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Items: 1 to 50 of 208

1.

A computational reconstruction of Papio phylogeny using Alu insertion polymorphisms.

Jordan VE, Walker JA, Beckstrom TO, Steely CJ, McDaniel CL, St Romain CP; Baboon Genome Analysis Consortium, Worley KC, Phillips-Conroy J, Jolly CJ, Rogers J, Konkel MK, Batzer MA.

Mob DNA. 2018 Apr 5;9:13. doi: 10.1186/s13100-018-0118-3. eCollection 2018.

2.

Analysis of lineage-specific Alu subfamilies in the genome of the olive baboon, Papio anubis.

Steely CJ, Baker JN, Walker JA, Loupe CD 3rd; Baboon Genome Analysis Consortium, Batzer MA.

Mob DNA. 2018 Mar 19;9:10. doi: 10.1186/s13100-018-0115-6. eCollection 2018.

3.

Recently integrated Alu insertions in the squirrel monkey (Saimiri) lineage and application for population analyses.

Baker JN, Walker JA, Denham MW, Loupe CD 3rd, Batzer MA.

Mob DNA. 2018 Feb 12;9:9. doi: 10.1186/s13100-018-0114-7. eCollection 2018.

4.

Alu Insertion Polymorphisms as Evidence for Population Structure in Baboons.

Steely CJ, Walker JA, Jordan VE, Beckstrom TO, McDaniel CL, St Romain CP, Bennett EC, Robichaux A, Clement BN, Raveendran M; Baboon Genome Analysis Consortium, Worley KC, Phillips-Conroy J, Jolly CJ, Rogers J, Konkel MK, Batzer MA.

Genome Biol Evol. 2017 Sep 1;9(9):2418-2427. doi: 10.1093/gbe/evx184.

5.

Evolution of Alu Subfamily Structure in the Saimiri Lineage of New World Monkeys.

Baker JN, Walker JA, Vanchiere JA, Phillippe KR, St Romain CP, Gonzalez-Quiroga P, Denham MW, Mierl JR, Konkel MK, Batzer MA.

Genome Biol Evol. 2017 Sep 1;9(9):2365-2376. doi: 10.1093/gbe/evx172.

6.

Papio Baboon Species Indicative Alu Elements.

Walker JA, Jordan VE, Steely CJ, Beckstrom TO, McDaniel CL, St Romain CP, Bennett EC, Robichaux A, Clement BN, Konkel MK; Baboon Genome Analysis Consortium, Batzer MA.

Genome Biol Evol. 2017 Jun 1;9(6):1788-1796. doi: 10.1093/gbe/evx130.

7.

Discovery of a new repeat family in the Callithrix jacchus genome.

Konkel MK, Ullmer B, Arceneaux EL, Sanampudi S, Brantley SA, Hubley R, Smit AF, Batzer MA.

Genome Res. 2016 May;26(5):649-59. doi: 10.1101/gr.199075.115. Epub 2016 Feb 25.

8.

DNA methylation variation of human-specific Alu repeats.

Bakshi A, Herke SW, Batzer MA, Kim J.

Epigenetics. 2016;11(2):163-73. doi: 10.1080/15592294.2015.1130518. Epub 2016 Feb 18.

9.

An integrated map of structural variation in 2,504 human genomes.

Sudmant PH, Rausch T, Gardner EJ, Handsaker RE, Abyzov A, Huddleston J, Zhang Y, Ye K, Jun G, Fritz MH, Konkel MK, Malhotra A, Stütz AM, Shi X, Casale FP, Chen J, Hormozdiari F, Dayama G, Chen K, Malig M, Chaisson MJP, Walter K, Meiers S, Kashin S, Garrison E, Auton A, Lam HYK, Mu XJ, Alkan C, Antaki D, Bae T, Cerveira E, Chines P, Chong Z, Clarke L, Dal E, Ding L, Emery S, Fan X, Gujral M, Kahveci F, Kidd JM, Kong Y, Lameijer EW, McCarthy S, Flicek P, Gibbs RA, Marth G, Mason CE, Menelaou A, Muzny DM, Nelson BJ, Noor A, Parrish NF, Pendleton M, Quitadamo A, Raeder B, Schadt EE, Romanovitch M, Schlattl A, Sebra R, Shabalin AA, Untergasser A, Walker JA, Wang M, Yu F, Zhang C, Zhang J, Zheng-Bradley X, Zhou W, Zichner T, Sebat J, Batzer MA, McCarroll SA; 1000 Genomes Project Consortium, Mills RE, Gerstein MB, Bashir A, Stegle O, Devine SE, Lee C, Eichler EE, Korbel JO.

