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Items: 1 to 20 of 54

1.

Contribution of retrotransposition to developmental disorders.

Gardner EJ, Prigmore E, Gallone G, Danecek P, Samocha KE, Handsaker J, Gerety SS, Ironfield H, Short PJ, Sifrim A, Singh T, Chandler KE, Clement E, Lachlan KL, Prescott K, Rosser E, FitzPatrick DR, Firth HV, Hurles ME.

Nat Commun. 2019 Oct 11;10(1):4630. doi: 10.1038/s41467-019-12520-y.

2.

Induction of Neural Crest Stem Cells From Bardet-Biedl Syndrome Patient Derived hiPSCs.

Barrell WB, Griffin JN, Harvey JL; HipSci Consortium, Danovi D, Beales P, Grigoriadis AE, Liu KJ.

Front Mol Neurosci. 2019 Jun 21;12:139. doi: 10.3389/fnmol.2019.00139. eCollection 2019.

3.

Low-frequency variation in TP53 has large effects on head circumference and intracranial volume.

Haworth S, Shapland CY, Hayward C, Prins BP, Felix JF, Medina-Gomez C, Rivadeneira F, Wang C, Ahluwalia TS, Vrijheid M, Guxens M, Sunyer J, Tachmazidou I, Walter K, Iotchkova V, Jackson A, Cleal L, Huffmann J, Min JL, Sass L, Timmers PRHJ; UK10K consortium, Davey Smith G, Fisher SE, Wilson JF, Cole TJ, Fernandez-Orth D, Bønnelykke K, Bisgaard H, Pennell CE, Jaddoe VWV, Dedoussis G, Timpson N, Zeggini E, Vitart V, St Pourcain B.

Nat Commun. 2019 Jan 21;10(1):357. doi: 10.1038/s41467-018-07863-x.

4.

Very low-depth whole-genome sequencing in complex trait association studies.

Gilly A, Southam L, Suveges D, Kuchenbaecker K, Moore R, Melloni GEM, Hatzikotoulas K, Farmaki AE, Ritchie G, Schwartzentruber J, Danecek P, Kilian B, Pollard MO, Ge X, Tsafantakis E, Dedoussis G, Zeggini E.

Bioinformatics. 2019 Aug 1;35(15):2555-2561. doi: 10.1093/bioinformatics/bty1032.

5.

Sixteen diverse laboratory mouse reference genomes define strain-specific haplotypes and novel functional loci.

Lilue J, Doran AG, Fiddes IT, Abrudan M, Armstrong J, Bennett R, Chow W, Collins J, Collins S, Czechanski A, Danecek P, Diekhans M, Dolle DD, Dunn M, Durbin R, Earl D, Ferguson-Smith A, Flicek P, Flint J, Frankish A, Fu B, Gerstein M, Gilbert J, Goodstadt L, Harrow J, Howe K, Ibarra-Soria X, Kolmogorov M, Lelliott CJ, Logan DW, Loveland J, Mathews CE, Mott R, Muir P, Nachtweide S, Navarro FCP, Odom DT, Park N, Pelan S, Pham SK, Quail M, Reinholdt L, Romoth L, Shirley L, Sisu C, Sjoberg-Herrera M, Stanke M, Steward C, Thomas M, Threadgold G, Thybert D, Torrance J, Wong K, Wood J, Yalcin B, Yang F, Adams DJ, Paten B, Keane TM.

Nat Genet. 2018 Nov;50(11):1574-1583. doi: 10.1038/s41588-018-0223-8. Epub 2018 Oct 1.

6.

Ancient human parallel lineages within North America contributed to a coastal expansion.

Scheib CL, Li H, Desai T, Link V, Kendall C, Dewar G, Griffith PW, Mörseburg A, Johnson JR, Potter A, Kerr SL, Endicott P, Lindo J, Haber M, Xue Y, Tyler-Smith C, Sandhu MS, Lorenz JG, Randall TD, Faltyskova Z, Pagani L, Danecek P, O'Connell TC, Martz P, Boraas AS, Byrd BF, Leventhal A, Cambra R, Williamson R, Lesage L, Holguin B, Ygnacio-De Soto E, Rosas J, Metspalu M, Stock JT, Manica A, Scally A, Wegmann D, Malhi RS, Kivisild T.

