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Items: 1 to 50 of 99

1.

Mammalian transposable elements and their impacts on genome evolution.

Platt RN 2nd, Vandewege MW, Ray DA.

Chromosome Res. 2018 Mar;26(1-2):25-43. doi: 10.1007/s10577-017-9570-z. Epub 2018 Feb 1. Review.

2.

Bat Biology, Genomes, and the Bat1K Project: To Generate Chromosome-Level Genomes for All Living Bat Species.

Teeling EC, Vernes SC, Dávalos LM, Ray DA, Gilbert MTP, Myers E; Bat1K Consortium.

Annu Rev Anim Biosci. 2018 Feb 15;6:23-46. doi: 10.1146/annurev-animal-022516-022811. Epub 2017 Nov 20.

PMID:
29166127
3.

Conflicting Evolutionary Histories of the Mitochondrial and Nuclear Genomes in New World Myotis Bats.

Platt RN 2nd, Faircloth BC, Sullivan KAM, Kieran TJ, Glenn TC, Vandewege MW, Lee TE Jr, Baker RJ, Stevens RD, Ray DA.

Syst Biol. 2018 Mar 1;67(2):236-249. doi: 10.1093/sysbio/syx070.

4.

Evolution and Diversity of Transposable Elements in Vertebrate Genomes.

Sotero-Caio CG, Platt RN 2nd, Suh A, Ray DA.

Genome Biol Evol. 2017 Jan 1;9(1):161-177. doi: 10.1093/gbe/evw264. Review.

5.

Improved genome assembly of American alligator genome reveals conserved architecture of estrogen signaling.

Rice ES, Kohno S, John JS, Pham S, Howard J, Lareau LF, O'Connell BL, Hickey G, Armstrong J, Deran A, Fiddes I, Platt RN 2nd, Gresham C, McCarthy F, Kern C, Haan D, Phan T, Schmidt C, Sanford JR, Ray DA, Paten B, Guillette LJ Jr, Green RE.

Genome Res. 2017 May;27(5):686-696. doi: 10.1101/gr.213595.116. Epub 2017 Jan 30.

6.

Bacteriostatic behavior of surface modulated silicon nitride in comparison to polyetheretherketone and titanium.

Bock RM, Jones EN, Ray DA, Sonny Bal B, Pezzotti G, McEntire BJ.

J Biomed Mater Res A. 2017 May;105(5):1521-1534. doi: 10.1002/jbm.a.35987. Epub 2017 Mar 20.

PMID:
28000413
7.
8.

Pinpointing the vesper bat transposon revolution using the Miniopterus natalensis genome.

Platt RN 2nd, Mangum SF, Ray DA.

Mob DNA. 2016 Jul 22;7:12. doi: 10.1186/s13100-016-0071-y. eCollection 2016.

9.

Transposable Element Targeting by piRNAs in Laurasiatherians with Distinct Transposable Element Histories.

Vandewege MW, Platt RN 2nd, Ray DA, Hoffmann FG.

Genome Biol Evol. 2016 May 9;8(5):1327-37. doi: 10.1093/gbe/evw078.

10.

Transposable elements and small RNAs: Genomic fuel for species diversity.

Hoffmann FG, McGuire LP, Counterman BA, Ray DA.

Mob Genet Elements. 2015 Jul 24;5(5):63-66. eCollection 2015 Sep-Oct.

11.

Contrasting Patterns of Evolutionary Diversification in the Olfactory Repertoires of Reptile and Bird Genomes.

Vandewege MW, Mangum SF, Gabaldón T, Castoe TA, Ray DA, Hoffmann FG.

Genome Biol Evol. 2016 Feb 9;8(3):470-80. doi: 10.1093/gbe/evw013.

12.

Accurate Transposable Element Annotation Is Vital When Analyzing New Genome Assemblies.

Platt RN 2nd, Blanco-Berdugo L, Ray DA.

Genome Biol Evol. 2016 Jan 21;8(2):403-10. doi: 10.1093/gbe/evw009.

13.

Targeted Capture of Phylogenetically Informative Ves SINE Insertions in Genus Myotis.

Platt RN 2nd, Zhang Y, Witherspoon DJ, Xing J, Suh A, Keith MS, Jorde LB, Stevens RD, Ray DA.

Genome Biol Evol. 2015 May 25;7(6):1664-75. doi: 10.1093/gbe/evv099.

14.

Differential SINE evolution in vesper and non-vesper bats.

Ray DA, Pagan HJ, Platt RN 2nd, Kroll AR, Schaack S, Stevens RD.

Mob DNA. 2015 May 15;6:10. doi: 10.1186/s13100-015-0038-4. eCollection 2015.

15.

Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs.

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, Caballero J, Hubley RM, Smit AF, Platt RN, Lavoie CA, Ramakodi MP, Finger JW Jr, Suh A, Isberg SR, Miles L, Chong AY, Jaratlerdsiri W, Gongora J, Moran C, Iriarte A, McCormack J, Burgess SC, Edwards SV, Lyons E, Williams C, Breen M, Howard JT, Gresham CR, Peterson DG, Schmitz J, Pollock DD, Haussler D, Triplett EW, Zhang G, Irie N, Jarvis ED, Brochu CA, Schmidt CJ, McCarthy FM, Faircloth BC, Hoffmann FG, Glenn TC, Gabaldón T, Paten B, Ray DA.

Science. 2014 Dec 12;346(6215):1254449. doi: 10.1126/science.1254449. Epub 2014 Dec 11.

16.

Comparative genomics reveals insights into avian genome evolution and adaptation.

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, Wang Z, Jin L, Zhang P, Hu H, Yang W, Hu J, Xiao J, Yang Z, Liu Y, Xie Q, Yu H, Lian J, Wen P, Zhang F, Li H, Zeng Y, Xiong Z, Liu S, Zhou L, Huang Z, An N, Wang J, Zheng Q, Xiong Y, Wang G, Wang B, Wang J, Fan Y, da Fonseca RR, Alfaro-Núñez A, Schubert M, Orlando L, Mourier T, Howard JT, Ganapathy G, Pfenning A, Whitney O, Rivas MV, Hara E, Smith J, Farré M, Narayan J, Slavov G, Romanov MN, Borges R, Machado JP, Khan I, Springer MS, Gatesy J, Hoffmann FG, Opazo JC, Håstad O, Sawyer RH, Kim H, Kim KW, Kim HJ, Cho S, Li N, Huang Y, Bruford MW, Zhan X, Dixon A, Bertelsen MF, Derryberry E, Warren W, Wilson RK, Li S, Ray DA, Green RE, O'Brien SJ, Griffin D, Johnson WE, Haussler D, Ryder OA, Willerslev E, Graves GR, Alström P, Fjeldså J, Mindell DP, Edwards SV, Braun EL, Rahbek C, Burt DW, Houde P, Zhang Y, Yang H, Wang J; Avian Genome Consortium, Jarvis ED, Gilbert MT, Wang J.

Science. 2014 Dec 12;346(6215):1311-20. doi: 10.1126/science.1251385. Epub 2014 Dec 11.

17.

Comparative genome analyses reveal distinct structure in the saltwater crocodile MHC.

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.

PLoS One. 2014 Dec 11;9(12):e114631. doi: 10.1371/journal.pone.0114631. eCollection 2014.

18.

Multiple lineages of ancient CR1 retroposons shaped the early genome evolution of amniotes.

Suh A, Churakov G, Ramakodi MP, Platt RN 2nd, Jurka J, Kojima KK, Caballero J, Smit AF, Vliet KA, Hoffmann FG, Brosius J, Green RE, Braun EL, Ray DA, Schmitz J.

Genome Biol Evol. 2014 Dec 11;7(1):205-17. doi: 10.1093/gbe/evu256.

19.

Early mesozoic coexistence of amniotes and hepadnaviridae.

Suh A, Weber CC, Kehlmaier C, Braun EL, Green RE, Fritz U, Ray DA, Ellegren H.

PLoS Genet. 2014 Dec 11;10(12):e1004559. doi: 10.1371/journal.pgen.1004559. eCollection 2014 Dec.

20.

Evolution and gene capture in ancient endogenous retroviruses - insights from the crocodilian genomes.

Chong AY, Kojima KK, Jurka J, Ray DA, Smit AF, Isberg SR, Gongora J.

Retrovirology. 2014 Dec 12;11:71. doi: 10.1186/s12977-014-0071-2.

21.

A 454 sequencing approach to dipteran mitochondrial genome research.

Ramakodi MP, Singh B, Wells JD, Guerrero F, Ray DA.

