By Dr Ruth Pidsley

Journal articles

Peters TJ; Meyer B; Ryan L; Achinger-Kawecka J; Song J; Campbell EM; Qu W; Nair S; Loi-Luu P; Stricker P; Lim E; Stirzaker C; Clark SJ; Pidsley R, 2024, 'Characterisation and reproducibility of the HumanMethylationEPIC v2.0 BeadChip for DNA methylation profiling', BMC Genomics, 25, http://dx.doi.org/10.1186/s12864-024-10027-5

Meyer B; Stirzaker C; Ramkomuth S; Harvey K; Chan B; Lee CS; Karim R; Deng N; Avery-Kiejda KA; Scott RJ; Lakhani S; Fox S; Robbins E; Shin JS; Beith J; Gill A; Sioson L; Chan C; Krishnaswamy M; Cooper C; Warrier S; Mak C; Rasko JEJ; Bailey CG; Swarbrick A; Clark SJ; O'Toole S; Pidsley R, 2024, 'Detailed DNA methylation characterisation of phyllodes tumours identifies a signature of malignancy and distinguishes phyllodes from metaplastic breast carcinoma', Journal of Pathology, 262, pp. 480 - 494, http://dx.doi.org/10.1002/path.6250

Achinger-Kawecka J; Stirzaker C; Portman N; Campbell E; Chia KM; Du Q; Laven-Law G; Nair SS; Yong A; Wilkinson A; Clifton S; Milioli HH; Alexandrou S; Caldon CE; Song J; Khoury A; Meyer B; Chen W; Pidsley R; Qu W; Gee JMW; Schmitt A; Wong ES; Hickey TE; Lim E; Clark SJ, 2024, 'The potential of epigenetic therapy to target the 3D epigenome in endocrine-resistant breast cancer', Nature Structural and Molecular Biology, 31, pp. 498 - 512, http://dx.doi.org/10.1038/s41594-023-01181-7

Meyer B; Stirzaker C; Ramkomuth S; Harvey K; Swarbrick A; Clark SJ; O'Toole S; Pidsley R, 2024, 'Detailed DNA methylation characterisation of phyllodes tumours identifies a signature of malignancy and distinguishes phyllodes from metaplastic breast carcinoma', Pathology, 56, pp. S70 - S71, http://dx.doi.org/10.1016/j.pathol.2023.12.241

Chitty JL; Yam M; Perryman L; Parker AL; Skhinas JN; Setargew YFI; Mok ETY; Tran E; Grant RD; Latham SL; Pereira BA; Ritchie SC; Murphy KJ; Trpceski M; Findlay AD; Melenec P; Filipe EC; Nadalini A; Velayuthar S; Major G; Wyllie K; Papanicolaou M; Ratnaseelan S; Phillips PA; Sharbeen G; Youkhana J; Russo A; Blackwell A; Hastings JF; Lucas MC; Chambers CR; Reed DA; Stoehr J; Vennin C; Pidsley R; Zaratzian A; Da Silva AM; Tayao M; Charlton B; Herrmann D; Nobis M; Clark SJ; Biankin AV; Johns AL; Croucher DR; Nagrial A; Gill AJ; Grimmond SM; Chantrill LA; Chou A; Dwarte T; Metcalf XL; Jeong G; Kenyon L; Waddell N; Pearson JV; Patch AM; Nones K; Newell F; Mukhopadhyay P; Addala V; Kazakoff S; Holmes O; Leonard C; Wood S; Hofmann O; Samra JS; Pavlakis N; Arena J; High HA; Asghari R; Merrett ND; Das A; Cosman PH; Ismail K; Stoita A; Williams D; Spigellman A; McLeo D; Kirk J; Kench JG; Grimison P; Sandroussi C; Goodwin A; Mead RS; Tucker K; Andrews L; Texler M; Forrest C; Ballal M; Fletcher D; Beilin M; Feeney K; Epari K; Mukhedkar S; Zeps N; Nguyen NQ; Ruszkiewicz AR; Worthley C; Chen J, 2023, 'A first-in-class pan-lysyl oxidase inhibitor impairs stromal remodeling and enhances gemcitabine response and survival in pancreatic cancer', Nature Cancer, 4, pp. 1326 - 1344, http://dx.doi.org/10.1038/s43018-023-00614-y

