Professor Susan Clark

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

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 Methods in Molecular Biology, pp. 375 - 392, http://dx.doi.org/10.1007/978-1-0716-1851-6_21

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

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

Brown LJ; Achinger-Kawecka J; Portman N; Clark S; Stirzaker C; Lim E, 2022, 'Epigenetic Therapies and Biomarkers in Breast Cancer', Cancers, vol. 14, pp. 474 - 474, http://dx.doi.org/10.3390/cancers14030474

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

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, vol. 38, pp. 516, http://dx.doi.org/10.1016/j.tig.2022.02.004

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

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, vol. 14, http://dx.doi.org/10.1177/17588359221092486

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, vol. 12, http://dx.doi.org/10.1002/ctm2.1030

Achinger-Kawecka J; Stirzaker C; Chia K-M; Portman N; Campbell E; Du Q; Laven-Law G; Nair SS; Yong A; Wilkinson A; Clifton S; Milioli HH; Schmitt A; Wong ES; Hickey TE; Lim E; Clark SJ, 2021, 'Epigenetic therapy suppresses endocrine-resistant breast tumour growth by re-wiring ER-mediated 3D chromatin interactions', , http://dx.doi.org/10.1101/2021.06.21.449340

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, vol. 36, http://dx.doi.org/10.1016/j.celrep.2021.109722

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, vol. 13, http://dx.doi.org/10.1186/s13148-021-01023-7

Luu P-L; Ong P-T; Tran THL; 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, vol. 37, pp. 2198 - 2200, http://dx.doi.org/10.1093/bioinformatics/btaa1060

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, vol. 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, vol. 49, pp. e109, http://dx.doi.org/10.1093/nar/gkab637

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

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

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, 2020, 'Epigenetic reprogramming at estrogen-receptor binding sites alters 3D chromatin landscape in endocrine-resistant breast cancer', Nature Communications, vol. 11, http://dx.doi.org/10.1038/s41467-019-14098-x

Du Q; Smith GC; Luu PL; Ferguson JM; Armstrong NJ; Caldon CE; Campbell E; Nair SS; Zotenko E; Gould CM; Buckley M; Kaczorowski D; Barton K; Deveson IW; Smith MA; Powell JE; Skvortsova K; Stirzaker C; Achinger-Kawecka J; Clark SJ, 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

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

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, vol. 48, pp. 6513 - 6529, http://dx.doi.org/10.1093/nar/gkaa435

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, vol. 11, http://dx.doi.org/10.1038/s41467-019-13753-7

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, vol. 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, vol. 12, pp. 90, 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, vol. 12, pp. 48, http://dx.doi.org/10.1186/s13148-020-00836-2

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, vol. 2, http://dx.doi.org/10.1093/nargab/lqaa054

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, vol. 16, pp. e1008531, http://dx.doi.org/10.1371/journal.pgen.1008531

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, vol. 39, http://dx.doi.org/10.15252/embj.2019104324

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, vol. 12, pp. 1 - 19, http://dx.doi.org/10.3390/cancers12123738

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, vol. 18, http://dx.doi.org/10.1186/s12915-020-00769-5

Stirzaker C; Skvortsova K; Masle-Farquhar E; Goodnow C; Clark SJ, 2020, 'Epigenetic changes during tumour development – Functional epigenetics study', Pathology, vol. 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, vol. 9, pp. 9511, http://dx.doi.org/10.1038/s41598-019-45777-w

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, vol. 21, pp. 773 - 788, http://dx.doi.org/10.1016/j.isci.2019.10.053

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, vol. 10, pp. 416, http://dx.doi.org/10.1038/s41467-019-08302-1

Giles KA; Gould CM; Du Q; Skvortsova K; Song JZ; Maddugoda MP; Achinger-Kawecka J; Stirzaker C; Clark SJ; Taberlay PC, 2019, 'Integrated epigenomic analysis stratifies chromatin remodellers into distinct functional groups', Epigenetics and Chromatin, vol. 12, pp. 12, http://dx.doi.org/10.1186/s13072-019-0258-9

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, vol. 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, vol. 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, vol. 35, pp. 560 - 570, http://dx.doi.org/10.1093/bioinformatics/bty675

Salazar-Roa M; Trakala M; Álvarez-Fernández M; Valdés-Mora F; Zhong C; Muñoz J; Yu Y; Peters T; Graña O; Serrano R; Zapatero-Solana E; Abad M; Bueno MJ; de Cedrón MG; Fernández-Piqueras J; Serrano M; Blasco M; Wang D-Z; Clark S; Izpisua-Belmonte JC; Ortega S; Malumbres M, 2019, 'A novel microRNA-based strategy to expand the differentiation potency of stem cells', , http://dx.doi.org/10.1101/826446

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, vol. 35, pp. 297 - 314.e8, http://dx.doi.org/10.1016/j.ccell.2019.01.004

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, vol. 9, http://dx.doi.org/10.1038/s41598-019-44765-4

Carpenter BL; Zhou W; Madaj Z; DeWitt AK; Ross JP; Grønbæk K; Liang G; Clark SJ; Molloy PL; Jones PA, 2018, 'Mother–child transmission of epigenetic information by tunable polymorphic imprinting', Proceedings of the National Academy of Sciences of the United States of America, vol. 115, pp. E11970 - E11977, http://dx.doi.org/10.1073/pnas.1815005115

Holliday H; Baker LA; Junankar SR; Clark SJ; Swarbrick A, 2018, 'Epigenomics of mammary gland development', Breast Cancer Research, vol. 20, http://dx.doi.org/10.1186/s13058-018-1031-x

Nair SS; Luu PL; Qu W; Maddugoda M; Huschtscha L; Reddel R; Chenevix-Trench G; Toso M; Kench JG; Horvath LG; Hayes VM; Stricker PD; Hughes TP; White DL; Rasko JEJ; Wong JJL; Clark SJ, 2018, 'Guidelines for whole genome bisulphite sequencing of intact and FFPET DNA on the Illumina HiSeq X Ten', Epigenetics and Chromatin, vol. 11, http://dx.doi.org/10.1186/s13072-018-0194-0

O'Donoghue SI; Baldi BF; Clark SJ; Darling AE; Hogan JM; Kaur S; Maier-Hein L; McCarthy DJ; Moore WJ; Stenau E; Swedlow JR; Vuong J; Procter JB, 2018, 'Visualization of Biomedical Data', ANNUAL REVIEW OF BIOMEDICAL DATA SCIENCE, VOL 1, vol. 1, pp. 275 - 304, http://dx.doi.org/10.1146/annurev-biodatasci-080917-013424

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, vol. 28, pp. 625 - 638, http://dx.doi.org/10.1101/gr.229070.117

Stirzaker C; Song JZ; Statham AL; Clark SJ, 2018, 'Bisulphite sequencing of chromatin immunoprecipitated DNA (BisChIP-seq)', Methods in Molecular Biology, vol. 1708, pp. 285 - 302, http://dx.doi.org/10.1007/978-1-4939-7481-8_15

Achinger-Kawecka J; Clark SJ, 2017, 'Disruption of the 3D cancer genome blueprint', Epigenomics, vol. 9, pp. 47 - 55, http://dx.doi.org/10.2217/epi-2016-0111

Clark SJ; Molloy PL, 2017, 'Smoke-Induced Changes to the Epigenome Provide Fertile Ground for Oncogenic Mutation', Cancer Cell, vol. 32, pp. 278 - 280, http://dx.doi.org/10.1016/j.ccell.2017.08.016

Knaupp AS; Buckberry S; Pflueger J; Lim SM; Ford E; Larcombe MR; Rossello FJ; de Mendoza A; Alaei S; Firas J; Holmes ML; Nair SS; Clark SJ; Nefzger CM; Lister R; Polo JM, 2017, 'Transient and Permanent Reconfiguration of Chromatin and Transcription Factor Occupancy Drive Reprogramming', Cell Stem Cell, vol. 21, pp. 834 - 845.e6, http://dx.doi.org/10.1016/j.stem.2017.11.007

Lawrence M; Pidlsey R; Zotenko E; Niranjan B; Nair S; French H; Statham A; Song J; Chabanon R; Papargiris M; Ellem S; Frydenberg M; Pedersen J; Stirzaker C; Taylor R; Clark S; Risbridger G, 2017, 'Hypomethylation of estrogen receptor alpha: a landmark in the epigenome landscape of prostate cancer stroma', CLINICAL ENDOCRINOLOGY, vol. 86, pp. 23 - 23, https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000393453600061&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1

Mahon KL; Qu W; Lin H-M; Spielman C; Cain D; Jacobs C; Chi KN; De Bono JS; Higano CS; Clark SJ; Horvath L, 2017, 'Post hoc analysis of a phase III study to test the association between circulating methylated glutathione s transferase (mGSTP1) DNA levels and response to docetaxel (DTX) in metastatic castration resistant prostate cancer (mCRPC).', Journal of Clinical Oncology, vol. 35, pp. 5014 - 5014, http://dx.doi.org/10.1200/jco.2017.35.15_suppl.5014

