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David A. Ray, B.S., M.A.T., Ph.D. - Publications

Affiliations: 
2005-2009 Biology West Virginia University, Morgantown, WV, United States 
 2009-2013 Biochemistry and Molecular Biology Mississippi State University, Starkville, MS, United States 
 2013- Biological Sciences Texas Tech University, Lubbock 
Area:
Molecular Evolution, Phylogenetics, Genomics
Website:
http://www.biol.ttu.edu/facultylist.aspx?id=david.a.ray@ttu.edu
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99 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Christmas MJ, Kaplow IM, Genereux DP, Dong MX, Hughes GM, Li X, Sullivan PF, Hindle AG, Andrews G, Armstrong JC, Bianchi M, Breit AM, Diekhans M, Fanter C, Foley NM, ... ... Ray DA, ... ... Ray DA, et al. Evolutionary constraint and innovation across hundreds of placental mammals. Science (New York, N.Y.). 380: eabn3943. PMID 37104599 DOI: 10.1126/science.abn3943  0.5
2023 Osmanski AB, Paulat NS, Korstian J, Grimshaw JR, Halsey M, Sullivan KAM, Moreno-Santillán DD, Crookshanks C, Roberts J, Garcia C, Johnson MG, Densmore LD, Stevens RD, Rosen J, Storer JM, ... ... Ray DA, ... ... Ray DA, et al. Insights into mammalian TE diversity through the curation of 248 genome assemblies. Science (New York, N.Y.). 380: eabn1430. PMID 37104570 DOI: 10.1126/science.abn1430  0.755
2023 Paulat NS, Storer JM, Moreno-Santillán DD, Osmanski AB, Sullivan KAM, Grimshaw JR, Korstian J, Halsey M, Garcia CJ, Crookshanks C, Roberts J, Smit AFA, Hubley R, Rosen J, Teeling EC, ... ... Ray DA, et al. Chiropterans are a hotspot for horizontal transfer of DNA transposons in Mammalia. Molecular Biology and Evolution. PMID 37071810 DOI: 10.1093/molbev/msad092  0.792
2023 De S, Kingan SB, Kitsou C, Portik DM, Foor SD, Frederick JC, Rana VS, Paulat NS, Ray DA, Wang Y, Glenn TC, Pal U. A high-quality Ixodes scapularis genome advances tick science. Nature Genetics. PMID 36658436 DOI: 10.1038/s41588-022-01275-w  0.458
2022 Paulat NS, McGuire E, Subramanian K, Osmanski AB, Moreno-Santillán DD, Ray DA, Xing J. Transposable Elements in Bats Show Differential Accumulation Patterns Determined by Class and Functionality. Life (Basel, Switzerland). 12. PMID 36013369 DOI: 10.3390/life12081190  0.715
2022 Doronina L, Hughes GM, Moreno-Santillan D, Lawless C, Lonergan T, Ryan L, Jebb D, Kirilenko BM, Korstian JM, Dávalos LM, Vernes SC, Myers EW, Teeling EC, Hiller M, Jermiin LS, ... ... Ray DA, et al. Contradictory Phylogenetic Signals in the Laurasiatheria Anomaly Zone. Genes. 13. PMID 35627151 DOI: 10.3390/genes13050766  0.807
2022 Korstian JM, Paulat NS, Platt RN, Stevens RD, Ray DA. SINE-Based Phylogenomics Reveal Extensive Introgression and Incomplete Lineage Sorting in . Genes. 13. PMID 35327953 DOI: 10.3390/genes13030399  0.78
2022 Vandewege MW, Platt RN, Merriman DK, Ray DA, Hoffmann FG. The PIWI/piRNA response is relaxed in a rodent that lacks mobilizing transposable elements. Rna (New York, N.Y.). PMID 35064043 DOI: 10.1261/rna.078862.121  0.357
2021 Gutierrez J, Platt R, Opazo JC, Ray DA, Hoffmann F, Vandewege M. Evolutionary history of the vertebrate Piwi gene family. Peerj. 9: e12451. PMID 34760405 DOI: 10.7717/peerj.12451  0.387
