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Items: 45

1.

DNA methylation aging clocks: challenges and recommendations.

Bell CG, Lowe R, Adams PD, Baccarelli AA, Beck S, Bell JT, Christensen BC, Gladyshev VN, Heijmans BT, Horvath S, Ideker T, Issa JJ, Kelsey KT, Marioni RE, Reik W, Relton CL, Schalkwyk LC, Teschendorff AE, Wagner W, Zhang K, Rakyan VK.

Genome Biol. 2019 Nov 25;20(1):249. doi: 10.1186/s13059-019-1824-y. Review.

2.

Early life diet conditions the molecular response to post-weaning protein restriction in the mouse.

Danson AF, Marzi SJ, Lowe R, Holland ML, Rakyan VK.

BMC Biol. 2018 May 2;16(1):51. doi: 10.1186/s12915-018-0516-5.

3.

Ageing-associated DNA methylation dynamics are a molecular readout of lifespan variation among mammalian species.

Lowe R, Barton C, Jenkins CA, Ernst C, Forman O, Fernandez-Twinn DS, Bock C, Rossiter SJ, Faulkes CG, Ozanne SE, Walter L, Odom DT, Mellersh C, Rakyan VK.

Genome Biol. 2018 Feb 16;19(1):22. doi: 10.1186/s13059-018-1397-1.

4.

Integration of human pancreatic islet genomic data refines regulatory mechanisms at Type 2 Diabetes susceptibility loci.

Thurner M, van de Bunt M, Torres JM, Mahajan A, Nylander V, Bennett AJ, Gaulton KJ, Barrett A, Burrows C, Bell CG, Lowe R, Beck S, Rakyan VK, Gloyn AL, McCarthy MI.

Elife. 2018 Feb 7;7. pii: e31977. doi: 10.7554/eLife.31977.

5.

Increased DNA methylation variability in type 1 diabetes across three immune effector cell types.

Paul DS, Teschendorff AE, Dang MA, Lowe R, Hawa MI, Ecker S, Beyan H, Cunningham S, Fouts AR, Ramelius A, Burden F, Farrow S, Rowlston S, Rehnstrom K, Frontini M, Downes K, Busche S, Cheung WA, Ge B, Simon MM, Bujold D, Kwan T, Bourque G, Datta A, Lowy E, Clarke L, Flicek P, Libertini E, Heath S, Gut M, Gut IG, Ouwehand WH, Pastinen T, Soranzo N, Hofer SE, Karges B, Meissner T, Boehm BO, Cilio C, Elding Larsson H, Lernmark Å, Steck AK, Rakyan VK, Beck S, Leslie RD.

Nat Commun. 2016 Nov 29;7:13555. doi: 10.1038/ncomms13555.

6.

eFORGE: A Tool for Identifying Cell Type-Specific Signal in Epigenomic Data.

Breeze CE, Paul DS, van Dongen J, Butcher LM, Ambrose JC, Barrett JE, Lowe R, Rakyan VK, Iotchkova V, Frontini M, Downes K, Ouwehand WH, Laperle J, Jacques PÉ, Bourque G, Bergmann AK, Siebert R, Vellenga E, Saeed S, Matarese F, Martens JHA, Stunnenberg HG, Teschendorff AE, Herrero J, Birney E, Dunham I, Beck S.

Cell Rep. 2016 Nov 15;17(8):2137-2150. doi: 10.1016/j.celrep.2016.10.059.

7.

Correlation of an epigenetic mitotic clock with cancer risk.

Yang Z, Wong A, Kuh D, Paul DS, Rakyan VK, Leslie RD, Zheng SC, Widschwendter M, Beck S, Teschendorff AE.

Genome Biol. 2016 Oct 3;17(1):205.

8.

Early-life nutrition modulates the epigenetic state of specific rDNA genetic variants in mice.

Holland ML, Lowe R, Caton PW, Gemma C, Carbajosa G, Danson AF, Carpenter AA, Loche E, Ozanne SE, Rakyan VK.

Science. 2016 Jul 29;353(6298):495-8. doi: 10.1126/science.aaf7040. Epub 2016 Jul 7.

9.

A donor-specific epigenetic classifier for acute graft-versus-host disease severity in hematopoietic stem cell transplantation.

Paul DS, Jones A, Sellar RS, Mayor NP, Feber A, Webster AP, Afonso N, Sergeant R, Szydlo RM, Apperley JF, Widschwendter M, Mackinnon S, Marsh SG, Madrigal JA, Rakyan VK, Peggs KS, Beck S.

