-
1
-
-
84975742565
-
A map of human genome variation from population-scale sequencing
-
The 1000 Genomes Project Consortium. 2010. A map of human genome variation from population-scale sequencing. Nature 467: 1061–1073.
-
(2010)
Nature
, vol.467
, pp. 1061-1073
-
-
-
2
-
-
84975795680
-
An integrated map of genetic variation from 1092 human genomes
-
The 1000 Genomes Project Consortium. 2012. An integrated map of genetic variation from 1092 human genomes. Nature 491: 56–65.
-
(2012)
Nature
, vol.491
, pp. 56-65
-
-
-
3
-
-
84943171338
-
A global reference for human genetic variation
-
The 1000 Genomes Project Consortium. 2015. A global reference for human genetic variation. Nature 526: 68–74.
-
(2015)
Nature
, vol.526
, pp. 68-74
-
-
-
4
-
-
81855178276
-
Somatic retrotransposition alters the genetic landscape of the human brain
-
Baillie JK, Barnett MW, Upton KR, Gerhardt DJ, Richmond TA, De Sapio F, Brennan PM, Rizzu P, Smith S, Fell M, et al. 2011. Somatic retrotransposition alters the genetic landscape of the human brain. Nature 479: 534–537.
-
(2011)
Nature
, vol.479
, pp. 534-537
-
-
Baillie, J.K.1
Barnett, M.W.2
Upton, K.R.3
Gerhardt, D.J.4
Richmond, T.A.5
De Sapio, F.6
Brennan, P.M.7
Rizzu, P.8
Smith, S.9
Fell, M.10
-
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
-
-
0030052666
-
Standarized nomenclature for Alu repeats
-
Batzer MA, Deininger PL, Hellman-Blumberg U, Jurka J, Labuda D, Rubin CM, Schmid CW, Zietkiewicz E, Zuckerkandl E. 1996. Standarized nomenclature for Alu repeats. J Mol Evol 42: 3–6.
-
(1996)
J Mol Evol
, vol.42
, pp. 3-6
-
-
Batzer, M.A.1
Deininger, P.L.2
Hellman-Blumberg, U.3
Jurka, J.4
Labuda, D.5
Rubin, C.M.6
Schmid, C.W.7
Zietkiewicz, E.8
Zuckerkandl, E.9
-
7
-
-
77953880842
-
LINE-1 retrotransposition activity in human genomes
-
Beck CR, Collier P, Macfarlane C, Malig M, Kidd JM, Eichler EE, Badge RM, Moran JV. 2010. LINE-1 retrotransposition activity in human genomes. Cell 141: 1159–1170.
-
(2010)
Cell
, vol.141
, pp. 1159-1170
-
-
Beck, C.R.1
Collier, P.2
Macfarlane, C.3
Malig, M.4
Kidd, J.M.5
Eichler, E.E.6
Badge, R.M.7
Moran, J.V.8
-
9
-
-
57149120574
-
Active Alu retrotransposons in the human genome
-
Bennett EA, Keller H, Mills RE, Schmidt S, Moran JV, Weichenrieder O, Devine SE. 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
Keller, H.2
Mills, R.E.3
Schmidt, S.4
Moran, J.V.5
Weichenrieder, O.6
Devine, S.E.7
-
10
-
-
0034086210
-
L1 (LINE-1) retrotransposon evolution and amplification in recent human history
-
Boissinot S, Chevret P, Furano AV. 2000. L1 (LINE-1) retrotransposon evolution and amplification in recent human history. Mol Biol Evol 17: 915–928.
-
(2000)
Mol Biol Evol
, vol.17
, pp. 915-928
-
-
Boissinot, S.1
Chevret, P.2
Furano, A.V.3
-
11
-
-
4544223707
-
Meiotic catastrophe and retrotransposon reactivation in Male germ cells lacking Dnmt3L
-
Borc’his D, Bestor TH. 2004. Meiotic catastrophe and retrotransposon reactivation in male germ cells lacking Dnmt3L. Nature 431: 96–99.
