Overview
Background
My current focus is on the application of deep learning models that read DNA sequences and predict cell type specific gene expression, chromatin accessibility, and transcription factor binding to human genetics. Specially, I am interested in 1) how well do current models trained on genetic variation across genomes generalize to genetic variation between individual genomes? 2) Can these models predict causal variants at loci that are associated with human traits? And if so, to what degree? 3) Can we utilize these models to link DNA sequences to the effect of genetic variants on human traits and disease?
Availability
- Dr Brad Balderson is:
- Available for supervision
Fields of research
Research impacts
In my previous research:
- CRISPR editing off-target detection (2025) - developed methods for the first technology ("Superb-seq") to measure genome editing locations in DNA in single cells, along with gene activity measurements. I found previously under-appreciated specificity issues with genome-editing, meaning there were many more locations in the genome edited than would be expected. This research has important implications for emerging CRISPR genome-editing therapeutics, such as Casgevy for sick cell disease, and VERVE-101 for LDL/cardiamyopathies, suggesting further research on the safety and efficacy of these approaches.
- Spatial transcriptomics (2021) - I analysed the first brain tumour maps of gene activity in conditions with and without CDK4/6 inhibitor treatment. I found the drug could not cross the blood-brain barrier (BBB), but could still penetrate the tumour since this barrier is not intact within the tumour. This means there is a niche where brain tumour cells could avoid drug treatment, which lead to recurrence. Now CDK4/6 inhibitors for brain tumours with better BBB penetrance are more widely used.
Works
Search Professor Brad Balderson’s works on UQ eSpace
2022
Journal Article
Engineering indel and substitution variants of diverse and ancient enzymes using Graphical Representation of Ancestral Sequence Predictions (GRASP)
Foley, Gabriel, Mora, Ariane, Ross, Connie M., Bottoms, Scott, Sützl, Leander, Lamprecht, Marnie L., Zaugg, Julian, Essebier, Alexandra, Balderson, Brad, Newell, Rhys, Thomson, Raine E. S., Kobe, Bostjan, Barnard, Ross T., Guddat, Luke, Schenk, Gerhard, Carsten, Jörg, Gumulya, Yosephine, Rost, Burkhard, Haltrich, Dietmar, Sieber, Volker, Gillam, Elizabeth M. J. and Bodén, Mikael (2022). Engineering indel and substitution variants of diverse and ancient enzymes using Graphical Representation of Ancestral Sequence Predictions (GRASP). PL o S Computational Biology, 18 (10) e1010633, e1010633. doi: 10.1371/journal.pcbi.1010633
2016
Journal Article
Emerging Role and Characterization of Immunometabolism: Relevance to HIV Pathogenesis, Serious Non-AIDS Events, and a Cure
Palmer, Clovis S., Henstridge, Darren C., Yu, Di, Singh, Amit, Balderson, Brad, Duette, Gabriel, Cherry, Catherine L., Anzinger, Joshua J., Ostrowski, Matias and Crowe, Suzanne M. (2016). Emerging Role and Characterization of Immunometabolism: Relevance to HIV Pathogenesis, Serious Non-AIDS Events, and a Cure. The Journal of Immunology, 196 (11), 4437-4444. doi: 10.4049/jimmunol.1600120
Supervision
Availability
- Dr Brad Balderson is:
- Available for supervision
Looking for a supervisor? Read our advice on how to choose a supervisor.
Media
Enquiries
For media enquiries about Dr Brad Balderson's areas of expertise, story ideas and help finding experts, contact our Media team: