-
1
-
-
51249171246
-
Nuclear DNA content of some important plant species
-
Arumuganathan K, Earle ED. 1991. Nuclear DNA content of some important plant species. Plant Mol Biol Rep. 9:208-218.
-
(1991)
Plant Mol Biol Rep
, vol.9
, pp. 208-218
-
-
Arumuganathan, K.1
Earle, E.D.2
-
2
-
-
4644242349
-
RNA silencing in plants
-
DOI 10.1038/nature02874
-
Baulcombe D. 2004. RNA silencing in plants. Nature 431:356-363. (Pubitemid 39265676)
-
(2004)
Nature
, vol.431
, Issue.7006
, pp. 356-363
-
-
Baulcombe, D.1
-
3
-
-
59949097135
-
Natural selection on gene function drives the evolution of LTR retrotransposon families in the rice genome
-
Baucom RS, Estill JC, Lessbens-Mack J, Bennetzen JL. 2009. Natural selection on gene function drives the evolution of LTR retrotransposon families in the rice genome. Genome Res. 19:243-254.
-
(2009)
Genome Res
, vol.19
, pp. 243-254
-
-
Baucom, R.S.1
Estill, J.C.2
Lessbens-Mack, J.3
Bennetzen, J.L.4
-
4
-
-
0033976643
-
Transposable element contributions to plant gene and genome evolution
-
DOI 10.1023/A:1006344508454
-
Bennetzen JL. 2000. Transposable element contributions to plant gene and genome evolution. Plant Mol Biol. 42:251-269. (Pubitemid 30096120)
-
(2000)
Plant Molecular Biology
, vol.42
, Issue.1
, pp. 251-269
-
-
Bennetzen, J.L.1
-
5
-
-
23844460513
-
What transposable elements tell us about genome organization and evolution: The case of Drosophila
-
DOI 10.1159/000084935
-
Biémont C, Vieira C. 2005. What transposable elements tell us about genome organization and evolution: the case of Drosophila. Cytogenet Genome Res. 110:25-34. (Pubitemid 41159880)
-
(2005)
Cytogenetic and Genome Research
, vol.110
, Issue.1-4
, pp. 25-34
-
-
Biemont, C.1
Vieira, C.2
-
6
-
-
0037633476
-
Plant LTR-retrotransposons and MITEs: Control of transposition and impact on the evolution of plant genes and genomes
-
DOI 10.1016/S0378-1119(03)00557-2
-
Casacuberta JM, Santiago N. 2003. Plant LTR-retrotransposons and MITEs: control of transposition and impact on the evolution of plant genes and genomes. Gene 311:1-11. (Pubitemid 36830797)
-
(2003)
Gene
, vol.311
, Issue.1-2
, pp. 1-11
-
-
Casacuberta, J.M.1
Santiago, N.2
-
7
-
-
58149189877
-
GtRNAdb: A database of transfer RNA genes detected in genomic sequence
-
Chan PP, Lowe TM. 2009. GtRNAdb: a database of transfer RNA genes detected in genomic sequence. Nucleic Acids Res. 37(Database Issue): D93-D97.
-
(2009)
Nucleic Acids Res
, vol.37
, Issue.DATABASE ISSUE
-
-
Chan, P.P.1
Lowe, T.M.2
-
8
-
-
33846108228
-
RetrOryza: A database of the rice LTR-retrotransposons
-
DOI 10.1093/nar/gkl780
-
Chaparro C, Guyot R, Zuccolo A, Piégu B, Panaud O. 2007. RetrOryza: a database of the rice LTR-retrotransposons. Nucleic Acids Res. 35(Database Issue): D66-D70. (Pubitemid 46056172)
-
(2007)
Nucleic Acids Research
, vol.35
, Issue.SUPPL. 1
-
-
Chaparro, C.1
Guyot, R.2
Zuccolo, A.3
Piegu, B.4
Panaud, O.5
-
9
-
-
0042121237
-
Multiple sequence alignment with the Clustal series of programs
-
DOI 10.1093/nar/gkg500
-
Chenna R, Sugawara H, Koike T, Lopez R, Gibson TJ, Higgins DB, Thompson D. 2003. Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res. 31:3497-3500. (Pubitemid 37442184)
-
(2003)
Nucleic Acids Research
, vol.31
, Issue.13
, pp. 3497-3500
-
-
Chenna, R.1
Sugawara, H.2
Koike, T.3
Lopez, R.4
Gibson, T.J.5
Higgins, D.G.6
Thompson, J.D.7
-
10
-
-
70349318211
-
The impact of retrotransposons on human genome evolution
-
Cordaux R, BatzerMA. 2009. The impact of retrotransposons on human genome evolution. Nat Rev Genet. 10:691-703.
-
(2009)
Nat Rev Genet
, vol.10
, pp. 691-703
-
-
Cordaux, R.1
Batzer, M.A.2
-
11
-
-
77955689247
-
Evolutionary conservation, diversity and specificity of LTR-retrotransposon in flowering plants: Insights from genome-wide analysis and multi-specific comparison
-
Du J, Tian Z, Hans C, Laten H, Cannon S, Jackson SA, Shoemaker RC, Ma J. 2010. Evolutionary conservation, diversity and specificity of LTR-retrotransposon in flowering plants: insights from genome-wide analysis and multi-specific comparison. Plant J. 63: 584-598.
