Mr John Toubia

Adjunct Associate Research Professor Centre for Cancer Biology

City West Campus (HB8-14)

email John.Toubia@unisa.edu.au

Alternative contact

Research Degree Supervisor

About me

Bioinformatics
Transcriptomics
Cancer Genomics
Next Generation Sequencing

John is a senior bioinformatician with over 15 years of experience in the analysis, interpretation, and visualisation of next-generation sequencing data. For the past 10 years, he has led bioinformatics efforts at the Australian Cancer Research Foundation (ACRF) Cancer Genomics Facility, Centre for Cancer Biology, where he has developed and maintained custom analysis pipelines for bulk and single-cell genomic and transcriptomic data.

John has extensive experience, knowledge, and expertise in large-scale genomic and transcriptomic data analyses, including the identification of differentially expressed and alternatively spliced genes, and the subsequent downstream gene set and over-representation analyses to interpret biological and... Read more

Centre for Cancer Biology

Making breakthrough discoveries in the fundamental causes of cancer, and translating these into prevention and treatment.

Tweets by @UniversitySA

Research

Research focus

Biochemistry and Cell Biology
Biological Sciences
Clinical Sciences
Medical and Health Sciences
Oncology and Carcinogenesis

Research

Outputs

Research outputs for the last seven years are shown below. Some long-standing staff members may have older outputs included. To see earlier years visit ORCID or Scopus

Open access indicates that an output is open access.

Highlights

Year	Output
2025	Toubia, J, Kusay, Y, Maqsood, M, Warnock, N I, Lawrence, DM, Bracken, CP, Gregory, PA, Kan, WL, Selth, LA, Conn, SJ, Lopez, AF, Branford, S, Scott, HS, Kok, CH, Goodall, GJ & Schreiber, AW 2025, 'TRanscriptome ANalysis of StratifiEd CohorTs (TRANSECT) enables automated assessment of global gene regulation linked to disparate expression in user defined genes and gene sets', NAR Genomics and Bioinformatics, vol. 7, no. 2, article no. lqaf041, pp. 1-13. Open access
2023	Conn, VM, Gabryelska, M, Toubia, J, Kirk, K, Powell, JA, Cildir, G, Samaraweera, SE, Bailey, S, Liu, D, Wallington-Gates, CT, D'Andrea, RJ, Pitson, SM, Goodall, GJ & Conn, SJ and 15 other authors 2023, 'Circular RNAs drive oncogenic chromosomal translocations within the MLL recombinome in leukemia', Cancer Cell, vol. 41, no. 7, pp. 1309-1326. Open access 38 36 279
2023	Kazenwadel, J, Venugopal, P, Oszmiana, A, Toubia, J, Panara, V, Piltz, SG, Brown, C, Ma, W, Schreiber, AW, Koltowska, K, Taoudi, S, Thomas, PQ, Scott, HS & Harvey, NL 2023, 'A Prox1 enhancer represses haematopoiesis in the lymphatic vasculature', Nature, vol. 614, no. 7947, pp 343-348. 23 21 162
2019	Cildir, G, Toubia, J, Yip, KH, Zhou, M, Pant, H, Hissaria, P, Zhang, J, Hong, W, Robinson, N, Grimbaldeston, MA, Lopez, AF & Tergaonkar, V 2019, 'Genome-wide analyses of chromatin state in human mast cells reveal molecular drivers and mediators of allergic and inflammatory diseases', Immunity, vol. 51, no. 5, pp. 949-965.e6. Open access 47 46 12
2018	Pillman, KA, Phillips, CA, Roslan, S, Toubia, J, Dredge, BK, Bert, AG, Lumb, R, Neumann, DP, Li, X, Conn, SJ, Liu, D, Bracken, CP, Lawrence, DM, Schreiber, AW, Khew-Goodall, Y, Goodall, GJ & Gregory, PA and 4 other authors 2018, 'miR‐200/375 control epithelial plasticity‐associated alternative splicing by repressing the RNA‐binding protein Quaking', The EMBO Journal, vol. 37, no. 13, article no. e99016, pp. 1-20. Open access 87 85 15