2020 Jebb D, Huang Z, Pippel M, Hughes GM, Lavrichenko K, Devanna P, Winkler S, Jermiin LS, Skirmuntt EC, Katzourakis A, Burkitt-Gray L, Ray DA, Sullivan KAM, Roscito JG, Kirilenko BM, et al. Six reference-quality genomes reveal evolution of bat adaptations. Nature. 583: 578-584. PMID 32699395 DOI: 10.1038/S41586-020-2486-3  0.514
2020 Louha S, Ray DA, Winker K, Glenn TC. A High-Quality Genome Assembly of the North American Song Sparrow, . G3 (Bethesda, Md.). PMID 32075855 DOI: 10.1534/G3.119.400929  0.531
2020 Lindsey LL, Platt RN, Phillips CD, Ray DA, Bradley RD. Differential Expression in Testis and Liver Transcriptomes from Four Species of Peromyscus (Rodentia: Cricetidae). Genome Biology and Evolution. PMID 31909812 DOI: 10.1093/Gbe/Evz280  0.303
2020 Volleth M, Volleth M, Müller S, Anwarali Khan FA, Yong H, Heller K, Baker RJ, Ray DA, Sotero-Caio CG. Cytogenetic Investigations in Emballonuroidea. I. Taphozoinae and Emballonurinae Karyotypes Evolve at Different Rates and Share No Derived Chromosomal Characters Acta Chiropterologica. 21: 257. DOI: 10.3161/15081109Acc2019.21.2.002  0.304
2019 Ghosh A, Johnson MG, Osmanski AB, Louha S, Bayona-Vásquez NJ, Glenn TC, Gongora J, Green RE, Isberg S, Stevens RD, Ray DA. A high-quality reference genome assembly of the saltwater crocodile, Crocodylus porosus, reveals patterns of selection in Crocodylidae. Genome Biology and Evolution. PMID 31821505 DOI: 10.1093/Gbe/Evz269  0.501
2019 Ray DA, Grimshaw JR, Halsey MK, Korstian JM, Osmanski AB, Am Sullivan K, Wolf KA, Reddy H, Foley N, Stevens RD, Knisbacher B, Levy O, Counterman B, Edelman NB, Mallet J. 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. PMID 31214686 DOI: 10.1093/Gbe/Evz125  0.848
2018 Doronina L, Reising O, Clawson H, Ray DA, Schmitz J. True Homoplasy of Retrotransposon Insertions in Primates. Systematic Biology. PMID 30445649 DOI: 10.1093/Sysbio/Syy076  0.541
2018 Platt RN, Vandewege MW, Ray DA. Mammalian transposable elements and their impacts on genome evolution. Chromosome Research : An International Journal On the Molecular, Supramolecular and Evolutionary Aspects of Chromosome Biology. PMID 29392473 DOI: 10.1007/S10577-017-9570-Z  0.563
2017 Teeling E, Vernes S, Davalos LM, Ray DA, Gilbert MTP, Myers E, Bat K Consortium. Bat Biology, Genomes, and the Bat1K Project: To Generate Chromosome-Level Genomes for all Living Bat Species. Annual Review of Animal Biosciences. PMID 29166127 DOI: 10.1146/Annurev-Animal-022516-022811  0.542
2017 Platt Ii RN, Faircloth BC, Sullivan KAM, Kieran TJ, Glenn TC, Vandewege MW, Lee TE, Baker RJ, Stevens RD, Ray DA. Conflicting Evolutionary Histories of the Mitochondrial and Nuclear Genomes in New World Myotis Bats. Systematic Biology. PMID 28945862 DOI: 10.1093/Sysbio/Syx070  0.513
2017 Sotero-Caio CG, Platt RN, Suh A, Ray DA. Evolution and Diversity of Transposable Elements in Vertebrate Genomes. Genome Biology and Evolution. PMID 28158585 DOI: 10.1093/Gbe/Evw264  0.581
2017 Rice ES, Kohno S, St John J, Pham S, Howard J, Lareau L, O'Connell BL, Hickey G, Armstrong J, Deran A, Fiddes I, Platt RN, Gresham C, McCarthy F, Kern C, ... ... Ray DA, et al. Improved genome assembly of American alligator genome reveals conserved architecture of estrogen signaling. Genome Research. PMID 28137821 DOI: 10.1101/Gr.213595.116  0.392
