Gene Regulation Bioinformatics Laboratory

Research Program Overview

We apply computational biology and bioinformatics to understand how gene regulation shapes development and disease, with a focus on childhood cancers such as neuroblastoma and brain cancer. Our work spans transcriptomics, regulatory networks, transcription factors, alternative splicing, microRNAs and circular RNAs. By integrating single-cell and bulk transcriptomic data with functional studies in stem cell differentiation and in vivo models, we uncover how gene regulatory programs drive cancer phenotypes and cell state transitions.

Research themes include:

Tumour heterogeneity in neuroblastoma – combining large-scale transcriptomics with machine learning to define subtypes that inform treatment and reveal new vulnerabilities, validated using CRISPR, iPSC and mouse models
Alternative splicing in epithelial–mesenchymal transition – investigating how splicing regulators reshape cell states during development and cancer
Non-coding RNA function in cancer – dissecting the roles of microRNAs and circular RNAs in transcriptional control and tumour progression

Our approach is grounded in biology and powered by data.

Working in close partnership with wet-lab collaborators, we design experiments to dissect systems, use computational biology to ask sharper questions, make more insightful predictions, and close the loop as collaborators take these findings back to the bench for validation.

Laboratory staff

Laboratory head

Dr Katherine Pillman

Senior Research Fellow, Centre for Cancer Biology

HB8-15, City West Campus

Katherine.Pillman@unisa.edu.au

Team Members

Research Assistants

Mrs Julie Bracken

Students

Miss Ayushi Notra (PhD)
Miss Tayla Albertini (PhD)
Mr Roopan Giri (PhD)
Dr Dione Gardner-Stephen (PhD)

