Prof Susan Clark

Research Leader - Genomics and Epigenetics
Lab Head - Epigenetics Research

Prof Susan Clark

Susan Clark is a molecular biologist by training and completed her BSc (Hons1) degree under the supervision of Drs Ken Reed and Lyn Dalgarno at the Australian National University, ACT, Australia in 1978. She studied for PhD (1982) in Biochemistry at University of Adelaide, South Australia, mapping a

Research Level

Head of the Epigenetics Laboratory; NHMRC Senior Principal Research Fellow; Fellow of the Australian Academy of Science

Biography

Susan Clark is a molecular biologist by training and completed her BSc (Hons1) degree under the supervision of Drs Ken Reed and Lyn Dalgarno at the Australian National University, ACT, Australia in 1978. She studied for PhD (1982) in Biochemistry at University of Adelaide, South Australia, mapping and sequencing human histone genes, under the supervision of Dr Julian Wells.

 Susan spent her postdoctoral years at Biotechnology Australia from 1983-1988 leading studies on the first recombinant vaccine development in Australia and eukaryotic expression of human inhibin, Il-3 and GMCSF. In 1992, she returned to basic research as Group Leader of the Gene Regulation Unit at the Kanematsu Laboratories, Royal Prince Alfred Hospital where she developed and implemented bisulphite sequencing for DNA methylation analysis. In 2000, she established and headed the Epigenetics Group at the Sydney Cancer Centre, Royal Prince Alfred Hospital and in 2004 moved her group to the Garvan Institute of Medical Research and initiated and led the growth of the Epigenetics Research Program in the Cancer Research Theme. In 2015 she was appointed the inaugural Head of the Genomics and Epigenetics Theme.

 Her DNA methylation studies over the last twenty five years have initiated profound questions about the importance of epigenetics in early development and in disease, especially in cancer. Susan has made extensive ground-breaking discoveries relating to DNA methylation patterns in normal and cancer genomes, that have led to the commercialization of new methylation-based tests for early cancer detection. The techniques she pioneered in the early 1990s, including bisulphite sequencing, have revolutionised and now underpin the new era in epigen"omic" research. She was founding member of IHEC (International Human Epigenome Consortium) and led the formation and is president of the AEpiA (Australian Epigenetics Alliance).

 She has a number of awards including the RPAH Research Medal (2002); the Julian Wells Medal (2003), for “outstanding contribution to gene action and genome structure”; the Ruby Payne-Scott Award (2004) for contribution of women in science; The German United Association Award for pioneering work in development of bisulphite sequencing; Australia’s “Top Ten” (NHMRC) Scientist Project Grant Award (2009); Rotary Award for Vocational Excellence (2012). She was awarded a NHMRC Senior Principal Research Fellowship (2014); elected a Fellow of the Australian Academy of Science (2015) and received a Cancer Institute NSW “Make a Difference award” (2015); awarded The Clive and Vera Ramaciotti Foundation: Medal of Excellence (2017), and in 2019 she was awarded a NHMRC Senior Principal Research Fellowship and received the NSW Premiers Prize for Excellence in Medical Biological Sciences.

Susan Clark is a molecular biologist by training and completed her BSc (Hons1) degree under the supervision of Drs Ken Reed and Lyn Dalgarno at the Australian National University, ACT, Australia in 1978. She studied for PhD (1982) in Biochemistry at University of Adelaide, South Australia, mapping and sequencing human histone genes, under the supervision of Dr Julian Wells.

 Susan spent her postdoctoral years at Biotechnology Australia from 1983-1988 leading studies on the first recombinant vaccine development in Australia and eukaryotic expression of human inhibin, Il-3 and GMCSF. In 1992, she returned to basic research as Group Leader of the Gene Regulation Unit at the Kanematsu Laboratories, Royal Prince Alfred Hospital where she developed and implemented bisulphite sequencing for DNA methylation analysis. In 2000, she established and headed the Epigenetics Group at the Sydney Cancer Centre, Royal Prince Alfred Hospital and in 2004 moved her group to the Garvan Institute of Medical Research and initiated and led the growth of the Epigenetics Research Program in the Cancer Research Theme. In 2015 she was appointed the inaugural Head of the Genomics and Epigenetics Theme.