-
(2010)
Plant J
, vol.63
, pp. 584-598
-
-
Du, J.1
Tian, Z.2
Hans, C.3
Laten, H.4
Cannon, S.5
Jackson, S.A.6
Shoemaker, R.C.7
Ma, J.8
-
12
-
-
39749179047
-
LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons
-
Ellinghaus D, Kurtz S, Willhoeft U. 2008. LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons. BMC Bioinformatics 9:18.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 18
-
-
Ellinghaus, D.1
Kurtz, S.2
Willhoeft, U.3
-
13
-
-
0034691159
-
Transposons and genome evolution in plants
-
Federoff N. 2000. Transposons and genome evolution in plants. Proc Natl Acad Sci USA. 97:7002-7007.
-
(2000)
Proc Natl Acad Sci USA
, vol.97
, pp. 7002-7007
-
-
Federoff, N.1
-
14
-
-
77952734605
-
Conservation and divergence of methylation patterning in plants and animals
-
(15 co-authors)
-
Feng S, Cokus SJ, Zhang Z, et al. (15 co-authors). 2010. Conservation and divergence of methylation patterning in plants and animals. Proc Natl Acad Sci USA. 107:8689-8694.
-
(2010)
Proc Natl Acad Sci USA
, vol.107
, pp. 8689-8694
-
-
Feng, S.1
Cokus, S.J.2
Zhang, Z.3
-
15
-
-
0036250001
-
Plant transposable elements: Where genetics meets genomics
-
DOI 10.1038/nrg793
-
Feschotte C, Jiang N, Wessler SR. 2002. Plant transposable elements: where genetics meets genomics. Nat Rev Genet. 3:329-341. (Pubitemid 34506715)
-
(2002)
Nature Reviews Genetics
, vol.3
, Issue.5
, pp. 329-341
-
-
Feschotte, C.1
Jiang, N.2
Wessler, S.R.3
-
16
-
-
75549090603
-
The Pfam protein families database
-
(14 co-authors)
-
Finn RD, Mistry J, Tate J, et al. (14 co-authors). 2010. The Pfam protein families database. Nucleic Acids Res. 38(Database Issue): D211-D222.
-
(2010)
Nucleic Acids Res
, vol.38
, Issue.DATABASE ISSUE
-
-
Finn, R.D.1
Mistry, J.2
Tate, J.3
-
17
-
-
62849117160
-
The domestication process and domesticaiton rate in rice: Spikelet bases from the Lower Yangtze
-
Fuller DQ, Qin L, Zheng Y, Zhao Z, Chen X, Hosoya LA, Sun GP. 2009. The domestication process and domesticaiton rate in rice: spikelet bases from the Lower Yangtze. Science 323:1607-1610.
-
(2009)
Science
, vol.323
, pp. 1607-1610
-
-
Fuller, D.Q.1
Qin, L.2
Zheng, Y.3
Zhao, Z.4
Chen, X.5
Hosoya, L.A.6
Sun, G.P.7
-
18
-
-
2442657861
-
Evolutionary history of Oryza sativa LTR retrotransposons: A preliminary surey of the rice genome sequences
-
Gao L, McCarthy EM, Ganko EW, McDonald JF. 2004. Evolutionary history of Oryza sativa LTR retrotransposons: a preliminary surey of the rice genome sequences. BMC Genomics 5:18.
-
(2004)
BMC Genomics
, vol.5
, pp. 18
-
-
Gao, L.1
McCarthy, E.M.2
Ganko, E.W.3
McDonald, J.F.4
-
19
-
-
0037023349
-
A draft sequence of the rice genome (Oryza sativa L. ssp. japonica)
-
DOI 10.1126/science.1068275
-
Goff SA, Ricke D, Lan TH, et al. (55 co-authors). 2002. A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 296: 92-100. (Pubitemid 34280065)
-
(2002)
Science
, vol.296
, Issue.5565
, pp. 92-100
-
-
Goff, S.A.1
Ricke, D.2
Lan, T.-H.3
Presting, G.4
Wang, R.5
Dunn, M.6
Glazebrook, J.7
Sessions, A.8
Oeller, P.9
Varma, H.10
Hadley, D.11
Hutchison, D.12
Martin, C.13
Katagiri, F.14
Lange, B.M.15
Moughamer, T.16
Xia, Y.17
Budworth, P.18
Zhong, J.19
Miguel, T.20
Paszkowski, U.21
Zhang, S.22
Colbert, M.23
Sun, W.-L.24
Chen, L.25
Cooper, B.26
Park, S.27
Wood, T.C.28
Mao, L.29
Quail, P.30
Wing, R.31
Deans, R.32
Yu, Y.33
Zharkikh, A.34
Shen, R.35
Sahasrabudhe, S.36
Thomas, A.37
Cannings, R.38
Gutin, A.39
Pruss, D.40
Reid, J.41
Tavtigian, S.42
Mitchell, J.43
Eldredge, G.44
Scholl, T.45
Miller, R.M.46
Bhatnagar, S.47
Adey, N.48
Rubano, T.49
Tusneem, N.50
Robinson, R.51
Feldhaus, J.52
Macalma, T.53
Oliphant, A.54
Briggs, S.55
more..
-
20
-
-
77949497797
-
BRAT: Bisulfite-treated reads analysis tool
-
Harris EY, Ponts N, Levchuk A, Roch KL, Lonardi S. 2010. BRAT: bisulfite-treated reads analysis tool. Bioinformatics 26:572-573.
