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},
   }

6. 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

   To appear

   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 = {To appear}
   }

Under Review

1. Am J Epidemiol

   Multi-Model Insights into Racial and Ethnic Heterogeneities in Early COVID-19 Transmission and Severity in the U.S.

   Samantha J. Bents, Spencer L. Larsen, Sicheol Jung, and 3 more authors

   American Journal of Epidemiology, 2026

   In revision

   Bib

   @article{bents2026heterogeneities,
     title = {Multi-Model Insights into Racial and Ethnic Heterogeneities in Early {COVID-19} Transmission and Severity in the {U.S.}},
     author = {Bents, Samantha J. and Larsen, Spencer L. and Jung, Sicheol and Howerton, Emily and Macdonald, Joshua C. and others},
     journal = {American Journal of Epidemiology},
     year = {2026},
     note = {In revision}
   }

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. 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}}
   }

2. 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}}
   }

3. What Should Structural Evaluation Mean?: Label-Free Structural Evaluation Scores for Scientific Prediction

   Joshua C. Macdonald, M. Marshall, and Shaun Truelove

   2026

   In preparation for \emphStatistical Science

   Bib

   @unpublished{macdonald2026structeval,
     title = {What Should Structural Evaluation Mean?: Label-Free Structural Evaluation Scores for Scientific Prediction},
     author = {Macdonald, Joshua C. and Marshall, M. and Truelove, Shaun},
     year = {2026},
     note = {In preparation for \emph{Statistical Science}}
   }

4. Decision Support Modeling for One Health Pathogens: Crimean-Congo Hemorrhagic Fever Surveillance and Control Design

   Joshua C. Macdonald, M. Kugler, Brianna Beechler, and 1 more author

   2026

   In preparation for \emphRoyal Society Interface

   Bib

   @unpublished{macdonald2026cchf,
     title = {Decision Support Modeling for One Health Pathogens: {Crimean-Congo} Hemorrhagic Fever Surveillance and Control Design},
     author = {Macdonald, Joshua C. and Kugler, M. and Beechler, Brianna and Jolles, Anna},
     year = {2026},
     note = {In preparation for \emph{Royal Society Interface}}
   }