Science. 2018 Jun 1;360(6392):1024-1027. doi: 10.1126/science.aar6851.

PMID:
29853687
7.

Response to Giem.

Haber M, Doumet-Serhal C, Scheib C, Xue Y, Danecek P, Mezzavilla M, Youhanna S, Martiniano R, Prado-Martinez J, Szpak M, Matisoo-Smith E, Schutkowski H, Mikulski R, Zalloua P, Kivisild T, Tyler-Smith C.

Am J Hum Genet. 2018 Feb 1;102(2):331. doi: 10.1016/j.ajhg.2018.01.002. No abstract available.

8.

Continuity and Admixture in the Last Five Millennia of Levantine History from Ancient Canaanite and Present-Day Lebanese Genome Sequences.

Haber M, Doumet-Serhal C, Scheib C, Xue Y, Danecek P, Mezzavilla M, Youhanna S, Martiniano R, Prado-Martinez J, Szpak M, Matisoo-Smith E, Schutkowski H, Mikulski R, Zalloua P, Kivisild T, Tyler-Smith C.

Am J Hum Genet. 2017 Aug 3;101(2):274-282. doi: 10.1016/j.ajhg.2017.06.013. Epub 2017 Jul 27.

9.

Rare Variant Analysis of Human and Rodent Obesity Genes in Individuals with Severe Childhood Obesity.

Hendricks AE, Bochukova EG, Marenne G, Keogh JM, Atanassova N, Bounds R, Wheeler E, Mistry V, Henning E, Körner A, Muddyman D, McCarthy S, Hinney A, Hebebrand J, Scott RA, Langenberg C, Wareham NJ, Surendran P, Howson JM, Butterworth AS, Danesh J, Nordestgaard BG, Nielsen SF, Afzal S, Papadia S, Ashford S, Garg S, Millhauser GL, Palomino RI, Kwasniewska A, Tachmazidou I, O'Rahilly S, Zeggini E, Barroso I, Farooqi IS; Understanding Society Scientific Group; EPIC-CVD Consortium; UK10K Consortium.

Sci Rep. 2017 Jun 29;7(1):4394. doi: 10.1038/s41598-017-03054-8.

10.

Corrigendum: Common genetic variation drives molecular heterogeneity in human iPSCs.

Kilpinen H, Goncalves A, Leha A, Afzal V, Alasoo K, Ashford S, Bala S, Bensaddek D, Casale FP, Culley OJ, Danecek P, Faulconbridge A, Harrison PW, Kathuria A, McCarthy D, McCarthy SA, Meleckyte R, Memari Y, Moens N, Soares F, Mann A, Streeter I, Agu CA, Alderton A, Nelson R, Harper S, Patel M, White A, Patel SR, Clarke L, Halai R, Kirton CM, Kolb-Kokocinski A, Beales P, Birney E, Danovi D, Lamond AI, Ouwehand WH, Vallier L, Watt FM, Durbin R, Stegle O, Gaffney DJ.

Nature. 2017 Jun 29;546(7660):686. doi: 10.1038/nature23012. Epub 2017 Jun 14.

PMID:
28614302
11.

Whole-Genome Sequencing Coupled to Imputation Discovers Genetic Signals for Anthropometric Traits.

