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Publications:  Prof Vardhman Rakyan

Bell C, Lowe R, Adams P, Baccarelli A, Beck S, Bell J, Christensen B, Gladyshev V et al.(2019). DNA methylation aging clocks: challenges and recommendations. Genome Biology Article 249 (2019),
10.1186/s13059-019-1824-y
https://qmro.qmul.ac.uk/xmlui/handle/123456789/62983
DANSON AF, MARZI SJ, LOWE R, HOLLAND ML, RAKYAN V(2018). Early life diet conditions the molecular response to post-weaning protein restriction in the mouse. BMC Biology vol. 16, (51)
10.1186/s12915-018-0516-5
https://qmro.qmul.ac.uk/xmlui/handle/123456789/36711
LOWE R, BARTON C, Jenkins C, Ernst C, Forman O, Fernandez-Twinn D, Bock C, ROSSITER S et al.(2018). Ageing-associated DNA methylation dynamics are a molecular readout of lifespan variation amongst mammalian species. Genome Biology vol. 19, Article 22,
10.1186/s13059-018-1397-1
https://qmro.qmul.ac.uk/xmlui/handle/123456789/36381
Paul DS, Teschendorff AE, Dang MAN, Lowe R, Hawa MI, Ecker S, Beyan H, Cunningham S et al.(2016). Increased DNA methylation variability in type 1 diabetes across three immune effector cell types. Nat Commun vol. 7, 13555-13555.
10.1038/ncomms13555
https://qmro.qmul.ac.uk/xmlui/handle/123456789/22321
Breeze CE, Paul DS, van Dongen J, Butcher LM, Ambrose JC, Barrett JE, Lowe R, Rakyan VK et al.(2016). eFORGE: A Tool for Identifying Cell Type-Specific Signal in Epigenomic Data. Cell Reports vol. 17, (8) 2137-2150.
10.1016/j.celrep.2016.10.059
https://qmro.qmul.ac.uk/xmlui/handle/123456789/18306
Yang Z, Wong A, Kuh D, Paul DS, Rakyan VK, Leslie RD, Zheng SC, Widschwendter M et al.(2016). Correlation of an epigenetic mitotic clock with cancer risk. Genome Biology vol. 17, (1)
10.1186/s13059-016-1064-3
https://qmro.qmul.ac.uk/xmlui/handle/123456789/22365
Holland ML, Lowe R, Caton P, Gemma C, Carbajosa G, DANSON AF, Loche E, Carpenter AAM et al.(2016). Early-life nutrition modulates the epigenetic state of specific rDNA genetic variants in mice. Science
10.1126/science.aaf7040
https://qmro.qmul.ac.uk/xmlui/handle/123456789/13450
Kraiczy J, Nayak K, Ross A, Raine T, Mak TN, Gasparetto M, Cario E, Rakyan V et al.(2016). Assessing DNA methylation in the developing human intestinal epithelium: Potential link to inflammatory bowel disease. Mucosal Immunology vol. 9, (3) 647-658.
10.1038/mi.2015.88
Paul DS, Jones A, Sellar RS, Mayor NP, Feber A, Webster AP, Afonso N, Sergeant R et al.(2015). A donor-specific epigenetic classifier for acute graft-versus-host disease severity in hematopoietic stem cell transplantation. Genome Medicine vol. 7, (1)
10.1186/s13073-015-0246-z
Lowe R, Overhoff MG, Ramagopalan SV, Garbe JC, Koh J, Stampfer MR, Beach DH, Rakyan VK et al.(2015). The senescent methylome and its relationship with cancer, ageing and germline genetic variation in humans. Genome Biology vol. 16, (1)
10.1186/s13059-015-0748-4
https://qmro.qmul.ac.uk/xmlui/handle/123456789/12249
Lowe R, Gemma C, Rakyan VK, Holland ML(2015). Sexually dimorphic gene expression emerges with embryonic genome activation and is dynamic throughout development. BMC Genomics vol. 16, (1)
10.1186/s12864-015-1506-4
https://qmro.qmul.ac.uk/xmlui/handle/123456789/14931
Lowe R, Slodkowicz G, Goldman N, Rakyan VK(2015). The human blood DNA methylome displays a highly distinctive profile compared with other somatic tissues. Epigenetics vol. 10, (4) 274-281.
