplicates. Harpak A, Lan, X, Gao, Z, Pritchard, JK PNAS 2017 114(48)12779-12784. [PDF]

Inferring Relevant Cell Types for Complex Traits by Using Single-Cell Gene Expression. Calderon D, Bhaskar A, Knowles, DA, Golan, D, Raj, T, Fu, AO, Pritchard, JK Am J Hum Genet. 2017 101(5):686-699. [PDF]

Quantification of transplant-derived circulating cell-free DNA in absence of a donor genotype. Sharon E, Shi H, Kharbanda S, Koh W, Martin LR, Khush KK, Valantine H, Pritchard JK, De Vlaminck I PLoS Comput Biol. 2017 13(8):e1005629. [PDF]

An Expanded View of Complex Traits: From Polygenic to Omnigenic. Boyle EA, Li YI, Pritchard JK Cell. 2017 169(7):1177-1186. [PDF]

Rapid evolution of the human mutation spectrum. Harris K, Pritchard JK Elife. 2017 6: e24284 [PDF]

Tracing the peopling of the world through genomics. Nielsen RR, Akey JM, Jakobsson M, Pritchard JK, Tishkoff S, Willersley E. Nature. 2017 541(7637):302-310. [PDF]

Batch effects and the effective design of single-cell gene expression studies. Tung PY, Blischak JD, Hsiao CJ, Knowles DA, Burnett JE, Pritchard JK, Gilad Y Sci Rep. 2017 7:39921. [PDF]

2016

Mutation Rate Variation is a Primary Determinant of the Distribution of Allele Frequencies in Humans. Harpak A, Bhaskar A, Pritchard JK PLoS Genet. 2016 12(12):e1006489. [PDF]

A Bibliometric History of the Journal GENETICS. Telis N, Lehmann BV, Feldman MW, Pritchard JK Genetics. 2016 204(4):1337-1342. [PDF]

Detection of human adaptation during the past 2000 years. Field Y, Boyle EA, Telis N, Gao Z, Gaulton KJ, Golan D, Yengo L, Rocheleau G, Froguel P, McCarthy MI, Pritchard JK Science. 2016 354(6313):760-764. [PDF]

Lineage-specific and single-cell chromatin accessibility charts human hematopoiesis and leukemia evolution. Corces MR, Buenrostro JD, Wu B, Greenside PG, Chan SM, Koenig JL, Snyder MP, Pritchard JK, Kundaje A, Greenleaf WJ, Majeti R, Chang HY Nat Genet. 2016 48(10):1193-203. [PDF]

Genetic variation in MHC proteins is associated with T cell receptor expression biases. Sharon E, Sibener LV, Battle A, Fraser HB, Garcia KC, Pritchard JK Nat Genet. 2016 48(9):995-1002 [PDF]

Genome-wide association study of behavioral, physiological and gene expression traits in outbred CFW mice. 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 Nat Genet. 2016 48(8):919-26 [PDF]

Whole Genome Sequencing Identifies a Novel Factor Required for Secretory Granule Maturation in Tetrahymena thermophila. Kontur C, Kumar S, Lan X, Pritchard JK, Turkewitz AP G3 (Bethesda). 2016 6(8):2505-16 [PDF]

Thousands of novel translated open reading frames in humans inferred by ribosome footprint profiling. Raj A, Wang SH, Shim H, Harpak A, Li YI, Engelmann B, Stephens M, Gilad Y, Pritchard JK Elife. 2016 5:e13328. [PDF]

Coregulation of tandem duplicate genes slows evolution of subfunctionalization in mammals. Lan X, Pritchard JK Science. 2016 352(6288):1009-13. [PDF]

RNA splicing is a primary link between genetic variation and disease. Li YI, van de Geijn B, Raj A, Knowles DA, Petti AA, Golan D, Gilad Y, Pritchard JK Science. 2016 352(6285):600-4. [PDF]

Genetic Variation, Not Cell Type of Origin, Underlies the Majority of Identifiable Regulatory Differences in iPSCs. Burrows CK, Banovich NE, Pavlovic BJ, Patterson K, Gallego Romero, Pritchard JK, Gilad Y PLoS Genet. 2016 12(1):e1005793 [PDF]