Nature. 2015 Oct 1;526(7571):75-81. doi: 10.1038/nature15394.

10.

Sequence Analysis and Characterization of Active Human Alu Subfamilies Based on the 1000 Genomes Pilot Project.

Konkel MK, Walker JA, Hotard AB, Ranck MC, Fontenot CC, Storer J, Stewart C, Marth GT; 1000 Genomes Consortium, Batzer MA.

Genome Biol Evol. 2015 Aug 29;7(9):2608-22. doi: 10.1093/gbe/evv167.

11.

Sequencing, identification and mapping of primed L1 elements (SIMPLE) reveals significant variation in full length L1 elements between individuals.

Streva VA, Jordan VE, Linker S, Hedges DJ, Batzer MA, Deininger PL.

BMC Genomics. 2015 Mar 21;16:220. doi: 10.1186/s12864-015-1374-y.

12.

Tangram: a comprehensive toolbox for mobile element insertion detection.

Wu J, Lee WP, Ward A, Walker JA, Konkel MK, Batzer MA, Marth GT.

BMC Genomics. 2014 Sep 16;15:795. doi: 10.1186/1471-2164-15-795.

13.

Gibbon genome and the fast karyotype evolution of small apes.

Carbone L, Harris RA, Gnerre S, Veeramah KR, Lorente-Galdos B, Huddleston J, Meyer TJ, Herrero J, Roos C, Aken B, Anaclerio F, Archidiacono N, Baker C, Barrell D, Batzer MA, Beal K, Blancher A, Bohrson CL, Brameier M, Campbell MS, Capozzi O, Casola C, Chiatante G, Cree A, Damert A, de Jong PJ, Dumas L, Fernandez-Callejo M, Flicek P, Fuchs NV, Gut I, Gut M, Hahn MW, Hernandez-Rodriguez J, Hillier LW, Hubley R, Ianc B, Izsvák Z, Jablonski NG, Johnstone LM, Karimpour-Fard A, Konkel MK, Kostka D, Lazar NH, Lee SL, Lewis LR, Liu Y, Locke DP, Mallick S, Mendez FL, Muffato M, Nazareth LV, Nevonen KA, O'Bleness M, Ochis C, Odom DT, Pollard KS, Quilez J, Reich D, Rocchi M, Schumann GG, Searle S, Sikela JM, Skollar G, Smit A, Sonmez K, ten Hallers B, Terhune E, Thomas GW, Ullmer B, Ventura M, Walker JA, Wall JD, Walter L, Ward MC, Wheelan SJ, Whelan CW, White S, Wilhelm LJ, Woerner AE, Yandell M, Zhu B, Hammer MF, Marques-Bonet T, Eichler EE, Fulton L, Fronick C, Muzny DM, Warren WC, Worley KC, Rogers J, Wilson RK, Gibbs RA.

Nature. 2014 Sep 11;513(7517):195-201. doi: 10.1038/nature13679.

14.

Analysis of western lowland gorilla (Gorilla gorilla gorilla) specific Alu repeats.

McLain AT, Carman GW, Fullerton ML, Beckstrom TO, Gensler W, Meyer TJ, Faulk C, Batzer MA.

Mob DNA. 2013 Nov 22;4(1):26. doi: 10.1186/1759-8753-4-26.

15.

APOE ϵ4, rated life experiences, and affect among centenarians.

Martin P, Jazwinski SM, Davey A, Green RC, Macdonald M, Margrett JA, Siegler IC, Arnold J, Woodard JL, Johnson MA, Kim S, Dai J, Li L, Batzer MA, Poon LW, For The Georgia Centenarian Study.

Aging Ment Health. 2014 Mar;18(2):240-7. doi: 10.1080/13607863.2013.827624. Epub 2013 Sep 2.

16.

Rates and patterns of great ape retrotransposition.

Hormozdiari F, Konkel MK, Prado-Martinez J, Chiatante G, Herraez IH, Walker JA, Nelson B, Alkan C, Sudmant PH, Huddleston J, Catacchio CR, Ko A, Malig M, Baker C; Great Ape Genome Project, Marques-Bonet T, Ventura M, Batzer MA, Eichler EE.

Proc Natl Acad Sci U S A. 2013 Aug 13;110(33):13457-62. doi: 10.1073/pnas.1310914110. Epub 2013 Jul 24.

17.

