By Professor Susan Clark

Books

Coolen MW; Clark SJ, 2011, Epigenetics: A Reference Manual, Original, Caister Academic Press, UK, http://www.horizonpress.com/epigenetics

Book Chapters

Warton K; Stirzaker C; Samimi G; Clark S, 2022, 'DNA Methylation Analysis of Circulating DNA Biomarkers', in Cell-Free Circulating DNA: Purification and Analysis Techniques, pp. 247 - 277, http://dx.doi.org/10.1142/9789811244681_0009

Sibbritt T; Schumann U; Shafik A; Guarnacci M; Clark SJ; Preiss T, 2022, 'Target-Specific Profiling of RNA m⁵C Methylation Level Using Amplicon Sequencing', in Post-Transcriptional Gene Regulation, pp. 375 - 392, http://dx.doi.org/10.1007/978-1-0716-1851-6_21

Sibbritt T; Shafik A; Clark SJ; Preiss T, 2016, 'Nucleotide-Level Profiling of m⁵C RNA Methylation.', in Post-Transcriptional Gene Regulation, pp. 269 - 284, http://dx.doi.org/10.1007/978-1-4939-3067-8_16

Coolen MW; Clark SJ, 2011, 'Genome-wide DNA Methylation Analysis', in Craig JM; Wong NC (ed.), EPIGENETICS: A REFERENCE MANUAL, CAISTER ACADEMIC PRESS, pp. 371 - 392, http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000293148200022&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1

Guerrero-Bosagna CM; Clark SJ, 2011, 'We are what we eat: how nutritional compounds such as isoflavones shape our epigenome', in Niculescu MD; Haggarty P (ed.), Nutrition in Epigenetics, Wiley-Blackwell, Oxford, UK, pp. 249 - 261, http://dx.doi.org/10.1002/9780470959824.ch15

Clark SJ, 2004, 'Studying mammalian DNA methylation: Bisulfite modification', in DNA Methylation: Approaches, Methods, and Applications, pp. 53 - 64, http://dx.doi.org/10.1201/9780203487013

Clark SJ; Millar DS; Molloy P, 2003, 'Bisulfite Methylation Analysis of Tumor Suppressor Genes in Prostate Cancer from Fresh and Archival Tissue Samples', in Prostate Cancer Methods and Protocols, Springer Nature, pp. 219 - 240, http://dx.doi.org/10.1385/1-59259-372-0:219

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

Conduit C; Mak B; Qu W; Yeung T; Bressel M; Cusick T; Dhillon HM; De Abreu Lourenço R; Underhill C; Torres J; Crumbaker M; Honeyball F; Linton A; Sewak S; Chau NMH; Allen R; Davis ID; Clark SJ; Horvath L; Mahon KL, 2023, 'GUIDE: A randomized non-comparative phase II trial of biomarker-driven intermittent docetaxel versus standard-of-care docetaxel in metastatic castration-resistant prostate cancer (ANZUP 1903).', Journal of Clinical Oncology, 41, pp. TPS5099 - TPS5099, http://dx.doi.org/10.1200/jco.2023.41.16_suppl.tps5099

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

Colino-Sanguino Y; Clark SJ; Valdes-Mora F, 2022, 'Erratum: The H2A.Z-nucleosome code in mammals: emerging functions (Trends in Genetics (2022) 38(3) (273–289), (S0168952521002870), (10.1016/j.tig.2021.10.003)): (Trends in Genetics, 38:3 p:273–289, 2022)', Trends in Genetics, 38, pp. 516, http://dx.doi.org/10.1016/j.tig.2022.02.004

Clark SJ; Molloy PL, 2022, 'Early Insights into Cancer Epigenetics: Gene Promoter Hypermethylation Emerges as a Potential Biomarker for Cancer Detection', Cancer Research, 82, pp. 1461 - 1463, http://dx.doi.org/10.1158/0008-5472.CAN-22-0657

Conduit C; Mak B; Qu W; Lulio JD; Burder R; Bressel M; Cusick T; Dhillon HM; Lourenço RDA; Underhill C; Torres J; Crumbaker M; Honeyball F; Linton A; Allen R; Davis ID; Clark SJ; Horvath LG; Mahon KL, 2022, 'GUIDE: a randomised non-comparative phase II trial of biomarker-driven intermittent docetaxel versus standard-of-care docetaxel in metastatic castration-resistant prostate cancer (clinical trial protocol)', Therapeutic Advances in Medical Oncology, 14, http://dx.doi.org/10.1177/17588359221092486

Colino-Sanguino Y; Clark SJ; Valdes-Mora F, 2022, 'The H2A.Z-nuclesome code in mammals: emerging functions', Trends in Genetics, 38, pp. 273 - 289, http://dx.doi.org/10.1016/j.tig.2021.10.003

Brown LJ; Achinger-Kawecka J; Portman N; Clark S; Stirzaker C; Lim E, 2022, 'Epigenetic Therapies and Biomarkers in Breast Cancer', Cancers, 14, http://dx.doi.org/10.3390/cancers14030474

