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Dr. Todd Castoe - Publications

(See personal or lab websites for updates and PDFs)

Lamers, R.P., G. Muthukrishnan, T.A. Castoe, S. Tafur, A.M. Cole, and C.L. Parkinson. In Press. Phylogenetic relationships among Staphylococcus species inferred from multilocus data. BMC Evolutionary Biology.

de Koning, A.P.J., Gu, W., T.A. Castoe, and D.D. Pollock. In Press. Phylogenetics, Likelihood, Evolution and Complexity (PLEX). Bioinformatics.

Castoe, T.A., E.L. Braun, A.M. Bronikowski, C.L. Cox, A.R. Davis, A.P.J. de Koning, J. Dobry, M. Fujita, M. Giorgianni, A. Hargreaves, C. Henkel, S.P. Mackessy, D. O'Meally, D. Rokyta, S.M. Secor, J. Streicher, K. Wray, K.D. Yokoyama, and D.D. Pollock. In Press. Meeting report from the first snake genomics and integrative biology meeting. Standards in Genomic Sciences.

Castoe, T.A., J.W. Streicher, J.M. Meik, M.J. Ingrasci, A.W. Poole, A.P.J. de Koning, J.A. Campbell, C.L. Parkinson, E.N. Smith, and D.D. Pollock. In Press. Thousands of microsatellite loci from the venomous coralsnake (Micrurus fulvius) and variability of select loci across populations and related species. Molecular Ecology Resources x:x-x.

Castoe, T.A., A.W. Poole, A.P.J. de Koning, K.L. Jones, D.F. Tomback, S.J. Oyler-McCance, J. Fike, S.L. Lance, J.W. Streicher, E.N. Smith, D.D. Pollock. 2012. Rapid microsatellite identification from Illumina paired-end genomic sequencing in two birds and a snake. PLoS ONE 7:e30953.

St. John, J., …, T.A. Castoe, [47 total authors], ...,  D.A. Ray. 2012. Sequencing three crocodilian genomes to illuminate the evolution of archosaurs and amniotes. Genome Biology 13:415. -Editor's Pick  -Highly Accessed  

Nakayama, M., T.A. Castoe, T. Sosinowski, X.L. He, K. Johnson, K. Haskins, D.A. Vignali, L. Gapin, D.D. Pollock, G.S. Eisenbarth. 2012. Germline TRAV5D-4 T cell receptor sequence targets a primary insulin peptide of NOD mice. Diabetes 61:857-865.

Sun, C., D.B. Shepard, R.A. Chong, J. Lopez-Arriaza, K.T. Hall, T.A. Castoe, C. Feschotte, D.D. Pollock, R.L. Mueller. 2012. LTR retrotransposons contribute to genomic gigantism in plethodontid salamanders. Genome Biology and Evolution 4:168-183.

Wang, B., R. Ekblom, T.A. Castoe, E.P. Jones, R. Kozma, E. Bongcam-Rudloff, D.D. Pollock, and J. Höglund. 2012. Transcriptome sequencing of black grouse (Tetrao tetrix) for immune gene discovery and microsatellite development. Open Biology 2:120054.

Jaden, R.C., J.H. Townsend, T.A. Castoe, and J.A. Campbell. 2012. Cryptic diversity in disjunct populations of Middle American Montane Pitvipers: a systematic reassessment of Cerrophidion godmani. Zoologica Scripta x:xx-xx (DOI:10.1111/j. 1463-6409.2012.00547.x).

de Koning, A.P.J., Gu, W., T.A. Castoe, and D.D. Pollock. 2011. Repetitive elements may comprise over two-thirds of the human genome. PLoS Genetics 7:e1002384. -Highly Accessed   -Featured Research Highlight in Nature Reviews Genetics

Castoe, T.A., A.P.J. de Koning, K. Hall, K.D. Yokoyama, W. Gu, E.N. Smith, C. Feschotte, P. Uetz, D.A. Ray, J. Dobry, R. Bogden, S.P. Mackessy, A.M. Bronikowski, W.C. Warren, S. Secor, and D.D. Pollock. 2011. Sequencing the genome of the Burmese python (Python molurus bivittatus) - a model for studying extreme adaptations in snakes. Genome Biology 12: 406.  -Highly Accessed

Alföldi J., ..., T.A. Castoe, [48 total authors]..., Lindblad-Toh. 2011. The genome of Anolis carolinensis, the green anole lizard, and a comparative analysis with birds and mammals. Nature 477: 587-591.