10.1080/15592294.2014.1003744
Hillman SL, Finer S, Smart MC, Mathews C, Lowe R, Rakyan VK, Hitman GA, Williams DJ(2015). Novel DNA methylation profiles associated with key gene regulation and transcription pathways in blood and placenta of growth-restricted neonates. Epigenetics vol. 10, (1) 50-61.
10.4161/15592294.2014.989741
https://qmro.qmul.ac.uk/xmlui/handle/123456789/15595
Finer S, Mathews C, Lowe R, Smart M, Hillman S, Foo L, Sinha A, Williams D et al.(2014). Maternal gestational diabetes is associated with genome-wide DNA methylation variation in placenta and cord blood of exposed offspring. Human Molecular Genetics vol. 24, (11) 3021-3029.
10.1093/hmg/ddv013
https://qmro.qmul.ac.uk/xmlui/handle/123456789/7020
Finer S, Iqbal S, Ogunkolade WB, Mathews C, Lowe R, Smart M, Rakyan VK, Alam DS et al.(2014). Variation in phenotype and DNA methylation is detectable in an observational cohort of young adult Bangladeshis exposed to famine during in utero and postnatal life. DIABETOLOGIA vol. 57, S105-S106.
https://qmro.qmul.ac.uk/xmlui/handle/123456789/7120
Lowe R, Rakyan VK(2014). Correcting for cell-type composition bias in epigenome-wide association studies. Genome Medicine vol. 6, (3)
10.1186/gm540
Hillman SL, Finer S, Smart MC, Rakyan V, Hitman GA, Williams DJ(2014). Identification of Novel DNA Methylation Profiles Associated with Gene Regulation and Metabolic Pathways in Growth Restricted Offspring. REPRODUCTIVE SCIENCES vol. 21, (3) 166A-166A.
Lowe R, Rakyan VK(2013). Marmal-aid--a database for Infinium HumanMethylation450. BMC Bioinformatics vol. 14,
10.1186/1471-2105-14-359
https://qmro.qmul.ac.uk/xmlui/handle/123456789/18026
Ke X, Cortina-Borja M, Silva BC, Lowe R, Rakyan V, Balding D(2013). Integrated analysis of genome-wide genetic and epigenetic association data for identification of disease mechanisms. Epigenetics vol. 8, (11) 1236-1244.
10.4161/epi.26407
Brugha R, Lowe R, Henderson J, Holloway J, Rakyan V, Shaheen S(2013). Comparison of DNA methylation profiles between airway epithelium and proxy tissues. EUROPEAN RESPIRATORY JOURNAL vol. 42,
Ramagopalan SV, Rakyan VK(2013). The promise and challenges of blood spot methylomics. Epigenetics vol. 8, (8) 775-777.
10.4161/epi.25357
Holland ML, Rakyan VK (2013). Transgenerational inheritance of non-genetically determined phenotypes. Biochemical Society Transactions. vol. 41, 769-776.
10.1042/BST20130043
Holland ML, Rakyan VK(2013). Transgenerational inheritance of non-genetically determined phenotypes. Biochem Soc Trans vol. 41, (3) 769-776.
10.1042/BST20130043
Gemma C, Ramagopalan SV, Down TA, Beyan H, Hawa MI, Holland ML, Hurd PJ, Giovannoni G et al.(2013). Inactive or moderately active human promoters are enriched for inter-individual epialleles. Genome Biol vol. 14, (5)
10.1186/gb-2013-14-5-r43
https://qmro.qmul.ac.uk/xmlui/handle/123456789/4899
Lowe R, Gemma C, Beyan H, Hawa MI, Bazeos A, Leslie RD, Montpetit A, Rakyan VK et al.(2013). Buccals are likely to be a more informative surrogate tissue than blood for epigenome-wide association studies. Epigenetics : official journal of the DNA Methylation Society vol. 8, (4) 445-454.