Skvortsova K; Zotenko E; Luu PL; Gould CM; Nair SS; Clark SJ; Stirzaker C, 2017, 'Comprehensive evaluation of genome-wide 5-hydroxymethylcytosine profiling approaches in human DNA', Epigenetics and Chromatin, vol. 10, http://dx.doi.org/10.1186/s13072-017-0123-7

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, vol. 36, pp. 1328 - 1338, http://dx.doi.org/10.1038/onc.2016.297

Valdés-Mora F; Gould CM; Colino-Sanguino Y; Qu W; Song JZ; Taylor KM; Buske FA; Statham AL; Nair SS; Armstrong NJ; Kench JG; Lee KML; Horvath LG; Qiu M; Ilinykh A; Yeo-Teh NS; Gallego-Ortega D; Stirzaker C; Clark SJ, 2017, 'Acetylated histone variant H2A.Z is involved in the activation of neo-enhancers in prostate cancer', Nature Communications, vol. 8, http://dx.doi.org/10.1038/s41467-017-01393-8

Achinger-Kawecka J; Taberlay PC; Clark SJ, 2016, 'Alterations in three-dimensional organization of the cancer genome and epigenome', Cold Spring Harbor Symposia on Quantitative Biology, vol. 81, pp. 41 - 51, http://dx.doi.org/10.1101/sqb.2016.81.031013

Bock C; Halbritter F; Carmona FJ; Tierling S; Datlinger P; Assenov Y; Berdasco M; Bergmann AK; Booher K; Busato F; Campan M; Dahl C; Dahmcke CM; Diep D; Fernández AF; Gerhauser C; Haake A; Heilmann K; Holcomb T; Hussmann D; Ito M; Kläver R; Kreutz M; Kulis M; Lopez V; Nair SS; Paul DS; Plongthongkum N; Qu W; Queirós AC; Reinicke F; Sauter G; Schlomm T; Statham A; Stirzaker C; Strogantsev R; Urdinguio RG; Walter K; Weichenhan D; Weisenberger DJ; Beck S; Clark SJ; Esteller M; Ferguson-Smith AC; Fraga MF; Guldberg P; Hansen LL; Laird PW; Martín-Subero JI; Nygren AOH; Peist R; Plass C; Shames DS; Siebert R; Sun X; Tost J; Walter J; Zhang K, 2016, 'Quantitative comparison of DNA methylation assays for biomarker development and clinical applications', Nature Biotechnology, vol. 34, pp. 726 - 737, http://dx.doi.org/10.1038/nbt.3605

Colino-Sanguino Y; Clark SJ; Valdes-Mora F, 2016, 'H2A.Z acetylation and transcription: Ready, steady, go!', Epigenomics, vol. 8, pp. 583 - 586, http://dx.doi.org/10.2217/epi-2016-0016

Hou L; Heilbronner U; Degenhardt F; Adli M; Akiyama K; Akula N; Ardau R; Arias B; Backlund L; Banzato CEM; Benabarre A; Bengesser S; Bhattacharjee AK; Biernacka JM; Birner A; Brichant-Petitjean C; Bui ET; Cervantes P; Chen GB; Chen HC; Chillotti C; Cichon S; Clark SR; Colom F; Cousins DA; Cruceanu C; Czerski PM; Dantas CR; Dayer A; Étain B; Falkai P; Forstner AJ; Frisén L; Fullerton JM; Gard S; Garnham JS; Goes FS; Grof P; Gruber O; Hashimoto R; Hauser J; Herms S; Hoffmann P; Hofmann A; Jamain S; Jiménez E; Kahn JP; Kassem L; Kittel-Schneider S; Kliwicki S; König B; Kusumi I; Lackner N; Laje G; Landén M; Lavebratt C; Leboyer M; Leckband SG; Jaramillo CAL; Macqueen G; Manchia M; Martinsson L; Mattheisen M; McCarthy MJ; McElroy SL; Mitjans M; Mondimore FM; Monteleone P; Nievergelt CM; Nöthen MM; Ösby U; Ozaki N; Perlis RH; Pfennig A; Reich-Erkelenz D; Rouleau GA; Schofield PR; Schubert KO; Schweizer BW; Seemüller F; Severino G; Shekhtman T; Shilling PD; Shimoda K; Simhandl C; Slaney CM; Smoller JW; Squassina A; Stamm T; Stopkova P; Tighe SK; Tortorella A; Turecki G; Volkert J; Witt S; Wright A; Young LT; Zandi PP; Potash JB; Depaulo JR, 2016, 'Genetic variants associated with response to lithium treatment in bipolar disorder: A genome-wide association study', The Lancet, vol. 387, pp. 1085 - 1093, http://dx.doi.org/10.1016/S0140-6736(16)00143-4

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, vol. 8, http://dx.doi.org/10.1186/s13148-016-0235-0

Mathe A; Wong-Brown M; Locke WJ; Stirzaker C; Braye SG; Forbes JF; Clark SJ; Avery-Kiejda KA; Scott RJ, 2016, 'DNA methylation profile of triple negative breast cancer-specific genes comparing lymph node positive patients to lymph node negative patients', Scientific Reports, vol. 6, http://dx.doi.org/10.1038/srep33435

Milevskiy MJG; Al-Ejeh F; Saunus JM; Northwood KS; Bailey PJ; Betts JA; Reed AEMC; Nephew KP; Stone A; Gee JMW; Dowhan DH; Dray E; Shewan AM; French JD; Edwards SL; Clark SJ; Lakhani SR; Brown MA, 2016, 'Long-range regulators of the lncRNA HOTAIR enhance its prognostic potential in breast cancer', Human Molecular Genetics, vol. 25, pp. 3269 - 3283, http://dx.doi.org/10.1093/hmg/ddw177

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, vol. 17, 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, vol. 17, http://dx.doi.org/10.1186/s13059-016-1066-1

Stirzaker C; Zotenko E; Clark SJ, 2016, 'Genome-wide DNA methylation profiling in triple-negative breast cancer reveals epigenetic signatures with important clinical value', Molecular and Cellular Oncology, vol. 3, http://dx.doi.org/10.1080/23723556.2015.1038424

Taberlay PC; Achinger-Kawecka J; Lun ATL; Buske FA; Sabir KS; Gould CM; Zotenko E; Bert SA; Giles KA; Bauer D; Smyth GK; Stirzaker C; O Donoghue SI; Clark SJ, 2016, 'Three-dimensional disorganisation of the cancer genome occurs coincident with long range genetic and epigenetic alterations', Genome Research, vol. 26, pp. 719 - 731, http://dx.doi.org/10.1101/gr.201517.115

Walton SJ; Lewis A; Jeffery R; Thompson H; Feakins R; Giannoulatou E; Yau C; Lindsay JO; Clark SK; Silver A, 2016, 'Familial adenomatous patients with desmoid tumours show increased expression of miR-34a in serum and high levels in tumours', Oncoscience, vol. 3, pp. 173 - 185, http://dx.doi.org/10.18632/oncoscience.312

Clark S; Sarlin P; Sharma A; Sisson SA, 2015, 'Increasing dependence on foreign water resources? An assessment of trends in global virtual water flows using a self-organizing time map', Ecological Informatics, vol. 26, pp. 192 - 202, http://dx.doi.org/10.1016/j.ecoinf.2014.05.012

Du Q; Luu PL; Stirzaker C; Clark SJ, 2015, 'Methyl-CpG-binding domain proteins: Readers of the epigenome', Epigenomics, vol. 7, pp. 1051 - 1073, http://dx.doi.org/10.2217/epi.15.39

Gallego-Ortega D; Ledger A; Roden DL; Law AMK; Magenau A; Kikhtyak Z; Cho C; Allerdice SL; Lee HJ; Valdes-Mora F; Herrmann D; Salomon R; Young AIJ; Lee BY; Sergio CM; Kaplan W; Piggin C; Conway JRW; Rabinovich B; Millar EKA; Oakes SR; Chtanova T; Swarbrick A; Naylor MJ; O’Toole S; Green AR; Timpson P; Gee JMW; Ellis IO; Clark SJ; Ormandy CJ, 2015, 'ELF5 Drives Lung Metastasis in Luminal Breast Cancer through Recruitment of Gr1+ CD11b+ Myeloid-Derived Suppressor Cells', PLoS Biology, vol. 13, http://dx.doi.org/10.1371/journal.pbio.1002330

Korbie D; Lin E; Wall D; Nair SS; Stirzaker C; Clark SJ; Trau M, 2015, 'Multiplex bisulfite PCR resequencing of clinical FFPE DNA', Clinical Epigenetics, vol. 7, http://dx.doi.org/10.1186/s13148-015-0067-3

