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Porter ML, Speiser DI, Zaharoff AK, Caldwell RL, Cronin TW, Oakley TH.  2013.  DATA FROM The evolution of complexity in the visual systems of stomatopods: insights from transcriptomics.
Porter ML, Speiser DI, Zaharoff AK, Caldwell RL, Cronin TW, Oakley TH.  2013.  The Evolution of Complexity in the Visual Systems of Stomatopods: Insights from Transcriptomics. Integrative and comparative biology. 53:39–49.
Plachetzki DC.  2009.  On the evolution of the animal phototransduction cascades. Ecology Evolution and Marine Biology. PhD:131. (2.56 MB)
Plachetzki DC, Oakley TH.  2007.  Key transitions during the evolution of animal phototransduction: novelty,“tree-thinking,” co-option, and co-duplication. Integrative and Comparative Biology. 47:759–769.
Plachetzki DC, Serb JM, Oakley TH.  2005.  New insights into the evolutionary history of photoreceptor cells. Trends in ecology & evolution. 20:465–467.
Plachetzki DC, Fong CR, Oakley TH.  2012.  Cnidocyte discharge is regulated by light and opsin-mediated phototransduction. BMC biology. 10:17.
Plachetzki DC, Degnan BM, Oakley TH.  2007.  The origins of novel protein interactions during animal opsin evolution. PLoS One. 2:e1054.
Plachetzki DC, Fong CR, Oakley TH.  2010.  The evolution of phototransduction from an ancestral cyclic nucleotide gated pathway. Proceedings of the Royal Society B: Biological Sciences. 277:1963.
Picciani N, Kerlin JR, Sierra N, Swafford AJM, M Ramirez D, Roberts NG, Cannon JT, Daly M, Oakley TH.  2018.  Prolific origination of eyes in Cnidaria with co-option of non-visual opsins. Current Biology. 28:2413–2419. (2.06 MB)
Phillips RB, Oakley TH, Davis EL.  1995.  Evidence supporting the paraphyly of Hucho (Salmonidae) based on ribosomal DNA restriction maps. Journal of fish biology. 47:956–961.
Phillips RB, Oakley TH, Kocher TD.  1997.  Phylogenetic relationships among the Salmoninae based on nuclear and mitochondrial DNA sequences.. Molecular systematics of fishes. Academic Press, London.
Peyer SM, M Pankey S, Oakley TH, McFall-Ngai MJ.  2014.  Eye-specification genes in the bacterial light organ of the bobtail squid Euprymna scolopes and their expression in response to symbiont cues. Mechanisms of development. 131:111-126. (3.54 MB)
Patek SN, Oakley TH.  2003.  Comparative tests of evolutionary trade-offs in a palinurid lobster acoustic system. Evolution. 57:2082–2100.
M. Pankey S, Minin VN, Imholte GC, Suchard MA, Oakley TH.  2014.  Predictable transcriptome evolution in the convergent and complex bioluminescent organs of squid. Proceedings of the National Academy of Sciences.