Genome Med. 2015 Dec 15;7:128. doi: 10.1186/s13073-015-0246-z.

10.

The senescent methylome and its relationship with cancer, ageing and germline genetic variation in humans.

Lowe R, Overhoff MG, Ramagopalan SV, Garbe JC, Koh J, Stampfer MR, Beach DH, Rakyan VK, Bishop CL.

Genome Biol. 2015 Sep 17;16:194. doi: 10.1186/s13059-015-0748-4.

11.

Sexually dimorphic gene expression emerges with embryonic genome activation and is dynamic throughout development.

Lowe R, Gemma C, Rakyan VK, Holland ML.

BMC Genomics. 2015 Apr 14;16:295. doi: 10.1186/s12864-015-1506-4.

12.

Maternal gestational diabetes is associated with genome-wide DNA methylation variation in placenta and cord blood of exposed offspring.

Finer S, Mathews C, Lowe R, Smart M, Hillman S, Foo L, Sinha A, Williams D, Rakyan VK, Hitman GA.

Hum Mol Genet. 2015 Jun 1;24(11):3021-9. doi: 10.1093/hmg/ddv013. Epub 2015 Jan 29.

PMID:
25634562
13.

The human blood DNA methylome displays a highly distinctive profile compared with other somatic tissues.

Lowe R, Slodkowicz G, Goldman N, Rakyan VK.

Epigenetics. 2015;10(4):274-81. doi: 10.1080/15592294.2014.1003744.

14.

Novel DNA methylation profiles associated with key gene regulation and transcription pathways in blood and placenta of growth-restricted neonates.

Hillman SL, Finer S, Smart MC, Mathews C, Lowe R, Rakyan VK, Hitman GA, Williams DJ.

Epigenetics. 2015;10(1):50-61. doi: 10.4161/15592294.2014.989741. Epub 2015 Jan 23.

15.

Correcting for cell-type composition bias in epigenome-wide association studies.

Lowe R, Rakyan VK.

Genome Med. 2014 Mar 25;6(3):23. doi: 10.1186/gm540. eCollection 2014.

16.

Marmal-aid--a database for Infinium HumanMethylation450.

Lowe R, Rakyan VK.

BMC Bioinformatics. 2013 Dec 12;14:359. doi: 10.1186/1471-2105-14-359.

17.

The promise and challenges of blood spot methylomics.

Ramagopalan SV, Rakyan VK.

Epigenetics. 2013 Aug;8(8):775-7. doi: 10.4161/epi.25357. Epub 2013 Jun 19. Review.

18.

Inactive or moderately active human promoters are enriched for inter-individual epialleles.

Gemma C, Ramagopalan SV, Down TA, Beyan H, Hawa MI, Holland ML, Hurd PJ, Giovannoni G, Leslie RD, Ebers GC, Rakyan VK.

Genome Biol. 2013 May 25;14(5):R43. doi: 10.1186/gb-2013-14-5-r43.

19.

Transgenerational inheritance of non-genetically determined phenotypes.

Holland ML, Rakyan VK.

Biochem Soc Trans. 2013 Jun;41(3):769-76. doi: 10.1042/BST20130043. Review.

PMID:
23697936
20.

Buccals are likely to be a more informative surrogate tissue than blood for epigenome-wide association studies.

Lowe R, Gemma C, Beyan H, Hawa MI, Bazeos A, Leslie RD, Montpetit A, Rakyan VK, Ramagopalan SV.

Epigenetics. 2013 Apr;8(4):445-54. doi: 10.4161/epi.24362. Epub 2013 Mar 28.

21.

Guthrie card methylomics identifies temporally stable epialleles that are present at birth in humans.

Beyan H, Down TA, Ramagopalan SV, Uvebrant K, Nilsson A, Holland ML, Gemma C, Giovannoni G, Boehm BO, Ebers GC, Lernmark Å, Cilio CM, Leslie RD, Rakyan VK.

Genome Res. 2012 Nov;22(11):2138-45. doi: 10.1101/gr.134304.111. Epub 2012 Aug 23.

22.

Protection against de novo methylation is instrumental in maintaining parent-of-origin methylation inherited from the gametes.

Proudhon C, Duffié R, Ajjan S, Cowley M, Iranzo J, Carbajosa G, Saadeh H, Holland ML, Oakey RJ, Rakyan VK, Schulz R, Bourc'his D.

Mol Cell. 2012 Sep 28;47(6):909-20. doi: 10.1016/j.molcel.2012.07.010. Epub 2012 Aug 16.

