-
1
-
-
33748803914
-
Identification of rDNA-specific non-LTR retrotransposons in Cnidaria
-
Kojima KK, Kuma K, Toh H, Fujiwara H, (2006) Identification of rDNA-specific non-LTR retrotransposons in Cnidaria. Mol Biol Evol 23: 1984-1993.
-
(2006)
Mol Biol Evol
, vol.23
, pp. 1984-1993
-
-
Kojima, K.K.1
Kuma, K.2
Toh, H.3
Fujiwara, H.4
-
2
-
-
70350221778
-
Rotifer-specific R9 retrotransposable elements generate an exceptionally long target site duplication upon insertion
-
Gladyshev EA, Arkhipova IR, (2009) Rotifer-specific R9 retrotransposable elements generate an exceptionally long target site duplication upon insertion. Gene 448: 145-150.
-
(2009)
Gene
, vol.448
, pp. 145-150
-
-
Gladyshev, E.A.1
Arkhipova, I.R.2
-
3
-
-
0032955930
-
The domain structure and retrotransposition mechanism of R2 elements are conserved throughout arthropods
-
Burke WD, Malik HS, Jones JP, Eickbush TH, (1999) The domain structure and retrotransposition mechanism of R2 elements are conserved throughout arthropods. Mol Biol Evol 16: 502-511.
-
(1999)
Mol Biol Evol
, vol.16
, pp. 502-511
-
-
Burke, W.D.1
Malik, H.S.2
Jones, J.P.3
Eickbush, T.H.4
-
4
-
-
0345466503
-
JAZ requires the double-stranded RNA-binding zinc finger motifs for nuclear localization
-
Yang M, May WS, Ito T, (1999) JAZ requires the double-stranded RNA-binding zinc finger motifs for nuclear localization. J Biol Chem 274: 27399-27406.
-
(1999)
J Biol Chem
, vol.274
, pp. 27399-27406
-
-
Yang, M.1
May, W.S.2
Ito, T.3
-
5
-
-
26444555977
-
Long-term inheritance of the 28S rDNA-specific retrotransposon R2
-
Kojima KK, Fujiwara H, (2005) Long-term inheritance of the 28S rDNA-specific retrotransposon R2. Mol Biol Evol 22: 2157-2165.
-
(2005)
Mol Biol Evol
, vol.22
, pp. 2157-2165
-
-
Kojima, K.K.1
Fujiwara, H.2
-
6
-
-
33845200930
-
RNA from the 50 end of the R2 retrotransposon controls R2 protein binding to and cleavage of its DNA target site
-
Christensen SM, Ye J, Eickbush TH, (2006) RNA from the 50 end of the R2 retrotransposon controls R2 protein binding to and cleavage of its DNA target site. Proc Natl Acad Sci USA 103: 17602-17607.
-
(2006)
Proc Natl Acad Sci USA
, vol.103
, pp. 17602-17607
-
-
Christensen, S.M.1
Ye, J.2
Eickbush, T.H.3
-
7
-
-
79952737753
-
The reverse transcriptase encoded by the non-LTR retrotransposon R2 is as error prone as that encoded by HIV-1
-
Jamburuthugoda VK, Eickbush TH, (2011) The reverse transcriptase encoded by the non-LTR retrotransposon R2 is as error prone as that encoded by HIV-1. J Mol Biol 407: 661-672.
-
(2011)
J Mol Biol
, vol.407
, pp. 661-672
-
-
Jamburuthugoda, V.K.1
Eickbush, T.H.2
-
8
-
-
0034856981
-
Dynamics of R1 and R2 elements in the rDNA locus of Drosophila simulans
-
Pérez-González CE, Eickbush TH, (2001) Dynamics of R1 and R2 elements in the rDNA locus of Drosophila simulans. Genetics 158: 1557-1567.
-
(2001)
Genetics
, vol.158
, pp. 1557-1567
-
-
Pérez-González, C.E.1
Eickbush, T.H.2
-
9
-
-
84874536367
-
Independently derived targeting of 28S rDNA by A- and D-clade R2 retrotransposons plasticity of integration mechanism
-
Available Accessed 2012 Nov 16
-
Thompson BK, Christensen SM (2011) Independently derived targeting of 28S rDNA by A- and D-clade R2 retrotransposons plasticity of integration mechanism. Mob Genet Elem 1: 29-37. Available: http://www.landesbioscience.com/journals/mge/article/16485/. Accessed 2012 Nov 16.