10.4161/epi.24362
Lowe R, Gemma C, Beyan H, Hawa MI, Bazeos A, Leslie RD, Montpetit A, Rakyan VK et al.(2013). Buccals are likely to be a more informative surrogate tissue than blood for epigenome-wide association studies. Epigenetics vol. 8, (4) 445-454.
10.4161/epi.24362
Saadeh H, Smallwood S, Proudhon C, Duffie R, Carbajosa G, Holland M, Rakyan V, Bourc'his D et al. (2012). A search for sequence-specific signals in maternally imprinted CGIs. GENETICS RESEARCH. vol. 94, 355-355.
Häsler R, Feng Z, Bäckdahl L, Spehlmann ME, Franke A, Teschendorff A, Rakyan VK, Down TA et al.(2012). A functional methylome map of ulcerative colitis. Genome Res vol. 22, (11) 2130-2137.
10.1101/gr.138347.112
Beyan H, Down TA, Ramagopalan SV, Uvebrant K, Nilsson A, Holland ML, Gemma C, Giovannoni G et al.(2012). Guthrie card methylomics identifies temporally stable epialleles that are present at birth in humans. Genome Res vol. 22, (11) 2138-2145.
10.1101/gr.134304.111
Proudhon C, Duffié R, Ajjan S, Cowley M, Iranzo J, Carbajosa G, Saadeh H, Holland ML et al.(2012). Protection against de novo methylation is instrumental in maintaining parent-of-origin methylation inherited from the gametes. Mol Cell vol. 47, (6) 909-920.
10.1016/j.molcel.2012.07.010
Mladkova N, McHugh A, Rakyan V, Proby C, Harwood C (2012). Methylation profiling of cutaneous squamous cell carcinoma reveals an embryonic stem cell signature among differentially methylated genes. BRITISH JOURNAL OF DERMATOLOGY. vol. 166, e23-e23.
Adams D, Altucci L, Antonarakis SE, Ballesteros J, Beck S, Bird A, Bock C, Boehm B et al.(2012). BLUEPRINT to decode the epigenetic signature written in blood. NATURE BIOTECHNOLOGY vol. 30, (3) 224-226.
10.1038/nbt.2153
Saied MH, Marzec J, Khalid S, Smith P, Down TA, Rakyan VK, Molloy G, Raghavan M et al.(2012). Genome wide analysis of acute myeloid leukemia reveal leukemia specific methylome and subtype specific hypomethylation of repeats. PLoS One vol. 7, (3)
10.1371/journal.pone.0033213
https://qmro.qmul.ac.uk/xmlui/handle/123456789/4829
Nanty L, Carbajosa G, Heap GA, Ratnieks F, van Heel DA, Down TA, Rakyan VK(2011). Comparative methylomics reveals gene-body H3K36me3 in Drosophila predicts DNA methylation and CpG landscapes in other invertebrates. Genome Res vol. 21, (11) 1841-1850.
10.1101/gr.121640.111
Mladkova N, McHugh A, Down T, Rakyan V, Proby C, Harwood C (2011). Identification of Differentially Methylated Genes in Cutaneous Squamous Cell Carcinoma from Epidermolysis Bullosa Patients and Normal Population. JOURNAL OF INVESTIGATIVE DERMATOLOGY. vol. 131, S24-S24.
Rakyan VK, Beyan H, Down TA, Hawa MI, Maslau S, Aden D, Daunay A, Busato F et al.(2011). Identification of type 1 diabetes-associated DNA methylation variable positions that precede disease diagnosis. PLoS Genet vol. 7, (9)
10.1371/journal.pgen.1002300
https://qmro.qmul.ac.uk/xmlui/handle/123456789/5415
Rakyan VK, Down TA, Balding DJ, Beck S(2011). Epigenome-wide association studies for common human diseases. Nat Rev Genet vol. 12, (8) 529-541.
