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    Peer-Reviewed Journals

  • Stevens, R.D., Gavilanez, M.M., Tello, J.S., & Ray, D. (Sep 2011). Phylogenetic Structure Illuminates the Mechanistic Role of Environmental Heterogeneity in Community Organization. Journal of Animal Ecology Wiley Online Library, 81(2), 455-462. DOI:10.1111/j.1365-2656.2011.01900.x. [Document Site]
  • Alfoldi, J., DiPalma, F., Grabherr, M., Williams, C., Kong, L., Mauceli, E., Russell, P., Lowe, C.B., Glor, R., Jaffe, J.D., Ray, D., Boissinot, S., Shedlock, A.M., Botka, C., Castoe, T.A., Colbourne, J.K., Fujita, M.K., Moreno, R.G., TenHallers, B.F., Haussler, D., Heger, A., Heiman, D., Janes, D.E., Johnston, J., DeJong, P.J., Koriabine, M.Y., Novick, P., Organ, C.L., Peach, S.E., Poe, S., Pollock, D.D., DeQueroz, K., Sanger, T., Searle, S., Smith, Z., Swofford, R., Turner-Maier, J., Wade, J., Young, S., Zadissa, A., Edwards, S.V., Glenn, T.C., Schneider, C.J., Losos, J.B., Lander, E.S., Breen, M., Ponting, C.P., & Lindblad-Toh, K. (Sep 2011). The Genome of Anolis Carolinensis, the Green Anole Lizard, and a Comparative Analysis with Birds and Mammals. Nature Nature Publishing Group, 477, 587-591.
  • Novick, P., Ray, D., & Boissinot, S. (Sep 2009). Independent and Parallel Lateral Transfer of DNA Transposons in Tetrapod Genomes. Gene, 449, 85-94. [Document Site]
  • Ray, D. (Nov 2011). Expedited Batch Processing and Analysis of Transposon Insertions. BMC Research Notes Biomed Central, 4, 482. DOI:10.1186/1756-0500-4-482. [Document Site]
  • Novick, P., Floumanhaft, M., Boissinot, S., & Ray, D. (Nov 2010). The Evolution and Diversity of DNA Transposons in the Genome of the Lizard Anolis Carolinensis. Genome Biology and Evolution, 2, 293-303. [Document Site]
  • Batzer, M.A., & Ray, D. (Nov 2009). Reading between the LINEs to See into the Past. Trends in Genetics, 25(11), 475-479. [Document Site]
  • Ray, D. (May 2012). A Non-LTR Retroelement Extinction in Spermophilus Tridecemlineatus. Gene Science Direct, 500, 47-53. [Document Site]
  • Ray, D., & Hubley, R.M. (May 2010). PiggyBac-ing on a Primate Genome: Novel Elements, Recent Activity and Horizontal Transfer. Genome Biology and Evolution, 2, 293-303. [Document Site]
  • Ray, D., Macas, J., Novak, P., McColloch, E.S., & Stevens, R.D. (Mar 2012). Survey Sequencing Reveals Elevated DNA Transposon Activity, Novel Elements, and Variation in Repetitive Landscapes among Vesper Bats. Genome Biology and Evolution Oxford Universtiy Press, 4(4), 575-585. DOI:10.1093/gbe/evs038. [Document Site]
  • Ray, D., & Batzer, M.A. (Jun 2011). Reading TE Leaves: New Approaches to the Identification of Transposable Element Insertions. Genome Research, 21, 813-820. [Document Site]
  • Ramakodi, M., Ray, D., Dubey, B., Batzer, M.A., & Haque, I. (Jun 2010). Molecular Phylogenetic Analyses of Genus Crocodylus (Eusuchia, Crocodylia, Crocodylidae) and the Taxonomic Position of Crocodylus Porosus. Molecular Phylogenetics and Evolution, 57, 393-402. [Document Site]
  • Castoe, T.A., DeKoning, A., Hall, K.T., Yokoyama, K.D., Gu, W., Smith, E.N., Feschotte, C., Uetz, P., Dobry, J., Bogden, R., Mackessy, S.P., Bronikowski, A.M., Warren, W.C., Secor, S.M., Pollock, D.D., & Ray, D. (Jul 2011). Sequencing the Genome of the Burmese Python (Python Molurus Bivittatus) as a Model for Studying Extreme Adaptations in Snakes. Genome Biology, 12, 406. DOI:10.1186/gb-2011-12-7-406. [Document Site]
  • Shan, X., Ray, D., Bunge, J.A., & Peterson, D. G. (Jul 2009). A Bacterial Artificial Chromosome Library for the Australian Saltwater Crocodile (Crocodylus Porosus) and Its Utilization in Gene Isolation and Genome Characterization. BMC Genomics, 10(Suppl), S9. [Abstract][Document]
  • Peterson, D. G., Ray, D., John, J.A., Braun, E.L., Isberg, S.R., Miles, L.G., Chong, A.Y., Gongora, J., Dalzell, P., Moran, C., Bed\\\'Hom, B., Abzhanov, A., Burgess, S.C., Cooksey, A.M., Castoe, T.A., Crawford, N.G., Densmore, L.D., Drew, J.C., Edwards, S.V., Faircloth, B.C., Fujita, M.K., Greenwold, M.J., Hoffmann, F.G., Howard, J.M., Iguchi, T., Janes, D.E., Khan, S.Y., Kohno, S., DeKoning, A., Lance, S.L., McCarthy, F.M., McCormack, J.E., Merchant, M.E., Pollock, D.D., Pourmand, N., Raney, B.J., Roessler, K.A., Sanford, J.R., Sawyer, R.H., Schmidt, C.J., Triplett, E.W., Tuberville, T.D., Venegas-Anaya, M., Howard, J.T., Jarvis, E.D., Guillette, L.J., Glenn, T.C., & Green, R.E. (Jan 2012). Sequencing Three Crocodilian Genomes to Illuminate the Evolution of Archosaurs and Amniotes. Genome Biology, 13(1), 415. DOI:10.1186/gb-2012-13-1-415. [Document Site]
  • Chouvarine, P., Cooksey, A.M., McCarthy, F.M., Ray, D., Baldwin, B.S., Burgess, S.C., & Peterson, D. G. (Jan 2012). Transcriptome-based Differentiation of Closely-related Miscanthus Lines. PLoS ONE, 7(1), e29850. DOI:10.1371/journal.pone.0029850. [Abstract][Document]
  • Ramakodi, M., Ray, D., McColloch, E.S., & Stevens, R.D. (Jan 2012). Complete Mitochondrial Genome Sequences of Three Bats Species and Whole Genome Mitochondrial Analyses Reveal Patterns of Codon Bias and Lend Support to a Basal Split in Chiroptera. Gene Science Direct, 492(1), 121-129. [Document Site]
  • Ray, D., Ramakodi, M., Dubey, B., Batzer, M.A., & Haque, I. (Feb 2011). Complete Mitochondrial Genome Sequences of Three Crocodylus Species and Their Comparison within the Order Crocodylia. Gene Science Direct, 478, 35-41. [Document Site]
  • Thomas, J., Sorourian, M., Baker, R.J., Pritham, E.J., & Ray, D. (Dec 2010). The Limited Distribution of Helitrons to Vesper Bats Supports Horizontal Transfer. Gene Science Direct, 474, 52-58. [Document Site]