2016 Andere AA, Platt RN, Ray DA, Picard CJ. Genome sequence of Phormia regina Meigen (Diptera: Calliphoridae): implications for medical, veterinary and forensic research. Bmc Genomics. 17: 842. PMID 27793085 DOI: 10.1186/S12864-016-3187-Z  0.484
2016 Platt RN, Mangum SF, Ray DA. Pinpointing the vesper bat transposon revolution using the Miniopterus natalensis genome. Mobile Dna. 7: 12. PMID 27489570 DOI: 10.1186/S13100-016-0071-Y  0.775
2016 Vandewege MW, Platt RN, Ray DA, Hoffmann FG. Transposable element targeting by piRNAs in Laurasiatherians with distinct transposable element histories. Genome Biology and Evolution. PMID 27060702 DOI: 10.1093/Gbe/Evw078  0.498
2016 Vandewege MW, Mangum SF, Gabaldón T, Castoe TA, Ray DA, Hoffmann FG. Contrasting patterns of evolutionary diversification in the olfactory repertoires of reptile and bird genomes. Genome Biology and Evolution. PMID 26865070 DOI: 10.1093/Gbe/Evw013  0.732
2016 Platt RN, Blanco-Berdugo L, Ray DA. Accurate transposable element annotation is vital when analyzing new genome assemblies. Genome Biology and Evolution. PMID 26802115 DOI: 10.1093/Gbe/Evw009  0.582
2015 Hoffmann FG, McGuire LP, Counterman BA, Ray DA. Transposable elements and small RNAs: Genomic fuel for species diversity. Mobile Genetic Elements. 5: 63-66. PMID 26904375 DOI: 10.1080/2159256X.2015.1066919  0.457
2015 Platt RN, Zhang Y, Witherspoon DJ, Xing J, Suh A, Keith MS, Jorde LB, Stevens RD, Ray DA. Targeted Capture of Phylogenetically Informative Ves SINE Insertions in Genus Myotis. Genome Biology and Evolution. 7: 1664-75. PMID 26014613 DOI: 10.1093/Gbe/Evv099  0.74
2015 Ray DA, Pagan HJ, Platt RN, Kroll AR, Schaack S, Stevens RD. Differential SINE evolution in vesper and non-vesper bats. Mobile Dna. 6: 10. PMID 25991928 DOI: 10.1186/S13100-015-0038-4  0.844
2015 Suh A, Churakov G, Ramakodi MP, Platt RN, Jurka J, Kojima KK, Caballero J, Smit AF, Vliet KA, Hoffmann FG, Brosius J, Green RE, Braun EL, Ray DA, Schmitz J. Multiple lineages of ancient CR1 retroposons shaped the early genome evolution of amniotes. Genome Biology and Evolution. 7: 205-17. PMID 25503085 DOI: 10.1093/Gbe/Evu256  0.525
2015 Ramakodi MP, Singh B, Wells JD, Guerrero F, Ray DA. A 454 sequencing approach to dipteran mitochondrial genome research. Genomics. 105: 53-60. PMID 25451744 DOI: 10.1016/J.Ygeno.2014.10.014  0.516
2014 Green RE, Braun EL, Armstrong J, Earl D, Nguyen N, Hickey G, Vandewege MW, St John JA, Capella-Gutiérrez S, Castoe TA, Kern C, Fujita MK, Opazo JC, Jurka J, Kojima KK, ... ... Ray DA, et al. Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs. Science (New York, N.Y.). 346: 1254449. PMID 25504731 DOI: 10.1126/Science.1254449  0.576
2014 Jarvis ED, Mirarab S, Aberer AJ, Li B, Houde P, Li C, Ho SY, Faircloth BC, Nabholz B, Howard JT, Suh A, Weber CC, da Fonseca RR, Li J, Zhang F, ... ... Ray D, et al. Whole-genome analyses resolve early branches in the tree of life of modern birds. Science (New York, N.Y.). 346: 1320-31. PMID 25504713 DOI: 10.1126/Science.1253451  0.542
2014 Zhang G, Li C, Li Q, Li B, Larkin DM, Lee C, Storz JF, Antunes A, Greenwold MJ, Meredith RW, Ödeen A, Cui J, Zhou Q, Xu L, Pan H, ... ... Ray DA, et al. Comparative genomics reveals insights into avian genome evolution and adaptation. Science (New York, N.Y.). 346: 1311-20. PMID 25504712 DOI: 10.1126/Science.1251385  0.573
