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2009
Crow KD, Amemiya CT, Roth J, Wagner GP.  2009.  Hypermutability of HoxA13A and functional divergence from its paralog are associated with the origin of a novel developmental feature in zebrafish and related taxa (Cypriniformes). Evolution. 63(6):1574-1592.
Leaché AD.  2009.  Species tree discordance traces to phylogeographic clade boundaries in North American fence lizards (Sceloporus).. Systematic biology. 58(6):547-59.
2008
Amemiya CT, Prohaska SJ, Hill-Force A, Cook A, Wasserscheid J, Ferrier DE, Pascual-Anaya J, Garcia-Fernandez J, Dewar K, Stadler PF.  2008.  The amphioxus Hox cluster: characterization, comparative genomics, and evolution. J Exp Zool B Mol Dev Evol. 310(5):465-477.
2004
Noonan JP, Grimwood J, Danke J, Schmutz J, Dickson M, Amemiya CT, Myers RM.  2004.  Coelacanth genome sequence reveals the evolutionary history of vertebrate genes. Genome Res. 14(12):2397-2405.