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Items: 26

1.

Detailed analysis of chick optic fissure closure reveals Netrin-1 as an essential mediator of epithelial fusion.

Hardy H, Prendergast JG, Patel A, Dutta S, Trejo-Reveles V, Kroeger H, Yung AR, Goodrich LV, Brooks B, Sowden JC, Rainger J.

Elife. 2019 Jun 4;8. pii: e43877. doi: 10.7554/eLife.43877.

2.

Examining the Impact of Imputation Errors on Fine-Mapping Using DNA Methylation QTL as a Model Trait.

Chundru VK, Marioni RE, Prendergast JGD, Vallerga CL, Lin T, Beveridge AJ; SGPD Consortium, Gratten J, Hume DA, Deary IJ, Wray NR, Visscher PM, McRae AF.

Genetics. 2019 Jul;212(3):577-586. doi: 10.1534/genetics.118.301861. Epub 2019 Apr 30.

3.

Arginine to Glutamine Variant in Olfactomedin Like 3 (OLFML3) Is a Candidate for Severe Goniodysgenesis and Glaucoma in the Border Collie Dog Breed.

Pugh CA, Farrell LL, Carlisle AJ, Bush SJ, Ewing A, Trejo-Reveles V, Matika O, de Kloet A, Walsh C, Bishop SC, Prendergast JGD, Rainger J, Schoenebeck JJ, Summers KM.

G3 (Bethesda). 2019 Mar 7;9(3):943-954. doi: 10.1534/g3.118.200944.

4.

Linked Mutations at Adjacent Nucleotides Have Shaped Human Population Differentiation and Protein Evolution.

Prendergast JGD, Pugh C, Harris SE, Hume DA, Deary IJ, Beveridge A.

Genome Biol Evol. 2019 Mar 1;11(3):759-775. doi: 10.1093/gbe/evz014.

5.

Shared regulatory sites are abundant in the human genome and shed light on genome evolution and disease pleiotropy.

Tong P, Monahan J, Prendergast JG.

PLoS Genet. 2017 Mar 10;13(3):e1006673. doi: 10.1371/journal.pgen.1006673. eCollection 2017 Mar.

6.

hapbin: An Efficient Program for Performing Haplotype-Based Scans for Positive Selection in Large Genomic Datasets.

Maclean CA, Chue Hong NP, Prendergast JG.

Mol Biol Evol. 2015 Nov;32(11):3027-9. doi: 10.1093/molbev/msv172. Epub 2015 Aug 6.

7.

Homozygous loss-of-function variants in European cosmopolitan and isolate populations.

Kaiser VB, Svinti V, Prendergast JG, Chau YY, Campbell A, Patarcic I, Barroso I, Joshi PK, Hastie ND, Miljkovic A, Taylor MS; Generation Scotland; UK10K, Enroth S, Memari Y, Kolb-Kokocinski A, Wright AF, Gyllensten U, Durbin R, Rudan I, Campbell H, Polašek O, Johansson Å, Sauer S, Porteous DJ, Fraser RM, Drake C, Vitart V, Hayward C, Semple CA, Wilson JF.

Hum Mol Genet. 2015 Oct 1;24(19):5464-74. doi: 10.1093/hmg/ddv272. Epub 2015 Jul 14.

8.

Exome sequencing to detect rare variants associated with general cognitive ability: a pilot study.

Luciano M, Svinti V, Campbell A, Marioni RE, Hayward C, Wright AF, Taylor MS, Porteous DJ, Thomson P, Prendergast JG, Hastie ND, Farrington SM, Scotland G, Dunlop MG, Deary IJ.

Twin Res Hum Genet. 2015 Apr;18(2):117-25. doi: 10.1017/thg.2015.10. Epub 2015 Mar 6.

PMID:
25744449
9.

Interactions with actin monomers, actin filaments, and Arp2/3 complex define the roles of WASP family proteins and cortactin in coordinately regulating branched actin networks.

