-
1
-
-
84975742565
-
A map of human genome variation from population- scale sequencing
-
Abecasis GR, et al. 2010. A map of human genome variation from population- scale sequencing. Nature 467:1061-1073.
-
(2010)
Nature
, vol.467
, pp. 1061-1073
-
-
Abecasis, G.R.1
-
2
-
-
84975795680
-
An integrated map of genetic variation from 1, 092 human genomes
-
Abecasis GR, et al. 2012. An integrated map of genetic variation from 1, 092 human genomes. Nature 491:56-65.
-
(2012)
Nature
, vol.491
, pp. 56-65
-
-
Abecasis, G.R.1
-
3
-
-
84890116607
-
Alu elements: An intrinsic source of human genome instability
-
Ade C, Roy-Engel AM, Deininger PL. 2013. Alu elements: An intrinsic source of human genome instability. Curr Opin Virol. 3:639-645.
-
(2013)
Curr Opin Virol.
, vol.3
, pp. 639-645
-
-
Ade, C.1
Roy-Engel, A.M.2
Deininger, P.L.3
-
4
-
-
84887382601
-
Identification of three new Alu Yb subfamilies by source tracking of recently integrated Alu Yb elements
-
Ahmed M, Li W, Liang P. 2013. Identification of three new Alu Yb subfamilies by source tracking of recently integrated Alu Yb elements. Mob DNA. 4:25.
-
(2013)
Mob DNA
, vol.4
, pp. 25
-
-
Ahmed, M.1
Li, W.2
Liang, P.3
-
5
-
-
0036250811
-
Alu repeats and human genomic diversity
-
Batzer MA, Deininger PL. 2002. Alu repeats and human genomic diversity. Nat Rev Genet. 3:370-379.
-
(2002)
Nat Rev Genet.
, vol.3
, pp. 370-379
-
-
Batzer, M.A.1
Deininger, P.L.2
-
6
-
-
0025633325
-
Structure and variability of recently inserted Alu family members
-
Batzer MA, et al. 1990. Structure and variability of recently inserted Alu family members. Nucleic Acids Res. 18:6793-6798.
-
(1990)
Nucleic Acids Res.
, vol.18
, pp. 6793-6798
-
-
Batzer, M.A.1
-
7
-
-
0030052666
-
Standardized nomenclature for Alu repeats
-
Batzer MA, et al. 1996. Standardized nomenclature for Alu repeats. J Mol Evol. 42:3-6.
-
(1996)
J Mol Evol.
, vol.42
, pp. 3-6
-
-
Batzer, M.A.1
-
8
-
-
77953880842
-
LINE-1 retrotransposition activity in human genomes
-
Beck CR, et al. 2010. LINE-1 retrotransposition activity in human genomes. Cell 141:1159-1170.
-
(2010)
Cell
, vol.141
, pp. 1159-1170
-
-
Beck, C.R.1
-
10
-
-
57149120574
-
Active Alu retrotransposons in the human genome
-
Bennett EA, et al. 2008. Active Alu retrotransposons in the human genome. Genome Res. 18:1875-1883.
-
(2008)
Genome Res.
, vol.18
, pp. 1875-1883
-
-
Bennett, E.A.1
-
11
-
-
34247344319
-
Retrotransposable elements and human disease
-
Callinan PA, Batzer MA. 2006. Retrotransposable elements and human disease. Genome Dyn. 1:104-115.
-
(2006)
Genome Dyn.
, vol.1
, pp. 104-115
-
-
Callinan, P.A.1
Batzer, M.A.2
-
12
-
-
0035800561
-
Large-scale analysis of the Alu Ya5 and Yb8 subfamilies and their contribution to human genomic diversity
-
Carroll ML, et al. 2001. Large-scale analysis of the Alu Ya5 and Yb8 subfamilies and their contribution to human genomic diversity. J Mol Biol. 311:17-40.
-
(2001)
J Mol Biol.
, vol.311
, pp. 17-40
-
-
Carroll, M.L.1
-
13
-
-
63849260592
-
Diverse cis factors controlling Alu retrotransposition: What causes Alu elements to die?
-
Comeaux MS, Roy-Engel AM, Hedges DJ, Deininger PL. 2009. Diverse cis factors controlling Alu retrotransposition: What causes Alu elements to die? Genome Res. 19:545-555.
-
(2009)
Genome Res.