Abundant contribution of short tandem repeats to gene expression variation in humans. Gymrek M, Willems T, Guilmatre A, Zeng H, Markus B, Georgiev S, Daly MJ, Price AL, Pritchard JK, Sharp AJ, Erlich Y. Nature Genetics. 2016 48(1):22-9. [PDF]

2015

msCentipede: Modeling Heterogeneity across Genomic Sites and Replicates Improves Accuracy in the Inference of Transcription Factor Binding. Raj A, Shim H, Gilad Y, Pritchard JK, Stephens M. PLoS One. 2015 10(9):e0138030. [PDF]

WASP: allele-specific software for robust molecular quantitative trait locus discovery. van de Geijn B, McVicker G, Gilad Y, Pritchard JK. Nature Methods. 2015 12(11):1061-3. [PDF]

The Genotype-Tissue Expression (GTEx) pilot analysis: multitissue gene regulation in humans. GTEx Consortium. Science. 2015 348(6235):648-60. [PDF]

Reprogramming LCLs to iPSCs Results in Recovery of Donor-Specific Gene Expression Signature. Thomas SM, Kagan C, Pavlovic BJ, Burnett J, Patterson K, Pritchard JK, Gilad Y. PLoS Genetics. 2015 11(5):e1005216. [PDF]

Impact of regulatory variation from RNA to protein. Battle A, Khan Z, Wang SH, Mitrano A, Ford MJ, Pritchard JK, Gilad Y. Science. 2015 347(6222):664-7. [PDF]

The genetic and mechanistic basis for variation in gene regulation. Pai AA, Pritchard JK, Gilad Y. PLoS Genetics. 2015 11(1):e1004857. [PDF]

2014

Epigenetic modifications are associated with inter-species gene expression variation in primates. Zhou X, Cain CE, Myrthil M, Lewellen N, Michelini K, Davenport ER, Stephens M, Pritchard JK, Gilad Y. Genome Biology. 2014;15(12):547. [PDF]

Methylation QTLs are associated with coordinated changes in transcription factor binding, histone modifications, and gene expression levels. Banovich NE, Lan X, McVicker G, van de Geijn B, Degner JF, Blischak JD, Roux J, Pritchard JK, Gilad Y. PLoS Genetics 2014 10(9):e1004663. [PDF]

The effect of freeze-thaw cycles on gene expression levels in lymphoblastoid cell lines. Caliskan M, Pritchard JK, Ober C, Gilad Y. PLoS One. 2014 9(9):e107166. [PDF]

fastSTRUCTURE: variational inference of population structure in large SNP data sets. Raj A, Stephens M, Pritchard JK. Genetics. 2014 197(2):573-89. [PDF]

The functional consequences of variation in transcription factor binding. Cusanovich DA, Pavlovic B, Pritchard JK, Gilad Y. PLoS Genetics. 2014 10(3):e1004226. [PDF]

Admixture facilitates genetic adaptations to high altitude in Tibet. Jeong C, Alkorta-Aranburu G, Basnyat B, Neupane M, Witonsky DB, Pritchard JK, Beall CM, Di Rienzo A. Nature Communications. 2014 5:3281. [PDF]

The deleterious mutation load is insensitive to recent population history. Simons YB, Turchin MC, Pritchard JK, Sella G. Nature Genetics. 2014 46(3):220-4. [PDF]

The chromatin architectural proteins HMGD1 and H1 bind reciprocally and have opposite effects on chromatin structure and gene regulation. Nalabothula N, McVicker G, Maiorano J, Martin R, Pritchard JK, Fondufe-Mittendorf YN. BMC Genomics 2014 15:92. [PDF]

Archaic humans: Four makes a party. Birney E, Pritchard JK. Nature. 2014 505(7481):32-4. [PDF]

2013

Identification of genetic variants that affect histone modifications in human cells. McVicker G, van de Geijn B, Degner JF, Cain CE, Banovich NE, Raj A, Lewellen N, Myrthil M, Gilad Y, Pritchard JK. Science 2013 342(6159):747-9. [PDF]

Primate transcript and protein expression levels evolve under compensatory selection pressures. Khan Z, Ford MJ, Cusanovich DA, Mitrano A, Pritchard JK, Gilad Y. Science 2013 342(6162):1100-4. [PDF]

