By Professor Susan Clark

Preprints

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

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

Salazar-Roa M; Trakala M; Álvarez-Fernández M; Valdés-Mora F; Zhong C; Muñoz J; Yu Y; Peters TJ; Graña O; Serrano R; Zapatero-Solana E; Abad M; Bueno MJ; de Cedrón MG; Fernández-Piqueras J; Serrano M; Blasco MA; Wang D-Z; Clark SJ; Izpisua-Belmonte JC; Ortega S; Malumbres M, A novel microRNA-based strategy to expand the differentiation potency of stem cells, http://dx.doi.org/10.1101/826446

Lam D; Clark S; Stirzaker C; Pidsley R, Advances in Prognostic Methylation Biomarkers for Prostate Cancer, http://dx.doi.org/10.20944/preprints202010.0154.v1

Campbell EM; Laven-Law G; Jones A; Challis D; Peters TJ; Smith G; Colino-Sanguino Y; Moulder D; Du Q; Giles KA; Thomson DW; Stirzaker C; Hickey TA; Mora FV; Khoury A; Clark SJ; Achinger-Kawecka J, Androgen stimulation rapidly reorganizes temporal 3D genome and epigenome states to trigger AR-mediated transcription in prostate cancer, http://dx.doi.org/10.1101/2024.12.17.628805

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

Angeloni A; Hammond JM; Peters TJ; Reis ALM; Kemp L; Amos T; Gamaarachchi H; Humphries S; Wilmott LA; Pal S; Masamsetti VP; Weatherstone M; Ip KCK; Pazaky K; Steel A; Lyons R; Walters ED; Liu N; Tam P; Polo JM; Waters P; Clark SJ; Richards LJ; Smith AD; Lee H; Deveson IW; Griffith OW; Skvortsova K, DNA methylation reprogramming in marsupial embryos is restricted to the extraembryonic lineage, http://dx.doi.org/10.1101/2025.11.09.686659

Skvortsova K; Angeloni A; Hammond J; Peters T; Reis ALM; Kemp L; Amos T; Gamaarachchi H; Humphries S; Wilmott L; Pal S; Masamsetti VP; Weatherstone M; Ip KCK; Pazaky K; Steel A; Lyons R; Walters E; Liu N; Tam P; Polo J; Waters P; Clark S; Richards L; Smith A; Lee H; Deveson I; Griffith O, DNA methylation reprogramming in marsupial embryos is restricted to the extraembryonic lineage, http://dx.doi.org/10.21203/rs.3.rs-8110586/v1

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, Epigenetic therapy targets the 3D epigenome in endocrine-resistant breast cancer, http://dx.doi.org/10.1101/2021.06.21.449340

González-Rajal Á; D’Araujo TY; Ovchinnikov V; Alcalá JLG-J; Wang T; Lausen B; Brethouwer T; Angeloni A; Ross SE; Burgos-Ruiz AM; Álvarez-Presas M; Mota-Gómez I; Acemel RD; Harris RJ; Loi-Luu P; Jimenez GE; Daners A; Ferguson JM; Hammond JM; Gamaarachchi H; Degnan BM; Degnan SM; Mackay JP; Undheim EAB; Ruiz-Trillo I; Clark SJ; Tena JJ; Lupiáñez DG; Church SH; Dunn CW; Marletaz F; Deveson IW; Cummins SF; Neely GG; de Mendoza A; Bogdanovic O, Integrative genomics of the siphonophore Physalia utriculus reveals the regulatory logic of colonial division of labour and the molecular basis of venom activity, http://dx.doi.org/10.64898/2026.08.01.742136

King HE; O’Connell S; Kavanagh D; Mason S; McCool C; Fernandez-Chamorro J; Chaffer C; Clark SJ; Vieira HGS; Sterne-Weiler T; Weatheritt RJ, Isoform-specific single-cell perturb-seq reveals distinct functions of alternative promoters in drug response, http://dx.doi.org/10.1101/2025.07.14.664827

Luu P-L; Ong P-T; Loc TTH; Lam D; Pidsley R; Stirzaker C; Clark SJ, 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

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

Schumann U; Zhang H-N; Sibbritt T; Pan A; Horvath A; Gross S; Clark SJ; Yang L; Preiss T, Multiple links between 5-methylcytosine content of mRNA and translation, http://dx.doi.org/10.1101/2020.02.04.933499

Tiedemann RL; Hrit J; Du Q; Wiseman AK; Eden HE; Dickson BM; Kong X; Chomiak AA; Vaughan RM; Hebert JM; David Y; Zhou W; Baylin SB; Jones PA; Clark SJ; Rothbart SB, UHRF1 ubiquitin ligase activity supports the maintenance of low-density CpG methylation, http://dx.doi.org/10.1101/2024.02.13.580169

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, 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, Visualization of Biomedical Data, http://dx.doi.org/10.7287/peerj.preprints.26896v1

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, Widespread aberrant alternative splicing despite molecular remission in chronic myeloid leukemia patients, http://dx.doi.org/10.1101/2020.07.31.20165597

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