Select Recent Publications

Orang A, Warnock NI, Migault M, Dredge BK, Bert AG, Bracken JM, Gregory PA, Pillman KA, Goodall GJ, Bracken CP (2025). Chasing non-existent "microRNAs" in cancer. Oncogenesis., 14(1):10. doi: 10.1038/s41389-025-00550-9. PMID: 40251190.Ngo LH, Bert AG, Dredge BK, Williams T, Murphy V, Li W, Hamilton WB, Carey KT, Toubia J,
Pillman KA, Liu D, Desogus J, Chao JA, Deans AJ, Goodall GJ, Wickramasinghe VO (2024). Nuclear export of circular RNA. Nature. 627(8002):212-220. doi: 10.1038/s41586-024-07060-5. PMID: 38355801.
Neumann DP, Pillman KA, Dredge BK, Bert AG, Phillips CA, Lumb R, Ramani Y, Bracken CP, Hollier BG, Selth LA, Beilharz TH, Goodall GJ, Gregory PA (2024). The landscape of alternative polyadenylation during EMT and its regulation by the RNA-binding protein Quaking. RNA Biol., 21(1):1-11. doi: 10.1080/15476286.2023.2294222. PMID: 38112323.
Liu D, Dredge BK, Bert AG, Pillman KA, Toubia J, Guo W, Dyakov BJA, Migault MM, Conn VM, Conn SJ, Gregory PA, Gingras AC, Patel D, Wu B, Goodall GJ (2024). ESRP1 controls biogenesis and function of a large abundant multiexon circRNA. Nucleic Acids Research., 52(3):1387-1403. doi: 10.1093/nar/gkad1138. PMID: 38015468.
Orang A, Dredge BK, Liu CY, Bracken JM, Chen CH, Sourdin L, Whitfield HJ, Lumb R, Boyle ST, Davis MJ, Samuel MS, Gregory PA, Khew-Goodall Y, Goodall GJ, Pillman KA*, Bracken CP* (2023). Basonuclin-2 regulates extracellular matrix production and degradation. Life Sci Alliance, 6(10):e202301984. *contributed equally. PMID: 37536977.
Sapkota S, Pillman KA, Dredge BK, Liu D, Bracken JM, Kachooei SA, Chereda B, Gregory PA, Bracken CP, Goodall GJ. On the rules of engagement for microRNAs targeting protein coding regions (2023). Nucleic Acids Research, 51(18)9938-9951. PMID: 37522357.
Smith MD, Leemaqz SY, Jankovic-Karasoulos T, McAninch D, McCullough D, Breen J, Roberts CT, Pillman KA (2022). Haemolysis detection in microRNA-seq from clinical plasma samples. Genes, 13(7):1288. PMID: 35886071.
Smith MD, Pillman KA, Jankovic-Karasoulos T, McAninch D, Wan Q, Bogias KJ, McCullough D, Bianco-Miotto T, Breen J, Roberts CT (2021). Large-scale transcriptome-wide profiling of microRNAs in human placenta and maternal plasma at early to mid gestation. RNA Biol, 18:507-520. doi:10.1080/15476286.2021.1963105. PMID: 34412547.
Fernandes RC, Toubia J, Townley S, Hanson AR, Dredge BK, Pillman KA, Bert AG, Winter JM, Iggo R, Das R, Obinata D; MURAL investigators, Sandhu S, Risbridger GP, Taylor RA, Lawrence MG, Butler LM, Zoubeidi A, Gregory PA, Tilley WD, Hickey TE, Goodall GJ, Selth LA (2021). Post-transcriptional Gene Regulation by MicroRNA-194 Promotes Neuroendocrine Transdifferentiation in Prostate Cancer. Cell Reports, 34 (1):108585. PMID: 33406413.
Pillman KA, Scheer KG, Hackett-Jones E, Saunders K, Bert AG, Toubia J, Whitfield HJ, Sapkota S, Sourdin L, Pham H, Le TD, Cursons J, Davis MJ, Gregory PA, Goodall GJ, Bracken CP (2019). Extensive transcriptional responses are co-ordinated by microRNAs as revealed by Exon-Intron Split Analysis (EISA). Nucleic Acids Research, 47 (16) 8606–19. PMID: 31372646.
Pillman KA, Goodall GJ, Bracken CP, Gantier MP (2019). miRNA length variation during macrophage stimulation confounds the interpretation of results: implications for miRNA quantification by RT-qPCR. RNA, 25 (2):232-38. PMID: 30487268.
Pillman KA*, Phillips C*, Roslan S*, Toubia J*, Dredge B, Bert A, Lumb R, Neumann D, Li X, Conn S, Liu D, Bracken CP, Lawrence D, Stylianou N, Schreiber A, Tilley W, Hollier B, Khew-Goodall Y, Selth L, Goodall G and Gregory PA (2018). miR-200/375 control widespread epithelial plasticity-associated alternative splicing through Quaking. The EMBO Journal, 37 (13) pii:e99016. *contributed equally. PMID: 29871889.
Cursons J, Pillman KA, Scheer KG, Gregory PA, Foroutan M, Hediyeh-Zadeh S, Toubia J, Crampin EJ, Goodall GJ, Bracken CP, Davis MJ (2018). Combinatorial Targeting by MicroRNAs Co-ordinates Post-transcriptional Control of EMT. Cell Systems, 7(1):77-91.e7. PMID: 30007539. doi: 10.1016/j.cels.2018.05.019.
Yu F, Pillman KA, Neilsen CT, Toubia J, Lawrence DM, Tsykin A, Gantier MP, Callen DF, Goodall GJ, Bracken CP. Naturally existing isoforms of miR-222 have distinct functions (2017). Nucleic Acids Research, 45 (19):11371-85.
Conn SJ, Pillman KA, Toubia J, Conn VM, Salmanidis M, Phillips CA, Roslan S, Schreiber AW, Gregory PA, Goodall GJ. (2015) The RNA binding protein Quaking regulates formation of circRNAs. Cell, 160 (6): 1125-34.
Yu F, Bracken CP, Pillman KA, Lawrence DM, Goodall GJ, Callen DF, Neilsen PM (2015). p53 represses the oncogenic sno-miR-28 derived from a snoRNA. PLoS One, 8 (9) e75517.
Thomson DW, Pillman KA, Anderson ML, Lawrence DM, Toubia J, Goodall GJ, Bracken CP (2015). Assessing the gene regulatory properties of Argonaute-bound small RNAs of diverse genomic origin. Nucleic Acids Research, 43 (1): 470-81.
Bracken CP, Li X, Wright JA, Lawrence DM, Pillman KA, Salmanidis M, Anderson MA, Dredge BK, Gregory PA, Tsykin A, Neilsen C, Thomson DW, Bert AG, Leerberg JM, Yap AS, Jensen KB, Khew-Goodall Y, Goodall GJ (2014). Genome-wide identification of miR-200 targets reveals a regulatory network controlling cell invasion. The EMBO Journal, 33 (18): 2040-56.