Articles in preparation
Exploring relationships between rates and patterns generated under state-dependent speciation and extinction models. Joint work with Michael Landis
Inferring epidemiological rate parameters under an SIR model with visitors. Joint work with Ammon Thompson and Michael Landis
Inferring rates under density-dependent GeoSSE with geographic overlap using deep learning approach. Joint work with Michael Landis and Ammon Thompson
Stochastic environmentally-driven model for the evolution of species. Joint work with Barbara Holland and Małgorzata O'Reilly
Journal Article
Soewongsono, A. C., Diao, J., Stark, T., Wilson, A. E., Holland, D. A., & O'Reilly, M. M. (2025). Matrix-analytic methods for the evolution of species trees, gene trees, and their reconciliation. Methodology and Computing in Applied Probability, 27(9). https://doi.org/10.1007/s11009-025-10135-z
Soewongsono, A.C., Landis, M.J. (2024). A diffusion-based approach for simulating forward-in-time state-dependent speciation and extinction dynamics. Bulletin of Mathematical Biology, 86, 101. https://doi.org/10.1007/s11538-024-01337-6
[code]
Soewongsono, A. C., Holland, B. R., & O’Reilly, M. M. (2022). The shape of phylogenies under phase-type distributed times to speciation and extinction. Bulletin of Mathematical Biology, 84(10), 118. https://doi.org/10.1007/s11538-022-01072-w.
Burden, C. J., & Soewongsono, A. C. (2019). Coalescence in the diffusion limit of a Bienaymé–Galton–Watson branching process. Theoretical Population Biology, 130, 50-59. https://doi.org/10.1016/j.tpb.2019.09.009.
Soewongsono, A. C., & Ariyanto, J. (2015). Teorema berbasis aksioma separasi dalam ruang topologi. Jurnal Matematika Integratif ISSN, 1412, 6184. https://doi.org/10.24198/jmi.v11.n2.9420.85-96.
Preprint
Soewongsono, A. C., & Landis, M. J. (2024). A diffusion-based approach for simulating forward-in-time state-dependent speciation and extinction dynamics. arXiv preprint arXiv:2402.00246 (*accepted for publication in Bulletin of Mathematical Biology) https://doi.org/10.48550/arXiv.2402.00246
Soewongsono, A.C., Holland, B.R., & O'Reilly, M. M. (2023). Stochastic niche-based models for the evolution of species, arXiv preprint arXiv:2309.02788v1 https://doi.org/10.48550/arXiv.2309.02788
Soewongsono, A. C., Diao, J., Stark, T., Wilson, A. E., Holland, D. A., & O'Reilly, M. M. (2023). Matrix-analytic methods for the evolution of species trees, gene trees, and their reconciliation. arXiv preprint arXiv:2309.06447 https://doi.org/10.48550/arXiv.2309.06447
Conference paper
Soewongsono, A. C., Holland, B. R., & O'Reilly, M. M. (2022). Stochastic niche-based models for the evolution of species. In MAM11 2022 (pp. 1-4).
Thesis
Soewongsono, A.C. (2023). Mathematical models for the evolution of species. PhD Thesis, University of Tasmania (Supervised by Prof. Barbara Holland and Assoc. Prof. Malgorzata O'Reilly) (e-access)
Soewongsono, A.C. (2018). The most recent common ancestor of a randomly chosen sample in a Galton-Watson process. Masters Thesis, Australian National University (Supervised by Assoc. Prof. Conrad J. Burden) (e-access)
Soewongsono, A.C. (2015). Teorema berbasis aksioma separasi dalam ruang topologi. Honors Thesis, Nusa Cendana University (Supervised by Dr. Jafaruddin Hamid and Ariyanto)
MATH1013: Mathematics and Applications 1, Mathematical Sciences Institute, ANU (Semester 1 & 2, 2018).
KMA153: Data Handling and Statistics, Mathematics, UTas (Semester 1 & 2, 2020; Semester 1 & 2, 2021; Semester 1 & 2, 2022).
KMA155: Computational Science and Discrete Mathematics 1 (Semester 2, 2020).
KME272: Engineering Mathematics 2B (Semester 2, 2020; Semester 2, 2021; Semester 2, 2022).
KMA252: Calculus and Applications 2 (Semester 1, 2021; Semester 1, 2022).
KMA154: Mathematics 1B (Semester 2, 2021; Semester 2, 2022).
Mathematical Biology, Mathematics, Nusa Cendana University (Contract, Semester 1 2019).
English for Specific Purposes, Mathematics, Nusa Cendana University (Contract, Semester 1 2019).