Publications

Found 21 results
Author Title Type [ Year(Asc)]
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2021
Lau ES, Oakley TH.  2021.  Multi-level convergence of complex traits and the evolution of bioluminescence. Biological Reviews. 96:673–691.
Hensley NM, Ellis EA, Leung NY, Coupart J, Mikhailovsky A, Taketa DA, Tessler M, Gruber DF, De Tomaso AW, Mitani Y et al..  2021.  Selection, drift, and constraint in cypridinid luciferases and the diversification of bioluminescent signals in sea fireflies. Molecular Ecology. 30:1864–1879.
2018
Jackrel SL, Narwani A, Bentlage B, Levine RB, Hietala DC, Savage PE, Oakley TH, Denef VJ, Cardinale BJ.  2018.  Ecological engineering helps maximize function in algal oil production. Applied and environmental microbiology. :AEM–00953.
2014
Bielecki J, Zaharoff AK, Leung NY, Garm A, Oakley TH.  2014.  Ocular and Extraocular Expression of Opsins in the Rhopalium of Tripedalia cystophora (Cnidaria: Cubozoa)). Plos One. 9(6)
Oakley T, Alexandrou M, Ngo R, Pankey M, Churchill C, Chen W, Lopker K.  2014.  Osiris: accessible and reproducible phylogenetic and phylogenomic analyses within the Galaxy workflow management system. BMC Bioinformatics. 15:230.
Speiser DI, M Pankey S, Zaharoff AK, Battelle BA, Bracken-Grissom HD, Breinholt JW, Bybee SM, Cronin TW, Garm A, Lindgren AR et al..  2014.  Using phylogenetically-informed annotation (PIA) to search for light-interacting genes in transcriptomes from non-model organisms. BMC bioinformatics. 15:350.
2013
Speiser DI, Lampe RI, Lovdahl VR, Carrillo-Zazueta B, Rivera AS, Oakley TH.  2013.  DATA FROM: Evasion of predators contributes to the maintenance of male eyes in sexually dimorphic Euphilomedes ostracods (Crustacea).
Speiser DI, Lampe RI, Lovdahl VR, Carrillo-Zazueta B, Rivera AS, Oakley TH.  2013.  DATA FROM: Evasion of predators contributes to the maintenance of male eyes in sexually dimorphic Euphilomedes ostracods (Crustacea).
Oakley TH, Wolfe JM, Lindgren AR, Zaharoff AK.  2013.  DATA FROM: Phylotranscriptomics to bring the understudied into the fold: monophyletic Ostracoda, fossil placement and pancrustacean phylogeny.
Speiser DI, Lampe RI, Lovdahl VR, Carrillo-Zazueta B, Rivera AS, Oakley TH.  2013.  Evasion of Predators Contributes to the Maintenance of Male Eyes in Sexually Dimorphic Euphilomedes ostracods (Crustacea). Integrative and comparative biology. 53:78–88. (254.54 KB)
Speiser DI, Lampe RI, Lovdahl VR, Carrillo-Zazueta B, Rivera AS, Oakley TH.  2013.  Evasion of Predators Contributes to the Maintenance of Male Eyes in Sexually Dimorphic Euphilomedes ostracods (Crustacea). Integrative and comparative biology. 53:78–88. (254.54 KB)
Oakley TH, Wolfe JM, Lindgren AR, Zaharoff AK.  2013.  Phylotranscriptomics to Bring the Understudied into the Fold: Monophyletic Ostracoda, Fossil Placement, and Pancrustacean Phylogeny. Molecular biology and evolution. 30:215–233. (1.19 MB)
2012
Lindgren A, Pankey M, Hochberg F, Oakley T.  2012.  A multi-gene phylogeny of Cephalopoda supports convergent morphological evolution in association with multiple habitat shifts in the marine environment. BMC Evolutionary Biology. 12:129.
2011
Lampe RI.  2011.  Support for the dimorphic niche hypothesis: Natural selection drives sexual eye dimorphism in ostracods. Ecology Evolution and Marine Biology. MA:42. (625.01 KB)
2008
Lum KE, Syme AE, Schwab AK, Oakley TH.  2008.  Euphilomedes chupacabra (Ostracoda: Myodocopida: Philomedidae), a new demersal marine species from coastal Puerto Rico with male-biased vespertine swimming activity. Zootaxa. 1684:35–57. (954.14 KB)
Larusso ND, Ruttenberg BE, Singh AK, Oakley TH.  2008.  Type II opsins: evolutionary origin by internal domain duplication? Journal of molecular evolution. 66:417–423. (321.78 KB)
2006
Lee C, Blay S, Mooers AØ, Singh A, Oakley TH.  2006.  CoMET: A Mesquite package for comparing models of continuous character evolution on phylogenies. Evolutionary Bioinformatics Online. 2:183.
2005
Oakley TH, Gu Z, Abouheif E, Patel NH, Li W-H.  2005.  Comparative methods for the analysis of gene-expression evolution: an example using yeast functional genomic data. Molecular biology and evolution. 22:40–50.
Lee C.  2005.  Testing Trait Evolution Models on Phylogenetic Trees. Computer Science. MS:34. (834.6 KB)
2004
Wang D, Oakley T, Mower J, Shimmin LC, Yim S, Honeycutt RL, Tsao H, Li W-H.  2004.  Molecular evolution of bat color vision genes. Molecular biology and evolution. 21:295–302.
1996
Setterquist RA, G Smith K, Oakley TH, Lee Y-H, Fox GE.  1996.  Sequence, overproduction and purification of Vibrio proteolyticus ribosomal protein L 18 for in vitro and in vivo studies. Gene. 183:237–242.