-
1
-
-
77952533015
-
Characterization of a novel SINE superfamily from invertebrates: "ceph-SINEs" from the genomes of squids and cuttlefish
-
Akasaki T, Nikaido M, Nishihara H, Tsuchiya K, Segawa S, Okada N. 2010. Characterization of a novel SINE superfamily from invertebrates: "Ceph-SINEs" from the genomes of squids and cuttlefish. Gene 454:8-19.
-
(2010)
Gene
, vol.454
, pp. 8-19
-
-
Akasaki, T.1
Nikaido, M.2
Nishihara, H.3
Tsuchiya, K.4
Segawa, S.5
Okada, N.6
-
2
-
-
0036250811
-
Alu repeats and human genomic diversity
-
DOI 10.1038/nrg798
-
Batzer MA, Deininger PL. 2002. Alu repeats and human genomic diversity. Nat Rev Genet 3:370-379. (Pubitemid 34506718)
-
(2002)
Nature Reviews Genetics
, vol.3
, Issue.5
, pp. 370-379
-
-
Batzer, M.A.1
Deininger, P.L.2
-
3
-
-
33646928347
-
A distal enhancer and an ultra-conserved exon are derived from a novel retroposon
-
Bejerano G, Lowe C, Ahituv N, King B, Siepel A, Salama S, Rubin E, Kent W, Haussler D. 2006. A distal enhancer and an ultra-conserved exon are derived from a novel retroposon. Nature 441:87-90.
-
(2006)
Nature
, vol.441
, pp. 87-90
-
-
Bejerano, G.1
Lowe, C.2
Ahituv, N.3
King, B.4
Siepel, A.5
Salama, S.6
Rubin, E.7
Kent, W.8
Haussler, D.9
-
4
-
-
0032865868
-
RNAs from all categories generate retrosequences that may be exapted as novel genes or regulatory elements
-
DOI 10.1016/S0378-1119(99)00227-9, PII S0378111999002279
-
Brosius J. 1999. RNAs from all categories generate retrosequences that may be exapted as novel genes or regulatory elements. Gene 238:115-134. (Pubitemid 29436103)
-
(1999)
Gene
, vol.238
, Issue.1
, pp. 115-134
-
-
Brosius, J.1
-
5
-
-
77950080387
-
The dynamic genome of Hydra
-
(74 co-authors)
-
Chapman JA, Kirkness EF, Simakov O, et al. (74 co-authors). 2010. The dynamic genome of Hydra. Nature 464:592-596.
-
(2010)
Nature
, vol.464
, pp. 592-596
-
-
Chapman, J.A.1
Kirkness, E.F.2
Simakov, O.3
-
6
-
-
42149157760
-
Broad phylogenomic sampling improves resolution of the animal tree of life
-
DOI 10.1038/nature06614, PII NATURE06614
-
Dunn CWD, Hejnol A, Matus DQ, et al. 2008. Broad phylogenomic sampling improves resolution of the animal tree of life. Nature 452:745-749. (Pubitemid 351522763)
-
(2008)
Nature
, vol.452
, Issue.7188
, pp. 745-749
-
-
Dunn, C.W.1
Hejnol, A.2
Matus, D.Q.3
Pang, K.4
Browne, W.E.5
Smith, S.A.6
Seaver, E.7
Rouse, G.W.8
Obst, M.9
Edgecombe, G.D.10
Sorensen, M.V.11
Haddock, S.H.D.12
Schmidt-Rhaesa, A.13
Okusu, A.14
Kristensen, R.M.15
Wheeler, W.C.16
Martindale, M.Q.17
Giribet, G.18
-
7
-
-
37549029474
-
DNA transposons and the evolution of eukaryotic genomes
-
Feschotte C, Pritham E. 2007. DNA transposons and the evolution of eukaryotic genomes. Annu Rev Genet. 41:331-368.
-
(2007)
Annu Rev Genet
, vol.41
, pp. 331-368
-
-
Feschotte, C.1
Pritham, E.2
-
9
-
-
0002051540
-
BioEdit: A user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT
-
Hall TA. 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser. 41:95-98.
