Epigenetics Research Lab

Selected Publications


Lam D, Clark S, Stirzaker C, Pidsley R (2020) Advances in Prognostic Methylation Biomarkers for Prostate Cancer. Cancers (Basel). 12(10):2993. doi:10.3390/cancers12102993. PMID: 33076494.

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.

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/10.1101/2020.02.09.94101

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


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

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

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


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


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.


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).


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.


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)


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.


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.


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.


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.


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