-
(2010)
Bioinformatics
, vol.26
, pp. 572-573
-
-
Harris, E.Y.1
Ponts, N.2
Levchuk, A.3
Roch, K.L.4
Lonardi, S.5
-
21
-
-
70449601785
-
Rapid DNA loss as a counterbalance to genome expansion through retrotransposon proliferation in plants
-
Hawkins JS, Proulx SR, Rapp RA, Wendel JF. 2009. Rapid DNA loss as a counterbalance to genome expansion through retrotransposon proliferation in plants. Proc Natl Acad Sci USA. 106: 17811-17816.
-
(2009)
Proc Natl Acad Sci USA
, vol.106
, pp. 17811-17816
-
-
Hawkins, J.S.1
Proulx, S.R.2
Rapp, R.A.3
Wendel, J.F.4
-
22
-
-
77950346035
-
Global epigenetic and transcriptional trends among two rice subspecies and their reciprocal hybrids
-
(13 co-authors)
-
He G, Zhu X, Elling A, et al. (13 co-authors). 2010. Global epigenetic and transcriptional trends among two rice subspecies and their reciprocal hybrids. Plant Cell 22:17-33.
-
(2010)
Plant Cell
, vol.22
, pp. 17-33
-
-
He, G.1
Zhu, X.2
Elling, A.3
-
23
-
-
84863116849
-
Widespread interspecific divergence in cis-regulation of transposable elements in the Arabidopsis genus
-
He F, Zhang X, Hu JY, Turck F, Dong X, Goebel U, Borevitz JO, de Meaux J. 2012. Widespread interspecific divergence in cis-regulation of transposable elements in the Arabidopsis genus. Mol Biol Evol. 29: 1081-1091.
-
(2012)
Mol Biol Evol
, vol.29
, pp. 1081-1091
-
-
He, F.1
Zhang, X.2
Hu, J.Y.3
Turck, F.4
Dong, X.5
Goebel, U.6
Borevitz, J.O.7
De Meaux, J.8
-
24
-
-
68149144366
-
Epigenetic silencing of transposable elements: A trade-off between reduced transposition and deleterious effects on neighboring gene expression
-
Hollister JD, Gaut BS. 2009. Epigenetic silencing of transposable elements: a trade-off between reduced transposition and deleterious effects on neighboring gene expression. Genome Res. 19: 1419-1428.
-
(2009)
Genome Res
, vol.19
, pp. 1419-1428
-
-
Hollister, J.D.1
Gaut, B.S.2
-
25
-
-
79952303685
-
Transposable elements and small RNAs contribute to gene expression divergence between Arabidopsis thaliana and Arabidopsis lyrata
-
Hollister JD, Smith LM, Guo YL, Ott F, Weigel D, Gaut BS. 2011. Transposable elements and small RNAs contribute to gene expression divergence between Arabidopsis thaliana and Arabidopsis lyrata. Proc Natl Acad Sci. 108:2322-2327.
-
(2011)
Proc Natl Acad Sci
, vol.108
, pp. 2322-2327
-
-
Hollister, J.D.1
Smith, L.M.2
Guo, Y.L.3
Ott, F.4
Weigel, D.5
Gaut, B.S.6
-
26
-
-
38649092410
-
An interactive viewer for large phylogenetic trees
-
Huson DH, Richter DC, Rausch C, Dezulian T, Franz M, Rupp R. 2007. An interactive viewer for large phylogenetic trees. BMC Bioinformatics 8:460.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 460
-
-
Huson, D.H.1
Richter, D.C.2
Rausch, C.3
Dezulian, T.4
Franz, M.5
Rupp, R.6
-
27
-
-
77955018899
-
Adephylo: New tools for investigating the phylogenetic signal in biological traits
-
Jombart T, Balloux F, Dray S. 2010. adephylo: new tools for investigating the phylogenetic signal in biological traits. Bioinformatics 26: 1907-1909.
-
(2010)
Bioinformatics
, vol.26
, pp. 1907-1909
-
-
Jombart, T.1
Balloux, F.2
Dray, S.3
-
28
-
-
23844525077
-
Repbase Update, a database of eukaryotic repetitive elements
-
DOI 10.1159/000084979
-
Jurka J, Kapitonov V, Pavlicek A, Klonowski P, Kohany O,Walichiewicz J. 2005. Repbase Update, a database of eukaryotic repetitive elements. Cytogenet Genome Res. 110:462-467. (Pubitemid 41159923)
-
(2005)
Cytogenetic and Genome Research
, vol.110
, Issue.1-4
, pp. 462-467
-
-
Jurka, J.1
Kapitonov, V.V.2
Pavlicek, A.3
Klonowski, P.4
Kohany, O.5
Walichiewicz, J.6
-
29
-
-
79953078781
-
Analysis of plant diversity with retrotransposon-based molecular markers
-
Kalendar R, Flavell A, Ellis THN, Sjakste T, Moisy C, Schulman AH. 2011. Analysis of plant diversity with retrotransposon-based molecular markers. Heredity 106:520-530.