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

Locke WJ; Zotenko E; Stirzaker C; Robinson MD; Hinshelwood RA; Stone A; Reddel RR; Huschtscha LI; Clark SJ, 2015, 'Coordinated epigenetic remodelling of transcriptional networks occurs during early breast carcinogenesis', Clinical Epigenetics, vol. 7, http://dx.doi.org/10.1186/s13148-015-0086-0

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, vol. 8, http://dx.doi.org/10.1186/1756-8935-8-6

Phua YW; Nguyen A; Roden DL; Elsworth B; Deng N; Nikolic I; Yang J; Mcfarland A; Russell R; Kaplan W; Cowley MJ; Nair R; Zotenko E; O'Toole S; Tan SX; James DE; Clark SJ; Kouros-Mehr H; Swarbrick A, 2015, 'MicroRNA profiling of the pubertal mouse mammary gland identifies miR-184 as a candidate breast tumour suppressor gene', Breast Cancer Research, vol. 17, http://dx.doi.org/10.1186/s13058-015-0593-0

Statham AL; Taberlay PC; Kelly TK; Jones PA; Clark SJ, 2015, 'Genome-wide nucleosome occupancy and DNA methylation profiling of four human cell lines', Genomics Data, vol. 3, pp. 94 - 96, http://dx.doi.org/10.1016/j.gdata.2014.11.012

Stirzaker C; Zotenko E; Song JZ; Qu W; Nair SS; Locke WJ; Stone A; Armstong NJ; Robinson MD; Dobrovic A; Avery-Kiejda KA; Peters KM; French JD; Stein S; Korbie DJ; Trau M; Forbes JF; Scott RJ; Brown MA; Francis GD; Clark SJ, 2015, 'Methylome sequencing in triple-negative breast cancer reveals distinct methylation clusters with prognostic value', Nature Communications, vol. 6, pp. 5899 - 5899, http://dx.doi.org/10.1038/ncomms6899

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, vol. 6, http://dx.doi.org/10.1038/ncomms8758

Valdés-Mora F; Clark SJ, 2015, 'Prostate cancer epigenetic biomarkers: next-generation technologies', Oncogene, vol. 34, pp. 1609 - 1618, http://dx.doi.org/10.1038/onc.2014.111

Van Dijk SJ; Molloy PL; Varinli H; Morrison JL; Muhlhausler BS; Buckley M; Clark SJ; McMillen IC; Noakes M; Samaras K; Tellam RL, 2015, 'Epigenetics and human obesity', International Journal of Obesity, vol. 39, pp. 85 - 97, http://dx.doi.org/10.1038/ijo.2014.34

Varinli H; Statham AL; Clark SJ; Molloy PL; Ross JP, 2015, 'COBRA-seq: Sensitive and quantitative methylome profiling', Genes, vol. 6, pp. 1140 - 1163, http://dx.doi.org/10.3390/genes6041140

Ali NA; Wu J; Hochgräfe F; Chan H; Nair R; Ye S; Zhang L; Lyons RJ; Pinese M; Lee HC; Armstrong N; Ormandy CJ; Clark SJ; Swarbrick A; Daly RJ, 2014, 'Profiling the tyrosine phosphoproteome of different mouse mammary tumour models reveals distinct, model-specific signalling networks and conserved oncogenic pathways', Breast Cancer Research, vol. 16, http://dx.doi.org/10.1186/s13058-014-0437-3

Buske FA; French HJ; Smith MA; Clark SJ; Bauer DC, 2014, 'NGSANE: a lightweight production informatics framework for high-throughput data analysis', Bioinformatics, vol. 30, pp. 1471 - 1472, http://dx.doi.org/10.1093/bioinformatics/btu036

Clark S; Sisson SA; Sharma A, 2014, 'A dimension range representation (DRR) measure for self-organizing maps', Pattern Recognition, http://dx.doi.org/10.1016/j.patcog.2015.11.002

Gloss B; Moran-Jones K; Lin V; Gonzalez M; Scurry J; Hacker NF; Sutherland RL; Clark SJ; Samimi G, 2014, 'ZNF300P1 Encodes a lincRNA that regulates cell polarity and is epigenetically silenced in type II epithelial ovarian cancer', Molecular Cancer, vol. 13, http://dx.doi.org/10.1186/1476-4598-13-3

Lin HM; Castillo L; Mahon KL; Chiam K; Lee BY; Nguyen Q; Boyer MJ; Stockler MR; Pavlakis N; Marx G; Mallesara G; Gurney H; Clark SJ; Swarbrick A; Daly RJ; Horvath LG, 2014, 'Circulating microRNAs are associated with docetaxel chemotherapy outcome in castration-resistant prostate cancer', British Journal of Cancer, vol. 110, pp. 2462 - 2471, http://dx.doi.org/10.1038/bjc.2014.181

Mahon KL; Qu W; Devaney J; Paul C; Castillo L; Wykes RJ; Chatfield MD; Boyer MJ; Stockler MR; Marx G; Gurney H; Mallesara G; Molloy PL; Horvath LG; Clark SJ, 2014, 'Methylated Glutathione S-transferase 1 (mGSTP1) is a potential plasma free DNA epigenetic marker of prognosis and response to chemotherapy in castrate-resistant prostate cancer', British Journal of Cancer, vol. 111, pp. 1802 - 1809, http://dx.doi.org/10.1038/bjc.2014.463

Riebler A; Menigatti M; Song JZ; Statham AL; Stirzaker C; Mahmud N; Mein CA; Clark SJ; Robinson MD, 2014, 'BayMeth:Improved DNA methylation quantification for affinity capture sequencing data using a flexible Bayesian approach', Genome Biology, vol. 15, http://dx.doi.org/10.1186/gb-2014-15-2-r35

Skulte KA; Phan L; Clark SJ; Taberlay PC, 2014, 'Chromatin remodeler mutations in human cancers: Epigenetic implications', Epigenomics, vol. 6, pp. 397 - 414, http://dx.doi.org/10.2217/epi.14.37

Stirzaker C; Taberlay PC; Statham AL; Clark SJ, 2014, 'Mining cancer methylomes: Prospects and challenges', Trends in Genetics, vol. 30, pp. 75 - 84, http://dx.doi.org/10.1016/j.tig.2013.11.004

Taberlay PC; Statham AL; Kelly TK; Clark SJ; Jones PA, 2014, 'Reconfiguration of nucleosome-depleted regions at distal regulatory elements accompanies DNA methylation of enhancers and insulators in cancer', Genome Research, vol. 24, pp. 1421 - 1432, http://dx.doi.org/10.1101/gr.163485.113

Warton K; Lin V; Navin T; Armstrong NJ; Kaplan W; Ying K; Gloss B; Mangs H; Nair SS; Hacker NF; Sutherland RL; Clark SJ; Samimi G, 2014, 'Methylation-capture and Next-Generation Sequencing of free circulating DNA from human plasma', BMC Genomics, vol. 15, http://dx.doi.org/10.1186/1471-2164-15-476

Bert SA; Robinson MD; Strbenac D; Statham AL; Song JZ; Hulf T; Sutherland RL; Coolen MW; Stirzaker C; Clark SJ, 2013, 'Regional Activation of the Cancer Genome by Long-Range Epigenetic Remodeling', Cancer Cell, vol. 23, pp. 9 - 22, http://dx.doi.org/10.1016/j.ccr.2012.11.006

Clark AK; Taubenberger AV; Taylor RA; Niranjan B; Chea ZY; Zotenko E; Sieh S; Pedersen JS; Norden S; Frydenberg M; Grummet JP; Pook DW; Stirzaker C; Clark SJ; Lawrence MG; Ellem SJ; Hutmacher DW; Risbridger GP, 2013, 'A bioengineered microenvironment to quantitatively measure the tumorigenic properties of cancer-associated fibroblasts in human prostate cancer', Biomaterials, vol. 34, pp. 4777 - 4785, http://dx.doi.org/10.1016/j.biomaterials.2013.03.005

Hulf T; Sibbritt T; Wiklund ED; Patterson K; Song JZ; Stirzaker C; Qu W; Nair S; Horvath LG; Armstrong NJ; Kench JG; Sutherland RL; Clark SJ, 2013, 'Epigenetic-induced repression of microRNA-205 is associated with MED1 activation and a poorer prognosis in localized prostate cancer', Oncogene, vol. 32, pp. 2891 - 2899, http://dx.doi.org/10.1038/onc.2012.300

Stone A; Cowley MJ; Valdes-Mora F; McCloy RA; Sergio CM; Gallego-Ortega D; Caldon CE; Ormandy CJ; Biankin AV; Gee JMW; Nicholson RI; Print CG; Clark SJ; Musgrove EA, 2013, 'BCL-2 hypermethylation is a potential biomarker of sensitivity to antimitotic chemotherapy in endocrine-resistant breast cancer', Molecular Cancer Therapeutics, vol. 12, pp. 1874 - 1885, http://dx.doi.org/10.1158/1535-7163.MCT-13-0012