Tachmazidou I, Süveges D, Min JL, Ritchie GRS, Steinberg J, Walter K, Iotchkova V, Schwartzentruber J, Huang J, Memari Y, McCarthy S, Crawford AA, Bombieri C, Cocca M, Farmaki AE, Gaunt TR, Jousilahti P, Kooijman MN, Lehne B, Malerba G, Männistö S, Matchan A, Medina-Gomez C, Metrustry SJ, Nag A, Ntalla I, Paternoster L, Rayner NW, Sala C, Scott WR, Shihab HA, Southam L, St Pourcain B, Traglia M, Trajanoska K, Zaza G, Zhang W, Artigas MS, Bansal N, Benn M, Chen Z, Danecek P, Lin WY, Locke A, Luan J, Manning AK, Mulas A, Sidore C, Tybjaerg-Hansen A, Varbo A, Zoledziewska M, Finan C, Hatzikotoulas K, Hendricks AE, Kemp JP, Moayyeri A, Panoutsopoulou K, Szpak M, Wilson SG, Boehnke M, Cucca F, Di Angelantonio E, Langenberg C, Lindgren C, McCarthy MI, Morris AP, Nordestgaard BG, Scott RA, Tobin MD, Wareham NJ; SpiroMeta Consortium; GoT2D Consortium, Burton P, Chambers JC, Smith GD, Dedoussis G, Felix JF, Franco OH, Gambaro G, Gasparini P, Hammond CJ, Hofman A, Jaddoe VWV, Kleber M, Kooner JS, Perola M, Relton C, Ring SM, Rivadeneira F, Salomaa V, Spector TD, Stegle O, Toniolo D, Uitterlinden AG; arcOGEN Consortium; Understanding Society Scientific Group; UK10K Consortium, Barroso I, Greenwood CMT, Perry JRB, Walker BR, Butterworth AS, Xue Y, Durbin R, Small KS, Soranzo N, Timpson NJ, Zeggini E.

Am J Hum Genet. 2017 Jun 1;100(6):865-884. doi: 10.1016/j.ajhg.2017.04.014. Epub 2017 May 25.

12.

Common genetic variation drives molecular heterogeneity in human iPSCs.

Kilpinen H, Goncalves A, Leha A, Afzal V, Alasoo K, Ashford S, Bala S, Bensaddek D, Casale FP, Culley OJ, Danecek P, Faulconbridge A, Harrison PW, Kathuria A, McCarthy D, McCarthy SA, Meleckyte R, Memari Y, Moens N, Soares F, Mann A, Streeter I, Agu CA, Alderton A, Nelson R, Harper S, Patel M, White A, Patel SR, Clarke L, Halai R, Kirton CM, Kolb-Kokocinski A, Beales P, Birney E, Danovi D, Lamond AI, Ouwehand WH, Vallier L, Watt FM, Durbin R, Stegle O, Gaffney DJ.

Nature. 2017 Jun 15;546(7658):370-375. doi: 10.1038/nature22403. Epub 2017 May 10. Erratum in: Nature. 2017 Jun 29;546(7660):686.

13.

BCFtools/csq: haplotype-aware variant consequences.

Danecek P, McCarthy SA.

Bioinformatics. 2017 Jul 1;33(13):2037-2039. doi: 10.1093/bioinformatics/btx100.

14.

Reference-based phasing using the Haplotype Reference Consortium panel.

Loh PR, Danecek P, Palamara PF, Fuchsberger C, A Reshef Y, K Finucane H, Schoenherr S, Forer L, McCarthy S, Abecasis GR, Durbin R, L Price A.

Nat Genet. 2016 Nov;48(11):1443-1448. doi: 10.1038/ng.3679. Epub 2016 Oct 3.

15.

A reference panel of 64,976 haplotypes for genotype imputation.