A statistical framework for joint eQTL analysis in multiple tissues. Flutre T, Wen X, Pritchard J, Stephens M. PLoS Genetics. 2013 May;9(5):e1003486. [PDF]

2012

The genetic architecture of adaptations to high altitude in Ethiopia. Alkorta-Aranburu G, Beall CM, Witonsky DB, Gebremedhin A, Pritchard JK, Di Rienzo A. PLoS Genetics. 2012 8:e1003110. [PDF]

Controls of nucleosome positioning in the human genome. Gaffney DJ, McVicker G, Pai AA, Fondufe-Mittendorf YN, Lewellen N, Michelini K, Widom J, Gilad Y, Pritchard JK. PLoS Genetics. 2012 8:e1003036. [PDF]

Inference of population splits and mixtures from genome-wide allele frequency data. Pickrell JK, Pritchard JK. PLoS Genetics. 2012 8:e1002967 [PDF] [TreeMix Software]

The contribution of RNA decay quantitative trait loci to inter-individual variation in steady-state gene expression levels. 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. PLoS Genetics. 2012 Oct;8(10):e1003000. [PDF],

Genomics: ENCODE explained. Ecker JR, Bickmore WA, Barroso I, Pritchard JK, Gilad Y, Segal E. Nature. 2012 89:52-5. [PDF],

DNA sequence-dependent compartmentalization and silencing of chromatin at the nuclear lamina. Zullo JM, Demarco IA, Pique-Regi R, Gaffney DJ, Epstein CB, Spooner CJ, Luperchio TR, Bernstein BE, Pritchard JK, Reddy KL, Singh H. Cell. 2012 149:1474-87. [PDF],

Comment on "Widespread RNA and DNA sequence differences in the human genome". Pickrell JK, Gilad Y, and Pritchard JK. Science 2012 335(6074):1302. [PDF], [Blog Post].

Exon-specific QTLs skew the inferred distribution of expression QTLs detected using gene expression array data. Veyrieras J-B, Gaffney DJ, Pickrell JK, Gilad Y, Stephens M, and Pritchard JK. PLoS One 2012 7(2):e30629. [PDF]

A systematic survey of loss-of-function variants in human protein-coding genes. MacArthur DG, Balasubramanian S, Frankish A, Huang N, Morris J, Walter K, Jostins L, Habegger L, Pickrell JK, <36 authors>, Pritchard JK, Barrett JC, Harrow J, Hurles ME, Gerstein MB, Tyler-Smith C. Science 2012 336(6079):296. [PDF]

DnaseI sensitivity QTLs are a major determinant of human expression variation. 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. Nature. 2012 482:390-4. [PDF]

Dissecting the regulatory architecture of gene expression QTLs. Gaffney DJ, Veyrieras JB, Degner JF, Roger PR, Pai AA, Crawford GE, Stephens M, Gilad Y, Pritchard JK. Genome Biology. 2012 13(1):R7. [PDF]

Comparative RNA sequencing reveals substantial genetic variation in endangered primates. Perry GH, Melsted P, Marioni JC, Wang Y, Bainer R, Pickrell JK, Michelini K, Zehr S, Yoder AD, Stephens M, Pritchard JK, Gilad Y. Genome Research 2012 22(4):602-10. [PDF]

A genome sequence resource for the aye-aye (Daubentonia madagascariensis), a nocturnal lemur from Madagascar. Perry GH, Reeves D, Melsted P, Ratan A, Miller W, Michelini K, Louis EE Jr, Pritchard JK, Mason CE, Gilad Y. Genome Biology Evol. 2011 [PDF]

2011

Whole-genome sequencing data offer insights into human demography. Pritchard JK. Nature Genetics. 2011 43:923-5. [PDF]

Efficient counting of k-mers in DNA sequences using a Bloom filter. Melsted P, Pritchard JK. BMC Bioinformatics. 2011 10;12:333. [PDF]

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

A genome-wide study of DNA methylation patterns and gene expression levels in multiple human and chimpanzee tissues. Pai AA, Bell JT, Marioni JC, Pritchard JK, Gilad Y. PLoS Genetics. 2011 7(2):e1001316. [PDF]

DNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines. Bell JT, Pai AA, Pickrell JK, Gaffney DJ, Pique-Regi R, Degner JF, Gilad Y, Pritchard JK. 2011 Genome Biology. [PDF] [correction]

Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data. Pique-Regi R, Degner JF, Pai AA, Gaffney DJ, Gilad Y, Pritchard JK. 2011 Genome Research. 21:447-455. [PDF] [data/software]

Adaptations to climate-mediated selective pressures in humans. Hancock AM, Witonsky DB, Alkorta-Aranburu G, Beall CM, Gebremedhin A, Sukernik R, Utermann G, Pritchard JK, Coop G, Di Rienzo A. PLoS Genetics. 2011 7(4):e1001375. [PDF]

Haplotype variation and genotype imputation in African populations. Huang L, Jakobsson M, Pemberton TJ, Ibrahim M, Nyambo T, Omar S, Pritchard JK, Tishkoff SA, Rosenberg NA. Genetic Epidemiology. 2011 35(8):766-80. [PDF]

2010

Noisy splicing drives mRNA isoform diversity in human cells. Pickrell JK, Pai AA, Gilad Y, Pritchard JK. 2010 PLoS Genetics 6:e1001236. [PDF] [data/software]

Understanding mechanisms underlying human gene expression variation with RNA sequencing. Pickrell JK, Marioni JC, Pai AA, Degner JF, Engelhardt BE, Nkadori E, Veyrieras JB, Stephens M, Gilad Y, Pritchard JK. 2010 Nature. 464:768-72. [PDF] [data/software]

Adaptation - not by sweeps alone. Pritchard JK, Di Rienzo A. 2010 Nature Reviews Genetics 11:665-7. [PDF]

The genetics of human adaptation: hard sweeps, soft sweeps, and polygenic adaptation. Pritchard JK, Pickrell JK, Coop G. 2010 Current Biology. 20:R208-15. [PDF]

How we are evolving. Pritchard JK 2010 Scientific American. 301(10):41-47. [link]

Using environmental correlations to identify loci underlying local adaptation. Coop G, Witonsky D, Di Rienzo A, Pritchard JK. 2010 Genetics. 185:1411-23. [PDF]

A rod cell marker of nocturnal ancestry. Perry GH, Pickrell JK. 2010 J Hum Evol. 58:207-10. [PDF]

2009

Characterizing natural variation using next-generation sequencing technologies. Gilad Y, Pritchard JK, Thornton K. 2009 Trends Genet. 25:463-71. [PDF]

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

Inferring weak population structure with the assistance of sample group information. Melissa J. Hubisz, Daniel Falush, Matthew Stephens and Pritchard JK. 2009 Molecular Ecology Resources. 9:1322-1332 [PDF]

The role of geography in human adaptation. Coop G, Pickrell JK, Novembre J, Kudaravalli S, Li J, Absher D, Myers RM, Cavalli-Sforza LL, Feldman MW, Pritchard JK. 2009 PLoS Genetics 5:e1000500. [PDF]

An approximate likelihood for genetic data under a model with recombination and population splitting. Davison D, Pritchard JK, Coop G. 2009. Theor Popul Biol. 75:331-45. [PDF]

Signals of recent positive selection in a worldwide sample of human populations. Pickrell JK, Coop G, Novembre J, Kudaravalli S, Li JZ, Absher D, Srinivasan BS, Barsh GS, Myers RM, Feldman MW, Pritchard JK. Genome Res. 2009 May;19(5):826-37. Epub 2009 Mar 23. [PDF]

Haplotypic background of a private allele at high frequency in the Americas. 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. 2009 Mol Biol Evol. 26:995-1016. [PDF]

Gene Expression Levels Are a Target of Recent Natural Selection in the Human Genome. Sridhar Kudaravalli, Jean-Baptiste Veyrieras, Barbara E. Stranger, Emmanouil T. Dermitzakis, and Jonathan K. Pritchard. 2009 Molecular Biology and Evolution 26:649-658. [PDF]

2008

High-Resolution Mapping of Expression-QTLs Yields Insight into Human Gene Regulation. Jean-Baptiste Veyrieras, Sridhar Kudaravalli, Su Yeon Kim, Emmanouil T. Dermitzakis, Yoav Gilad, Matthew Stephens, Jonathan K. Pritchard. 2008 PLoS Genetics Vol 4. (10):1-15. [PDF]

