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35. Shan, X., D. A. Ray, and D. G. Peterson (Submitted) A bacterial artificial chromosome (BAC) library for the Australian saltwater crocodile (Crocodylus porosus) and its utilization in comparative genomics. BMC Genomics. 34. Ray, D. A., K. Han, J. A. Walker and M. A. Batzer (Submitted) Laboratory methods for the analysis of primate mobile elements. In "Methods in Molecular Biology - Genetic Variation Edition", M. R. Barnes and G. Breen (Eds.), Humana Press Inc., Totowa, NJ. 33. Ray, D. A., C. Feschotte, H. J. T. Pagan, J. D. Smith, E. Pritham, P. Arensburger, P. W. Atkinson, N. L. Craig. (2008) Multiple waves of recent DNA transposon activity in the bat, Myotis lucifugus. Genome Research 18:717-728. Cover illustration. 32. Warren W. C., L. W. Hillier, J. A. M. Graves, E. Birney, C. P. Ponting, F. Grützner, K. Belov, W. Miller, L. Clarke, A. T. Chinwalla, S.-P. Yang, A. Heger, D. Locke, P. Miethke, P. D. Waters, F. Veyrunes, L. Fulton, B. Fulton, T. Graves, J. Wallis, X. S. Puente, C. López-Otín, G. R. Ordóñez, E. E. Eichler, L. Chen, Z. Cheng, J. E. Deakin, A. Alsop, K. Thompson, P. Kirby, A. T. Papenfuss, M. J. Wakefield, T. Olender, D. Lancet, G. A. Huttley, A. F. A. Smit, A. Pask, P. Temple-Smith, M. A. Batzer, J. A. Walker, M. K. Konkel, R. S. Harris, C. M. Whittington, E. S. W. Wong, N. Gemmell, E. Buschiazzo, I. V. Jentzsch, A. Merkel, J. Schmitz, A. Zemann, G. Churakov, J. O. Kriegs, J. Brosius, E. Murchison, R. Sachidanandam, C. Smith, A. Stark, P. Kheradpour, G. Hannon, E. Tsend-Ayush, D. McMillan, R. Attenborough, W. Rens, M. Ferguson-Smith, C. M. Lefèvre, J. A. Sharp, K. R. Nicholas, D. A. Ray, M. Kube, R. Reinhard, T. H. Pringle, J. Taylor, R. C. Jones, B. Nixon, J.-L. Dacheux, H. Niwa, Y. Sekita, X. Huang, P. Flicek, C. Webber, R. Hardison, J. Nelson, K. Hallsworth-Pepin, M. Renfree, Washington University Genome Sequencing Center, E. R. Mardis and R. K. Wilson. (2008) Genome analysis of the platypus reveals unique signatures of evolution. Nature 453:175-183. 31. Rainwater T. R., K. W. Selcer, L. M. Nespoli, A. G. Finger, D. A. Ray, S. G. Platt, P. N. Smith, L. D. Densmore, T. A. Anderson, S. T. McMurry (2008) Plasma vitellogenin in Morelet's crocodiles from contaminated habitats in northern Belize. Environmental Pollution 153:101-109. 30. Xing J., D. J. Witherspoon, D. A. Ray, M. A. Batzer, and L. B. Jorde (2007) Mobile Elements and Primate Evolution. Yearbook of Physical Anthropology 50:2-19. 