-2024-

118. EA Wright, JD Manthey, MR Buchalski, BR McKinney, DA Ray, CD Phillips, RD Bradley (2024) Genomic affinity following restoration of a locally extirpated species: a case study of desert bighorn sheep in Texas. Conservation Genetics (2024). https://doi.org/10.1007/s10592-024-01635-5

117. JM Korstian, RD Stevens, TE Lee Jr., RJ Baker, DA Ray (2024) Unraveling the Myotis morass: ultraconserved-element analysis reveals introgression, cryptic diversity, and taxonomic trouble. Journal of Mammalogy 2024 105(2):259-276. https://doi.org/10.1093/jmammal/gyad119

116. JR Grimshaw, D Donner, R Perry, WM Ford, A Silvis, CJ Garcia, RD Stevens, DA Ray (2024) Disentangling genetic diversity of Myotis septentrionalis: population structure, demographic history, and effective population size. Journal of Mammalogy 105(4):854-864. https://doi.org/10.1093/jmammal/gyae056

115. F Cicconardi, BJ Morris, J Martelossi, DA Ray, SH Montgomery (2024) Novel sex-specific genes and diverse interspecific expression in the antennal transcriptomes of ithomiine butterflies. Genome Biology and Evolution. https://doi.org/10.1093/gbe/evae218

114. AE Morales, Y Dong, T Brown, K Baid, DG Kontopoulos, V Gonzalez, Z Huang, A-W Ahmed, L Hilgers, S Winkler, G Hughes, X Li, B M Kirilenko, P Devanna, TM Lama, Y Nissan, M Pippel, LM Dávalos, SC Vernes, SJ Puechmaille, SJ Rossiter, Y Yossi, JB Prescott, A Kurth, DA Ray, BK Lim, E Myers, EC Teeling, A Banerjee, AT Irving, M Hiller (Submitted) Reference-quality bat genomes illuminate adaptations to viral tolerance and disease resistance. Nature.

-2023-

113. FX Castellanos, D Moreno-Santillan, GM Hughes, NS Paulat, N Sipperly, A Brown, K Martin, GM Poterewicz, MCW Lim, AL Russell, MS Moore, M Johnson, AP Corthals, DA Ray, and LM Davalos (2023) The evolution of antimicrobial peptides in Chiroptera. Frontiers in Immunology 14:1250229. https://www.frontiersin.org/articles/10.3389/fimmu.2023.1250229.

112. NS Paulat, JM Storer, DD Moreno-Santillan, AB Osmanski, KAM Sullivan, JR Grimshaw, J Korstian, M Halsey, CJ Garcia, C Crookshanks, J Roberts, AFA Smit, R Hubley, J Rosen, EC Teeling, SC Vernes, E Myers, Zoonomia Consortium, D Rojas, LM Davalos, DA Ray. (2023) Chiropterans are a hotspot for horizontal transfer of DNA transposons in Mammalia. Molecular Biology and Evolution.40:5 (msad092). Supplemental Data. https://doi.org/10.1093/molbev/msad092

111. RD Bradley, AT Pham, KA Rich, EK Roberts, TJ Soniat, CM Poehlein, MN Mills, M Ballard, RM Pitts, LL Lindsey, MK Halsey, DA Ray, RD Stevens, DJ Schmidly and EA Wright (2023) Genetic identification of pocket gophers (Genera Cratogeomys, Geomys, and Thomomys) in Texas and surrounding areas. Special Publications, Museum of Texas Tech University 78 (1 November 2023):1-120.

110. MJ Christmas, IM Kaplow, DP Genereux, MX Dong, GM Hughes, X Li, PF Sullivan, AG Hindle, G Andrews, JC Armstrong, M Bianchi, M Diekhans, C Fanter, NM Foley, DB Goodman, L Goodman, KC Keough, B Kirilenko, A Kowalcyk, C Lawless, AL Lind, JRS Meadows, LR Moreira, RW Redlich, L Ryan, R Swofford, A Valenzuela, F Wagner, O Waterman, AR Brown, J Damas, K Fan, J Gatesy, J Grimshaw, J Johnson, SV Kozyrev AJ Lawler, VD Marinescu, KM Morrill, A Osmanski, NS Paulat, BN Phan, SK Reilly, DE Schaffer, C Steiner, MA Supple, AP Wilder, ME Wirthlin, JR Xue, Zoonomia Consortium, BW Birren, S Gaza RM Hubley, K-P Koepflii, T Marques-Bonet, WK Meyer, M Nweeia PC Sabeli B Shapiro, AFA Smit, MS Springer, EC Teeling, Z Wang, M Hiller, DL Levesque, HA Lewin, WJ Murphy, A Navarro, B Paten, KS Pollard, DA Ray, I Ruf, OA Ryder, AR Pfenning, K Lindblad-Toh, EK Karlsson (2023) Evolutionary constraint and innovation across hundreds of placental mammals. Science 380, eabn3943 https://doi.org/10.1101/2023.03.09.531574

109. AB Osmanski, NS Paulat, JM Korstian, JR Grimshaw, M Halsey, KAM Sullivan, DD Moreno-Santillan, C Crookshanks, J Roberts, CJ Garcia, LM Davalos, MG Johnson, LD Densmore, RD Stevens, Zoonomia Consortium, J Rosen, JM Storer, R. Hubley, AFA Smit, DA Ray. (2023) Insights into mammalian TE diversity via the curation of 200+ genome assemblies. Science 380, eabn1430. https://doi.org/10.1126/science.abn1430