Genomics. 2015 Jan;105(1):53-60. doi: 10.1016/j.ygeno.2014.10.014. Epub 2014 Nov 11.

22.

Large numbers of novel miRNAs originate from DNA transposons and are coincident with a large species radiation in bats.

Platt RN 2nd, Vandewege MW, Kern C, Schmidt CJ, Hoffmann FG, Ray DA.

Mol Biol Evol. 2014 Jun;31(6):1536-45. doi: 10.1093/molbev/msu112. Epub 2014 Apr 1.

PMID:
24692655
23.

The Burmese python genome reveals the molecular basis for extreme adaptation in snakes.

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, Polanco D, Dobry J, Vandewege MW, Li Q, Schott RK, Kapusta A, Minx P, Feschotte C, Uetz P, Ray DA, Hoffmann FG, Bogden R, Smith EN, Chang BS, Vonk FJ, Casewell NR, Henkel CV, Richardson MK, Mackessy SP, Bronikowski AM, Yandell M, Warren WC, Secor SM, Pollock DD.

Proc Natl Acad Sci U S A. 2013 Dec 17;110(51):20645-50. doi: 10.1073/pnas.1314475110. Epub 2013 Dec 2. Erratum in: Proc Natl Acad Sci U S A. 2013 Dec 17;110(51). doi:10.1073/pnas.1324133111. Bronikowsi, Anne M [corrected to Bronikowski, Anne M]. Proc Natl Acad Sci U S A. 2014 Feb 25;111(8):3194.

24.

Transposable element evolution in Heliconius suggests genome diversity within Lepidoptera.

Lavoie CA, Platt RN 2nd, Novick PA, Counterman BA, Ray DA.

Mob DNA. 2013 Oct 2;4(1):21. doi: 10.1186/1759-8753-4-21.

25.

Genomic architecture of adaptive color pattern divergence and convergence in Heliconius butterflies.

Supple MA, Hines HM, Dasmahapatra KK, Lewis JJ, Nielsen DM, Lavoie C, Ray DA, Salazar C, McMillan WO, Counterman BA.

Genome Res. 2013 Aug;23(8):1248-57. doi: 10.1101/gr.150615.112. Epub 2013 May 14.

26.

Draft genome sequence of the Tibetan antelope.

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, Ou X, Xu J, Zhang Y, Wu K, Geng C, Zhou W, Zhou T, Irwin DM, Yang Y, Ying L, Bao H, Kim J, Larkin DM, Ma J, Lewin HA, Xing J, Platt RN 2nd, Ray DA, Auvil L, Capitanu B, Zhang X, Zhang G, Murphy RW, Wang J, Zhang YP, Wang J.

Nat Commun. 2013;4:1858. doi: 10.1038/ncomms2860.

27.

Survey sequencing reveals elevated DNA transposon activity, novel elements, and variation in repetitive landscapes among vesper bats.

Pagán HJ, Macas J, Novák P, McCulloch ES, Stevens RD, Ray DA.

Genome Biol Evol. 2012;4(4):575-85. doi: 10.1093/gbe/evs038. Epub 2012 Apr 4.

28.

A non-LTR retroelement extinction in Spermophilus tridecemlineatus.

Platt RN 2nd, Ray DA.

Gene. 2012 May 25;500(1):47-53. doi: 10.1016/j.gene.2012.03.051. Epub 2012 Mar 21.

PMID:
22465530
29.

Sequencing three crocodilian genomes to illuminate the evolution of archosaurs and amniotes.

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, Drew JC, Edwards SV, Faircloth BC, Fujita MK, Greenwold MJ, Hoffmann FG, Howard JM, Iguchi T, Janes DE, Khan SY, Kohno S, de Koning AJ, Lance SL, McCarthy FM, McCormack JE, Merchant ME, Peterson DG, Pollock DD, Pourmand N, Raney BJ, Roessler KA, Sanford JR, Sawyer RH, Schmidt CJ, Triplett EW, Tuberville TD, Venegas-Anaya M, Howard JT, Jarvis ED, Guillette LJ Jr, Glenn TC, Green RE, Ray DA.

Genome Biol. 2012 Jan 31;13(1):415. doi: 10.1186/gb-2012-13-1-415.

30.

Transcriptome-based differentiation of closely-related Miscanthus lines.