Stone A; Valdes-Mora F; Clark SJ, 2013, 'Exploring and exploiting the aberrant DNA methylation profile of endocrine-resistant breast cancer', Epigenomics, vol. 5, pp. 595 - 598, http://dx.doi.org/10.2217/epi.13.70

Warton K; Vita L; Armstrong NJ; Kaplan W; Ying K; Mangs H; Hacker NF; Sutherland RL; Clark SJ; Samimi G, 2013, 'Whole genome sequencing of free circulating DNA from plasma of HGSOC patients', CLINICAL CANCER RESEARCH, vol. 19, http://dx.doi.org/10.1158/1078-0432.OVCA13-A4

Beck S; Bernstein BE; Campbell RM; Costello JF; Dhanak D; Ecker JR; Greally JM; Issa JP; Laird PW; Polyak K; Tycko B; Jones PA; Force ACET, 2012, 'A blueprint for an international cancer epigenome consortium. A report from the AACR Cancer Epigenome Task Force', Cancer Res, vol. 72, pp. 6319 - 6324, http://dx.doi.org/10.1158/0008-5472.CAN-12-3658

Gloss B; Patterson K; Barton CA; Gonzalez M; Scurry JP; Hacker NF; Sutherland RL; O''brien P; Clark SJ, 2012, 'Integrative genome-wide expression and promoter DNA methylation profiling identifies a potential novel panel of ovarian cancer epigenetic biomarkers', Cancer Letters, vol. 318, pp. 76 - 85, http://dx.doi.org/10.1016/j.canlet.2011.12.003

Kalyuga M; Gallego-Ortega D; Lee H; Roden DL; Cowley MJ; Caldon CE; Stone A; Allerdice SL; Valdes-Mora F; Rosalind launchbury R; Statham A; Armstrong NJ; Alles MC; Adelaide young A; Egger A; Au W; Piggin CL; Evans C; Ledger A; Brummer T; Oakes SR; Kaplan W; Gee JMW; Robert i nicholson RI; Sutherland RL; Swarbrick A; Naylor MJ; Clark SJ; Carroll JS; Ormandy CJ, 2012, 'ELF5 Suppresses Estrogen Sensitivity and Underpins the Acquisition of Antiestrogen Resistance in Luminal Breast Cancer', PLoS Biology, vol. 10, pp. e1001461, http://dx.doi.org/10.1371/journal.pbio.1001461

Peters K; Edwards S; Nair SS; French J; Bailey PJ; Salkield K; Stein SR; Wagner S; Francis G; Clark SJ; Brown M, 2012, 'Androgen receptor expression predicts breast cancer survival: The role of genetic and epigenetic events', BMC Cancer, vol. 12, pp. 132, http://dx.doi.org/10.1186/1471-2407-12-132

Robinson MD; Strbenac D; Stirzaker C; Statham A; Song JZ; Speed TP; Clark SJ, 2012, 'Copy-number-aware differential analysis of quantitative DNA sequencing data', Genome Research, vol. 22, pp. 2490 - 2496, http://dx.doi.org/10.1101/gr.139055.112

Valdes-Mora F; Song JZ; Statham AL; Strbenac D; Robinson MD; Nair SS; Patterson K; Tremethick DJ; Stirzaker C; Clark SJ, 2012, 'Acetylation of H2A.Z is a key epigenetic modification associated with gene deregulation and epigenetic remodeling in cancer', Genome Research, vol. 22, pp. 307 - 321, http://dx.doi.org/10.1101/gr.118919.110

Wee EJH; Peters K; Nair SS; Hulf T; Stein S; Wagner S; Bailey PJ; Lee SY; Qu WJ; Brewster B; French JD; Dobrovic A; Francis GD; Clark SJ; Brown MA, 2012, 'Mapping the regulatory sequences controlling 93 breast cancer-associated miRNA genes leads to the identification of two functional promoters of the Hsa-mir-200b cluster, methylation of which is associated with metastasis or hormone receptor status in advanced breast cancer', Oncogene, vol. 31, pp. 4182 - 4195, http://dx.doi.org/10.1038/onc.2011.584

Braithwaite J; Westbrook J; Johnston BW; Clarke S; Brandon M; Banks M; Hughes C; Greenfield DR; Pawsey M; Corbett AD; Georgiou A; Callen J; Ovreveit J; Pope C; Suñol R; Shaw C; Debono DS; Westbrook MT; Hinchcliff R; Moldovan M, 2011, 'Strengthening organizational performance through accreditation research - a framework for twelve interrelated studies: the ACCREDIT project study protocol', BMC Research Notes, vol. 4, pp. 390 - 399, http://dx.doi.org/10.1186/1756-0500-4-390

Coolen MW; Statham A; Qu W; Campbell M; Henders AK; Montgomery GW; Martin N; Clark SJ, 2011, 'Impact of the genome on the epigenome is manifested in DNA methylation patterns of imprinted regions in monozygotic and dizygotic twins', PLoS One, vol. 6, pp. e25590, http://dx.doi.org/10.1371/journal.pone.0025590

Devaney J; Stirzaker C; Qu W; Song JZ; Statham AL; Patterson K; Horvath LG; Tabor B; Coolen MW; Hulf T; Kench JG; Henshall SM; Pe benito R; Haynes AM; Mayor R; Peinado M; Sutherland RL; Clark SJ, 2011, 'Epigenetic deregulation across chromosome 2q14.2 differentiates normal from prostate cancer and provides a regional panel of novel DNA methylation cancer biomarkers', Cancer Epidemiology Biomarkers and Prevention, vol. 20, pp. 148 - 159, http://dx.doi.org/10.1158/1055-9965.EPI-10-0719

Hansen TK; Wiklund ED; Bramsen J; Villadsen S; Statham AL; Clark SJ; Kjems J, 2011, 'miRNA-dependent gene silencing involving Ago2-mediated cleavage of a circular antisense RNA', European Molecular Biology Organization, vol. 30, pp. 4414 - 4422, http://dx.doi.org/10.1038/emboj.2011.359

Horvath L; Mahon KL; Qu W; Devaney J; Chatfield MD; Paul C; Wykes R; Boyer MJ; Stockler MR; Marx GM; Sutherland RL; Clark SJ, 2011, 'A study of methylated glutathione s-transferase 1 (mGSTP1)as a potential plasma epigenetic marker of response to chemotherapy and prognosis in men with castration-resistant prostate cancer (CRPC).', J Clin Oncol, vol. 29, pp. 4603, http://www.ncbi.nlm.nih.gov/pubmed/28024014

Hulf T; Sibbritt T; Wikland K; Bert S; Strbenac D; Statham AL; Robinson M; Clark SJ, 2011, 'Discovery pipeline for epigenetically deregulated miRNAs in cancer: integration of primary miRNA transcription', BMC Genomics, vol. 12, pp. 54 - 64, http://dx.doi.org/10.1186/1471-2164-12-54

Jeronimo C; Bastian PJ; Bjartell A; Carbone GM; Catto JWF; Clark SJ; Henrique R; Nelson WG; Shariat SF, 2011, 'Epigenetics in prostate cancer: Biologic and clinical relevance', European Urology, vol. 60, pp. 753 - 766, http://dx.doi.org/10.1016/j.eururo.2011.06.035

Lee HJ; Hinshelwood R; Bouras T; Gallego-Ortega D; Valdes-Mora F; Blazek K; Visvader JE; Clark SJ; Ormandy CJ, 2011, 'Lineage specific methylation of the Elf5 promoter in mammary epithelial cells', Stem Cells, vol. 29, pp. 1611 - 1619, http://dx.doi.org/10.1002/stem.706

Mayor R; Munoz M; Coolen MW; Custodio J; Esteller M; Clark SJ; Peinado M, 2011, 'Dynamics of bivalent chromatin domains upon drug induced reactivation and resilencing in cancer cells', Epigenetics, vol. 6, pp. 1138 - 1148, http://dx.doi.org/10.4161/epi.6.9.16066

Nair SS; Coolen MW; Stirzaker C; Song J; Statham AL; Strbenac D; Robinson MR; Clark SJ, 2011, 'Comparison of methyl-DNA immunoprecipitation (MeDIP) and methyl-CpG binding domain (MBD) protein capture for genome-wide DNA methylation analysis reveal CpG sequence coverage bias', Epigenetics, vol. 6, pp. 34 - 44, http://dx.doi.org/10.4161/epi.6.1.13313

Patterson K; Molloy L; Qu W; Clark S, 2011, 'DNA methylation: Bisulphite modification and analysis', Journal of Visualized Experiments, http://dx.doi.org/10.3791/3170

Patterson K; Molloy L; Qu W; Clark S, 2011, 'DNA methylation: bisulphite modification and analysis.', Journal of visualized experiments : JoVE