108. CJ Garcia, DA Ray, RW Perry, RD Stevens (2023) Seasonal differences in day-roost selection of Northern long-eared bats (Myotis septentrionalis) in Louisiana and a meta-analytical comparison across North America. Forest Ecology and Management 530:120749. https://doi.org/10.1016/j.foreco.2022.120749

107. D Sandip, SB Kingan, C Kitsou, DM Portik, SD Foor, JC Frederick, VS Rana, NS Paulat, DA Ray, Y Wang, TC Glenn, and U Pal. (2023) A high-quality Ixodes scapularis genome advances tick science. Nature Genetics 55:301-333. https://doi.org/10.1038/s41588-022-01275-w

-2022-

106. JD Stuhler, MK Halsey, JR Goetze, RD Bradley, DA Ray, RD Stevens (2023) Updated distribution of the Texas kangaroo rat (Dipodomys elator) and patterns of rodent species associations from county road surveys in Texas. Therya 14(1). https://doi.org/10.12933/therya-23-2306

105. AP Dorador, M Dalikova, S Cerbin, C Stillman, M Zych, RC Hawley, DE Miller, DA Ray, SY Funikov, MB Evven’ev, and JP Blumenstiel (2022) Paramutation-like epigenetic conversion by piRNA at the telomere of Drosophila virilis. Biology 2022 11(10):1480. https://doi.org/10.3390/biology11101480

104. NS Paulat, E McGuire, K Subramanian, AB Osmanski, DD Moreno-Santillan, DA Ray, J Xing (2022) Transposable elements in bats show differential accumulation patterns determined by class and functionality. Life 2022, 12(8):1190. https://doi.org/10.3390/life12081190

103. EE Stukenholz, TA Hailu, S Childers, C Leatherwood, L Evans, D Roulain, D Townsley, M Treider, RN Platt II, SR Fritts, DA Ray, JC Zak, RD Stevens (2022) A pigeon’s eye view of a university campus. The Southwestern Naturalist. 66(1):13-14. https://doi.org/10.1894/0038-4909-66.1.13

102. L Doronina, GM Hughes, D Moreno-Santillan, C Lawless, T Lonergan, L. Ryan, D Jebb, BM Kirilenko, JM Korstian, LM Davalos, SC Vernes, EW Myers, EC Teeling, M Hiller, LS Jermin J Schmitz, MS Springer, DA Ray. (2022) Contradictory phylogenetic signals in the Laurasiatheria anomaly zone. Genes 13(5):766. Cover article. https://doi.org/10.3390/genes13050766

101. JM Korstian, NS Paulat, RN Platt II, RD Stevens, DA Ray. (2022) SINE-based phylogenomics reveal extensive introgression and incomplete lineage sorting in Myotis. Genes 2022, 13, 399. https://doi.org/10.3390/genes13030399

100. MK Halsey, JD Stuhler, NJ Bayona-Vasquez, RN Platt II, JR Goetze, RE Martin, KG Matocha, RD Bradley, RD Stevens, DA Ray. (2022) Comparison of genetic variation between rare and common congeners of Dipodomys with estimates of contemporary and historical effective population size. PLoS ONE 17(9):e0274554. https://doi.org/10.1371/journal.pone.0274554

99. MW Vandewege, RN Platt II, DK Merriman, DA Ray, FG Hoffmann. (2022) The PIWI/piRNA response is relaxed in a rodent that lacks mobilizing transposable elements. RNA 28:609-621.

98. JR Grimshaw, JD Manthey, NS Paulat, RD Stevens, and DA Ray (2022) Landscape level patterns of genetic diversity of bat species of greatest conservation need in Louisiana. Occasional Papers of the Museum of Texas Tech University. 380:1-12.

-2021-

97. J Gutierrez, RN Platt II, JC Opazo, DA Ray, FG Hoffmann, MW Vandewege. (2021) Evolutionary history of the vertebrate Piwi gene family. PeerJ e12451.

96. JR Grimshaw, DA Ray, and R. D. Stevens. (2021) Ecological niche models for bat species of greatest conservation need in Louisiana. Occasional Papers in Museum of the Texas Tech University. 378:1-15.

95. DD Moreno- Santillán, TM Lama, YT Guttierez Guerrero, AM Brown, P Donat, H Zhao, SJ Rossiter, LR Yohe, JH Potter, EC Teeling, SC Vernes, K Davies, E Myers, GM Hughes, Z Huang, FG Hoffmann, AP Corthals, DA Ray, and Liliana Davalos. (2021) Large -scale genome sampling reveals unique immunity and metabolic adaptations in bats. Molecular Ecology 30(23):6449-6467. https://doi.org/10.1111/mec.16027

94. MK Halsey, JD Stuhler, RN Platt II, RD Bradley, RD Stevens, and DA Ray. (2021) Cheeky Business: Comparing DNA yield of buccal, whisker, and fecal samples for minimally invasive genetic research. Occasional Papers of the Museum of Texas Tech University 374:March30,2021.