 Her DNA methylation studies over the last twenty five years have initiated profound questions about the importance of epigenetics in early development and in disease, especially in cancer. Susan has made extensive ground-breaking discoveries relating to DNA methylation patterns in normal and cancer genomes, that have led to the commercialization of new methylation-based tests for early cancer detection. The techniques she pioneered in the early 1990s, including bisulphite sequencing, have revolutionised and now underpin the new era in epigen"omic" research. She was founding member of IHEC (International Human Epigenome Consortium) and led the formation and is president of the AEpiA (Australian Epigenetics Alliance).

 She has a number of awards including the RPAH Research Medal (2002); the Julian Wells Medal (2003), for “outstanding contribution to gene action and genome structure”; the Ruby Payne-Scott Award (2004) for contribution of women in science; The German United Association Award for pioneering work in development of bisulphite sequencing; Australia’s “Top Ten” (NHMRC) Scientist Project Grant Award (2009); Rotary Award for Vocational Excellence (2012). She was awarded a NHMRC Senior Principal Research Fellowship (2014); elected a Fellow of the Australian Academy of Science (2015) and received a Cancer Institute NSW “Make a Difference award” (2015); awarded The Clive and Vera Ramaciotti Foundation: Medal of Excellence (2017), and in 2019 she was awarded a NHMRC Senior Principal Research Fellowship and received the NSW Premiers Prize for Excellence in Medical Biological Sciences.

Awards and Honours

2019 - NSW Premiers Prize for Excellence in Medical Biological Sciences
2019 - Senior Principal Research Fellowship (NHMRC)
2017 - The Clive and Vera Ramaciotti Foundation: 2017 Medal of Excellence ($50K)
2015 - Elected a Fellow of the Australian Academy of Science
2015 - The Rob Sutherland Make a Difference ($20K), CINSW
2015 - Nadine Watson Lecture Award for a Leading Female Scientist
2014 - Senior Principal Research Fellowship (NHMRC)
2012 - Rotary Award for Vocational Excellence
2011 - Victor Chang Medal (Barbara Ell Seminar Series Lecturer)
2010 - Service to Science and Industry, North Shore Times, 50 year medal
2009 - Australia’s “Top Ten” (NHMRC) Scientist Award for 2009
2009 - Promoted Senior Principal Research Fellow (Garvan Institute)
2008 - Principal Research Fellowship (NHMRC)
2008 - Adjunct Professor, Faculty Medicine, University of NSW
2008 - Director’s Inaugural Women in Science Lecture Award (WEHI)
2006 - World Technology Award, finalist for 2006 for Biotechnology: the most innovative people in the science and technology world in 2006
2006 - Elected a Fellow of the World Technology Network for Biotechnology for contribution to Epigenetics technology
2004 - Principal Research Fellowship (NHMRC)
2004 - The Ruby Payne-Scott Award for women in Australian science
2004 - German Science Prize “Biochemisch Analytik Preis” (50,000 Euros) for outstanding contribution for Methylation analysis. Since 1970, this award has recognized the work of 27 world-renowned scientists, four of whom have subsequently gone on to win a Nobel Prize
2003 - Julian Wells Medal for “outstanding contribution to gene action and genome structure”, Lorne Genome conference
2002 - RPAH Research Medal for $50,000 for major contribution to research
1998 - Cancer Council NSW Travelling Award
1997 - DNA Methylation Imprinting and the Epigenetics of Cancer, AACR, Research Presentation Award, Puerto Rico
1978 - Commonwealth Post Graduate Research Award
1976 - CRAC Undergraduate Exchange Travelling Award to study at Cambridge

Education

1982 - PhD, University of Adelaide, South Australia - Australia
1978 - BSc (Hons1) - Australian National University, ACT - Australia
1977 - BSc, Australian National University, ACT - Australia

Selected Publications

 

2020

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-203enhances the differentiation capacity of established pluripotent stem cells. EMBO J.:e104324. doi:10.15252/embj.2019104324. Epub ahead of print.