, vol.19
, pp. 545-555
-
-
Comeaux, M.S.1
Roy-Engel, A.M.2
Hedges, D.J.3
Deininger, P.L.4
-
14
-
-
84859763538
-
Alu pair exclusions in the human genome
-
Cook GW, et al. 2011. Alu pair exclusions in the human genome. Mob DNA. 2:10.
-
(2011)
Mob DNA
, vol.2
, pp. 10
-
-
Cook, G.W.1
-
15
-
-
70349318211
-
The impact of retrotransposons on human genome evolution
-
Cordaux R, Batzer MA. 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
-
16
-
-
4444358450
-
Retrotransposition of Alu elements: How many sources?
-
Cordaux R, Hedges DJ, Batzer MA. 2004. Retrotransposition of Alu elements: how many sources? Trends Genet 20:464-467.
-
(2004)
Trends Genet
, vol.20
, pp. 464-467
-
-
Cordaux, R.1
Hedges, D.J.2
Batzer, M.A.3
-
17
-
-
33646247399
-
Estimating the retrotransposition rate of human Alu elements
-
Cordaux R, Hedges DJ, Herke SW, Batzer MA. 2006. Estimating the retrotransposition rate of human Alu elements. Gene 373:134-137.
-
(2006)
Gene
, vol.373
, pp. 134-137
-
-
Cordaux, R.1
Hedges, D.J.2
Herke, S.W.3
Batzer, M.A.4
-
19
-
-
84855281420
-
Repetitive elements may comprise over two-thirds of the human genome
-
de Koning, AP, Gu W, Castoe TA, Batzer MA, Pollock DD. 2011. Repetitive elements may comprise over two-thirds of the human genome. PLoS Genet. 7:e1002384.
-
(2011)
PLoS Genet.
, vol.7
, pp. e1002384
-
-
Gu, W.1
Castoe, T.A.2
Batzer, M.A.3
Pollock, D.D.4
De Koning, A.P.5
-
20
-
-
84855199454
-
Alu elements: Know the SINEs
-
Deininger P. 2011. Alu elements: know the SINEs. Genome Biol. 12:236.
-
(2011)
Genome Biol.
, vol.12
, pp. 236
-
-
Deininger, P.1
-
23
-
-
0041353551
-
LINE-mediated retrotransposition of marked Alu sequences
-
Dewannieux M, Esnault C, Heidmann T. 2003. LINE-mediated retrotransposition of marked Alu sequences. Nat Genet. 35:41-48.
-
(2003)
Nat Genet.
, vol.35
, pp. 41-48
-
-
Dewannieux, M.1
Esnault, C.2
Heidmann, T.3
-
24
-
-
23244439083
-
Role of poly(A) tail length in Alu retrotransposition
-
Dewannieux M, Heidmann T. 2005. Role of poly(A) tail length in Alu retrotransposition. Genomics 86:378-381.
-
(2005)
Genomics
, vol.86
, pp. 378-381
-
-
Dewannieux, M.1
Heidmann, T.2
-
25
-
-
0009969062
-
Human L1 retrotransposon encodes a conserved endonuclease required for retrotransposition
-
Feng Q, Moran JV, Kazazian HH Jr, Boeke JD. 1996. Human L1 retrotransposon encodes a conserved endonuclease required for retrotransposition. Cell 87:905-916.
-
(1996)
Cell
, vol.87
, pp. 905-916
-
-
Feng, Q.1
Moran, J.V.2
Kazazian, H.H.3
Boeke, J.D.4
-
26
-
-
7944228189
-
The Alu Yc1 subfamily: Sorting the wheat from the chaff
-
Garber RK, Hedges DJ, Herke SW, Hazard NW, Batzer MA. 2005. The Alu Yc1 subfamily: sorting the wheat from the chaff. Cytogenet Genome Res. 110:537-542.
-
(2005)
Cytogenet Genome Res.
, vol.110
, pp. 537-542
-
-
Garber, R.K.1
Hedges, D.J.2
Herke, S.W.3
Hazard, N.W.4
Batzer, M.A.5
-
27
-
-
0002051540
-
BioEdit: A user-friendly biological sequence alignment editor and analysis program forWindows 95/98/NT
-
Hall TA. 1999. BioEdit: A user-friendly biological sequence alignment editor and analysis program forWindows 95/98/NT. Nucleic Acids Symp Ser. 41:95-98.
-
(1999)
Nucleic Acids Symp Ser.
, vol.41
, pp. 95-98
-
-
Hall, T.A.1
-
28
-
-
19844382341
-
Under the genomic radar: The stealth model of Alu amplification
-
Han K, et al. 2005. Under the genomic radar: The stealth model of Alu amplification. Genome Res. 15:655-664.