A comparison of 100 human genes using an alu element-based instability model.

Cook GW, Konkel MK, Walker JA, Bourgeois MG, Fullerton ML, Fussell JT, Herbold HD, Batzer MA.

PLoS One. 2013 Jun 3;8(6):e65188. doi: 10.1371/journal.pone.0065188. Print 2013.

18.

Mobile element scanning (ME-Scan) identifies thousands of novel Alu insertions in diverse human populations.

Witherspoon DJ, Zhang Y, Xing J, Watkins WS, Ha H, Batzer MA, Jorde LB.

Genome Res. 2013 Jul;23(7):1170-81. doi: 10.1101/gr.148973.112. Epub 2013 Apr 18.

19.

Genomic impact of eukaryotic transposable elements.

Arkhipova IR, Batzer MA, Brosius J, Feschotte C, Moran JV, Schmitz J, Jurka J.

Mob DNA. 2012 Nov 21;3(1):19. doi: 10.1186/1759-8753-3-19.

20.

An alu-based phylogeny of lemurs (infraorder: Lemuriformes).

McLain AT, Meyer TJ, Faulk C, Herke SW, Oldenburg JM, Bourgeois MG, Abshire CF, Roos C, Batzer MA.

PLoS One. 2012;7(8):e44035. doi: 10.1371/journal.pone.0044035. Epub 2012 Aug 28. Erratum in: PLoS One. 2012;7(8). doi:10.1371/annotation/378aaec2-599e-4cd4-8941-3a14c208b757.

21.

An Alu-based phylogeny of gibbons (hylobatidae).

Meyer TJ, McLain AT, Oldenburg JM, Faulk C, Bourgeois MG, Conlin EM, Mootnick AR, de Jong PJ, Roos C, Carbone L, Batzer MA.

Mol Biol Evol. 2012 Nov;29(11):3441-50. doi: 10.1093/molbev/mss149. Epub 2012 Jun 7.

22.

Centromere remodeling in Hoolock leuconedys (Hylobatidae) by a new transposable element unique to the gibbons.

Carbone L, Harris RA, Mootnick AR, Milosavljevic A, Martin DI, Rocchi M, Capozzi O, Archidiacono N, Konkel MK, Walker JA, Batzer MA, de Jong PJ.

Genome Biol Evol. 2012;4(7):648-58. doi: 10.1093/gbe/evs048. Epub 2012 May 16.

23.

Orangutan Alu quiescence reveals possible source element: support for ancient backseat drivers.

Walker JA, Konkel MK, Ullmer B, Monceaux CP, Ryder OA, Hubley R, Smit AF, Batzer MA.

Mob DNA. 2012 Apr 30;3:8. doi: 10.1186/1759-8753-3-8.

24.

Repetitive elements may comprise over two-thirds of the human genome.

de Koning AP, Gu W, Castoe TA, Batzer MA, Pollock DD.

PLoS Genet. 2011 Dec;7(12):e1002384. doi: 10.1371/journal.pgen.1002384. Epub 2011 Dec 1.

25.

Alu pair exclusions in the human genome.

Cook GW, Konkel MK, Major JD 3rd, Walker JA, Han K, Batzer MA.

Mob DNA. 2011 Sep 23;2:10. doi: 10.1186/1759-8753-2-10.

26.

A comprehensive map of mobile element insertion polymorphisms in humans.

Stewart C, Kural D, Strömberg MP, Walker JA, Konkel MK, Stütz AM, Urban AE, Grubert F, Lam HY, Lee WP, Busby M, Indap AR, Garrison E, Huff C, Xing J, Snyder MP, Jorde LB, Batzer MA, Korbel JO, Marth GT; 1000 Genomes Project.

PLoS Genet. 2011 Aug;7(8):e1002236. doi: 10.1371/journal.pgen.1002236. Epub 2011 Aug 18.

27.

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.

28.

Nuclear versus mitochondrial DNA: evidence for hybridization in colobine monkeys.

Roos C, Zinner D, Kubatko LS, Schwarz C, Yang M, Meyer D, Nash SD, Xing J, Batzer MA, Brameier M, Leendertz FH, Ziegler T, Perwitasari-Farajallah D, Nadler T, Walter L, Osterholz M.

BMC Evol Biol. 2011 Mar 24;11:77. doi: 10.1186/1471-2148-11-77.

29.

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
30.

Mapping copy number variation by population-scale genome sequencing.

Mills RE, Walter K, Stewart C, Handsaker RE, Chen K, Alkan C, Abyzov A, Yoon SC, Ye K, Cheetham RK, Chinwalla A, Conrad DF, Fu Y, Grubert F, Hajirasouliha I, Hormozdiari F, Iakoucheva LM, Iqbal Z, Kang S, Kidd JM, Konkel MK, Korn J, Khurana E, Kural D, Lam HY, Leng J, Li R, Li Y, Lin CY, Luo R, Mu XJ, Nemesh J, Peckham HE, Rausch T, Scally A, Shi X, Stromberg MP, Stütz AM, Urban AE, Walker JA, Wu J, Zhang Y, Zhang ZD, Batzer MA, Ding L, Marth GT, McVean G, Sebat J, Snyder M, Wang J, Ye K, Eichler EE, Gerstein MB, Hurles ME, Lee C, McCarroll SA, Korbel JO; 1000 Genomes Project.

Nature. 2011 Feb 3;470(7332):59-65. doi: 10.1038/nature09708.

31.

Comparative and demographic analysis of orang-utan genomes.

Locke DP, Hillier LW, Warren WC, Worley KC, Nazareth LV, Muzny DM, Yang SP, Wang Z, Chinwalla AT, Minx P, Mitreva M, Cook L, Delehaunty KD, Fronick C, Schmidt H, Fulton LA, Fulton RS, Nelson JO, Magrini V, Pohl C, Graves TA, Markovic C, Cree A, Dinh HH, Hume J, Kovar CL, Fowler GR, Lunter G, Meader S, Heger A, Ponting CP, Marques-Bonet T, Alkan C, Chen L, Cheng Z, Kidd JM, Eichler EE, White S, Searle S, Vilella AJ, Chen Y, Flicek P, Ma J, Raney B, Suh B, Burhans R, Herrero J, Haussler D, Faria R, Fernando O, Darré F, Farré D, Gazave E, Oliva M, Navarro A, Roberto R, Capozzi O, Archidiacono N, Della Valle G, Purgato S, Rocchi M, Konkel MK, Walker JA, Ullmer B, Batzer MA, Smit AF, Hubley R, Casola C, Schrider DR, Hahn MW, Quesada V, Puente XS, Ordoñez GR, López-Otín C, Vinar T, Brejova B, Ratan A, Harris RS, Miller W, Kosiol C, Lawson HA, Taliwal V, Martins AL, Siepel A, Roychoudhury A, Ma X, Degenhardt J, Bustamante CD, Gutenkunst RN, Mailund T, Dutheil JY, Hobolth A, Schierup MH, Ryder OA, Yoshinaga Y, de Jong PJ, Weinstock GM, Rogers J, Mardis ER, Gibbs RA, Wilson RK.

Nature. 2011 Jan 27;469(7331):529-33. doi: 10.1038/nature09687.

32.

LINEs and SINEs of primate evolution.

Konkel MK, Walker JA, Batzer MA.

Evol Anthropol. 2010 Nov 1;19(6):236-249. No abstract available.

33.

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
34.

Mobile element scanning (ME-Scan) by targeted high-throughput sequencing.

Witherspoon DJ, Xing J, Zhang Y, Watkins WS, Batzer MA, Jorde LB.

BMC Genomics. 2010 Jun 30;11:410. doi: 10.1186/1471-2164-11-410.

35.

HRAS1 and LASS1 with APOE are associated with human longevity and healthy aging.

Jazwinski SM, Kim S, Dai J, Li L, Bi X, Jiang JC, Arnold J, Batzer MA, Walker JA, Welsh DA, Lefante CM, Volaufova J, Myers L, Su LJ, Hausman DB, Miceli MV, Ravussin E, Poon LW, Cherry KE, Welsch MA; Georgia Centenarian Study and the Louisiana Healthy Aging Study.

Aging Cell. 2010 Oct;9(5):698-708. doi: 10.1111/j.1474-9726.2010.00600.x. Epub 2010 Aug 4.

36.

The genome of a songbird.