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.Clin Epigenetics. 12(1):90. doi: 10.1186/s13148-020-00880-y.

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 JJ. (2020). Macrophage development and activation involve coordinated intron retention in key inflammatory regulators. Nucleic Acids Res. gkaa435. doi: 10.1093/nar/gkaa435. Online ahead of print.

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 Biol. 18(1):40. doi: 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. Clin Epigenetics. 12(1):48. doi: 10.1186/s13148-020-00836-2

Phuc LL, Phuc TO, Tran THL, 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.  (BioRixvs preprint) doi: https://doi.org/10.1101/2020.02.09.941013

Piggin C, Roden D, Law A, Molloy M, Krisp C, Swarbrick A, Naylor M, Kalyuga M, Kaplan W, Oakes S, Gallego-Ortega D, Clark S, Carroll J, Bartonicek N, Ormandy CJ. (2020) ELF5 modulates the estrogen receptor cistrome 4in breast cancer. PLOS Genetics. 6(1):e1008531. PMID: 31895944

J Achinger-Kawecka J, Valdes-Mora F, Luu PL, Giles KA, Caldon CE, Qu W, Nair SS, Soto S, Locke WJ, Yeo-The NS, Gould CM, Du Q, Smith GC, Ramos IR, Fernandez K, Hoon D, Gee JMW, Stirzaker C, Clark, SJ. (2020) Epigenetic reprogramming at estrogen-receptor binding sites alters 3D landscape in endocrine resistant breast cancer. Nature Communications. 11(1):320. PMID: 31949157

2019

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. 21:773-788.  PMID: 31727574 * Equal Authors

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. (2019) Constitutively bound CTCF sites maintain 3D chromatin architecture and long-range epigenetically regulated domains. Nature Communications. 11(1):54 , PMID: 31911579

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, Arnold 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(1):9511, PMID: 31266983, * Equal Authors

Tarr IS, McCann EP, Benyamin B, Peters T. J, Twine NA, Zhang KY, Zhao Q, Zhang ZH, Rowe DB, Nicholson GA, Bauer D, Clark S J, Blair IP Williams KL. (2019) Monozygotic twins and triplets discordant for amyotrophic lateral sclerosis display differential methylation and gene expression. Scientific Reports 9 (1):8254, PMID: 31164693

Milevskiy MJG, Gujral U, Del Lama Marques C, Stone A, Northwood K, Burke L, 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(6):621-632 PMID: 30783203

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 & Chromatin 12(1):12 PMID: 30755246 * Equal Authors

Skvortsova K, Masle-Farquhar E, Luu PL, Song JZ, Qu W, Zotenko E, Gould CM, Du Q, Peters T, 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 C, Stirzaker C*, Clark SJ*. (2019). DNA hypermethylation encroachment at CpG island borders in cancer is predisposed by H2K4 mono-methylation patterns. Cancer Cell 35(2):297-314 PMID: 30753827 *Equal Authors

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 (mGSTP1) 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 (pii:S0302-2838(18)30855-8 (epub ahead of print) PMID: 30466891 * Equal Authors

Du Q, Bert SA, Armstrong N, Caldon CE, Song JZ, Nair SS, Gould CM, Luu PL, Peters TJ, 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(1):416. PMID: 30679435

2018

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. Proc Natl Acad Sci USA. 115(51):E11970-E11977. Epub PMID: 30509985

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*.  (2018) Evaluation of cross-platform and interlaboratory concordance via consensus modelling of genomic measurements. Bioinformatics. 35(4):560-570 PMID: 30084929. *Equal Authors

Nair SS, Luu P-L, 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 JJ-L and Clark SJ (2018). Guidelines for whole genome bisulphite sequencing of intact and FFPET DNA on the Illumina HiSeq X Ten. Epigenetics & Chromatin 11:24. PMID: 29807544

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 R. J, Horvath L. G, Stricker P, Frydenberg M, Taylor R. A, Stirzaker C, Risbridger GP,* Clark SJ* (2018). Enduring epigenetic landmarks define the cancer microenvironment. Genome Res. 28:625-638. PMID: 29650553 *Equal Authors

Stirzaker C, Song JZ, Statham AL, Clark SJ (2018). Bisulphite Sequencing of Chromatin Immunoprecipitated DNA (BisChIP-seq). Methods Mol Biol. 1708:285-302. PMID: 29224150

2017

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.  721:834-845. PMID: 29220667

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 8:1346. doi: 10.1038/s41467-017-01393-8.