-
(2005)
Genome Res.
, vol.15
, pp. 655-664
-
-
Han, K.1
-
29
-
-
35948983427
-
Alu recombination-mediated structural deletions in the chimpanzee genome
-
Han K, et al. 2007. Alu recombination-mediated structural deletions in the chimpanzee genome. PLoS Genet. 3:1939-1949.
-
(2007)
PLoS Genet.
, vol.3
, pp. 1939-1949
-
-
Han, K.1
-
30
-
-
84975806579
-
Alu repeat discovery and characterization within human genomes
-
Hormozdiari F, et al. 2011. Alu repeat discovery and characterization within human genomes. Genome Res. 21:840-849.
-
(2011)
Genome Res.
, vol.21
, pp. 840-849
-
-
Hormozdiari, F.1
-
31
-
-
0037693743
-
Potential for retroposition by old Alu subfamilies
-
Johanning K, et al. 2003. Potential for retroposition by old Alu subfamilies. J Mol Evol. 56:658-664.
-
(2003)
J Mol Evol.
, vol.56
, pp. 658-664
-
-
Johanning, K.1
-
32
-
-
0031055331
-
Sequence patterns indicate an enzymatic involvement in integration of mammalian retroposons
-
Jurka J. 1997. Sequence patterns indicate an enzymatic involvement in integration of mammalian retroposons. Proc Natl Acad Sci U S A. 94:1872-1877.
-
(1997)
Proc Natl Acad Sci U S A
, vol.94
, pp. 1872-1877
-
-
Jurka, J.1
-
33
-
-
0034284437
-
Repbase update: A database and an electronic journal of repetitive elements
-
Jurka J. 2000. Repbase update: A database and an electronic journal of repetitive elements. Trends Genet. 16:418-420.
-
(2000)
Trends Genet.
, vol.16
, pp. 418-420
-
-
Jurka, J.1
-
34
-
-
23844525077
-
Repbase Update, a database of eukaryotic repetitive elements
-
Jurka J, 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
-
35
-
-
0036598649
-
Active Alu elements are passed primarily through paternal germlines
-
Jurka J, Krnjajic M, Kapitonov VV, Stenger JE, Kokhanyy O. 2002. Active Alu elements are passed primarily through paternal germlines. Theor Popul Biol. 61:519-530.
-
(2002)
Theor Popul Biol.
, vol.61
, pp. 519-530
-
-
Jurka, J.1
Krnjajic, M.2
Kapitonov, V.V.3
Stenger, J.E.4
Kokhanyy, O.5
-
36
-
-
0036226603
-
BLAT-The BLAST-like alignment tool
-
Kent WJ. 2002. BLAT-the BLAST-like alignment tool. Genome Res. 12:656-664.
-
(2002)
Genome Res.
, vol.12
, pp. 656-664
-
-
Kent, W.J.1
-
37
-
-
0036079158
-
The human genome browser at UCSC
-
Kent WJ, et al. 2002. The human genome browser at UCSC. Genome Res. 12:996-1006.
-
(2002)
Genome Res.
, vol.12
, pp. 996-1006
-
-
Kent, W.J.1
-
38
-
-
77956858478
-
A mobile threat to genome stability: The impact of non-LTR retrotransposons upon the human genome
-
Konkel MK, Batzer MA. 2010. A mobile threat to genome stability: The impact of non-LTR retrotransposons upon the human genome. Semin Cancer Biol. 20:211-221.
-
(2010)
Semin Cancer Biol.
, vol.20
, pp. 211-221
-
-
Konkel, M.K.1
Batzer, M.A.2
-
40
-
-
0024558422
-
Sequence conservation in Alu evolution
-
Labuda D, Striker G. 1989. Sequence conservation in Alu evolution. Nucleic Acids Res. 17:2477-2491.
-
(1989)
Nucleic Acids Res.
, vol.17
, pp. 2477-2491
-
-
Labuda, D.1
Striker, G.2
-
41
-
-
2042437650
-
Initial sequencing and analysis of the human genome
-
Lander ES, et al. 2001. Initial sequencing and analysis of the human genome. Nature 409:860-921.
