Daniel Thomson

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)

Daniel Thomson

SAIGENCI

College of Health

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.

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

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

Year Citation
2023 Mullany, S., Diaz-Torres, S., Schmidt, J. M., Thomson, D., Qassim, A., Marshall, H., . . . Craig, J. E. (2023). No Strong Association Between the Apolipoprotein E E4 Allele and Glaucoma: a Multicohort Study.. Ophthalmology Science, 3(3), 100287.
DOI Scopus3 WoS4 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 Scopus7 WoS7 Europe PMC7
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 Scopus18 WoS18 Europe PMC15
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 Scopus17 WoS16 Europe PMC18
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 WoS3 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 Scopus25 WoS23 Europe PMC24
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 WoS7 Europe PMC7
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 Scopus7 WoS6 Europe PMC7
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 Scopus8 WoS6 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 Scopus44 WoS40 Europe PMC38
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 Scopus35 WoS34 Europe PMC29
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 Scopus168 WoS157 Europe PMC140
2016 Thomson, D. W., & Dinger, M. E. (2016). Endogenous microRNA sponges: evidence and controversy. NATURE REVIEWS GENETICS, 17(5), 272-283.
DOI WoS1752 Europe PMC1559
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 WoS422 Europe PMC392
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 Scopus37 WoS35 Europe PMC38
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 Scopus124 WoS121 Europe PMC114
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 WoS102 Europe PMC99
2011 Thomson, D., Bracken, C., & Goodall, G. (2011). Experimental strategies for microRNA target identification. Nucleic Acids Research, 39(16), 6845-6853.
DOI Scopus482 WoS452 Europe PMC412
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 WoS68 Europe PMC71
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 WoS113 Europe PMC104

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). FL, Orlando: ELSEVIER.
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 WoS2

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