Clark SJ, Molloy PL (2017). Smoke-Induced Changes to the Epigenome Provide Fertile Ground for Oncogenic Mutation. Cancer Cell 32:278-280. doi: 10.1016/j.ccell.2017.08.016 (Commentary).

Achinger­Kawecka J, Taberlay PC, Clark SJ (2017). Alterations in Three­Dimensional Organization of the Cancer Genome and Epigenome. Cold Spring Harb Symp Quant Biol 81:41­51. doi: 10.1101/sqb.2016.81.031013

Skvortsova K, Zotenko E, Luu PL, Gould CM, Nair SS, Clark SJ*, Stirzaker C* (2017). Comprehensive evaluation of genome-wide hydroxymethylcytosine profiling approaches in human DNA. Epigenetics & Chromatin 10:16. doi: 10.1186/s13072-017-0123-7. * Equal Last Authors

Stirzaker C, Song J, Ng W, Du Q, Armstrong N, Locke W, Statham A, 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 of CpG islands and shores in cancer. Oncogene 36:1328-1338. doi: 10.1038/onc.2016.297.

2016

Pidsley R, Zotenko E, Peters T, Lawrence MG, Risbridger GP, Molloy P, Van Dijk S, Muhlhausler B, Stirzaker C*, Clark SJ* (2016). Critical evaluation of the Illumina MethylationEPIC BeadChip microarray for whole-genome DNA methylation profiling. Genome Biology 17:208. * Equal Last Authors

Taberlay PC, Achinger-Kawecka A, Lun ATL, Buske FA, Sabir K, Gould CM, Zotenko E, Bert SA, Giles KA, Bauer DC, Smyth GK, Stirzaker C, O’Donoghue SI, Clark SJ (2016). Three-dimensional disorganization of the cancer genome occurs coincident with long-range genetic and epigenetic alterations. Genome Research, 26:719-31.

BLUEPRINT consortium (Qu W, Nair S, Statham A, Stirzaker C, Clark SJ (2016). Quantitative comparison of DNA methylation assays for biomarker development and clinical applications. Nat Biotechnology, 34:726-37.

Colino-Sanguino Y, Clark SJ*, Valdes-Mora F* (2016). H2A.Z acetylation and transcription: ready, steady, go! Epigenomics, 8:583-6 *Equal Last Authors (Review).

2015

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 and Clark SJ (2015). Methylome sequencing in triple-negative breast cancer reveals distinct methylation clusters with prognostic value. Nat Communications 6:5899.

Stone A, Zotenko E, Locke WJ, Korbie D, Millar EK, Pidsley R, Stirzaker C, Graham P, Trau M, Musgrove EA, Nicholson RI, Gee JM and Clark SJ (2015). DNA

methylation of oestrogen-regulated enhancers defines endocrine sensitivity in breast cancer. Nat Communications 6:7758.

Du Q, Luu PL, Stirzaker C and Clark SJ (2015). Methyl-CpG-binding domain proteins: readers of the epigenome. Epigenomics 1-23 (Review).

Locke WJ, Zotenko E, Stirzaker C, Robinson MD, Hinshelwood RA, Stone A, Reddel RR, Huschtscha LI and Clark SJ (2015). Coordinated epigenetic remodelling of transcriptional networks occurs during early breast carcinogenesis. Clinical Epigenetics 7(1):52.

