publications

Published

1. Am Nat

   Within-host viral growth and immune response rates predict FMDV transmission dynamics for African buffalo

   Joshua C. Macdonald, Hayriye Gulbudak, Brianna Beechler, and 4 more authors

   The American Naturalist, 2024

   DOI Bib HTML

   @article{macdonald2024fmdv,
     title = {Within-host viral growth and immune response rates predict {FMDV} transmission dynamics for {African} buffalo},
     author = {Macdonald, Joshua C. and Gulbudak, Hayriye and Beechler, Brianna and Gorsich, Erin and Gubbins, Simon and Perez, Eduardo and Jolles, Anna},
     journal = {The American Naturalist},
     year = {2024},
     doi = {10.1086/730703},
   }

2. EHS

   Cultural transmission, networks, and clusters among Austronesian-speaking peoples

   Joshua C. Macdonald, Javier Blanco-Portillo, Marcus W. Feldman, and 1 more author

   Evolutionary Human Sciences, 2024

   DOI Bib HTML

   @article{macdonald2024austronesian,
     title = {Cultural transmission, networks, and clusters among {Austronesian}-speaking peoples},
     author = {Macdonald, Joshua C. and Blanco-Portillo, Javier and Feldman, Marcus W. and Ram, Yoav},
     journal = {Evolutionary Human Sciences},
     volume = {6},
     pages = {e45},
     year = {2024},
     doi = {10.1017/ehs.2024.45},
   }

3. J Math Biol

   Forward hysteresis and Hopf bifurcation in an NPZD model with application to harmful algal blooms

   Joshua C. Macdonald and Hayriye Gulbudak

   Journal of Mathematical Biology, 2023

   DOI Bib HTML

   @article{macdonald2023npzd,
     title = {Forward hysteresis and {Hopf} bifurcation in an {NPZD} model with application to harmful algal blooms},
     author = {Macdonald, Joshua C. and Gulbudak, Hayriye},
     journal = {Journal of Mathematical Biology},
     volume = {87},
     pages = {45},
     year = {2023},
     doi = {10.1007/s00285-023-01969-7},
   }

4. J Theor Biol

   First and second wave outbreak size with reactive quarantine measures: a COVID-19 model applied to an epidemic in China

   Cameron J. Browne, Hayriye Gulbudak, and Joshua C. Macdonald

   Journal of Theoretical Biology, 2022

   DOI Bib HTML

   @article{browne2022covid,
     title = {First and second wave outbreak size with reactive quarantine measures: a {COVID-19} model applied to an epidemic in {China}},
     author = {Browne, Cameron J. and Gulbudak, Hayriye and Macdonald, Joshua C.},
     journal = {Journal of Theoretical Biology},
     volume = {538},
     pages = {110919},
     year = {2022},
     doi = {10.1016/j.jtbi.2021.110919},
   }

5. R Soc Open Sci

   Modeling COVID-19 outbreaks in the United States with distinct testing, lockdown speed, and fatigue rates

   Joshua C. Macdonald, Cameron J. Browne, and Hayriye Gulbudak

   Royal Society Open Science, 2021

   DOI Bib HTML

   @article{macdonald2021covid,
     title = {Modeling {COVID-19} outbreaks in the {United States} with distinct testing, lockdown speed, and fatigue rates},
     author = {Macdonald, Joshua C. and Browne, Cameron J. and Gulbudak, Hayriye},
     journal = {Royal Society Open Science},
     volume = {8},
     pages = {210227},
     year = {2021},
     doi = {10.1098/rsos.210227},
   }

Under Review

1. Bull Math Biol

   An immuno-epidemiological model of foot-and-mouth disease in African buffalo with carrier transmission

   Samuel Atkins, Hayriye Gulbudak, Sarah Welker, and 4 more authors

   Bulletin of Mathematical Biology, 2026

   Under review

   Bib

   @article{atkins2026fmdcarrier,
     title = {An immuno-epidemiological model of foot-and-mouth disease in {African} buffalo with carrier transmission},
     author = {Atkins, Samuel and Gulbudak, Hayriye and Welker, Sarah and Smith, Hayden and Macdonald, Joshua C. and Beechler, Brianna R. and Jolles, Anna E.},
     journal = {Bulletin of Mathematical Biology},
     year = {2026},
     note = {Under review}
   }

Preprints

1. arXiv

   Bayesian estimation of the number of significant principal components for cultural data

   Joshua C. Macdonald, Javier Blanco-Portillo, Marcus W. Feldman, and 1 more author

   2024

   DOI Bib HTML

   @article{macdonald2024vbpca,
     title = {{Bayesian} estimation of the number of significant principal components for cultural data},
     author = {Macdonald, Joshua C. and Blanco-Portillo, Javier and Feldman, Marcus W. and Ram, Yoav},
     year = {2024},
     archiveprefix = {arXiv},
     doi = {10.48550/arXiv.2409.12129},
   }

In Preparation

1. Lawful Learning: Embedding Physical Laws into Surrogate Representations for Robust Extrapolation

   Joshua C. Macdonald

   2026

   In preparation for \emphProceedings of the Royal Society A

   Bib

   @unpublished{macdonald2026lawful,
     title = {Lawful Learning: Embedding Physical Laws into Surrogate Representations for Robust Extrapolation},
     author = {Macdonald, Joshua C.},
     year = {2026},
     note = {In preparation for \emph{Proceedings of the Royal Society A}}
   }

2. Structured observables: recovering dynamical structure from parameter-indexed generators

   Joshua C. Macdonald

   2026

   In preparation for \emphSIAM Journal on Applied Dynamical Systems

   Bib

   @unpublished{macdonald2026structured,
     title = {Structured observables: recovering dynamical structure from parameter-indexed generators},
     author = {Macdonald, Joshua C.},
     year = {2026},
     note = {In preparation for \emph{SIAM Journal on Applied Dynamical Systems}}
   }

3. Shapelet analysis of infectious disease forecasts reveals heterogeneity across epidemic phases

   Kimberlyn Roosa, Lauren A. White, Tomás M. Leon, and 3 more authors

   2026

   In preparation for \emphEpidemics

   Bib

   @unpublished{roosa2026shapelet,
     title = {Shapelet analysis of infectious disease forecasts reveals heterogeneity across epidemic phases},
     author = {Roosa, Kimberlyn and White, Lauren A. and Leon, Tom\'{a}s M. and Macdonald, Joshua C. and Srivastava, Ajitesh and Truelove, Shaun},
     year = {2026},
     note = {In preparation for \emph{Epidemics}}
   }

4. Convergence characterization of coordinate-ascent variational inference for Bayesian PCA

   Joshua C. Macdonald and Yoav Ram

   2026

   In preparation

   Bib

   @unpublished{macdonald2026convergence,
     title = {Convergence characterization of coordinate-ascent variational inference for {Bayesian} {PCA}},
     author = {Macdonald, Joshua C. and Ram, Yoav},
     year = {2026},
     note = {In preparation}
   }

5. Posterior predictive eigenvalue testing for spectral dimensionality selection

   Joshua C. Macdonald, Shany Naim, and Yoav Ram

   2026

   In preparation for \emphBioinformatics or \emphPLOS Computational Biology

   Bib

   @unpublished{macdonald2026eigentest,
     title = {Posterior predictive eigenvalue testing for spectral dimensionality selection},
     author = {Macdonald, Joshua C. and Naim, Shany and Ram, Yoav},
     year = {2026},
     note = {In preparation for \emph{Bioinformatics} or \emph{PLOS Computational Biology}}
   }