-
(2011)
Heredity
, vol.106
, pp. 520-530
-
-
Kalendar, R.1
Flavell, A.2
Ellis, T.H.N.3
Sjakste, T.4
Moisy, C.5
Schulman, A.H.6
-
30
-
-
0035105221
-
Perspective: Transposable elements, parasitic DNA, and genome evolution
-
KidwellMG, Lisch DR. 2001. Perspective: transposable elements, parasitic DNA, and genome evolution. Evolution 55:1-24. (Pubitemid 32175281)
-
(2001)
Evolution
, vol.55
, Issue.1
, pp. 1-24
-
-
Kidwell, M.G.1
Lisch, D.R.2
-
31
-
-
77952299411
-
On the estimation of the insertion time of LTR retrotransposable elements
-
Kijima TE, Innan H. 2010. On the estimation of the insertion time of LTR retrotransposable elements. Mol Biol Evol. 27:896-904.
-
(2010)
Mol Biol Evol
, vol.27
, pp. 896-904
-
-
Kijima, T.E.1
Innan, H.2
-
32
-
-
0019296687
-
A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences
-
DOI 10.1007/BF01731581
-
Kimura M. 1980. A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. J Mol Evol. 16:111-120. (Pubitemid 11166431)
-
(1980)
Journal of Molecular Evolution
, vol.16
, Issue.2
, pp. 111-120
-
-
Kimura, M.1
-
33
-
-
35748969870
-
New insights into the history of rice domestication
-
DOI 10.1016/j.tig.2007.08.012, PII S0168952507003046
-
Kovach MJ, Sweeney MT, McCouch SR. 2007. New insights into the history of rice domestication. Trends Genet. 23:578-587. (Pubitemid 350052354)
-
(2007)
Trends in Genetics
, vol.23
, Issue.11
, pp. 578-587
-
-
Kovach, M.J.1
Sweeney, M.T.2
McCouch, S.R.3
-
34
-
-
40749139473
-
TEnest: Automated chronological annotation and visualization of nested plant transposable elements
-
DOI 10.1104/pp.107.110353
-
Kronmiller BA, Wise RP. 2008. TEnext: automated chronological annotation and visualization of nested plant transposable elements. Plant Physiol. 146:45-59. (Pubitemid 351380032)
-
(2008)
Plant Physiology
, vol.146
, Issue.1
, pp. 45-59
-
-
Kronmiller, B.A.1
Wise, R.P.2
-
36
-
-
0024210911
-
On the role of unequal exchange in the containment of transposable element copy number
-
Langley CH, Montgomery E, Hudson R, Kaplan N, Charlesworth B. 1988. On the role of unequal exchange in the containment of transposable element copy number. Genet Res. 52:223-235. (Pubitemid 19031127)
-
(1988)
Genetical Research
, vol.52
, Issue.3
, pp. 223-235
-
-
Langley, C.H.1
Montgomery, E.2
Hudson, R.3
Kaplan, N.4
Charlesworth, B.5
-
37
-
-
36448991500
-
ClustalW and ClustalX version 2
-
(13 co-authors)
-
Larkin MA, Blachshields G, Brown NP, et al. (13 co-authors). 2007. ClustalW and ClustalX version 2. Bioinformatics 23:2947-2948.
-
(2007)
Bioinformatics
, vol.23
, pp. 2947-2948
-
-
Larkin, M.A.1
Blachshields, G.2
Brown, N.P.3
-
38
-
-
77952670452
-
Identifying repeats and transposable elements in sequenced genomes: How to find your way through the dense forest of programs
-
Lerat E. 2010. Identifying repeats and transposable elements in sequenced genomes: how to find your way through the dense forest of programs. Heredity 104:520-533.
-
(2010)
Heredity
, vol.104
, pp. 520-533
-
-
Lerat, E.1
-
39
-
-
80051997952
-
Dynamic interactions between transposable elements and their hosts
-
Levin HL, Moran JV. 2011. Dynamic interactions between transposable elements and their hosts. Nat Rev Genet. 12:615-627.
-
(2011)
Nat Rev Genet
, vol.12
, pp. 615-627
-
-
Levin, H.L.1
Moran, J.V.2
-
40
-
-
3342927934
-
Role of transposable elements in heterochromatin and epigenetic control
-
DOI 10.1038/nature02651
-
Lippman Z, Gendrel AV, Black M, et al. (14 co-authors). 2004. Role of transposable elements in heterochromatin and epigenetic control. Nature 430:471-476. (Pubitemid 38987911)
-
(2004)
Nature
, vol.430
, Issue.6998
, pp. 471-476
-
-
Lippman, Z.1
Gendrel, A.-V.2
Black, M.3
Vaughn, M.W.4
Dedhia, N.5
McCombie, W.R.6
Lavine, K.7
Mittal, V.8
May, B.9
Kasschau, K.B.10
Carrington, J.C.11
Doerge, R.W.12
Colot, V.13
Martienssen, R.14
-
41
-
-
66449124318
-
Epigenetic regulation of transposable elements in plants
-
Lisch DR. 2009. Epigenetic regulation of transposable elements in plants. Annu Rev Plant Biol. 60:43-66.
-
(2009)
Annu Rev Plant Biol
, vol.60
, pp. 43-66
-
-
Lisch, D.R.1
-
42
-
-
79955082486
-
Transposable element origins of epigenetic gene regulation
-
Lisch D, Bennetzen J. 2011. Transposable element origins of epigenetic gene regulation. Curr Opin Plant Biol. 14:156-161.
-
(2011)
Curr Opin Plant Biol
, vol.14
, pp. 156-161
-
-
Lisch, D.1
Bennetzen, J.2
-
43
-
-
42749087226
-
Highly integrated single-base resolution maps of the epigenome in Arabidopsis
-
Lister R, O'Malley RC, Tonti-Filippini J, Gregory BD, Berry CC, Millar AH, Ecker JR. 2008. Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 133:523-536.
