By Professor Susan Clark

Journal articles

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

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

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

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

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

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

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

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

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

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

Luu PL; Ong PT; Loc TTH; Lam D; Pidsley R; Stirzaker C; Clark SJ, 2021, 'MethPanel: a parallel pipeline and interactive analysis tool for multiplex bisulphite PCR sequencing to assess DNA methylation biomarker panels for disease detection', Bioinformatics, vol. 37, pp. 2198 - 2200, http://dx.doi.org/10.1093/bioinformatics/btaa1060

Achinger-Kawecka J; Stirzaker C; Portman N; Campbell E; Chia K-M; Du Q; Laven-Law G; Nair SS; Yong A; Wilkinson A; Clifton S; Milioli HH; Alexandrou S; Caldon CE; Song J; Khoury A; Meyer B; Gee JMW; Schmitt A; Wong ES; Hickey TE; Lim E; Clark SJ, 2021, 'Epigenetic therapy targets the 3D epigenome in endocrine-resistant breast cancer', , http://dx.doi.org/10.1101/2021.06.21.449340

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

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

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

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

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

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

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

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

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

Lam D; Luu PL; Song JZ; Qu W; Risbridger GP; Lawrence MG; Lu J; Trau M; Korbie D; Clark SJ; Pidsley R; Stirzaker C, 2020, 'Comprehensive evaluation of targeted multiplex bisulphite PCR sequencing for validation of DNA methylation biomarker panels', Clinical Epigenetics, vol. 12, pp. 90, http://dx.doi.org/10.1186/s13148-020-00880-y

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

Lawrence MG; Pidsley R; Niranjan B; Papargiris M; Pereira BA; Richards M; Teng L; Norden S; Ryan A; Frydenberg M; Stirzaker C; Taylor RA; Risbridger GP; Clark SJ, 2020, 'Alterations in the methylome of the stromal tumour microenvironment signal the presence and severity of prostate cancer', Clinical Epigenetics, vol. 12, pp. 48, http://dx.doi.org/10.1186/s13148-020-00836-2

Piggin CL; Roden DL; Law AMK; Molloy MP; Krisp C; Swarbrick A; Naylor MJ; Kalyuga M; Kaplan W; Oakes SR; Gallego-Ortega D; Clark SJ; Carroll JS; Bartonicek N; Ormandy CJ, 2020, 'ELF5 modulates the estrogen receptor cistrome in breast cancer', PLoS Genetics, vol. 16, pp. e1008531, http://dx.doi.org/10.1371/journal.pgen.1008531

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

Stirzaker C; Skvortsova K; Masle-Farquhar E; Goodnow C; Clark SJ, 2020, 'Epigenetic changes during tumour development – Functional epigenetics study', Pathology, 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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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