Pidsley R; Lam D; Qu W; Peters TJ; Phuc-Loi L; Korbie D; Stirzaker C; Daly RJ; Stricker P; Kench JG; Horvath LG; Clark SJ, 2022, 'Comprehensive methylome sequencing reveals prognostic epigenetic biomarkers for prostate cancer mortality', CLINICAL AND TRANSLATIONAL MEDICINE, 12, http://dx.doi.org/10.1002/ctm2.1030

Meyer B; Clifton S; Locke W; Luu PL; Du Q; Lam D; Armstrong NJ; Kumar B; Deng N; Harvey K; Swarbrick A; Ganju V; Clark SJ; Pidsley R; Stirzaker C, 2021, 'Identification of DNA methylation biomarkers with potential to predict response to neoadjuvant chemotherapy in triple-negative breast cancer', Clinical Epigenetics, 13, http://dx.doi.org/10.1186/s13148-021-01210-6

Luu PL; Ong PT; Loc TTH; Lam D; Pidsley R; Stirzaker C; Clark SJ, 2021, 'MethPanel: a parallel pipeline and interactive analysis tool for multiplex bisulphite PCR sequencing to assess DNA methylation biomarker panels for disease detection', Bioinformatics, 37, pp. 2198 - 2200, http://dx.doi.org/10.1093/bioinformatics/btaa1060

Lam D; Clark S; Stirzaker C; Pidsley R, 2020, 'Advances in Prognostic Methylation Biomarkers for Prostate Cancer', , http://dx.doi.org/10.20944/preprints202010.0154.v1

Lam D; Clark S; Stirzaker C; Pidsley R, 2020, 'Advances in prognostic methylation biomarkers for prostate cancer', Cancers, 12, pp. 1 - 39, http://dx.doi.org/10.3390/cancers12102993

Lam D; Luu PL; Song JZ; Qu W; Risbridger GP; Lawrence MG; Lu J; Trau M; Korbie D; Clark SJ; Pidsley R; Stirzaker C, 2020, 'Comprehensive evaluation of targeted multiplex bisulphite PCR sequencing for validation of DNA methylation biomarker panels', Clinical Epigenetics, 12, http://dx.doi.org/10.1186/s13148-020-00880-y

Lawrence MG; Pidsley R; Niranjan B; Papargiris M; Pereira BA; Richards M; Teng L; Norden S; Ryan A; Frydenberg M; Stirzaker C; Taylor RA; Risbridger GP; Clark SJ, 2020, 'Alterations in the methylome of the stromal tumour microenvironment signal the presence and severity of prostate cancer', Clinical Epigenetics, 12, http://dx.doi.org/10.1186/s13148-020-00836-2

Peters TJ; French HJ; Bradford ST; Pidsley R; Stirzaker C; Varinli H; Nair S; Qu W; Song J; Giles KA; Statham AL; Speirs H; Speed TP; Clark SJ, 2019, 'Evaluation of cross-platform and interlaboratory concordance via consensus modelling of genomic measurements', Bioinformatics, 35, pp. 560 - 570, http://dx.doi.org/10.1093/bioinformatics/bty675

Skvortsova K; Masle-Farquhar E; Luu PL; Song JZ; Qu W; Zotenko E; Gould CM; Du Q; Peters TJ; Colino-Sanguino Y; Pidsley R; Nair SS; Khoury A; Smith GC; Miosge LA; Reed JH; Kench JG; Rubin MA; Horvath L; Bogdanovic O; Lim SM; Polo JM; Goodnow CC; Stirzaker C; Clark SJ, 2019, 'DNA Hypermethylation Encroachment at CpG Island Borders in Cancer Is Predisposed by H3K4 Monomethylation Patterns', Cancer Cell, 35, pp. 297 - 314.e8, http://dx.doi.org/10.1016/j.ccell.2019.01.004