 2014

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 and Clark SJ; PRIMe consortium (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 111:1802-9

Taberlay P, Statham A, Kelly TK, Clark SJ* and Jones PA* (2014). Reconfiguration of nucleosome depleted regions at distal regulatory elements accompanies DNA methylation of enhancers and insulators in cancer. Genome Res: doi:10.1101/gr.163485.113. * Equal Last Authors

Skulte KA, Phan L, Clark SJ* and Taberlay PC* (2014). Chromatin remodeler mutations in human cancers: epigenetic implications. Epigenomics 6:397-414. * Equal Last Authors (Review)

2013

Robinson MD, Strbenac D, Stirzaker C, Statham AL, Song J, Speed TP and Clark SJ (2013). Copy-number-aware differential analysis of DNA sequencing data.

Genome Research 22:2489-2496.

Bert SA, Robinson MD, Strbenac D, Statham AL, Song JZ, Hulf T, Sutherland RL, Coolen MW, Stirzaker C and Clark SJ (2013). Regional activation of the cancer genome by long range epigenetic remodelling. Cancer Cell 23:9-22.

Hulf T, Sibbritt T, Wiklund ED, Patterson K, Song JZ, Stirzaker C, Qu W, Nair S, Horvath LG, Armstrong NJ, Kench JG, Sutherland RL and Clark SJ (2013). Epigenetic-induced repression of microRNA-205 is associated with MED1 activation and a poorer prognosis in localized prostate cancer. Oncogene 32:2891-9.

2012

Valdes-Mora F, Song JZ, Statham AL, Strbenac D, Robinson MD, Nair SS, Patterson KI, Tremethick DJ, Stirzaker C and Clark SJ (2012). Acetylation of H2A.Z is a key epigenetic modification associated with gene deregulation and epigenetic remodeling in cancer. Genome Res 22:307-321.

Statham AL, Robinson MD, Song JZ, Coolen MW, Stirzaker C and Clark SJ (2012). Bisulfite sequencing of chromatin immunoprecipitated DNA (BisChIP-seq)

directly informs methylation status of histone-modified DNA. Genome Res 22:1120-1127.

Locke WJ and Clark SJ (2012). Epigenome remodelling in breast cancer: insights from an early in vitro model of carcinogenesis. Breast Cancer Res

14:10.1186/bcr3237 (Review)

Gloss BS, Patterson KI, Barton CA, Gonzalez M, Scurry JP, Hacker NF, Sutherland RL, O'Brien PM and Clark SJ (2012). Integrative genome-wide expression and promoter DNA methylation profiling identifies a novel panel of ovarian cancer epigenetic biomarkers. Cancer Lett 318:76-85.

2011

Wiklund ED, Gao S, Hulf T, Sibbritt T, Nair S, Costea DE, Villadsen SB, Bakholdt V, Bramsen JB, Sorensen JA, Krogdahl A, Clark SJ* and Kjems J* (2011). MicroRNA alterations and associated aberrant DNA methylation patterns across multiple sample types in oral squamous cell carcinoma. PLoS One 2011; 6:e27840. *Equal Last Authors

Patterson K, Molloy L, Qu W and Clark SJ (2011). DNA methylation: bisulphite modification and analysis. JoVE 56:e3170.

Nair SS, Coolen MW, Stirzaker C, Song JZ, Statham AL, Strbenac D, Robinson MD and 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

6:34-44.

Lee HJ, Hinshelwood RA, Bouras T, Gallego-Ortega D, Valdes-Mora F, Blazek K, Visvader JE, Clark SJ* and Ormandy CJ* (2011). Lineage specific methylation of the Elf5 promoter in mammary epithelial cells. Stem Cells 29:1611-1619. * Equal Last Authors

Hulf T, Sibbritt T, Wiklund ED, Bert S, Strbenac D, Statham AL, Robinson MD and Clark SJ (2011). Discovery pipeline for epigenetically deregulated miRNAs in cancer: integration of primary miRNA transcription. BMC Genomics 12:54.

Hansen TB, Wiklund ED, Bramsen JB, Villadsen SB, Statham AL, Clark SJ and Kjems J (2011). miRNA-dependent gene silencing involving Ago2-mediated cleavage of a circular antisense RNA. EMBO J 2011; 30:4414-4422.

