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.
DOI 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.
DOI
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.
DOI 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.
DOI 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.
DOI 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.
DOI 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.
DOI 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.
DOI 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.
DOI 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.
DOI 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

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