By Professor Susan Clark

Journal articles

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

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, 15, http://dx.doi.org/10.1186/1471-2164-15-476

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, 110, pp. 2462 - 2471, http://dx.doi.org/10.1038/bjc.2014.181

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, 15, pp. r35, http://dx.doi.org/10.1186/gb-2014-15-2-r35

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

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, 13, http://dx.doi.org/10.1186/1476-4598-13-3

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

Stone A; Valdes-Mora F; Clark SJ, 2013, 'Exploring and exploiting the aberrant DNA methylation profile of endocrine-resistant breast cancer', Epigenomics, 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, 19, http://dx.doi.org/10.1158/1078-0432.OVCA13-A4

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, 12, pp. 1874 - 1885, http://dx.doi.org/10.1158/1535-7163.MCT-13-0012

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, 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, 32, pp. 2891 - 2899, http://dx.doi.org/10.1038/onc.2012.300

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, 23, pp. 9 - 22, http://dx.doi.org/10.1016/j.ccr.2012.11.006

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, 72, pp. 6319 - 6324, http://dx.doi.org/10.1158/0008-5472.CAN-12-3658

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, 22, pp. 307 - 321, http://dx.doi.org/10.1101/gr.118919.110

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, 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, 22, pp. 2490 - 2496, http://dx.doi.org/10.1101/gr.139055.112

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, 10, pp. e1001461, http://dx.doi.org/10.1371/journal.pbio.1001461

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, 318, pp. 76 - 85, http://dx.doi.org/10.1016/j.canlet.2011.12.003

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, 31, pp. 4182 - 4195, http://dx.doi.org/10.1038/onc.2011.584

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

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, 29, pp. 4603, http://www.ncbi.nlm.nih.gov/pubmed/28024014

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

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, 21, pp. 146

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, 6, pp. 34 - 44, http://dx.doi.org/10.4161/epi.6.1.13313

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, 128, pp. 1327 - 1334, http://dx.doi.org/10.1002/ijc.25461

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, 12, pp. 54 - 64, http://dx.doi.org/10.1186/1471-2164-12-54

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, 6, pp. 1138 - 1148, http://dx.doi.org/10.4161/epi.6.9.16066

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, 20, pp. 148 - 159, http://dx.doi.org/10.1158/1055-9965.EPI-10-0719

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, 60, pp. 753 - 766, http://dx.doi.org/10.1016/j.eururo.2011.06.035

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, 6, pp. e25590, http://dx.doi.org/10.1371/journal.pone.0025590

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, 29, pp. 1611 - 1619, http://dx.doi.org/10.1002/stem.706

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, 6, pp. e27840 - e27851, http://dx.doi.org/10.1371/journal.pone.0027840

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, 30, pp. 4414 - 4422, http://dx.doi.org/10.1038/emboj.2011.359

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, 4, pp. 390 - 399, http://www.biomedcentral.com/1756-0500/4/390

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

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, 27, pp. S7 - S8, http://dx.doi.org/10.1016/j.nbt.2010.01.303

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, 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, 12, pp. 235 - 246, http://dx.doi.org/10.1038/ncb2023

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, 20, pp. 1719 - 1729, http://dx.doi.org/10.1101/gr.110601.110

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

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, 26, pp. 1662 - 1663, http://dx.doi.org/10.1093/bioinformatics/btq247

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, 3, pp. 838 - 843, http://dx.doi.org/10.1017/S1751731109003966

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, 18, pp. 3098 - 3109

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, 100, pp. 1534 - 1539

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, 71, pp. 226 - 233

Hinshelwood R; Clark SJ, 2008, 'Breast cancer epigenetics: normal human mammary epithelial cells as a model system', Journal of Molecular Medicine - Jmm, 86, pp. 1315 - 1328

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, 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, 8, pp. 1 - 19

Barton CA; Clark SJ; Hacker NF; O Brien P, 2008, 'Epigenetic markers of ovarian cancer', Advances in Experimental Medicine and Biology, 622, pp. 35 - 51

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