Castoe, T.A., K. Hall, M.L. Guibotsy Mboulas, W. Gu, A.P.J. de Koning, A.W. Poole, V. Vemulapalli, J.M. Daza, C. Feschotte, and D.D. Pollock. 2011. Discovery of highly divergent repeat landscapes in snake genomes using high throughput sequencing. Genome Biology and Evolution 3: 641-653.

Pollock, D.D., A.P.J. de Koning, H. Kim, T.A. Castoe, M. Churchill, and K.J. Kechris. 2011. Bayesian analysis of high-throughput quantitative measurement of protein-DNA interactions. PLoS ONE 6:e26105.

Castoe, T.A., S.E. Fox, A.P.J. de Koning, A.W. Poole, J. M. Daza, E.N. Smith, T. Mockler, S. Secor, and D.D. Pollock. 2011. A multi-organ transcriptome resource for the Burmese python (Python molurus bivittatus). BMC Research Notes 4: 310.

Castoe, T.A., A.M. Bronikowski, E.D. Brodie III, S.V. Edwards, M.E. Pfrender, M.D. Shipiro, D.D. Pollock, W.C. Warren. 2011. A proposal to sequence the genome of a garter snake. Standards in Genomic Sciences4: 257-270.

Castoe, T.A., A.P.J. de Koning, and D.D. Pollock. 2010. Adaptive molecular convergence – molecular evolution versus molecular phylogenetics. Communicative and Integrative Biology3: 67-69.

Harris, J.K., J.W. Sahl, T.A. Castoe, D.D. Pollock, and J.R. Spear. 2010. Comparison of normalization methods for construction of large multiplex amplicon pools for next-generation sequencing. Applied and Environmental Microbiology 76: 3863-3868.

Castoe, T.A., A.P.J. de Koning, D.D. Pollock. 2010. Molecular structure and evolution of genomes. In: Evolutionary Genomics and Systems Biology, G. Caetano-Anolles (Ed.), John Wiley & Sons, New York, NY, pp. 183-202.

Castoe, T.A., A.W. Poole, W. Gu, A.P.J. de Koning, J.M Daza, E.N. Smith, and D.D. Pollock. 2010. Rapid identification of thousands of microsatellite loci for the copperhead snake (Agkistrodon contortrix) from modest amounts of 454 shotgun genome sequence. Molecular Ecology Resources 10: 341-347.

Daza, J.M.*, T.A. Castoe*, and C.L. Parkinson. 2010. Using regional comparative phylogeographic data from snake lineages to infer historical processes in Middle America. Ecography 33: 343-354. [*joint primary authors]

Castoe, T.A., A.P.J. de Koning, H.M. Kim, W. Gu, B.P. Noonan, G. Naylor, Z.J. Jiang, C.L. Parkinson, and D.D. Pollock. 2009. Evidence for an ancient adaptive episode of convergent molecular evolution. Proceedings of the National Academy of Sciences USA106: 8986-8991. -Cover Feature -Faculty of 1000

Castoe, T.A., A.P.J. de Koning, W. Gu, J.M. Daza, Z.J. Jiang, C.L. Parkinson, and D.D. Pollock. 2009. Dynamic mutational gradients and control region usage in squamate reptile mitochondrial genomes. Cytogenetic and Genome Research 127: 112-127.

Tonnsman, G., D.D. Pollock, W. Gu, and T.A. Castoe. 2009. Identifying DNA strands using a kernel of classified sequences. 2009 WRI World Congress on Computer Science and Information Engineering 3: 703-707.

Castoe, T.A., J.M. Daza, E.N. Smith, M. Sasa, U. Kuch, P.T. Chippindale, J.A. Campbell, and C.L. Parkinson. 2009. Comparative phylogeography of pitvipers suggests a consensus of ancient Middle American highland biogeography. Journal of Biogeography 36:83-103. -Cover Article-

Burbrink, F.T., and T.A. Castoe. 2009. Molecular phylogeography of snakes. In: Snakes: Ecology and Conservation, R. Seigel and S. Mullin (Eds.), Cornell Univ. Press, Ithaca, NY, pp. 38-77.

Gu, W., T.A. Castoe, D.L. Hedges, M.A. Batzer, and D.D. Pollock. 2008. Analysis of the repeat structure in large genomes using repeat probability clouds. Analytical Biochemistry380:77-83.