2014 Jaratlerdsiri W, Deakin J, Godinez RM, Shan X, Peterson DG, Marthey S, Lyons E, McCarthy FM, Isberg SR, Higgins DP, Chong AY, John JS, Glenn TC, Ray DA, Gongora J. Comparative genome analyses reveal distinct structure in the saltwater crocodile MHC. Plos One. 9: e114631. PMID 25503521 DOI: 10.1371/Journal.Pone.0114631  0.378
2014 Suh A, Weber CC, Kehlmaier C, Braun EL, Green RE, Fritz U, Ray DA, Ellegren H. Early mesozoic coexistence of amniotes and hepadnaviridae. Plos Genetics. 10: e1004559. PMID 25501991 DOI: 10.1371/Journal.Pgen.1004559  0.479
2014 Chong AY, Kojima KK, Jurka J, Ray DA, Smit AF, Isberg SR, Gongora J. Evolution and gene capture in ancient endogenous retroviruses - insights from the crocodilian genomes. Retrovirology. 11: 71. PMID 25499090 DOI: 10.1186/S12977-014-0071-2  0.541
2014 Platt RN, Vandewege MW, Kern C, Schmidt CJ, Hoffmann FG, Ray DA. Large numbers of novel miRNAs originate from DNA transposons and are coincident with a large species radiation in bats. Molecular Biology and Evolution. 31: 1536-45. PMID 24692655 DOI: 10.1093/Molbev/Msu112  0.314
2014 Castoe TA, De Koning APJ, Hall KT, Card DC, Schield DR, Fujita MK, Ruggiero RP, Degner JF, Daza JM, Gu W, Reyes-Velasco J, Shaney KJ, Castoe JM, Fox SE, Poole AW, ... ... Ray DA, et al. The Burmese python genome reveals the molecular basis for extreme adaptation in snakes (Proceedings of the National Academy of Sciences of the United States of America (2013) 110, 51, (20645-20650) DOI: 10.1073/pnas. 1314475110) Proceedings of the National Academy of Sciences of the United States of America. 111: 3194. DOI: 10.1073/Pnas.1324133111  0.39
2014 Johnson JB, Roberts JH, King TL, Edwards JW, Ford WM, Ray DA. Genetic structuring of northern myotis (Myotis septentrionalis) at multiple spatial scales Acta Theriologica. 59: 223-231. DOI: 10.1007/S13364-013-0163-8  0.305
2013 Castoe TA, de Koning AP, Hall KT, Card DC, Schield DR, Fujita MK, Ruggiero RP, Degner JF, Daza JM, Gu W, Reyes-Velasco J, Shaney KJ, Castoe JM, Fox SE, Poole AW, ... ... Ray DA, et al. The Burmese python genome reveals the molecular basis for extreme adaptation in snakes. Proceedings of the National Academy of Sciences of the United States of America. 110: 20645-50. PMID 24297902 DOI: 10.1073/Pnas.1314475110  0.468
2013 Lavoie CA, Platt RN, Novick PA, Counterman BA, Ray DA. Transposable element evolution in Heliconius suggests genome diversity within Lepidoptera. Mobile Dna. 4: 21. PMID 24088337 DOI: 10.1186/1759-8753-4-21  0.596
2013 Supple MA, Hines HM, Dasmahapatra KK, Lewis JJ, Nielsen DM, Lavoie C, Ray DA, Salazar C, McMillan WO, Counterman BA. Genomic architecture of adaptive color pattern divergence and convergence in Heliconius butterflies. Genome Research. 23: 1248-57. PMID 23674305 DOI: 10.1101/Gr.150615.112  0.484
2013 Ge RL, Cai Q, Shen YY, San A, Ma L, Zhang Y, Yi X, Chen Y, Yang L, Huang Y, He R, Hui Y, Hao M, Li Y, Wang B, ... ... Ray DA, et al. Draft genome sequence of the Tibetan antelope. Nature Communications. 4: 1858. PMID 23673643 DOI: 10.1038/Ncomms2860  0.683
2012 Pagán HJ, Macas J, Novák P, McCulloch ES, Stevens RD, Ray DA. Survey sequencing reveals elevated DNA transposon activity, novel elements, and variation in repetitive landscapes among vesper bats. Genome Biology and Evolution. 4: 575-85. PMID 22491057 DOI: 10.1093/Gbe/Evs038  0.829
