By Dr Ruth Pidsley

Book Chapters

Pidsley R; Stirzaker C, 2019, 'Cancer Methylation Biomarkers in Circulating Cell-Free DNA', in Clinical Epigenetics, pp. 217 - 245, http://dx.doi.org/10.1007/978-981-13-8958-0_10

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

Conference Papers

Lawrence MG; Pidsley R; Zotenko E; Niranjan B; Statham A; Song J; Armstrong N; Pedersen J; Frydenberg M; Taylor R; Stirzaker C; Risbridger G; Clark S, 2017, 'Abstract 1997: Charting the DNA methylation landscape of prostate cancer associated fibroblasts', in Cancer Research, American Association for Cancer Research (AACR), pp. 1997 - 1997, http://dx.doi.org/10.1158/1538-7445.am2017-1997

Conference Abstracts

Blazevski A; Pidsley R; Qu W; Korbie D; Luu L; Chang J; Yuen B; Scheltema MJ; Masand N; Haynes A-M; Quoc N; Stirzaker C; Song J; Stricker P; Clark S, 2018, 'When Focal Therapy Fails for Localised Prostate Cancer - Can Epigenetics Predict Which Patients Fail and Improve Patient Selection?', in ASIA-PACIFIC JOURNAL OF CLINICAL ONCOLOGY, WILEY, Vol. 14, pp. 33 - 33, https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000437670700023&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1

Pidsley R, 2015, 'Mining the microenvironment methylome to identify novel prostate cancer biomarkers', in Prostate Cancer, Hindawi Publishing Corporation, Brisbane, presented at Prostate Cancer Collaborative Symposium, Brisbane, 26 November 2015 - 28 November 2015

Pidsley R, 2015, 'Charting the epigenomic landscape of the prostate cancer microenvironment', in Epigenetics, Taylor & Francis: STM, Behavioural Science and Public Health Titles, Hobart, presented at Illumina Early Career Awards, Hobart, 12 November 2015 - 14 November 2015

Lawrence M; Pidsley R; Ellem S; Furic L; Nair S; French H; Statham A; Larsson O; Frydenberg M; Pedersen J; Buchanan G; Taylor R; Clark S; Risbridger G, 2015, 'Surveying the epigenome landscape of the prostate cancer microenvironment: identification of estrogen receptor alpha as a key differentially methylated gene', in CLINICAL ENDOCRINOLOGY, WILEY, AUSTRALIA, Adelaide, Vol. 84, pp. 20 - 20, presented at Annual Scientific Meeting of the Endocrine-Society-of-Australia, AUSTRALIA, Adelaide, 23 August 2015 - 26 August 2015, https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000372310400056&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1

Pidsley R, 2015, 'Peeling back the layers of the Prostate Cancer microenvironment', in ASMR, ASMR 23rd NSW Annual Scientific Meeting, Sydney, presented at ASMR 23rd NSW Annual Scientific Meeting, Sydney, 01 June 2015 - 02 June 2015

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