-
(2011)
Mob Genet Elem
, vol.1
, pp. 29-37
-
-
Thompson, B.K.1
Christensen, S.M.2
-
10
-
-
0032976398
-
The age and evolution of non-LTR retrotransposons
-
Malik HS, Burke WD, Eickbush TH, (1999) The age and evolution of non-LTR retrotransposons. Mol Biol Evol 16: 793-805.
-
(1999)
Mol Biol Evol
, vol.16
, pp. 793-805
-
-
Malik, H.S.1
Burke, W.D.2
Eickbush, T.H.3
-
11
-
-
34247899003
-
Finely orchestrated movements: evolution of the ribosomal RNA genes
-
Eickbush TH, Eickbush DG, (2007) Finely orchestrated movements: evolution of the ribosomal RNA genes. Genetics 175: 477-485.
-
(2007)
Genetics
, vol.175
, pp. 477-485
-
-
Eickbush, T.H.1
Eickbush, D.G.2
-
12
-
-
59449095107
-
Role of recombination in the long-term retention of transposable elements in rRNA gene loci
-
Zhang X, Eickbush MT, Eickbush TH, (2008) Role of recombination in the long-term retention of transposable elements in rRNA gene loci. Genetics 180: 1617-1626.
-
(2008)
Genetics
, vol.180
, pp. 1617-1626
-
-
Zhang, X.1
Eickbush, M.T.2
Eickbush, T.H.3
-
13
-
-
79953107625
-
R2 dynamics in Triops cancriformis (Bosc, 1801) (Crustacea, Branchiopoda, Notostraca): turnover rate and 28S concerted evolution
-
Mingazzini V, Luchetti A, Mantovani B, (2011) R2 dynamics in Triops cancriformis (Bosc, 1801) (Crustacea, Branchiopoda, Notostraca): turnover rate and 28S concerted evolution. Heredity 106: 567-575.
-
(2011)
Heredity
, vol.106
, pp. 567-575
-
-
Mingazzini, V.1
Luchetti, A.2
Mantovani, B.3
-
14
-
-
0020478245
-
Molecular drive: a cohesive mode of species evolution
-
Dover GA, (1982) Molecular drive: a cohesive mode of species evolution. Nature 299: 111-117.
-
(1982)
Nature
, vol.299
, pp. 111-117
-
-
Dover, G.A.1
-
15
-
-
0036843291
-
Molecular drive
-
Dover GA, (2002) Molecular drive. Trends Genet 18: 587-589.
-
(2002)
Trends Genet
, vol.18
, pp. 587-589
-
-
Dover, G.A.1
-
16
-
-
0032510519
-
Are retrotransposons long-term hitchhikers?
-
Burke WD, Malik HS, Lathe WC 3rd, Eickbush TH
-
Burke WD, Malik HS, Lathe WC 3rd, Eickbush TH (1998) Are retrotransposons long-term hitchhikers? Nature 392: 141-142.
-
(1998)
Nature
, vol.392
, pp. 141-142
-
-
-
17
-
-
1542316940
-
Cross-genome screening of novel sequence-specific non-LTR retrotransposons: various multicopy RNA genes and microsatellites are selected as targets
-
Kojima KK, Fujiwara H, (2004) Cross-genome screening of novel sequence-specific non-LTR retrotransposons: various multicopy RNA genes and microsatellites are selected as targets. Mol Biol Evol 21: 207-217.
-
(2004)
Mol Biol Evol
, vol.21
, pp. 207-217
-
-
Kojima, K.K.1
Fujiwara, H.2
-
18
-
-
0028870386
-
Vertical transmission of the retrotransposable elements R1 and R2 during the evolution of the Drosophila melanogaster species subgroup
-
Eickbush DG, Eickbush TH, (1995) Vertical transmission of the retrotransposable elements R1 and R2 during the evolution of the Drosophila melanogaster species subgroup. Genetics 139: 671-684.
-
(1995)
Genetics
, vol.139
, pp. 671-684
-
-
Eickbush, D.G.1
Eickbush, T.H.2
-
19
-
-
79953651062
-
The Non-LTR retrotransposon R2 in termites (Insecta, Isoptera): characterization and dynamics
-
Ghesini S, Luchetti A, Marini M, Mantovani B, (2011) The Non-LTR retrotransposon R2 in termites (Insecta, Isoptera): characterization and dynamics. J Mol Evol 72: 296-305.