Giles KA; Gould CM; Achinger-Kawecka J; Page SG; Kafer GR; Rogers S; Luu PL; Cesare AJ; Clark SJ; Taberlay PC, 2021, 'BRG1 knockdown inhibits proliferation through multiple cellular pathways in prostate cancer', Clinical Epigenetics, 13, http://dx.doi.org/10.1186/s13148-021-01023-7

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

Peters TJ; Buckley MJ; Chen Y; Smyth GK; Goodnow CC; Clark SJ, 2021, 'Calling differentially methylated regions from whole genome bisulphite sequencing with DMRcate', Nucleic Acids Research, 49, http://dx.doi.org/10.1093/nar/gkab637

Ushijima T; Clark SJ; Tan P, 2021, 'Mapping genomic and epigenomic evolution in cancer ecosystems', Science, 373, pp. 1474 - 1479, http://dx.doi.org/10.1126/science.abh1645

Du Q; Smith GC; Luu PL; Ferguson JM; Armstrong NJ; Caldon CE; Campbell EM; Nair SS; Zotenko E; Gould CM; Buckley M; Chia KM; Portman N; Lim E; Kaczorowski D; Chan CL; Barton K; Deveson IW; Smith MA; Powell JE; Skvortsova K; Stirzaker C; Achinger-Kawecka J; Clark SJ, 2021, 'DNA methylation is required to maintain both DNA replication timing precision and 3D genome organization integrity', Cell Reports, 36, http://dx.doi.org/10.1016/j.celrep.2021.109722

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

Stirzaker C; Skvortsova K; Clark SJ, 2021, 'Epigenetic changes during tumour development – functional epigenetics study', Pathology, 53, pp. S10 - S11, http://dx.doi.org/10.1016/j.pathol.2021.05.040

Achinger-Kawecka J; Stirzaker C; Portman N; Campbell E; Chia K-M; Du Q; Laven-Law G; Nair S; Yong A; Wilkinson A; Clifton S; Milioli H; Alexandrou S; Caldon E; Song J; Khoury A; Meyer B; Gee JMW; Schmitt A; Wong E; Hickey T; Lim E; Clark S, 2021, 'Epigenetic therapy targets the 3D epigenome in endocrine-resistant breast cancer', , http://dx.doi.org/10.1101/2021.06.21.449340

Khoury A; Achinger-Kawecka J; Bert SA; Smith GC; French HJ; Luu PL; Peters TJ; Du Q; Parry AJ; Valdes-Mora F; Taberlay PC; Stirzaker C; Statham AL; Clark SJ, 2020, 'Constitutively bound CTCF sites maintain 3D chromatin architecture and long-range epigenetically regulated domains', Nature Communications, 11, http://dx.doi.org/10.1038/s41467-019-13753-7

Achinger-Kawecka J; Valdes-Mora F; Luu PL; Giles KA; Caldon CE; Qu W; Nair S; Soto S; Locke WJ; Yeo-Teh NS; Gould CM; Du Q; Smith GC; Ramos IR; Fernandez KF; Hoon DS; Gee JMW; Stirzaker C; Clark SJ; Valdes Mora F, 2020, 'Epigenetic reprogramming at estrogen-receptor binding sites alters 3D chromatin landscape in endocrine-resistant breast cancer', Nature Communications, 11, pp. 320, http://dx.doi.org/10.1038/s41467-019-14098-x

Schmitz U; Shah JS; Dhungel BP; Monteuuis G; Luu PL; Petrova V; Metierre C; Nair SS; Bailey CG; Saunders VA; Turhan AG; White DL; Branford S; Clark SJ; Hughes TP; Wong JJL; Rasko JEJ, 2020, 'Widespread aberrant alternative splicing despite molecular remission in chronic myeloid leukaemia patients', Cancers, 12, pp. 1 - 19, http://dx.doi.org/10.3390/cancers12123738

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

Luu PL; Ong PT; Dinh TP; Clark SJ, 2020, 'Benchmark study comparing liftover tools for genome conversion of epigenome sequencing data', NAR Genomics and Bioinformatics, 2, http://dx.doi.org/10.1093/nargab/lqaa054

Salazar-Roa M; Trakala M; Álvarez-Fernández M; Valdés-Mora F; Zhong C; Muñoz J; Yu Y; Peters TJ; Graña-Castro O; Serrano R; Zapatero-Solana E; Abad M; Bueno MJ; de Cedrón MG; Fernández-Piqueras J; Serrano M; Blasco MA; Wang DZ; Clark SJ; Izpisua-Belmonte JC; Ortega S; Malumbres M, 2020, 'Transient exposure to miR-203 enhances the differentiation capacity of established pluripotent stem cells', EMBO Journal, 39, http://dx.doi.org/10.15252/embj.2019104324

Green ID; Pinello N; Song R; Lee Q; Halstead JM; Kwok CT; Wong ACH; Nair SS; Clark SJ; Roediger B; Schmitz U; Larance M; Hayashi R; Rasko JEJ; Wong JJL, 2020, 'Macrophage development and activation involve coordinated intron retention in key inflammatory regulators', Nucleic Acids Research, 48, pp. 6513 - 6529, http://dx.doi.org/10.1093/nar/gkaa435