Devaney J, Stirzaker C, Qu W, Song JZ, Statham AL, Patterson KI, Horvath LG, Tabor B, Coolen MW, Hulf T, Kench JG, Henshall SM, Benito RP, Haynes A-M, Mayor R, Peinado MA, Sutherland RL and 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 Epidemiol Biomarkers Prev 20:148-159.

2006-2010

Wiklund ED, Kjems J and Clark SJ (2010). Epigenetic architecture and miRNA: reciprocal regulators. Epigenomics 2:823-840 (Review).

Wiklund ED, Bramsen JB, Hulf T, Dyrskjøt L, Ramanathan R, Hansen TB, Villadsen SB, Gao S, Ostenfeld MS, Borre M, Peter ME, Ørntoft TF, Kjems J* and Clark SJ* (2010). Coordinated epigenetic repression of the miR-200 family and miR-205 in invasive bladder cancer. Int J Cancer128:1327-1334. * Equal Last Authors

Statham AL, Strbenac D, Coolen MW, Stirzaker C, Clark SJ and Robinson MD (2010). Repitools: an R package for the analysis of enrichment-based epigenomic data. Bioinformatics 26:1662-1663.

Robinson MD, Stirzaker C, Statham AL, Coolen MW, Song JZ, Nair SS, Strbenac D, Speed TP and Clark SJ (2010). Evaluation of affinity-based genome-wide DNA

methylation data: effects of CpG density, amplification bias, and copy number variation. Genome Research 20:1719-1729.

Robinson MD, Statham AL, Speed TP and Clark SJ (2010). Protocol matters: which methylome are you actually studying? Epigenomics 2:587-598 (Review).

Coolen MW, Stirzaker C, Song JZ, Statham AL, Kassir Z, Moreno CS, Young AN, Varma V, Speed TP, Cowley M, Lacaze P, Kaplan W, Robinson MD and 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 12:235-246.

Hinshelwood RA, Melki JR, Huschtscha LI, Paul C, Song JZ, Stirzaker C, Reddel RR and Clark SJ (2009). Aberrant de novo methylation of the p16(INK4A) CpG

island is initiated post gene silencing in association with chromatin remodelling and mimics nucleosome positioning. Hum Mol Genet 18:3098-3109.

Hinshelwood RA, Huschtscha LI, Melki J, Stirzaker C, Abdipranoto A, Vissel B, Ravasi T, Wells CA, Hume DA, Reddel RR and Clark SJ (2007). Concordant epigenetic silencing of transforming growth factor-beta signaling pathway genes occurs early in breast carcinogenesis. Cancer Research 67:11517-11527.

Coolen MW, Statham AL, Gardiner-Garden M and Clark SJ (2007). Genomic profiling of CpG methylation and allelic specificity using quantitative high- throughput mass spectrometry: critical evaluation and improvements. Nucleic Acids Res 35:e119.

Frigola J, Song J, Stirzaker C, Hinshelwood RA, Peinado MA and Clark SJ (2006). Epigenetic remodeling in colorectal cancer results in coordinate gene suppression across an entire chromosome band. Nature Genetics 38:540-549.

Clark SJ, Statham A, Stirzaker C, Molloy PL and Frommer M (2006). DNA methylation: Bisulphite modification and analysis. Nature Protocols 1:2353-2364.

Prior to 2006

Stirzaker C, Song JZ, Davidson B and Clark SJ (2004). Transcriptional gene silencing promotes DNA hypermethylation through a sequential change in chromatin modifications in cancer cells. Cancer Res, 64:3871-3877.

Song JZ, Stirzaker C, Harrison J, Melki JR and Clark SJ (2002). Hypermethylation trigger of the glutathione-S-transferase gene (GSTP1) in prostate cancer cells. Oncogene, 21:1048-1061.

Stirzaker C, Millar DS, Paul CL, Warnecke PM, Harrison J, Vincent PC, Frommer M and Clark SJ (1997). Extensive DNA methylation spanning the Rb promoter in retinoblastoma tumors. Cancer Res, 57:2229-2237.

Clark SJ, Harrison J and Frommer M (1995). CpNpG methylation in mammalian-cells. Nat Genet, 10:20-27.