-
1
-
-
33847749916
-
Recurrent insertion and duplication generate networks of transposable element sequences in the Drosophila melanogaster genome
-
Bergman CM, et al. (2006) Recurrent insertion and duplication generate networks of transposable element sequences in the Drosophila melanogaster genome. Genome Biol 7:R112
-
(2006)
Genome. Biol.
, vol.7
-
-
Bergman, C.M.1
-
2
-
-
28844444029
-
Combined evidence annotation of transposable elements in genome sequences
-
Quesneville H, et al. (2005) Combined evidence annotation of transposable elements in genome sequences. PLoS Comput Biol 1: 166-175
-
(2005)
PLoS Comput Biol.
, vol.1
, pp. 166-175
-
-
Quesneville, H.1
-
3
-
-
2042437650
-
Initial sequencing and analysis of the human genome
-
DOI 10.1038/35057062
-
Lander ES, et al. (2001) Initial sequencing and analysis of the human genome. Nature 409:860-921 (Pubitemid 32165345)
-
(2001)
Nature
, vol.409
, Issue.6822
, pp. 860-921
-
-
Lander, E.S.1
-
4
-
-
70450202132
-
The B73 maize genome: Complexity, diversity, and dynamics
-
Schnable PS, et al. (2009) The B73 maize genome: complexity, diversity, and dynamics. Science 326:1112-1115
-
(2009)
Science
, vol.326
, pp. 1112-1115
-
-
Schnable, P.S.1
-
5
-
-
0024505998
-
Eukaryotic transposable elements and genome evolution
-
DOI 10.1016/0168-9525(89)90039-5
-
Finnegan DJ (1989) Eukaryotic transposable elements and genome evolution. Trends Genet 5:103-107 (Pubitemid 19107063)
-
(1989)
Trends in Genetics
, vol.5
, Issue.4
, pp. 103-107
-
-
Finnegan, D.J.1
-
6
-
-
36249023071
-
A unified classification system for eukaryotic transposable elements
-
DOI 10.1038/nrg2165, PII NRG2165
-
Wicker T, et al. (2007) A unifi ed classifi cation 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
-
7
-
-
36549035839
-
Discovering and detecting transposable elements in genome sequences
-
DOI 10.1093/bib/bbm048
-
Bergman CM, Quesneville H (2007) Discovering and detecting transposable elements in genome sequences. Brief Bioinform 8:382-392 (Pubitemid 350186918)
-
(2007)
Briefings in Bioinformatics
, vol.8
, Issue.6
, pp. 382-392
-
-
Bergman, C.M.1
Quesneville, H.2
-
8
-
-
0346120025
-
Detection of New Transposable Element Families in Drosophila melanogaster and Anopheles gambiae Genomes
-
DOI 10.1007/s00239-003-0007-2
-
Quesneville H, Nouaud D, Anxolabehere D (2003) Detection of new transposable element families in Drosophila melanogaster and Anopheles gambiae genomes. J Mol Evol 57 Suppl 1:S50-59 (Pubitemid 37543995)
-
(2003)
Journal of Molecular Evolution
, vol.57
, Issue.SUPPL. 1
-
-
Quesneville, H.1
Nouaud, D.2
Anxolabehere, D.3
-
9
-
-
34548669353
-
The Fusarium graminearum genome reveals a link between localized polymorphism and pathogen specialization
-
DOI 10.1126/science.1143708
-
Cuomo CA, et al. (2007) The Fusarium graminearum genome reveals a link between localized polymorphism and pathogen specialization. Science 317:1400-1402 (Pubitemid 47417482)
-
(2007)
Science
, vol.317
, Issue.5843
, pp. 1400-1402
-
-
Cuomo, C.A.1
-
10
-
-
34250902354
-
Genome sequence of Aedes aegypti, a major arbovirus vector
-
DOI 10.1126/science.1138878
-
Nene V, et al. (2007) Genome sequence of Aedes aegypti, a major arbovirus vector. Science 316:1718-1723 (Pubitemid 46988541)
-
(2007)
Science
, vol.316
, Issue.5832
, pp. 1718-1723
-
-
Nene, V.1
Wortman, J.R.2
Lawson, D.3
Haas, B.4
Kodira, C.5
Tu, Z.6
Loftus, B.7
Xi, Z.8
Megy, K.9
Grabherr, M.10
Ren, Q.11
Zdobnov, E.M.12
Lobo, N.F.13