29. Mikkelsen, T. S., B. Aken, C. T. Amemiya, J. L. Chang, S. Duke, M. Garber, A. J. Gentles, L. Goodstadt, A. Heger, J. Jurka, M. Kamal, E. Mauceli, S. M. J. Searle, T. Sharpe, M. L. Baker, M. A. Batzer, P. V. Benos, K. Belov, M. Clamp, A. Cook, J. Cuff, R. Das, J. E. Deakin, M. Grabherr, J. M. Greally, W. Gu, R. L. Jirtle, S. Mahony, M. A. Marra, R. D. Miller, R. D. Nicholls, A. T. Papenfuss, Z. E. Parra, D. D. Pollock, D. A. Ray, J. E. Schein, T. P. Speed, J. L. VandeBerg, M. J. Wakefield, C. M. Wade, J. A. Walker, C. Webber, J. R. Weidman, X. Xie, M. C. Zody, Broad Institute Genome Sequencing Platform, Broad Institute Whole Genome Assembly Team, J. A. Marshall Graves, C. P. Ponting, M. Breen, P. B. Samollow, E. S. Lander, K. Lindblad-Toh (2007) Genome of the marsupial Monodelphis domestica reveals lineage-specific innovation in coding and non-coding sequences. Nature 447(7141):115-230. 28. Gu, W.*, D. A. Ray*, J. A. Walker, E. Barnes, A. J. Gentles, P. B. Somollow, J. Jurka, M. A. Batzer, and D. D. Pollock (2007) SINEs, evolution and genome structure in the opossum. GENE 396(1):46-58. * These authors contributed equally to this work. 27. Xing, J. H. Wang, Y. Zhang, D. A. Ray, A. J. Tosi, T. R. Disotell and M. A. Batzer (2007) A mobile element based evolutionary history of guenons (Tribe Cercopithicini). BMC Biology 5:5.
26. Ray, D. A, H. J. T. Pagan, M. L. Thompson, R. D. Stevens (2007) Bats with hATs: Evidence for recent DNA transposon activity in genus Myotis. Molecular Biology and Evolution 24:632-639. Supplemental Table and Figures, Supplemental Alignments.
25. Herke S. W., J. Xing, D. A. Ray, J. W. Zimmerman, R. Cordaux and M. A. Batzer (2007) A SINE-based dichotomous key for primate identification. GENE 390:39-51.
24. Ray, D. A.*, J. A. Walker*, and M. A. Batzer.(2007) Mobile element-based forensics. Mutation Research 616: 24-33. *These authors contributed equally to this work.
22. Witherspoon, D. J., E. E. Marchani, W. S. Watkins, C. T. Ostler, S. P. Wooding, B. A. Anders, J. D. Fowlkes, S. Boissinot, A. V. Furano, D. A. Ray, A. R. Rogers, M. A. Batzer and L. B. Jorde (2006) Human population genetic structure and diversity inferred from polymorphic L1 (LINE-1) and Alu insertions. Human Heredity 62:30-46.
21. Ray, D. A., J. Xing, A.-H. Salem and M. A. Batzer (2006) SINEs of a nearly perfect character: Applications of the SINE method to phylogeny and population biology. Systematic Biology 55:928-935.
20. Selcer, K. W., L. M. Nespoli, T. R. Rainwater, A. G. Finger, D. A. Ray, S. G. Platt, P. N. Smith, L. D. Densmore, and S. T. McMurry (2006) Development of an enzyme-linked immunosorbent assay for vitellogenin of Morelet's crocodile (Crocodylus moreletti). Comparative Biochemistry and Physiology Part C: Toxicology & Pharmacology 143(1):50-58
19. Ray, D. A,
and M. A. Batzer (2005) Tracking
Alu evolution in New World primates. BMC
Evolutionary Biology 5:51.
18. McAliley, L.R., R.E. Willis, D.A. Ray, P.S. White, C. A. Brochu and L.D. Densmore (2006) Are crocodiles really monophyletic?—Evidence for subdivisions from sequence and morphological data. Molecular Phylogenetics and Evolution 39:16-32.