2012 Platt RN, Ray DA. A non-LTR retroelement extinction in Spermophilus tridecemlineatus. Gene. 500: 47-53. PMID 22465530 DOI: 10.1016/J.Gene.2012.03.051  0.421
2012 St John JA, Braun EL, Isberg SR, Miles LG, Chong AY, Gongora J, Dalzell P, Moran C, Bed'hom B, Abzhanov A, Burgess SC, Cooksey AM, Castoe TA, Crawford NG, Densmore LD, ... ... Ray DA, et al. Sequencing three crocodilian genomes to illuminate the evolution of archosaurs and amniotes. Genome Biology. 13: 415. PMID 22293439 DOI: 10.1186/Gb-2012-13-1-415  0.743
2012 Chouvarine P, Cooksey AM, McCarthy FM, Ray DA, Baldwin BS, Burgess SC, Peterson DG. Transcriptome-based differentiation of closely-related Miscanthus lines. Plos One. 7: e29850. PMID 22253803 DOI: 10.1371/Journal.Pone.0029850  0.47
2012 Meganathan PR, Pagan HJ, McCulloch ES, Stevens RD, Ray DA. 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. 492: 121-9. PMID 22041054 DOI: 10.1016/J.Gene.2011.10.038  0.827
2012 Stevens RD, Gavilanez MM, Tello JS, Ray DA. Phylogenetic structure illuminates the mechanistic role of environmental heterogeneity in community organization. The Journal of Animal Ecology. 81: 455-62. PMID 21895648 DOI: 10.1111/J.1365-2656.2011.01900.X  0.341
2011 Smith JD, Ray DA. Expedited batch processing and analysis of transposon insertions. Bmc Research Notes. 4: 482. PMID 22054356 DOI: 10.1186/1756-0500-4-482  0.478
2011 Alföldi J, Di Palma F, Grabherr M, Williams C, Kong L, Mauceli E, Russell P, Lowe CB, Glor RE, Jaffe JD, Ray DA, Boissinot S, Shedlock AM, Botka C, Castoe TA, et al. The genome of the green anole lizard and a comparative analysis with birds and mammals. Nature. 477: 587-91. PMID 21881562 DOI: 10.1038/Nature10390  0.573
2011 Castoe TA, de Koning JA, Hall KT, Yokoyama KD, Gu W, Smith EN, Feschotte C, Uetz P, Ray DA, Dobry J, Bogden R, Mackessy SP, Bronikowski AM, Warren WC, Secor SM, et al. Sequencing the genome of the Burmese python (Python molurus bivittatus) as a model for studying extreme adaptations in snakes. Genome Biology. 12: 406. PMID 21801464 DOI: 10.1186/Gb-2011-12-7-406  0.528
2011 Ray DA, Batzer MA. Reading TE leaves: new approaches to the identification of transposable element insertions. Genome Research. 21: 813-20. PMID 21632748 DOI: 10.1101/Gr.110528.110  0.685
2011 Meganathan PR, Dubey B, Batzer MA, Ray DA, Haque I. Complete mitochondrial genome sequences of three Crocodylus species and their comparison within the Order Crocodylia. Gene. 478: 35-41. PMID 21310220 DOI: 10.1016/J.Gene.2011.01.012  0.662
2011 Thomas J, Sorourian M, Ray D, Baker RJ, Pritham EJ. The limited distribution of Helitrons to vesper bats supports horizontal transfer. Gene. 474: 52-8. PMID 21193022 DOI: 10.1016/J.Gene.2010.12.007  0.565
2011 Novick PA, Smith JD, Floumanhaft M, Ray DA, Boissinot S. The evolution and diversity of DNA transposons in the genome of the Lizard Anolis carolinensis. Genome Biology and Evolution. 3: 1-14. PMID 21127169 DOI: 10.1093/Gbe/Evq080  0.577
2010 Pagan HJ, Smith JD, Hubley RM, Ray DA. PiggyBac-ing on a primate genome: novel elements, recent activity and horizontal transfer. Genome Biology and Evolution. 2: 293-303. PMID 20624734 DOI: 10.1093/Gbe/Evq021  0.827
2010 Meganathan PR, Dubey B, Batzer MA, Ray DA, Haque I. Molecular phylogenetic analyses of genus Crocodylus (Eusuchia, Crocodylia, Crocodylidae) and the taxonomic position of Crocodylus porosus. Molecular Phylogenetics and Evolution. 57: 393-402. PMID 20601012 DOI: 10.1016/J.Ympev.2010.06.011  0.593
