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Items: 28

1.

PhenoSpD: an integrated toolkit for phenotypic correlation estimation and multiple testing correction using GWAS summary statistics.

Zheng J, Richardson TG, Millard LAC, Hemani G, Elsworth BL, Raistrick CA, Vilhjalmsson B, Neale BM, Haycock PC, Smith GD, Gaunt TR.

Gigascience. 2018 Aug 1;7(8). doi: 10.1093/gigascience/giy090.

2.

The nature of nurture: Effects of parental genotypes.

Kong A, Thorleifsson G, Frigge ML, Vilhjalmsson BJ, Young AI, Thorgeirsson TE, Benonisdottir S, Oddsson A, Halldorsson BV, Masson G, Gudbjartsson DF, Helgason A, Bjornsdottir G, Thorsteinsdottir U, Stefansson K.

Science. 2018 Jan 26;359(6374):424-428. doi: 10.1126/science.aan6877.

PMID:
29371463
3.

Covariate selection for association screening in multiphenotype genetic studies.

Aschard H, Guillemot V, Vilhjalmsson B, Patel CJ, Skurnik D, Ye CJ, Wolpin B, Kraft P, Zaitlen N.

Nat Genet. 2017 Dec;49(12):1789-1795. doi: 10.1038/ng.3975. Epub 2017 Oct 16.

4.

Nationwide Genomic Study in Denmark Reveals Remarkable Population Homogeneity.

Athanasiadis G, Cheng JY, Vilhjálmsson BJ, Jørgensen FG, Als TD, Le Hellard S, Espeseth T, Sullivan PF, Hultman CM, Kjærgaard PC, Schierup MH, Mailund T.

Genetics. 2016 Oct;204(2):711-722. Epub 2016 Aug 17.

5.

Response to Day et al.

Aschard H, Vilhjálmsson BJ, Joshi AD, Price AL, Kraft P.

Am J Hum Genet. 2016 Feb 4;98(2):394-5. doi: 10.1016/j.ajhg.2015.12.020. No abstract available.

6.

Modeling Linkage Disequilibrium Increases Accuracy of Polygenic Risk Scores.

Vilhjálmsson BJ, Yang J, Finucane HK, Gusev A, Lindström S, Ripke S, Genovese G, Loh PR, Bhatia G, Do R, Hayeck T, Won HH; Schizophrenia Working Group of the Psychiatric Genomics Consortium, Discovery, Biology, and Risk of Inherited Variants in Breast Cancer (DRIVE) study, Kathiresan S, Pato M, Pato C, Tamimi R, Stahl E, Zaitlen N, Pasaniuc B, Belbin G, Kenny EE, Schierup MH, De Jager P, Patsopoulos NA, McCarroll S, Daly M, Purcell S, Chasman D, Neale B, Goddard M, Visscher PM, Kraft P, Patterson N, Price AL.

Am J Hum Genet. 2015 Oct 1;97(4):576-92. doi: 10.1016/j.ajhg.2015.09.001.

7.

DNA methylation in Arabidopsis has a genetic basis and shows evidence of local adaptation.

Dubin MJ, Zhang P, Meng D, Remigereau MS, Osborne EJ, Paolo Casale F, Drewe P, Kahles A, Jean G, Vilhjálmsson B, Jagoda J, Irez S, Voronin V, Song Q, Long Q, Rätsch G, Stegle O, Clark RM, Nordborg M.

Elife. 2015 May 5;4:e05255. doi: 10.7554/eLife.05255.

8.

Mixed model with correction for case-control ascertainment increases association power.

Hayeck TJ, Zaitlen NA, Loh PR, Vilhjalmsson B, Pollack S, Gusev A, Yang J, Chen GB, Goddard ME, Visscher PM, Patterson N, Price AL.

Am J Hum Genet. 2015 May 7;96(5):720-30. doi: 10.1016/j.ajhg.2015.03.004. Epub 2015 Apr 16.

9.

Polygenic Risk Score, Parental Socioeconomic Status, Family History of Psychiatric Disorders, and the Risk for Schizophrenia: A Danish Population-Based Study and Meta-analysis.

Agerbo E, Sullivan PF, Vilhjálmsson BJ, Pedersen CB, Mors O, Børglum AD, Hougaard DM, Hollegaard MV, Meier S, Mattheisen M, Ripke S, Wray NR, Mortensen PB.