Pidsley R; Lawrence MG; Zotenko E; Niranjan B; Statham A; Song J; Chabanon RM; Qu W; Wang H; Richards M; Nair SS; Armstrong NJ; Nim HT; Papargiris M; Balanathan P; French H; Peters T; Norden S; Ryan A; Pedersen J; Kench J; Daly RJ; Horvath LG; Stricker P; Frydenberg M; Taylor RA; Stirzaker C; Risbridger GP; Clark SJ, 2018, 'Enduring epigenetic landmarks define the cancer microenvironment', Genome Research, 28, pp. 625 - 638, http://dx.doi.org/10.1101/gr.229070.117

O'Toole SA; Pidsley R; Harvey K; Karim R; Lee CS; Chan B; Stirzaker C, 2018, 'Using the epigenome to understand and better classify phyllodes tumours', Pathology, 50, pp. S7 - S8, http://dx.doi.org/10.1016/j.pathol.2017.12.015

Lunnon K; Keohane A; Pidsley R; Newhouse S; Riddoch-Contreras J; Thubron EB; Devall M; Soininen H; Kłoszewska I; Mecocci P; Tsolaki M; Vellas B; Schalkwyk L; Dobson R; Malik AN; Powell J; Lovestone S; Hodges A, 2017, 'Mitochondrial genes are altered in blood early in Alzheimer's disease', Neurobiology of Aging, 53, pp. 36 - 47, http://dx.doi.org/10.1016/j.neurobiolaging.2016.12.029

Stirzaker C; Song JZ; Ng W; Du Q; Armstrong NJ; Locke WJ; Statham AL; French H; Pidsley R; Valdes-Mora F; Zotenko E; Clark SJ, 2017, 'Methyl-CpG-binding protein MBD2 plays a key role in maintenance and spread of DNA methylation at CpG islands and shores in cancer', Oncogene, 36, pp. 1328 - 1338, http://dx.doi.org/10.1038/onc.2016.297

Viana J; Hannon E; Dempster E; Pidsley R; Macdonald R; Knox O; Spiers H; Troakes C; Al-Saraj S; Turecki G; Schalkwyk LC; Mill J, 2017, 'Schizophrenia-associated methylomic variation: Molecular signatures of disease and polygenic risk burden across multiple brain regions', Human Molecular Genetics, 26, pp. 210 - 225, http://dx.doi.org/10.1093/hmg/ddw373

Pidsley R; Zotenko E; Peters TJ; Lawrence MG; Risbridger GP; Molloy P; Van Djik S; Muhlhausler B; Stirzaker C; Clark SJ, 2016, 'Critical evaluation of the Illumina MethylationEPIC BeadChip microarray for whole-genome DNA methylation profiling', Genome Biology, 17, pp. 208, http://dx.doi.org/10.1186/s13059-016-1066-1

Pidsley R; Zotenko E; Peters TJ; Lawrence MG; Risbridger GP; Molloy P; Van Djik S; Muhlhausler B; Stirzaker C; Clark SJ, 2016, 'Critical evaluation of the Illumina MethylationEPIC BeadChip microarray for whole-genome DNA methylation profiling', GENOME BIOLOGY, 17, http://dx.doi.org/10.1186/s13059-016-1066-1

Lim AM; Wong NC; Pidsley R; Zotenko E; Corry J; Dobrovic A; Clark SJ; Rischin D; Solomon B, 2016, 'Genome-scale methylation assessment did not identify prognostic biomarkers in oral tongue carcinomas', Clinical Epigenetics, 8, http://dx.doi.org/10.1186/s13148-016-0235-0

Yeung KR; Chiu CL; Pidsley R; Makris A; Hennessy A; Lind JM, 2016, 'DNA methylation profiles in preeclampsia and healthy control placentas', American Journal of Physiology - Heart and Circulatory Physiology, 310, pp. H1295 - H1303, http://dx.doi.org/10.1152/ajpheart.00958.2015

