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Items: 21

1.

npInv: accurate detection and genotyping of inversions using long read sub-alignment.

Shao H, Ganesamoorthy D, Duarte T, Cao MD, Hoggart CJ, Coin LJM.

BMC Bioinformatics. 2018 Jul 13;19(1):261. doi: 10.1186/s12859-018-2252-9.

2.

Diagnostic Test Accuracy of a 2-Transcript Host RNA Signature for Discriminating Bacterial vs Viral Infection in Febrile Children.

Herberg JA, Kaforou M, Wright VJ, Shailes H, Eleftherohorinou H, Hoggart CJ, Cebey-López M, Carter MJ, Janes VA, Gormley S, Shimizu C, Tremoulet AH, Barendregt AM, Salas A, Kanegaye J, Pollard AJ, Faust SN, Patel S, Kuijpers T, Martinón-Torres F, Burns JC, Coin LJ, Levin M; IRIS Consortium.

JAMA. 2016 Aug 23-30;316(8):835-45. doi: 10.1001/jama.2016.11236. Erratum in: JAMA. 2017 Feb 7;317(5):538.

3.

Predicting IVIG resistance in UK Kawasaki disease.

Davies S, Sutton N, Blackstock S, Gormley S, Hoggart CJ, Levin M, Herberg JA.

Arch Dis Child. 2015 Apr;100(4):366-8. doi: 10.1136/archdischild-2014-307397. Epub 2015 Feb 10.

4.

Novel approach identifies SNPs in SLC2A10 and KCNK9 with evidence for parent-of-origin effect on body mass index.

Hoggart CJ, Venturini G, Mangino M, Gomez F, Ascari G, Zhao JH, Teumer A, Winkler TW, Tšernikova N, Luan J, Mihailov E, Ehret GB, Zhang W, Lamparter D, Esko T, Macé A, Rüeger S, Bochud PY, Barcella M, Dauvilliers Y, Benyamin B, Evans DM, Hayward C, Lopez MF, Franke L, Russo A, Heid IM, Salvi E, Vendantam S, Arking DE, Boerwinkle E, Chambers JC, Fiorito G, Grallert H, Guarrera S, Homuth G, Huffman JE, Porteous D; Generation Scotland Consortium; LifeLines Cohort study; GIANT Consortium, Moradpour D, Iranzo A, Hebebrand J, Kemp JP, Lammers GJ, Aubert V, Heim MH, Martin NG, Montgomery GW, Peraita-Adrados R, Santamaria J, Negro F, Schmidt CO, Scott RA, Spector TD, Strauch K, Völzke H, Wareham NJ, Yuan W, Bell JT, Chakravarti A, Kooner JS, Peters A, Matullo G, Wallaschofski H, Whitfield JB, Paccaud F, Vollenweider P, Bergmann S, Beckmann JS, Tafti M, Hastie ND, Cusi D, Bochud M, Frayling TM, Metspalu A, Jarvelin MR, Scherag A, Smith GD, Borecki IB, Rousson V, Hirschhorn JN, Rivolta C, Loos RJ, Kutalik Z.

PLoS Genet. 2014 Jul 31;10(7):e1004508. doi: 10.1371/journal.pgen.1004508. eCollection 2014 Jul.

5.

Genome-wide association study of primary tooth eruption identifies pleiotropic loci associated with height and craniofacial distances.

Fatemifar G, Hoggart CJ, Paternoster L, Kemp JP, Prokopenko I, Horikoshi M, Wright VJ, Tobias JH, Richmond S, Zhurov AI, Toma AM, Pouta A, Taanila A, Sipila K, Lähdesmäki R, Pillas D, Geller F, Feenstra B, Melbye M, Nohr EA, Ring SM, St Pourcain B, Timpson NJ, Davey Smith G, Jarvelin MR, Evans DM.

Hum Mol Genet. 2013 Sep 15;22(18):3807-17. doi: 10.1093/hmg/ddt231. Epub 2013 May 23.

6.

The effect of genomic inversions on estimation of population genetic parameters from SNP data.

Seich Al Basatena NK, Hoggart CJ, Coin LJ, O'Reilly PF.

Genetics. 2013 Jan;193(1):243-53. doi: 10.1534/genetics.112.145599. Epub 2012 Nov 12.

7.

A multi-SNP locus-association method reveals a substantial fraction of the missing heritability.

Ehret GB, Lamparter D, Hoggart CJ; Genetic Investigation of Anthropometric Traits Consortium, Whittaker JC, Beckmann JS, Kutalik Z.

Am J Hum Genet. 2012 Nov 2;91(5):863-71. doi: 10.1016/j.ajhg.2012.09.013.

8.

MultiPhen: joint model of multiple phenotypes can increase discovery in GWAS.

O'Reilly PF, Hoggart CJ, Pomyen Y, Calboli FC, Elliott P, Jarvelin MR, Coin LJ.