-
(1999)
Nucleic Acids Symp ser
, vol.41
, pp. 95-98
-
-
Hall, T.A.1
-
10
-
-
0028861735
-
Ubiquitous mammalian-wide interspersed repeats (MIRs) are molecular fossils from the mesozoic era
-
Jurka J, Zietkiewicz E, Labuda D. 1995. Ubiquitous mammalian-wide interspersed repeats (MIRs) are molecular fossils from the mesozoic era. Nucleic Acids Res. 23:170-175.
-
(1995)
Nucleic Acids Res
, vol.23
, pp. 170-175
-
-
Jurka, J.1
Zietkiewicz, E.2
Labuda, D.3
-
11
-
-
0036849412
-
LINEs mobilize SINEs in the eel through a shared 3′ sequence
-
DOI 10.1016/S0092-8674(02)01041-3
-
Kajikawa M, Okada N. 2002. LINEs mobilize SINEs in the eel through a shared 3# sequence. Cell 111:433-444. (Pubitemid 35341395)
-
(2002)
Cell
, vol.111
, Issue.3
, pp. 433-444
-
-
Kajikawa, M.1
Okada, N.2
-
12
-
-
0036021699
-
Transposable elements and the evolution of genome size in eukaryotes
-
DOI 10.1023/A:1016072014259
-
Kidwell MG. 2002. Transposable elements and the evolution of genome size in eukaryotes. Genetica 115:49-63. (Pubitemid 34842170)
-
(2002)
Genetica
, vol.115
, Issue.1
, pp. 49-63
-
-
Kidwell, M.G.1
-
13
-
-
0035105221
-
Perspective: Transposable elements, parasitic DNA, and genome evolution
-
Kidwell MG, 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
-
14
-
-
39149110563
-
The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans
-
DOI 10.1038/nature06617, PII NATURE06617
-
King N, Westbrook MJ, Young SL, et al. (36 co-authors). 2008. The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans. Nature 451:783-788. (Pubitemid 351253174)
-
(2008)
Nature
, vol.451
, Issue.7180
, pp. 783-788
-
-
King, N.1
Westbrook, M.J.2
Young, S.L.3
Kuo, A.4
Abedin, M.5
Chapman, J.6
Fairclough, S.7
Hellsten, U.8
Isogai, Y.9
Letunic, I.10
Marr, M.11
Pincus, D.12
Putnam, N.13
Rokas, A.14
Wright, K.J.15
Zuzow, R.16
Dirks, W.17
Good, M.18
Goodstein, D.19
Lemons, D.20
Li, W.21
Lyons, J.B.22
Morris, A.23
Nichols, S.24
Richter, D.J.25
Salamov, A.26
Bork, P.27
Lim, W.A.28
Manning, G.29
Miller, W.T.30
McGinnis, W.31
Shapiro, H.32
Tjian, R.33
Grigoriev, I.V.34
Rokhsar, D.35
more..
-
15
-
-
2042437650
-
Initial sequencing and analysis of the human genome
-
DOI 10.1038/35057062
-
Lander ES, Linton LM, Birren B, et al. (256 co-authors). 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
Linton, L.M.2
Birren, B.3
Nusbaum, C.4
Zody, M.C.5
Baldwin, J.6
Devon, K.7
Dewar, K.8
Doyle, M.9
Fitzhugh, W.10
Funke, R.11
Gage, D.12
Harris, K.13
Heaford, A.14
Howland, J.15
Kann, L.16
Lehoczky, J.17
Levine, R.18
McEwan, P.19
McKernan, K.20
Meldrim, J.21
Mesirov, J.P.22
Miranda, C.23
Morris, W.24
Naylor, J.25
Raymond, C.26
Rosetti, M.27
Santos, R.28
Sheridan, A.29
Sougnez, C.30
Stange-Thomann, N.31