Adaptations to Climate in Candidate Genes for Common Metabolic Disorders. Angela M. Hancock, David B. Witonsky, Adam S. Gordon, Gidon Eshel Jonathan K. Pritchard, Graham Coop, Anna Di Rienzo. 2008 PLoS Genetics Vol 4. (2):1-13. [PDF]

Revealing the architecture of gene regulation: the promise of eQTL studies. Gilad Y., Rifkin SA, Pritchard JK. 2008 Trends Genet Vol.24 No.8:408-413. [PDF]

Using population mixtures to optimize the utility of genomic databases: linkage disequilibrium and association study design in India. Pemberton TJ, Jakobsson M, Conrad DF, Coop G, Wall JD, Pritchard JK, Patel PI, Rosenberg NA. 2008 Ann Hum Genet(72):535-546. [PDF]

High-resolution mapping of crossovers reveals extensive variation in fine-scale recombination patterns among humans. 2008 Science. Coop G, Wen X,Ober C, Pritchard JK, Przeworski M. 2008 Science(319):1395-1398. [PDF]

The timing of selection at the human FOXP2 gene. Coop G, Bullaughey K, Luca F, Przeworski M. 2008 Mol Biol Evol 25(7):1257-1259. [PDF]

No effect of recombination on the efficacy of natural selection in primates. Bullaughey K, Przeworski M, Coop G. 2008 Genome Res(18):544-554. [PDF]

2007

The population genetics of structual variation. Conrad DF, Hurles ME. 2007 Nat Genet(39):S30-S35. [PDF]

Adaptive Evolution of Conserved Noncoding Elements in Mammals. S.Y. Kim and J.K. Pritchard. 2007 PLoS Genet. 3(9):e147:1572-1586. [PDF]

Inference of population structure using multilocus genotype data: dominant markers and null alleles. D. Falush, M. Stephens and J. K. Pritchard. 2007 Molecular Ecology(?):895-908. [PDF]

Overcoming the Winner's Curse: Estimating Penetrance Parameters from Case-Control Data. S. Zöllner and J. K. Pritchard. 2007 Am J Hum Genet. 80(4):605-615. [PDF]

Adaptive drool in the gene pool. J. Novembre, J.K. Pritchard and G. Coop 2007 Nat Genet 39(10):1188-1190. [News & Views on article by Perry et al.] [PDF]

Convergent adaptation of human lactase persistence in Africa and Europe. S. A. Tishkoff, F. A. Reed , A. Ranciaro, B. F. Voight, C. C. Babbitt, J. S. Silverman, K. Powell, H. M. Mortensen, J. B. Hirbo, M. Osman, M. Ibrahim, S. A. Omar, G. Lema, T. B. Nyambo, J. Ghori, S. Bumpstead, J. K. Pritchard, G. A. Wray and P. Deloukas. 2007 Nat Genet. 39(1):31-40 [PDF]

Live Hot, Die Young: Transmission Distortion in Recombination Hotspots. G. Coop and S. R. Myers. 2007 PLoS Genet. 3(3):e35:1-10. [PDF]

An evolutionary view of human recombination. G. Coop and M. Przeworski. 2007 Nat Rev Genet. 8(1):23-34 [PDF]

2006

Sequencing and Analysis of Neanderthal Genomic DNA. JP Noonan, G Coop, S Kudaravalli, D Smith, J Krause, J Alessi, F Chen, D Platt, S Paabo, JK Pritchard, EM Rubin. 2006. Science. 314:1113-1118. [PDF]

DF Conrad, M Jakobsson, G Coop, X Wen, JD Wall, NA Rosenberg, JK Pritchard. 2006. A worldwide survey of haplotype variation and linkage disequilibrium in the human genome. Nature Genetics. 38:1251-60. [PDF]

A Map of Recent Positive Selection in the Human Genome. B. F. Voight, S. Kudaravalli, X. Wen and J. K. Pritchard   2006. PLoS Biol 4(3): e72:446-458. [PDF], [Haplotter]

A high-resolution survey of deletion polymorphism in the human genome. D. F. Conrad, T D. Andrews, N. P. Carter, M. E. Hurles and J. K. Pritchard   2006. Nature Genetics., 38:75-81. [PDF]

Clonal origin and evolution of a transmissible cancer. C. Murgia, J. K. Pritchard, S.Y. Kim, A. Fassati, R.A. Weiss. Cell. 2006 126:477-87. [PDF]