JAMA Psychiatry. 2015 Jul;72(7):635-41. doi: 10.1001/jamapsychiatry.2015.0346.

PMID:
25830477
10.

Efficient Bayesian mixed-model analysis increases association power in large cohorts.

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.

Nat Genet. 2015 Mar;47(3):284-90. doi: 10.1038/ng.3190. Epub 2015 Feb 2.

11.

Adjusting for heritable covariates can bias effect estimates in genome-wide association studies.

Aschard H, Vilhjálmsson BJ, Joshi AD, Price AL, Kraft P.

Am J Hum Genet. 2015 Feb 5;96(2):329-39. doi: 10.1016/j.ajhg.2014.12.021. Epub 2015 Jan 29.

12.

Partitioning heritability of regulatory and cell-type-specific variants across 11 common diseases.

Gusev A, Lee SH, Trynka G, Finucane H, Vilhjálmsson BJ, Xu H, Zang C, Ripke S, Bulik-Sullivan B, Stahl E; Schizophrenia Working Group of the Psychiatric Genomics Consortium; SWE-SCZ Consortium, Kähler AK, Hultman CM, Purcell SM, McCarroll SA, Daly M, Pasaniuc B, Sullivan PF, Neale BM, Wray NR, Raychaudhuri S, Price AL; Schizophrenia Working Group of the Psychiatric Genomics Consortium; SWE-SCZ Consortium.

Am J Hum Genet. 2014 Nov 6;95(5):535-52. doi: 10.1016/j.ajhg.2014.10.004. Epub 2014 Nov 6.

13.

Leveraging population admixture to characterize the heritability of complex traits.

Zaitlen N, Pasaniuc B, Sankararaman S, Bhatia G, Zhang J, Gusev A, Young T, Tandon A, Pollack S, Vilhjálmsson BJ, Assimes TL, Berndt SI, Blot WJ, Chanock S, Franceschini N, Goodman PG, He J, Hennis AJ, Hsing A, Ingles SA, Isaacs W, Kittles RA, Klein EA, Lange LA, Nemesure B, Patterson N, Reich D, Rybicki BA, Stanford JL, Stevens VL, Strom SS, Whitsel EA, Witte JS, Xu J, Haiman C, Wilson JG, Kooperberg C, Stram D, Reiner AP, Tang H, Price AL.

Nat Genet. 2014 Dec;46(12):1356-62. doi: 10.1038/ng.3139. Epub 2014 Nov 10.

14.

Genome-wide association study of Arabidopsis thaliana leaf microbial community.

Horton MW, Bodenhausen N, Beilsmith K, Meng D, Muegge BD, Subramanian S, Vetter MM, Vilhjálmsson BJ, Nordborg M, Gordon JI, Bergelson J.

Nat Commun. 2014 Nov 10;5:5320. doi: 10.1038/ncomms6320.

15.

Maximizing the power of principal-component analysis of correlated phenotypes in genome-wide association studies.

Aschard H, Vilhjálmsson BJ, Greliche N, Morange PE, Trégouët DA, Kraft P.

Am J Hum Genet. 2014 May 1;94(5):662-76. doi: 10.1016/j.ajhg.2014.03.016. Epub 2014 Apr 17.

16.

Quantifying missing heritability at known GWAS loci.

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.

PLoS Genet. 2013;9(12):e1003993. doi: 10.1371/journal.pgen.1003993. Epub 2013 Dec 26.

17.

Effect of genetic variation in a Drosophila model of diabetes-associated misfolded human proinsulin.

He BZ, Ludwig MZ, Dickerson DA, Barse L, Arun B, Vilhjálmsson BJ, Jiang P, Park SY, Tamarina NA, Selleck SB, Wittkopp PJ, Bell GI, Kreitman M.

Genetics. 2014 Feb;196(2):557-67. doi: 10.1534/genetics.113.157800. Epub 2013 Nov 26. Erratum in: Genetics. 2014 Apr;196(4):1357. Jiang, Pengyao [added].

18.

Massive genomic variation and strong selection in Arabidopsis thaliana lines from Sweden.

