Alkes Price's Faculty Website

Publications

2024

    • Kim SS, Truong B*, Jagadeesh K*, KK Dey*, Shen AZ, Raychaudhuri S, Manolis K, Price AL. Leveraging single-cell ATAC-seq and RNA-seq to identify disease-critical fetal and adult brain cell types. Nat Commun. Epub January 17 2024. PMCID in progress.

2023

    • Amariuta T, Siewert-Rocks K, Price AL. Modeling tissue co-regulation estimates tissue-specific contributions to disease. Nat Genet. 2023 Sep;55(9):1503-1511.  PMCID PMC10904330
    • Jiang X, Zhang MJ*, Zhang Y*, Durvasula A*, Inouye M, Holmes C, Price AL**, McVean G**. Age-dependent topic modeling of comorbidities in UK Biobank identifies disease subtypes with differential genetic risk. Nat Genet. 2023 Oct; 55:1854-1865. PMCID 10632146.
    • Gupta A, Weinand K, Nathan A, Sakaue S, Zhang MJ … Donlin L, Wei K, Price AL, Amariuta T, Raychaudhuri S. Dynamic regulatory elements in single-cell multimodal data implicate key immune cell states enriched for autoimmune disease heritability. Nat Genet. 2023 Nov; 55:2200-2210. PMCID 10787644.

2022

    • Siewert-Rocks K, Kim SS, Yao DW, Shi H, Price AL. Leveraging gene co-regulation to identify gene sets enriched for disease heritability. Am J Hum Genet. 2022 Feb;109(3):393-404. PMCID: 8948163.
    • Weissbrod O, Kanai M, Shi H, Gazal S, Peyrot WJ, Khera AV, Okada Y, Martin AR, Finucane HK, Price AL. Leveraging fine-mapping and multipopulation training data to improve cross-population polygenic risk scores. Nat Genet. 2022 Apr; 54(4):450-458. PMCID: 9009299 .
    • Gazal S, Weissbrod O, Hormozdiari F, Dey K, Nasser J, Jagadeesh K, Weiner D, Shi H, Fulco C, O’Connor L, Pasaniuc B, Engreitz J, Price AL. Combining SNP-to-gene linking strategies to pinpoint disease genes and assess disease omnigenicity. Nat Genet. 2022 Jun 6:450-458. PMCID: 9894581.
    • Dey KK, Gazal S, van de Geijn B, Kim SS, Nasser J, Engreitz J, Price AL. SNP-to-gene linking strategies reveal contributions of enhancer-related and candidate master-regulator genes to autoimmune disease. Cell Genom. 2022 Jul 13;2(7):100145. PMCID: 9306342 .
    • Hujoel MLA, Loh PR, Neale BM, Price AL. Incorporating family history of disease improves polygenic risk scores in diverse populations. Cell Genom. 2022 Jul 13;2(7)100152. PMCID: 9351615.
    • Nathan A, Asgari S, Ishigaki K, Valencia C, Amariuta T, Luo Y…Suliman S, Price AL, Lecca L, Murray MB, Moody DB, Raychaudhuri S. Single-cell eQTL models reveal dynamic T cell state dependence of disease loci. Nature. 2022 Jun; 606(7912):120-128. PMCID: PMC9842455.
    • Zhang MJ*, Hou K*, Dey KK, Sakaue S, Jagadeesh KA, Weinand K, Taychameekiatchai A, Rao P, Pisco AO, Zou J, Wang B, Gandal M, Raychaudhuri S, Pasaniuc B**, Price AL**. Polygenic enrichment distinguishes disease associations of individual cells in single-cell RNA-seq data. Nat Genet. 2022 Oct;54(10):1572-1580. PMCID: 9891382.
    • Jagadeesh KA*, Dey KK*, Montoro DT, Mohan R, Gazal S, Engreitz JM, Xavier RJ, Price AL**, Regev A**. Identifying disease-critical cell types and cellular processes by integrating single-cell RNA-sequencing and human genetics. Nat Genet. 2022 Oct;54(10):1479-1492. PMCID: PMC9910198.

2021

    • Peyrot WJ, Price AL. Identifying loci with different allele frequencies among cases of eight psychiatric disorders using CC-GWAS. Nat Genet. 2021 April;53(4):445-454. PMCID: 8038973.
    • Shi H, Gazal S, Kanai M, Koch EM, Schoech AP, Siewert KM, …, Amariuta T, Huang H, Okada Y, Raychaudhuri S, Sunyaev SR, Price AL. Population-specific causal disease effect sizes in functionally important regions impacted by selection. Nat Commun. 2021 February 17;12(1):1098. PMCID: 7889654.
    • Nasser J, Bergman DT, Fulco CP, Guckelberger P, Doughty BR, Patwardhan TA, …, Price AL, …, Daly MJ, Huang H, Finucane HK, Hacohen N, Lander ES, Engreitz JM. Genome-wide enhancer maps link risk variants to disease genes. Nature. 2021 May;593(7858):238-243. PMCID:9153265.
    • Delorey TM*, Ziegler CGK*, Heimberg G*, Normand R*, Yang Y*, Segerstolpe A*, Abbondanza D*, Fleming SJ*, Subramanian A*, Montoro DT*, Jagadeesh KA*, Dey KK*, …, Price AL, …, Porter CBM, Li B, Shalek AK, Villani AC, Rozenblatt-Rosen O, Regev A. COVID-19 tissue atlases reveal SARS-CoV-2 pathology and cellular targets. Nature. 2021 April 29;595(7865): 1-8. PMCID:8919505
    • Luo Y, Li X, Wang X, Gazal S, Mercader JP, 23 and Me Research Team, …, Neale BM, Florez JC, Auton A, Price AL, Finucane HK, Raychaudhuri S. Estimating heritability and its enrichment in tissue-specific gene sets in admixed populations. Hum. Mol. Genet. 2021 May 13;30(16): 1521-1534. PMCID: 8330913
    • Márquez-Luna C, Gazal S, Loh PR, Kim SS, Furlotte N, Auton A, & Price AL. Incorporating functional priors improves polygenic prediction accuracy in UK Biobank and 23andMe data sets. Nat. Commun. 2021 October;12(1), 1-11. PMCID: 8523709.