Hannon E; Spiers H; Viana J; Pidsley R; Burrage J; Murphy TM; Troakes C; Turecki G; O'Donovan MC; Schalkwyk LC; Bray NJ; Mill J, 2015, 'Methylation QTLs in the developing brain and their enrichment in schizophrenia risk loci', Nature Neuroscience, 19, pp. 48 - 54, http://dx.doi.org/10.1038/nn.4182

Watkins-Chow DE; Cooke J; Pidsley R; Edwards A; Slotkin R; Leeds KE, 2015, 'Correction To: Mutation of the Diamond-Blackfan Anemia Gene Rps7 in Mouse Results in Morphological and Neuroanatomical Phenotypes (PLoS Genet, 11, 11)', PLoS Genetics, 11, http://dx.doi.org/10.1371/journal.pgen.1005682

Stone A; Zotenko E; Locke WJ; Korbie D; Millar EKA; Pidsley R; Stirzaker C; Graham P; Trau M; Musgrove EA; Nicholson RI; Gee JMW; Clark SJ, 2015, 'DNA methylation of oestrogen-regulated enhancers defines endocrine sensitivity in breast cancer', Nature Communications, 6, http://dx.doi.org/10.1038/ncomms8758

Lawrence M; Pidsley R; Ellem S; Furic L; Nair S; French H; Stratham A; Larsson O; Frydenberg M; Pedersen J; Buchanan G; Taylor R; Clark S; Risbridger G, 2015, 'Oestrogen receptor α promotes prostate cancer progression through dual actions in both epithelia and stroma', Endocrine Abstracts, http://dx.doi.org/10.1530/endoabs.37.oc8.5

Peters TJ; Buckley MJ; Statham AL; Pidsley R; Samaras K; V Lord R; Clark SJ; Molloy PL, 2015, 'De novo identification of differentially methylated regions in the human genome', Epigenetics and Chromatin, 8, http://dx.doi.org/10.1186/1756-8935-8-6

Fisher HL; Murphy TM; Arseneault L; Caspi A; Moffitt TE; Viana J; Hannon E; Pidsley R; Burrage J; Dempster EL; Wong CCY; Pariante CM; Mill J, 2015, 'Methylomic analysis of monozygotic twins discordant for childhood psychotic symptoms', Epigenetics, 10, pp. 1014 - 1023, http://dx.doi.org/10.1080/15592294.2015.1099797

Spiers H; Bray NJ; Hannon E; Schalkwyk LC; Wong CC; Pidsley R; Smith RG; Mill J, 2015, 'ISDN2014_0171: Dynamic and sex‐specific changes in DNA methylation during human fetal brain development', International Journal of Developmental Neuroscience, 47, pp. 50 - 51, http://dx.doi.org/10.1016/j.ijdevneu.2015.04.142

Lim A; Wong N; Pidsley R; Zontenko E; Corry J; Dobrovic A; Solomon B; Rischin D; Clark S, 2015, 'PO-097: Genome-scale methylation assessment did not identify prognostic biomarkers in oral tongue carcinomas', Radiotherapy and Oncology, 114, pp. 49 - 49, http://dx.doi.org/10.1016/s0167-8140(15)34857-x

Viana J; Pidsley R; Troakes C; Spiers H; Wong CC; Al-Sarraj S; Craig I; Schalkwyk L; Mill J, 2014, 'Epigenomic and transcriptomic signatures of a Klinefelter syndrome (47,XXY) karyotype in the brain', Epigenetics, 9, pp. 587 - 599, http://dx.doi.org/10.4161/epi.27806

Pidsley R; Viana J; Hannon E; Spiers HH; Troakes C; Al-Saraj S; Mechawar N; Turecki G; Schalkwyk LC; Bray NJ; Mill J, 2014, 'Methylomic profiling of human brain tissue supports a neurodevelopmental origin for schizophrenia', Genome Biol, 15, pp. 483, http://dx.doi.org/10.1186/PREACCEPT-1621721621132088

Pidsley R; Viana J; Hannon E; Spiers HH; Troakes C; Al-Saraj S; Mechawar N; Turecki G; Schalkwyk LC; Bray NJ; Mill J, 2014, 'Methylomic profiling of human brain tissue supports a neurodevelopmental origin for schizophrenia', Genome Biology, 15, pp. 483 - 483, http://dx.doi.org/10.1186/preaccept-1621721621132088

