-
1
-
-
33646928347
-
A distal enhancer and an ultraconserved exon are derived from a novel retroposon
-
10.1038/nature04696, 16625209
-
Bejerano G, Lowe CB, Ahituv N, King B, Siepel A, Salama SR, Rubin EM, Kent WJ, Haussler D. A distal enhancer and an ultraconserved exon are derived from a novel retroposon. Nature 2006, 441:87-90. 10.1038/nature04696, 16625209.
-
(2006)
Nature
, vol.441
, pp. 87-90
-
-
Bejerano, G.1
Lowe, C.B.2
Ahituv, N.3
King, B.4
Siepel, A.5
Salama, S.R.6
Rubin, E.M.7
Kent, W.J.8
Haussler, D.9
-
2
-
-
33746801653
-
A family of conserved noncoding elements derived from an ancient transposable element
-
10.1073/pnas.0604768103, 1518811, 16864796
-
Xie X, Kamal M, Lander ES. A family of conserved noncoding elements derived from an ancient transposable element. Proc Natl Acad Sci U S A 2006, 103:11659-11664. 10.1073/pnas.0604768103, 1518811, 16864796.
-
(2006)
Proc Natl Acad Sci U S A
, vol.103
, pp. 11659-11664
-
-
Xie, X.1
Kamal, M.2
Lander, E.S.3
-
3
-
-
33644503176
-
A large family of ancient repeat elements in the human genome is under strong selection
-
10.1073/pnas.0511238103, 1413850, 16477033
-
Kamal M, Xie X, Lander ES. A large family of ancient repeat elements in the human genome is under strong selection. Proc Natl Acad Sci U S A 2006, 103:2740-2745. 10.1073/pnas.0511238103, 1413850, 16477033.
-
(2006)
Proc Natl Acad Sci U S A
, vol.103
, pp. 2740-2745
-
-
Kamal, M.1
Xie, X.2
Lander, E.S.3
-
4
-
-
33745620751
-
Functional noncoding sequences derived from SINEs in the mammalian genome
-
10.1101/gr.5255506, 1484453, 16717141
-
Nishihara H, Smit AF, Okada N. Functional noncoding sequences derived from SINEs in the mammalian genome. Genome Res 2006, 16:864-874. 10.1101/gr.5255506, 1484453, 16717141.
-
(2006)
Genome Res
, vol.16
, pp. 864-874
-
-
Nishihara, H.1
Smit, A.F.2
Okada, N.3
-
5
-
-
34249937354
-
Thousands of human mobile element fragments undergo strong purifying selection near developmental genes
-
10.1073/pnas.0611223104, 1876562, 17463089
-
Lowe CB, Bejerano G, Haussler D. Thousands of human mobile element fragments undergo strong purifying selection near developmental genes. Proc Natl Acad Sci U S A 2007, 104:8005-8010. 10.1073/pnas.0611223104, 1876562, 17463089.
-
(2007)
Proc Natl Acad Sci U S A
, vol.104
, pp. 8005-8010
-
-
Lowe, C.B.1
Bejerano, G.2
Haussler, D.3
-
6
-
-
34248576291
-
Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences
-
10.1038/nature05805, 17495919
-
Mikkelsen TS, Wakefield MJ, Aken B, Amemiya CT, Chang JL, Duke S, Garber M, Gentles AJ, Goodstadt L, Heger A, et al. Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences. Nature 2007, 447:167-177. 10.1038/nature05805, 17495919.
-
(2007)
Nature
, vol.447
, 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
-
7
-
-
34248512741
-
Evolutionary dynamics of transposable elements in the short-tailed opossum Monodelphis domestica
-
10.1101/gr.6070707, 1899126, 17495012
-
Gentles AJ, Wakefield MJ, Kohany O, Gu W, Batzer MA, Pollock DD, Jurka J. Evolutionary dynamics of transposable elements in the short-tailed opossum Monodelphis domestica. Genome Research 2007, 17:992-1004. 10.1101/gr.6070707, 1899126, 17495012.
-
(2007)
Genome Research
, vol.17
, pp. 992-1004
-
-
Gentles, A.J.1
Wakefield, M.J.2
Kohany, O.3
Gu, W.4
Batzer, M.A.5
Pollock, D.D.6
Jurka, J.7
-
8
-
-
41949093041
-
Possible involvement of SINEs in mammalian-specific brain formation
-
10.1073/pnas.0709398105, 2393765, 18334644
-
Sasaki T, Nishihara H, Hirakawa M, Fujimura K, Tanaka M, Kokubo N, Kimura-Yoshida C, Matsuo I, Sumiyama K, Saitou N, et al. Possible involvement of SINEs in mammalian-specific brain formation. Proc Natl Acad Sci U S A 2008, 105:4220-4225. 10.1073/pnas.0709398105, 2393765, 18334644.
