Daniel Thomson

South Australian Immunogenomics Cancer Institute

Faculty of Health and Medical Sciences

Dr Daniel Thomson is a computational/molecular biologist passionate about applying genomic technology for cancer research and new diagnostic tests. Joining SAIGENCI in 2025, Daniel is using genomic and transcriptomic approaches to understand mechanisms of cancer therapy resistance, in order to develop new bioinformatic tools to predict patient outcomes.

He has held postdoctoral positions at the Garvan Institute, SA Pathology and Flinders University, and has a proven capacity to translate research findings into clinical diagnostic applications, having lead the bioinformatic development and NATA accreditation of multiple genomic tests currently in the clinic. This includes development of variant and fusion-gene calling pipelines for solid and haematological tumours as lead clinical bioinformatician at Monash Pathology, and a polygenic risk score for glaucoma predisposition testing at an Adelaide-based biotech start-up SeonixBio,

With proven expertise in genomic computational biology in research and biotech industry roles, Daniel is highly motivated with strong research background ( 25 research publications, >4000 citations), This includes first author publications in Nature Reviews Genetics, Nucleic Acids Research and Leukaemia.

Career
Publications
Contact

Appointments

Date	Position	Institution name
2025 - ongoing	Senior Postdoctoral Researcher	SAIGENCI
2023 - 2025	Senior Bioinformatician	South Australian Genomic Centre
2020 - 2021	Clinical Bioinformatics Lead	Monash Health
2017 - 2020	Research Scientist	SAPathology
2014 - 2017	Postdoctoral researcher	Garvan Institute of Medical Research
2011 - 2023	Senior Bioinformatician	SeonixBio

Education

Date Institution name Country Title

2010 - 2014 University of Adelaide Australia PhD
Research Interests

Genomics and transcriptomics Cancer Diagnosis Bioinformatics and computational biology Cancer Genetics Cancer Cell Biology Gene expression (incl. microarray and other genome-wide approaches)

Date	Institution name	Country	Title
2010 - 2014	University of Adelaide	Australia	PhD