Giles KA; Gould CM; Achinger-Kawecka J; Page SG; Kafer G; Luu P-L; Cesare AJ; Clark SJ; Taberlay PC, 2020, 'BRG1 promotes transcriptional patterns that are permissive to proliferation in cancer cells', , http://dx.doi.org/10.1101/2020.07.03.187385

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

Schumann U; Zhang HN; Sibbritt T; Pan A; Horvath A; Gross S; Clark SJ; Yang L; Preiss T, 2020, 'Multiple links between 5-methylcytosine content of mRNA and translation', BMC Biology, 18, http://dx.doi.org/10.1186/s12915-020-00769-5

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

Piggin CL; Roden DL; Law AMK; Molloy MP; Krisp C; Swarbrick A; Naylor MJ; Kalyuga M; Kaplan W; Oakes SR; Gallego-Ortega D; Clark SJ; Carroll JS; Bartonicek N; Ormandy CJ, 2020, 'ELF5 modulates the estrogen receptor cistrome in breast cancer', PLoS Genetics, 16, http://dx.doi.org/10.1371/journal.pgen.1008531

Du Q; Smith G; Luu PL; Ferguson J; Armstrong N; Caldon E; Campbell E; Nair S; Zotenko E; Gould C; Buckley M; Kaczorowski D; Barton K; Deveson I; Smith M; Powell J; Skvortsova K; Stirzaker C; Achinger-Kawecka J; Clark S, 2020, 'DNA methylation is required to maintain DNA replication timing precision and 3D genome integrity', , http://dx.doi.org/10.1101/2020.10.15.338855

Stirzaker C; Skvortsova K; Masle-Farquhar E; Goodnow C; Clark SJ, 2020, 'Epigenetic changes during tumour development – Functional epigenetics study', Pathology, 52, pp. S29 - S29, http://dx.doi.org/10.1016/j.pathol.2020.01.121

Bradford ST; Nair SS; Statham AL; van Dijk SJ; Peters TJ; Anwar F; French HJ; von Martels JZH; Sutcliffe B; Maddugoda MP; Peranec M; Varinli H; Arnoldy R; Buckley M; Ross JP; Zotenko E; Song JZ; Stirzaker C; Bauer DC; Qu W; Swarbrick MM; Lutgers HL; Lord RV; Samaras K; Molloy PL; Clark SJ, 2019, 'Methylome and transcriptome maps of human visceral and subcutaneous adipocytes reveal key epigenetic differences at developmental genes', Scientific Reports, 9, pp. 9511, http://dx.doi.org/10.1038/s41598-019-45777-w

Tarr IS; McCann EP; Benyamin B; Peters TJ; Twine NA; Zhang KY; Zhao Q; Zhang ZH; Rowe DB; Nicholson GA; Bauer D; Clark SJ; Blair IP; Williams KL, 2019, 'Monozygotic twins and triplets discordant for amyotrophic lateral sclerosis display differential methylation and gene expression', Scientific Reports, 9, http://dx.doi.org/10.1038/s41598-019-44765-4

Du Q; Bert SA; Armstrong NJ; Caldon CE; Song JZ; Nair SS; Gould CM; Luu PL; Peters T; Khoury A; Qu W; Zotenko E; Stirzaker C; Clark SJ, 2019, 'Replication timing and epigenome remodelling are associated with the nature of chromosomal rearrangements in cancer', Nature Communications, 10, http://dx.doi.org/10.1038/s41467-019-08302-1

Colino-Sanguino Y; Cornett EM; Moulder D; Smith GC; Hrit J; Cordeiro-Spinetti E; Vaughan RM; Krajewski K; Rothbart SB; Clark SJ; Valdés-Mora F, 2019, 'A Read/Write Mechanism Connects p300 Bromodomain Function to H2A.Z Acetylation', iScience, 21, pp. 773 - 788, http://dx.doi.org/10.1016/j.isci.2019.10.053

Mahon KL; Qu W; Lin HM; Spielman C; Cain D; Jacobs C; Stockler MR; Higano CS; de Bono JS; Chi KN; Clark SJ; Horvath LG, 2019, 'Serum Free Methylated Glutathione S-transferase 1 DNA Levels, Survival, and Response to Docetaxel in Metastatic, Castration-resistant Prostate Cancer: Post Hoc Analyses of Data from a Phase 3 Trial', European Urology, 76, pp. 306 - 312, http://dx.doi.org/10.1016/j.eururo.2018.11.001

Milevskiy MJG; Gujral U; Del Lama Marques C; Stone A; Northwood K; Burke LJ; Gee JMW; Nephew K; Clark S; Brown MA, 2019, 'MicroRNA-196a is regulated by ER and is a prognostic biomarker in ER+ breast cancer', British Journal of Cancer, 120, pp. 621 - 632, http://dx.doi.org/10.1038/s41416-019-0395-8

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

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