Robinson MD; Stirzaker C; Statham AL; Coolen MW; Song JZ; Nair SS; Strbenac D; Speed TP; Clark SJ, 2011, 'Evaluation of affinity-based genome-wide DNA methylation data: Effects of CpG density, amplification bias, and copy number variation (Genome Research (2010), 20 (1719-1729))', Genome Research, vol. 21, pp. 146

Wikland E; Bramsen J; Hulf T; Dyrskjot L; Ramanathan P; Hansen TK; Villadsen S; Gao SJ; Ostenfeld MS; Borre M; Peters M; Ortntoft T; Kjems J; Clark SJ, 2011, 'Coordinated epigenetic repression of the miR-200 family and miR-205 in invasive bladder cancer', International Journal of Cancer, vol. 128, pp. 1327 - 1334, http://dx.doi.org/10.1002/ijc.25461

Wikland E; Gao SJ; Hulf T; Sibbritt T; Nair SS; Costea A; Villadsen S; Bakholdt V; Bramsen J; Sorensen J; Krogdahl A; Clark SJ; Kjems J, 2011, 'MicroRNA alterations and associated aberrant DNA methylation patterns across multiple sample types in oral squamous cell carcinoma', PLoS One, vol. 6, pp. e27840 - e27851, http://dx.doi.org/10.1371/journal.pone.0027840

Barton CA; Gloss B; Qu W; Statham AL; Hacker NF; Sutherland RL; Clark SJ; O Brien P, 2010, 'Collagen and calcium-binding EGF domains 1 is frequently inactivated in ovarian cancer by aberrant promoter hypermethylation and modulates cell migration and survival', British Journal of Cancer, vol. 102, pp. 87 - 96, http://dx.doi.org/10.1038/sj.bjc.6605429

Coolen M; Stirzaker C; Song JZ; Statham AL; Kassir Z; Moreno CS; Young AM; Varma V; Speed TP; Cowley MJ; Lacaze P; Kaplan W; Robinson M; Clark SJ, 2010, 'Consolidation of the cancer genome into domains of repressive chromatin by long-range epigenetic silencing (LRES) reduces transcriptional plasticity', Nature Cell Biology, vol. 12, pp. 235 - 246, http://dx.doi.org/10.1038/ncb2023

Kjems J; Wiklund ED; Bramsen JB; Hulf T; Dyrskjot L; Clark SJ, 2010, 'Coordinated epigenetic repression of the miR-200 family and miR-205 in invasive bladder cancer', NEW BIOTECHNOLOGY, vol. 27, pp. S7 - S8, http://dx.doi.org/10.1016/j.nbt.2010.01.303

Robinson M; Statham AL; Speed TP; Clark SJ, 2010, 'Protocol matters: Which methylome are you actually studying?', Epigenomics, vol. 2, pp. 587 - 598, http://dx.doi.org/10.2217/epi.10.36

Robinson M; Stirzaker C; Statham AL; Coolen M; Song J; Nair S; Strbenac D; Speed TP; Clark SJ, 2010, 'Evaluation of affinity-based genome-wide DNA methylation data: Effects of CpG density, amplification bias, and copy number variation', Genome Research, vol. 20, pp. 1719 - 1729, http://dx.doi.org/10.1101/gr.110601.110

Statham AL; Strbenac D; Coolen M; Stirzaker C; Robinson M; Clark SJ, 2010, 'Repitools: an R package for the analysis of enrichment-based epigenomic data', Bioinformatics, vol. 26, pp. 1662 - 1663, http://dx.doi.org/10.1093/bioinformatics/btq247

Wiklund ED; Kjems J; Clark SJ, 2010, 'Epigenetic architecture and miRNA: Reciprocal regulators', Epigenomics, vol. 2, pp. 823 - 840, http://dx.doi.org/10.2217/epi.10.51

Hinshelwood R; Melki J; Huschtscha L; Paul C; Song JZ; Stirzaker C; Reddel RR; Clark SJ, 2009, 'Aberrant de novo methylation of the p16INK4A CpG island is initiated post gene silencing in association with chromatin remodelling and mimics nucleosome positioning', Human Molecular Genetics, vol. 18, pp. 3098 - 3109, http://dx.doi.org/10.1093/hmg/ddp251

Hynd PI; Edwards NM; Hebart M; McDowall M; Clark S, 2009, 'Wool fibre crimp is determined by mitotic asymmetry and position of final keratinisation and not ortho- and para-cortical cell segmentation', Animal, vol. 3, pp. 838 - 843, http://dx.doi.org/10.1017/S1751731109003966

Mayor R; Casadome L; Azuara D; Moreno V; Clark SJ; Capella G; Peinado M, 2009, 'Long-range epigenetic silencing at 2q14.2 affects most human colorectal cancers and may have application as a non-invasive biomarker of disease', British Journal of Cancer, vol. 100, pp. 1534 - 1539, http://dx.doi.org/10.1038/sj.bjc.6605045

McCormack A; McDonald K; Gill A; Clark SJ; Burt MG; Campbell K; Braund W; Little N; Cook R; Grossman AB; Robinson BG; Clifton-Bligh R, 2009, 'Low O6-methylguanine-DNA methyltransferase (MGMT) expression and response to temozolomide in aggressive pituitary tumours', Clinical Endocrinology, vol. 71, pp. 226 - 233, http://dx.doi.org/10.1111/j.1365-2265.2008.03487.x

Barton CA; Clark SJ; Hacker NF; O Brien P, 2008, 'Epigenetic markers of ovarian cancer', Advances in Experimental Medicine and Biology, vol. 622, pp. 35 - 51, http://dx.doi.org/10.1007/978-0-387-68969-2_4

Barton CA; Hacker NF; Clark SJ; O Brien P, 2008, 'DNA methylation changes in ovarian cancer: Implications for early diagnosis, prognosis and treatment', Gynecologic Oncology, vol. 109, pp. 129 - 139, http://dx.doi.org/10.1016/j.ygyno.2007.12.017

Guerrero-Bosagna CM; Sabat P; Valdovinos FS; Valladares LE; Clark SJ, 2008, 'Epigenetic and phenotypic changes result from a continuous pre and post dietary exposure to phytoestrogens in an experimental population of mice', BMC Physiology, vol. 8, pp. 1 - 19, http://dx.doi.org/10.1186/1472-6793-8-17

Hinshelwood R; Clark SJ, 2008, 'Breast cancer epigenetics: normal human mammary epithelial cells as a model system', Journal of Molecular Medicine - Jmm, vol. 86, pp. 1315 - 1328, http://dx.doi.org/10.1007/s00109-008-0386-3

jones PD; Archer T; Baylin S; Beck S; Berger SM; Bernstein B; Carpten J; Clark SJ; Costello J; Doerge R; Esteller M; Feinberg A; Gingeras T; Greally J; Henikoff S; Herman J; Jackson-Grusby L; Jenuwein T; Jirtle R; Lim B; Laird P; Lim B; Martienssen R; Polyak K; Stunnenberg H; Tlsty T; Tycko B; Ushijima T; Zhu J; Pirrotta V; Allis C; Elgin S; Rine J; Wu C, 2008, 'Moving AHEAD with an international human epigenome project', Nature, vol. 454, pp. 711 - 715, http://dx.doi.org/10.1038/454711a

Clark SJ, 2007, 'Action at a distance: epigenetic silencing of large chromosomal regions in carcinogenesis', Human Molecular Genetics, vol. 16, pp. R88 - R95, http://dx.doi.org/10.1093/hmg/ddm051

Coolen M; Statham A; Gardiner-Garden M; Clark SJ, 2007, 'Genomic profiling of CpG methylation and allelic specificity using quantitative high-throughput mass spectrometry: critical evaluation and improvements', Nucleic Acids Research, vol. 35, http://dx.doi.org/10.1093/nar/gkm662

Hinshelwood R; Huschtscha L; Melki J; Stirzaker C; Abdipranoto A; Vissel B; Ravasi T; Wells C; Hume DP; Reddel R; Clark SJ, 2007, 'Concordant epigenetic silencing of transforming growth factor-beta signaling pathway genes occurs early in breast carcinogenesis', Cancer research, vol. 67, pp. 11517 - 11527, http://dx.doi.org/10.1158/0008-5472.CAN-07-1284

Hitchins MP; Ap Lin V; Buckle AD; Cheong KF; Halani N; Ku S; Kwok C; Packham D; Suter CM; Meagher AP; Stirzaker C; Clark SJ; Hawkins NJ; Ward RL, 2007, 'Epigenetic inactivation of a cluster of genes flanking MLH1 in microsatellite-unstable colorectal cancer', Cancer research, vol. 67, pp. 9107 - 9116, http://dx.doi.org/10.1158/0008-5472.CAN-07-0869