Campbell, K.S.14
Brown, S.E.15
Bonaldo, M.F.16
Zhu, J.17
Sinkins, S.P.18
Hogenkamp, D.G.19
Amedeo, P.20
Arensburger, P.21
Atkinson, P.W.22
Bidwell, S.23
Biedler, J.24
Birney, E.25
Bruggner, R.V.26
Costas, J.27
Coy, M.R.28
Crabtree, J.29
Crawford, M.30
DeBruyn, B.31
DeCaprio, D.32
Eiglmeier, K.33
Eisenstadt, E.34
El-Dorry, H.35
Gelbart, W.M.36
Gomes, S.L.37
Hammond, M.38
Hannick, L.I.39
Hogan, J.R.40
Holmes, M.H.41
Jaffe, D.42
Johnston, J.S.43
Kennedy, R.C.44
Koo, H.45
Kravitz, S.46
Kriventseva, E.V.47
Kulp, D.48
LaButti, K.49
Lee, E.50
Li, S.51
Lovin, D.D.52
Mao, C.53
Mauceli, E.54
Menck, C.F.M.55
Miller, J.R.56
Montgomery, P.57
Mori, A.58
Nascimento, A.L.59
Naveira, H.F.60
Nusbaum, C.61
O'Leary, S.62
Orvis, J.63
Pertea, M.64
Quesneville, H.65
Reidenbach, K.R.66
Rogers, Y.-H.67
Roth, C.W.68
Schneider, J.R.69
Schatz, M.70
Shumway, M.71
Stanke, M.72
Stinson, E.O.73
Tubio, J.M.C.74
VanZee, J.P.75
Verjovski-Almeida, S.76
Werner, D.77
White, O.78
Wyder, S.79
Zeng, Q.80
Zhao, Q.81
Zhao, Y.82
Hill, C.A.83
Raikhel, A.S.84
Soares, M.B.85
Knudson, D.L.86
Lee, N.H.87
Galagan, J.88
Salzberg, S.L.89
Paulsen, I.T.90
Dimopoulos, G.91
Collins, F.H.92
Birren, B.93
Fraser-Liggett, C.M.94
Severson, D.W.95
more..
-
11
-
-
34547740136
-
Ltr retrotransposons in rice (Oryza sativa, L.): Recent burst amplifi cations followed by rapid DNA loss
-
Vitte C, Panaud O, Quesneville H (2007) LTR retrotransposons in rice (Oryza sativa, L.): recent burst amplifi cations 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
-
12
-
-
49449094873
-
Genome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita
-
Abad P, et al. (2008) Genome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita. Nat Biotechnol 26:909-915
-
(2008)
Nat. Biotechnol
, vol.26
, pp. 909-915
-
-
Abad, P.1
-
13
-
-
42149187766
-
Improved detection and annotation of transposable elements in sequenced genomes using multiple reference sequence sets
-
Buisine N, Quesneville H, Colot V (2008) Improved detection and annotation of transposable elements in sequenced genomes using multiple reference sequence sets. Genomics 91:467-475
-
(2008)
Genomics
, vol.91
, pp. 467-475
-
-
Buisine, N.1
Quesneville, H.2
Colot, V.3
-
14
-
-
40449120632
-
The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis
-
DOI 10.1038/nature06556, PII NATURE06556
-
Martin F, et al. (2008) The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis. Nature 452:88-92 (Pubitemid 351355085)
-
(2008)
Nature
, vol.452
, Issue.7183
, pp. 88-92
-
-
Martin, F.1
Aerts, A.2
Ahren, D.3
Brun, A.4
Danchin, E.G.J.5
Duchaussoy, F.6
Gibon, J.7
Kohler, A.8
Lindquist, E.9
Pereda, V.10
Salamov, A.11
Shapiro, H.J.12
Wuyts, J.13
Blaudez, D.14
Buee, M.15
Brokstein, P.16
Canback, B.17
Cohen, D.18
Courty, P.E.19
Coutinho, P.M.20
Delaruelle, C.21
Detter, J.C.22
Deveau, A.23
DiFazio, S.24
Duplessis, S.25
Fraissinet-Tachet, L.26
Lucic, E.27
Frey-Klett, P.28
Fourrey, C.29
Feussner, I.30
Gay, G.31
Grimwood, J.32
Hoegger, P.J.33
Jain, P.34
Kilaru, S.35
Labbe, J.36
Lin, Y.C.37
Legue, V.38
Le Tacon, F.39
Marmeisse, R.40
Melayah, D.41
Montanini, B.42
Muratet, M.43
Nehls, U.44
Niculita-Hirzel, H.45
Secq, M.P.O.-L.46
Peter, M.47
Quesneville, H.48
Rajashekar, B.49
Reich, M.50
Rouhier, N.51
Schmutz, J.52
Yin, T.53
Chalot, M.54
Henrissat, B.55
Kues, U.56
Lucas, S.57
Van De Peer, Y.58
Podila, G.K.59
Polle, A.60
Pukkila, P.J.61
Richardson, P.M.62
Rouze, P.63
Sanders, I.R.64
Stajich, J.E.65
Tunlid, A.66
Tuskan, G.67
Grigoriev, I.V.68
more..