-
(2008)
Cell
, vol.133
, pp. 523-536
-
-
Lister, R.1
O'Malley, R.C.2
Tonti-Filippini, J.3
Gregory, B.D.4
Berry, C.C.5
Millar, A.H.6
Ecker, J.R.7
-
44
-
-
66449121652
-
Finding the fifth base: Genome-wide sequencing of cytosine methylation
-
Lister R, Ecker JR. 2009. Finding the fifth base: genome-wide sequencing of cytosine methylation. Genome Res. 19:959-966.
-
(2009)
Genome Res
, vol.19
, pp. 959-966
-
-
Lister, R.1
Ecker, J.R.2
-
46
-
-
2342466982
-
Analyses of LTR-retrotransposon structures reveal recent and rapid genomic DNA loss in rice
-
DOI 10.1101/gr.1466204
-
Ma J, Devos KM, Bennetzen JL. 2004. Analyses of LTR-retrotransposon structure reveal recent and rapid genomic loss of DNA in rice. Genome Res. 14:860-869. (Pubitemid 38660503)
-
(2004)
Genome Research
, vol.14
, Issue.5
, pp. 860-869
-
-
Ma, J.1
Devos, K.M.2
Bennetzen, J.L.3
-
48
-
-
0037433054
-
LTR-STRUC: A novel search and identification program for LTR retrotransposons
-
McCarthy EM, McDonald JF. 2003. LTR-STRUC: a novel search and identification program for LTR retrotransposons. Bioinformatics 19: 362-367.
-
(2003)
Bioinformatics
, vol.19
, pp. 362-367
-
-
McCarthy, E.M.1
McDonald, J.F.2
-
49
-
-
0031441380
-
LTR retrotransposons and the evolution of the eukaryotic enhancers
-
McDonald JF, Matyunina LV, Wilson S, Jordan IK, Bowen JN, Miller W. 1997. LTR retrotransposons and the evolution of the eukaryotic enhancers. Genetics 100:111-115.
-
(1997)
Genetics
, vol.100
, pp. 111-115
-
-
McDonald, J.F.1
Matyunina, L.V.2
Wilson, S.3
Jordan, I.K.4
Bowen, J.N.5
Miller, W.6
-
50
-
-
70350515004
-
Unexpected consequences of a sudden and massive transposon amplification on rice gene expression
-
Naito K, Zhang R, Tsukiyama T, Saito H, Hancock CN, Richardson AO, Okumoto Y, Tanisaka T, Wessler SR. 2009. Unexpected consequences of a sudden and massive transposon amplification on rice gene expression. Nature 461:1130-1135.
-
(2009)
Nature
, vol.461
, pp. 1130-1135
-
-
Naito, K.1
Zhang, R.2
Tsukiyama, T.3
Saito, H.4
Hancock, C.N.5
Richardson, A.O.6
Okumoto, Y.7
Tanisaka, T.8
Wessler, S.R.9
-
51
-
-
0035212395
-
Silencing of transposable elements in plants
-
DOI 10.1016/S1360-1385(01)02105-7, PII S1360138501021057
-
Okamoto H, Hirochika H. 2001. Silencing of transposable elements in plants. Trends Plant Sci. 6:527-534. (Pubitemid 33145972)
-
(2001)
Trends in Plant Science
, vol.6
, Issue.11
, pp. 527-534
-
-
Okamoto, H.1
Hirochika, H.2
-
52
-
-
37849013027
-
Testing for phylogenetic signal in phenotypic traits: New matrices of phylogenetic proximities
-
Pavoine S, Ollier S, Ponteir D, Chessel D. 2008. Testing for phylogenetic signal in phenotypic traits: new matrices of phylogenetic proximities. Theor Popul Biol. 73:79-91.
-
(2008)
Theor Popul Biol
, vol.73
, pp. 79-91
-
-
Pavoine, S.1
Ollier, S.2
Ponteir, D.3
Chessel, D.4
-
53
-
-
0038247887
-
Size matters: Non-LTR retrotransposable elements and ectopic recombination in drosophila
-
DOI 10.1093/molbev/msg102
-
Petrov DA, Aminetzach YT, Davis JC, Bensasson D, Hirsh AE. 2003. Size matters: non-LTR retrotransposable elements and ectopic recombination in Drosophila. Mol Biol Evol. 20:880-892. (Pubitemid 36578714)
-
(2003)
Molecular Biology and Evolution
, vol.20
, Issue.6
, pp. 880-892
-
-
Petrov, D.A.1
Aminetzach, Y.T.2
Davis, J.C.3
Bensasson, D.4
Hirsh, A.E.5
-
54
-
-
79953729211
-
Population genomics of transposable elements in Drosophila melanogaster
-
Petrov DA, Fiston-Lavier AS, Lipatov M, Lenkov K, González J. 2010. Population genomics of transposable elements in Drosophila melanogaster. Mol Bio Evol. 28:1633-1644.
