Selected Publications

Elyssa M Campbell, Geraldine Laven-Law, Grady Smith, Timothy J Peters, Yolanda Colino Sanguino, David Moulder, Qian Du, Alicia Jones, Katherine Giles, Amanda Khoury, Clare Stirzaker, Theresa Hickey, Fatima Valdes Mora, Susan Clark*, Joanna Achinger-Kawecka* (2025) Androgen stimulation rapidly reorganizes temporal 3D genome and epigenome states to trigger AR-mediated transcription in prostate cancer.https://doi.org/10.1101/2024.12.17.628805

Chen W, Zeng I, Achinger-Kawecka J, Campbell E, Jones A, Steward A, Khoury A, Clark S (2024) Machine learning enables pan-cancer identification of mutational hotspots at persistent CTCF binding sites. Nucleic Acids Research, https://doi.org/10.1093/nar/gkae530

Achinger-Kawecka J*, Stirzaker C, Portman N, Chia K-M, Campbell E, 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, Chen W, Pidsley R, Qu W, Gee JMW, Schmitt A, Wong ES, Hickey TE, Lim E, Clark SJ* (2024) The potential of epigenetic therapy to target the 3D epigenome in endocrine-resistant breast cancer. Nature Structural and Molecular Biology (*Co-corresponding author) doi:10.1038/s41594-023-01181-7

Du Q, Smith GA, Luu PL, Ferguson JM, Armstrong NJ, Nair S, Gould CA, Buckley M, Kaczorowski D, Campbell E, Barton K, Deveson I, Smith MA, Powell JE, Skvortsova K, Stirzaker C, Achinger-Kawecka J*, Clark SJ*. (2021) DNA methylation is required for DNA replication timing precision and 3D genome integrity. Cell Reports 36 (12), 109722

Achinger-Kawecka J, Valdes-Mora F, Luu PL, Giles KA, Caldon CE, Qu W, Nair S, Soto S, Locke WJ, Yeo-The 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 the 3D chromatin landscape in endocrine resistant breast cancer. Nature Communications 11, 320

Khoury A, Achinger-Kawecka J, Bert SA, Smith GC, French H, Luu PL, Peters T, Du Q, Parry A, Valdes-Mora F, Taberlay P, Stirzaker C, Statham AL, Clark SJ (2020) Constitutively bound CTCF sites maintain 3D chromatin architecture and long-range epigenetically regulated domains. Nature Communications 11, 54

Taberlay PC*, Achinger-Kawecka J*, 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. Three-dimensional disorganisation of the cancer genome occurs coincident with long range genetic and epigenetic alterations. Genome Research 26: 719-731 2016 *Equal first authors