Helgeson LA, Prendergast JG, Wagner AR, Rodnick-Smith M, Nolen BJ.

J Biol Chem. 2014 Oct 17;289(42):28856-69. doi: 10.1074/jbc.M114.587527. Epub 2014 Aug 26.

10.

Sequence-level mechanisms of human epigenome evolution.

Prendergast JG, Chambers EV, Semple CA.

Genome Biol Evol. 2014 Jun 24;6(7):1758-71. doi: 10.1093/gbe/evu142.

11.

A promoter-level mammalian expression atlas.

FANTOM Consortium and the RIKEN PMI and CLST (DGT), Forrest AR, Kawaji H, Rehli M, Baillie JK, de Hoon MJ, Haberle V, Lassmann T, Kulakovskiy IV, Lizio M, Itoh M, Andersson R, Mungall CJ, Meehan TF, Schmeier S, Bertin N, Jørgensen M, Dimont E, Arner E, Schmidl C, Schaefer U, Medvedeva YA, Plessy C, Vitezic M, Severin J, Semple C, Ishizu Y, Young RS, Francescatto M, Alam I, Albanese D, Altschuler GM, Arakawa T, Archer JA, Arner P, Babina M, Rennie S, Balwierz PJ, Beckhouse AG, Pradhan-Bhatt S, Blake JA, Blumenthal A, Bodega B, Bonetti A, Briggs J, Brombacher F, Burroughs AM, Califano A, Cannistraci CV, Carbajo D, Chen Y, Chierici M, Ciani Y, Clevers HC, Dalla E, Davis CA, Detmar M, Diehl AD, Dohi T, Drabløs F, Edge AS, Edinger M, Ekwall K, Endoh M, Enomoto H, Fagiolini M, Fairbairn L, Fang H, Farach-Carson MC, Faulkner GJ, Favorov AV, Fisher ME, Frith MC, Fujita R, Fukuda S, Furlanello C, Furino M, Furusawa J, Geijtenbeek TB, Gibson AP, Gingeras T, Goldowitz D, Gough J, Guhl S, Guler R, Gustincich S, Ha TJ, Hamaguchi M, Hara M, Harbers M, Harshbarger J, Hasegawa A, Hasegawa Y, Hashimoto T, Herlyn M, Hitchens KJ, Ho Sui SJ, Hofmann OM, Hoof I, Hori F, Huminiecki L, Iida K, Ikawa T, Jankovic BR, Jia H, Joshi A, Jurman G, Kaczkowski B, Kai C, Kaida K, Kaiho A, Kajiyama K, Kanamori-Katayama M, Kasianov AS, Kasukawa T, Katayama S, Kato S, Kawaguchi S, Kawamoto H, Kawamura YI, Kawashima T, Kempfle JS, Kenna TJ, Kere J, Khachigian LM, Kitamura T, Klinken SP, Knox AJ, Kojima M, Kojima S, Kondo N, Koseki H, Koyasu S, Krampitz S, Kubosaki A, Kwon AT, Laros JF, Lee W, Lennartsson A, Li K, Lilje B, Lipovich L, Mackay-Sim A, Manabe R, Mar JC, Marchand B, Mathelier A, Mejhert N, Meynert A, Mizuno Y, de Lima Morais DA, Morikawa H, Morimoto M, Moro K, Motakis E, Motohashi H, Mummery CL, Murata M, Nagao-Sato S, Nakachi Y, Nakahara F, Nakamura T, Nakamura Y, Nakazato K, van Nimwegen E, Ninomiya N, Nishiyori H, Noma S, Noma S, Noazaki T, Ogishima S, Ohkura N, Ohimiya H, Ohno H, Ohshima M, Okada-Hatakeyama M, Okazaki Y, Orlando V, Ovchinnikov DA, Pain A, Passier R, Patrikakis M, Persson H, Piazza S, Prendergast JG, Rackham OJ, Ramilowski JA, Rashid M, Ravasi T, Rizzu P, Roncador M, Roy S, Rye MB, Saijyo E, Sajantila A, Saka A, Sakaguchi S, Sakai M, Sato H, Savvi S, Saxena A, Schneider C, Schultes EA, Schulze-Tanzil GG, Schwegmann A, Sengstag T, Sheng G, Shimoji H, Shimoni Y, Shin JW, Simon C, Sugiyama D, Sugiyama T, Suzuki M, Suzuki N, Swoboda RK, 't Hoen PA, Tagami M, Takahashi N, Takai J, Tanaka H, Tatsukawa H, Tatum Z, Thompson M, Toyodo H, Toyoda T, Valen E, van de Wetering M, van den Berg LM, Verado R, Vijayan D, Vorontsov IE, Wasserman WW, Watanabe S, Wells CA, Winteringham LN, Wolvetang E, Wood EJ, Yamaguchi Y, Yamamoto M, Yoneda M, Yonekura Y, Yoshida S, Zabierowski SE, Zhang PG, Zhao X, Zucchelli S, Summers KM, Suzuki H, Daub CO, Kawai J, Heutink P, Hide W, Freeman TC, Lenhard B, Bajic VB, Taylor MS, Makeev VJ, Sandelin A, Hume DA, Carninci P, Hayashizaki Y.