-
(2004)
Nature
, vol.431
, pp. 96-99
-
-
Borc’his, D.1
Bestor, T.H.2
-
12
-
-
0036077271
-
Evidence consistent with human L1 retrotransposition in maternal meiosis I
-
Brouha B, Meischl C, Ostertag E, de Boer M, Zhang Y, Neijens H, Roos D, Kazazian HH Jr. 2002. Evidence consistent with human L1 retrotransposition in maternal meiosis I. Am J Hum Genet 71: 327–336.
-
(2002)
Am J Hum Genet
, vol.71
, pp. 327-336
-
-
Brouha, B.1
Meischl, C.2
Ostertag, E.3
De Boer, M.4
Zhang, Y.5
Neijens, H.6
Roos, D.7
Jr, K.H.H.8
-
13
-
-
0037965788
-
Hot L1s account for the bulk of retrotransposition activity in the human population
-
Brouha B, Schustak J, Badge RM, Lutz-Prigge S, Farley AH, Moran JV, Kazazian HH Jr. 2003. Hot L1s account for the bulk of retrotransposition activity in the human population. Proc Natl Acad Sci 100: 5280–5285.
-
(2003)
Proc Natl Acad Sci
, vol.100
, pp. 5280-5285
-
-
Brouha, B.1
Schustak, J.2
Badge, R.M.3
Lutz-Prigge, S.4
Farley, A.H.5
Moran, J.V.6
Jr, K.H.H.7
-
14
-
-
84892789989
-
Increased L1 retrotransposition in the neuronal genome in schizophrenia
-
Bundo M, Toyoshima M, Okada Y, Akamatsu W, Ueda J, Nemoto-Miyauchi T, Sunaga F, Toritsuka M, Ikawa D, Kakita A, et al. 2014. Increased L1 retrotransposition in the neuronal genome in schizophrenia. Neuron 81: 306–313.
-
(2014)
Neuron
, vol.81
, pp. 306-313
-
-
Bundo, M.1
Toyoshima, M.2
Okada, Y.3
Akamatsu, W.4
Ueda, J.5
Nemoto-Miyauchi, T.6
Sunaga, F.7
Toritsuka, M.8
Ikawa, D.9
Kakita, A.10
-
15
-
-
38049078812
-
Detection of two Alu insertions in the CFTR gene
-
Chen JM, Masson E, Macek M, Raguenes O, Piskackova T, Fercot B, Fila L, Cooper DN, Audrezet MP, Ferec C. 2008. Detection of two Alu insertions in the CFTR gene. J Cyst Fibros 7: 37–43.
-
(2008)
J Cyst Fibros
, vol.7
, pp. 37-43
-
-
Chen, J.M.1
Masson, E.2
Macek, M.3
Raguenes, O.4
Piskackova, T.5
Fercot, B.6
Fila, L.7
Cooper, D.N.8
Audrezet, M.P.9
Ferec, C.10
-
16
-
-
0242690915
-
De novo insertion of an Alu sequence in the coding region of the CLCN5 gene results in Dent’s disease
-
Claverie-Martin F, Gonzalez-Acosta H, Flores C, Anton-Gamero M, Garcia-Nieto V. 2003. De novo insertion of an Alu sequence in the coding region of the CLCN5 gene results in Dent’s disease. Hum Genet 113: 480–485.
-
(2003)
Hum Genet
, vol.113
, pp. 480-485
-
-
Claverie-Martin, F.1
Gonzalez-Acosta, H.2
Flores, C.3
Anton-Gamero, M.4
Garcia-Nieto, V.5
-
17
-
-
69349096044
-
L1 retrotransposition in human neural progenitor cells
-
Coufal NG, Garcia-Perez JL, Peng GE, Yeo GW, Mu Y, Lovci MT, Morell M, O’Shea KS, Moran JV, Gage FH. 2009. L1 retrotransposition in human neural progenitor cells. Nature 460: 1127–1131.
-
(2009)
Nature
, vol.460
, pp. 1127-1131
-
-
Coufal, N.G.1
Garcia-Perez, J.L.2
Peng, G.E.3
Yeo, G.W.4
Mu, Y.5
Lovci, M.T.6
Morell, M.7
O’Shea, K.S.8
Moran, J.V.9
Gage, F.H.10
-
18
-
-
79960405019
-
The variant call format and VCFtools
-
Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, Handsaker RE, Lunter G, Marth GT, Sherry ST, et al. 2011. The variant call format and VCFtools. Bioinformatics 27: 2156–2158.