Warren WC, Clayton DF, Ellegren H, Arnold AP, Hillier LW, Künstner A, Searle S, White S, Vilella AJ, Fairley S, Heger A, Kong L, Ponting CP, Jarvis ED, Mello CV, Minx P, Lovell P, Velho TA, Ferris M, Balakrishnan CN, Sinha S, Blatti C, London SE, Li Y, Lin YC, George J, Sweedler J, Southey B, Gunaratne P, Watson M, Nam K, Backström N, Smeds L, Nabholz B, Itoh Y, Whitney O, Pfenning AR, Howard J, Völker M, Skinner BM, Griffin DK, Ye L, McLaren WM, Flicek P, Quesada V, Velasco G, Lopez-Otin C, Puente XS, Olender T, Lancet D, Smit AF, Hubley R, Konkel MK, Walker JA, Batzer MA, Gu W, Pollock DD, Chen L, Cheng Z, Eichler EE, Stapley J, Slate J, Ekblom R, Birkhead T, Burke T, Burt D, Scharff C, Adam I, Richard H, Sultan M, Soldatov A, Lehrach H, Edwards SV, Yang SP, Li X, Graves T, Fulton L, Nelson J, Chinwalla A, Hou S, Mardis ER, Wilson RK.

Nature. 2010 Apr 1;464(7289):757-62. doi: 10.1038/nature08819.

37.

A mobile threat to genome stability: The impact of non-LTR retrotransposons upon the human genome.

Konkel MK, Batzer MA.

Semin Cancer Biol. 2010 Aug;20(4):211-21. doi: 10.1016/j.semcancer.2010.03.001. Epub 2010 Mar 20. Review.

38.

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.

39.

Computational methods for the analysis of primate mobile elements.

Cordaux R, Sen SK, Konkel MK, Batzer MA.

Methods Mol Biol. 2010;628:137-51. doi: 10.1007/978-1-60327-367-1_8. Review.

40.

Heads or tails: L1 insertion-associated 5' homopolymeric sequences.

Meyer TJ, Srikanta D, Conlin EM, Batzer MA.

Mob DNA. 2010 Feb 1;1(1):7. doi: 10.1186/1759-8753-1-7.

41.

Alu repeats increase local recombination rates.

Witherspoon DJ, Watkins WS, Zhang Y, Xing J, Tolpinrud WL, Hedges DJ, Batzer MA, Jorde LB.

BMC Genomics. 2009 Nov 16;10:530. doi: 10.1186/1471-2164-10-530.

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.

Distribution of four HIV type 1-resistance polymorphisms (CCR5-Delta32, CCR5-m303, CCR2-64I, and SDF1-3'A) in the Bahraini population.

Salem AH, Farid E, Fadel R, Abu-Hijleh M, Almawi W, Han K, Batzer MA.

AIDS Res Hum Retroviruses. 2009 Oct;25(10):973-7. doi: 10.1089/aid.2009.0066.

PMID:
19803715
44.

The impact of retrotransposons on human genome evolution.

Cordaux R, Batzer MA.

Nat Rev Genet. 2009 Oct;10(10):691-703. doi: 10.1038/nrg2640. Review.

45.

5'-Transducing SVA retrotransposon groups spread efficiently throughout the human genome.

Damert A, Raiz J, Horn AV, Löwer J, Wang H, Xing J, Batzer MA, Löwer R, Schumann GG.

Genome Res. 2009 Nov;19(11):1992-2008. doi: 10.1101/gr.093435.109. Epub 2009 Aug 3.

46.

High frequency of the D allele of the angiotensin-converting enzyme gene in Arabic populations.

Salem AH, Batzer MA.

BMC Res Notes. 2009 Jun 8;2:99. doi: 10.1186/1756-0500-2-99.

47.

Internal priming: an opportunistic pathway for L1 and Alu retrotransposition in hominins.

Srikanta D, Sen SK, Conlin EM, Batzer MA.

Gene. 2009 Dec 15;448(2):233-41. doi: 10.1016/j.gene.2009.05.014. Epub 2009 Jun 6.

48.

Phylogeny of the macaques (Cercopithecidae: Macaca) based on Alu elements.

Li J, Han K, Xing J, Kim HS, Rogers J, Ryder OA, Disotell T, Yue B, Batzer MA.

Gene. 2009 Dec 15;448(2):242-9. doi: 10.1016/j.gene.2009.05.013. Epub 2009 Jun 2.

49.

Allele frequencies of the human platelet antigen-1 in the Egyptian population.

Salem AH, Han K, Batzer MA.

BMC Res Notes. 2009 May 20;2:90. doi: 10.1186/1756-0500-2-90.

50.

Mobile elements create structural variation: analysis of a complete human genome.

Xing J, Zhang Y, Han K, Salem AH, Sen SK, Huff CD, Zhou Q, Kirkness EF, Levy S, Batzer MA, Jorde LB.

Genome Res. 2009 Sep;19(9):1516-26. doi: 10.1101/gr.091827.109. Epub 2009 May 13.

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