-
(2011)
J Mol Evol
, vol.72
, pp. 296-305
-
-
Ghesini, S.1
Luchetti, A.2
Marini, M.3
Mantovani, B.4
-
20
-
-
27744438186
-
Ticks have R2 retrotransposons but not the consensus transposon target site of other arthropods
-
Bunikis J, Barbour AG, (2005) Ticks have R2 retrotransposons but not the consensus transposon target site of other arthropods. Insect Mol Biol 14: 465-474.
-
(2005)
Insect Mol Biol
, vol.14
, pp. 465-474
-
-
Bunikis, J.1
Barbour, A.G.2
-
21
-
-
84862758973
-
28S junctions and chimeric elements of the rDNA targeting non-LTR retrotransposon R2 in crustacean living fossils (Branchiopoda, Notostraca)
-
Luchetti A, Mingazzini V, Mantovani B, (2012) 28S junctions and chimeric elements of the rDNA targeting non-LTR retrotransposon R2 in crustacean living fossils (Branchiopoda, Notostraca). Genomics 100: 51-56.
-
(2012)
Genomics
, vol.100
, pp. 51-56
-
-
Luchetti, A.1
Mingazzini, V.2
Mantovani, B.3
-
22
-
-
0027535644
-
Sequence relationship of retrotransposable elements R1 and R2 within and between divergent insect species
-
Burke WD, Eickbush DG, Xiong Y, Jakubczak J, Eickbush TH, (1993) Sequence relationship of retrotransposable elements R1 and R2 within and between divergent insect species. Mol Biol Evol 10: 163-185.
-
(1993)
Mol Biol Evol
, vol.10
, pp. 163-185
-
-
Burke, W.D.1
Eickbush, D.G.2
Xiong, Y.3
Jakubczak, J.4
Eickbush, T.H.5
-
23
-
-
75649110860
-
Maintenance of multiple lineages of R1 and R2 retrotransposable elements in the ribosomal RNA gene loci of Nasonia
-
Stage DE, Eickbush TH (2010) Maintenance of multiple lineages of R1 and R2 retrotransposable elements in the ribosomal RNA gene loci of Nasonia. Insect Mol Biol (suppl. 1): 37-48.
-
(2010)
Insect Mol Biol
, Issue.SUPPL. 1
, pp. 37-48
-
-
Stage, D.E.1
Eickbush, T.H.2
-
24
-
-
23844525077
-
Repbase Update, a database of eukaryotic repetitive elements
-
Jurka J, Kapitonov VV, Pavlicek A, Klonowski P, Kohany O, et al. (2005) Repbase Update, a database of eukaryotic repetitive elements. Cytogenet Genome Res 110: 462-467.
-
(2005)
Cytogenet Genome Res
, vol.110
, pp. 462-467
-
-
Jurka, J.1
Kapitonov, V.V.2
Pavlicek, A.3
Klonowski, P.4
Kohany, O.5
-
25
-
-
45949107473
-
Recent developments in the MAFFT multiple sequence alignment program
-
Recent developments in the MAFFT multiple sequence alignment program. Brief Bioinform 9: 286-298.
-
Brief Bioinform
, vol.9
, pp. 286-298
-
-
-
26
-
-
47949097485
-
Noisy: Identification of problematic columns in multiple sequence alignments
-
Available. Accessed 2012 Nov 16
-
Dress AWM, Flamm C, Fritzsch G, Grünewald S, Kruspe M, et al. (2008) Noisy: Identification of problematic columns in multiple sequence alignments. Algorithms Mol Biol 3: 7. Available: http://www.almob.org/content/3/1/7. Accessed 2012 Nov 16.
-
(2008)
Algorithms Mol Biol
, vol.3
, pp. 7
-
-
Dress, A.W.M.1
Flamm, C.2
Fritzsch, G.3
Grünewald, S.4
Kruspe, M.5
-
27
-
-
0031002417
-
Likelihood-mapping: A simple method to visualize phylogenetic content of a sequence alignment
-
Strimmer K, von Haeseler A, (1997) Likelihood-mapping: A simple method to visualize phylogenetic content of a sequence alignment. Proc Natl Acad Sci USA 94: 6815-6819.