10.1038/nrg3000
Mladkova N, McHugh A, Down T, Rakyan V, South A, Proby C, Harwood C (2011). Methylation profiling of cutaneous squamous cell carcinoma. BRITISH JOURNAL OF DERMATOLOGY. vol. 164, 932-933.
Feber A, Wilson GA, Zhang L, Presneau N, Idowu B, Down TA, Rakyan VK, Noon LA et al.(2011). Comparative methylome analysis of benign and malignant peripheral nerve sheath tumors. GENOME RESEARCH vol. 21, (4) 515-524.
10.1101/gr.109678.110
Finer S, Holland ML, Nanty L, Rakyan VK(2011). The hunt for the epiallele. Environ Mol Mutagen vol. 52, (1) 1-11.
10.1002/em.20590
Beyan H, Rakyan VK, Down TA, Hawa MI, Maslau S, Wallace C, Aden D, Mein CA et al. (2010). Identification of type 1 diabetes-associated methylation variable positions that precede disease diagnosis. DIABETOLOGIA. vol. 53, S145-S146.
10.1371/journal.pgen.1002300
Bell CG, Teschendorff AE, Rakyan VK, Maxwell AP, Beck S, Savage DA(2010). Genome-wide DNA methylation analysis for diabetic nephropathy in type 1 diabetes mellitus. BMC Med Genomics vol. 3,
10.1186/1755-8794-3-33
https://qmro.qmul.ac.uk/xmlui/handle/123456789/242
Beyan H, Rakyan VK, Down TA, Maslau S, Hawa MI, Boehm BO, Beck S, Leslie RD (2010). Whole-Genome Identification and Functional Analysis of Type 1 Diabetes-Associated Epigenetic Variation. DIABETES. vol. 59, A56-A56.
Rakyan VK, Down TA, Maslau S, Andrew T, Yang T-P, Beyan H, Whittaker P, McCann OT et al.(2010). Human aging-associated DNA hypermethylation occurs preferentially at bivalent chromatin domains. Genome Res vol. 20, (4) 434-439.
10.1101/gr.103101.109
Novakovic B, Wong NC, Sibson M, Ng H-K, Morley R, Manuelpillai U, Down T, Rakyan VK et al.(2010). DNA methylation-mediated down-regulation of DNA methyltransferase-1 (DNMT1) is coincident with, but not essential for, global hypomethylation in human placenta. J Biol Chem vol. 285, (13) 9583-9593.
10.1074/jbc.M109.064956
Finer S, Holland M, Rakyan V, Hitman G (2010). A model of intrauterine hyperglycaemia provides evidence for fetal programming of glucose tolerance and a platform for epigenomic studies in mouse and human. Longitudinal and Life Course Studies: international journal. Conference: The 5th Conference on Epidemiology and Longitudonal Studies in Europe (Paphos, Cyprus) from: 13/10/2010 to: 15/10/2010, vol. 1,
Bell CG, Finer S, Lindgren CM, Wilson GA, Rakyan VK, Teschendoff AE, Akan P, Stupka E et al.(2010). Integrated Genetic and Epigenetic Analysis Identifies Haplotype-Specific Methylation in the FTO Type 2 Diabetes and Obesity Susceptibility Locus. PLOS One
10.1371/journal.pone.0014040
https://qmro.qmul.ac.uk/xmlui/handle/123456789/14550
Rakyan VK (2009). The Hunt for Epialleles. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS. vol. 50, 543-543.
10.1002/em.20590
Novakovic B, Sibson M, Ng HK, Manuelpillai U, Rakyan V, Down T, Beck S, Fournier T et al.(2009). Placenta-specific methylation of the vitamin D 24-hydroxylase gene: implications for feedback autoregulation of active vitamin D levels at the fetomaternal interface. J Biol Chem vol. 284, (22) 14838-14848.
10.1074/jbc.M809542200
Papageorgiou EA, Fiegler H, Rakyan V, Beck S, Hulten M, Lamnissou K, Carter NP, Patsalis PC(2009). Sites of differential DNA methylation between placenta and peripheral blood: molecular markers for noninvasive prenatal diagnosis of aneuploidies. Am J Pathol vol. 174, (5) 1609-1618.