-2020-

93. DP Genereux, A Serres, J Armstrong, J Johnson, VD Marinescu, E Murén, D Juan, G Bejerano, NR Casewell, LG Chemnick, J Damas, F Di Palma, M Diekhans, IT Fiddes, M Garber, VN Gladyshev, L Goodman, W Haerty, ML Houck, R Hubley, T Kivioja, K-P Koepfli, LFK Kuderna, ES Lander, JRS Meadows, WJ Murphy, W Nash, HJ Noh, M Nweeia, AR Pfenning, KS Pollard, D Ray, B Shapiro, A Smit, Mark Springer, CC Steiner, R Swofford, J Taipale, EC Teeling, J Turner-Maier, J Alfoldi, B Birren, OA Ryder, H Lewin, B Paten, T Marques-Bonet, K Lindblad-Toh, and EK Karlsson (2020) A comparative genomics multitool for scientific discovery and conservation. Nature:240-245.

92. D Jebb, Z Huang, M Pippel, M Hughes, K Lavrichenko, P Devanna, S Winkler, LS Jermiin, EC Skirmuntt, A Katzourakis, L Burkitt-Gray, DA Ray, KAM Sullivan, JG Roscito, BM Kirilenko, LM Dávalos, AP Corthals, ML Power, G Jones, RD Ransome, D Dechmann, AG Locatelli, SJ Puechmaille, O Fedrigo, ED Jarvis, M Hiller, SC Vernes, EW Myers, C Teeling (2020) Six reference-quality genomes reveal evolution of bat adaptations. Nature 583:578–584. Cover article.

91. A Ghosh, RN Platt II, MW Vandewege, R Tabassum, C-Y Hsu, SR Isberg, DG Peterson, JW Finger, TJ Kieran, TC Glenn, J Gongora, and DA Ray (2020) Identification and characterization of microRNAs (miRNAs) and their transposable element origins in the saltwater crocodile, Crocodylus porosus. Analytical Biochemistry 602:113781.

90. LL Lindsey, RN Platt II, CD Phillips, DA Ray, and RD Bradley (2020) Differential expression in testis and liver transcriptomes from four species of Peromyscus (Rodentia: Cricetidae). Genome Biology and Evolution 12(1):3698-3709.

89. S Louha, DA Ray, K Winker, TC Glenn (2020) A high-quality genome assembly of the North American Song Sparrow, Melospiza melodia. G3: Genes, Genomes, Genetics 10(4):1159-1166.

88. A Ghosh, MG Johnson, AB Osmanski, S Louha, NJ Bayona-Vásquez, TC Glenn, J Gongora, RE Green, S Isberg, RD Stevens, and DA Ray (2020) A high-quality reference genome assembly of the saltwater crocodile, Crocodylus porosus, reveals patterns of selection in Crocodylidae. Genome Biology and Evolution 12(1): 3635–3646.

-2019-

87. DA Ray, N Paulat, W An, S Boissinot, R Cordaux, T Kaul, B Freeman, V Belancio (2019) The 2019 FASEB Science Research Conference on The Mobile DNA Conference: 25 Years of Discussion and Research, June 23–28, Palm Springs, California, USA. The FASEB Journal 33 (11), 11625-1162.

86. M Volleth, S Muller, FA Anwarali Khan, H-S Yong, K-G Heller, RJ Baker, DA Ray, and CG Sotero-Caio (2019) Cytogenetic investigations in Emballonuroidea. I. Taphozoinae and Emallonurinae karyotypes evolve at different rates and share no derived chromosomal characters. Acta Chiropterologica 21(2):257-269.

85. EE Stukenholtz, TA Hailu, S Childers, C Leatherwood, L Evans, D Roulain, D Townsley, M Treider, RN Platt II, DA Ray, JC Zak, and RD Stevens (2019) Ecology of Feral Pigeons: Population Monitoring, Resource Selection, and Management Practices, Wildlife Population Monitoring, Marco Ferretti, IntechOpen, DOI: 10.5772/intechopen.84612.

84. DA Ray, JR Grimshaw, MK Halsey, JM Korstian, AB Osmanski, KAM Sullivan, KA Wolf, H Reddy, N Foley, RD Stevens, BA Knisbacher, O Levy, B Counterman, NB Edelman, and J Mallet (2019) Simultaneous TE Analysis of 19 Heliconiine Butterflies Yields Novel Insights into Rapid TE-Based Genome Diversification and Multiple SINE Births and Deaths. Genome Biology and Evolution 11(8):2162–2177.

-2018-

83. L Doronina, O Reising, H Clawson, D Ray, and J Schmitz (2018) True homoplasy of retrotransposon insertions in primates. Systematic Biology 68(3):482–493.

82. Platt II, RN, MW Vandewege, DA Ray. (2018) Mammalian transposable elements and their impacts on genome evolution. Chromosome Research 26:25-43.

81. E Teeling, S Vernes, L Davalos, DA Ray, MTP Gilbert, E Myers, and Bat1K Consortium (2018) Bat1K: A proposal to generate chromosome-level genomes for all living bat species. Annual Review of Animal Biosciences 6:23-46.

-2017-

80. Platt, RN, BC Faircloth, KAM Sullivan, T Kieran, TC Glenn, MW Vandewege, TE Lee, RJ Baker, RD Stevens, DA Ray (2017) Conflicting evolutionary histories of the mitochondrial and nuclear genomes in New World Myotis. Systematic Biology 67:236-249.