Chouvarine P, Cooksey AM, McCarthy FM, Ray DA, Baldwin BS, Burgess SC, Peterson DG.

PLoS One. 2012;7(1):e29850. doi: 10.1371/journal.pone.0029850. Epub 2012 Jan 10.

31.

Expedited batch processing and analysis of transposon insertions.

Smith JD, Ray DA.

BMC Res Notes. 2011 Nov 4;4:482. doi: 10.1186/1756-0500-4-482.

32.

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.

Meganathan PR, Pagan HJ, McCulloch ES, Stevens RD, Ray DA.

Gene. 2012 Jan 15;492(1):121-9. doi: 10.1016/j.gene.2011.10.038. Epub 2011 Oct 24.

PMID:
22041054
33.

Phylogenetic structure illuminates the mechanistic role of environmental heterogeneity in community organization.

Stevens RD, Gavilanez MM, Tello JS, Ray DA.

J Anim Ecol. 2012 Mar;81(2):455-62. doi: 10.1111/j.1365-2656.2011.01900.x. Epub 2011 Sep 5.

PMID:
21895648
34.

The genome of the green anole lizard and a comparative analysis with birds and mammals.

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, Colbourne JK, Fujita MK, Moreno RG, ten Hallers BF, Haussler D, Heger A, Heiman D, Janes DE, Johnson J, de Jong PJ, Koriabine MY, Lara M, Novick PA, Organ CL, Peach SE, Poe S, Pollock DD, de Queiroz K, Sanger T, Searle S, Smith JD, Smith Z, Swofford R, Turner-Maier J, Wade J, Young S, Zadissa A, Edwards SV, Glenn TC, Schneider CJ, Losos JB, Lander ES, Breen M, Ponting CP, Lindblad-Toh K.

Nature. 2011 Aug 31;477(7366):587-91. doi: 10.1038/nature10390.

35.

Sequencing the genome of the Burmese python (Python molurus bivittatus) as a model for studying extreme adaptations in snakes.

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, Pollock DD.

Genome Biol. 2011 Jul 28;12(7):406. doi: 10.1186/gb-2011-12-7-406.

36.

Reading TE leaves: new approaches to the identification of transposable element insertions.

Ray DA, Batzer MA.

Genome Res. 2011 Jun;21(6):813-20. doi: 10.1101/gr.110528.110.

37.

Complete mitochondrial genome sequences of three Crocodylus species and their comparison within the Order Crocodylia.

Meganathan PR, Dubey B, Batzer MA, Ray DA, Haque I.

Gene. 2011 Jun 1;478(1-2):35-41. doi: 10.1016/j.gene.2011.01.012. Epub 2011 Feb 17.

PMID:
21310220
38.

The evolution and diversity of DNA transposons in the genome of the Lizard Anolis carolinensis.

Novick PA, Smith JD, Floumanhaft M, Ray DA, Boissinot S.

Genome Biol Evol. 2011;3:1-14. doi: 10.1093/gbe/evq080. Epub 2010 Dec 2.

39.

PiggyBac-ing on a primate genome: novel elements, recent activity and horizontal transfer.

Pagan HJ, Smith JD, Hubley RM, Ray DA.

Genome Biol Evol. 2010 Jul 12;2:293-303. doi: 10.1093/gbe/evq021.

40.

Molecular phylogenetic analyses of genus Crocodylus (Eusuchia, Crocodylia, Crocodylidae) and the taxonomic position of Crocodylus porosus.

Meganathan PR, Dubey B, Batzer MA, Ray DA, Haque I.

Mol Phylogenet Evol. 2010 Oct;57(1):393-402. doi: 10.1016/j.ympev.2010.06.011. Epub 2010 Jun 19.

PMID:
20601012
41.

Laboratory methods for the analysis of primate mobile elements.

Ray DA, Han K, Walker JA, Batzer MA.

Methods Mol Biol. 2010;628:153-79. doi: 10.1007/978-1-60327-367-1_9.

42.

Reading between the LINEs to see into the past.

Ray DA, Platt RN, Batzer MA.

Trends Genet. 2009 Nov;25(11):475-9. doi: 10.1016/j.tig.2009.09.006.

43.

Multiple chicken repeat 1 lineages in the genomes of oestroid flies.

Thompson ML, Gauna AE, Williams ML, Ray DA.