Journal Articles

Year	Output
2025	Bayram Catak, F, Catak, MC, Babayeva, R, Toubia, J, Warnock, N I, Kok, CH, Cildir, G & Baris, S and 16 other authors 2025, 'Ruxolitinib treatment ameliorates clinical, immunologic, and transcriptomic aberrations in patients with STAT3 gain-of-function disease', Journal of Allergy and Clinical Immunology, vol. 155, no. 3, pp. 784-791. 1 5
2025	Davies, LT, Ganesen, R, Toubia, J, Hong, S-H, Kumar, KS, Oehler, MK, Ricciardelli, C, Szili, EJ, Robinson, N & Pitman, MR 2025, 'Plasma-activated media selectively induces apoptotic death via an orchestrated oxidative stress pathway in high-grade serous ovarian cancer cells', Molecular Oncology, vol. 19, no. 4, pp. 1170-1187. Open access 4
2025	Thompson, EJ, Dorward, EL, Jurrius, K, Nataren, N, Tondl, M, Myo Min, KK, Cockshell, MP, Fouladzadeh, A, Toubia, J, Denichilo, M, Merino, D & Bonder, CS 2025, 'Inhibitor of DNA binding-1 is a key regulator of cancer cell vasculogenic mimicry', Molecular Oncology, online, pp. 1-20. Open access
2025	Toubia, J, Kusay, Y, Maqsood, M, Warnock, N I, Lawrence, DM, Bracken, CP, Gregory, PA, Kan, WL, Selth, LA, Conn, SJ, Lopez, AF, Branford, S, Scott, HS, Kok, CH, Goodall, GJ & Schreiber, AW 2025, 'TRanscriptome ANalysis of StratifiEd CohorTs (TRANSECT) enables automated assessment of global gene regulation linked to disparate expression in user defined genes and gene sets', NAR Genomics and Bioinformatics, vol. 7, no. 2, article no. lqaf041, pp. 1-13. Open access
2024	De Sousa, SM, McCormack, A, Orsmond, A, Shen, A, Yates, CJ, Clifton-Bligh, R, Santoreneos, S, King, J, Feng, J, Toubia, J, Torpy, DJ & Scott, HS 2024, 'Increased prevalence of germline pathogenic CHEK2 variants in individuals with pituitary adenomas', Journal of Clinical Endocrinology and Metabolism, vol. 109, no. 11, pp. 2720-2728. Open access 3 2
2024	Li, M, Bennett, MK, Toubia, J, Pope, VS, Tea, MN, Tamang, S, Samuel, MS, Anderson, PH, Gliddon, BL, Powell, JA & Pitson, SM 2024, 'An orthotopic syngeneic mouse model of bortezomib-resistant multiple myeloma', British Journal of Haematology, 204, no. 2, pp. 566-570. Open access 1
2024	Liu, D, Dredge, BK, Bert, AG, Pillman, KA, Toubia, J, Guo, W, Dyakov, BJ, Migault, MM, Conn, VM, Conn, SJ, Gregory, PA, Gingras, A-C, Patel, D, Wu, B & Goodall, GJ 2024, 'ESRP1 controls biogenesis and function of a large abundant multiexon circRNA', Nucleic Acids Research, vol. 52, no. 3, pp. 1387-1403. Open access 11 13 2
2024	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, vol. 627, no 8002, pp. 212-220. 50 49 116
2024	Wang, H, Yip, KH, Keam, SP, Vlahos, R, Nichol, K, Wark, P, Toubia, J, Kral, AC, Cildir, G, Pant, H, Hercus, TR, Wilson, N, Owczarek, C, Lopez, AF, Bozinovski, S & Tumes, DJ 2024, 'Dual inhibition of airway inflammation and fibrosis by common β cytokine receptor blockade', Journal of Allergy and Clinical Immunology, vol. 153, no. 3, pp. 672-683.e6. Open access 5 4 67
2023	Byrne, AB, Arts, P, Ha, TT, Kassahn, KS, Babic, M, Frank, MS, Feng, J, Wang, P, Lawrence, DM, Eshraghi, L, Arriola, L, Toubia, J, Gardner, AE, Morrow, R, Schreiber, AW, King-Smith, SL, Jackson, MR & Scott, HS 182 other authors and 2 consortia 2023, 'Genomic autopsy to identify underlying causes of pregnancy loss and perinatal death', Nature Medicine, vol. 29, no. 1, pp. 180-189. Open access 31 32 76
2023	Conn, VM, Gabryelska, M, Toubia, J, Kirk, K, Powell, JA, Cildir, G, Samaraweera, SE, Bailey, S, Liu, D, Wallington-Gates, CT, D'Andrea, RJ, Pitson, SM, Goodall, GJ & Conn, SJ and 15 other authors 2023, 'Circular RNAs drive oncogenic chromosomal translocations within the MLL recombinome in leukemia', Cancer Cell, vol. 41, no. 7, pp. 1309-1326. Open access 38 36 279