Nature. 2014 Mar 27;507(7493):462-70. doi: 10.1038/nature13182.

12.

Side effects: substantial non-neutral evolution flanking regulatory sites.

Prendergast JG, Semple CA.

PLoS Genet. 2013 May;9(5):e1003528. doi: 10.1371/journal.pgen.1003528. Epub 2013 May 30. No abstract available.

13.

Redistribution of H3K27me3 upon DNA hypomethylation results in de-repression of Polycomb target genes.

Reddington JP, Perricone SM, Nestor CE, Reichmann J, Youngson NA, Suzuki M, Reinhardt D, Dunican DS, Prendergast JG, Mjoseng H, Ramsahoye BH, Whitelaw E, Greally JM, Adams IR, Bickmore WA, Meehan RR.

Genome Biol. 2013 Mar 25;14(3):R25. doi: 10.1186/gb-2013-14-3-r25.

14.

Transcription forms and remodels supercoiling domains unfolding large-scale chromatin structures.

Naughton C, Avlonitis N, Corless S, Prendergast JG, Mati IK, Eijk PP, Cockroft SL, Bradley M, Ylstra B, Gilbert N.

Nat Struct Mol Biol. 2013 Mar;20(3):387-95. doi: 10.1038/nsmb.2509. Epub 2013 Feb 17.

15.

A genome-wide screen in human embryonic stem cells reveals novel sites of allele-specific histone modification associated with known disease loci.

Prendergast JG, Tong P, Hay DC, Farrington SM, Semple CA.

Epigenetics Chromatin. 2012 May 19;5(1):6. doi: 10.1186/1756-8935-5-6.

16.

Abundant pleiotropy in human complex diseases and traits.

Sivakumaran S, Agakov F, Theodoratou E, Prendergast JG, Zgaga L, Manolio T, Rudan I, McKeigue P, Wilson JF, Campbell H.

Am J Hum Genet. 2011 Nov 11;89(5):607-18. doi: 10.1016/j.ajhg.2011.10.004. Review.

17.

Genome-wide methylation profiling in Crohn's disease identifies altered epigenetic regulation of key host defense mechanisms including the Th17 pathway.

Nimmo ER, Prendergast JG, Aldhous MC, Kennedy NA, Henderson P, Drummond HE, Ramsahoye BH, Wilson DC, Semple CA, Satsangi J.

Inflamm Bowel Dis. 2012 May;18(5):889-99. doi: 10.1002/ibd.21912. Epub 2011 Oct 21.

PMID:
22021194
18.