-
(2008)
Proc Natl Acad Sci U S A
, vol.105
, 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
-
9
-
-
10744222156
-
Identification and characterization of multi-species conserved sequences
-
10.1101/gr.1602203, 403793, 14656959
-
Margulies EH, Blanchette M, Haussler D, Green ED. Identification and characterization of multi-species conserved sequences. Genome Res 2003, 13:2507-2518. 10.1101/gr.1602203, 403793, 14656959.
-
(2003)
Genome Res
, vol.13
, pp. 2507-2518
-
-
Margulies, E.H.1
Blanchette, M.2
Haussler, D.3
Green, E.D.4
-
10
-
-
23744458086
-
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
-
10.1101/gr.3715005, 1182216, 16024819
-
Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, Rosenbloom K, Clawson H, Spieth J, Hillier LW, Richards S, et al. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res 2005, 15:1034-1050. 10.1101/gr.3715005, 1182216, 16024819.
-
(2005)
Genome Res
, vol.15
, pp. 1034-1050
-
-
Siepel, A.1
Bejerano, G.2
Pedersen, J.S.3
Hinrichs, A.S.4
Hou, M.5
Rosenbloom, K.6
Clawson, H.7
Spieth, J.8
Hillier, L.W.9
Richards, S.10
-
11
-
-
23844525077
-
Repbase Update, a database of eukaryotic repetitive elements
-
10.1159/000084979, 16093699
-
Jurka J, Kapitonov VV, Pavlicek A, Klonowski P, Kohany O, Walichiewicz J. Repbase Update, a database of eukaryotic repetitive elements. Cytogenet Genome Res 2005, 110:462-467. 10.1159/000084979, 16093699.
-
(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
Walichiewicz, J.6
-
12
-
-
33750831582
-
Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor
-
10.1186/1471-2105-7-474, 1634758, 17064419
-
Kohany O, Gentles AJ, Hankus L, Jurka J. Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor. BMC Bioinformatics 2006, 7:474. 10.1186/1471-2105-7-474, 1634758, 17064419.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 474
-
-
Kohany, O.1
Gentles, A.J.2
Hankus, L.3
Jurka, J.4
-
13
-
-
0000378875
-
Evidence for higher rates of nucleotide substitution in rodents than in man
-
10.1073/pnas.82.6.1741, 397348, 3856856
-
Wu CI, Li WH. Evidence for higher rates of nucleotide substitution in rodents than in man. Proc Natl Acad Sci U S A 1985, 82:1741-1745. 10.1073/pnas.82.6.1741, 397348, 3856856.
-
(1985)
Proc Natl Acad Sci U S A
, vol.82
, pp. 1741-1745
-
-
Wu, C.I.1
Li, W.H.2
-
14
-
-
80051914599
-
Three periods of regulatory innovation during vertebrate evolution
-
10.1126/science.1202702, 21852499
-
Lowe CB, Kellis M, Siepel A, Raney BJ, Clamp M, Salama SR, Kingsley DM, Lindblad-Toh K, Haussler D. Three periods of regulatory innovation during vertebrate evolution. Science 2011, 333:1019-1024. 10.1126/science.1202702, 21852499.
-
(2011)
Science
, vol.333
, pp. 1019-1024
-
-
Lowe, C.B.1
Kellis, M.2
Siepel, A.3
Raney, B.J.4
Clamp, M.5
Salama, S.R.6
Kingsley, D.M.7
Lindblad-Toh, K.8
Haussler, D.9
-
15
-
-
0030794201
-
Molecular evidence from retroposons that whales form a clade within even-toed ungulates
-
10.1038/41759, 9262399
-
Shimamura M, Yasue H, Ohshima K, Abe H, Kato H, Kishiro T, Goto M, Munechika I, Okada N. Molecular evidence from retroposons that whales form a clade within even-toed ungulates. Nature 1997, 388:666-670. 10.1038/41759, 9262399.
