Thulin, C.-G., J. Stone, H. Tegelström, and C. W. Walker. 2006. Species assignment and hybrid identification among Scandinavian hares. Wildlife Biology 12:29-38.
Stone, J. and M. Telford. 2005. Fractal dimensions characterizing mammalian teeth. Mammal Review 35:123-128.
Stone, Jon R. and Brian K. Hall. 2004. Latent homologues for the neural crest as an evolutionary novelty. Evolution & Development 6:123-129.
Stone, J. R. 2003. Pectinate and symmetric cladogram probabilities. Cladistics 19:565-566.
Spong, G., J. Stone, S. Creel, and M. Björklund. 2002. Genetic structure of lions ( Panthera leo L.) in the Selous Game Reserve: implications for the evolution of sociality. Journal of Evolutionary Biology 15:945-953.
Stone, Jonathon R. and Gregory A. Wray. 2001. Rapid evolution of cis-regulatory sequences via local point mutations. Molecular Biology and Evolution 18:1764-1770.
Shorey, Lisa, Stuart Piertney, Jon Stone, and Jacob Högland. 2000. Fine-scale genetic structuring on Manacus leks. nature 408:352-353.