-
15
-
-
77953001382
-
The Ectocarpus genome and the independent evolution of multicellularity in brown algae
-
Cock JM, et al. (2010) The Ectocarpus genome and the independent evolution of multicellularity in brown algae. Nature 465:617-621
-
(2010)
Nature.
, vol.465
, pp. 617-621
-
-
Cock, J.M.1
-
16
-
-
77952403419
-
Extensive synteny conservation of holocentric chromosomes in Lepidoptera despite high rates of local genome rearrangements
-
D'Alencon E, et al. (2010) Extensive synteny conservation of holocentric chromosomes in Lepidoptera despite high rates of local genome rearrangements. Proc Natl Acad Sci USA 107:7680-7685
-
(2010)
Proc. Natl. Acad. Sci. USA
, vol.107
, pp. 7680-7685
-
-
D'Alencon, E.1
-
17
-
-
77951144839
-
Perigord black truffle genome uncovers evolutionary origins and mechanisms of symbiosis
-
Martin F, et al. (2010) Perigord black truffle genome uncovers evolutionary origins and mechanisms of symbiosis. Nature 464: 1033-1038
-
(2010)
Nature.
, vol.464
, pp. 1033-1038
-
-
Martin, F.1
-
18
-
-
78650122420
-
Genome expansion and gene loss in powdery mildew fungi reveal tradeoffs in extreme parasitism
-
Spanu PD, et al. (2010) Genome expansion and gene loss in powdery mildew fungi reveal tradeoffs in extreme parasitism. Science 330:1543-1546
-
(2010)
Science.
, vol.330
, pp. 1543-1546
-
-
Spanu, P.D.1
-
19
-
-
79551624472
-
Considering transposable element diversifi cation in de novo annotation approaches
-
Flutre T, et al. (2011) Considering transposable element diversifi cation in de novo annotation approaches. PLoS One 6:e16526
-
(2011)
PLoS One.
, vol.6
-
-
Flutre, T.1
-
20
-
-
47149117454
-
Evolution of genes and genomes on the Drosophila phylogeny
-
DOI 10.1038/nature06341, PII NATURE06341
-
Clark AG, et al. (2007) Evolution of genes and genomes on the Drosophila phylogeny. Nature 450:203-218 (Pubitemid 351972300)
-
(2007)
Nature
, vol.450
, Issue.7167
, pp. 203-218
-
-
Clark, A.G.1
-
21
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
DOI 10.1093/nar/25.17.3389
-
Altschul SF, et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389-3402 (Pubitemid 27359211)
-
(1997)
Nucleic Acids Research
, vol.25
, Issue.17
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schaffer, A.A.3
Zhang, J.4
Zhang, Z.5
Miller, W.6
Lipman, D.J.7
-
22
-
-
0036673472
-
Automated de novo identification of repeat sequence families in sequenced genomes
-
DOI 10.1101/gr.88502
-
Bao Z, Eddy SR (2002) Automated de novo identifi cation of repeat sequence families in sequenced genomes. Genome Res 12: 1269-1276 (Pubitemid 41264428)
-
(2002)
Genome Research
, vol.12
, Issue.8
, pp. 1269-1276
-
-
Bao, Z.1
Eddy, S.R.2
-
23
-
-
84860513986
-
Piler: Identifi - Cation and classifi cation of genomic repeats
-
Edgar RC, Myers EW (2005) PILER: identifi - cation and classifi cation of genomic repeats, Bioinformatics 21 Suppl 1:i152-158
-
(2005)
Bioinformatics
, vol.21
, Issue.SUPPL. 1
-
-
Edgar, R.C.1
Myers, E.W.2
-
25
-
-
0037100671
-
MAFFT: A novel method for rapid multiple sequence alignment based on fast Fourier transform
-
Katoh K, et al. (2002) MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res 30:3059-3066 (Pubitemid 34851225)
-
(2002)
Nucleic Acids Research
, vol.30
, Issue.14
, pp. 3059-3066
-
-
Katoh, K.1
Misawa, K.2
Kuma, K.-I.3
Miyata, T.4
-
27
-
-
23844525077
-
Repbase Update, a database of eukaryotic repetitive elements
-
DOI 10.1159/000084979
-
Jurka J, et al. (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
-
28
-
-
75549090603
-
The Pfam protein families database
-
Finn RD, et al. (2010) The Pfam protein families database. Nucleic Acids Res 38:D211-222
-
(2010)
Nucleic. Acids. Res.