10.2353/ajpath.2009.081038
Ottaviani D, Lever E, Mitter R, Jones T, Forshew T, Christova R, Tomazou EM, Rakyan VK et al.(2008). Reconfiguration of genomic anchors upon transcriptional activation of the human major histocompatibility complex. Genome Res vol. 18, (11) 1778-1786.
10.1101/gr.082313.108
Rakyan VK, Down TA, Thorne NP, Flicek P, Kulesha E, Gräf S, Tomazou EM, Bäckdahl L et al.(2008). An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs). Genome Res vol. 18, (9) 1518-1529.
10.1101/gr.077479.108
Novakovic B, Rakyan V, Ng HK, Manuelpillai U, Dewi C, Wong NC, Morley R, Down T et al.(2008). Specific tumour-associated methylation in normal human term placenta and first-trimester cytotrophoblasts. Mol Hum Reprod vol. 14, (9) 547-554.
10.1093/molehr/gan046
Down TA, Rakyan VK, Turner DJ, Flicek P, Li H, Kulesha E, Gräf S, Johnson N et al.(2008). A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis. Nat Biotechnol vol. 26, (7) 779-785.
10.1038/nbt1414
Tomazou EM, Rakyan VK, Lefebvre G, Andrews R, Ellis P, Jackson DK, Langford C, Francis MD et al.(2008). Generation of a genomic tiling array of the human Major Histocompatibility Complex (MHC) and its application for DNA methylation analysis. BMC Med Genomics vol. 1, (1)
10.1186/1755-8794-1-19
https://qmro.qmul.ac.uk/xmlui/handle/123456789/13161
Beck S, Rakyan VK(2008). The methylome: approaches for global DNA methylation profiling. TRENDS IN GENETICS vol. 24, (5) 231-237.
10.1016/j.tig.2008.01.006
Eckhardt F, Lewin J, Cortese R, Rakyan VK, Attwood J, Burger M, Burton J, Cox TV et al.(2006). DNA methylation profiling of human chromosomes 6, 20 and 22. Nat Genet vol. 38, (12) 1378-1385.
10.1038/ng1909
Rakyan VK, Beck S(2006). Epigenetic variation and inheritance in mammals. Curr Opin Genet Dev vol. 16, (6) 573-577.
10.1016/j.gde.2006.09.002
Murrell A, Rakyan VK, Beck S(2005). From genome to epigenome. Hum Mol Genet vol. 14 Spec No 1, R3-R10.
10.1093/hmg/ddi110
RAKYAN V, Novik KL, Hildmann T, Lewin J(2004). DNA Methylation Profiling of the Human Major Histocompatibility Complex: A Pilot Study for the Human Epigenome Project. PLoS Biol vol. 2, (12) e405-e405.
10.1371/journal.pbio.0020405
Rakyan VK, Chong S, Champ ME, Cuthbert PC, Morgan HD, Luu KVK, Whitelaw E(2003). Transgenerational inheritance of epigenetic states at the murine Axin(Fu) allele occurs after maternal and paternal transmission. Proc Natl Acad Sci U S A vol. 100, (5) 2538-2543.
10.1073/pnas.0436776100
Rakyan V, Whitelaw E(2003). Transgenerational epigenetic inheritance. Curr Biol vol. 13, (1)
10.1016/s0960-9822(02)01377-5
Rakyan VK, Blewitt ME, Druker R, Preis JI, Whitelaw E(2002). Metastable epialleles in mammals. Trends Genet vol. 18, (7) 348-351.
10.1016/s0168-9525(02)02709-9
Rakyan VK, Preis J, Morgan HD, Whitelaw E(2001). The marks, mechanisms and memory of epigenetic states in mammals. Biochem J vol. 356, (Pt 1) 1-10.
10.1042/0264-6021:3560001
Morgan H, Preis J, Rakyan V, Whitelaw E(2001). Inheritance: Not only DNA. Today's Life Science vol. 13, (1) 32-36.
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