-
(2010)
Mol Bio Evol
, vol.28
, pp. 1633-1644
-
-
Petrov, D.A.1
Fiston-Lavier, A.S.2
Lipatov, M.3
Lenkov, K.4
González, J.5
-
55
-
-
33749392949
-
Doubling genome size without polyploidization: Dynamics of retrotransposition-driven genomic expansions in Oryza australiensis, a wild relative of rice
-
DOI 10.1101/gr.5290206
-
Piegu B, Guyot R, Picault N, et al. (12 co-authors). 2006. Doubling genome size without polyploidization: dynamics of retrotransposition-driven genomic expansions in Oryza australiensis, a wild relative of rice. Genome Res. 16:1262-1269. (Pubitemid 44506959)
-
(2006)
Genome Research
, vol.16
, Issue.10
, pp. 1262-1269
-
-
Piegu, B.1
Guyot, R.2
Picault, N.3
Roulin, A.4
Saniyal, A.5
Kim, H.6
Collura, K.7
Brar, D.S.8
Jackson, S.9
Wing, R.A.10
Panaud, O.11
-
56
-
-
77955056912
-
Rice genomics moves ahead
-
Raghuvanshi S, Kapoor M, Tyagi S, Kapoor S, Khurana P, Tyagi A. 2011. Rice genomics moves ahead. Mol Breeding 26:257-273.
-
(2011)
Mol Breeding
, vol.26
, pp. 257-273
-
-
Raghuvanshi, S.1
Kapoor, M.2
Tyagi, S.3
Kapoor, S.4
Khurana, P.5
Tyagi, A.6
-
57
-
-
33846857991
-
Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana
-
Rice Annotation Project
-
Rice Annotation Project. 2007. Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana. Genome Res. 17:175-183.
-
(2007)
Genome Res
, vol.17
, pp. 175-183
-
-
-
58
-
-
38549136871
-
The Rice Annotation Project Database (RAP-DB): 2008 update
-
Rice Annotation Project
-
Rice Annotation Project. 2008. The Rice Annotation Project Database (RAP-DB): 2008 update. Nucleic Acids Res. 36: D1028-D1033.
-
(2008)
Nucleic Acids Res
, vol.36
-
-
-
59
-
-
36549064298
-
Genetics and phylogenetics of rice domestication
-
DOI 10.1016/j.gde.2007.09.005, PII S0959437X07001700, Genomes and Evolution
-
Sang T, Ge S. 2007. Genetics and phylogenetics of rice domestication. Curr Opin Genet Dev. 17:533-538. (Pubitemid 350184312)
-
(2007)
Current Opinion in Genetics and Development
, vol.17
, Issue.6
, pp. 533-538
-
-
Sang, T.1
Ge, S.2
-
60
-
-
0031707062
-
The paleontology of intergene retrotransposons of maize
-
DOI 10.1038/1695
-
SanMiguel P, Gaut BS, Tikhonov A, Nakajima Y, Bennetzen JL. 1998. The paleontology of intergene retrotransposons of maize. Nat Genet. 20: 43-45. (Pubitemid 28410341)
-
(1998)
Nature Genetics
, vol.20
, Issue.1
, pp. 43-45
-
-
SanMiguel, P.1
Gaut, B.S.2
Tikhonov, A.3
Nakajima, Y.4
Bennetzen, J.L.5
-
61
-
-
80054837794
-
Transgenerational epigenetic instability is a source of novel methylation variants
-
Schmitz JR, Schultz MD, Lewsey MG, O'Malley RC, Urich MA, Libiger O, Schork NJ, Ecker JR. 2011. Transgenerational epigenetic instability is a source of novel methylation variants. Science 334: 369-373.
-
(2011)
Science
, vol.334
, pp. 369-373
-
-
Schmitz, J.R.1
Schultz, M.D.2
Lewsey, M.G.3
O'Malley, R.C.4
Urich, M.A.5
Libiger, O.6
Schork, N.J.7
Ecker, J.R.8
-
62
-
-
33947303168
-
Transposable elements and the epigenetic regulation of the genome
-
DOI 10.1038/nrg2072, PII NRG2072
-
Slotkin RK, Martienssen R. 2007. Transposable elements and the epigenetic regulation of the genome. Nat Rev Genet. 8:272-285. (Pubitemid 46439291)
-
(2007)
Nature Reviews Genetics
, vol.8
, Issue.4
, pp. 272-285
-
-
Slotkin, R.K.1
Martienssen, R.2
-
63
-
-
33750403801
-
RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
-
DOI 10.1093/bioinformatics/btl446
-
Stamatakis A. 2006. RAxML-VI-HPC: Maximum likelihood phylogenetic analsyis with thousands of taxa and mixed models. Bioinformatics 22:2688-2690. (Pubitemid 44642609)
-
(2006)
Bioinformatics
, vol.22
, Issue.21
, pp. 2688-2690
-
-
Stamatakis, A.1
-
64
-
-
75349090212
-
Fine-grained annotation and classification of de novo predicted LTR retrotransposons
-
Steinbiss S, Willhoeft U, Gremme G, Kurtz S. 2009. Fine-grained annotation and classification of de novo predicted LTR retrotransposons. Nucleic Acids Res. 37:7002-7013.