2020

    • Hujoel MLA, Gazal S, Loh PR, Patterson N, Price AL. Liability threshold modeling of case-control status and family history of disease increases association power. Nat Genet. 2020 May;52(5):541-547. PMCID: 7210076
    • van de Geijn B, Finucane H, Gazal S, Hormozdiari F, Amariuta T, Liu X, Gusev A, Loh PR, Reshef Y, Kichaev G, Raychauduri S, Price AL. Annotations capturing cell-type-specific TF binding explain a large fraction of disease heritability. Hum Mol Genet. 2020 Apr 1;29(7):1057-1067. PMCID: 7206853
    • Yao DW, O’Connor LJ, Price AL, Gusev A. Quantifying genetic effects on disease mediated by assayed gene expression levels. Nat Genet. 2020 Jun;52(6):626-633. PMCID: 7276299
    • Liu X, Mefford JA, Dahl A, He Y, Subramaniam M, Battle A, Price AL, Zaitlen N. GBAT: a gene-based association test for robust detection of trans-gene regulation. Genome Biol. 2020 Aug 24;21(1):211. PMCID: 7444084
    • Dey KK, van de Geijn B, Kim SS, Hormozdiari F, Kelley DR, Price AL. Evaluating the informativeness of deep learning annotations for human complex diseases. Nat Commun. 2020 Sep 17;11(1):4703. PMCID: 7499261
    • Weissbrod O, Hormozdiari F, Benner C, Cui R, Ulirsch J, Gazal S, Schoech AP, van de Geijn B, Reshef Y, Marquez-Luna C, O’Connor L, Pirinen M, Finucane HK, Price AL. Functionally informed fine-mapping and polygenic localization of complex trait heritability. Nat Genet. 2020 Dec;52(12):1355-1363. PMCID: 7710571
    • Kim SS, Dey KK, Marquez-Luna C, Gazal S, Price AL. Improving the informativeness of Mendelian disease-derived pathogenicity scores for common disease. Nat Commun. 2020 Dec 7;11(1):6258. PMCID: 7721881
    • Amariuta T, Ishigaki K, Sugishita H, Ohta T, Koido M, Dey KK, Matsuda K, Murakami Y, Price AL, Kawakami E, Terao C, Raychaudhuri S. Improving the trans-ancestry portability of poygenic risk scores by prioritizing variants in predicted cell-type-specific regulatory elements. Nat Genet. 2020 Dec;52(12):1346-1354. PMCID: 8049522.

2019

    • Kichaev G, Bhatia G, Loh PR, Gazal S, Burch K, Freund MK, Schoech A, Pasaniuc B**, Price AL**. (2019). Leveraging Polygenic Functional Enrichment to Improve GWAS Power. Am J Hum Genet. 2019 Jan 3;104(1):65-75. PMCID: 6323418
    • Galinsky KJ, Reshef YA, Finucane HK, Loh PR, Zaitlen N, Patterson NJ, Brown BC, Price AL. (2019). Estimating cross-population genetic correlations of causal effect sizes. Genet Epidemiol 43, 180-188. PMCID: 6375794
    • Pollack S, Igo RP, Jr., Jensen RA, Christiansen M, Li X, Cheng CY,… Klein BEK, Klein R, Rotter JI, Iyengar SK, Price A**, Sobrin L**. (2019). Multiethnic Genome-wide Association Study of Diabetic Retinopathy using Liability Threshold Modeling of Duration of Diabetes and Glycemic Control. Diabetes 68, 441-456. PMCID: 6341299
    • Schoech AP, Jordan DM, Loh PR, Gazal S, O’Connor LJ, Balick DJ, Palamara PF, Finucane HK, Sunyaev SR, Price AL. (2019). Quantification of frequency-dependent genetic architectures in 25 UK Biobank traits reveals action of negative selection. Nat Commun 10, 1-10. PMCID: 6377669
    • Jiang X, Finucane HK, Schumacher FR, Schmit SL, Tyrer JP, Han Y…Pharoah PDP, Price AL, Pasaniuc B, Amos CI, Kraft P, Lindstrom S. (2019). Shared heritability and functional enrichment across six solid cancers. Nat Commun 10, 1-23. PMCID: 6347624
    • Hujoel MLA, Gazal S, Hormozdiari F, van de Geijn B, Price AL. (2019). Disease Heritability Enrichment of Regulatory Elements Is Concentrated in Elements with Ancient Sequence Age and Conserved Function across Species. Am J Hum Genet. 2019 Apr 4;104(4):611-624. PMCID: 6451699
    • Kim SS, Dai C, Hormozdiari F, van de Geijn B, Gazal S, Park Y, O’Connor L, Amariuta, Loh PR, Finucane H, Raychaudhuri S, Price AL. (2019). Genes with High Network Connectivity Are Enriched for Disease Heritability. Am J Hum Genet. 2019 May 2;104(5):896-913. PMCID: 6506868
    • Amariuta T, Luo Y, Gazal S, Davenport EE, van de Geijn B, Ishigaki K, Westra HJ, Teslovich N, Okada Y, Yamamoto K, Price AL, Raychaudhuri S. (2019). IMPACT: Genomic Annotation of Cell-State-Specific Regulatory Elements Inferred from the Epigenome of Bound Transcription Factors. Am J Hum Genet. 2019 May 2;104(5):879-895. PMCID: 6506796
    • Gazal S, Marquez-Luna C, Finucane HK, Price AL (2019). Reconciling S-LDSC and LDAK functional enrichment estimates. Nat Genet 51, 1202-1204. PMCID: 7006477
    • O’Connor LJ, Schoech AP, Hormozdiari F, Gazal S, Patterson N, Price AL (2019). Extreme polygenicity of complex traits is explained by negative selection. Am J Hum Genet. 2019 Sep 5;105(3):456-476. PMCID: 6732528
    • Hormozdiari F, van de Geijn B, Nasser J, Weissbrod O, Gazal S, Ju CJT, O’Connor L, Hujoel MLA, Engreitz J, Hormozdiari F, Price AL (2019). Functional disease architectures reveal unique biological role of transposable elements. Nat Commun. Sep 6;10(1):1-8 . PMCID: 6731302

