Publication and Teaching

Scientific Publications

Articles in preparation

1. Investigating parameter identifiability in state-dependent speciation-extinction models. Joint work with Muhammad Ardiyansyah and Michael Landis.

2. Investigating the effect of information loss on parameter estimation in phylogenetic diversification models. Joint work with Helen He and Michael Landis.

3. Outlier detection method for SSE models. Joint work with Michael Landis.

4. Visitor SIR model with multiple hosts. Joint work with Ammon Thompson, Anna Nagel, and Michael Landis.

Journal Article

1. Soewongsono, A. C., Thompson, A., Landis, M. J. (2026). Inferring epidemiological parameters under an infectious phylogeography model with visitor dynamics. Proceedings of the National Academy of Sciences, 123 (27), e2535042123 (https://doi.org/10.1073/pnas.2535042123) [GitHub][research showcase]

2. 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 

3. 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][research showcase]

4. 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.

5. 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.

6. 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

1. Soewongsono, A. C., & Lanids, M.J. (2026). On the mapping between evolutionary scenarios and governing rules in state-dependent speciation-extinction models. bioRxiv preprint https://doi.org/10.64898/2026.09.24.754193 (*under review in Journal of Mathematical Biology)

2. Soewongsono, A. C., & Landis, M. J. (2026). Phylogenetic estimation of diversity-dependent biogeographic rates using deep learning. bioRxiv preprint https://doi.org/10.64898/2026.02.17.706216 (*under minor revision in Systematic Biology)

3. Soewongsono, A. C., Thompson A., & Landis, M. J. (2025). Inferring epidemiological parameters under an infectious phylogeography model with visitor dynamics. medRxiv preprint (*accepted for publication in Proceedings of the National Academy of Sciences) https://doi.org/10.64898/2025.12.16.25342415

4. 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  

5. 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

6. 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 (*accepted for publication in Methodology and Computing in Applied Probability)

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

1. 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)

2. 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)

3. Soewongsono, A.C. (2015). Teorema berbasis aksioma separasi dalam ruang topologi. Honors Thesis, Nusa Cendana University (Supervised by Dr. Jafaruddin Hamid and Ariyanto)

Tutoring Experience

1. MATH1013: Mathematics and Applications 1, Mathematical Sciences Institute, ANU (Semester 1 & 2, 2018).

2. KMA153: Data Handling and Statistics, Mathematics, UTas (Semester 1 & 2, 2020; Semester 1 & 2, 2021; Semester 1 & 2, 2022).

3. KMA155: Computational Science and Discrete Mathematics 1 (Semester 2, 2020).

4. KME272: Engineering Mathematics 2B (Semester 2, 2020; Semester 2, 2021; Semester 2, 2022).

5. KMA252: Calculus and Applications 2 (Semester 1, 2021; Semester 1, 2022).

6. KMA154: Mathematics 1B (Semester 2, 2021; Semester 2, 2022).

Teaching Experience

1. Mathematical Biology, Mathematics, Nusa Cendana University (Contract, Semester 1 2019).

2. English for Specific Purposes, Mathematics, Nusa Cendana University (Contract, Semester 1 2019).