79. KAM Sullivan, RN Platt II, RD Bradley, and DA Ray (2017) Whole mitochondrial genomes provide increased resolution and indicate paraphyly in deermice. BMC Zoology 2:11.

78. ES Rice, S Kohno, J St. John, S Pham, J Howard, L Lareau, B O'Connell, G Hickey, J Armstrong, A Deran, I Fiddes, RN Platt II, C Gresham, F McCarthy, C Kern, D Haan, Schmidt, J Sanford, DA Ray, B Paten, LJ Guillette Jr, and RE Green. (2017) Improved assembly of American alligator genome reveals conserved architecture of estrogen signaling. Genome Research 27:686-696.

77. CG Sotero-Caio, RN Platt II, A Suh, and DA Ray (2017) Evolution and diversity of transposable elements in vertebrate genomes. Genome Biology and Evolution 9(1):161-177.

- 2016 -

76. A Andere, RN Platt II, DA Ray, and C Picard (2016) Genome sequence of Phormia regina Meigen (Diptera: Calliphoridae): Implications for medical, veterinary and forensic research. BMC Genomics 17:842. 

75. RN Platt II, S Mangum, and DA Ray (2016) Pinpointing the vesper bat transposon revolution using the Miniopterus natalensis genome. Mobile DNA 7:12.

74. MW Vandewege, RN Platt II, DA Ray, and FG Hoffmann (2016) Transposable element targeting by piRNAs in Laurasiatherians with distinct transposable element histories.  Genome Biology and Evolution 8(5):1327-1337.

73. MW Vandewege, S Mangum, T Gabaldon, TA Castoe, DA Ray, and FG Hoffmann (2016) Contrasting patterns of evolutionary diversification in the olfactory repertoires of reptile and bird genomes.  Genome Biology and Evolution 8(3):470-480.

72. RN Platt II, L Blanco-Berdugo and DA Ray (2016) Accurate transposable element annotation is vital when analyzing new genome assemblies. Genome Biology and Evolution 8(2):403-410.

- 2015 -

71. FG Hoffmann, LP McGuire, BA Counterman, and DA Ray (2015) Transposable elements and small RNAs: Genomic fuel for species diversity. Mobile Genetic Elements 5(5):1-4).

70. RN Platt II, Y Zhang, DJ Witherspoon, J Xing, A Suh, MS Keith, LB Jorde, RD Stevens, and DA Ray (2015) Targeted capture of phylogenetically informative Ves SINE insertions in genus Myotis. Genome Biology and Evolution 7(6):1664-1675.

69. DA Ray, HJT Pagan, RN Platt II, AR Kroll, S Schaack, RD Stevens (2015) Differential SINE evolution in vesper and non-vesper bats. Mobile DNA 6:10.

68. A Suh, G Churakov, MP Ramakodi, RN Platt II, J Jurka, KK Kojima, J Caballero, A Smit, FG Hoffmann, J Brosius, RE Green, EL Braun, DA Ray and J Schmitz (2015) Multiple lineages of ancient CR1 retroposons shaped the early genome evolution of amniotes. Genome Biology and Evolution 7(1):205-217.

67. MP Ramakodi, B Singh, JD Wells, F Guerrero and DA Ray (2015) A 454 sequencing approach to dipteran mitochondrial genomes research. Genomics 105(1):53-60. 

- 2014 -

66. AY Chong, KK Kojima, J Jurka, AFA Smit, DA Ray, SR Isberg and J Gongora (2014) Replication and evolution of ancient endogenous retroviruses - insights from the crocodilian genomes. Retrovirology 11:71.

65. A Suh, CC Weber, C Khlmaier, EL Braun, RE Green, U Fritz, DA Ray and H Ellegren (2014) Early Mesozoic coexistence of amniotes and hepadnaviridae. PloS Genetics 10(12):e1004559.

64. RE Green, EL Braun, J Armstrong, D Earl, N Nguyen, G Hickey, MW Vandewege, JA St John, S Capella-Gutiérrez, TA Castoe, C Kern, MK Fujita, JC Opazo, J Jurka, KK Kojima, J Caballero, RM Hubley,  A Smit, RN Platt, CA Lavoie, MP Ramakodi, JW Finger Jr,  A Suh, SR Isberg, L Miles, AY Chong, W Jaratlerdsiri, J Gongora, C Moran, A Iriarte, BC Faircloth, J McCormack, SC Burgess, SV Edwards, E Lyons, C Williams, M Breen, JT Howard, CR Gresham, DG Peterson, J Schmitz, DD Pollock, D Haussler, EW Triplett, G Zhang, N Irie, ED Jarvis, CA Brochu, CJ Schmidt, FM McCarthy, FG Hoffmann, TC Glenn, T Gabaldón, B Paten, and DA Ray (2014) The genomes of three crocodilians provide insight into archosaur evolution. Science 346:125449.

63. W Jaratlerdsiri, J Deakin, RM Godinez, X Shan, DG Peterson, S Marthey, E Lyons, FM McCarthy, SR Isberg, DP Higgins, AY Chong, J St John, TC Glenn, DA Ray, J Gongora (2014) Comparative analyses reveal adaptive MHC structure in the saltwater crocodile (Crocodylus porosus). PLoS ONE 9(12):e11463.