PLoS One. 2012;7(5):e34861. doi: 10.1371/journal.pone.0034861. Epub 2012 May 2.

9.

Fine-scale estimation of location of birth from genome-wide single-nucleotide polymorphism data.

Hoggart CJ, O'Reilly PF, Kaakinen M, Zhang W, Chambers JC, Kooner JS, Coin LJ, Jarvelin MR.

Genetics. 2012 Feb;190(2):669-77. doi: 10.1534/genetics.111.135657. Epub 2011 Nov 17.

10.

Pathway-driven gene stability selection of two rheumatoid arthritis GWAS identifies and validates new susceptibility genes in receptor mediated signalling pathways.

Eleftherohorinou H, Hoggart CJ, Wright VJ, Levin M, Coin LJ.

Hum Mol Genet. 2011 Sep 1;20(17):3494-506. doi: 10.1093/hmg/ddr248. Epub 2011 Jun 8.

PMID:
21653640
11.

Genome-wide association study reveals multiple loci associated with primary tooth development during infancy.

Pillas D, Hoggart CJ, Evans DM, O'Reilly PF, Sipilä K, Lähdesmäki R, Millwood IY, Kaakinen M, Netuveli G, Blane D, Charoen P, Sovio U, Pouta A, Freimer N, Hartikainen AL, Laitinen J, Vaara S, Glaser B, Crawford P, Timpson NJ, Ring SM, Deng G, Zhang W, McCarthy MI, Deloukas P, Peltonen L, Elliott P, Coin LJ, Smith GD, Jarvelin MR.

PLoS Genet. 2010 Feb 26;6(2):e1000856. doi: 10.1371/journal.pgen.1000856.

12.

invertFREGENE: software for simulating inversions in population genetic data.

O'Reilly PF, Coin LJ, Hoggart CJ.

Bioinformatics. 2010 Mar 15;26(6):838-40. doi: 10.1093/bioinformatics/btq029. Epub 2010 Jan 26.

PMID:
20106819
13.

Fregene: simulation of realistic sequence-level data in populations and ascertained samples.

Chadeau-Hyam M, Hoggart CJ, O'Reilly PF, Whittaker JC, De Iorio M, Balding DJ.

BMC Bioinformatics. 2008 Sep 8;9:364. doi: 10.1186/1471-2105-9-364.

14.

Simultaneous analysis of all SNPs in genome-wide and re-sequencing association studies.

Hoggart CJ, Whittaker JC, De Iorio M, Balding DJ.

PLoS Genet. 2008 Jul 25;4(7):e1000130. doi: 10.1371/journal.pgen.1000130.

15.

Genome-wide significance for dense SNP and resequencing data.

Hoggart CJ, Clark TG, De Iorio M, Whittaker JC, Balding DJ.

Genet Epidemiol. 2008 Feb;32(2):179-85. doi: 10.1002/gepi.20292.

PMID:
18200594
16.

Sequence-level population simulations over large genomic regions.

Hoggart CJ, Chadeau-Hyam M, Clark TG, Lampariello R, Whittaker JC, De Iorio M, Balding DJ.

Genetics. 2007 Nov;177(3):1725-31. Epub 2007 Oct 18.

17.

Assessing the relative ages of admixture in the bovine hybrid zones of Africa and the Near East using X chromosome haplotype mosaicism.

Freeman AR, Hoggart CJ, Hanotte O, Bradley DG.

Genetics. 2006 Jul;173(3):1503-10. Epub 2006 Apr 2.

18.

Relation of type 2 diabetes to individual admixture and candidate gene polymorphisms in the Hispanic American population of San Luis Valley, Colorado.

Parra EJ, Hoggart CJ, Bonilla C, Dios S, Norris JM, Marshall JA, Hamman RF, Ferrell RE, McKeigue PM, Shriver MD.

J Med Genet. 2004 Nov;41(11):e116. No abstract available.

19.

Design and analysis of admixture mapping studies.

Hoggart CJ, Shriver MD, Kittles RA, Clayton DG, McKeigue PM.

Am J Hum Genet. 2004 May;74(5):965-78. Epub 2004 Apr 14.

20.

Control of confounding of genetic associations in stratified populations.

Hoggart CJ, Parra EJ, Shriver MD, Bonilla C, Kittles RA, Clayton DG, McKeigue PM.

Am J Hum Genet. 2003 Jun;72(6):1492-1504.

21.

Skin pigmentation, biogeographical ancestry and admixture mapping.

Shriver MD, Parra EJ, Dios S, Bonilla C, Norton H, Jovel C, Pfaff C, Jones C, Massac A, Cameron N, Baron A, Jackson T, Argyropoulos G, Jin L, Hoggart CJ, McKeigue PM, Kittles RA.

Hum Genet. 2003 Apr;112(4):387-99. Epub 2003 Feb 11.

PMID:
12579416

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