2018

    • Gusev A, Mancuso N, Won H, Kousi M, Finucane HK, Reshef Y,…Crawford GE, Geschwind DH, Katsanis N, Sullivan PF, Pasaniuc B, Price AL. (2018). Transcriptome-wide association study of schizophrenia and chromatin activity yields mechanistic disease insights. Nat Genet 50, 538-548. PMCID: 5942893
    • Finucane HK, Reshef Y, Anttila V, Slowikowski K, Gusev A, Byrnes A,…Buenrostro JD, Bernstein BE, Raychaudhuri S, McCarroll S, Neale BM, Price AL. (2018). Heritability enrichment of specifically expressed genes identifies disease-relevant tissues and cell types. Nat Genet 50, 621-629. PMCID: 5896795
    • Kaplanis J, Gordon A, Shor T, Weissbrod O, Geiger D, Wahl M,…Sheikh M, Gymrek M, Bhatia G, MacArthur DG, Price AL, Erlich Y. (2018). Quantitative analysis of population-scale family trees with millions of relatives. Science Apr 13; 360(6385):171-175. PMCID: 6593158
    • Loh, PR, Kichaev G, Gazal S, Schoech AP, Price AL. (2018). Mixed-model association for biobank-scale datasets. Nat Genet 50, 906-908. PMCID: 6309610
    • Brainstorm Consortium, Anttila V, Bulik-Sullivan B, Finucane H, Walters RK, Bras J, Duncan L…Price A…Palotie A, Smoller JW, Sullivan P, Rosand J, Corvin A, Neale BM. (2018). Analysis of shared heritability in common disorders of the brain. Science 360. PMCID: 6097237
    • Hormozdiari F, Gazal S, van de Geijn B, Finucane HK, Ju CJ, Loh PR, Schoech A, Reshef Y, Liu X, O’Connor L, Gusev A, Eskin E, Price AL. (2018). Leveraging molecular quantitative trait loci to understand the genetic architecture of diseases and complex traits. Nat Genet 50, 1041-1047. PMCID: 6030458
    • Loh PR*, Genovese G*, Handsaker RE, Finucane HK, Reshef YA, Palamara PF, Birmann BM, Talkowski ME, Bakhoum SF, McCarroll SA**, Price AL**. (2018). Insights into clonal haematopoiesis from 8,342 mosaic chromosomal alterations. Nature 559, 350-355. PMCID: 6054542
    • Palamara P, Terhorst J, Song YS, Price AL. (2018). High-throughput inference of pairwise coalescence times identifies signals of selection and enriched disease heritability. Nat Genet 50, 1311-1317. PMCID: 6145075
    • Reshef Y, Finucane H, Kelley D, Gusev A, Kotlair D, Ulirsch J…Gazal S, Palamara P, Pinello L, Patterson N, Adams RP, Price AL. (2018). Detecting genome-wide directional effects of transcription factor binding on polygenic disease risk. Nat Genet 50, 1483-1493. PMCID: 6202062
    • Gazal S, Loh PR, Finucane HK, Ganna A, Schoech A, Sunyaev S, Price AL. (2018). Functional architecture of low-frequency variants highlights strength of negative selection across coding and non-coding annotations. Nat Genet 50, 1600-1607. PMCID: 6236676
    • O’Connor L, Price AL. (2018). Distinguishing genetic correlation from causation across 52 diseases and complex traits. Nat Genet 50, 1728-1734. PMCID: 6684375.
    • Meng W, Shah KP, Pollack S, Toppila I, Hebert HL, McCarthy MI,… Price AL, Burdon KP, Groop PH, Sandholm N, Grassi MA, Sobrin L, Palmer CNA. (2018). A genome-wide association study suggests new evidence for an association of the NADPH Oxidase 4 (NOX4) gene with severe diabetic retinopathy in type 2 diabetes. Acta ophthalmologica 96, e811-e819. PMCID: 6263819

2017

    • Hayeck TJ, Loh PR, Pollack S, Gusev A, Patterson N, Zaitlen NA, Price AL. (2017). Mixed Model Association with Family-Biased Case-Control Ascertainment. Am J Hum Genet. 2017 Jan 5;100(1):31-39. PMCID: 5223022
    • Zheng J, Mesut Erzurumluoglu A, Elsworth BL, Howe L, Haycock PC, …Price AL, …Anttila V, Paternoster L,Gaunt TR, Evans DM, Neale BM. (2017). LD Hub: a centralized database and web interface to perform LD score regression that maximizes the potential of summary level GWAS data for SNP heritability and genetic correlation analysis. Bioinformatics. 2017 Jan 15;33(2):272-279. PMCID: 5542030
    • Pasaniuc B, Price AL. (2017). Dissecting the genetics of complex traits using summary association statistics. Nat Rev Genet. 2017 Feb;18(2):117-127. PMCID:5449190
    • Liu X, Finucane HK, Gusev A, Bhatia G, Gazal S, O’Connor L, Bulik-Sullivan B, Wright FA, Sullivan PF, Neale BM, Price AL. (2017). Functional architectures of local and distal regulation of gene expression in multiple human tissues. Am J Hum Genet. 2017 Apr 6;100(4):605-616. PMCID: 5384099
    • Day FR, Thompson DJ, Helgason H, Chasman DI, Finucane H,…Price AL,…Murray A, Murabito JM, Stefansson K, Ong KK, Perry JRB. (2017). Genomic analyses identify hundreds of variants associated with age at menarche and support a role for puberty timing in cancer risk. Nat Genet (2017) 49, 834-841. PMCID: 4661791
    • Lindstrom S, Finucane H, Bulik-Sullivan B, Schumacher FR, Amos CI,…Haiman CA, Hunter DJ, Neale B, Price AL, Kraft P. (2017). Quantifying the Genetic Correlation between Multiple Cancer Types. Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology 26, 1427-1435. PMCID:5592139
    • Gazal S, Finucane HK, Furlotte NA, Loh P-R, Palamara PF, Liu X, Schoech A, Bulik-Sullivan B, Neale BM, Gusev A, Price AL. (2017). Linkage disequilibrium-dependent architecture of human complex traits shows action of negative selection. Nat Genet 49, 1421-1427. (2017)  PMCID: 6133304
    • Marquez-Luna C, Loh PR, Price AL. (2017). Multiethnic polygenic risk scores improve risk prediction in diverse populations. Genetic epidemiology 41, 811-823. PMCID: 5726434
    • Sobrin L, Chong YH, Fan Q, Gan A, Stanwyck LK, Kaidonis G,…Price AL,…Rotter JI, Tsai FJ, Hanis CL, Burdon KP, Wong TY, Cheng CY. (2017). Genetically Determined Plasma Lipid Levels and Risk of Diabetic Retinopathy: A Mendelian Randomization Study. Diabetes 66, 3130-3141. PMCID:5697951