2023	De Sousa, SM, Shen, A, Yates, CJ, Clifton-Bligh, R, Santoreneos, S, King, J, Toubia, J, Trivellin, G, Lania, AG, Stratakis, CA, Torpy, DJ & Scott, HS 2023, 'PAM variants in patients with thyrotrophinomas, cyclical Cushing's disease and prolactinomas', Frontiers in Endocrinology, vol. 14, article no. 1305606, pp. 1-10. Open access 3
2023	Kan, WL, Dhagat, U, Kaufmann, KB, Hercus, TR, Toubia, J, Barry, EF, Gomez, GA, Dottore, M, Samaraweera, SE, Goodall, GJ, Thomas, D, Tvorogov, D, D'Andrea, RJ & Lopez, AF and 12 other authors 2023, 'Distinct assemblies of heterodimeric cytokine receptors govern stemness programs in leukemia', Cancer Discovery, vol. 13, no. 8, pp. 1922-1947. Open access 8 8 19
2023	Kazenwadel, J, Venugopal, P, Oszmiana, A, Toubia, J, Panara, V, Piltz, SG, Brown, C, Ma, W, Schreiber, AW, Koltowska, K, Taoudi, S, Thomas, PQ, Scott, HS & Harvey, NL 2023, 'A Prox1 enhancer represses haematopoiesis in the lymphatic vasculature', Nature, vol. 614, no. 7947, pp 343-348. 23 21 162
2022	Alizadeh-Ghodsi, M, Owen, KL, Townley, SL, Zanker, D, Toubia, J, Gargett, T, Thierry, B & Selth, LA and 17 other authors 2022, 'Potent stimulation of the androgen receptor instigates a viral mimicry response in prostate cancer', Cancer Research Communications, vol. 2, no. 7, pp. 706-724. Open access 9 9 15
2022	Bassal, MA, Samaraweera, SE, Lim, K, Bernard, BA, Bailey, S, Toubia, J, Nguyen, T, Maung, KZY, Casolari, DA, Iarossi, DG, Powell, J, Pitson, S, Brown, AL, Robinson, N, Ross, DM, Gonda, TJ & D'Andrea, RJ and 10 other authors 2022, 'Germline mutations in mitochondrial complex I reveal genetic and targetable vulnerability in IDH1-mutant acute myeloid leukaemia', Nature Communications, vol. 13, article no. 2614, pp. 1-12. Open access 14 14 9
2022	Bennett, MK, Li, M, Tea, MN, Pitman, MR, Toubia, J, Wang, PP, Anderson, D, Creek, DJ, Orlowski, RZ, Gliddon, BL, Powell, JA, Wallington-Beddoe, CT & Pitson, SM 2022, 'Resensitising proteasome inhibitor-resistant myeloma with sphingosine kinase 2 inhibition', Neoplasia, vol. 24, no. 1, pp. 1-11. Open access 15 14 3
2022	Bournazos, AM, Riley, LG, Bommireddipalli, S, Ades, L, Cooper, ST & Toubia, J and 104 other authors and 1 consortium 2022, 'Standardized practices for RNA diagnostics using clinically accessible specimens reclassifies 75% of putative splicing variants', Genetics in Medicine, vol. 24, no. 1, pp. 130-145. 63 67
2022	Kollis, PM, Ebert, LM, Toubia, J, Bastow, CR, Ormsby, RJ, Poonnoose, S I, Lenin, S, Tea, MN, Pitson, SM, Gomez, GA, Brown, MP & Gargett, T 2022, 'Characterising distinct migratory profiles of infiltrating T-Cell subsets in human glioblastoma', Frontiers in Immunology, vol.13, pp. 1-19. Open access 21 18
2021	Fernandes, RC, Toubia, J, Townley, S, Hanson, AR, Dredge, BK, Pillman, KA, Bert, AG, Gregory, PA, Goodall, GJ & Selth, LA and 12 other authors 2021, 'Post-transcriptional gene regulation by microRNA-194 promotes neuroendocrine transdifferentiation in prostate cancer', Cell Reports, vol. 34, no. 1, article no. 108585, pp. 1-24. Open access 36 36 120
2021	Jensen, KB, Dredge, BK, Toubia, J, Jin, X, Iadevaia, V, Goodall, GJ & Proud, CG 2021, 'capCLIP: a new tool to probe translational control in human cells through capture and identification of the eIF4E-mRNA interactome', Nucleic Acids Research, vol. 49, no. 18, pp. e105 -1-e105-15. Open access 16 16
2021	Mansilla, MO, Salazar-Hernandez, C, Perrin, SL, Scheer, KG, Cildir, G, Toubia, J, Sedivakova, K, Tea, MN, Lenin, S, Ponthier, E, Yeo, EC, Tergaonkar, V, Poonnoose, S, Ormsby, RJ, Pitson, SM, Brown, MP, Ebert, LM & Gomez, GA 2021, '3D-printed microplate inserts for long term high-resolution imaging of live brain organoids', BMC Biomedical Engineering, vol. 3, article no. 6, pp. 1-13. Open access 13
2021	Prompsy, PB, Toubia, J, Gearing, LJ, Knight, RL, Forster, SC, Bracken, CP & Gantier, MP 2021, 'Making use of transcription factor enrichment to identify functional microRNA-regulons', Computational and Structural Biotechnology Journal, vol. 19, pp. 4896-4903. Open access 3 3 2