Stojanovic, N.32
Subramanian, A.33
Wyman, D.34
Rogers, J.35
Sulston, J.36
Ainscough, R.37
Beck, S.38
Bentley, D.39
Burton, J.40
Clee, C.41
Carter, N.42
Coulson, A.43
Deadman, R.44
Deloukas, P.45
Dunham, A.46
Dunham, I.47
Durbin, R.48
French, L.49
Grafham, D.50
Gregory, S.51
Hubbard, T.52
Humphray, S.53
Hunt, A.54
Jones, M.55
Lloyd, C.56
McMurray, A.57
Matthews, L.58
Mercer, S.59
Milne, S.60
Mullikin, J.C.61
Mungall, A.62
Plumb, R.63
Ross, M.64
Shownkeen, R.65
Sims, S.66
Waterston, R.H.67
Wilson, R.K.68
Hillier, L.W.69
McPherson, J.D.70
Marra, M.A.71
Mardis, E.R.72
Fulton, L.A.73
Chinwalla, A.T.74
Pepin, K.H.75
Gish, W.R.76
Chissoe, S.L.77
Wendl, M.C.78
Delehaunty, K.D.79
Miner, T.L.80
Delehaunty, A.81
Kramer, J.B.82
Cook, L.L.83
Fulton, R.S.84
Johnson, D.L.85
Minx, P.J.86
Clifton, S.W.87
Hawkins, T.88
Branscomb, E.89
Predki, P.90
Richardson, P.91
Wenning, S.92
Slezak, T.93
Doggett, N.94
Cheng, J.-F.95
Olsen, A.96
Lucas, S.97
Elkin, C.98
Uberbacher, E.99
more..
-
16
-
-
34248576291
-
Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences
-
DOI 10.1038/nature05805, PII NATURE05805
-
Mikkelsen T, Wakefield MJ, Aken B, et al. (64 co-authors). 2007. Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences. Nature 447:167-177. (Pubitemid 46763085)
-
(2007)
Nature
, vol.447
, Issue.7141
, pp. 167-177
-
-
Mikkelsen, T.S.1
Wakefield, M.J.2
Aken, B.3
Amemiya, C.T.4
Chang, J.L.5
Duke, S.6
Garber, M.7
Gentles, A.J.8
Goodstadt, L.9
Heger, A.10
Jurka, J.11
Kamal, M.12
Mauceli, E.13
Searle, S.M.J.14
Sharpe, T.15
Baker, M.L.16
Batzer, M.A.17
Benos, P.V.18
Belov, K.19
Clamp, M.20
Cook, A.21
Cuff, J.22
Das, R.23
Davidow, L.24
Deakin, J.E.25
Fazzari, M.J.26
Glass, J.L.27
Grabherr, M.28
Greally, J.M.29
Gu, W.30
Hore, T.A.31
Huttley, G.A.32
Kleber, M.33
Jirtle, R.L.34
Koina, E.35
Lee, J.T.36
Mahony, S.37
Marra, M.A.38
Miller, R.D.39
Nicholls, R.D.40
Oda, M.41
Papenfuss, A.T.42
Parra, Z.E.43
Pollock, D.D.44
Ray, D.A.45
Schein, J.E.46
Speed, T.P.47
Thompson, K.48
VandeBerg, J.L.49
Wade, C.M.50
Walker, J.A.51
Waters, P.D.52
Webber, C.53
Weidman, J.R.54
Xie, X.55
Zody, M.C.56
Baldwin, J.57
Abdouelleil, A.58
Abdulkadir, J.59
Abebe, A.60
Abera, B.61
Abreu, J.62
Acer, St.C.63
Aftuck, L.64
Alexander, A.65
An, P.66
Anderson, E.67
Anderson, S.68
Arachi, H.69
Azer, M.70
Bachantsang, P.71
Barry, A.72
Bayul, T.73
Berlin, A.74
Bessette, D.75
Bloom, T.76
Blye, J.77
Boguslavskiy, L.78
Bonnet, C.79
Boukhgalter, B.80
Bourzgui, I.81
Brown, A.82
Cahill, P.83
Channer, S.84
Cheshatsang, Y.85
Chuda, L.86
Citroen, M.87
Collymore, A.88
Cooke, P.89
Costello, M.90
D'Aco, K.91
Daza, R.92
De Haan, G.93
DeGray, S.94
DeMaso, C.95
Dhargay, N.96
Dooley, K.97
Dooley, E.98
Doricent, M.99
more..
