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

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. Nuclear export of circular RNA. Nature. 627:212-220, 2024.
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. ESRP1 controls biogenesis and function of a large abundant multiexon circRNA. Nucleic Acids Res. 52(3):1387-1403, 2024
Neumann DP, Phillips CA, Lumb R, Palethorpe HM, Ramani Y, Hollier BG, Selth LA, Bracken CP, Goodall GJ, Gregory PA. Quaking isoforms cooperate to promote the mesenchymal phenotype. Mol Biol Cell. 2024 Feb 1;35(2):ar17.
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. Nucleic Acids Res. 519938-9951, 2023.
Conn VM, Gabryelska M, Toubia J, Kirk K, Gantley L, Powell JA, Cildir G, Marri S, Liu R, Stringer BW, Townley S, Webb ST, Lin H, Samaraweera SE, Bailey S, Moore AS, Maybury M, Liu D, Colella AD, Chataway T, Wallington-Gates CT, Walters L, Sibbons J, Selth LA, Tergaonkar V, D'Andrea RJ, Pitson SM, Goodall GJ, Conn SJ. Circular RNAs drive oncogenic chromosomal translocations within the MLL recombinome in leukemia. Cancer Cell. 41:1309-1326, 2023.
Bracken CP, Goodall GJ. The many regulators of epithelial-mesenchymal transition. Nat Rev Mol Cell Biol. 23:89-90 2022
RC Fernandes, J Toubia, S Townley, AR Hanson, BK Dredge, KA Pillman, AG Bert, JM Winter, R Iggo, R Das, D Obinata, S Sandhu, GP Risbridger, RA Taylor, MG Lawrence, LM Butler, A Zoubeidi, P Gregory, WD Tilley, TE Hickey, GJ Goodall, LA Selth. Post-transcriptional Gene Regulation by MicroRNA-194 Promotes Neuroendocrine Trans-differentiation in Prostate Cancer. Cell Reports 34:108585, 2021
Goodall GJ and Wickramasinghe V. RNA in cancer Nat Rev Cancer 21:22-36, 2021
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. Extensive transcriptional responses are co-ordinated by microRNAs as revealed by Exon-Intron Split Analysis (EISA). Nucleic Acids Res. 47:8606-8619. 2019.
Pillman KA, Phillips ca, Roslan S, Toubia J, Dredge BK, Bert AG, Lumb R, Neumann DP, Li X, Conn SJ, Liu D, Lawrence DM, Stylianou N, Schreiber AW, Tilley WD, Hollier BG, Khew-Goodall Y, Selth LA, Goodall GJ, Gregory PA. miR-200-375 control epithelial plasticity-associated alternative splicing by repressing the RNA-binding protein Quaking. EMBO J. 37(13): e99016.
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. Nucleic Acids Res. 45:11371-11385, 2017.
Conn SJ, Pillman KA, Toubia J, Conn VM, Salmanidis M, Phillips CA, Roslan S, Schreiber AW, Gregory PA and Goodall GJ. The RNA binding protein Quaking regulates formation of circRNAs. Cell 160:1125-1134, 2015.
Bracken CP, Li X, Wright JA, Lawrence D, 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. Genome-wide identification of miR-200 targets reveals a regulatory network controlling cell invasion. EMBO J. 33:2040-2056, 2014.
Li X, Roslan S, Johnstone CN, Wright JA, Bracken CP, Anderson M, Bert AG, Selth LA, Anderson RA, Goodall GJ, Gregory PA, Khew-Goodall Y. MiR-200 can repress breast cancer metastasis through ZEB1-independent, but moesin-dependent pathways. Oncogene 33:4077-4088, 2014.
Lim YY, Wright JA, Attema JA, Gregory PA, Bert AG, Smith E, Thomas D, Lopez AF, Drew PA, Khew-Goodall Y and Goodall GJ. Epigenetic modulation of the miR-200 family is associated with transition to a breast cancer stem cell-like state. J. Cell Sci. 126:2256-2266, 2013.
Paterson EL, Kazenwadel J, Bert AG, Khew-Goodall Y, Ruszkiewicz A, Goodall GJ Downregulation of the miRNA-200 family at the invasive front of colorectal cancers with degraded basement membrane indicates EMT is involved in cancer progression. Neoplasia 15:180-191, 2013.
Bracken CP, Gregory PA, Kolesnikoff N, Bert AG, Wang J, Shannon MF, Goodall GJ. A double-negative feedback loop between ZEB1-SIP1 and the microRNA-200 family regulates epithelial-mesenchymal transition. Cancer Res. 68: 7846-7854, 2008.
Gregory PA, Bert AG, Paterson EL, Barry SC, Tsykin A, Farshid G, Vadas MA, Khew-Goodall Y, Goodall GJ. The microRNA-200 family and miR-205 regulate epithelial-mesenchymal transition by targeting the E-cadherin repressors, ZEB1 and SIP1. Nature Cell Biol. 10;593-601, 2008.