Dwyer, Greg, Jonathan Dushoff, Joseph Elkinton, and Simon Levin. (2000) 2000. “Pathogen-Driven Outbreaks in Forest Defoliators Revisited: Building Models from Experimental Data.”. The American Naturalist 156 (2): 105-20. doi:10.1086/303379.

Levin, Simon, Jonathan Dushoff, and Joshua Plotkin. (2004) 2004. “Evolution and Persistence of Influenza A and Other Diseases.”. Mathematical Biosciences 188: 17-28.

Smith, David, Jonathan Dushoff, Eli Perencevich, Anthony Harris, and Simon Levin. (2004) 2004. “Persistent Colonization and the Spread of Antibiotic Resistance in Nosocomial Pathogens: Resistance Is a Regional Problem.”. Proceedings of the National Academy of Sciences of the United States of America 101 (10): 3709-14.

Kryazhimskiy, Sergey, Ulf Dieckmann, Simon Levin, and Jonathan Dushoff. (2007) 2007. “On State-Space Reduction in Multi-Strain Pathogen Models, With an Application to Antigenic Drift in Influenza A.”. PLoS Computational Biology 3 (8): e159.

Ndifon, Wilfred, Jonathan Dushoff, and Simon Levin. (2009) 2009. “On the Use of Hemagglutination-Inhibition for Influenza Surveillance: Surveillance Data Are Predictive of Influenza Vaccine Effectiveness.”. Vaccine 27 (18): 2447-52. doi:10.1016/j.vaccine.2009.02.047.

Plotkin, Joshua, Jonathan Dushoff, and Simon Levin. (2002) 2002. “Hemagglutinin Sequence Clusters and the Antigenic Evolution of Influenza A Virus.”. Proceedings of the National Academy of Sciences of the United States of America 99 (9): 6263-8.

Dushoff, Jonathan, Lee Worden, Juan Keymer, and Simon Levin. (2002) 2002. “Metapopulations, Community Assembly, and Scale Invariance in Aspect Space.”. Theoretical Population Biology 62 (4): 329-38.

Jiang, Xingpeng, Morgan Langille, Russell Neches, Marie Elliot, Simon Levin, Jonathan Eisen, Joshua Weitz, and Jonathan Dushoff. (2012) 2012. “Functional Biogeography of Ocean Microbes Revealed through Non-Negative Matrix Factorization.”. PloS One 7 (9): e43866. doi:10.1371/journal.pone.0043866.

Bazykin, Georgii, Jonathan Dushoff, Simon Levin, and Alexey Kondrashov. (2006) 2006. “Bursts of Nonsynonymous Substitutions in HIV-1 Evolution Reveal Instances of Positive Selection at Conservative Protein Sites.”. Proceedings of the National Academy of Sciences of the United States of America 103 (51): 19396-401.

Dushoff, Jonathan, Joshua Plotkin, Simon Levin, and David Earn. (2004) 2004. “Dynamical Resonance Can Account for Seasonality of Influenza Epidemics.”. Proceedings of the National Academy of Sciences of the United States of America 101 (48): 16915-6.

Lichstein, Jeremy, Jonathan Dushoff, Simon Levin, and Stephen Pacala. (2007) 2007. “Intraspecific Variation and Species Coexistence.”. The American Naturalist 170 (6): 807-18. doi:10.1086/522937.

Pulliam, Juliet, Jonathan Dushoff, Simon Levin, and Andrew Dobson. (2007) 2007. “Epidemic Enhancement in Partially Immune Populations.”. PloS One 2 (1): e165.