23.

A functional methylome map of ulcerative colitis.

Häsler R, Feng Z, Bäckdahl L, Spehlmann ME, Franke A, Teschendorff A, Rakyan VK, Down TA, Wilson GA, Feber A, Beck S, Schreiber S, Rosenstiel P.

Genome Res. 2012 Nov;22(11):2130-7. doi: 10.1101/gr.138347.112. Epub 2012 Jul 23.

24.

Genome wide analysis of acute myeloid leukemia reveal leukemia specific methylome and subtype specific hypomethylation of repeats.

Saied MH, Marzec J, Khalid S, Smith P, Down TA, Rakyan VK, Molloy G, Raghavan M, Debernardi S, Young BD.

PLoS One. 2012;7(3):e33213. doi: 10.1371/journal.pone.0033213. Epub 2012 Mar 29.

25.

Identification of type 1 diabetes-associated DNA methylation variable positions that precede disease diagnosis.

Rakyan VK, Beyan H, Down TA, Hawa MI, Maslau S, Aden D, Daunay A, Busato F, Mein CA, Manfras B, Dias KR, Bell CG, Tost J, Boehm BO, Beck S, Leslie RD.

PLoS Genet. 2011 Sep;7(9):e1002300. doi: 10.1371/journal.pgen.1002300. Epub 2011 Sep 29.

26.

Comparative methylomics reveals gene-body H3K36me3 in Drosophila predicts DNA methylation and CpG landscapes in other invertebrates.

Nanty L, Carbajosa G, Heap GA, Ratnieks F, van Heel DA, Down TA, Rakyan VK.

Genome Res. 2011 Nov;21(11):1841-50. doi: 10.1101/gr.121640.111. Epub 2011 Sep 22.

27.

Epigenome-wide association studies for common human diseases.

Rakyan VK, Down TA, Balding DJ, Beck S.

Nat Rev Genet. 2011 Jul 12;12(8):529-41. doi: 10.1038/nrg3000. Review.

28.

Comparative methylome analysis of benign and malignant peripheral nerve sheath tumors.

Feber A, Wilson GA, Zhang L, Presneau N, Idowu B, Down TA, Rakyan VK, Noon LA, Lloyd AC, Stupka E, Schiza V, Teschendorff AE, Schroth GP, Flanagan A, Beck S.

Genome Res. 2011 Apr;21(4):515-24. doi: 10.1101/gr.109678.110. Epub 2011 Feb 1.

29.

Integrated genetic and epigenetic analysis identifies haplotype-specific methylation in the FTO type 2 diabetes and obesity susceptibility locus.

Bell CG, Finer S, Lindgren CM, Wilson GA, Rakyan VK, Teschendorff AE, Akan P, Stupka E, Down TA, Prokopenko I, Morison IM, Mill J, Pidsley R; International Type 2 Diabetes 1q Consortium, Deloukas P, Frayling TM, Hattersley AT, McCarthy MI, Beck S, Hitman GA.

PLoS One. 2010 Nov 18;5(11):e14040. doi: 10.1371/journal.pone.0014040.

30.

The hunt for the epiallele.

Finer S, Holland ML, Nanty L, Rakyan VK.

Environ Mol Mutagen. 2011 Jan;52(1):1-11. doi: 10.1002/em.20590. Review.

PMID:
20839222
31.

Genome-wide DNA methylation analysis for diabetic nephropathy in type 1 diabetes mellitus.

Bell CG, Teschendorff AE, Rakyan VK, Maxwell AP, Beck S, Savage DA.

BMC Med Genomics. 2010 Aug 5;3:33. doi: 10.1186/1755-8794-3-33.

32.

Human aging-associated DNA hypermethylation occurs preferentially at bivalent chromatin domains.

Rakyan VK, Down TA, Maslau S, Andrew T, Yang TP, Beyan H, Whittaker P, McCann OT, Finer S, Valdes AM, Leslie RD, Deloukas P, Spector TD.

Genome Res. 2010 Apr;20(4):434-9. doi: 10.1101/gr.103101.109. Epub 2010 Mar 10.

33.

DNA methylation-mediated down-regulation of DNA methyltransferase-1 (DNMT1) is coincident with, but not essential for, global hypomethylation in human placenta.

Novakovic B, Wong NC, Sibson M, Ng HK, Morley R, Manuelpillai U, Down T, Rakyan VK, Beck S, Hiendleder S, Roberts CT, Craig JM, Saffery R.