Widespread signatures of recent selection linked to nucleosome positioning in the human lineage.

Prendergast JG, Semple CA.

Genome Res. 2011 Nov;21(11):1777-87. doi: 10.1101/gr.122275.111. Epub 2011 Sep 8.

19.

Multiple common susceptibility variants near BMP pathway loci GREM1, BMP4, and BMP2 explain part of the missing heritability of colorectal cancer.

Tomlinson IP, Carvajal-Carmona LG, Dobbins SE, Tenesa A, Jones AM, Howarth K, Palles C, Broderick P, Jaeger EE, Farrington S, Lewis A, Prendergast JG, Pittman AM, Theodoratou E, Olver B, Walker M, Penegar S, Barclay E, Whiffin N, Martin L, Ballereau S, Lloyd A, Gorman M, Lubbe S; COGENT Consortium; CORGI Collaborators; EPICOLON Consortium, Howie B, Marchini J, Ruiz-Ponte C, Fernandez-Rozadilla C, Castells A, Carracedo A, Castellvi-Bel S, Duggan D, Conti D, Cazier JB, Campbell H, Sieber O, Lipton L, Gibbs P, Martin NG, Montgomery GW, Young J, Baird PN, Gallinger S, Newcomb P, Hopper J, Jenkins MA, Aaltonen LA, Kerr DJ, Cheadle J, Pharoah P, Casey G, Houlston RS, Dunlop MG.

PLoS Genet. 2011 Jun;7(6):e1002105. doi: 10.1371/journal.pgen.1002105. Epub 2011 Jun 2.

20.

Sequencing illustrates the transcriptional response of Legionella pneumophila during infection and identifies seventy novel small non-coding RNAs.

Weissenmayer BA, Prendergast JG, Lohan AJ, Loftus BJ.

PLoS One. 2011 Mar 3;6(3):e17570. doi: 10.1371/journal.pone.0017570.

21.

Meta-analysis of three genome-wide association studies identifies susceptibility loci for colorectal cancer at 1q41, 3q26.2, 12q13.13 and 20q13.33.

Houlston RS, Cheadle J, Dobbins SE, Tenesa A, Jones AM, Howarth K, Spain SL, Broderick P, Domingo E, Farrington S, Prendergast JG, Pittman AM, Theodoratou E, Smith CG, Olver B, Walther A, Barnetson RA, Churchman M, Jaeger EE, Penegar S, Barclay E, Martin L, Gorman M, Mager R, Johnstone E, Midgley R, Niittymäki I, Tuupanen S, Colley J, Idziaszczyk S; COGENT Consortium, Thomas HJ, Lucassen AM, Evans DG, Maher ER; CORGI Consortium; COIN Collaborative Group; COINB Collaborative Group, Maughan T, Dimas A, Dermitzakis E, Cazier JB, Aaltonen LA, Pharoah P, Kerr DJ, Carvajal-Carmona LG, Campbell H, Dunlop MG, Tomlinson IP.

Nat Genet. 2010 Nov;42(11):973-7. doi: 10.1038/ng.670. Epub 2010 Oct 24.

22.

Sequencing and analysis of an Irish human genome.

Tong P, Prendergast JG, Lohan AJ, Farrington SM, Cronin S, Friel N, Bradley DG, Hardiman O, Evans A, Wilson JF, Loftus B.

Genome Biol. 2010;11(9):R91. doi: 10.1186/gb-2010-11-9-r91. Epub 2010 Sep 7.

23.

Meta-analysis of genome-wide association data identifies four new susceptibility loci for colorectal cancer.