Castoe, T.A., Z.J. Jiang, W. Gu, Z. Wang, and D.D. Pollock. 2008. Adaptive evolution and functional redesign of core metabolic proteins in snakes. PLoS ONE3:e2201. –Faculty of 1000-

Jiang, Z.J./T.A. Castoe*, C.C. Austin, F.T. Burbrink, M.D. Herron, J.A. McGuire, C.L. Parkinson, and D.D. Pollock. 2007. Comparative mitochondrial genomics of snakes: substitution rate dynamics and functionality of the duplicate control region. BMC Evolutionary Biology 7:123. [*joint primary authors]

Castoe, T.A., T.S. Stephens, B.P. Noonan, C.L. Calestani. 2007. A novel group of type I polyketide synthases (PKS) in animals and the complex phylogenomics of PKSs. Gene 392:47-58.

Castoe, T.A., E.N. Smith, R.M. Brown, and C.L. Parkinson. 2007. Higher-level phylogeny of Asian and American coralsnakes, their placement within the Elapidae (Squamata), and the systematic affinities of the enigmatic Asian coralsnake Hemibungarus calligaster. Zoological Journal of the Linnean Society 151:809-831.

Castoe, T.A., C.L. Spencer, and C.L. Parkinson. 2007. Phylogeographic structure and historical demography of the western diamondback rattlesnake (Crotalus atrox): a perspective on North American desert biogeography. Molecular Phylogenetics and Evolution 42:193-212.

Castoe, T.A., and C.L. Parkinson. 2006. Bayesian mixed models and the phylogeny of pitvipers (Serpentes: Viperidae). Molecular Phylogenetics and Evolution 39:91-110.

Castoe, T.A., M. Sasa, and C. L. Parkinson. 2005. Modeling nucleotide evolution at the mesoscale: The phylogeny of the Neotropical pitvipers of the Porthidium Group (Viperidae: Crotalinae). Molecular Phylogenetics and Evolution 37:881-898.

Doan, T.M., T.A. Castoe, and W. Arizábal Arriaga. 2005. Phylogenetic relationships of the genus Proctoporus sensu stricto (Squamata: Gymnophthalmidae), with a new species from Puno, southeastern Peru. Herpetologica 61:325-336.

Reece, J.S., T.A. Castoe, and C.L. Parkinson. 2005. Historical perspectives on population genetics and conservation of three sea turtle species. Conservation Genetics 6:235-251.

Doan, T.M., and T.A. Castoe. 2005. Phylogenetic taxonomy of the Cercosaurini (Squamata: Gymnophthalmidae), with new genera for species of Neusticurus and Proctoporus. Zoological Journal of the Linnean Society 143:405-416.

Mulvaney, A., T.A. Castoe, K.G. Ashton, K.L. Krysko, and C.L. Parkinson. 2005. Evidence of population genetic structure within the Florida worm lizard, Rhineura floridana (Amphisbaenia: Rhineuridae). Journal of Herpetology 39:118-124.

Castoe, T.A., T.M. Doan, and C.L. Parkinson. 2004. Data partitions and complex models in Bayesian analysis: the phylogeny of gymnophthalmid lizards. Systematic Biology 53:448-469.

Herron, M.D., T.A. Castoe, and C.L. Parkinson. 2004. Sciurid phylogeny and the paraphyly of Holarctic ground squirrels (Spermophilus). Molecular Phylogenetics and Evolution 31:1015-1030.

Schargel, W.E. and T.A. Castoe. 2003. The hemipenes of some snakes of the semifossorial genus Atractus with comments on variation within the genus. Journal of Herpetology 37: 718-721.

Castoe, T.A., P.T. Chippindale, J.A. Campbell, L.A. Ammerman, and C.L. Parkinson. 2003. The evolution and phylogeography of the Middle American jumping pitvipers, genus Atropoides, based on mtDNA sequences. Herpetologica 59: 421-432.

Doan, T.M. and T.A. Castoe. 2003. Using morphological and molecular evidence to infer species boundaries within Proctoporus bolivianus Werner (Gymnophthalmidae). Herpetologica 59: 433-450.

Castoe, T.A. 2002. Microhabitat selection in Porthidium nasutum (Serpentes: Viperidae) in Costa Rica, with comments on ontogenetic variation. Herpetological Review 33: 174-175.