2020	Ebert, LM, Yu, W, Gargett, T, Toubia, J, Kollis, PM, Tea, MN, Ebert, BW, Bonder, CS, Oksdath Mansilla, M, Scheer, KG, Perrin, SL, Pitson, SM, Gomez, GA & Brown, MP and 8 other authors 2020, 'Endothelial, pericyte and tumor cell expression in glioblastoma identifies fibroblast activation protein (FAP) as an excellent target for immunotherapy', Clinical and Translational Immunology, vol. 9, no. 10, article no. e1191. Open access 51 46 4
2020	McCalmont, H, Li, KL, Jones, L, Toubia, J, Bray, SC, Casolari, DA, Mayoh, C, Samaraweera, SE, Lewis, ID, Prinjha, RK, Smithers, N, Wang, S & Lock, RB 2020, 'Efficacy of combined CDK9/BET inhibition in preclinical models of MLL-rearranged acute leukemia', Blood Advances, vol. 4, no. 2, pp. 296-300. Open access 23 22
2020	Saunders, K, Bert, AG, Dredge, BK, Toubia, J, Gregory, PA, Pillman, KA, Goodall, GJ & Bracken, CP 2020, 'Insufficiently complex unique-molecular identifiers (UMIs) distort small RNA sequencing', Scientific Reports, vol. 10, no. 1, pp. 1-9. Open access 12 10 9
2019	Baek, S, Oh, TG, Secker, G, Sutton, DL, Okuda, KS, Paterson, S, Bower, N I, Toubia, J, Koltowska, K, Capon, SJ, Baillie, GJ, Simons, C, Muscat, GE, Lagendijk, AK, Smith, KA, Harvey, NL & Hogan, BM 2019, 'The alternative splicing regulator nova2 constrains vascular erk signaling to limit specification of the lymphatic lineage', Developmental Cell, vol. 49, no. 2, pp. 279-292.e5. Open access 30 30 4
2019	Cildir, G, Toubia, J, Yip, KH, Zhou, M, Pant, H, Hissaria, P, Zhang, J, Hong, W, Robinson, N, Grimbaldeston, MA, Lopez, AF & Tergaonkar, V 2019, 'Genome-wide analyses of chromatin state in human mast cells reveal molecular drivers and mediators of allergic and inflammatory diseases', Immunity, vol. 51, no. 5, pp. 949-965.e6. Open access 47 46 12
2019	Dorstyn, L, Hackett-Jones, E, Nikolic, A, Norris, MD, Lim, Y, Toubia, J, Haber, M & Kumar, S 2019, 'Transcriptome profiling of caspase-2 deficient EμMyc and Th-MYCN mouse tumors identifies distinct putative roles for caspase-2 in neuronal differentiation and immune signaling', Cell Death and Disease, vol. 10, no. 2, pp. 1-16. Open access 7 6 6
2019	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, vol. 47, no. 16, pp. 8606-8619. Open access 7 6 5
2018	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, vol. 7, no. 1, pp. 77-91. Open access 73 68 28
2018	Pillman, KA, Phillips, CA, Roslan, S, Toubia, J, Dredge, BK, Bert, AG, Lumb, R, Neumann, DP, Li, X, Conn, SJ, Liu, D, Bracken, CP, Lawrence, DM, Schreiber, AW, Khew-Goodall, Y, Goodall, GJ & Gregory, PA and 4 other authors 2018, 'miR‐200/375 control epithelial plasticity‐associated alternative splicing by repressing the RNA‐binding protein Quaking', The EMBO Journal, vol. 37, no. 13, article no. e99016, pp. 1-20. Open access 87 85 15
2017	Yu, F, Pillman, KA, Neilsen, CT, Toubia, J, Lawrence, DM, Tsykin, A, Gantier, MP, Callen, DF, Goodall, GJ & Bracken, CP 2017, 'Naturally existing isoforms of miR-222 have distinct functions', Nucleic Acids Research, vol. 45, no. 19, pp. 1137-11385. Open access 61 58 7
2016	Plett, D, Baumann, U, Schreiber, AW, Holtham, L, Kalashyan, E, Toubia, J, Nau, J, Beatty, M, Rafalski, A, Dhugga, KS, Tester, M, Garnett, T & Kaiser, BN 2016, 'Maize maintains growth in response to decreased nitrate supply through a highly dynamic and developmental stage-specific transcriptional response', Plant Biotechnology Journal, vol. 14, no. 1, pp. 342-353. Open access 17 16
2016	Plett, D, Holtham, L, Baumann, U, Kalashyan, E, Francis, K, Enju, A, Toubia, J, Roessner, U, Bacic, A, Rafalski, A, Dhugga, K, Tester, M, Garnett, T & Kaiser, B 2016, 'Nitrogen assimilation system in maize is regulated by developmental and tissue-specific mechanisms', Plant Molecular Biology: An International Journal on Molecular Biology, Molecular Genetics and Biochemistry, vol. 92, no. 3, pp. 293-312. 18