Long Q, Rabanal FA, Meng D, Huber CD, Farlow A, Platzer A, Zhang Q, Vilhjálmsson BJ, Korte A, Nizhynska V, Voronin V, Korte P, Sedman L, Mandáková T, Lysak MA, Seren Ü, Hellmann I, Nordborg M.

Nat Genet. 2013 Aug;45(8):884-890. doi: 10.1038/ng.2678. Epub 2013 Jun 23.

19.

Genetic architecture of skin and eye color in an African-European admixed population.

Beleza S, Johnson NA, Candille SI, Absher DM, Coram MA, Lopes J, Campos J, Araújo II, Anderson TM, Vilhjálmsson BJ, Nordborg M, Correia E Silva A, Shriver MD, Rocha J, Barsh GS, Tang H.

PLoS Genet. 2013 Mar;9(3):e1003372. doi: 10.1371/journal.pgen.1003372. Epub 2013 Mar 21.

20.

JAWAMix5: an out-of-core HDF5-based java implementation of whole-genome association studies using mixed models.

Long Q, Zhang Q, Vilhjalmsson BJ, Forai P, Seren Ü, Nordborg M.

Bioinformatics. 2013 May 1;29(9):1220-2. doi: 10.1093/bioinformatics/btt122. Epub 2013 Mar 11.

PMID:
23479353
21.

GWAPP: a web application for genome-wide association mapping in Arabidopsis.

Seren Ü, Vilhjálmsson BJ, Horton MW, Meng D, Forai P, Huang YS, Long Q, Segura V, Nordborg M.

Plant Cell. 2012 Dec;24(12):4793-805. doi: 10.1105/tpc.112.108068. Epub 2012 Dec 31.

22.

The nature of confounding in genome-wide association studies.

Vilhjálmsson BJ, Nordborg M.

Nat Rev Genet. 2013 Jan;14(1):1-2. doi: 10.1038/nrg3382. Epub 2012 Nov 20.

PMID:
23165185
23.

A mixed-model approach for genome-wide association studies of correlated traits in structured populations.

Korte A, Vilhjálmsson BJ, Segura V, Platt A, Long Q, Nordborg M.

Nat Genet. 2012 Sep;44(9):1066-71. doi: 10.1038/ng.2376. Epub 2012 Aug 19.

24.

An efficient multi-locus mixed-model approach for genome-wide association studies in structured populations.

Segura V, Vilhjálmsson BJ, Platt A, Korte A, Seren Ü, Long Q, Nordborg M.

Nat Genet. 2012 Jun 17;44(7):825-30. doi: 10.1038/ng.2314.

25.

Genome-wide patterns of genetic variation in worldwide Arabidopsis thaliana accessions from the RegMap panel.

Horton MW, Hancock AM, Huang YS, Toomajian C, Atwell S, Auton A, Muliyati NW, Platt A, Sperone FG, Vilhjálmsson BJ, Nordborg M, Borevitz JO, Bergelson J.

Nat Genet. 2012 Jan 8;44(2):212-6. doi: 10.1038/ng.1042.

26.

Analysis and visualization of Arabidopsis thaliana GWAS using web 2.0 technologies.

Huang YS, Horton M, Vilhjálmsson BJ, Seren U, Meng D, Meyer C, Ali Amer M, Borevitz JO, Bergelson J, Nordborg M.

Database (Oxford). 2011 May 23;2011:bar014. doi: 10.1093/database/bar014. Print 2011.

27.

Conditions under which genome-wide association studies will be positively misleading.

Platt A, Vilhjálmsson BJ, Nordborg M.

Genetics. 2010 Nov;186(3):1045-52. doi: 10.1534/genetics.110.121665. Epub 2010 Sep 2.

28.

Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines.

Atwell S, Huang YS, Vilhjálmsson BJ, Willems G, Horton M, Li Y, Meng D, Platt A, Tarone AM, Hu TT, Jiang R, Muliyati NW, Zhang X, Amer MA, Baxter I, Brachi B, Chory J, Dean C, Debieu M, de Meaux J, Ecker JR, Faure N, Kniskern JM, Jones JD, Michael T, Nemri A, Roux F, Salt DE, Tang C, Todesco M, Traw MB, Weigel D, Marjoram P, Borevitz JO, Bergelson J, Nordborg M.

Nature. 2010 Jun 3;465(7298):627-31. doi: 10.1038/nature08800. Epub 2010 Mar 24.

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