J Biol Chem. 2010 Mar 26;285(13):9583-93. doi: 10.1074/jbc.M109.064956. Epub 2010 Jan 13.

34.

Reconfiguration of genomic anchors upon transcriptional activation of the human major histocompatibility complex.

Ottaviani D, Lever E, Mitter R, Jones T, Forshew T, Christova R, Tomazou EM, Rakyan VK, Krawetz SA, Platts AE, Segarane B, Beck S, Sheer D.

Genome Res. 2008 Nov;18(11):1778-86. doi: 10.1101/gr.082313.108. Epub 2008 Oct 10.

35.

A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis.

Down TA, Rakyan VK, Turner DJ, Flicek P, Li H, Kulesha E, Gräf S, Johnson N, Herrero J, Tomazou EM, Thorne NP, Bäckdahl L, Herberth M, Howe KL, Jackson DK, Miretti MM, Marioni JC, Birney E, Hubbard TJ, Durbin R, Tavaré S, Beck S.

Nat Biotechnol. 2008 Jul;26(7):779-85. doi: 10.1038/nbt1414.

36.

An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs).

Rakyan VK, Down TA, Thorne NP, Flicek P, Kulesha E, Gräf S, Tomazou EM, Bäckdahl L, Johnson N, Herberth M, Howe KL, Jackson DK, Miretti MM, Fiegler H, Marioni JC, Birney E, Hubbard TJ, Carter NP, Tavaré S, Beck S.

Genome Res. 2008 Sep;18(9):1518-29. doi: 10.1101/gr.077479.108. Epub 2008 Jun 24.

37.

Generation of a genomic tiling array of the human major histocompatibility complex (MHC) and its application for DNA methylation analysis.

Tomazou EM, Rakyan VK, Lefebvre G, Andrews R, Ellis P, Jackson DK, Langford C, Francis MD, Bäckdahl L, Miretti M, Coggill P, Ottaviani D, Sheer D, Murrell A, Beck S.

BMC Med Genomics. 2008 May 30;1:19. doi: 10.1186/1755-8794-1-19.

38.

The methylome: approaches for global DNA methylation profiling.

Beck S, Rakyan VK.

Trends Genet. 2008 May;24(5):231-7. doi: 10.1016/j.tig.2008.01.006. Epub 2008 Mar 5. Review.

PMID:
18325624
39.

DNA methylation profiling of human chromosomes 6, 20 and 22.

Eckhardt F, Lewin J, Cortese R, Rakyan VK, Attwood J, Burger M, Burton J, Cox TV, Davies R, Down TA, Haefliger C, Horton R, Howe K, Jackson DK, Kunde J, Koenig C, Liddle J, Niblett D, Otto T, Pettett R, Seemann S, Thompson C, West T, Rogers J, Olek A, Berlin K, Beck S.

Nat Genet. 2006 Dec;38(12):1378-85. Epub 2006 Oct 29.

40.

Epigenetic variation and inheritance in mammals.

Rakyan VK, Beck S.

Curr Opin Genet Dev. 2006 Dec;16(6):573-7. Epub 2006 Sep 26. Review.

PMID:
17005390
41.

From genome to epigenome.

Murrell A, Rakyan VK, Beck S.

Hum Mol Genet. 2005 Apr 15;14 Spec No 1:R3-R10. Review.

PMID:
15809270
42.

DNA methylation profiling of the human major histocompatibility complex: a pilot study for the human epigenome project.

Rakyan VK, Hildmann T, Novik KL, Lewin J, Tost J, Cox AV, Andrews TD, Howe KL, Otto T, Olek A, Fischer J, Gut IG, Berlin K, Beck S.

PLoS Biol. 2004 Dec;2(12):e405. Epub 2004 Nov 23.

43.

Transgenerational inheritance of epigenetic states at the murine Axin(Fu) allele occurs after maternal and paternal transmission.

Rakyan VK, Chong S, Champ ME, Cuthbert PC, Morgan HD, Luu KV, Whitelaw E.

Proc Natl Acad Sci U S A. 2003 Mar 4;100(5):2538-43. Epub 2003 Feb 24.

44.

Metastable epialleles in mammals.

Rakyan VK, Blewitt ME, Druker R, Preis JI, Whitelaw E.

Trends Genet. 2002 Jul;18(7):348-51. Review.

PMID:
12127774
45.

The marks, mechanisms and memory of epigenetic states in mammals.

Rakyan VK, Preis J, Morgan HD, Whitelaw E.

Biochem J. 2001 May 15;356(Pt 1):1-10. Review.

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