Journals

Year	Citation
2023	Mullany, S., Diaz-Torres, S., Schmidt, J. M., Thomson, D., Qassim, A., Marshall, H. N., . . . Craig, J. E. (2023). No Strong Association between the Apolipoprotein E E4 Allele and Glaucoma: A Multicohort Study. Ophthalmology Science, 3(3), 13 pages. DOI Scopus3 Europe PMC3
2023	Berry, E. C., Marshall, H. N., Mullany, S., Torres, S. D., Schmidt, J., Thomson, D., . . . Craig, J. E. (2023). Physical Activity Is Associated With Macular Thickness: A Multi-Cohort Observational Study. Investigative Ophthalmology and Visual Science, 64(3), 11-1-11-8. DOI Scopus4 WoS1 Europe PMC3
2023	Shanmuganathan, N., Wadham, C., Shahrin, N., Feng, J., Thomson, D., Wang, P., . . . Branford, S. (2023). Impact of additional genetic abnormalities at diagnosis of chronic myeloid leukemia for first-line imatinib-treated patients receiving proactive treatment intervention. Haematologica, 108(9), 2380-2395. DOI Scopus12 WoS2 Europe PMC6
2023	Marshall, H. N., Mullany, S., Han, X., Qassim, A., He, W., Hassall, M. M., . . . Craig, J. E. (2023). High Polygenic Risk is Associated with Earlier Initiation and Escalation of Treatment in Early Primary Open Angle Glaucoma. Ophthalmology, 130(8), 830-836. DOI Scopus14 Europe PMC11
2023	Hollitt, G. L., Qassim, A., Thomson, D., Schmidt, J. M., Nguyen, T. T., Landers, J., . . . Craig, J. E. (2023). Genetic Risk Assessment of Degenerative Eye Disease (GRADE): study protocol of a prospective assessment of polygenic risk scores to predict diagnosis of glaucoma and age-related macular degeneration. BMC OPHTHALMOLOGY, 23(1), 9 pages. DOI Europe PMC5
2023	Marshall, H., Berry, E. C., Torres, S. D., Mullany, S., Schmidt, J., Thomson, D., . . . Craig, J. E. (2023). Association between Body Mass Index and Primary Open-Angle Glaucoma in Three Cohorts. American Journal of Ophthalmology, 245, 126-133. DOI Scopus24 WoS4 Europe PMC22
2022	Mullany, S., Marshall, H., Zhou, T., Thomson, D., Schmidt, J. M., Qassim, A., . . . Craig, J. E. (2022). RNA Sequencing of Lens Capsular Epithelium Implicates Novel Pathways in Pseudoexfoliation Syndrome. Investigative Ophthalmology and Visual Science, 63(3), 26-1-26-17. DOI Scopus7 WoS4 Europe PMC4
2022	Mullany, S., Marshall, H., Diaz-Torres, S., Berry, E. C., Schmidt, J. M., Thomson, D., . . . Craig, J. E. (2022). The APOE E4 allele is associated with faster rates of neuroretinal thinning in a prospective cohort study of suspect and early glaucoma. Ophthalmology Science, 2(2), 1-13. DOI Scopus5 WoS1 Europe PMC5
2022	Shanmuganathan, N., Wadham, C., Thomson, D., Shahrin, N. H., Vignaud, C., Obourn, V., . . . Branford, S. (2022). RNA-Based Targeted Gene Sequencing Improves the Diagnostic Yield of Mutant Detection in Chronic Myeloid Leukemia.. The Journal of molecular diagnostics : JMD, 24(7), 803-822. DOI Scopus6 WoS1 Europe PMC5
2021	Adnan Awad, S., Dufva, O., Ianevski, A., Ghimire, B., Koski, J., Maliniemi, P., . . . Mustjoki, S. (2021). RUNX1 mutations in blast-phase chronic myeloid leukemia associate with distinct phenotypes, transcriptional profiles, and drug responses. Leukemia, 35(4), 1087-1099. DOI Scopus42 WoS25 Europe PMC31
2020	Thomson, D. W., Shahrin, N. H., Wang, P. P. S., Wadham, C., Shanmuganathan, N., Scott, H. S., . . . Branford, S. (2020). Aberrant RAG-mediated recombination contributes to multiple structural rearrangements in lymphoid blast crisis of chronic myeloid leukemia. Leukemia, 34(8), 2051-2063. DOI Scopus33 WoS22 Europe PMC23
2018	Branford, S., Wang, P., Yeung, D. T., Thomson, D., Purins, A., Wadham, C., . . . Hughes, T. P. (2018). Integrative genomic analysis reveals cancer-associated mutations at diagnosis of CML in patients with high-risk disease. Blood, 132(9), 948-961. DOI Scopus161 WoS121 Europe PMC126
2016	Thomson, D. W., & Dinger, M. E. (2016). Endogenous microRNA sponges: evidence and controversy. NATURE REVIEWS GENETICS, 17(5), 272-283. DOI Europe PMC1355
2015	Quek, X. C., Thomson, D. W., Maag, J. L. V., Bartonicek, N., Signal, B., Clark, M. B., . . . Dinger, M. E. (2015). lncRNAdb v2.0: expanding the reference database for functional long noncoding RNAs. NUCLEIC ACIDS RESEARCH, 43(D1), D168-D173. DOI Europe PMC359
2015	Thomson, D., Pillman, K., Anderson, M., Lawrence, D., Toubia, J., Goodall, G., & Bracken, C. (2015). Assessing the gene regulatory properties of Argonaute-bound small RNAs of diverse genomic origin. Nucleic Acids Research, 43(1), 470-481. DOI Scopus35 WoS27 Europe PMC33
2014	Bracken, C. P., Li, X., Wright, J. A., Lawrence, D., Pillman, K. A., Salmanidis, M., . . . Goodall, G. (2014). Genome-wide identification of miR-200 targets reveals a regulatory network controlling cell invasion. The EMBO Journal, 33(18), 1979-2134. DOI Scopus123 WoS116 Europe PMC108
2013	Thomson, D., Bracken, C., Szubert, J., & Goodall, G. (2013). On measuring miRNAs after transient transfection of mimics or antisense inhibitors. PLoS One, 8(1), 1-10. DOI Scopus105 WoS92 Europe PMC93
2011	Thomson, D., Bracken, C., & Goodall, G. (2011). Experimental strategies for microRNA target identification. Nucleic Acids Research, 39(16), 6845-6853. DOI Scopus477 WoS426 Europe PMC387
2011	Bracken, C., Szubert, J., Mercer, T., Dinger, M., Thomson, D., Mattick, J., . . . Goodall, G. (2011). Global analysis of the mammalian RNA degradome reveals widespread miRNA-dependent and miRNA-independent endonucleolytic cleavage. Nucleic Acids Research, 39(13), 5658-5668. DOI Scopus71 WoS64 Europe PMC65
2011	Fowler, A., Thomson, D., Giles, K., Maleki, S., Mreich, E., Wheeler, H., . . . McDonald, K. (2011). MiR-124a is frequently down-regulated in glioblastoma and is involved in migration and invasion. European Journal of Cancer, 47(6), 953-963. DOI Scopus116 WoS106 Europe PMC101