-
(2009)
Nucleic Acids Res
, vol.37
, pp. 7002-7013
-
-
Steinbiss, S.1
Willhoeft, U.2
Gremme, G.3
Kurtz, S.4
-
65
-
-
43749098985
-
DNA methylation landscapes: Provocative insights from epigenomics
-
DOI 10.1038/nrg2341, PII NRG2341
-
Suzuki MM, Bird A. 2008. DNA methylation landscapes: provocative insights from epigenomics. Nat Rev Genet. 9:465-476. (Pubitemid 351693975)
-
(2008)
Nature Reviews Genetics
, vol.9
, Issue.6
, pp. 465-476
-
-
Suzuki, M.M.1
Bird, A.2
-
66
-
-
35348934368
-
The complex history of the domestication of rice
-
DOI 10.1093/aob/mcm128
-
Sweeney M, McCouch S. 2007. The complex history of the domestication of rice. Ann Bot. 100:951-957. (Pubitemid 47614323)
-
(2007)
Annals of Botany
, vol.100
, Issue.5
, pp. 951-957
-
-
Sweeney, M.1
McCouch, S.2
-
67
-
-
79957613599
-
MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods
-
Tamura KJD, Nei M, Kumar S. 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.J.D.1
Nei, M.2
Kumar, S.3
-
68
-
-
77955273950
-
A triptych of the evolution of plant transposable elements
-
Tenaillon MI, Hollister JD, Gaut BS. 2010. A triptych of the evolution of plant transposable elements. Trends Plant Sci. 15:471-478.
-
(2010)
Trends Plant Sci
, vol.15
, pp. 471-478
-
-
Tenaillon, M.I.1
Hollister, J.D.2
Gaut, B.S.3
-
69
-
-
79960095966
-
Genome size and transposable element content as determined by high-throughput sequencing in maize and Zea luxurians
-
Advance access published February 4, 2011 doi:10. 1093/gbe/evr008
-
Tenaillon MI, Hufford M, Gaut BS, Ross-Ibarra J. 2011. Genome size and transposable element content as determined by high-throughput sequencing in maize and Zea luxurians. Genome Biol Evol. Advance access published February 4, 2011, doi:10. 1093/gbe/evr008.
-
(2011)
Genome Biol Evol
-
-
Tenaillon, M.I.1
Hufford, M.2
Gaut, B.S.3
Ross-Ibarra, J.4
-
70
-
-
73249153383
-
Do genetic recombination and gene density shape the pattern of DNA elimination in rice long terminal repeat retrotransposons?
-
Tian Z, Rizzon C, Du J, Zhu L, Bennetzen JL, Jackson SA, Gaut BS, Ma J. 2009. Do genetic recombination and gene density shape the pattern of DNA elimination in rice long terminal repeat retrotransposons? Genome Res. 19:2221-2230.
-
(2009)
Genome Res
, vol.19
, pp. 2221-2230
-
-
Tian, Z.1
Rizzon, C.2
Du, J.3
Zhu, L.4
Bennetzen, J.L.5
Jackson, S.A.6
Gaut, B.S.7
Ma, J.8
-
71
-
-
0037387430
-
Formation of solo-LTRs through unequal homologous recombination counterbalances amplifications of LTR retrotransposons in rice Oryza sativa L
-
DOI 10.1093/molbev/msg055
-
Vitte C, Panaud O. 2003. Formation of solo-LTRs through unequal homologous recombination counterbalances amplification of LTR retrotransposons in rice Oryza sativa L. Mol Biol Evol. 20:528-540. (Pubitemid 36437903)
-
(2003)
Molecular Biology and Evolution
, vol.20
, Issue.4
, pp. 528-540
-
-
Vitte, C.1
Panaud, O.2
-
72
-
-
34547740136
-
LTR retrotransposon in rice (Oryza sativa, L. ): Recent burst amplifications followed by rapid DNA loss
-
Vitte C, Panaud O, Quesneville H. 2007. LTR retrotransposon in rice (Oryza sativa, L. ): recent burst amplifications followed by rapid DNA loss. BMC Genomics 8:218.
-
(2007)
BMC Genomics
, vol.8
, pp. 218
-
-
Vitte, C.1
Panaud, O.2
Quesneville, H.3
-
73
-
-
51749095104
-
Phylocom: Software for the analysis of phylogenetic community structure and character evolution
-
Webb CO, Ackerly DD, Kembel SW. 2008. Phylocom: software for the analysis of phylogenetic community structure and character evolution. Bioinformatics 24:2098-2100.
-
(2008)
Bioinformatics
, vol.24
, pp. 2098-2100
-
-
Webb, C.O.1
Ackerly, D.D.2
Kembel, S.W.3
-
75
-
-
33745634395
-
Cd-hit: A fast program for clustering and comparing large sets of protein or nucleotide sequences
-
DOI 10.1093/bioinformatics/btl158
-
Weizhong L, Godzik A. 2006. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22:1658-1659. (Pubitemid 43985301)
-
(2006)
Bioinformatics
, vol.22
, Issue.13
, pp. 1658-1659
-
-
Li, W.1
Godzik, A.2
-
76
-
-
34347381116
-
Genome-wide comparative analysis of copia retrotransposons in Triticeae, rice, and Arabidopsis reveals conserved ancient evolutionary lineages and distinct dynamics of individual copia families
-
DOI 10.1101/gr.6214107
-
Wicker T, Keller B. 2007. Genome-wide comparative analysis of copia retrotransposons in Triticeae, rice and Arabidopsis reveals conserved ancient evolutionary lineages and distinct dynamics of individual copia families. Genome Res. 17:1072-1081. (Pubitemid 47026354)
-
(2007)
Genome Research
, vol.17
, Issue.7
, pp. 1072-1081
-
-
Wicker, T.1
Keller, B.2
-
77
-
-
36249023071
-
A unified classification system for eukaryotic transposable elements
-
DOI 10.1038/nrg2165, PII NRG2165
-
Wicker T, Sabot F, Hua-Van A, et al. (13 co-authors). 2007. A unified classification system for eukaryotic transposable elements. Nat Rev Genet. 8:973-982. (Pubitemid 350129169)
-
(2007)
Nature Reviews Genetics
, vol.8
, Issue.12
, pp. 973-982
-
-
Wicker, T.1
Sabot, F.2
Hua-Van, A.3
Bennetzen, J.L.4
Capy, P.5
Chalhoub, B.6
Flavell, A.7
Leroy, P.8
Morgante, M.9
Panaud, O.10
Paux, E.11
SanMiguel, P.12
Schulman, A.H.13
-
78
-
-
77952950482
-
Structure and evolution of full-length LTR retrotransposons in rice genome
-
Xu L, Zhang YP, Su Y, Liu L, Yang J, Zhu Y, Li C. 2010. Structure and evolution of full-length LTR retrotransposons in rice genome. Plant Syst Evol. 287:19-28.