2010 Ray DA, Han K, Walker JA, Batzer MA. Laboratory methods for the analysis of primate mobile elements. Methods in Molecular Biology (Clifton, N.J.). 628: 153-79. PMID 20238081 DOI: 10.1007/978-1-60327-367-1_9  0.746
2010 Novick P, Smith J, Ray D, Boissinot S. Independent and parallel lateral transfer of DNA transposons in tetrapod genomes. Gene. 449: 85-94. PMID 19747963 DOI: 10.1016/J.Gene.2009.08.017  0.513
2010 Thompson ML, Gauna AE, Williams ML, Ray DA. Corrigendum to Multiple Chicken Repeat 1 (CR1) lineages in the genomes of oestroid flies [GENE 448/1 (2009) 40-45] Gene. 468: 58. DOI: 10.1016/J.Gene.2010.07.010  0.444
2010 Thompson ML, Gauna AE, Williams ML, Ray DA. Corrigendum to Multiple Chicken Repeat 1 (CR1) lineages in the genomes of oestroid flies [GENE 448/1 (2009) 40-45] Gene. 468: 58. DOI: 10.1016/j.gene.2010.07.010  0.335
2009 Ray DA, Platt RN, Batzer MA. Reading between the LINEs to see into the past. Trends in Genetics : Tig. 25: 475-9. PMID 19837475 DOI: 10.1016/J.Tig.2009.09.006  0.7
2009 Thompson ML, Gauna AE, Williams ML, Ray DA. Multiple chicken repeat 1 lineages in the genomes of oestroid flies. Gene. 448: 40-5. PMID 19716865 DOI: 10.1016/J.Gene.2009.08.010  0.573
2009 Shan X, Ray DA, Bunge JA, Peterson DG. A bacterial artificial chromosome library for the Australian saltwater crocodile (Crocodylus porosus) and its utilization in gene isolation and genome characterization. Bmc Genomics. 10: S9. PMID 19607660 DOI: 10.1186/1471-2164-10-S2-S9  0.502
2008 Warren WC, Hillier LW, Marshall Graves JA, Birney E, Ponting CP, Grützner F, Belov K, Miller W, Clarke L, Chinwalla AT, Yang SP, Heger A, Locke DP, Miethke P, Waters PD, ... ... Ray DA, et al. Genome analysis of the platypus reveals unique signatures of evolution. Nature. 453: 175-83. PMID 18464734 DOI: 10.1038/Nature06936  0.668
2008 Ray DA, Feschotte C, Pagan HJ, Smith JD, Pritham EJ, Arensburger P, Atkinson PW, Craig NL. Multiple waves of recent DNA transposon activity in the bat, Myotis lucifugus. Genome Research. 18: 717-28. PMID 18340040 DOI: 10.1101/Gr.071886.107  0.841
2008 Rainwater TR, Selcer KW, Nespoli LM, Finger AG, Ray DA, Platt SG, Smith PN, Densmore LD, Anderson TA, McMurry ST. Plasma vitellogenin in Morelet's crocodiles from contaminated habitats in northern Belize. Environmental Pollution (Barking, Essex : 1987). 153: 101-9. PMID 17826876 DOI: 10.1016/J.Envpol.2007.07.018  0.619
2008 Warren WC, Hillier LW, Marshall Graves JA, Birney E, Ponting CP, Grützner F, Belov K, Miller W, Clarke L, Chinwalla AT, Yang SP, Heger A, Locke DP, Miethke P, Waters PD, ... ... Ray DA, et al. Genome analysis of the platypus reveals unique signatures of evolution (Nature (2008) 453, (175-183)) Nature. 455: 256. DOI: 10.1038/Nature07253  0.699
2008 Warren WC, Hillier LW, Marshall Graves JA, Birney E, Ponting CP, Grützner F, Belov K, Miller W, Clarke L, Chinwalla AT, Yang SP, Heger A, Locke DP, Miethke P, Waters PD, ... ... Ray DA, et al. Genome analysis of the platypus reveals unique signatures of evolution (Nature (2008) 453, (175-183)) Nature. 455: 256. DOI: 10.1038/nature07253  0.433
2007 Xing J, Witherspoon DJ, Ray DA, Batzer MA, Jorde LB. Mobile DNA elements in primate and human evolution. American Journal of Physical Anthropology. 2-19. PMID 18046749 DOI: 10.1002/Ajpa.20722  0.794