    2016

    • Galinsky KJ, Bhatia G, Loh PR, Georgiev S, Mukherjee S, Patterson NJ, Price AL. Fast Principal-Component Analysis Reveals Convergent Evolution of ADH1B in Europe and East Asia. Am J Hum Genet. 2016 Mar 3;98(3):456-72. PMCID: 4827102.
    • Gusev A, Ko A, Shi H, Bhatia G, Chung W, Penninx BW, other authors, Raitakari OT, Kuusisto J, Laakso M, Price AL, Pajukanta P, Pasaniuc B. Integrative approaches for large-scale transcriptome-wide association studies. Nat Genet. 2016 Mar;48(3):245-52. PMCID: 4767558.
    • Mensah-Ablorh A, Lindstrom S, Haiman CA, Henderson BE, Marchand LL, Lee S, Stram DO, Eliassen AH, Price A, Kraft P. Meta-Analysis of Rare Variant Association Tests in Multiethnic Populations. Genet Epidemiol. 2016 Jan;40(1):57-65. PMCID: 4968883.
    • 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. PMCID: 4909355.
    • Gusev A, Shi H, Kichaev G, Pomerantz M, Li F, Long HW, …, Raychaudhuri S, Schumacher FR, Price AL, Freedman ML, Haiman CA, Pasaniuc B. Atlas of prostate cancer heritability in European and African-American men pinpoints tissue-specific regulation. Nat Commun. 2016 Apr 7;7:1-13. PMCID: 4829663.
    • Loh PR, Palamara PF, Price AL. Fast and accurate long-range phasing in a UK Biobank cohort. Nat Genet. 2016 Jul;48(7):811-6. PMCID: 4925291.
    • Brown BC, Price AL, Patsopoulos NA, ZaitlenNA. Local joint testing improves power and identifies missing heritability in association studies. Genetics. 2016 Jul;203(3):1105-16. PMCID: 4937483.
    • Brown BC, Asian Genetic Epidemiology Network-Type 2 Diabetes (AGEN-T2D) Consortium, Ye CJ, Price AL, Zaitlen NA. Transethnic genetic correlation estimates from summary statistics support. Am J Hum Genet. 2016 Jul;99(1):76-88. PMCID: 50057434.
    • Loh LR, Danecek P, Palamara PF, Fuchsberger C, Reshef YA, Finucane HK, Schoenherr S, Forer L, McCarthy S, Abecasis GR, Durbin R, Price AL. Reference-based phasing using the Haplotype Reference Consortium panel. Nat Genet. 2016 Nov;48(11):1443-1448. PMCID: 5096458.
    • Galinsky KJ, Loh PR, Mallick S, Patterson NJ, Price AL. Population structure of UK Biobank and ancient Eurasians reveals adaptation at genes influencing blood pressure. Am J Hum Genet. 2016 Nov 3;99(5):1130-1139. PMCID: 5097941.
    • Lindstroem S, Ablorh A, Chapman B, Gusev A, Chen G, Turman C, …, Price AL, Henderson BE, Le Marchand L, Hofmann O, Haiman CA, Kraft P. Deep targeted sequencing of 12 breast cancer susceptibility regions in 4611 women across four different ethnicities. Breast Cancer Res. 2016 Nov 5;18(1):1-13. PMCID: 5097387