-
(1997)
Proc Natl Acad Sci USA
, vol.94
, pp. 6815-6819
-
-
Strimmer, K.1
von Haeseler, A.2
-
28
-
-
0036205377
-
TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing
-
Schmidt HA, Strimmer K, Vingron M, von Haeseler A, (2002) TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 18: 502-504.
-
(2002)
Bioinformatics
, vol.18
, pp. 502-504
-
-
Schmidt, H.A.1
Strimmer, K.2
Vingron, M.3
von Haeseler, A.4
-
29
-
-
79957613599
-
MEGA5: molecular evolutionary genetics analysis using Maximum Likelihood, evolutionary distance, and Maximum Parsimony methods
-
Tamura K, Peterson D, Peterson N, Stecher G, Nei M, et al. (2011) MEGA5: molecular evolutionary genetics analysis using Maximum Likelihood, evolutionary distance, and Maximum Parsimony methods. Mol Biol Evol 28: 2731-2739.
-
(2011)
Mol Biol Evol
, vol.28
, pp. 2731-2739
-
-
Tamura, K.1
Peterson, D.2
Peterson, N.3
Stecher, G.4
Nei, M.5
-
30
-
-
0242578620
-
A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood
-
Guindon S, Gascuel O, (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52: 696-704.
-
(2003)
Syst Biol
, vol.52
, pp. 696-704
-
-
Guindon, S.1
Gascuel, O.2
-
31
-
-
77954067056
-
DIVEIN: a web server to analyze phylogenies, sequence divergence, diversity, and informative sites
-
Deng W, Maust BS, Nickle DC, Learn GH, Liu Y, et al. (2010) DIVEIN: a web server to analyze phylogenies, sequence divergence, diversity, and informative sites. BioTechniques 48: 405-408.
-
(2010)
BioTechniques
, vol.48
, pp. 405-408
-
-
Deng, W.1
Maust, B.S.2
Nickle, D.C.3
Learn, G.H.4
Liu, Y.5
-
32
-
-
84860109324
-
MrBayes 3.2: Effcient Bayesian phylogenetic inference and model choice across a large model space
-
Ronquist F, Teslenko M, van der Mark P, Ayres D, Darling A, et al. (2011) MrBayes 3.2: Effcient Bayesian phylogenetic inference and model choice across a large model space. Syst Biol 61: 539-542.
-
(2011)
Syst Biol
, vol.61
, pp. 539-542
-
-
Ronquist, F.1
Teslenko, M.2
van der Mark, P.3
Ayres, D.4
Darling, A.5
-
34
-
-
43049094016
-
The diversity of retrotransposons and the properties of their reverse transcriptases
-
Eickbush TH, Jamburuthugoda VK, (2008) The diversity of retrotransposons and the properties of their reverse transcriptases. Virus Res 134: 221-234.
-
(2008)
Virus Res
, vol.134
, pp. 221-234
-
-
Eickbush, T.H.1
Jamburuthugoda, V.K.2
-
35
-
-
0036092497
-
Ancient lineages of non-LTR retrotransposons in the primitive eukaryote, Giardia lamblia
-
Burke WD, Malik HS, Rich SM, Eickbush TH, (2002) Ancient lineages of non-LTR retrotransposons in the primitive eukaryote, Giardia lamblia. Mol Biol Evol 19: 619-630.
-
(2002)
Mol Biol Evol
, vol.19
, pp. 619-630
-
-
Burke, W.D.1
Malik, H.S.2
Rich, S.M.3
Eickbush, T.H.4
-
36
-
-
33846063713
-
Macroevolution and macroecology through deep time
-
Butterfield NJ, (2007) Macroevolution and macroecology through deep time. Palaeontology 50: 41-55.
-
(2007)
Palaeontology
, vol.50
, pp. 41-55
-
-
Butterfield, N.J.1
-
37
-
-
0035141595
-
Multiple lineages of R1 retrotransposable elements can coexist in the rDNA loci of Drosophila
-
Gentile KL, Burke WD, Eickbush TH, (2001) Multiple lineages of R1 retrotransposable elements can coexist in the rDNA loci of Drosophila. Mol Biol Evol 18: 235-245.
