Publications

Found 26 results
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Oakley TH.  1996.  Duplicated growth hormone genes from a tetraploid family of fishes: DNA sequence evolution and implications for salmonid systematics.
Oakley TH.  2019.  Evolving witnesses of changing environments: An introduction to the 18th International Symposium on Ostracoda. Journal of Crustacean Biology. 39:199–201.
Oakley T.  2018.  Eyes to See: The Astonishing Variety of Vision in Nature. Nature. 563:182–183.
Oakley TH.  2017.  Furcation and fusion: The phylogenetics of evolutionary novelty. Developmental Biology. 431:69-76.
Oakley TH, Speiser DI.  2015.  How Complexity Originates: The Evolution of Animal Eyes. Annual Review of Ecology, Evolution, and Systematics. 46 (351.15 KB)
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.
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.
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)
Oakley TH.  2009.  A Critique of Experimental Phylogenetics.
Oakley TH.  2008.  Jay Hosler, An Evolutionary Novelty: Optical Allusions. Evolution: Education and Outreach. 1:548–551. (212.35 KB)
Oakley TH.  2001.  Phylogenetic reconstruction of ancestral character states.
Oakley TH.  2007.  A review of Gene Sharing and Evolution: The Diversity of Protein Functions, by Joram Piatigorsky. Evolution & Development. 9:514–516.
Oakley TH.  2007.  Today's multiple choice exam:(a) gene duplication;(b) structural mutation;(c) co-option;(d) regulatory mutation;(e) all of the above. Evolution & Development. 9:523–524.
Oakley TH, Cunningham CW.  2000.  Independent contrasts succeed where ancestor reconstruction fails in a known bacteriophage phylogeny. Evolution. 54:397–405.
Oakley TH, Rivera AS.  2008.  Genomics and the evolutionary origins of nervous system complexity. Current opinion in genetics & development. 18:479–492.
Oakley TH, M Pankey S.  2008.  Opening the “black box”: the genetic and biochemical basis of eye evolution. Evolution: Education and Outreach. 1:390–402. (342.38 KB)
Oakley TH.  2005.  Myodocopa (Crustacea: Ostracoda) as models for evolutionary studies of light and vision: multiple origins of bioluminescence and extreme sexual dimorphism. Hydrobiologia. 538:179–192.
Oakley TH, Plachetzki DC, Rivera AS.  2007.  Furcation, field-splitting, and the evolutionary origins of novelty in arthropod photoreceptors. Arthropod structure & development. 36:386–400.
Oakley TH, Huber DR.  2004.  Differential expression of duplicated opsin genes in two eyetypes of ostracod crustaceans. Journal of molecular evolution. 59:239–249.
Oakley TH, Østman B, Wilson ACV.  2006.  Repression and loss of gene expression outpaces activation and gain in recently duplicated fly genes. Proceedings of the National Academy of Sciences. 103:11637.
Oakley TH.  2003.  Maximum likelihood models of trait evolution. Comments on Theoretical Biology. 8:609–625.
Oakley TH.  2003.  The eye as a replicating and diverging, modular developmental unit. TRENDS in Ecology and Evolution. 18:623–627.
Oakley TH.  2003.  On homology of arthropod compound eyes. Integrative and comparative biology. 43:522–530.
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.
Oakley TH, Cunningham CW.  2002.  Molecular phylogenetic evidence for the independent evolutionary origin of an arthropod compound eye. Proceedings of the National Academy of Sciences. 99:1426.

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