-
(2010)
Plant Syst Evol
, vol.287
, pp. 19-28
-
-
Xu, L.1
Zhang, Y.P.2
Su, Y.3
Liu, L.4
Yang, J.5
Zhu, Y.6
Li, C.7
-
79
-
-
34547417996
-
Transposition of the rice miniature inverted repeat transposable element mPing in Arabidopsis thaliana
-
DOI 10.1073/pnas.0702080104
-
Yang G, Zhang F, Hancock CN, Wessler SR. 2007. Transposition of the rice minature inverted repeat transposable element mPing in Arabidopsis thaliana. Proc Natl Acad Sci. 104:10962-10967. (Pubitemid 47175209)
-
(2007)
Proceedings of the National Academy of Sciences of the United States of America
, vol.104
, Issue.26
, pp. 10962-10967
-
-
Yang, G.1
Zhang, F.2
Hancock, C.N.3
Wessler, S.R.4
-
80
-
-
0037023384
-
A draft sequence of the rice genome (Oryza sativa L. ssp. indica)
-
DOI 10.1126/science.1068037
-
Yu J, Hu S, Wang J, Wong GK, Li S, et al. (95 co-authors). 2002. A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 296: 79-92. (Pubitemid 34280064)
-
(2002)
Science
, vol.296
, Issue.5565
, pp. 79-92
-
-
Yu, J.1
Hu, S.2
Wang, J.3
Wong, G.K.-S.4
Li, S.5
Liu, B.6
Deng, Y.7
Dai, L.8
Zhou, Y.9
Zhang, X.10
Cao, M.11
Liu, J.12
Sun, J.13
Tang, J.14
Chen, Y.15
Huang, X.16
Lin, W.17
Ye, C.18
Tong, W.19
Cong, L.20
Geng, J.21
Han, Y.22
Li, L.23
Li, W.24
Hu, G.25
Huang, X.26
Li, W.27
Li, J.28
Liu, Z.29
Li, L.30
Liu, J.31
Qi, Q.32
Liu, J.33
Li, L.34
Li, T.35
Wang, X.36
Lu, H.37
Wu, T.38
Zhu, M.39
Ni, P.40
Han, H.41
Dong, W.42
Ren, X.43
Feng, X.44
Cui, P.45
Li, X.46
Wang, H.47
Xu, X.48
Zhai, W.49
Xu, Z.50
Zhang, J.51
He, S.52
Zhang, J.53
Xu, J.54
Zhang, K.55
Zheng, X.56
Dong, J.57
Zeng, W.58
Tao, L.59
Ye, J.60
Tan, J.61
Ren, X.62
Chen, X.63
He, J.64
Liu, D.65
Tian, W.66
Tian, C.67
Xia, H.68
Bao, Q.69
Li, G.70
Gao, H.71
Cao, T.72
Wang, J.73
Zhao, W.74
Li, P.75
Chen, W.76
Wang, X.77
Zhang, Y.78
Hu, J.79
Wang, J.80
Liu, S.81
Yang, J.82
Zhang, G.83
Xiong, Y.84
Li, Z.85
Mao, L.86
Zhou, C.87
Zhu, Z.88
Chen, R.89
Hao, B.90
Zheng, W.91
Chen, S.92
Guo, W.93
Li, G.94
Liu, S.95
Tao, M.96
Wang, J.97
Zhu, L.98
Yang, H.99
more..
-
81
-
-
77952355762
-
Genome-wide evolutionary analysis of eukaryotic DNA methylation
-
Zemach A, McDaniel IE, Silva P, Zilberman D. 2010. Genome-wide evolutionary analysis of eukaryotic DNA methylation. Science 328: 916-919.
-
(2010)
Science
, vol.328
, pp. 916-919
-
-
Zemach, A.1
McDaniel, I.E.2
Silva, P.3
Zilberman, D.4
-
82
-
-
33845880624
-
Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription
-
DOI 10.1038/ng1929, PII NG1929
-
Zilberman D, Gehring M, Tran RK, Ballinger T, Henikoff S. 2007. Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription. Nat Genet. 39:61-69. (Pubitemid 46026502)
-
(2007)
Nature Genetics
, vol.39
, Issue.1
, pp. 61-69
-
-
Zilberman, D.1
Gehring, M.2
Tran, R.K.3
Ballinger, T.4
Henikoff, S.5
|