-
17
-
-
33745620751
-
Functional noncoding sequences derived from SINEs in the mammalian genome
-
DOI 10.1101/gr.5255506
-
Nishihara H, Smit AF, Okada N. 2006. Functional noncoding sequences derived from SINEs in the mammalian genome. Genome Res. 16:864-874. (Pubitemid 43992910)
-
(2006)
Genome Research
, vol.16
, Issue.7
, pp. 864-874
-
-
Nishihara, H.1
Smit, A.F.A.2
Okada, N.3
-
18
-
-
0036177682
-
V-SINEs: A new superfamily of vertebrate SINEs that are widespread in vertebrate genomes and retain a strongly conserved segment within each repetitive unit
-
DOI 10.1101/gr.212302
-
Ogiwara I, Miya M, Ohshima K, Okada N. 2002. V-SINEs: a new superfamily of vertebrate SINEs that are widespread in vertebrate genomes and retain a strongly conserved segment within each repetitive unit. Genome Res. 12:316-324. (Pubitemid 34162998)
-
(2002)
Genome Research
, vol.12
, Issue.2
, pp. 316-324
-
-
Ogiwara, I.1
Miya, M.2
Ohshima, K.3
Okada, N.4
-
19
-
-
23844437243
-
SINEs and LINEs: Symbionts of eukaryotic genomes with a common tail
-
DOI 10.1159/000084981
-
Ohshima K, Okada N. 2005. SINEs and LINEs: symbionts of eukaryotic genomes with a common tail. Cytogenet Genome Res. 110:475-490. (Pubitemid 41159925)
-
(2005)
Cytogenetic and Genome Research
, vol.110
, Issue.1-4
, pp. 475-490
-
-
Ohshima, K.1
Okada, N.2
-
20
-
-
79953716259
-
Resolving difficult phylogenetic questions: Why more sequences are not enough
-
Philippe H, Brinkmann H, Lavrov DV, Littlewood DTJ, Manuel M, Wörheide G, Baurain D. 2011. Resolving difficult phylogenetic questions: why more sequences are not enough. PLoS Biol. 9:e1000602.
-
(2011)
PLoS Biol
, vol.9
-
-
Philippe, H.1
Brinkmann, H.2
Lavrov, D.V.3
Littlewood, D.T.J.4
Manuel, M.5
Wörheide, G.6
Baurain, D.7
-
21
-
-
77955497041
-
Improved phylogenomic taxon sampling noticeably affects non-bilaterian relationships
-
(11 co-authors)
-
Pick K, Hervé P, Fabian S, et al. (11 co-authors). 2010. Improved phylogenomic taxon sampling noticeably affects non-bilaterian relationships. Mol Biol Evol. 27:1983-1987.
-
(2010)
Mol Biol Evol.
, vol.27
, pp. 1983-1987
-
-
Pick, K.1
Hervé, P.2
Fabian, S.3
-
22
-
-
35948981635
-
Ancient exaptation of a CORE-SINE retroposon into a highly conserved mammalian neuronal enhancer of the proopiomelanocortin gene
-
DOI 10.1371/journal.pgen.0030166
-
Santangelo AM, de Souza FSJ, Franchini LF, Bumaschny VF, Low MJ, Rubinstein M. 2007. Ancient exaptation of a CORE-SINE retroposon into a highly conserved mammalian neuronal enhancer of the proopiomelanocortin gene. PLoS Genet. 3:1813-1826. (Pubitemid 350072048)
-
(2007)
PLoS Genetics
, vol.3
, Issue.10
, pp. 1813-1826
-
-
Santangelo, A.M.1
De Souza, F.S.J.2
Franchini, L.F.3
Bumaschny, V.F.4
Low, M.J.5
Rubinstein, M.6
-
23
-
-
41949093041
-
Possible involvement of SINEs in mammalian-specific brain formation
-
DOI 10.1073/pnas.0709398105
-
Sasaki T, Nishihara H, Hirakawa M, et al. (12 co-authors). 2008. Possible involvement of SINEs in mammalian brain formation. Proc Natl Acad Sci USA. 105:4220-4225. (Pubitemid 351754361)
-
(2008)
Proceedings of the National Academy of Sciences of the United States of America
, vol.105
, Issue.11
, pp. 4220-4225
-
-
Sasaki, T.1
Nishihara, H.2
Hirakawa, M.3
Fujimura, K.4
Tanaka, M.5
Kokubo, N.6
Kimura-Yoshida, C.7
Matsuo, I.8
Sumiyama, K.9
Saitou, N.10
Shimogori, T.11
Okada, N.12
-
24
-
-
58849142045
-
Concatenated analysis sheds light on early metazoan evolution and fuels a modern "urmetazoon" hypothesis
-
Schierwater B, Eitel M, Jakob W, Osigus HJ, Hadrys H, Dellaporta SL, Kolokotronis SO, Desalle R. 2009. Concatenated analysis sheds light on early metazoan evolution and fuels a modern "urmetazoon" hypothesis. PLoS Biol. 7:e20.