, vol.38
-
-
Finn, R.D.1
-
29
-
-
65549101705
-
TEclass - A tool for automated classifi cation of unknown eukaryotic transposable elements
-
Abrusan G, et al. (2009) TEclass - a tool for automated classifi cation of unknown eukaryotic transposable elements. Bioinformatics 25: 1329-1330
-
(2009)
Bioinformatics
, vol.25
, pp. 1329-1330
-
-
Abrusan, G.1
-
31
-
-
13244255415
-
MUSCLE: A multiple sequence alignment method with reduced time and space complexity
-
Edgar RC (2004) MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 5:113
-
(2004)
BMC Bioinformatics
, vol.5
, pp. 113
-
-
Edgar, R.C.1
-
32
-
-
0242578620
-
A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood
-
DOI 10.1080/10635150390235520
-
Guindon S, Gascuel O (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52:696-704 (Pubitemid 37365050)
-
(2003)
Systematic Biology
, vol.52
, Issue.5
, pp. 696-704
-
-
Guindon, S.1
Gascuel, O.2
-
34
-
-
0030094146
-
Censor - A program for identification and elimination of repetitive elements from DNA sequences
-
Jurka J, et al. (1996) CENSOR - a program for identifi cation and elimination of repetitive elements from DNA sequences. Comput Chem 20:119-121 (Pubitemid 126405358)
-
(1996)
Computers and Chemistry
, vol.20
, Issue.1
, pp. 119-121
-
-
Jurka, J.1
Klonowski, P.2
Dagman, V.3
Pelton, P.4
-
35
-
-
33750831582
-
Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor
-
Kohany O, et al. (2006) Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor. BMC Bioinformatics 7:474
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 474
-
-
Kohany, O.1
-
36
-
-
0033555906
-
Tandem repeats finder: A program to analyze DNA sequences
-
DOI 10.1093/nar/27.2.573
-
Benson G (1999) Tandem repeats fi nder: a program to analyze DNA sequences. Nucleic Acids Res 27:573-580 (Pubitemid 29210025)
-
(1999)
Nucleic Acids Research
, vol.27
, Issue.2
, pp. 573-580
-
-
Benson, G.1
-
37
-
-
0043123037
-
Mreps: Efficient and flexible detection of tandem repeats in DNA
-
DOI 10.1093/nar/gkg617
-
Kolpakov R, Bana G, Kucherov G (2003) mreps: Effi cient and fl exible detection of tandem repeats in DNA. Nucleic Acids Res 31:3672-3678 (Pubitemid 37442220)
-
(2003)
Nucleic Acids Research
, vol.31
, Issue.13
, pp. 3672-3678
-
-
Kolpakov, R.1
Bana, G.2
Kucherov, G.3
-
38
-
-
56549086632
-
A new method to compute K-mer frequencies and its application to annotate large repetitive plant genomes
-
Kurtz S, et al. (2008) A new method to compute K-mer frequencies and its application to annotate large repetitive plant genomes. BMC Genomics 9:517
-
(2008)
BMC Genomics.
, vol.9
, pp. 517
-
-
Kurtz, S.1
-
39
-
-
46649114729
-
Identifi cation of repeat structure in large genomes using repeat probability clouds
-
Gu W, et al. (2008) Identifi cation of repeat structure in large genomes using repeat probability clouds. Anal Biochem 380:77-83
-
(2008)
Anal. Biochem.
, vol.380
, pp. 77-83
-
-
Gu, W.1
-
40
-
-
55449118548
-
ReAS: Recovery of ancestral sequences for transposable elements from the unassembled reads of a whole genome shotgun
-
Li R, et al. (2005) ReAS: Recovery of ancestral sequences for transposable elements from the unassembled reads of a whole genome shotgun. PLoS Comput Biol 1:e43
-
(2005)
PLoS Comput Biol.