62. GZhang, C Li, Q Li, B Li, DM Larkin, C Lee, JF Storz, A Antunes, RW Meredith, A Ödeen, J Cui, Q Zhou, L Xu, H Pan, Z Wang, L Jin, P Zhang, H Hu, W Yang, J Hu, J Xiao, Z Yang, Y Liu, Q Xie, J Lian, P Wen, F Zhang, H Li, Y Zeng, Z Xiong, S Liu, L Zhou, Z Huang, N An, J Wang, Q Zheng, Y Xiong, G Wang, B Wang, J Wang, Y Fang, R da Fonseca, A Alfaro-Núñez, M Schubert, L Orlando, T Mourier, J Howard, G Ganapathy, J Smith, M Farré, J Narayan, G Slavov, MN Romanov, R Borges, JP Machado, I Khan, MS Springer, J Gatesy, FG Hoffmann, JC Opazo, O Håstad, MJ Greenwold, RH Sawyer, HK Kim, K-W Kim, N Li, Y Huang, MW Bruford, X Zhan, A Dixon, M Bertelsen, E Derryberry, W Warren, S Li, DA Ray, RE Green, SJ O’Brien, D Griffin, WE Johnson, D Haussler, OA Ryder, E Willerslev, G Graves, P Alström, J Fjeldså, D Mindell, SV Edwards, EL Braun, C Rahbek, DW Burt, P Houde, Y Zhang, H Yang, J Wang, ED Jarvis, MTP Gilbert, J Wang, and the Avian Genome Consortium (2014) Comparative genomics reveals insights into avian genome evolution and adaptation. Science 346:1311-1320.

61. ED Jarvis, S Mirarab, AJ Aberer, B Li, P Houde, C Li, SYW Ho, BC Faircloth, B Nabholz, JT Howard, A Suh, CC Weber, RR da Fonseca, J Li, F Zhang, H Li, L Zhou, N Narula, L Liu, G Ganapathy, B Boussau, MS Bayzid, V Zavidovych, S Subramanian, T Gabaldón, S Capella-Gutiérrez, J Huerta-Cepas, B Rekepalli, K Munch, M Schierup, B Lindow, WC Warren, D Ray, RE Green, M Bruford, X Zhan, A Dixon, S Li, N Li, Y Huang, EP Derryberry, MF Bertelsen, F Sheldon, RT Brumfield, C Mello, PV Lovell, M Wirthlin, JA Samaniego, AMV Velazquez, A Alfaro-Núñez, PF Campos, T Sicheritz-Ponten, A Pas, T Bailey, P Scofield, M Bunce, D Lambert, Q Zhou, P Perelman, AC Driskell, G Ruby, B Shapiro, Z Xiong, Y Zeng, S Liu, Z Li, B Liu, K Wu, J Xiao, X Yinqi, Q Zheng, Y Zhang, H Yang, J Wang, L Smeds, FE Rheindt, M Braun, J Fjeldsa, L Orlando, K Barker, KA Jønsson, W Johnson, K-P Koepfli, S O'Brien, D Haussler, OA Ryder, C Rahbek, E Willerslev, GR Graves, TC Glenn, J McCormack, D Burt, H Ellegren, P Alström, S Edwards, A Stamatakis, DP Mindell, J Cracraft, EL Braun, T Warnow, W Jun, MTP Gilbert and G Zhang (2014) Whole genome analyses resolve the early branches in the tree of life of modern birds. Science 346:1320-1321

60. RN Platt, MW Vandewege, C Kern, CJ Schmidt, FG Hoffmann, DA Ray (2014) Large numbers of novel miRNAs originate from DNA transposons and are coincident with a large species radiation in bats. Molecular Biology and Evolution 31(6):1536-1545.

59. JB Johnson, JH Roberts, TL King, JW Edwards, WM Ford, DA Ray (2014) Genetic structuring of northern myotis (Myotis septentrionalis) at multiple spatial scales. Acta Theriologica 59(2):223-231).

- 2013 -

58. TA Castoe, APJ de Koning, KT Hall, DC Card, DR Schield, MK Fujita, RP Ruggiero, JF Degner, JM Daza, W Gu, J Reyes-Velasco, KJ Shaney, JM Castoe, SE Fox, AW Poole, D Polanco, J Dobry, MW Vandewege, Q Li, R Schott, A Kapusta, P Minx, C Feschotte, P Uetz, DA Ray, FG Hoffman, R Bogden, EN Smith, BSW Chang, F Vonk, NR Casewell, CV Henkel, MK Richardson, SP Mackessy, AM Bronikowski, M Yandell, WC Warren, SM Secor, and DD Pollock (2013) The Burmese python genome reveals the molecular basis for extreme adaptation in snakes. Proceedings of the National Academy of Sciences, USA 110(51):20645-20650.

57. CA Lavoie, RN Platt, PA Novick, BA Counterman and DA Ray (2013) Transposable element evolution in Heliconius suggests genome diversity within Lepidoptera. Mobile DNA 2013 4:21.

56. M Supple, H Hines, C Lavoie, DA Ray, D Nielson, C Salazar, D Dasmahapatra, WO McMillan and B Counterman (2013) Genomic architecture of adaptive color pattern divergence and convergence in Heliconius butterflies. Genome Research 2013 23:1248-1257.