McCarthy S, Das S, Kretzschmar W, Delaneau O, Wood AR, Teumer A, Kang HM, Fuchsberger C, Danecek P, Sharp K, Luo Y, Sidore C, Kwong A, Timpson N, Koskinen S, Vrieze S, Scott LJ, Zhang H, Mahajan A, Veldink J, Peters U, Pato C, van Duijn CM, Gillies CE, Gandin I, Mezzavilla M, Gilly A, Cocca M, Traglia M, Angius A, Barrett JC, Boomsma D, Branham K, Breen G, Brummett CM, Busonero F, Campbell H, Chan A, Chen S, Chew E, Collins FS, Corbin LJ, Smith GD, Dedoussis G, Dorr M, Farmaki AE, Ferrucci L, Forer L, Fraser RM, Gabriel S, Levy S, Groop L, Harrison T, Hattersley A, Holmen OL, Hveem K, Kretzler M, Lee JC, McGue M, Meitinger T, Melzer D, Min JL, Mohlke KL, Vincent JB, Nauck M, Nickerson D, Palotie A, Pato M, Pirastu N, McInnis M, Richards JB, Sala C, Salomaa V, Schlessinger D, Schoenherr S, Slagboom PE, Small K, Spector T, Stambolian D, Tuke M, Tuomilehto J, Van den Berg LH, Van Rheenen W, Volker U, Wijmenga C, Toniolo D, Zeggini E, Gasparini P, Sampson MG, Wilson JF, Frayling T, de Bakker PI, Swertz MA, McCarroll S, Kooperberg C, Dekker A, Altshuler D, Willer C, Iacono W, Ripatti S, Soranzo N, Walter K, Swaroop A, Cucca F, Anderson CA, Myers RM, Boehnke M, McCarthy MI, Durbin R; Haplotype Reference Consortium.

Nat Genet. 2016 Oct;48(10):1279-83. doi: 10.1038/ng.3643. Epub 2016 Aug 22.

16.

A Method for Checking Genomic Integrity in Cultured Cell Lines from SNP Genotyping Data.

Danecek P, McCarthy SA; HipSci Consortium, Durbin R.

PLoS One. 2016 May 13;11(5):e0155014. doi: 10.1371/journal.pone.0155014. eCollection 2016.

17.

An organelle-specific protein landscape identifies novel diseases and molecular mechanisms.

Boldt K, van Reeuwijk J, Lu Q, Koutroumpas K, Nguyen TM, Texier Y, van Beersum SE, Horn N, Willer JR, Mans DA, Dougherty G, Lamers IJ, Coene KL, Arts HH, Betts MJ, Beyer T, Bolat E, Gloeckner CJ, Haidari K, Hetterschijt L, Iaconis D, Jenkins D, Klose F, Knapp B, Latour B, Letteboer SJ, Marcelis CL, Mitic D, Morleo M, Oud MM, Riemersma M, Rix S, Terhal PA, Toedt G, van Dam TJ, de Vrieze E, Wissinger Y, Wu KM, Apic G, Beales PL, Blacque OE, Gibson TJ, Huynen MA, Katsanis N, Kremer H, Omran H, van Wijk E, Wolfrum U, Kepes F, Davis EE, Franco B, Giles RH, Ueffing M, Russell RB, Roepman R; UK10K Rare Diseases Group.

Nat Commun. 2016 May 13;7:11491. doi: 10.1038/ncomms11491.

18.

BCFtools/RoH: a hidden Markov model approach for detecting autozygosity from next-generation sequencing data.

Narasimhan V, Danecek P, Scally A, Xue Y, Tyler-Smith C, Durbin R.

Bioinformatics. 2016 Jun 1;32(11):1749-51. doi: 10.1093/bioinformatics/btw044. Epub 2016 Jan 30.

19.

Timing, rates and spectra of human germline mutation.

Rahbari R, Wuster A, Lindsay SJ, Hardwick RJ, Alexandrov LB, Turki SA, Dominiczak A, Morris A, Porteous D, Smith B, Stratton MR; UK10K Consortium, Hurles ME.

Nat Genet. 2016 Feb;48(2):126-133. doi: 10.1038/ng.3469. Epub 2015 Dec 14.

20.

A global reference for human genetic variation.

1000 Genomes Project Consortium, Auton A, Brooks LD, Durbin RM, Garrison EP, Kang HM, Korbel JO, Marchini JL, McCarthy S, McVean GA, Abecasis GR.

Nature. 2015 Oct 1;526(7571):68-74. doi: 10.1038/nature15393.

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