Clark SJ; Statham A; Stirzaker C; Molloy PL; Frommer M, 2006, 'DNA methylation: Bisulphite modification and analysis', Nature Protocols, vol. 1, pp. 2353 - 2364, http://dx.doi.org/10.1038/nprot.2006.324

Frigola J; Song J; Stirzaker C; Hinshelwood R; Peinado M; Clark SJ, 2006, 'Epigenetic remodeling in colorectal cancer results in coordinate gene suppression across an entire chromosome band', Nature Genetics, vol. 38, pp. 540 - 549, http://dx.doi.org/10.1038/ng1781

Rand KN; Mitchell SM; Clark SJ; Molloy PL, 2006, 'Bisulphite differential denaturation PCR for analysis of DNA methylation', Epigenetics, vol. 1, pp. 94 - 100, http://dx.doi.org/10.4161/epi.1.2.2680

Wen VW; Wu K; Baksh S; Hinselwood RA; Lock RB; Clark SJ; Moore MA; Mackenzie K, 2006, 'Telomere-driven karyotypic complexity concurs with p16INK4a inactivation in TP53 competent immortal endothelial cells', Cancer research, vol. 66, pp. 10691 - 10700, http://dx.doi.org/10.1158/0008-5472.CAN-06-0979

Wong NC; Wong LH; Quach JM; Canham P; Craig JM; Song JZ; Clark SJ; Choo KHA, 2006, 'Permissive transcriptional activity at the centromere through pockets of DNA hypomethylation', PLoS Genetics, vol. 2, pp. 172 - 186, http://dx.doi.org/10.1179/146531205225021589

Broad A; Links MR; Rosenthal M; Abraham R; Clark SJ; Burns I; Dilulio J; Mitchell P, 2005, 'Oxaliplatin and gemcitabine in advanced NSCLC: A multicentre phase 2 Australian study', Lung Cancer, vol. 49, pp. S239 - S239

Frigola J; Munoz MA; Clark SJ; Moreno V; Capella G; Peinado M, 2005, 'Hypermethylation of the prostacyclin synthase (PTGIS) promoter is a frequent event in colorectal cancer and associated with aneuploidy', Oncogene, vol. 24, pp. 7320 - 7326, http://dx.doi.org/10.1038/sj.onc.1208883

Rand KN; Ho T; Qu W; Mitchell SM; White R; Clark SJ; Molloy PL, 2005, 'Headloop suppression PCR and its application to selective amplification of methylated DNA sequences', Nucleic Acids Research, vol. 33, pp. 1 - 11, http://dx.doi.org/10.1093/nar/gni120

Rand KN; Ho T; Qu W; Mitchell SM; White R; Clark SJ; Molloy PL, 2005, 'Headloop suppression PCR and its application to selective amplification of methylated DNA sequences.', Nucleic acids research, vol. 33

Sidhu S; Martin E; Gicquel C; Melki J; Clark SJ; Campbell P; Magarey CJ; Schulte KM; Roher HD; Delbridge L; Robinson BG, 2005, 'Mutation and methylation analysis of TP53 in adrenal carcinogenesis', Eur J Surg Oncol, vol. 31, pp. 549 - 554, http://dx.doi.org/10.1016/j.ejso.2005.01.013

Wong NC-L; Wong LH; Quach JM; Canham P; Craig JM; Song JZ; Clark SJ; Choo A, 2005, 'Permissive transcriptional activity at the centromere through pockets of DNA hypomethylation', PLoS Genetics, vol. preprint, pp. e17 - e17, http://dx.doi.org/10.1371/journal.pgen.0020017.eor

Noble JR; Zhong ZH; Neumann AA; Melki JR; Clark SJ; Reddel RR, 2004, 'Alterations in the p16(INK4a) and p53 tumor suppressor genes of hTERT-immortalized human fibroblasts', Oncogene, vol. 23, pp. 3116 - 3121, http://dx.doi.org/10.1038/sj.onc.1207440

Stirzaker C; Song J; Davidson B; Clark SJ, 2004, 'Transcriptional Gene Silencing Promotes DNA Hypermethylation through a sequential Change in Chromatin Modifications in Cancer Cells', Cancer research, vol. 64, pp. 3871 - 3877, http://dx.doi.org/10.1158/0008-5472.CAN-03-3690

Clark SJ; Millar DS; Molloy P, 2003, 'Bisulfite methylation analysis of tumor suppressor genes in prostate cancer from fresh and archival tissue samples', Methods Mol Med, vol. 81, pp. 219 - 240, http://dx.doi.org/10.1385/1-59259-372-0:219

Clark SJ; Melki J, 2002, 'DNA methylation and gene silencing in cancer: which is the guilty party?', Oncogene, vol. 21, pp. 5380 - 5387, http://dx.doi.org/10.1038/sj.onc.1205598

Clark SJ; Warnecke PM, 2002, 'DNA methylation analysis in mammalian cells', Methods, vol. 27, pp. 99 - 100, http://dx.doi.org/10.1016/S1046-2023(02)00059-2

Melki JR; Clark SJ, 2002, 'DNA methylation changes in leukaemia', Semin Cancer Biol, vol. 12, pp. 347 - 357, http://dx.doi.org/10.1016/S1044-579X(02)00055-X

Millar DS; Warnecke PM; Melki JR; Clark SJ, 2002, 'Methylation sequencing from limiting DNA: embryonic, fixed, and microdissected cells', Methods, vol. 27, pp. 108 - 113, http://dx.doi.org/10.1016/S1046-2023(02)00061-0

Rand K; Qu W; Ho T; Clark SJ; Molloy P, 2002, 'Conversion-specific detection of DNA methylation using real-time polymerase chain reaction (ConLight-MSP) to avoid false positives', Methods, vol. 27, pp. 114 - 120, http://dx.doi.org/10.1016/S1046-2023(02)00062-2

Schmitt JF; Millar DS; Pedersen JS; Clark SL; Venter DJ; Frydenberg M; Molloy PL; Risbridger GP, 2002, 'Hypermethylation of the inhibin alpha-subunit gene in prostate carcinoma', Mol Endocrinol, vol. 16, pp. 213 - 220, http://dx.doi.org/10.1210/mend.16.2.0771

Schmitt JF; Millar DS; Pedersen JS; Clark SL; Venter DJ; Frydenberg M; Molloy PL; Risbridger GP, 2002, 'Hypermethylation of the inhibin α-subunit gene in prostate carcinoma', Molecular Endocrinology, vol. 16, pp. 213 - 220, http://dx.doi.org/10.1210/me.16.2.213

Song JZ; Stirzaker C; Harrison J; Melki JR; Clark SJ, 2002, 'Hypermethylation trigger of the glutathione-S-transferase gene (GSTP1) in prostate cancer cells', Oncogene, vol. 21, pp. 1048 - 1061, http://dx.doi.org/10.1038/sj.onc.1205153

Warnecke PM; Stirzaker C; Song J; Grunau C; Melki JR; Clark SJ, 2002, 'Identification and resolution of artifacts in bisulfite sequencing', Methods, vol. 27, pp. 101 - 107, http://dx.doi.org/10.1016/S1046-2023(02)00060-9

Chetcuti A; Margan SH; Russell P; Mann S; Millar DS; Clark SJ; Rogers J; Handelsman DJ; Dong Q, 2001, 'Loss of annexin II heavy and light chains in prostate cancer and its precursors', Cancer Res, vol. 61, pp. 6331 - 6334, http://www.ncbi.nlm.nih.gov/pubmed/11522620

Grunau C; Clark SJ; Rosenthal A, 2001, 'Bisulfite genomic sequencing: systematic investigation of critical experimental parameters', Nucleic Acids Res, vol. 29, pp. E65 - E65, http://www.ncbi.nlm.nih.gov/pubmed/11433041

Grunau C; Renault E; Rosenthal A; Roizes G, 2001, 'MethDB - a public database for DNA methylation data', NUCLEIC ACIDS RESEARCH, vol. 29, pp. 270 - 274, http://dx.doi.org/10.1093/nar/29.1.270

Welch J; Millar D; Goldman A; Heenan P; Stark M; Eldon M; Clark S; Martin NG; Hayward NK, 2001, 'Lack of genetic and epigenetic changes in CDKN2A in melanocytic nevi', J Invest Dermatol, vol. 117, pp. 383 - 384, http://dx.doi.org/10.1046/j.0022-202x.2001.01391.x

Jackson P; Millar D; Kingsley E; Yardley G; Ow K; Clark S; Russell PJ, 2000, 'Methylation of a CpG island within the promoter region of the KAI1 metastasis suppressor gene is not responsible for down-regulation of KAI1 expression in invasive cancers or cancer cell lines', Cancer Letters, vol. 157, pp. 169 - 176, http://dx.doi.org/10.1016/S0304-3835(00)00483-3

Jackson P; Mills DR; Kingsley EA; Yardley G; Ow KT; Clark SJ; Russell PJ, 2000, 'Methylation of a CpG island within the KAI1 promoter region is not responsible for reduced KAI1 expression in invasive bladder cancer or bladder cancer cell lines', Cancer Letters, vol. 157, pp. 169 - 175

