Funding period: 2024-2029
Lead: Jason O'Brien
Total GRDI funding: $220,446
Gene expression technology (i.e. transcriptomics) has been used in toxicology and conservation biology research for decades. However, transcriptomics has seen limited adoption in regulatory applications such as chemical safety assessment and environmental monitoring. This project will address many of the barriers identified by regulatory agencies that have prevented the effective use of transcriptomics for regulatory applications. This includes addressing uncertainties and developing recommendations for experimental design and bioinformatic analysis of transcriptomic experiments and optimizing the technology for environmentally relevant species and animal-free alternative models. In addition, this project will also advance existing approaches with cutting-edge technologies such as single-cell sequencing and machine learning. The project does not specifically address issues related to gender, underrepresented groups, or vulnerable populations.
Publications
- O'Brien J, Mitchell C, Auerbach S, Doonan L, Ewald J, Everett L, Faranda A, Johnson K, Reardon A, Rooney J, Shao K, Stainforth R, Wheeler M, Dalmas Wilk D, Williams A, Yauk C, Costa E. 2025. Bioinformatic workflows for deriving transcriptomic points of departure: current status, data gaps, and research priorities. Toxicol Sci. 2025 Feb 1;203(2):147-159. https://doi.org/10.1093/toxsci/kfae145
- Stead JD, Lee H, Williams A, Ramírez SAC, Atlas E, Mennigen JA, O'Brien JM, Yauk C. 2025. Gene Set Enrichment Analysis in Zebrafish Embryos Is Susceptible to False-Positive Results in the Absence of Differentially Expressed Genes. Bioinform. Biol. Insights. 2025 Mar 4;19:11779322251321071. https://doi.org/10.1177/11779322251321071
Contact us
For additional information, please contact:
Genomics R&D Initiative
Email: info@grdi-irdg.collaboration.gc.ca