-
(1997)
Nature
, vol.388
, pp. 666-670
-
-
Shimamura, M.1
Yasue, H.2
Ohshima, K.3
Abe, H.4
Kato, H.5
Kishiro, T.6
Goto, M.7
Munechika, I.8
Okada, N.9
-
16
-
-
16344366343
-
A novel abundant family of retroposed elements (DAS-SINEs) in the nine-banded armadillo (Dasypus novemcinctus)
-
10.1093/molbev/msi071, 15616140
-
Churakov G, Smit AF, Brosius J, Schmitz J. A novel abundant family of retroposed elements (DAS-SINEs) in the nine-banded armadillo (Dasypus novemcinctus). Mol Biol Evol 2005, 22:886-893. 10.1093/molbev/msi071, 15616140.
-
(2005)
Mol Biol Evol
, vol.22
, pp. 886-893
-
-
Churakov, G.1
Smit, A.F.2
Brosius, J.3
Schmitz, J.4
-
17
-
-
78650470086
-
Recent expansion of a new Ingi-related clade of Vingi non-LTR retrotransposons in hedgehogs
-
10.1093/molbev/msq220, 3002237, 20716533
-
Kojima KK, Kapitonov VV, Jurka J. Recent expansion of a new Ingi-related clade of Vingi non-LTR retrotransposons in hedgehogs. Mol Biol Evol 2011, 28:17-20. 10.1093/molbev/msq220, 3002237, 20716533.
-
(2011)
Mol Biol Evol
, vol.28
, pp. 17-20
-
-
Kojima, K.K.1
Kapitonov, V.V.2
Jurka, J.3
-
18
-
-
34548032355
-
MyrSINEs: a novel SINE family in the anteater genomes
-
10.1016/j.gene.2007.06.003, 17628355
-
Nishihara H, Kuno S, Nikaido M, Okada N. MyrSINEs: a novel SINE family in the anteater genomes. Gene 2007, 400:98-103. 10.1016/j.gene.2007.06.003, 17628355.
-
(2007)
Gene
, vol.400
, pp. 98-103
-
-
Nishihara, H.1
Kuno, S.2
Nikaido, M.3
Okada, N.4
-
19
-
-
64149088221
-
5S rRNA-derived and tRNA-derived SINEs in fruit bats
-
10.1016/j.ygeno.2009.02.001, 19442632
-
Gogolevsky KP, Vassetzky NS, Kramerov DA. 5S rRNA-derived and tRNA-derived SINEs in fruit bats. Genomics 2009, 93:494-500. 10.1016/j.ygeno.2009.02.001, 19442632.
-
(2009)
Genomics
, vol.93
, pp. 494-500
-
-
Gogolevsky, K.P.1
Vassetzky, N.S.2
Kramerov, D.A.3
-
20
-
-
4544222472
-
SINEs of speciation: tracking lineages with retroposons
-
10.1016/j.tree.2004.08.002, 16701320
-
Shedlock AM, Takahashi K, Okada N. SINEs of speciation: tracking lineages with retroposons. Trends Ecol Evol 2004, 19:545-553. 10.1016/j.tree.2004.08.002, 16701320.
-
(2004)
Trends Ecol Evol
, vol.19
, pp. 545-553
-
-
Shedlock, A.M.1
Takahashi, K.2
Okada, N.3
-
21
-
-
21744461035
-
Malazy, a degenerate, species-specific transposable element in Cercospora zeae-maydis
-
10.3852/mycologia.97.2.349, 16396343
-
Shim WB, Dunkle LD. Malazy, a degenerate, species-specific transposable element in Cercospora zeae-maydis. Mycologia 2005, 97:349-355. 10.3852/mycologia.97.2.349, 16396343.
-
(2005)
Mycologia
, vol.97
, pp. 349-355
-
-
Shim, W.B.1
Dunkle, L.D.2
-
22
-
-
33749389724
-
Differential lineage-specific amplification of transposable elements is responsible for genome size variation in Gossypium
-
10.1101/gr.5282906, 1581434, 16954538
-
Hawkins JS, Kim H, Nason JD, Wing RA, Wendel JF. Differential lineage-specific amplification of transposable elements is responsible for genome size variation in Gossypium. Genome Res 2006, 16:1252-1261. 10.1101/gr.5282906, 1581434, 16954538.
-
(2006)
Genome Res
, vol.16
, pp. 1252-1261
-
-
Hawkins, J.S.1
Kim, H.2
Nason, J.D.3
Wing, R.A.4
Wendel, J.F.5
-
23
-
-
43549088103
-
Abundant and species-specific DINE-1 transposable elements in 12 Drosophila genomes
-
10.1186/gb-2008-9-2-r39, 2374699, 18291035
-
Yang HP, Barbash DA. Abundant and species-specific DINE-1 transposable elements in 12 Drosophila genomes. Genome Biol 2008, 9:R39. 10.1186/gb-2008-9-2-r39, 2374699, 18291035.