The effects of genotype-dependent recombination, and transmission asymmetry, on linkage disequilibrium. G. Hellenthal, J. K. Pritchard and M. Stephens   2006. Genetics, 172(3):2001-5. [PDF]

2005

Interrogating multiple aspects of variation in a full resequencing data set to infer human population size changes. B. F. Voight, A. M. Adams, L. A. Frisse, Y. Qian, R. R. Hudson and A. Di Rienzo.   PNAS, 102(51):18508-13. [PDF]

Can a genome change its (hot)spots? G. Coop   2005. Trends in Ecology and Evolution, 20(12):643-645. [PDF]

The signature of positive selection on standing genetic variation. M. Przeworski, G. Coop and J. D. Wall   2005. Evolution Int J Org Evolution, 59(11):2312-23. [PDF]

Clines, clusters, and the effect of study design on the inference of human population structure. N. A. Rosenberg, S. Mahajan, S. Ramachandran, C. Zhao, J. K. Pritchard and M. W. Feldman   2005. PLoS Genetics,1(6):e70 [PDF]

Confounding from Cryptic Relatedness in Case-Control Association Studies. B. F. Voight and J. K. Pritchard  2005. PLoS Genetics,1(3):e32 p1-10 .[PDF]

Association mapping and fine mapping with TreeLD. S. Zöllner, X. Wen and J. K. Pritchard  2005 Bioinfomatics,21(14):3168-70 [PDF]

Coalescent-based association mapping and fine mapping of complex trait loci S. Zöllner and J. K. Pritchard  2005. Genetics,169(2):1071-92 [PDF]

2004

Statistical Tests for Admixture Mapping with Case-Control and Cases-Only Data. G.Montana and J. K. Pritchard  2004. Am J. Hum Genet.,75:771-789 [PDF]

Evidence for Extensive Transmission Distortion in the Human Genome. S. Zöllner, X. Wen, NA Hanchard, MA Herbert, C. Ober, and J.K. Pritchard 2004. Am J. Hum Genet., 74:62-72 [PDF]

2003

Comparative Linkage-Disequilibrium Analysis of the Beta-Globin Hotspot in Primates. J.D. Wall, L.A. Frisse, RR Hudson, and A Di Rienzo 2003. Am J. Hum. Genet., 73:1330-1340. [PDF]

Informativeness of Genetic Markers for Inference of Ancestry.  N.A. Rosenberg, L.M. Li, R. Ward, and J. K. Pritchard  2003. Am. J. Hum. Genet., 73:1402-1422 [PDF]

Inference of population structure using multilocus genotype data: Linked loci and correlated allele frequencies.  D. Falush, M. Stephens and J.K. Pritchard. 2003. Genetics, 164: 1567-1587. [PDF]

Assessing the performance of the haplotype block model of linkage disequilibrium. J.D. Wall and J.K. Pritchard. 2003. Am J. Hum. Genet., 73: 502-516.[PDF]

Haplotype blocks and linkage disequilibrium in the human genome. J.D. Wall and J.K. Pritchard. 2003. Nature Reviews Genetics, 4: 587-597. [PDF]

Selection on human genes as revealed by comparisons to chimpanzee cDNA.  Hellmann I, Zöllner S, Enard W, Ebersberger I, Nickel B, Paabo S. 2003. Genome Res. 13:831-7. [PDF]

Traces of human migrations in Helicobacter pylori populations. D. Falush, T. Wirth, B. Linz, J.K. Pritchard and 14 others, 2003.  Science, 299: 1582-1585. [PDF]

Estimating ancestral population sizes and divergence times. J.D. Wall, 2003 Genetics  63:395-404. [PDF]

2002

The genetic structure of human populations.  N.A. Rosenberg, J.K. Pritchard, J.L. Weber, H.M. Cann, K.K. Kidd, L.A. Zhivotovsky and M.W. Feldman, 2002. Science, 298: 2381-2385. (and technical comment, 2003) [PDF]

The allelic architecture of human disease genes: common disease--common variant--or not?  J.K. Pritchard and N.J. Cox, 2002.   Human Molecular Genetics, 11:2417-2423 [PDF]