    2015

    • Loh PR, Tucker G, Bulik-Sullivan BK, Vilhjálmsson BJ, Finucane HK, Salem RM, Chasman DI, Ridker PM, Neale BM, Berger B, Patterson N, Price AL.  Efficient Bayesian mixed-model analysis increases association power in large cohorts.  Nat Genet. 2015 Mar;47(3):284-90. PMCID: 4342297.
    • Bulik-Sullivan BK, Loh PR, Finucane HK, Ripke S, Yang J; Schizophrenia Working Group of the Psychiatric Genomics Consortium, Patterson N, Daly MJ, Price AL, Neale BM.  LD Score regression distinguishes confounding from polygenicity in genome-wide association studies.  Nat Genet. 2015 Mar;47(3):291-5. PMCID: 4495769.
    • Cornelis MC, Zaitlen N, Hu FB, Kraft P, Price AL.  Genetic and environmental components of family history in type 2 diabetes.  Hum Genet. 2015 Feb;134(2):259-67.  PMCID: 4293229.
    • Aschard H, Vilhjalmsson BJ, Joshi AD, Price AL, Kraft P.  Adjusting for heritable covariates can bias effect estimates in genome-wide association studies. AJHG. 2015 Feb 5;96(2):329-39.  PMCID: 4320269.
    • Hayeck TJ, Zaitlen NA, Loh PR, Vilhjalmsson B, Pollack S, Gusev A, Yang J, Chen GB, Goddard ME, Visscher PM, Patterson N, Price AL.  Mixed model with correction for case-control ascertainment increases association power.  AJHG. 2015 May 7;96(5):720-30. PMCID: 4570278.
    • Chen CY, Han J, Hunter DJ, Kraft P, Price AL. Explicit modeling of ancestry improves polygenic risk scores and BLUP prediction. Genet Epidemiol. 2015 Sep;39(6):427-38. PMCID: 4734143
    • Finucane HK*, Bulik-Sullivan B*, Gusev A, Trynka G, Reshef Y, Loh PR, …, Okada Y, Raychaudhuri S, Daly MJ, Patterson N, Neale BM**, Price AL**. Partitioning heritability by functional annotation using genome-wide association summary statistics. Nat Genet. 2015 Nov;47(11):1228-35. PMCID: 4626285.
    • Bulik-Sullivan B*, Finucane HK*, Anttila V, Gusev A, Day FR, Loh PR, …, Perry JR, Patterson N, Robinson EB, Daly MJ, Price AL**, Neale BM**. An atlas of genetic correlations across human diseases and traits. Nat Genet. 2015 Nov;47(11):1236-41. PMCID: 4797329
    • Day FR, Ruth KS, Thompson DJ, Lunetta KL, Pervjakova N, …Price AL, …Ong KK, Chang-Claude J, Murabito JM, Perry JR, Murray A. Large-scale genomic analyses link reproductive aging to hypothalamic signaling, breast cancer susceptibility and BRCA1-mediated DNA repair. Nat Genet. 2015 Nov;47(11):1294-303. PMCID: 4661791.
    • Vilhjálmsson BJ, Yang J, Finucane HK, Gusev A, Lindström S, Ripke S, …Goddard M, Visscher PM, Kraft P, Patterson N, Price AL; Discovery Biology and Risk of Inherited Variants in Breast Cancer DRIVE study. Modeling Linkage Disequilibrium Increases Accuracy of Polygenic Risk Scores. Am J Hum Genet. 2015 Oct 1;97(4):576-92. PMCID: 4596916.
    • Loh PR, Bhatia G, Gusev A, Finucane HK, Bulik-Sullivan BK, Pollack SJ; Schizophrenia Working Group of the Psychiatric Genomics Consortium, de Candia TR, Lee SH, Wray NR, Kendler KS, O’Donovan MC, Neale BM, Patterson N, Price AL. Contrasting genetic architectures of schizophrenia and other complex diseases using fast variance-components analysis. Nat Genet. 2015 Dec;47(12):1385-92. PMCID: 4666835.
    • Tucker G*, Loh PR*, MacLeod IM, Hayes BJ, Goddard ME, Berger B, Price AL. Two-Variance-Component Model Improves Genetic Prediction in Family Datasets. AJHG. 2015 Nov;97(5):677-90. PMCID: 4667134.
    • Lee SH, Byrne EM, Hultman CM, Kähler A, Vinkhuyzen AA, …, Price AL, …,  Klareskog L, Mariette X, Plenge RM, van Laar M, van Riel P. New data and an old puzzle: the negative association between schizophrenia and rheumatoid arthritis. Int J Epidemiol. 2015 Oct 1;44(5)1706-21. PMCID: 4881824
    • Palamara PF, Francioli LC, Wilton PR, Genovese G, Gusev A, Finucane HK, Sankararaman S, Genome of the Netherlands Consortium, Sunyaev SR, de Bakker PIW, Wakeley J, Pe’er I, Price AL. Leveraging Distant Relatedness to Quantify Human Mutation and Gene-Conversion Rates. AJHG. 2015 Dec;97(6):775-89. PMCID: 4678427
    • Price AL, Spencer CC, Donnelly P. Progress and promise in understanding the genetic basis of common diseases. Proc Biol Sci. 2015 Dec;282(1821). PMCID: 4707742

    2014

    • Yang J, Zaitlen NA, Goddard ME, Visscher PM, Price AL.  Advantages and pitfalls in the application of mixed-model association methods.  Nat Genet.  2014 Feb;46(2):100-6.  PMCID: 3989144.
    • Chimusa ER*, Zaitlen N*, Daya M, Moeller M, Mulder NJ, Price AL*, Hoal E*.  Genome-wide association study of ancestry-specific TB risk in the South African Coloured population.  Hum Mol Genet. 2014 Feb;23(3):796-809. PMCID: 3888262.
    • Tucker G, Price AL, Berger BA.  Improving the power of GWAS and avoiding confounding from population stratification with PC-Select.  Genetics.  2014 Apr 29;197(3);1045-9. PMCID: 4096359.
    • 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 Oct;30(20):2906-14.  PMCID: 4184260.
    • Schizophrenia Working Group of the Psychiatric Genomics Consortium.  Biological insights from 108 schizophrenia-associated genetic loci.  Nature.  2014 Jul 24;511(7510):421.  PMCID: 4112379.
    • Price AL, Loh P.  Genomic prediction and genome-wide association in humans with whole genome sequence data.  2014 Aug.  Proceedings of the 10th World Congress of Genetics Applied to Livestock Production.
    • Bhatia G, Tandon A, Patterson N, Aldrich MC, Ambrosone CB, other authors, Ziegler RG, Chanock SJ, Haiman CA, Reich D, Price AL.  Genome-wide scan of 29,141 African Americans finds no evidence of directional selection since admixture.  AJHG.  2014 Sept 18;95(4):437-44.  PMCID: 4185117.
    • Wood AR, Esko T, Yang J, Vedantam S, Pers TH, …, Price AL, …, Chasman DI, Goddard ME, Visscher PM, Hirschhorn JN, Frayling TM.  Defining the role of common variation in the genomic and biological architecture of adult human height.  Nat Genet. 2014 Nov;46(11):1173-86.  PMCID: 4250049.
    • Kichaev G, Yang WY, Lindstroem S, Hormozdiari F, Eskin E, Price AL, Kraft P, Pasaniuc B.  Integrating functional data to prioritize causal variants in statistical fine-mapping studies.  PLoS Genet. 2014 Oct;10(10): e1004722.  PMCID: 4214605.
    • Zaitlen N, Pasaniuc B, Sankararaman S, Bhatia G, Zhang J, …, Kooperberg C, Stram D, Reiner AP, Tang H, Price AL.  Leveraging population admixture to characterize the heritability of complex traits.  Nat Genet. 2014 Dec;46(12):1356-62. PMCID: 4244251.
    • Gusev A, Lee SH, Trynka G, Finucane H, Vilhjalmsson BJ, …, Sullivan PF, Neale BM, Wray NR, Raychaudhuri S, Price AL.  Partitioning heritability of regulatory and cell-type-specific variants across 11 common diseases.  AJHG. 2014 Nov;95: 535-552.  PMCID: 4225595.