55. R-L Ge, Q Cai, Y-Y Shen, A San, L Ma,Y Zhang, X Yi, Y Chen, L Yang, Y Huang, R He, Y Hui, M Hao, Y Li, B Wang, X Ou, J Xu, Y Zhang, K Wu, C Geng, W Zhou, Y Zhou, DM Irwin, Y Yang, L Ying, H Bao, J Kim, DM Larkin, J Ma, HA Lewin, J Xing, RN Platt, DA Ray, L Auvil,  B Capitanu, X Zhang, G Zhang, RW Murphy, J Wang, Y-P Zhang, and J Wang (2013) Draft genome sequence of the Tibetan antelope. Nature Communications 4: 1858.

- 2012 -

54. The Heliconius Genome Consortium (2012) Butterfly genome reveals promiscuous exchange of mimicry adaptations among species. Nature 487:94-98.

53. RN Platt and DA Ray (2012) A non-LTR retroelement extinction in Spermophilus tridecemlineatus. Gene 500:47-53.

52. HJT Pagan, J Macas, P Novak, ES McColloch, RD Stevens, and DA Ray (2012) Survey sequencing reveals elevated DNA transposon activity, novel elements, and variation in repetitive landscapes among bats. Genome Biology and Evolution 4(4):575-585.

51. JA St. John, EL Braun, SR Isberg, LG Miles, AY Chong, J Gongora, P Dalzell, C Moran, B Bed'Hom, A Abzhanov, SC Burgess AM Cooksey, TA Castoe, NG Crawford, LD Densmore, JC Drew, SV Edwards, BC Faircloth, MK Fujita, MJ Greenwold, FG Hoffmann, JM Howard, T Iguchi, DE Janes, SY Khan, S Kohno, APJ de Koning, SL Lance, FM McCarthy, JE McCormack ME Merchant, DG Peterson, DD Pollock, N Pourmand, BJ Raney, KA Roessler, JR Sanford, RH Sawyer, CJ Schmidt, EW Triplett, TD Tuberville, M Venegas-Anaya, JT Howard, ED JArvis, LJ Guillette, TC Glenn, RE Green, DA Ray (2012)  Sequencing three crocodilian genomes to illuminate the evolution of archosaurs and amniotes. Genome Biology 13:415.

50. RD Stevens, MM Gavilanez, JS Tello and DA Ray (2012) Phylogenetic structure illuminates mechanistic role of environmental heterogeneity on community organization. Journal of Animal Ecology 81(2) 455-462.

49. P Chouvarine, AM Cooksey, FM McCarthy, DA Ray, BB Baldwin, SC Burgess, and DG Peterson (2012) Transcriptome-based differentiation of closely-related Miscanthus lines. PLoS ONE 7(1): e29850.

48. PR Meganathan, HJT Pagan, ES McColloch, RD Stevens and DA Ray (2012) Complete mitochondrial genome sequences of three bat species and whole genome mitochonrial analyses reveal patterns of codon bias and lend support to a basal split in Chiroptera. Gene 492:121-129.

- 2011 -

47. JD Smith and DA Ray (2011) Expedited batch processing and analysis of transposon insertions. BMC Research Notes 4:482.

46. J Alfoldi, F Di Palma, M Grabherr, C Williams, L Kong, E Mauceli, P Russell, CB Lowe, R Glor, JD Jaffe, DA Ray, S Boissinot, AM Shedlock, C Botka, TA Castoe, JK Colbourne, MK Fujita, RG Moreno, BF ten Hallers, D Haussler, A Heger, D Heiman, DE Janes, J Johnson, PJ de Jong, MY Koriabine, P Novick, CL Organ, SE Peach, S Poe, DD Pollock, K de Queiroz, T Sanger, S Searle, JD Smith, Z Smith, R Swofford, J Turner-Maier, J Wade, S Young, A Zadissa, Genome Sequencing Platform and Whole Genome Assembly Team, SV Edwards, TC Glenn, CJ Schneider, JB Losos, ES Lander, M Breen, CP Ponting and K Lindblad-Toh (2011) The genome of Anolis carolinensis, the green anole lizard, and a comparative analysis with birds and mammals. Nature 477:587-591.

45. TA Castoe, APJ de Koning, KT Hall, KD Yokoyama, W Gu, EN Smith, C Feschotte, P Uetz, DA Ray, J Dobry, R Bogden, SP Mackessy, AM Bronikowski, WC Warren, SM Secor and DD Pollock (2011) Sequencing the genome of the Burmese python (Python molurus bivittatus) as a model for studying extreme adaptations in snakes. Genome Biology 12:406.

44. PR Meganathan, B Dubey, MA Batzer, DA Ray and I Haque (2011) Complete mitochondrial genome sequences of three Crocodylus species and their comparison within the order Crocodylia. Gene 478:35-41.

43. J Thomas, M Sorourian, D Ray, RJ Baker and EJ Pritham (2011) The limited distribution of Helitrons to vesper bats supports horizontal transfer. Gene 474:52-58.

42. DA Ray and MA Batzer (2011) Reading TE leaves: New approaches to the identification of transposable element insertions. Genome Research 21:813-820.