2007 Mikkelsen TS, Wakefield MJ, Aken B, Amemiya CT, Chang JL, Duke S, Garber M, Gentles AJ, Goodstadt L, Heger A, Jurka J, Kamal M, Mauceli E, Searle SM, Sharpe T, ... ... Ray DA, et al. Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences. Nature. 447: 167-77. PMID 17495919 DOI: 10.1038/Nature05805  0.696
2007 Gu W, Ray DA, Walker JA, Barnes EW, Gentles AJ, Samollow PB, Jurka J, Batzer MA, Pollock DD. SINEs, evolution and genome structure in the opossum. Gene. 396: 46-58. PMID 17442506 DOI: 10.1016/J.Gene.2007.02.028  0.684
2007 Xing J, Wang H, Zhang Y, Ray DA, Tosi AJ, Disotell TR, Batzer MA. A mobile element-based evolutionary history of guenons (tribe Cercopithecini). Bmc Biology. 5: 5. PMID 17266768 DOI: 10.1186/1741-7007-5-5  0.757
2007 Ray DA. SINEs of progress: Mobile element applications to molecular ecology. Molecular Ecology. 16: 19-33. PMID 17181718 DOI: 10.1111/J.1365-294X.2006.03104.X  0.42
2007 Ray DA, Walker JA, Batzer MA. Mobile element-based forensic genomics. Mutation Research. 616: 24-33. PMID 17161440 DOI: 10.1016/J.Mrfmmm.2006.11.019  0.696
2007 Ray DA, Pagan HJ, Thompson ML, Stevens RD. Bats with hATs: evidence for recent DNA transposon activity in genus Myotis. Molecular Biology and Evolution. 24: 632-9. PMID 17150974 DOI: 10.1093/Molbev/Msl192  0.843
2007 Herke SW, Xing J, Ray DA, Zimmerman JW, Cordaux R, Batzer MA. A SINE-based dichotomous key for primate identification. Gene. 390: 39-51. PMID 17056208 DOI: 10.1016/J.Gene.2006.08.015  0.78
2006 Ray DA, Xing J, Salem AH, Batzer MA. SINEs of a nearly perfect character. Systematic Biology. 55: 928-35. PMID 17345674 DOI: 10.1080/10635150600865419  0.717
2006 Witherspoon DJ, Marchani EE, Watkins WS, Ostler CT, Wooding SP, Anders BA, Fowlkes JD, Boissinot S, Furano AV, Ray DA, Rogers AR, Batzer MA, Jorde LB. Human population genetic structure and diversity inferred from polymorphic L1(LINE-1) and Alu insertions. Human Heredity. 62: 30-46. PMID 17003565 DOI: 10.1159/000095851  0.617
2006 McAliley LR, Willis RE, Ray DA, White PS, Brochu CA, Densmore LD. Are crocodiles really monophyletic?--Evidence for subdivisions from sequence and morphological data. Molecular Phylogenetics and Evolution. 39: 16-32. PMID 16495085 DOI: 10.1016/J.Ympev.2006.01.012  0.705
2006 Selcer KW, Nespoli LM, Rainwater TR, Finger AG, Ray DA, Platt SG, Smith PN, Densmore LD, McMurry ST. Development of an enzyme-linked immunosorbent assay for vitellogenin of Morelet's crocodile (Crocodylus moreletii). Comparative Biochemistry and Physiology. Toxicology & Pharmacology : Cbp. 143: 50-8. PMID 16448857 DOI: 10.1016/J.Cbpc.2005.12.001  0.61
2006 Wang J, Song L, Gonder MK, Azrak S, Ray DA, Batzer MA, Tishkoff SA, Liang P. Whole genome computational comparative genomics: A fruitful approach for ascertaining Alu insertion polymorphisms. Gene. 365: 11-20. PMID 16376498 DOI: 10.1016/J.Gene.2005.09.031  0.718
2005 Ray DA, Batzer MA. Tracking Alu evolution in New World primates. Bmc Evolutionary Biology. 5: 51. PMID 16209711 DOI: 10.1186/1471-2148-5-51  0.73
2005 Ray DA, Hedges DJ, Herke SW, Fowlkes JD, Barnes EW, LaVie DK, Goodwin LM, Densmore LD, Batzer MA. Chompy: an infestation of MITE-like repetitive elements in the crocodilian genome. Gene. 362: 1-10. PMID 16183215 DOI: 10.1016/J.Gene.2005.07.010  0.848