    2013

    • Zaitlen N, Kraft P, Patterson N, Pasaniuc B, Bhatia G, Pollack S, Price AL.  Using extended genealogy to estimate components of heritability for 23 quantitative and dichotomous traits.  PLoS Genet.  2013 May;9(5):e1003520.  PMCID: 3667752.
    • Chen CY, Pollack S, Hunter DJ, Hirschhorn JN, Kraft P, Price AL.  Improved ancestry inference using weights from external reference panels.  Bioinformatics.  2013 Mar 28;29(11):1399-1406.  PMCID: 3661048.
    • Bhatia G*, Patterson N*, Sankararaman S, Price AL.  Estimating and interpreting Fst: the impact of rare variants. Genome Res. 2013 Sept;23(9):1514-21.  PMCID: 3759727.
    • Price AL, Zaitlen NA, Reich D, Patterson N.  Response to Sul and Eskin.  Nat Rev Genet.  2013 Apr14;(4):300. doi: 10.1038/nrg2813-c2.
    • Gokcumen O, Zhu Q, Mulder L, Iskow RC, Austermann C, Scharer CD, Raj T, Boss JM, Sunyaev S, Price AL, Stranger B, Simon V, Lee C.  Balancing selection on a regulatory region exhibiting ancient variation that predates Human-Neandertal divergence.  PLoS Genet.  2013 Apr;9(4):e1003404.  PMCID: 3623772.
    • Genovese G, Handsaker RE, Li H, Altemose N, Lindgren AM, Chambert K, Pasaniuc B, Price AL, Reich D, Morton CC, Pollak MR, Wilson JG, McCarroll SA.  Using population admixture to help complete maps of the human genome.  Nat Genet.  2013 Apr;45(4):406-14. doi: 10.1038/ng.2565. PMCID: 3683849.
    • Kantor DB, Palmer CD, Young TR, Meng Y, Gajdos ZK, Lyon H, Price AL, Pollack S, London SJ, Loehr LR, Smith LJ, Kumar R, Jacobs Jr DR, Petrini MF, O’Connor GT, White WB, Papanicolaou G, Burkart KM, Heckbert SR, Barr RG, Hirschhorn JN.  Replication and fine mapping of asthma-associated loci in individuals of African ancestry.  Hum Genet. 2013 Sept;132(9):1039-47.  PMCID: 3975655.
    • Wray NR, Yang J, Hayes BJ, Price AL, Goddard ME, Visscher PM.  Pitfalls of predicting complex traits from SNPs.  Nat Rev Genet. 2013 Jul;14(7):507-15.  PMCID: 4096801.
    • Wray NR, Yang J, Hayes BJ, Price AL, Goddard ME, Visscher PM.  Author reply to A commentary on Pitfalls of predicting complex traits from SNPs.  Nat Rev Genet. 2013 Dec;14(12):894.  PMCID: 4266985.
    • Gusev A, Bhatia G, Zaitlen N, Vilhjalmsson BJ, Diogo D, Stahl EA, Gregersen PK, Worthington J, Klareskog L, Raychaudhuri S, Plenge RM, Pasaniuc B, Price AL.  Quantifying missing heritability at known GWAS loci.  PLoS Genetics. 2013 Dec;9(12):e1003993.  PMCID: 3873246.

    2012

    • Pasaniuc B, Rohland N, McLaren PJ, Garimella K, Zaitlen N, other authors, Sunyaev S, Patterson N, de Bakker PIW, Reich D*, Price AL*.  Extremely low-coverage sequencing and imputation increases power for genome-wide association studies. Nat Genet. 2012 May 20;44(6): 631-635. PMCID:3400344.
    • Kiezun A*, Garimella K*, Do R*, Stitziel NO*, Neale BM, other authors, Shugart YY, Price AL*, de Bakker PI*, Purcell SM*, Sunyaev SR*.  Exome sequencing and the genetic basis of complex traits. Nat Genet. 2012 May 29;44(6):623-630.  PMCID: 3727622.
    • Zaitlen N, Pasaniuc B, Patterson N, Pollack S, Voight B, other authors, Haiman CA, Stranger BE, Dermitzakis ET, Kraft P, Price AL.  Analysis of case-control association studies with known risk variants. Bioinformatics. 2012 Jul 1;28(13):1729-1737. PMCID: 3381970.
    • Campbell DD, Parra MV, Duque C, Gallego N, Franco L, Tandon A, Hunemeier T, Bortolini C, Villegas A, Bedoya G, McCarthy MI, Price AL, Reich D, Ruiz-Linares A.  Amerind Ancestry, Socioeconomic Status and the Genetics of Type 2 Diabetes in a Colombian Population.  PLoS One. 2012; 7(4): e33570. PMCID: 3328483.
    • Stranger BE, Montgomery SB, Dimas AS, Parts L, Stegle O, Ingle CE, Sekowska M, Smith GD, Evans D, Gutierrez-Arcelus M, Price A, Raj T, Nisbett J, Nica AC, Beazley C, Durbin R, Deloukas P, Dermitzakis ET.  Patterns of cis regulatory variation in diverse human populations.  PLoS Genet. 2012 Apr;8(4):e1002639. PMCID:3330104.
    • Epstein MM, Kasperzyk JL, Mucci LA, Giovannucci E, Price A, Wolk A, Hakansson N, Fall K, Andersson SO, Andren O.  Dietary Fatty Acid Intake and Prostate Cancer Survival in Orebro County, Sweden.  Am J Epidemiol.  2012 Aug 1;176(3):240-252.  PMCID:3491963.
    • Reich D, Patterson N, Campbell D, Tandon A, Mazieres S, other authors, Kidd K, Di Rienzo A, Freimer NB, Price AL, Ruiz-Linares A.  Reconstructing Native American population history.  Nature. 2012 Aug 16;488(7411):370-374. PMCID: 3615710.
    • Zaitlen N, Lindstrom S, Pasaniuc B, Cornelis M, Genovese G, other authors, Altshuler D, Voight B, Kraft P, Patterson N, Price AL.  Informed conditioning on clinical covariates increases power in case-control association studies.  PLoS Genet. 2012 Nov;8(11):e1003032.  PMCID: 3493452.