41. P Novick, JD Smith, M Floumanhaft, DA Ray and S Boissinot (2011) The evolution and diversity of DNA transposons in the genome of the lizard Anolis carolinensis. Genome Biology and Evolution 3:1-14. 

- 2010 -

40. PR Meganathan, B Dubey, MA Batzer, DA Ray and I Haque (2010) Molecular phylogenetic analyses of Genus Crocodylus (Eusuchia, Crocodylia, Crocodylidae) and the taxonomic position of Crocodylus porosus. Molecular Phylogenetics and Evolution 57:393-402. 

39. HJT Pagan, JD Smith, RM Hubley and DA Ray (2010) PiggyBac-ing on a primate genome: Novel elements, recent activity and horizontal transfer. Genome Biology and Evolution 2:293-303.

38. DA Ray, K Han, JA Walker and MA Batzer (2010) Laboratory methods for the analysis of primate mobile elements. Pp 153-179 in "Genetic Variation: Methods and Protocols (Methods in Molecular Biology)", MR Barnes and G Breen (Eds.), Humana Press Inc., Totowa, NJ.

37. P Novick, JD Smith, DA Ray and S Boissinot (2010) Independent and parallel lateral transfer of DNA transposons in tetrapod genomes. Gene 449:85-94.

- 2009 -

36. DA Ray, RN Platt and MA Batzer (2009) Reading between the LINEs to see into the past. Trends in Genetics 25(11):475-479.

35. ML Thompson, AE Gauna, ML Williams and DA Ray (2009) Multiple chicken repeat 1 (CR1) lineages in the genomes of oestroid flies. Gene 448:40-45. 

34. X Shan, DA Ray, JA Bunge and DG 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.

- 2008 -

33. DA Ray, C Feschotte, HJT Pagan, JD Smith, E Pritham, P Arensburger, PW Atkinson and NL Craig (2008) Multiple waves of recent DNA transposon activity in the bat, Myotis lucifugus. Genome Research 18:717-728. Cover illustration.

32. WC Warre, LW Hillier, JAM Graves, E Birney, CP Ponting, F Grutzner, K Belov, W Miller, L Clarke, AT Chinwalla, S-P Yang, A Heger, D Locke, P Miethke, PD Waters, F Veyrunes, L Fulton, B Fulton, T Graves, J Wallis, XS Puente, C Lopez-Otin, GR Ordonez, EE Eichler, L Chen, Z Cheng, JE Deakin, A Alsop, K Thompson, P Kirby, AT Papenfuss, MJ Wakefield, T Olender, D Lancet, GA Huttley, AFA Smit, A Pask, P Temple-Smith, MA Batzer, JA Walker, MK Konkel, RS Harris, CM Whittington, ESW Wong, N Gemmell, E Buschiazzo, IV Jentzsch, A Merkel, J Schmitz, A Zemann, G Churakov, JO 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, CM Lefevre, JA Sharp, KR Nicholas, DA Ray, M Kube, R Reinhard, TH Pringle, J Taylor, RC 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, ER Mardis and RK Wilson (2008) Genome analysis of the platypus reveals unique signatures of evolution. Nature 453:175-183.

31. TR Rainwater, KW Selcer, LM Nespoli, AG Finger, DA Ray, SG Platt, PN Smith, LD Densmore, TA Anderson and ST McMurry (2008) Plasma vitellogenin in Morelet's crocodiles from contaminated habitats in northern Belize. Environmental Pollution 153:101-109.

- 2007 -

30. J Xing, DJ Witherspoon, DA Ray, MA Batzer and LB Jorde (2007) Mobile Elements and Primate Evolution. Yearbook of Physical Anthropology 50:2-19.

29. TS Mikkelsen, B Aken, CT Amemiya, JL Chang, S Duke, M Garber, AJ Gentles, L Goodstadt, A Heger, J Jurka, M Kamal, E Mauceli, SMJ Searle, T Sharpe, ML Baker, MA Batzer, PV Benos, K Belov, M Clamp, A Cook, J Cuff, R Das, JE Deakin, M Grabherr, JM Greally, W Gu, RL Jirtle, S Mahony, MA Marra, RD Miller, RD Nicholls, AT Papenfuss, ZE Parra, DD Pollock, DA Ray, JE Schein, TP Speed, JL VandeBerg, MJ Wakefield, CM Wade, JA Walker, C Webber, JR Weidman, X Xie, MC Zody, Broad Institute Genome Sequencing Platform, Broad Institute Whole Genome Assembly Team, JA Marshall Graves, CP Ponting, M Breen, PB Samollow, ES Lander and 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. W Gu*, DA Ray*, JA Walker, E Barnes, AJ Gentles, PB Somollow, J Jurka, MA Batzer and DD Pollock (2007) SINEs, evolution and genome structure in the opossum. Gene 396(1):46-58. * These authors contributed equally to this work.

27. J Xing, H Wang, Y Zhang, DA Ray, AJ Tosi, TR Disotell and MA Batzer (2007) A mobile element based evolutionary history of guenons (Tribe Cercopithicini). BMC Biology 5:5.

26. DA Ray, HJT Pagan, ML Thompson, RD Stevens (2007) Bats with hATs: Evidence for recent DNA transposon activity in genus Myotis. Molecular Biology and Evolution 24:632-639.