Signatures of domain shuffling in the human genome.  H. Kaessmann, S. Zöllner, A. Nekrutenko A, W.H. Li, 2003. Genome Research 12:1642-50. [PDF]

2001 

Case-control studies of association in structured or admixed populations. J.K. Pritchard and P. Donnelly, 2001. Theor. Pop. Biol. 60:227-237 [Abstract] [PDF]

Deconstructing maize population structure. J.K. Pritchard, 2001. Nature Genetics 28: 203-204 (N & V for article by Thornsberry et al) [PDF]

Linkage disequilibrium in humans: models and data. J.K. Pritchard and M. Przeworski, 2001. Am. J. Hum. Genet. 69:1-14 [Abstract] [PDF]

Are rare variants responsible for susceptibility to complex diseases? J.K. Pritchard, 2001. Am. J. Hum. Genet. 69:124-137 [Abstract] [PDF]

Genetic diversity and introgression in the Scottish wildcat. M.A. Beaumont, E.M. Barratt, D. Gottelli, A.C. Kitchener, M.J. Daniels, J.K. Pritchard & M.W. Bruford, 2001. Molec. Ecol. 10:319-336. [Abstract], [PDF]

Distinctive genetic signatures in the Libyan Jews. N. A. Rosenberg, E. Woolf, J. K. Pritchard, T. Schaap, D. Gefel, I. Shpirer, U. Lavi, B. Bonne'-Tamir, J. Hillel, and M.W. Feldman, 2001. PNAS 98:858-863. [Abstract], [PDF]

2000 

Association mapping in structured populations. J.K. Pritchard, M. Stephens, N.A. Rosenberg and P. Donnelly, 2000. Am J. Hum Genet. 67:170-181. [Abstract], [PDF], [Software]

Inference of population structure using multilocus genotype data. J.K. Pritchard, M. Stephens and P. J. Donnelly, 2000. Genetics 155: 945-959. [Abstract], [PDF], [Software]. 

Recent common ancestry of human Y chromsomes: Evidence from DNA sequence data. R. Thompson, J.K. Pritchard, P. Shen, P.J. Oefner and M.W. Feldman, 2000. PNAS 97:7360-7365. [Abstract]. [PDF], 

1999. 

Use of unlinked genetic markers to detect population stratification in association studies. JK Pritchard and NA Rosenberg 1999. Am. J. of Hum. Gen. 65: 220-228. [Abstract], [PDF]

Population growth of human Y chromosomes: a study of Y chromosome microsatellites. JK Pritchard, MT Seielstad, A Perez-Lezaun and MW Feldman 1999. Mol. Biol. Evol., 16:1791-1798. [Abstract], [PDF], [Data]

Risky Business: sex and selfing in an unpredictable world. AJ Robson, CT Bergstrom and JK Pritchard 1999. J. Theor. Biol. 197: 541-556. [Abstract], [PDF]

Mutation and migration in models of microsatellite evolution. MW Feldman, J Kumm, and JK Pritchard 1999. In ``Microsatellites: Evolution and Applications'', DG Goldstein and C Schloetterer, eds., pp 98-115. Oxford University Press, Oxford. [Abstract], [PDF]

1998 

Germline bottlenecks and the evolutionary maintenance of mitochondrial genomes. CT Bergstrom and JK Pritchard 1998. Genetics 149: 2135-2146. [Abstract], [PDF]

A test for heterogeneity of microsatellite variation. JK Pritchard and MW Feldman 1998. In ``Proceedings of the Trinational Workshop on Molecular Evolution", M. K. Uyenoyama and A. von Haeseler, eds. pp. 47-56. Duke University Publications Group, Durham, NC. [Abstract], [PDF]

1997 

Polymorphism and divergence at a Drosophila melanogaster pseudogene locus. JK Pritchard and SW Schaeffer 1997. Genetics 147: 199-208. [Abstract], [PDF]

1996

Statistics for microsatellite variation based on coalescence. JK Pritchard and MW Feldman 1996. Theor. Pop. Biol. 50: 325-344. [Abstract], [PDF]

Genetic data and the African origin of modern humans. JK Pritchard and MW Feldman 1996. Science 274: 1548. [Synopsis]

1994

Mathematical models of running. WG Pritchard and JK Pritchard 1994. American Scientist 82: 546-553. [Synopsis]