COGENT Study, Houlston RS, Webb E, Broderick P, Pittman AM, Di Bernardo MC, Lubbe S, Chandler I, Vijayakrishnan J, Sullivan K, Penegar S; Colorectal Cancer Association Study Consortium, Carvajal-Carmona L, Howarth K, Jaeger E, Spain SL, Walther A, Barclay E, Martin L, Gorman M, Domingo E, Teixeira AS; CoRGI Consortium, Kerr D, Cazier JB, Niittymäki I, Tuupanen S, Karhu A, Aaltonen LA, Tomlinson IP, Farrington SM, Tenesa A, Prendergast JG, Barnetson RA, Cetnarskyj R, Porteous ME, Pharoah PD, Koessler T, Hampe J, Buch S, Schafmayer C, Tepel J, Schreiber S, Völzke H, Chang-Claude J, Hoffmeister M, Brenner H, Zanke BW, Montpetit A, Hudson TJ, Gallinger S, Campbell H, Dunlop MG.

Nat Genet. 2008 Dec;40(12):1426-35. doi: 10.1038/ng.262. Epub 2008 Nov 16.

24.

A genome-wide association study identifies colorectal cancer susceptibility loci on chromosomes 10p14 and 8q23.3.

Tomlinson IP, Webb E, Carvajal-Carmona L, Broderick P, Howarth K, Pittman AM, Spain S, Lubbe S, Walther A, Sullivan K, Jaeger E, Fielding S, Rowan A, Vijayakrishnan J, Domingo E, Chandler I, Kemp Z, Qureshi M, Farrington SM, Tenesa A, Prendergast JG, Barnetson RA, Penegar S, Barclay E, Wood W, Martin L, Gorman M, Thomas H, Peto J, Bishop DT, Gray R, Maher ER, Lucassen A, Kerr D, Evans DG; CORGI Consortium, Schafmayer C, Buch S, Völzke H, Hampe J, Schreiber S, John U, Koessler T, Pharoah P, van Wezel T, Morreau H, Wijnen JT, Hopper JL, Southey MC, Giles GG, Severi G, Castellví-Bel S, Ruiz-Ponte C, Carracedo A, Castells A; EPICOLON Consortium, Försti A, Hemminki K, Vodicka P, Naccarati A, Lipton L, Ho JW, Cheng KK, Sham PC, Luk J, Agúndez JA, Ladero JM, de la Hoya M, Caldés T, Niittymäki I, Tuupanen S, Karhu A, Aaltonen L, Cazier JB, Campbell H, Dunlop MG, Houlston RS.

Nat Genet. 2008 May;40(5):623-30. doi: 10.1038/ng.111. Epub 2008 Mar 30.

PMID:
18372905
25.

Genome-wide association scan identifies a colorectal cancer susceptibility locus on 11q23 and replicates risk loci at 8q24 and 18q21.

Tenesa A, Farrington SM, Prendergast JG, Porteous ME, Walker M, Haq N, Barnetson RA, Theodoratou E, Cetnarskyj R, Cartwright N, Semple C, Clark AJ, Reid FJ, Smith LA, Kavoussanakis K, Koessler T, Pharoah PD, Buch S, Schafmayer C, Tepel J, Schreiber S, Völzke H, Schmidt CO, Hampe J, Chang-Claude J, Hoffmeister M, Brenner H, Wilkening S, Canzian F, Capella G, Moreno V, Deary IJ, Starr JM, Tomlinson IP, Kemp Z, Howarth K, Carvajal-Carmona L, Webb E, Broderick P, Vijayakrishnan J, Houlston RS, Rennert G, Ballinger D, Rozek L, Gruber SB, Matsuda K, Kidokoro T, Nakamura Y, Zanke BW, Greenwood CM, Rangrej J, Kustra R, Montpetit A, Hudson TJ, Gallinger S, Campbell H, Dunlop MG.

Nat Genet. 2008 May;40(5):631-7. doi: 10.1038/ng.133. Epub 2008 Mar 30.

26.

Chromatin structure and evolution in the human genome.

Prendergast JG, Campbell H, Gilbert N, Dunlop MG, Bickmore WA, Semple CA.

BMC Evol Biol. 2007 May 9;7:72.

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