-
(2009)
PLoS Biol
, vol.7
-
-
Schierwater, B.1
Eitel, M.2
Jakob, W.3
Osigus, H.J.4
Hadrys, H.5
Dellaporta, S.L.6
Kolokotronis, S.O.7
Desalle, R.8
-
25
-
-
0030479536
-
The origin of interspersed repeats in the human genome
-
DOI 10.1016/S0959-437X(96)80030-X
-
Smit AF. 1996. The origin of interspersed repeats in the human genome. Curr Opin Genet Dev. 6:743-748. (Pubitemid 27010635)
-
(1996)
Current Opinion in Genetics and Development
, vol.6
, Issue.6
, pp. 743-748
-
-
Smit, A.F.A.1
-
26
-
-
50049092481
-
The Trichoplax genome and the nature of placozoans
-
(21 co-authors)
-
Srivastava M, Begovic E, Chapman J, et al. (21 co-authors). 2008. The Trichoplax genome and the nature of placozoans. Nature 454:955-960.
-
(2008)
Nature
, vol.454
, pp. 955-960
-
-
Srivastava, M.1
Begovic, E.2
Chapman, J.3
-
27
-
-
77955490196
-
The Amphimedon queenslandica genome and the evolution of animal complexity
-
(33 co-authors)
-
Srivastava M, Simakov O, Chapman J, et al. (33 co-authors). 2010. The Amphimedon queenslandica genome and the evolution of animal complexity. Nature 466:720-727.
-
(2010)
Nature
, vol.466
, pp. 720-727
-
-
Srivastava, M.1
Simakov, O.2
Chapman, J.3
-
28
-
-
42649132446
-
A novel SINE family occurs frequently in both genomic DNA and transcribed sequences in ixodid ticks of the arthropod sub-phylum Chelicerata
-
Sunter JD, Patel SP, Skilton RA, Githaka N, Knowles DP, Scoles GA, Nene V, de Villiers E, Bishop RP. 2008. A novel SINE family occurs frequently in both genomic DNA and transcribed sequences in ixodid ticks of the arthropod sub-phylum Chelicerata. Gene 415:13-22.
-
(2008)
Gene
, vol.415
, pp. 13-22
-
-
Sunter, J.D.1
Patel, S.P.2
Skilton, R.A.3
Githaka, N.4
Knowles, D.P.5
Scoles, G.A.6
Nene, V.7
De Villiers, E.8
Bishop, R.P.9
-
29
-
-
34547781750
-
MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0
-
DOI 10.1093/molbev/msm092
-
Tamura K, Dudley J, Nei M, Kumar S. 2007. MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol. 24:1596-1599. (Pubitemid 47236692)
-
(2007)
Molecular Biology and Evolution
, vol.24
, Issue.8
, pp. 1596-1599
-
-
Tamura, K.1
Dudley, J.2
Nei, M.3
Kumar, S.4
-
30
-
-
0032509302
-
Genome sequence of the nematode C. elegans: A platform for investigating biology
-
The C. elegans sequencing consortium
-
The C. elegans sequencing consortium. 1998. Genome sequence of the nematode C. elegans: a platform for investigating biology. Science 282:2012-2018.
-
(1998)
Science
, vol.282
, pp. 2012-2018
-
-
|