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38. Thompson, M.L., A.E. Gauna, M.L. Williams, D.A. Ray (Under revision) Multiple chicken repeat 1 (CR1) lineages in the genomes of oestroid flies. GENE

37. Pagan, H.J.T., J.D. Smith, and D.A. Ray (Submitted) Lineage specific Class II transposon activity in mouse lemurs (Microcebus). BMC Evolutionary Biology.

36. Novick, P., J.D. Smith, D.A. Ray, S. Boissinot (Under revision) Jumping genes: Independent and parallel lateral transfer of DNA transposons in tetrapod genomes. GENE.

35. Shan, X., D.A. Ray, J.A. Bunge, and D.G. Peterson (2009) A bacterial artificial chromosome (BAC) library for the Australian saltwater crocodile (Crocodylus porosus) and its utilization in gene isolation and genome characterization. BMC Genomics 10:S9.

34. Ray, D.A., K. Han, J.A. Walker and M.A. Batzer (In press) 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.

23. Ray, D.A. (2007) SINEs of progress: Mobile element applications for molecular
ecology. Molecular Ecology 16:19-33. Legend for Box 1 (omitted in published version, see subsequent issue for correction)


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. Supplementary Data


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 using Alu insertion polymorphisms. Forensic Science International. 153:117-124. Supplementary Data: 1 -  Primer and amplification conditions,

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 Old World monkeys. Molecular Phylogenetics and Evolution 37: 872-880. Supplementary Data: Supplemental Table, Supplemental Alignments


13. Salem, A-H, D.A. Ray, D.J. Hedges, J. Jurka and M. A. Batzer (2005) Analysis of the human Alu Ye lineage.  BMC Evolutionary Biology 5:18.


12. Ho, H.J., D.A. Ray, A.H. Salem, J.S. Myers, and M.A. Batzer (2005) Straightening out the LINEs: LINE-1 element orthologous loci. Genomics 85:201-207.


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. Supplementary Data:  Locus and primer data, Alignments


10. Salem, A-H, D.A. Ray, and M.A. Batzer (2005) Identity by descent and DNA sequence variation of human SINE and LINE elements.  Cytogenetic and Genome Research 108: 63-72. Supplementary Data: Tables  Alignments


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, and M.A. Batzer (2004) Analysis of the human Alu Ya-lineage. Journal of Molecular Biology 342: 109-118.


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


5. Stafford, P.J., S.T. McMurry, T.R. Rainwater, D.A. Ray, L.D. Densmore and B. Barr (2003) Morelet's crocodile (Crocodylus moreletii) in the Macal River watershed, Maya Mountains, Belize. Herpetological Bulletin 85: 15-23.


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 Panamapp. 136-150 Asociacon Panamena de Manejadores y

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. Surrey Beatty and Sons, Chipping Norton.