    2011

    • Price AL, Helgason A, Thorleifsson G, McCarroll SA, Kong A, Stefansson K.  Single-tissue and cross-tissue heritability of gene expression via identity-by-descent in related or unrelated individuals.  PLoS Genet.  2011 Feb; 7(2): e1001317. PMCID: 3044684.
    • Pasaniuc B, Zaitlen N, Lettre G, Chen GK, Tandon A, other authors, Haiman CA, Reich D, Patterson N, Wilson JG, Price AL. Enhanced statistical tests for GWAS in admixed populations: assessment using African Americans from CARe and a breast cancer consortium. PLoS Genet.  2011 April; 7(4): e1001371.  PMCID: 3080860.
    • Moorjani P, Patterson N, Hirschhorn JN, Keinan A, Hao L, Atzmon G, Burns E, Ostrer H, Price AL, Reich D. The History of African Gene Flow into Southern Europeans, Levantines and Jews. PLoS Genet.  2011 April; 7(4): e1001373. PMCID: 3080861.
    • Seldin MF, Pasaniuc B, Price AL.  New approaches to disease mapping in admixed populations.  Nat Rev Genet.  2011 June 28;12(8):523-8.  doi: 10.1038/nrg3002.  PMCID: 3142784.
    • Hinch AG, Tandon A, Patterson N, Song Y, Rohland N, other authors, Price AL, Hakonarson H, Chanock SJ, Haiman CA, Wilson JG, Reich D, Myers S.  The landscape of recombination in African-Americans.  Nature.  2011 July 20;476(7359):170-5. doi: 10.1038/nature10336.  PMCID: 3154982.
    • Bhatia G, Patterson N, Pasaniuc B, Zaitlen N, Genovese G, other authors, Zhu X, Cooper R, Reich D, Wilson JG, Price AL.  Genome-wide Comparison of African-Ancestry Populations from CARe and Other Cohorts Reveals Signals of Natural Selection.  AJHG.  2011 Sept 9; 89 (3): 368-381.  PMCID: 3169818.

    2010

    • Price AL, Zaitlen NA, Reich D, Patterson N.  New approaches to population stratification in genome-wide association studies.  Nat Rev Genet. 2010 Jun 15;11(7):459-463. PMCID: 2975875
    • Price AL*, Kryukov GV*, de Bakker PI, Purcell SM, Staples J, Wei LJ, Sunyaev SR. Pooled Association Tests for Rare Variants in Exon-Resequencing Studies. Am J Hum Genet. 2010 Jun 11;86(6):832-8. PMCID: 3032073.
    • International HapMap 3 Consortium. Integrating common and rare genetic variation in diverse human populations. Nature. 2010 Sep  2;467(7311):52-8.  PMCID: 3173859.
    • Meyer MS, Penney KL, Stark JR, Schumacher FR, Sesso HD, Loda M, Fiorentino M, Finn S, Flavin RJ, Kurth T, Price AL, Giovannucci EL, Fall K, Stampfer MJ, Ma J, Mucci LA. Genetic variation in RNASEL associated with prostate cancer risk and progression. Carcinogenesis. 2010 Sep;31(9):1597-603. PMCID: 2930803

    2009

    • Reich D*, Thangaraj K*, Patterson N*, Price AL*, Singh L. Reconstructing Indian population history. Nature. 2009 Sep 24;461(7263):489-94.  PMCID: 2842210.
    • Florez JC*, Price AL*, Campbell D, Riba L, Parra MV, Yu F, Duque C, Saxena R, Gallego N, Tello-Ruiz M, Franco L, Rodríguez-Torres M, Villegas A, Bedoya G, Aguilar-Salinas CA, Tusié-Luna MT, Ruiz-Linares A, Reich D. Strong association of socioeconomic status with genetic ancestry in Latinos: implications for admixture studies of type 2 diabetes. Diabetologia. 2009 Aug;52(8):1528-36. PMCID: 3113605.
    • Price AL, Tandon A, Patterson N, Barnes KC, Rafaels N, Ruczinski I, Beaty TH, Mathias R, Reich D, Myers S. Sensitive detection of chromosomal segments of distinct ancestry in admixed populations. PLoS Genet. 2009 Jun;5(6):e1000519. PMCID: 2689842
    • Price AL, Helgason A, Palsson S, Stefansson H, St Clair D, Andreassen OA, Reich D, Kong A, Stefansson K. The impact of divergence time on the nature of population structure: an example from Iceland. PLoS Genet. 2009 Jun;5(6):e1000505. PMCID: 2684636
    • De Jager PL, Baecher-Allan C, Maier LM, Arthur AT, Ottoboni L, Barcellos L, McCauley JL, Sawcer S, Goris A, Saarela J, Yelensky R, Price AL, Leppa V, Patterson N, de Bakker PI, Tran D, Aubin C, Pobywajlo S, Rossin E, Hu X, Ashley CW, Choy E, Rioux JD, Pericak-Vance MA, Ivinson A, Booth DR, Stewart GJ, Palotie A, Peltonen L, Dubois B, Haines JL, Weiner HL, Compston A, Hauser SL, Daly MJ, Reich D, Oksenberg JR, Hafler DA. The role of the CD58 locus in multiple sclerosis. Proc Natl Acad Sci U S A. 2009 Mar 31;106(13):5264-9. PMCID: 2664005
    • Dhandapany PS, Sadayappan S, Xue Y, Powell GT, Rani DS, Nallari P, Rai TS, Khullar M, Soares P, Bahl A, Tharkan JM, Vaideeswar P, Rathinavel A, Narasimhan C, Ayapati DR, Ayub Q, Mehdi SQ, Oppenheimer S, Richards MB, Price AL, Patterson N, Reich D, Singh L, Tyler-Smith C, Thangaraj K. A common MYBPC3 (cardiac myosin binding protein C) variant associated with cardiomyopathies in South Asia. Nat Genet. 2009 Feb;41(2):187-91. PMCID: 2697598