-
(2001)
Nature
, vol.409
, pp. 860-921
-
-
Lander, E.S.1
-
42
-
-
58149191245
-
Chromosomal inversions between human and chimpanzee lineages caused by retrotransposons
-
Lee J, Han K, Meyer TJ, Kim HS, Batzer MA. 2008. Chromosomal inversions between human and chimpanzee lineages caused by retrotransposons. PLoS One 3:e4047.
-
(2008)
PLoS One
, vol.3
, pp. e4047
-
-
Lee, J.1
Han, K.2
Meyer, T.J.3
Kim, H.S.4
Batzer, M.A.5
-
43
-
-
0027450385
-
Reverse transcription of R2Bm RNA is primed by a nick at the chromosomal target site: A mechanism for non-LTR retrotransposition
-
Luan DD, Korman MH, Jakubczak JL, Eickbush TH. 1993. Reverse transcription of R2Bm RNA is primed by a nick at the chromosomal target site: A mechanism for non-LTR retrotransposition. Cell 72:595-605.
-
(1993)
Cell
, vol.72
, pp. 595-605
-
-
Luan, D.D.1
Korman, M.H.2
Jakubczak, J.L.3
Eickbush, T.H.4
-
45
-
-
33645464594
-
Recently mobilized transposons in the human and chimpanzee genomes
-
Mills RE, et al. 2006. Recently mobilized transposons in the human and chimpanzee genomes. Am J Hum Genet. 78:671-679.
-
(2006)
Am J Hum Genet.
, vol.78
, pp. 671-679
-
-
Mills, R.E.1
-
46
-
-
84975804424
-
Mapping copy number variation by population-scale genome sequencing
-
Mills RE, et al. 2011. Mapping copy number variation by population-scale genome sequencing. Nature 470:59-65.
-
(2011)
Nature
, vol.470
, pp. 59-65
-
-
Mills, R.E.1
-
47
-
-
0030606320
-
High frequency retrotransposition in cultured mammalian cells
-
Moran JV, et al. 1996. High frequency retrotransposition in cultured mammalian cells. Cell 87:917-927.
-
(1996)
Cell
, vol.87
, pp. 917-927
-
-
Moran, J.V.1
-
48
-
-
0036613245
-
DNA repair mediated by endonuclease-independent LINE-1 retrotransposition
-
Morrish TA, et al. 2002. DNA repair mediated by endonuclease-independent LINE-1 retrotransposition. Nat Genet. 31:159-165.
-
(2002)
Nat Genet.
, vol.31
, pp. 159-165
-
-
Morrish, T.A.1
-
49
-
-
84864676886
-
Alu expression in human cell lines and their retrotranspositional potential
-
Oler AJ, et al. 2012. Alu expression in human cell lines and their retrotranspositional potential. Mob DNA. 3:11.
-
(2012)
Mob DNA
, vol.3
, pp. 11
-
-
Oler, A.J.1
-
50
-
-
8744242187
-
Whole-genome analysis of Alu repeat elements reveals complex evolutionary history
-
Price AL, Eskin E, Pevzner PA. 2004. Whole-genome analysis of Alu repeat elements reveals complex evolutionary history. Genome Res. 14:2245-2252.
-
(2004)
Genome Res.
, vol.14
, pp. 2245-2252
-
-
Price, A.L.1
Eskin, E.2
Pevzner, P.A.3
-
51
-
-
0033787169
-
Potential gene conversion and source genes for recently integrated Alu elements
-
Roy AM, et al. 2000. Potential gene conversion and source genes for recently integrated Alu elements. Genome Res. 10:1485-1495.
-
(2000)
Genome Res.
, vol.10
, pp. 1485-1495
-
-
Roy, A.M.1
-
52
-
-
0034817362
-
Alu insertion polymorphisms for the study of human genomic diversity
-
Roy-Engel et al. 2001. Alu insertion polymorphisms for the study of human genomic diversity. Genetics 159:279-290.
-
(2001)
Genetics
, vol.159
, pp. 279-290
-
-
Roy-Engel1
-
53
-
-
0036737222
-
Active Alu element "A-tails": Size does matter
-
Roy-Engel AM, et al. 2002. Active Alu element "A-tails": size does matter. Genome Res. 12:1333-1344.
-
(2002)
Genome Res.
, vol.12
, pp. 1333-1344
-
-
Roy-Engel, A.M.1
-
54
-
-
0004222748
-
-
Code available at
-
Rozen S, Skaletsky HJ. 1998. Primer3. Code available at http://wwwgenome.wi.mit.edu/genome-software/other/primer3.html.