Gene. 2009 Dec 1;448(1):40-5. doi: 10.1016/j.gene.2009.08.010. Epub 2009 Aug 28. Erratum in: Gene. 2010 Nov 15;468(1-2):58.

PMID:
19716865
44.
45.

Genome analysis of the platypus reveals unique signatures of evolution.

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, Veyrunes F, Fulton L, Fulton B, Graves T, Wallis J, Puente XS, López-Otín C, Ordóñez GR, Eichler EE, Chen L, Cheng Z, Deakin JE, Alsop A, Thompson K, Kirby P, Papenfuss AT, Wakefield MJ, Olender T, Lancet D, Huttley GA, Smit AF, Pask A, Temple-Smith P, Batzer MA, Walker JA, Konkel MK, Harris RS, Whittington CM, Wong ES, Gemmell NJ, Buschiazzo E, Vargas Jentzsch IM, Merkel A, Schmitz J, Zemann A, Churakov G, Kriegs JO, Brosius J, Murchison EP, Sachidanandam R, Smith C, Hannon GJ, Tsend-Ayush E, McMillan D, Attenborough R, Rens W, Ferguson-Smith M, Lefèvre CM, Sharp JA, Nicholas KR, Ray DA, Kube M, Reinhardt R, Pringle TH, Taylor J, Jones RC, Nixon B, Dacheux JL, Niwa H, Sekita Y, Huang X, Stark A, Kheradpour P, Kellis M, Flicek P, Chen Y, Webber C, Hardison R, Nelson J, Hallsworth-Pepin K, Delehaunty K, Markovic C, Minx P, Feng Y, Kremitzki C, Mitreva M, Glasscock J, Wylie T, Wohldmann P, Thiru P, Nhan MN, Pohl CS, Smith SM, Hou S, Nefedov M, de Jong PJ, Renfree MB, Mardis ER, Wilson RK.

Nature. 2008 May 8;453(7192):175-83. doi: 10.1038/nature06936. Erratum in: Nature. 2008 Sep 11;455(7210):256. Nefedov, Mikhail [added]; de Jong, Pieter J [added].

46.

Multiple waves of recent DNA transposon activity in the bat, Myotis lucifugus.

Ray DA, Feschotte C, Pagan HJ, Smith JD, Pritham EJ, Arensburger P, Atkinson PW, Craig NL.

Genome Res. 2008 May;18(5):717-28. doi: 10.1101/gr.071886.107. Epub 2008 Mar 13.

47.

Mobile DNA elements in primate and human evolution.

Xing J, Witherspoon DJ, Ray DA, Batzer MA, Jorde LB.

Am J Phys Anthropol. 2007;Suppl 45:2-19. Review.

PMID:
18046749
48.

Plasma vitellogenin in Morelet's crocodiles from contaminated habitats in northern Belize.

Rainwater TR, Selcer KW, Nespoli LM, Finger AG, Ray DA, Platt SG, Smith PN, Densmore LD, Anderson TA, McMurry ST.

Environ Pollut. 2008 May;153(1):101-9. Epub 2007 Sep 10.

PMID:
17826876
49.

Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences.

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, Baker ML, Batzer MA, Benos PV, Belov K, Clamp M, Cook A, Cuff J, Das R, Davidow L, Deakin JE, Fazzari MJ, Glass JL, Grabherr M, Greally JM, Gu W, Hore TA, Huttley GA, Kleber M, Jirtle RL, Koina E, Lee JT, Mahony S, Marra MA, Miller RD, Nicholls RD, Oda M, Papenfuss AT, Parra ZE, Pollock DD, Ray DA, Schein JE, Speed TP, Thompson K, VandeBerg JL, Wade CM, Walker JA, Waters PD, Webber C, Weidman JR, Xie X, Zody MC; Broad Institute Genome Sequencing Platform; Broad Institute Whole Genome Assembly Team, Graves JA, Ponting CP, Breen M, Samollow PB, Lander ES, Lindblad-Toh K.

Nature. 2007 May 10;447(7141):167-77.

PMID:
17495919
50.

SINEs, evolution and genome structure in the opossum.

Gu W, Ray DA, Walker JA, Barnes EW, Gentles AJ, Samollow PB, Jurka J, Batzer MA, Pollock DD.

Gene. 2007 Jul 1;396(1):46-58. Epub 2007 Mar 19.

PMID:
17442506

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