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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.
Patek SN, Oakley TH.  2003.  Comparative tests of evolutionary trade-offs in a palinurid lobster acoustic system. Evolution. 57:2082–2100.
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)
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.
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)
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.
Plachetzki DC.  2009.  On the evolution of the animal phototransduction cascades. Ecology Evolution and Marine Biology. PhD:131. (2.56 MB)
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.