-
(2008)
Genome Biol
, vol.9
-
-
Yang, H.P.1
Barbash, D.A.2
-
24
-
-
80052854314
-
Families of transposable elements, population structure and the origin of species
-
10.1186/1745-6150-6-44, 3183009, 21929767
-
Jurka J, Bao W, Kojima KK. Families of transposable elements, population structure and the origin of species. Biol Direct 2011, 6:44. 10.1186/1745-6150-6-44, 3183009, 21929767.
-
(2011)
Biol Direct
, vol.6
, pp. 44
-
-
Jurka, J.1
Bao, W.2
Kojima, K.K.3
-
25
-
-
21344443661
-
Disparity, adaptation, exaptation, bookkeeping, and contingency at the genome level
-
Brosius J. Disparity, adaptation, exaptation, bookkeeping, and contingency at the genome level. Paleobiology 2005, 31:1-16.
-
(2005)
Paleobiology
, vol.31
, pp. 1-16
-
-
Brosius, J.1
-
26
-
-
80053266481
-
Mobile DNA and the TE-Thrust hypothesis: supporting evidence from the primates
-
10.1186/1759-8753-2-8, 3123540, 21627776
-
Oliver KR, Greene WK. Mobile DNA and the TE-Thrust hypothesis: supporting evidence from the primates. Mob DNA 2011, 2:8. 10.1186/1759-8753-2-8, 3123540, 21627776.
-
(2011)
Mob DNA
, vol.2
, pp. 8
-
-
Oliver, K.R.1
Greene, W.K.2
-
27
-
-
70349339300
-
Transposable elements: powerful facilitators of evolution
-
10.1002/bies.200800219, 19415638
-
Oliver KR, Greene WK. Transposable elements: powerful facilitators of evolution. Bioessays 2009, 31:703-714. 10.1002/bies.200800219, 19415638.
-
(2009)
Bioessays
, vol.31
, pp. 703-714
-
-
Oliver, K.R.1
Greene, W.K.2
-
28
-
-
84866126396
-
Mutation induced extinction in finite populations: lethal mutagenesis and lethal isolation
-
10.1371/journal.pcbi.1002609, 3410861, 22876168
-
Wylie CS, Shakhnovich EI. Mutation induced extinction in finite populations: lethal mutagenesis and lethal isolation. PLoS Comput Biol 2012, 8:e1002609. 10.1371/journal.pcbi.1002609, 3410861, 22876168.
-
(2012)
PLoS Comput Biol
, vol.8
-
-
Wylie, C.S.1
Shakhnovich, E.I.2
-
29
-
-
77954946300
-
Natural hybridization generates mammalian lineage with species characteristics
-
10.1073/pnas.1000133107, 2895066, 20534512
-
Larsen PA, Marchan-Rivadeneira MR, Baker RJ. Natural hybridization generates mammalian lineage with species characteristics. Proc Natl Acad Sci U S A 2010, 107:11447-11452. 10.1073/pnas.1000133107, 2895066, 20534512.
-
(2010)
Proc Natl Acad Sci U S A
, vol.107
, pp. 11447-11452
-
-
Larsen, P.A.1
Marchan-Rivadeneira, M.R.2
Baker, R.J.3
-
30
-
-
2042437650
-
Initial sequencing and analysis of the human genome
-
10.1038/35057062, 11237011
-
Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, et al. Initial sequencing and analysis of the human genome. Nature 2001, 409:860-921. 10.1038/35057062, 11237011.
-
(2001)
Nature
, vol.409
, 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
-
32
-
-
1542563409
-
Initial sequencing and comparative analysis of the mouse genome
-
10.1038/nature01262, 12466850
-
Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, Agarwal P, Agarwala R, Ainscough R, Alexandersson M, An P, et al. Initial sequencing and comparative analysis of the mouse genome. Nature 2002, 420:520-562. 10.1038/nature01262, 12466850.
-
(2002)
Nature
, vol.420
, pp. 520-562
-
-
Waterston, R.H.1
Lindblad-Toh, K.2
Birney, E.3
Rogers, J.4
Abril, J.F.5
Agarwal, P.6
Agarwala, R.7
Ainscough, R.8
Alexandersson, M.9
An, P.10
|