2005 Ray DA, Walker JA, Hall A, Llewellyn B, Ballantyne J, Christian AT, Turteltaub K, Batzer MA. Inference of human geographic origins using Alu insertion polymorphisms. Forensic Science International. 153: 117-24. PMID 16139099 DOI: 10.1016/J.Forsciint.2004.10.017  0.572
2005 Xing J, Wang H, Han K, Ray DA, Huang CH, Chemnick LG, Stewart CB, Disotell TR, Ryder OA, Batzer MA. A mobile element based phylogeny of Old World monkeys. Molecular Phylogenetics and Evolution. 37: 872-80. PMID 15936216 DOI: 10.1016/J.Ympev.2005.04.015  0.826
2005 Ray DA, Xing J, Hedges DJ, Hall MA, Laborde ME, Anders BA, White BR, Stoilova N, Fowlkes JD, Landry KE, Chemnick LG, Ryder OA, Batzer MA. Alu insertion loci and platyrrhine primate phylogeny. Molecular Phylogenetics and Evolution. 35: 117-26. PMID 15737586 DOI: 10.1016/J.Ympev.2004.10.023  0.853
2005 Salem AH, Ray DA, Hedges DJ, Jurka J, Batzer MA. Analysis of the human Alu Ye lineage. Bmc Evolutionary Biology. 5: 18. PMID 15725352 DOI: 10.1186/1471-2148-5-18  0.833
2005 Ho HJ, Ray DA, Salem AH, Myers JS, Batzer MA. Straightening out the LINEs: LINE-1 orthologous loci. Genomics. 85: 201-7. PMID 15676278 DOI: 10.1016/J.Ygeno.2004.10.016  0.804
2005 Salem AH, Ray DA, Batzer MA. Identity by descent and DNA sequence variation of human SINE and LINE elements. Cytogenetic and Genome Research. 108: 63-72. PMID 15545717 DOI: 10.1159/000080803  0.66
2004 Otieno AC, Carter AB, Hedges DJ, Walker JA, Ray DA, Garber RK, Anders BA, Stoilova N, Laborde ME, Fowlkes JD, Huang CH, Perodeau B, Batzer MA. Analysis of the human Alu Ya-lineage. Journal of Molecular Biology. 342: 109-18. PMID 15313610 DOI: 10.1016/J.Jmb.2004.07.016  0.808
2004 Gonzalez Z, Ray DA, McAliley LR, Gray MJ, Perchellet C, Smith LM, Densmore LD. Five polymorphic microsatellite markers for the Great Plains toad, Bufo cognatus Molecular Ecology Notes. 4: 9-10. DOI: 10.1046/J.1471-8286.2003.00546.X  0.736
2004 Ray DA, Dever JA, Platt SG, Rainwater TR, Finger AG, McMurry ST, Batzer MA, Barr B, Stafford PJ, McKnight J, Densmore LD. Low levels of nucleotide diversity in Crocodylus moreletii and evidence of hybridization with C. acutus Conservation Genetics. 5: 449-462. DOI: 10.1023/B:Coge.0000041024.96928.Fe  0.785
2003 Salem AH, Ray DA, Xing J, Callinan PA, Myers JS, Hedges DJ, Garber RK, Witherspoon DJ, Jorde LB, Batzer MA. Alu elements and hominid phylogenetics. Proceedings of the National Academy of Sciences of the United States of America. 100: 12787-91. PMID 14561894 DOI: 10.1073/Pnas.2133766100  0.815
2003 Ray DA, Densmore LD. Repetitive sequences in the crocodilian mitochondrial control region: poly-A sequences and heteroplasmic tandem repeats. Molecular Biology and Evolution. 20: 1006-13. PMID 12716979 DOI: 10.1093/Molbev/Msg117  0.713
2003 Stafford PJ, McMurry ST, Rainwater TR, Ray DA, Densmore LD, Barr B. Morelet's Crocodile (Crocodylus moreletii) in the Macal River watershed, Maya Mountains, Belize Herpetological Bulletin. 15-23.  0.699
2002 Ray DA, Densmore L. The crocodilian mitochondrial control region: general structure, conserved sequences, and evolutionary implications. The Journal of Experimental Zoology. 294: 334-45. PMID 12461813 DOI: 10.1002/Jez.10198  0.702
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