Levin, R. A., G. Bernardello,  C. Whiting'2010 and J. S. Miller. A new generic circumscription in tribe Lycieae (Solanaceae). Taxon 60:681-690.

Miller J. S. and J. L. Kostyun'2009. 2011. Functional self-incompatibility in a peripheral population of Solanum peruvianum (Solanaceae). Heredity 107:30-39.

Miller, JS, A Kamath'2011, J Damashek'2009, and RA Levin. 2011. Out of America to Africa or Asia: Inference of dispersal histories using nuclear and plastid DNA and the S-RNase self-incompatibility locus. Molecular Biology and Evolution 28:793–801

Stiefkens, L, M Las Peñas, G Bernardello, RA Levin, and JS Miller. 2010. Karyotypes and fluorescent chromosome banding patterns in southern African Lycium (Solanaceae). Caryologia, 63, 50-61. 

Temeles, E. J., J. S. Miller, and J. R. Rifkin '2009. 2010. Evolution of sexual dimorphism in bill size and shape of hermit hummingbirds (Phaethornithinae): A role for ecological causation? Philosophical Transactions of the Royal Society B: Biological Sciences. (Link to on-line article; pdf available on request)

Levin, R. A., A. P. Whelan'2008, and J. S. Miller. 2009. The characterization and utility of nuclear conserved ortholog set II (COSII) genomic regions for species-level phylogenetic inference. Molecular Phylogenetics and Evolution, 53, 881-890.

Miller, J. S., A. Kamath'2011, and R. A. Levin. 2009. Do multiple tortoises equal a hare? The utility of nine noncoding plastid regions for species-level phylogenetics in tribe Lycieae (Solanaceae). Systematic Botany, 34, 796-804.

Levin, R. A., J. M. Blanton'2006E, and J. S. Miller. 2009. Phylogenetic utility of nuclear NIA: A multi-locus comparison of nuclear and chloroplast sequence data for inference of relationships among American Lycieae (Solanaceae). Molecular Phylogenetics and Evolution, 50, 608-617.

Miller, J. S., R. A. Levin, and N. M. Feliciano'2008. 2008. A tale of two continents: Baker’s rule and the maintenance of self-incompatibility in Lycium (Solanaceae). Evolution, 62, 1052-1065.

Miller, J. S. and J. L. Stanton-Geddes'2004. 2007. Gynodioecy in Lobelia siphilitica and L. spicata (Lobeliaceae) from western Massachusetts. Journal of the Torrey Botanical Society, 134, 349-361.

Miller, J. S. and P. K. Diggle. 2007. Correlated evolution of fruit size and sexual expression in andromonoecious Solanum sections Acanthophora and Lasiocarpa (Solanaceae). American Journal of Botany, 94, 1706-1715.

Levin, R. A., G. Bernardello, A. M. Venter, J. R. Shak'2006, and J. S. Miller. 2007. Evolutionary relationships in tribe Lycieae (Solanaceae). Acta Horticulturae, 745, 225-239.

Savage, A. E.'2004 and J. S. Miller. 2006. Gametophytic self-incompatibility in Lycium parishii (Solanaceae): Allelic diversity, genealogical structure, and patterns of molecular evolution. Heredity, 96, 434-444.

Levin, R. A. and J. S. Miller. 2005. Relationships within tribe Lycieae (Solanaceae): paraphyly of Lycium and multiple origins of gender dimorphism. American Journal of Botany, 92, 2044-2053.

Yeung, K., J. S. Miller, A. E. Savage'2004, B. C. Husband, B. Igic, and J. R. Kohn. 2005. Association of ploidy and sexual system in Lycium californicum (Solanaceae). Evolution, 59, 2048-2055.

Diggle, P. K. and J. S. Miller.  2004. Architectural effects mimic floral sexual dimorphism in Solanum (Solanaceae). American Journal of Botany, 91, 2030-40.

Miller, J. S. and P. K. Diggle. 2003. Diversification of andromonoecy in Solanum section Lasiocarpa (Solanaceae): the roles of phenotypic plasticity and architecture. American Journal of Botany, 90, 707-715.

Miller, J. S. and D. L. Venable. 2003. Floral morphometrics and the evolution of sexual dimorphism in Lycium (Solanaceae). Evolution, 57, 74-86.

Miller, J. S. and D. L. Venable. 2002. The transition to gender dimorphism on an evolutionary background of self-incompatibility: an example from Lycium (Solanaceae). American Journal of Botany, 89, 1907-1915.

Miller, J. S. 2002. Phylogenetic relationships and the evolution of gender dimorphism in Lycium (Solanaceae). Systematic Botany, 27, 416-428.

Brunet, J., A. Liston, J. S. Miller, and D. L. Venable. 2001. Polyploidy and gender dimorphism. Science, 291, 1441a.

Miller, J. S. and D. L. Venable. 2000. Polyploidy and the evolution of gender dimorphism in plants. Science, 289, 2335-2338.

Miller, J. S., Kelso, S., Litvak, M., & A. Vargo. 1994. Comparative reproductive biology of two alpine species of primrose. Arctic and Alpine Research, 26, 297-303.