External engagement & recognition

Collaborations

External engagement & recognition

Collaborations

Organisation	Country
Adelaide Oncology and Haematology	AUSTRALIA
A-Star, Institute of Molecular and Cell Biology	SINGAPORE
Central Queensland University	AUSTRALIA
CSL Limited	AUSTRALIA
DuPont	UNITED STATES
DuPont Pioneer Hi-Bred International	UNITED STATES
Flinders Medical Centre	AUSTRALIA
Flinders University	AUSTRALIA
Friedrich Miescher Institute for Biomedical Research	SWITZERLAND
Garvan Institute of Medical Research	AUSTRALIA
Genentech, Inc.	UNITED STATES
GlaxoSmithKline	AUSTRALIA
Harvard University	UNITED STATES
Hudson Institute of Medical Research	AUSTRALIA
Humanitas University	ITALY
Kids Research Institute	AUSTRALIA
King Abdullah University of Science and Technology (KAUST)	SAUDI ARABIA
La Trobe University	AUSTRALIA
Marmara University	TURKEY
Memorial Sloan Kettering Cancer Centre	UNITED STATES
Monash University	AUSTRALIA
Mount Sinai Hospital	UNITED STATES
Northwestern University Feinberg School of Medicine	UNITED STATES
NSW Health	AUSTRALIA
Peter MacCallum Cancer Centre	AUSTRALIA
RMIT University	AUSTRALIA
Royal Adelaide Hospital	AUSTRALIA
Royal Melbourne Hospital	AUSTRALIA
Royal North Shore Hospital	AUSTRALIA
SA Pathology	AUSTRALIA
South Australian Health and Medical and Research Institute (SAHMRI)	AUSTRALIA
St Vincent's Hospital	AUSTRALIA
St. Vincent's Institute of Medical Research	AUSTRALIA
Stanford University	UNITED STATES
Sun Yat-Sen University	CHINA
University Health Network	CANADA
University of Adelaide	AUSTRALIA
University of Basel	SWITZERLAND
University of Melbourne	AUSTRALIA
University of New South Wales	AUSTRALIA
University of Newcastle	AUSTRALIA
University of Queensland	AUSTRALIA
University of South Australia	AUSTRALIA
University of Surrey	UNITED KINGDOM
University of Sydney	AUSTRALIA
University of Texas	UNITED STATES
University of Toronto	CANADA
Uppsala University	SWEDEN
Walter and Eliza Hall Institute of Medical Research	AUSTRALIA

Teaching & student supervision

Research degree supervision

Supervisions from 2010 shown

Thesis title	Student status
Enhanced bioinformatics and machine learning for improved risk stratification and outcome prediction in chronic myeloid leukaemia	Current

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Mr John Toubia

Alternative contact

Alternative contact details

About me

About me

Centre for Cancer Biology

About me

Professional Associations

Research

Research focus

Projects

Other projects

Outputs

Highlights

Journal Articles

External engagement & recognition

Collaborations

Collaborations

Teaching & student supervision

Courses and programs

Research degree supervision

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