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Heimberg, A.M, Sempere, L.F., Moy, V.N., Donoghue, P.C.J. and Peterson, K.J. (2008) MicroRNAs and the advent of vertebrate morphological complexity. Proceedings of the National Academy of Sciences 105: 2946-2750.

Peterson, K.J., Cotton, J.A., Gehling, J.G. and Pisani, D. The Ediacaran emergence of bilaterians: congruence between the genetic and the geological fossil records. Philosophical Transactions of the Royal Society B: doi:10.1098/rstb.2007.2233

Peterson, K.J. and Sperling, E.A. (2007). Poriferan ANTP genes - primitively simple or secondarily reduced? Evolution & Development 9:405-408.

Sempere, L.F., Martinez, P., Cole, C., Baguna, J., & Peterson, K.J. (2007). Phylogenetic distribution of microRNAs supports the basal position of acoels and the polyphyly of Platyhelminthes. Evolution & Development 9:409-415.

Peterson, K.J., Summons, R. S., and Donoghue, P. C. J. (2007) Molecular Palaeobiology. Palaeontology, 50:775-809.

Dunn, E.F, Moy, V.N., Angerer, L.M., Angerer, R.C., Morris,R.L.
and K. J. Peterson (2007). Molecular paleoecology: using gene regulatory analysis to address the origins of complex life cycles in the late Precambrian. Evolution & Development 9:1, 10–24

Bottjer, D.J., Davidson, E.H., Peterson, K. J. and Cameron, R. A. (2006). Paleogenomics of Echinoderms. Science, 314: 956-959

Sperling, E.A., Pisani, D. and Peterson, K.J. Poriferan paraphyly and its implications for Precambrian paleobiology. Journal of Geological Society of London Special Publications 286:355-368.

Sempere, L.F., Cole, C.N., McPeek, M.A., and Peterson, K.J. (2006). The Phylogenetic Distribution of Metazoan microRNAs: Insights into Evolutionary Complexity and Constraint. Journal of Experimental Zoology (MOL DEV EVOL) 306B

Peterson, K.J. and Butterfield, N.J. (2005). Origin of the Eumetazoa: testing ecological predictions of molecular clocks against he Proterozoic fossil record. Proceedings of the National Academy of Sciences 102: 9547-9552.

Peterson, K.J. (2005).  Macroevolutionary interplay between planktic larvae and benthic predators.  Geology, 33(12):  929-932

Peterson, K.J., McPeek, M.A., and Evan, D.A.D. (2005). Tempo and mode of early animal evolution: inferences from rocks, Hox, and molecular clocks. Paleobiology, 31 (2, supp.): 36-55.

Peterson, K.J. (2004).  Isolation  of Hox and Parahox genes in the hemichordate Ptychodera flava: Insights into the Evolution of Deuterostome Hox genesMolecular Phylogenetics and Evolution, 31: 1208-1215.

Takacs, C.M., Amore, G., Oliveri, P., Poustka, A.J., Wang, D., Burke, R.B., and Peterson, K.J. (2004). Expression of an NK2 homeodomain gene in the apical ectoderm defines a new territory in the early sea urchin embryoDevelopmental Biology, 269: 152-164.

Peterson, K.J., Lyons, J.B., Nowak, K.S., Takacs, C.M., Wargo, M.T., and McPeek, M.A. (2004). Estimating metazoan divergence times with a molecular clock. Proceedings of the National Academy of Sciences, USA, 101: 6536-6541.

Peterson, K.J., Waggoner, B., and Hagadorn, J.W. (2003). A Fungal Analog for Newfoundland Ediacaran Fossils? Intreg. Comp. Biol. 43: 127-136.