-
(1998)
Primer3
-
-
Rozen, S.1
Skaletsky, H.J.2
-
55
-
-
17444390904
-
Analysis of the human Alu Ye lineage
-
Salem AH, Ray DA, Hedges DJ, Jurka J, Batzer MA. 2005. Analysis of the human Alu Ye lineage. BMC Evol Biol. 5:18.
-
(2005)
BMC Evol Biol.
, vol.5
, pp. 18
-
-
Salem, A.H.1
Ray, D.A.2
Hedges, D.J.3
Jurka, J.4
Batzer, M.A.5
-
57
-
-
0025008168
-
Sequence logos: A new way to display consensus sequences
-
Schneider TD, Stephens RM. 1990. Sequence logos: A new way to display consensus sequences. Nucleic Acids Res. 18:6097-6100.
-
(1990)
Nucleic Acids Res.
, vol.18
, pp. 6097-6100
-
-
Schneider, T.D.1
Stephens, R.M.2
-
58
-
-
33745244299
-
Human genomic deletions mediated by recombination between Alu elements
-
Sen SK, et al. 2006. Human genomic deletions mediated by recombination between Alu elements. Am J Hum Genet. 79:41-53.
-
(2006)
Am J Hum Genet.
, vol.79
, pp. 41-53
-
-
Sen, S.K.1
-
61
-
-
80052318161
-
A comprehensive map of mobile element insertion polymorphisms in humans
-
Stewart C, et al. 2011. A comprehensive map of mobile element insertion polymorphisms in humans. PLoS Genet. 7:e1002236.
-
(2011)
PLoS Genet.
, vol.7
, pp. e1002236
-
-
Stewart, C.1
-
62
-
-
84878637862
-
The role of recombination in the origin and evolution of Alu subfamilies
-
Teixeira-Silva A, Silva RM, Carneiro J, Amorim A, Azevedo L. 2013. The role of recombination in the origin and evolution of Alu subfamilies. PLoS One 8:e64884.
-
(2013)
PLoS One
, vol.8
, pp. e64884
-
-
Teixeira-Silva, A.1
Silva, R.M.2
Carneiro, J.3
Amorim, A.4
Azevedo, L.5
-
63
-
-
84866166604
-
Rescuing Alu: Recovery of new inserts shows LINE-1 preserves Alu activity through A-tail expansion
-
Wagstaff BJ, et al. 2012. Rescuing Alu: Recovery of new inserts shows LINE-1 preserves Alu activity through A-tail expansion. PLoS Genet. 8:e1002842.
-
(2012)
PLoS Genet.
, vol.8
, pp. e1002842
-
-
Wagstaff, B.J.1
-
64
-
-
31844449262
-
Whole genome computational comparative genomics: A fruitful approach for ascertaining Alu insertion polymorphisms
-
Wang J, et al. 2006. Whole genome computational comparative genomics: A fruitful approach for ascertaining Alu insertion polymorphisms. Gene 365:11-20.
-
(2006)
Gene
, vol.365
, pp. 11-20
-
-
Wang, J.1
-
65
-
-
0042044628
-
Comprehensive analysis of two Alu Yd subfamilies
-
Xing J, et al. 2003. Comprehensive analysis of two Alu Yd subfamilies. J Mol Evol. 57(Suppl 1):S76-S89.
-
(2003)
J Mol Evol.
, vol.57
, pp. S76-S89
-
-
Xing, J.1
-
66
-
-
7944232060
-
Alu element mutation spectra: Molecular clocks and the effect of DNA methylation
-
Xing J, et al. 2004. Alu element mutation spectra: molecular clocks and the effect of DNA methylation. J Mol Biol. 344:675-682.
-
(2004)
J Mol Biol.
, vol.344
, pp. 675-682
-
-
Xing, J.1
-
67
-
-
67649982842
-
Mobile elements create structural variation: Analysis of a complete human genome
-
Xing J, et al. 2009. Mobile elements create structural variation: Analysis of a complete human genome. Genome Res. 19:1516-1526.
-
(2009)
Genome Res.
, vol.19
, pp. 1516-1526
-
-
Xing, J.1
-
68
-
-
84876799103
-
Mobile element biology: New possibilities with high-throughput sequencing
-
Xing J, Witherspoon DJ, Jorde LB. 2013. Mobile element biology: new possibilities with high-throughput sequencing. Trends Genet. 29:280-289.
-
(2013)
Trends Genet.
, vol.29
, pp. 280-289
-
-
Xing, J.1
Witherspoon, D.J.2
Jorde, L.B.3
|