    2008

    • Price AL, Patterson N, Hancks DC, Myers S, Reich D, Cheung VG, Spielman RS. Effects of cis and trans genetic ancestry on gene expression in African Americans. PLoS Genet. 2008 Dec;4(12):e1000294. PMCID: 2586034
    • Keating BJ, Tischfield S, Murray SS, Bhangale T, Price TS, Glessner JT, Galver L, Barrett JC, Grant SF, Farlow DN, Chandrupatla HR, Hansen M, Ajmal S, Papanicolaou GJ, Guo Y, Li M, Derohannessian S, de Bakker PI, Bailey SD, Montpetit A, Edmondson AC, Taylor K, Gai X, Wang SS, Fornage M, Shaikh T, Groop L, Boehnke M, Hall AS, Hattersley AT, Frackelton E, Patterson N, Chiang CW, Kim CE, Fabsitz RR, Ouwehand W, Price AL, Munroe P, Caulfield M, Drake T, Boerwinkle E, Reich D, Whitehead AS, Cappola TP, Samani NJ, Lusis AJ, Schadt E, Wilson JG, Koenig W, McCarthy MI, Kathiresan S, Gabriel SB, Hakonarson H, Anand SS, Reilly M, Engert JC, Nickerson DA, Rader DJ, Hirschhorn JN, Fitzgerald GA. Concept, design and implementation of a cardiovascular gene-centric 50 k SNP array for large-scale genomic association studies. PLoS One. 2008;3(10):e3583. PMCID: 2571995
    • Gajdos ZK, Butler JL, Henderson KD, He C, Supelak PJ, Egyud M, Price AL, Reich D, Clayton PE, Le Marchand L, Hunter DJ, Henderson BE, Palmert MR, Hirschhorn JN. ssociation studies of common variants in 10 hypogonadotropic hypogonadism genes with age at menarche. J Clin Endocrinol Metab. 2008 Nov;93(11):4290-8. PMCID: 2582573
    • Price AL, Weale ME, Patterson N, Myers SR, Need AC, Shianna KV, Ge D, Rotter JI, Torres E, Taylor KD, Goldstein DB, Reich D. Long-range LD can confound genome scans in admixed populations. Am J Hum Genet. 2008 Jul;83(1):132-5; author reply 135-9. PMCID: 2443852
    • Reich D, Price AL, Patterson N. Principal component analysis of genetic data. Nat Genet. 2008 May;40(5):491-2.
    • Seldin MF, Price AL. Application of ancestry informative markers to association studies in European Americans. PLoS Genet. 2008 Jan;4(1):e5. PMCID: 2211545
    • Price AL, Butler J, Patterson N, Capelli C, Pascali VL, Scarnicci F, Ruiz-Linares A, Groop L, Saetta AA, Korkolopoulou P, Seligsohn U, Waliszewska A, Schirmer C, Ardlie K, Ramos A, Nemesh J, Arbeitman L, Goldstein DB, Reich D, Hirschhorn JN. Discerning the ancestry of European Americans in genetic association studies. PLoS Genet. 2008 Jan;4(1):e236. PMCID: 2211542

    2007

    • Plenge RM, Cotsapas C, Davies L, Price AL, de Bakker PI, Maller J, Pe’er I, Burtt NP, Blumenstiel B, DeFelice M, Parkin M, Barry R, Winslow W, Healy C, Graham RR, Neale BM, Izmailova E, Roubenoff R, Parker AN, Glass R, Karlson EW, Maher N, Hafler DA, Lee DM, Seldin MF, Remmers EF, Lee AT, Padyukov L, Alfredsson L, Coblyn J, Weinblatt ME, Gabriel SB, Purcell S, Klareskog L, Gregersen PK, Shadick NA, Daly MJ, Altshuler D. Two independent alleles at 6q23 associated with risk of rheumatoid arthritis. Nat Genet. 2007 Dec;39(12):1477-82. PMCID: 2652744
    • Sabeti PC, Varilly P, Fry B, Lohmueller J, Hostetter E, Cotsapas C, Xie X, Byrne EH, McCarroll SA, Gaudet R, Schaffner SF, Lander ES; International HapMap Consortium. Genome-wide detection and characterization of positive selection in human populations. Nature. 2007 Oct 18;449(7164):913-8. PMCID: 2687721
    • International HapMap Consortium. A second generation human haplotype map of over 3.1 million SNPs. Nature. 2007 Oct 18;449(7164):851-61. PMCID: PMC2689609
    • Ayodo G, Price AL, Keinan A, Ajwang A, Otieno MF, Orago AS, Patterson N, Reich D. Combining proof of natural selection with association analysis increases power to detect malaria-resistance variants. Am J Hum Genet. 2007 Aug;81(2):234-42. PMCID: 1950820
    • Price AL, Patterson N, Yu F, Cox DR, Waliszewska A, McDonald GJ, Tandon A, Schirmer C, Neubauer J, Bedoya G, Duque C, Villegas A, Bortolini MC, Salzano FM, Gallo C, Mazzotti G, Tello-Ruiz M, Riba L, Aguilar-Salinas CA, Canizales-Quinteros S, Menjivar M, Klitz W, Henderson B, Haiman CA, Winkler C, Tusie-Luna T, Ruiz-Linares A, Reich D. A genomewide admixture map for Latino populations. Am J Hum Genet. 2007 Jun;80(6):1024-36. PMCID: 1867092

    2006

    • Patterson N, Price AL, Reich D. Population structure and eigenanalysis. PLoS Genet. 2006 Dec;2(12):e190. PMCID: 1713260
    • Price AL, Patterson NJ, Plenge RM, Weinblatt ME, Shadick NA, Reich D. Principal components analysis corrects for stratification in genome-wide association studies. Nat Genet. 2006 Aug;38(8):904-9.
    • Zhi D, Raphael BJ, Price AL, Tang H, Pevzner PA. Identifying repeat domains in large genomes. Genome Biol. 2006;7(1):1-14. PMCID: 1431705

    2003-2005

    • Bashir A, Ye C, Price AL, Bafna V. Orthologous repeats and mammalian phylogenetic inference. Genome Res. 2005 Jul;15(7):998-1006. PMCID: 1172044
    • Price AL, Jones NC, Pevzner PA. De novo identification of repeat families in large genomes. Bioinformatics. 2005 Jun;21 Suppl 1:i351-8. Proceedings of the 13th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB-05). Detroit, Michigan.
    • Price AL, Eskin E, Pevzner PA. Whole-genome analysis of Alu repeat elements reveals complex evolutionary history. Genome Res. 2004 Nov;14(11):2245-52. PMCID: 525682
    • Price AL, Ramabhadran S, Pevzner PA. Finding subtle motifs by branching from sample strings. Bioinformatics. 2003 Oct;19 Suppl 2:ii149-55.