Melki JR; Vincent PC; Brown RD; Clark SJ, 2000, 'Hypermethylation of E-cadherin in leukemia', Blood, vol. 95, pp. 3208 - 3213, http://www.ncbi.nlm.nih.gov/pubmed/10807790

Millar DS; Paul CL; Molloy PL; Clark SJ, 2000, 'A distinct sequence (ATAAA)n separates methylated and unmethylated domains at the 5'-end of the GSTP1 CpG island', J Biol Chem, vol. 275, pp. 24893 - 24899, http://dx.doi.org/10.1074/jbc.M906538199

Melki JR; Vincent PC; Clark SJ, 1999, 'Cancer-specific region of hypermethylation identified within the HIC1 putative tumour suppressor gene in acute myeloid leukaemia', Leukemia, vol. 13, pp. 877 - 883, http://dx.doi.org/10.1038/sj.leu.2401401

Melki JR; Vincent PC; Clark SJ, 1999, 'Concurrent DNA hypermethylation of multiple genes in acute myeloid leukemia', Cancer Res, vol. 59, pp. 3730 - 3740, http://www.ncbi.nlm.nih.gov/pubmed/10446989

Millar DS; Ow KT; Paul CL; Russell PJ; Molloy PL; Clark SJ, 1999, 'Detailed methylation analysis of the glutathione S-transferase pi (GSTP1) gene in prostate cancer', Oncogene, vol. 18, pp. 1313 - 1324, http://dx.doi.org/10.1038/sj.onc.1202415

Molloy PL; Millar DS; Russell PJ; Clark SJ, 1999, 'Prostate Cancer DNA Methylation assay', Today's Life Science, vol. 11, pp. 34 - 35

Veitch C; Harte J; Hays R; Pashen D; Clark S, 1999, 'Community participation in the recruitment and retention of rural doctors: methodological and logistical considerations.', The Australian journal of rural health, vol. 7, pp. 206 - 211, http://dx.doi.org/10.1046/j.1440-1584.1999.00213.x

Warnecke PM; Clark SJ, 1999, 'DNA methylation profile of the mouse skeletal alpha-actin promoter during development and differentiation', Mol Cell Biol, vol. 19, pp. 164 - 172, http://www.ncbi.nlm.nih.gov/pubmed/9858541

Harrison J; Stirzaker C; Clark SJ, 1998, 'Cytosines adjacent to methylated CpG sites can be partially resistant to conversion in genomic bisulfite sequencing leading to methylation artifacts', Anal Biochem, vol. 264, pp. 129 - 132, http://dx.doi.org/10.1006/abio.1998.2833

Huschtscha LI; Noble JR; Neumann AA; Moy EL; Barry P; Melki JR; Clark SJ; Reddel RR, 1998, 'Loss of p16INK4 expression by methylation is associated with lifespan extension of human mammary epithelial cells', Cancer Res, vol. 58, pp. 3508 - 3512, http://www.ncbi.nlm.nih.gov/pubmed/9721850

Melki JR; Warnecke P; Vincent PC; Clark SJ, 1998, 'Increased DNA methyltransferase expression in leukaemia', Leukemia, vol. 12, pp. 311 - 316, http://dx.doi.org/10.1038/sj.leu.2400932

Warnecke PM; Biniszkiewicz D; Jaenisch R; Frommer M; Clark SJ, 1998, 'Sequence-specific methylation of the mouse H19 gene in embryonic cells deficient in the Dnmt-1 gene', Dev Genet, vol. 22, pp. 111 - 121, http://dx.doi.org/10.1002/(SICI)1520-6408(1998)22:2<111::AID-DVG1>3.0.CO;2-9

Warnecke PM; Mann JR; Frommer M; Clark SJ, 1998, 'Bisulfite sequencing in preimplantation embryos: DNA methylation profile of the upstream region of the mouse imprinted H19 gene', Genomics, vol. 51, pp. 182 - 190, http://dx.doi.org/10.1006/geno.1998.5371

Clark SJ; Harrison J; Molloy PL, 1997, 'Sp1 binding is inhibited by (m)Cp(m)CpG methylation', Gene, vol. 195, pp. 67 - 71, http://dx.doi.org/10.1016/S0378-1119(97)00164-9

Melki JR; Vincent PC; Clark SJ, 1997, 'DNA methylation in leukemia', Experimental Hematology, vol. 25, pp. 855

Stirzaker C; Millar DS; Paul CL; Warnecke PM; Harrison J; Vincent PC; Frommer M; Clark SJ, 1997, 'Extensive DNA methylation spanning the Rb promoter in retinoblastoma tumors', Cancer Research, vol. 57, pp. 2229 - 2237

Warnecke PM; Stirzaker C; Melki JR; Millar DS; Paul CL; Clark SJ, 1997, 'Detection and measurement of PCR bias in quantitative methylation analysis of bisulphite-treated DNA', Nucleic Acids Res, vol. 25, pp. 4422 - 4426, http://dx.doi.org/10.1093/nar/25.21.4422

Paul CL; Clark SJ, 1996, 'Cytosine methylation: quantitation by automated genomic sequencing and GENESCAN analysis', Biotechniques, vol. 21, pp. 126 - 133, http://www.ncbi.nlm.nih.gov/pubmed/8816247

Clark SJ; Harrison J; Frommer M, 1995, 'CpNpG methylation in mammalian cells', Nat Genet, vol. 10, pp. 20 - 27, http://dx.doi.org/10.1038/ng0595-20

Clark SJ; Harrison J; Paul CL; Frommer M, 1994, 'High sensitivity mapping of methylated cytosines', Nucleic Acids Res, vol. 22, pp. 2990 - 2997, http://dx.doi.org/10.1093/nar/22.15.2990

Grigg G; Clark S, 1994, 'Sequencing 5-methylcytosine residues in genomic DNA', Bioessays, vol. 16, pp. 431 - 436, http://dx.doi.org/10.1002/bies.950160612

Harrison J; Molloy PL; Clark SJ, 1994, 'Direct cloning of polymerase chain reaction products in an XcmI T-vector', Anal Biochem, vol. 216, pp. 235 - 236, http://dx.doi.org/10.1006/abio.1994.1033

Greenwood PE; Clark SJ; Cahill AD; Trevallyn-Jones J; Tzipori S, 1988, 'Development and protective efficacy of a recombinant-DNA derived fimbrial vaccine against enterotoxic colibacillosis in neonatal piglets', Vaccine, vol. 6, pp. 389 - 392, http://www.ncbi.nlm.nih.gov/pubmed/3057758

Lichtler AC; Sierra F; Clark S; Wells JR; Stein JL; Stein GS, 1982, 'Multiple H4 histone mRNAs of HeLa cells are encoded in different genes', Nature, vol. 298, pp. 195 - 198, http://dx.doi.org/10.1038/298195a0

Rickles R; Marashi F; Sierra F; Clark S; Wells J; Stein J; Stein G, 1982, 'Analysis of histone gene expression during the cell cycle in HeLa cells by using cloned human histone genes', Proc Natl Acad Sci U S A, vol. 79, pp. 749 - 753, http://dx.doi.org/10.1073/pnas.79.3.749

Rickles R; Marashi F; Sierra F; Clark S; Wells J; Stein J; Stein G, 1982, 'Analysis of histone gene expression during the cell cycle in HeLa cells by using cloned human histone genes', Proceedings of the National Academy of Sciences of the United States of America, vol. 79, pp. 749 - 753, http://dx.doi.org/10.1073/pnas.79.3.749

Sierra F; Leza A; Marashi F; Plumb M; Rickles R; Van Dyke T; Clark S; Wells J; Stein GS; Stein JL, 1982, 'Human histone genes are interspersed with members of the Alu family and with other transcribed sequences', Biochem Biophys Res Commun, vol. 104, pp. 785 - 792, http://dx.doi.org/10.1016/0006-291X(82)90706-9

Sierra F; Lichtler A; Marashi F; Rickles R; Van Dyke T; Clark S; Wells J; Stein G; Stein J, 1982, 'Organization of human histone genes', Proc Natl Acad Sci U S A, vol. 79, pp. 1795 - 1799, http://dx.doi.org/10.1073/pnas.79.6.1795

Clark SJ; Krieg PA; Wells JR, 1981, 'Isolation of a clone containing human histone genes', Nucleic Acids Res, vol. 9, pp. 1583 - 1590, http://dx.doi.org/10.1093/nar/9.7.1583

Luu P-L; Ong P-T; Loc TTH; Lam D; Pidsley R; Stirzaker C; Clark SJ, 2020, MethPanel: a parallel pipeline and interactive analysis tool for multiplex bisulphite PCR sequencing to assess DNA methylation biomarker panels for disease detection, http://dx.doi.org/10.1101/2020.02.09.941013