Pidsley R; Y Wong CC; Volta M; Lunnon K; Mill J; Schalkwyk LC, 2013, 'A data-driven approach to preprocessing Illumina 450K methylation array data', BMC Genomics, 14, http://dx.doi.org/10.1186/1471-2164-14-293

Dempster E; Viana J; Pidsley R; Mill J, 2013, 'Epigenetic studies of schizophrenia: Progress, predicaments, and promises for the future', Schizophrenia Bulletin, 39, pp. 11 - 16, http://dx.doi.org/10.1093/schbul/sbs139

Watkins-Chow DE; Cooke J; Pidsley R; Edwards A; Slotkin R; Leeds KE; Mullen R; Baxter LL; Campbell TG; Salzer MC; Biondini L; Gibney G; Phan Dinh Tuy F; Chelly J; Morris HD; Riegler J; Lythgoe MF; Arkell RM; Loreni F; Flint J; Pavan WJ; Keays DA, 2013, 'Mutation of the Diamond-Blackfan Anemia Gene Rps7 in Mouse Results in Morphological and Neuroanatomical Phenotypes', PLoS Genetics, 9, http://dx.doi.org/10.1371/journal.pgen.1003094

Pidsley R; Fernandes C; Viana J; Paya-Cano JL; Liu L; Smith RG; Schalkwyk LC; Mill J, 2012, 'DNA methylation at the Igf2/H19 imprinting control region is associated with cerebellum mass in outbred mice', Molecular Brain, 5, http://dx.doi.org/10.1186/1756-6606-5-42

Bell JT; Tsai PC; Yang TP; Pidsley R; Nisbet J; Glass D; Mangino M; Zhai G; Zhang F; Valdes A; Shin SY; Dempster EL; Murray RM; Grundberg E; Hedman AK; Nica A; Small KS; Dermitzakis ET; McCarthy MI; Mill J; Spector TD; Deloukas P, 2012, 'Epigenome-wide scans identify differentially methylated regions for age and age-related phenotypes in a healthy ageing population', PLoS Genetics, 8, http://dx.doi.org/10.1371/journal.pgen.1002629

Pidsley R; Dempster E; Troakes C; Al-Sarraj S; Mill J, 2012, 'Epigenetic and genetic variation at the IGF2/H19 imprinting control region on 11p15.5 is associated with cerebellum weight', Epigenetics, 7, pp. 155 - 163, http://dx.doi.org/10.4161/epi.7.2.18910

Davies MN; Volta M; Pidsley R; Lunnon K; Dixit A; Lovestone S; Coarfa C; Harris RA; Milosavljevic A; Troakes C; Al-Sarraj S; Dobson R; Schalkwyk LC; Mill J, 2012, 'Functional annotation of the human brain methylome identifies tissue-specific epigenetic variation across brain and blood.', Genome biology, 13, http://dx.doi.org/10.1186/gb-2012-13-6-r43

Boks MP; Pidsley R; van Eijk K; Dempster EL; Bank NB; de Jong S; Pol HEH; van Haren NE; Murray R; Kahn RS; Mill J; Ophoff RA, 2012, 'Poster #105 MONOZYGOTIC TWINS DISCORDANT FOR BIPOLAR DISORDER SHOW FUNCTIONAL DNA METHYLATION CHANGES IN WHOLE BLOOD AND BRAIN', Schizophrenia Research, 136, pp. S129 - S129, http://dx.doi.org/10.1016/s0920-9964(12)70420-6

Dempster EL; Pidsley R; Schalkwyk LC; Owens S; Georgiades A; Kane F; Kalidindi S; Picchioni M; Kravariti E; Toulopoulou T; Murray RM; Mill J, 2011, 'Disease-associated epigenetic changes in monozygotic twins discordant for schizophrenia and bipolar disorder', Human Molecular Genetics, 20, pp. 4786 - 4796, http://dx.doi.org/10.1093/hmg/ddr416

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