Dr Ryan Murphy

Research at the interface of mathematics, statistics, and biology.

Publications

A link to my Google Scholar is here.

All articles are also accessible on preprint servers, with links included below.

Preprints

  1. Cassidy T, Johnston ST, Plank M, Botha I, Flegg JA, Murphy RJ, Hamis S. (2025). A nonparametric approach to practical identifiability of nonlinear mixed effects models. [preprint-arxiv]
  2. Murphy RJ, Coster ACF, Flegg JA, Ndenda JP, Myerscough MR, Byrne HM. (2025). Quantifying bead accumulation inside a cannibalistic macrophage population.
  3. Chambers KL, Coster ACF, Flegg JA, Murphy RJ, Myerscough MR, Ndenda JP, Pan J, Watson MG. (2025). Atherosclerosis: reflections on mathematical modelling, data and other matters.

Published

  1. Browning AP, Flegg JA, Murphy RJ. (2025). A cautionary tale of model misspecification and identifiability. Bulletin of Mathematical Biology. doi:10.1007/s11538-025-01573-4 [preprint – arxiv]
  2. Murphy RJ, Faria M, Osborne JM, Johnston ST. (2025). Quantifying biological heterogeneity in nano-engineered particle-cell interaction experiments. Journal of the Royal Society Interface. doi:10.1098/rsif.2025.0206 [preprint-bioRxiv]
  3. Buenzli PR, Kuba S, Murphy RJ, Simpson MJ. (2025) Mechanical cell interactions on curved interfaces. Bulletin of Mathematical Biology. doi:10.1007/s11538-024-01406-w [preprint – arXiv]
  4. Murphy RJ, Maclaren OJ, Simpson MJ. (2024) Implementing measurement error models with mechanistic mathematical models in a likelihood-based framework for estimation, identifiability analysis, and prediction in the life sciences. Journal of the Royal Society Interface. doi:10.1098/rsif.2023.0402 [preprint – arXiv]
  5. Murphy RJ, Gunasingh G, Haass NK, Simpson MJ. (2024). Formation and growth of co-culture tumour spheroids: new mathematical models and experiments. Bulletin of Mathematical Biology. doi:10.1007/s11538-023-01229-1 [preprint – bioRxiv]
  6. Simpson MJ, Murphy RJ, Maclaren OJ. (2024) Modelling count data with partial differential equation models in biology. Journal of Theoretical Biology. doi:10.1016/j.jtbi.2024.111732 [preprint – bioRxiv]
  7. Murphy RJ, Gunasingh G, Haass NK, Simpson MJ. (2023). Growth and adaptation mechanisms of tumour spheroids with time-dependent oxygen availability. PLoS Computational Biology. doi:10.1371/journal.pcbi.1010833 [preprint – bioRxiv]
  8. Simpson MJ, Walker S, Studerus E, McCue SW, Murphy RJ, Maclaren OJ. (2023). Profile likelihood-based parameter and predictive interval analysis guides model choice for population dynamics. Mathematical Biosciences. doi:10.1016/j.mbs.2022.108950[preprint – bioRxiv]
  9. Murphy RJ, Maclaren OJ, Calabrese AR, Thomas PB, Warne DJ, Williams ED, Simpson MJ. (2022). Computationally efficient framework for diagnosing, understanding, and predicting biphasic population growth. Journal of the Royal Society Interface doi:10.1098/rsif.2022.0560 [preprint – bioRxiv]
  10. Murphy RJ, Browning AP, Gunasingh G, Haass NK, Simpson J. (2022). Designing and interpreting 4D tumour spheroid experiments. Communications Biology doi:10.1038/s42003-022-03018-3 [preprint – bioRxiv]
  11. Klowss J, Browning AP, Murphy RJ, Carr EJ, Plank MJ, Gunasingh G, Haass NK, Simpson MJ. (2022). A stochastic mathematical model of 4D tumour spheroids with real-time fluorescent cell cycle labelling. Journal of the Royal Society Interface doi:10.1098/rsif.2021.0903 [preprint – bioRxiv]
  12. Jolly MK, Murphy RJ, Bhatia S, Whitfield H, Redfern A, Davis MJ, Thompson EW. (2022). Measuring and modelling the epithelial mesenchymal hybrid state in cancer: clinical implications. Cells Tissues Organs. https://doi.org/10.1159/000515289 [preprint]
  13. Murphy RJ, Buenzli PR, Baker RE, Simpson MJ (2021). Travelling waves in a free boundary mechanobiological model of an epithelial tissue. Applied Mathematics Letters. https://doi.org/10.1016/j.aml.2020.106636
  14. Murphy RJ, Buenzli PR, Tambyah TA, Thompson EW, Hugo H, Baker RE, Simpson MJ. (2021). The role of mechanical interactions in EMT. Physical Biology. doi:10.1088/1478-3975/abf425 [preprint – bioRxiv]
  15. Browning AP, Sharp JA, Murphy RJ, Gunasingh G, Lawson B, Burrage K, Haass NK, Simpson MJ. (2021). Quantitative analysis of tumour spheroid structure. eLife doi:10.7554/eLife.73020 [preprint – bioRxiv]
  16. Reye G, Huang X, Haupt L, Murphy RJ, Northey JJ, Thompson EW, Momot K, Hugo H. (2021). Mechanical pressure driving proteoglycan expression in mammographic density: a self-perpetuating cycle? Journal of Mammary Gland Biology and Neoplasia. https://doi.org/10.1007/s10911-021-09494-3 [preprint]
  17. Murphy RJ, Buenzli PR, Baker RE, Simpson MJ (2020). Mechanical cell competition in heterogeneous epithelial tissues. Bulletin of Mathematical Biology. https://doi.org/10.1007/s11538-020-00807-x [preprint – bioRxiv]
  18. Tambyah T, Murphy RJ, Buenzli PR, Simpson MJ (2020). A free boundary mechanobiological model of epithelial tissues. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences. https://doi.org/10.1098/rspa.2020.0528 [preprint – bioRxiv]
  19. Murphy RJ, Buenzli PR, Baker RE, Simpson MJ (2019). A one-dimensional individual-based mechanical model of cell movement in heterogeneous tissues and its coarse-grained approximation. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences. https://doi.org/10.1098/rspa.2018.0838[preprint – bioRxiv]. This article was selected as cover image.

Book Chapters

  • Spoerri L, Beaumont KA, Anfosso A, Murphy RJ, Browning AP, Gunasingh G, Haass NK. (2024). Real-time cell cycle imaging in a 3D cell culture model of melanoma, quantitative analysis, optical clearing, and mathematical modelling. In: Sumbalova Koledova, Z. (eds) 3D Cell Culture. Methods in Molecular Biology, vol 2764. Humana, New York, NY. doi:10.1007/978-1-0716-3674-9_19

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