, vol.1
-
-
Li, R.1
-
41
-
-
29144455282
-
De novo identification of repeat families in large genomes
-
DOI 10.1093/bioinformatics/bti1018
-
Price AL, Jones NC, Pevzner PA (2005) De novo identifi cation of repeat families in large genomes. Bioinformatics 21 Suppl 1:i351-358 (Pubitemid 41794508)
-
(2005)
Bioinformatics
, vol.21
, Issue.SUPPL. 1
-
-
Price, A.L.1
Jones, N.C.2
Pevzner, P.A.3
-
42
-
-
39749179047
-
Ltrharvest, an effi cient and fl exible software for de novo detection of LTR retrotransposons
-
Ellinghaus D, Kurtz S, Willhoeft U (2008) LTRharvest, an effi cient and fl exible 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
-
43
-
-
69149101693
-
Structure-based discovery and description of plant and animal Helitrons
-
Yang L, Bennetzen JL (2009) Structure-based discovery and description of plant and animal Helitrons. Proc Natl Acad Sci USA 106:12832-12837
-
(2009)
Proc. Natl. Acad. Sci. USA
, vol.106
, pp. 12832-12837
-
-
Yang, L.1
Bennetzen, J.L.2
-
44
-
-
62549105255
-
MUST: A system for identifi cation of miniature inverted-repeat transposable elements and applications to anabaena variabilis and haloquadratum walsbyi
-
Chen Y, et al. (2009) MUST: a system for identifi cation of miniature inverted-repeat transposable elements and applications to Anabaena variabilis and Haloquadratum walsbyi. Gene 436:1-7
-
(2009)
Gene.
, vol.436
, pp. 1-7
-
-
Chen, Y.1
-
45
-
-
77952670452
-
Identifying repeats and transposable elements in sequenced genomes: How to fi nd your way through the dense forest of programs
-
Lerat E (2010) Identifying repeats and transposable elements in sequenced genomes: how to fi nd your way through the dense forest of programs. Heredity 104:520-533
-
(2010)
Heredity.
, vol.104
, pp. 520-533
-
-
Lerat, E.1
-
46
-
-
32044447172
-
Identification of transposable elements using multiple alignments of related genomes
-
DOI 10.1101/gr.4361206
-
Caspi A, Pachter L (2006) Identifi cation of transposable elements using multiple alignments of related genomes. Genome Res 16:260-270 (Pubitemid 43200275)
-
(2006)
Genome Research
, vol.16
, Issue.2
, pp. 260-270
-
-
Caspi, A.1
Pachter, L.2
-
48
-
-
33646000287
-
Effi cient q-gram fi lters for fi nding all e-matches over a given length
-
Rasmussen K, Stoye J, Myers EW (2006) Effi cient q-gram fi lters for fi nding all e-matches over a given length. J Comput Biol 13:296-308
-
(2006)
J. Comput Biol.
, vol.13
, pp. 296-308
-
-
Rasmussen, K.1
Stoye, J.2
Myers, E.W.3
-
49
-
-
71749089142
-
Exploring repetitive DNA landscapes using repclass, a tool that automates the classifi cation of transposable elements in eukaryotic genomes
-
Feschotte C, et al. (2009) Exploring repetitive DNA landscapes using REPCLASS, a tool that automates the classifi cation of transposable elements in eukaryotic genomes. Genome Biol Evol 1:205-220
-
(2009)
Genome. Biol. Evol.
, vol.1
, pp. 205-220
-
-
Feschotte, C.1
-
50
-
-
4944239027
-
Pack-MULE transposable elements mediate gene evolution in plants
-
DOI 10.1038/nature02953
-
Jiang N, et al. (2004) Pack-MULE transposable elements mediate gene evolution in plants. Nature 431:569-573 (Pubitemid 39336337)
-
(2004)
Nature
, vol.431
, Issue.7008
, pp. 569-573
-
-
Jiang, N.1
Bao, Z.2
Zhang, X.3
Eddy, S.R.4
Wessler, S.R.5
-
51
-
-
25144488228
-
Gene duplication and exon shuffling by helitron-like transposons generate intraspecies diversity in maize
-
DOI 10.1038/ng1615, PII NG1615
-
Morgante M, et al. (2005) Gene duplication and exon shuffl ing by helitron-like transposons generate intraspecies diversity in maize. Nat Genet 37:997-1002 (Pubitemid 43086159)
-
(2005)
Nature Genetics
, vol.37
, Issue.9
, pp. 997-1002
-
-
Morgante, M.1
Brunner, S.2
Pea, G.3
Fengler, K.4
Zuccolo, A.5
Rafalski, A.6
-
53
-
-
0034307716
-
It takes two transposons to tango: Transposable-element-mediated chromosomal rearrangements
-
Gray YH (2000) It takes two transposons to tango: transposable-element- mediated chromosomal rearrangements. Trends Genet 16:461-468
-
(2000)
Trends. Genet.
, vol.16
, pp. 461-468
-
-
Gray, Y.H.1
|