Dr Sasha Gavryushkina
Lecturer
School of Mathematical Sciences
College of Science
Eligible to supervise Masters and PhD (as Co-Supervisor) - email supervisor to discuss availability.
I am a Lecturer in Data Science and Statistics at the School of Computer and Mathematical Sciences at the University of Adelaide, where I develop methods for genomics data analysis with applications in macroevolution, epidemiology, and cancer research
My research focuses on developing statistical and computational methods for genomics data analysis, with applications in macroevolution, epidemiology, and cancer research.
Understanding the evolutionary relationships among tumour cells provides critical insights into how cancers develop, adapt, and spread. The advent and growing accessibility of single-cell sequencing technologies present an opportunity to reconstruct detailed cell lineage trees from tumour samples. My work focuses on testing and developing robust, accurate, and scalable methods to enhance our ability to interpret the complex evolutionary history of cancer at single-cell resolution.
Evolutionary histories reconstructed from genetic data carry information about population dynamics parameters across various application areas—for example, diversification rates in macroevolutionary studies, transmission rates in infectious disease epidemiology, and tumour growth rates in cancer research, among others. I am working on extensions and applications of birth–death models to improve such phylodynamic inference.
Classical statistical methods for inferring phylogenetic trees are well-established and reliable, but can be computationally intensive. My research focuses on developing likelihood-free inference techniques for phylogenetic analysis. My other research interests include machine learning techniques for sequencing data pre-processing, genotype–phenotype association studies, and other related problems.
| Date | Position | Institution name |
|---|---|---|
| 2025 - ongoing | Lecturer | University of Adelaide |
| 2024 - 2025 | Senior Research Fellow | Max Planck Institute of Geoanthropology |
| 2021 - 2024 | Research Fellow | University of Canterbury |
| 2018 - 2021 | Postdoctoral Research Fellow | University of Otago |
| 2016 - 2018 | Postdoctoral Research Fellow | ETH Zurich |
| Date | Institution name | Country | Title |
|---|---|---|---|
| 2013 - 2017 | University of Auckland | New Zealand | PhD |
| Year | Citation |
|---|---|
| 2025 | Truman, K., Vaughan, T. G., Gavryushkin, A., & Gavryushkina, A. S. (2025). The Fossilized Birth-Death Model Is Identifiable.. Syst Biol, 74(1), 112-123. Scopus5 WoS4 Europe PMC9 |
| 2025 | Gavryushkina, A. S., Pinkney, H. R., Diermeier, S. D., & Gavryushkin, A. (2025). Filtering for Highly Variable Genes and High-Quality Spots Improves Phylogenetic Analysis of Cancer Spatial Transcriptomics Visium Data.. J Comput Biol, 32(8), 738-752. |
| 2025 | Smith, J. A., Dowding, E. M., Abdelhady, A. A., Abondio, P., Araújo, R., Aze, T., . . . Ranaivosoa, V. (2025). Identifying the Big Questions in paleontology: a community-driven project. Paleobiology, 51(3), 408-431. Scopus1 WoS2 |
| 2020 | Biggs, H., Parthasarathy, P., Gavryushkina, A., & Gardner, P. P. (2020). ncVarDB: A manually curated database for pathogenic non-coding variants and benign controls. Database, 2020, baaa105. Scopus14 Europe PMC14 |
| 2019 | Bouckaert, R., Vaughan, T. G., Barido-Sottani, J., Duchêne, S., Fourment, M., Gavryushkina, A., . . . Drummond, A. J. (2019). BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis. Plos Computational Biology, 15(4), e1006650. Scopus3182 Europe PMC2177 |
| 2018 | Silvestro, D., Warnock, R. C. M., Gavryushkina, A., & Stadler, T. (2018). Closing the gap between palaeontological and neontological speciation and extinction rate estimates. Nature Communications, 9(1), 5237. Scopus69 Europe PMC47 |
| 2018 | Stadler, T., Gavryushkina, A., Warnock, R. C. M., Drummond, A. J., & Heath, T. A. (2018). The fossilized birth-death model for the analysis of stratigraphic range data under different speciation modes. Journal of Theoretical Biology, 447, 41-55. Scopus82 Europe PMC67 |
| 2016 | Ratmann, O., Van Sighem, A., Bezemer, D., Gavryushkina, A., Jurriaans, S., Wensing, A., . . . Fraser, C. (2016). Sources of HIV infection among men having sex with men and implications for prevention. Science Translational Medicine, 8(320), 320ra2. Scopus103 Europe PMC91 |
| 2014 | Gavryushkina, A., Welch, D., Stadler, T., & Drummond, A. J. (2014). Bayesian Inference of Sampled Ancestor Trees for Epidemiology and Fossil Calibration. Plos Computational Biology, 10(12), e1003919. Scopus262 Europe PMC214 |
| 2013 | Gavryushkina, A., Welch, D., & Drummond, A. J. (2013). Recursive algorithms for phylogenetic tree counting. Algorithms for Molecular Biology, 8(1), 26. Scopus9 |
| Year | Citation |
|---|---|
| 2021 | Gavryushkina, A., & Zhang, C. (2021). Total-evidence dating and the fossilized birth-death model. In S. Y. W. Ho (Ed.), The Molecular Evolutionary Clock: Theory and Practice (pp. 175-193). Springer International Publishing. DOI Scopus2 |
| Year | Citation |
|---|---|
| 2017 | Gavryushkina, A., Heath, T. A., Ksepka, D. T., Stadler, T., Welch, D., & Drummond, A. J. (2017). Bayesian total-evidence dating reveals the recent crown radiation of penguins. In Systematic Biology Vol. 66 (pp. 57-73). England: Oxford University Press (OUP). DOI Scopus224 Europe PMC195 |