-
(2001)
Mol Biol Evol
, vol.18
, pp. 235-245
-
-
Gentile, K.L.1
Burke, W.D.2
Eickbush, T.H.3
-
38
-
-
38349081152
-
Satellite DNAs between selfishness and functionality: structure, genomics and evolution of tandem repeats in centromeric (hetero)chromatin
-
Plohl M, Luchetti A, Meštrović N, Mantovani B, (2008) Satellite DNAs between selfishness and functionality: structure, genomics and evolution of tandem repeats in centromeric (hetero)chromatin. Gene 409: 72-82.
-
(2008)
Gene
, vol.409
, pp. 72-82
-
-
Plohl, M.1
Luchetti, A.2
Meštrović, N.3
Mantovani, B.4
-
39
-
-
0031903901
-
Evolution of satellite DNAs from the genus Palorus - Experimental evidence for the "library" hypothesis
-
Meštrović N, Plohl M, Mravinac B, Ugarković D{stroke}, (1998) Evolution of satellite DNAs from the genus Palorus - Experimental evidence for the "library" hypothesis. Mol Biol Evol 15: 1062-1068.
-
(1998)
Mol Biol Evol
, vol.15
, pp. 1062-1068
-
-
Meštrović, N.1
Plohl, M.2
Mravinac, B.3
Ugarković, D.4
-
40
-
-
57649236065
-
Relevance of satellite DNA genomic distribution in phylogenetic analysis: a case study with root-knot nematodes of the genus Meloidogyne
-
Meštrović N, Plohl M, Castagnone-Sereno P, (2009) Relevance of satellite DNA genomic distribution in phylogenetic analysis: a case study with root-knot nematodes of the genus Meloidogyne. Mol Phylogenet Evol 50: 204-208.
-
(2009)
Mol Phylogenet Evol
, vol.50
, pp. 204-208
-
-
Meštrović, N.1
Plohl, M.2
Castagnone-Sereno, P.3
-
41
-
-
0141430063
-
Polymerase chain reaction amplification of the Bag320 satellite family reveals the ancestral library and past gene conversion events in Bacillus rossius (Insecta Phasmatodea)
-
Cesari M, Luchetti A, Passamonti M, Scali V, Mantovani B, (2003) Polymerase chain reaction amplification of the Bag320 satellite family reveals the ancestral library and past gene conversion events in Bacillus rossius (Insecta Phasmatodea). Gene 312: 289-295.
-
(2003)
Gene
, vol.312
, pp. 289-295
-
-
Cesari, M.1
Luchetti, A.2
Passamonti, M.3
Scali, V.4
Mantovani, B.5
-
42
-
-
53549088060
-
Epigenetic regulation of retrotransposons within the nucleolus of Drosophila
-
Eickbush DG, Ye J, Zhang X, Burke WD, Eickbush TH, (2008) Epigenetic regulation of retrotransposons within the nucleolus of Drosophila. Mol Cell Biol 28: 6452-6461.
-
(2008)
Mol Cell Biol
, vol.28
, pp. 6452-6461
-
-
Eickbush, D.G.1
Ye, J.2
Zhang, X.3
Burke, W.D.4
Eickbush, T.H.5
-
43
-
-
0026729098
-
Turnover of R1 (type I) and R2 (type II) retrotransposable elements in the ribosomal DNA of Drosophila melanogaster
-
Jakubczak JL, Zenni MK, Woodruff RC, Eickbush TH, (1992) Turnover of R1 (type I) and R2 (type II) retrotransposable elements in the ribosomal DNA of Drosophila melanogaster. Genetics 131: 129-142.
-
(1992)
Genetics
, vol.131
, pp. 129-142
-
-
Jakubczak, J.L.1
Zenni, M.K.2
Woodruff, R.C.3
Eickbush, T.H.4
-
44
-
-
43549088103
-
Abundant and species-specific DINE-1 transposable elements in 12 Drosophila genomes
-
Available Accessed 2012 Nov 16
-
Yang H-P, Barbash DA (2008) Abundant and species-specific DINE-1 transposable elements in 12 Drosophila genomes. Genome Biol 9: R39. Available: http://genomebiology.com/content/9/2/r39. Accessed 2012 Nov 16.
-
(2008)
Genome Biol
, vol.9
-
-
Yang, H.-P.1
Barbash, D.A.2
|