Schmitz U; Shah JS; Dhungel BP; Monteuuis G; Luu P-L; Petrova V; Metierre C; Nair SS; Bailey CG; Saunders VA; Turhan AG; White DL; Branford S; Clark S; Hughes TP; Wong JJ-L; Rasko JEJ, 2020, Widespread aberrant alternative splicing despite molecular remission in chronic myeloid leukemia patients, http://dx.doi.org/10.1101/2020.07.31.20165597

Schumann U; Zhang H-N; 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, http://dx.doi.org/10.1101/2020.02.04.933499

Tiedemann R; Du Q; Dickson B; Kong X; Chomiak A; Zhou W; Johnson B; Baylin S; Jones P; Clark S; Rothbart S, 2020, 'High-resolution Epigenome Mapping Reveals Distinct and Divergent Roles for UHRF1 in the Maintenance of DNA Methylation', in FASEB JOURNAL, WILEY, CA, San Diego, Vol. 34, presented at Annual Meeting on Experimental Biology, CA, San Diego, 04 April 2020 - 07 April 2020, http://dx.doi.org/10.1096/fasebj.2020.34.s1.05966

Stirzaker C; Chia KM; Portman N; Milioli HH; Clifton S; Achinger-Kawecka J; Nair S; Lim E; Clark S, 2019, 'DNA demethylation agents as a therapeutic approach in endocrine-resistant breast cancer', in Oncolabs, presented at 7th PacRim Breast & Prostate Cancer Meeting, http://dx.doi.org/10.1530/oncolabs.1.P049

Du Q; Bert SA; Armstrong NJ; Caldon CE; Song JZ; Nair SS; Gould CM; Luu PL; Khoury A; Qu W; Zotenko E; Stirzaker C; Clark SJ, 2018, Replication timing shapes the cancer epigenome and the nature of chromosomal rearrangements, http://dx.doi.org/10.1101/251280

Horvath LG; Mahon KL; Qu W; Lin HM; Spielman C; Cain D; Jacobs C; Stockler MR; de Bono JS; Higano CS; Chi KN; Clark SJ, 2018, 'Post Hoc Analysis of a Phase III Study to Test the Association Between Circulating Methylated Glutathione S Transferase (mGSTP1) DNA Levels and Response to Docetaxel (DTX) in Metastatic Castration-Resistant Prostate Cancer (mCRPC)', in ASIA-PACIFIC JOURNAL OF CLINICAL ONCOLOGY, WILEY, Vol. 14, pp. 51 - 52, https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000439493100013&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1

Mathe A; Wong-Brown M; Morten BC; Braye SG; Locke WJ; Stirzaker C; Clark SJ; Scott R; Avery-Kiejda KA, 2018, 'Defining the Key Mediators of Breast Cancer Progression and Treatment Resistance in the triple Negative Subtype', in ASIA-PACIFIC JOURNAL OF CLINICAL ONCOLOGY, WILEY, Vol. 14, pp. 9 - 9, https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000446654600003&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1

Milevskiy MJG; Gujral U; Lama Marques CD; Stone A; Northwood K; Burke LJ; Gee JMW; Nephew K; Clark S; Brown MA, 2018, MicroRNA-196a is regulated by ER and is a prognostic biomarker in ER+ Breast Cancer, http://dx.doi.org/10.1101/329227

O'Donoghue SI; Baldi BF; Clark SJ; Darling AE; Hogan JM; Kaur S; Maier-Hein L; McCarthy DJ; Moore WJ; Stenau E; Swedlow JR; Vuong J; Procter JB, 2018, Visualization of Biomedical Data, http://dx.doi.org/10.7287/peerj.preprints.26896

O'Donoghue SI; Baldi BF; Clark SJ; Darling AE; Hogan JM; Kaur S; Maier-Hein L; McCarthy DJ; Moore WJ; Stenau E; Swedlow JR; Vuong J; Procter JB, 2018, Visualization of Biomedical Data, http://dx.doi.org/10.7287/peerj.preprints.26896v1

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, presented at Proceedings: AACR Annual Meeting 2017; April 1-5, 2017; Washington, DC, http://dx.doi.org/10.1158/1538-7445.am2017-1997

Mathe A; Wong-Brown M; Locke W; Stirzaker C; Braye S; Forbes J; Clark S; Avery-Kiejda K; Scott R, 2016, 'DNA METHYLATION PROFILE OF TRIPLE NEGATIVE BREAST CANCER-SPECIFIC GENES COMPARING LYMPH NODE POSITIVE PATIENTS TO LYMPH NODE NEGATIVE PATIENTS', in ASIA-PACIFIC JOURNAL OF CLINICAL ONCOLOGY, WILEY-BLACKWELL, Vol. 12, pp. 27 - 27, https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000387772400056&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1

Milevskiy MJ; Al-Ejeh F; Saunus JM; Northwood KS; McCart-Reed AE; Dray E; Nephew K; Bailey PJ; Betts JA; Stone A; Gee JMW; Shewan AM; French JD; Edwards SL; Clark SJ; Lakhani SR; Brown MA, 2016, 'Abstract 1980: Long-range regulation of HOTAIR identifies novel biomarkers of breast cancer outcome and suggests a role in genome instability', in Cancer Research, American Association for Cancer Research (AACR), pp. 1980 - 1980, presented at Proceedings: AACR 107th Annual Meeting 2016; April 16-20, 2016; New Orleans, LA, http://dx.doi.org/10.1158/1538-7445.am2016-1980

Vuocolo T; Statham A; Bauer DC; McWilliam S; Nair SS; Morrison JL; Zhang S; Buckley M; McMillen IC; Clark SJ; Tellam RL, 2016, 'A hierarchy of epigenetic changes in the developmental transition from brown to white perirenal adipose tissue.', in JOURNAL OF ANIMAL SCIENCE, OXFORD UNIV PRESS INC, Vol. 94, pp. 9 - 10, http://dx.doi.org/10.2527/jas2016.94supplement49a

Gallego-Ortega D; Ledger A; Roden D; Cho C; Allerdice SL; Lee HJ; Valdes-Mora F; Lee B; Kaplan W; Salomon R; Piggin C; Rabinovich B; Millar E; Chtanova T; Swarbrick A; Clark S; Ormandy C, 2015, 'The ETS transcription factor ELF5 drives metastasis via angiogenesis and recruitment of Gr-1+ CD11b+ myeloid derived suppressor cells in luminal breast cancer', in Clinical and Experimental Metastasis, Springer Verlag (Germany), Vol. 32, pp. 203 - 203, presented at MRS 15th International biennial congress of the metastasis research society, http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000351601900067&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a

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

Clark S, 2014, 'WHOLE GENOME METHYLATION SEQUENCING IDENTIFIES POTENTIAL EPIGENETIC-BASED CANCER BIOMARKERS', in ASIA-PACIFIC JOURNAL OF CLINICAL ONCOLOGY, WILEY-BLACKWELL, pp. 18 - 19, https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000344745100037&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1

Clark SJ, 2014, 'EPIGENETIC REMODELING AND REPLICATION TIMING IN CANCER', in ASIA-PACIFIC JOURNAL OF CLINICAL ONCOLOGY, WILEY-BLACKWELL, pp. 28 - 28, https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000339716200018&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1

Mahon K; Qu W; Devaney J; Paul C; Castillo L; Chatfield M; Boyer M; Stockler M; Marx G; Gurney H; Mallesara G; Molloy P; Horvath L; Clark S, 2014, 'METHYLATED GLUTATHIONE S-TRANSFERASE 1 (MGSTP1) ASA POTENTIAL PLASMA EPIGENETIC MARKER OF PROGNOSIS AND RESPONSE TO CHEMOTHERAPY IN CASTRATE-RESISTANT PROSTATE CANCER (CRPC)', in ASIA-PACIFIC JOURNAL OF CLINICAL ONCOLOGY, WILEY-BLACKWELL, pp. 27 - 27, https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000339716200013&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1

Mahon KL; Chiam K; Lee BY; Nguyen Q; Boyer MJ; Stockler M; Pavlakis N; Marx G; Mallesara G; Gurney H; Clark S; Swarbrick A; Daly R; Horvath L, 2014, 'CIRCULATING MICRORNAS ASSOCIATED WITH DOCETAXEL-RESISTANT CASTRATION-RESISTANT PROSTATE CANCER', in ASIA-PACIFIC JOURNAL OF CLINICAL ONCOLOGY, WILEY-BLACKWELL, pp. 26 - 27, https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000339716200012&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1

Riebler A; Menigatti M; Song JZ; Statham AL; Stirzaker C; Mahmud N; Mein CA; Clark SJ; Robinson MD, 2013, BayMeth: Improved DNA methylation quantification for affinity capture sequencing data using a flexible Bayesian approach, http://dx.doi.org/10.48550/arxiv.1312.3115

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