17. Ray, D. A, D. J. Hedges, S. W. Herke, J. D. Fowlkes, E. W. Barnes, D. K. LaVie, L. M. Goodwin and M. A. Batzer (2005) Chompy: An infestation of MITE-like repetitive elements in the crocodilian genome. GENE 362 (2005) 1-10. Supplementary Data
16. Wang J., L. Song, M.K. Gonder, S.A.Tishkoff, S. Azrak, D.A. Ray, M.A. Batzer and Ping Liang (2006) Whole genome computational comparative genomics: a fruitful approach for ascertaining Alu insertion polymorphisms. GENE 365:11-20. Supplementary Data
15. Ray,
D.A., J.A. Walker, A. Hall, B. Llewellyn, J Ballantyne,
A.T. Christian, K. Turtletaub and M.A. Batzer (2005)
Inference
of human geographic origins 2 - Genotype information, 3 - Structure output, 4 - WGA results
14. Xing, J., H. Wang,
K. Han, D.A. Ray, C.H. Huang, L.G. Chemnick, C.-B. Stewart,
T. Disotell, O.A. Ryder and
M.A. Batzer (2005)
A mobile element based phylogeny
of
12.
Ho, H.J., D.A. Ray, A.H. Salem, J.S. Myers, and M.A. Batzer
(2005)
11.
Ray, D.A., J. Xing, D.J. Hedges, M.A.Hall, M.E. Laborde, B.A.Anders,
B.R. White, N. Stoilova, J.D. Fowlkes, K.E. Landry, L.G. Chemnick,
O.A. Ryder, and M.A. Batzer (2005) Alu
insertion loci and platyrrhine primate phylogeny. Molecular Phylogenetics
and Evolution 35(1):117-126.
9. Otieno, A.C., A.B.
Carter, D.J. Hedges, J.A. Walker, D.A. Ray, R.K. Garber, B.A.
Anders,
N. Stoilova, M.E. Laborde, J.D. Fowlkes, C.H. Huang, B. Perodeau,
8.
Ray, D.A.,
J.A. Dever, S.G. Platt, T.R. Rainwater, A.G. Finger, S.T. McMurry,
M.A. Batzer, B. Barr, P.J. Stafford, J. McKnight and L.D. Densmore (2004)
Low
levels
of nucleotide diversity in Crocodylus moreletii and evidence
of hybridization with C. acutus.
Conservation Genetics 5(4): 449-462. 7. Gonzalez, Z., D. A. Ray, L. R. McAliley, M. J. Gray, C. Perchellet, L. M. Smith and L. D. Densmore (2004) A set of polymorphic microsatellite markers for the Great Plains Toad, Bufo cognatus. Molecular Ecology Notes 4(1): 9-10.
6. Salem, A.-H.*, D.A. Ray*, J. Xing, P.A. Callinan, J.S. Myers, D.J. Hedges, R.K. Garber, D. J. Witherspoon, L.B. Jorde and M.A. Batzer (2003) Alu elements and hominid phylogenetics. Proceedings of the National Academy of Sciences, USA 100(22):12787-12791. *These authors contributed equally to this work. Supplementary Data: AluYe_alignment Appendix_1 Appendix_II
4.
Ray, D. A.
and L. D. Densmore (2003) Repetitive
sequences in the crocodilian mitochondrial
control region: Poly-A sequences and heteroplasmic tandem
repeats.
Molecular Biology and Evolution 20(6): 1006-1013.
3.
Ray, D. A.
and L. D. Densmore (2002) The
crocodilian control region: General
structure, conserved sequences and evolutionary implications. Journal
of Experimental Zoology (Molecular Development and Evolution) 294
(4): 334-345. 2.
Densmore, L. D and D. A. Ray. (2002) Genetic Markers as Tools
for Management of Captive
Crocodilian Populations. In “Memoria Primer Seminario
Taller: Capacitacion y Actualizacion en el Manejo Sostenible de Cocodrilos
en Especialistas
de Crocodylia, Panama,
Republica de Panama. (English
version: pp.
205-214.). 1.
Ray, D. A.,
P. S. White, H. V. Duong, T. Cullen, and L. D. Densmore (2001)
High levels of variation
in the African Dwarf Crocodile (Osteolaemus tetraspis)
In: Crocodilian Biology and Evolution (G. Grigg, F. Seebacherand C.
Franklin, eds). pp. 58-69. |
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