Conference Papers

Year	Citation
2019	Shanmuganathan, N., Thomson, D., Wadham, C., Saunders, V. A., Shahrin, N. H., Yeung, D. T., . . . Branford, S. (2019). RNA Splicing Defects in Cancer-Linked Genes Indicate Mutation or Focal Gene Deletion and Are Associated with TKI Resistance in CML. In BLOOD Vol. 134 (pp. 4 pages). Orlando, FL: AMER SOC HEMATOLOGY. DOI WoS1
2019	Branford, S., Wadham, C., Shanmuganathan, N., Thomson, D., Shahrin, N. U. R. H., Feng, J., . . . Hughes, T. P. (2019). An RNA-Based Next Generation Sequencing (NGS) Strategy Detects More Cancer Gene Mutations Than a DNA-Based Approach for the Prediction and Assessment of Resistance in CML. In BLOOD Vol. 134 (pp. 4 pages). Orlando, FL: AMER SOC HEMATOLOGY. DOI
2019	Shahrin, N. H., Thomson, D., Wadham, C., Schreiber, A., & Branford, S. (2019). IMATINIB INDUCES MARKED UPREGULATION OF RECOMBINATION ACTIVATING GENE (RAG) EXPRESSION IN BCR-ABL1 POSITIVE LYMPHOID CELLS. In EXPERIMENTAL HEMATOLOGY Vol. 76 (pp. S85). ELSEVIER SCIENCE INC.
2018	Thomson, D., Shahrin, H., Wang, P., Wadham, C., Hughes, T. P., Schreiber, A., & Branford, S. (2018). High Recombination Activating Gene (RAG) Expression and RAG Mediated Recombination Is Associated with Oncogenic Rearrangement Observed with Tyrosine Kinase Inhibitor Resistant CML. In BLOOD Vol. 132 (pp. 4 pages). CA, San Diego: AMER SOC HEMATOLOGY. DOI WoS1

Conference Items

Year	Citation
2022	Berry, E. C., Marshall, H., Mullany, S., Torres, S. D., Schmidt, J., Thomson, D., . . . Craig, J. E. (2022). Greater physical activity is associated with neuroretinal thinning in glaucomatous and normative cohorts. Poster session presented at the meeting of Abstracts of the Association for Research in Vision & Ophthalmology 2022 Annual Meeting (ARVO), as published in Investigative Ophthalmology & Visual Science. Denver, CO, USA & online: Association for Research in Vision & Ophthalmology.

Year

Citation

2022

Berry, E. C., Marshall, H., Mullany, S., Torres, S. D., Schmidt, J., Thomson, D., . . . Craig, J. E. (2022). Greater physical activity is associated with neuroretinal thinning in glaucomatous and normative cohorts. Poster session presented at the meeting of Abstracts of the Association for Research in Vision & Ophthalmology 2022 Annual Meeting (ARVO), as published in Investigative Ophthalmology & Visual Science. Denver, CO, USA & online: Association for Research in Vision & Ophthalmology.

Email: daniel.thomson@adelaide.edu.au

Daniel Thomson

Appointments

Education

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Conference Papers

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