25. SW Herke, J Xing, DA Ray, JW Zimmerman, R Cordaux and MA Batzer (2007) A SINE-based dichotomous key for primate identification. Gene 390:39-51. 

24. DA Ray*, JA Walker* and MA Batzer (2007) Mobile element-based forensic genomics. Mutation Research 616: 24-33. *These authors contributed equally to this work.

23. DA Ray (2007) SINEs of progress: Mobile element applications for molecular ecology. Molecular Ecology 16:19-33. 

- 2006 -

22. DJ Witherspoon, EE Marchani, WS Watkins, CT Ostler, SP Wooding, BA Anders, JD Fowlkes, S Boissinot, AV Furano, DA Ray, AR Rogers, MA Batzer and LB Jorde (2006) Human population genetic structure and diversity inferred from polymorphic L1 (LINE-1) and Alu insertions. Human Heredity 62:30-46.

21. DA Ray, J Xing, A-H Salem and MA Batzer (2006) SINEs of a nearly perfect character: Applications of the SINE method to phylogeny and population biology. Systematic Biology 55:928-935.

20. KW Selcer, LM Nespoli, TR Rainwater, AG Finger, DA Ray, SG Platt, PN Smith, LD Densmore and ST 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. LR McAliley, RE Willis, DA Ray, PS White, CA Brochu and LD Densmore (2006) Are crocodiles really monophyletic? Evidence for subdivisions from sequence and morphological data. Molecular Phylogenetics and Evolution 39:16-32.

18. J Wang, L Song, MK Gonder, SA Tishkoff, S Azrak, DA Ray, MA Batzer and P Liang (2006) Whole genome computational comparative genomics:  a fruitful approach for ascertaining Alu insertion polymorphisms. Gene 365:11-20.

- 2005 -

17. DA Ray and M.A. Batzer (2005) Tracking Alu evolution in New World primates. BMC Evolutionary Biology 5:51.

16. DA Ray, DJ Hedges, SW Herke, JD Fowlkes, EW Barnes, DK LaVie, LM Goodwin and MA Batzer (2005) Chompy: An infestation of MITE-like repetitive elements in the crocodilian genome. Gene 362 (2005) 1-10.

15. DA Ray, JA Walker, A Hall, B Llewellyn, J Ballantyne, AT Christian, K Turtletaub and  MA Batzer (2005) Inference of human geographic origins using Alu insertion polymorphisms. Forensic Science International. 153:117-124. 

14. J Xing, H Wang, K Han, DA Ray, CH Huang, LG Chemnick, C-B Stewart, T Disotell, OA Ryder and MA Batzer (2005) A mobile element based phylogeny of Old World monkeys. Molecular Phylogenetics and Evolution 37: 872-880. 

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

12. HJ Ho, DA Ray, AH Salem, JS Myers and MA Batzer (2005) Straightening out the LINEs: LINE-1 element orthologous loci. Genomics 85:201-207.

11. DA Ray, J Xing, DJ Hedges, MA Hall, ME Laborde, BA Anders, BR White, N Stoilova, JD Fowlkes, KE Landry, LG Chemnick, OA Ryder and MA Batzer (2005) Alu insertion loci and platyrrhine primate phylogeny. Molecular Phylogenetics and Evolution 35(1):117-126. 

10. A-H Salem, DA Ray and MA Batzer (2005) Identity by descent and DNA sequence variation of human SINE and LINE elements.  Cytogenetic and Genome Research 108: 63-72.

- 2004 -

9. AC Otieno, AB Carter, DJ Hedges, JA Walker, DA Ray, RK Garber, BAAnders, N Stoilova, ME Laborde, JD Fowlkes, CH Huang, B Perodeau and MA Batzer (2004) Analysis of the human Alu Ya-lineage. Journal of Molecular Biology 342: 109-118.

8. DA Ray, JA Dever, SG Platt, TR Rainwater, AG Finger, ST McMurry, MA Batzer, B Barr, PJ Stafford, J McKnight and LD Densmore (2004) Low levels of nucleotide diversity in Crocodylus moreletii and evidence of hybridization with C. acutus. Conservation Genetics 5(4): 449-462.

7. Z Gonzalez, DA Ray, LR McAliley, MJ Gray, C Perchellet, LMSmith and LD Densmore (2004) A set of polymorphic microsatellite markers for the Great Plains Toad, Bufo cognatus. Molecular Ecology Notes 4(1): 9-10.

- 2003 -

6. A-H Salem*, DA Ray*, J Xing, PA Callinan, JS Myers, DJ Hedges, RK Garber, DJ Witherspoon, LB Jorde and MA 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. 

5. PJ Stafford, ST McMurry, TR Rainwater, DA Ray, LD Densmore and BBarr (2003) Morelet's crocodile (Crocodylus moreletii) in the Macal River watershed, Maya Mountains, Belize. Herpetological Bulletin 85: 15-23.

4. DA Ray and LD 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.

- 2002 -

3. DA Ray and LD 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. LD Densmore and DA 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 Panama" pp. 136-150 Asociacon Panamena de Manejadores y Especialistas de Crocodylia, Panama, Republica de Panama. (English version: pp. 205-214.).

- 2001 -

1. DA Ray, PS White, HV Duong, T Cullen and LD 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.