On State-Space Reduction in Multi-Strain Pathogen Models, with an Application to Antigenic Drift in Influenza A. - Sergey Kryazhimskiy; Ulf Dieckmann; Simon A. Levin; Jonathan Dushoff (PLoS Comput. Biol., 2007)

Unsupervised statistical clustering of environmental shotgun sequences. - Andrey Kislyuk; Srijak Bhatnagar; Jonathan Dushoff; Joshua S. Weitz (BMC Bioinform., 2009)

On the Accessibility of Adaptive Phenotypes of a Bacterial Metabolic Network. - Wilfred Ndifon; Joshua B. Plotkin; Jonathan Dushoff (PLoS Comput. Biol., 2009)

Incorporating Stochasticity in Simple Models of Disease Spread. - Jonathan Dushoff (Modeling Paradigms and Analysis of Disease Trasmission Models, 2010)

Finding Attractors on a Folding Energy Landscape. - Wilfred Ndifon; Jonathan Dushoff (Handbook of Research on Computational and Systems Biology, 2011)

Identifying enterotype in human microbiome by decomposing probabilistic topics into components. - Xingpeng Jiang; Jonathan Dushoff; Xin Chen 041; Xiaohua Hu 001 (BIBM, 2012)

Effects of mixing in threshold models of social behavior - Andrei R. Akhmetzhanov; Lee Worden; Jonathan Dushoff (CoRR, 2013)

Equivalence of the Erlang-Distributed SEIR Epidemic Model and the Renewal Equation. - David Champredon; Jonathan Dushoff; David J. D. Earn (SIAM J. Appl. Math., 2018)

Calibration of individual-based models to epidemiological data: A systematic review. - C. Marijn Hazelbag; Jonathan Dushoff; Emanuel M. Dominic; Zinhle E. Mthombothi; Wim Delva (PLoS Comput. Biol., 2020)

Best practices for estimating and reporting epidemiological delay distributions of infectious diseases. - Kelly Charniga; Sang Woo Park; Andrei R. Akhmetzhanov; Anne Cori; Jonathan Dushoff; Sebastian Funk; Katelyn M. Gostic; Natalie M. Linton; Adrian Lison; Christopher E. Overton; Juliet R. C. Pulliam; Thomas Ward; et al. (PLoS Comput. Biol., 2024)