Sasha Gavryushkina

Sasha Gavryushkina

School of Computer and Mathematical Sciences

Faculty of Sciences, Engineering and Technology

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 provide a powerful tool for inferring 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.

 

  • Journals

    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 Scopus4 Europe PMC6
    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. JOURNAL OF COMPUTATIONAL BIOLOGY, 15 pages.
    DOI
    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 Scopus11 Europe PMC10
    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 Scopus2824 Europe PMC1781
    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 Scopus65 Europe PMC39
    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 Scopus74 Europe PMC50
    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 Scopus101 Europe PMC86
    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 Scopus252 Europe PMC195
    2013 Gavryushkina, A., Welch, D., & Drummond, A. J. (2013). Recursive algorithms for phylogenetic tree counting. Algorithms for Molecular Biology, 8(1), 26.
    DOI Scopus9
  • Book Chapters

    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
  • Conference Papers

    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 Scopus218 Europe PMC160

Connect With Me
External Profiles