Tam, P.P.C., Barrette-Ng, I. H., Simon, D. M., Tam, M. W. C., Ang, A. L., and Muench, D. G. 2010. The Puf family of RNA-binding proteins in plants: phylogeny, structural modeling, activity and subcellular localization. BMC Plant Biology 10:44.
Simon, D. M., Kelchner, S. A., and Zimmerly, S. 2009. A broadscale phylogenetic analysis of group II intron RNAs and intron-encoded reverse transcriptases. Molecular Biology and Evolution 26(12):2795-2808.
Simon, D. M., and Zimmerly, S. 2008. A diversity of uncharacterized reverse transcriptases in bacteria. Nucleic Acids Research 36(22):7219–7229.
Simon, D. M., Clarke, N. A. C., McNeil, B. A., Johnson, I., Pantuso, D., Dai, L., Chai, D., and Zimmerly, S. 2008. Group II introns in Eubacteria and Archaea: ORF-Iess introns and new varieties. RNA 14:1704-1713.
Hausner G., Olson, R., Simon, D. M., Johnson, I., Sanders, E. R., Karol, K. G., McCourt, R. M., and Zimmerly, S. 2006. Origin and evolution of the chloroplast trnK (matK) intron: a model for evolution of group II intron RNA structures. Molecular Biology and Evolution 23:380-391.
Bhattacharya, D., Reeb, V., Simon, D. M., and François Lutzoni, F. 2005. Phylogenetic analyses suggest reverse splicing spread of group I introns in fungal ribosomal DNA. BMC Evolutionary Biology 5:68. (11 pp)
Haugen, P., Simon, D. M., & Bhattacharya, D. 2005. The natural history of group I introns. Trends in Genetics 21(2):111-119.
Simon, D. M., Moline, J., Helms, G., Friedl, T., and Bhattacharya, D. 2005. Divergent histories of rDNA group I introns in the lichen family Physciaceae. Journal of Molecular Evolution 60:434-446.
Simon, D. M., Hummel, C. L., Sheeley, S. L., & Bhattacharya, D. 2005. Heterogeneity of intron presence or absence in rDNA genes of the lichen species Physcia aipolia and P. stellaris. Current Genetics 47(6):389-399.
Bhattacharya, D., Simon, D. M., Huang, J., Cannone, J. J., & Gutell, R. R. 2003. The exon context and distribution of Euascomycetes rRNA introns. BMC Evolutionary Biology 3:7.
Simon, D. M., Fewer, D., Friedl, T., & Bhattacharya, D. 2003. Phylogeny and self-splicing ability of the plastid tRNA-Leu group I intron. Journal of Molecular Evolution 57:710–720.
Dollhopf, M. E., Nealson K. H., Simon, D. M., and Luther, G.W., III. 2000. Kinetics of Fe(III) and Mn(IV) reduction by the Black Sea strain of Shewanella putrefaciens using in situ solid state voltammetric Au/Hg electrodes. Marine Chemistry 70:171-180.
Bhattacharya, D., Lutzoni, F., Reeb, V., Simon, D. M., & Fernandez, F. 2000. Widespread occurrence of spliceosomal introns in the rDNA genes of ascomycetes. Molecular Biology and Evolution 17:1971–1984.