-
(2011)
Bioinformatics
, vol.27
, pp. 2156-2158
-
-
Danecek, P.1
Auton, A.2
Abecasis, G.3
Albers, C.A.4
Banks, E.5
DePristo, M.A.6
Handsaker, R.E.7
Lunter, G.8
Marth, G.T.9
Sherry, S.T.10
-
19
-
-
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
-
20
-
-
0003248174
-
A novel mechanism of β-thalassemia. The insertion of L1 retrotransposable element into β globin IVSII
-
Divoky V, Indra K, Mrug M, Brabec V, Huisman THJ, Prchal JT. 1996. A novel mechanism of β-thalassemia. The insertion of L1 retrotransposable element into β globin IVSII. Blood 88: 148a.
-
(1996)
Blood
, vol.88
, pp. 148a
-
-
Divoky, V.1
Indra, K.2
Mrug, M.3
Brabec, V.4
Huisman, T.H.J.5
Prchal, J.T.6
-
21
-
-
0027248510
-
Two additional potential retrotransposons isolated from a human L1 subfamily that contains an active retrotransposable element
-
Dombroski BA, Scott AF, Kazazian HH Jr. 1993. Two additional potential retrotransposons isolated from a human L1 subfamily that contains an active retrotransposable element. Proc Natl Acad Sci 90: 6513–6517.
-
(1993)
Proc Natl Acad Sci
, vol.90
, pp. 6513-6517
-
-
Dombroski, B.A.1
Scott, A.F.2
Jr, K.H.H.3
-
22
-
-
84940979605
-
LINE-1 expression and retrotransposition in Barrett’s esophagus and esophageal carcinoma
-
Doucet-O’Hare TT, Rodic N, Sharma R, Darbari I, Abril G, Choi JA, Young Ahn J, Cheng Y, Anders RA, Burns KH, et al. 2015. LINE-1 expression and retrotransposition in Barrett’s esophagus and esophageal carcinoma. Proc Natl Acad Sci 112: E4894–E4900.
-
(2015)
Proc Natl Acad Sci
, vol.112
, pp. E4894-E4900
-
-
Doucet-O’Hare, T.T.1
Rodic, N.2
Sharma, R.3
Darbari, I.4
Abril, G.5
Choi, J.A.6
Young Ahn, J.7
Cheng, Y.8
Anders, R.A.9
Burns, K.H.10
-
23
-
-
84868032982
-
Single-neuron sequencing analysis of L1 retrotransposition and somatic mutation in the human brain
-
Evrony GD, Cai X, Lee E, Hills LB, Elhosary PC, Lehmann HS, Parker JJ, Atabay KD, Gilmore EC, Poduri A, et al. 2012. Single-neuron sequencing analysis of L1 retrotransposition and somatic mutation in the human brain. Cell 151: 483–496.
-
(2012)
Cell
, vol.151
, pp. 483-496
-
-
Evrony, G.D.1
Cai, X.2
Lee, E.3
Hills, L.B.4
Elhosary, P.C.5
Lehmann, H.S.6
Parker, J.J.7
Atabay, K.D.8
Gilmore, E.C.9
Poduri, A.10
-
24
-
-
77955160719
-
High throughput sequencing reveals extensive variation in human-specific L1 content in individual human genomes
-
Ewing AD, Kazazian HH Jr. 2010. High throughput sequencing reveals extensive variation in human-specific L1 content in individual human genomes. Genome Res 20: 1262–1270.
-
(2010)
Genome Res
, vol.20
, pp. 1262-1270
-
-
Ewing, A.D.1
Jr, K.H.H.2
-
25
-
-
84941923663
-
Widespread somatic L1 retrotransposition occurs early during gastrointestinal cancer evolution
-
Ewing AD, Gacita A, Wood LD, Ma F, Xing D, Kim MS, Manda SS, Abril G, Pereira G, Makohon-Moore A, et al. 2015. Widespread somatic L1 retrotransposition occurs early during gastrointestinal cancer evolution. Genome Res 25: 1536–1545.
-
(2015)
Genome Res
, vol.25
, pp. 1536-1545
-
-
Ewing, A.D.1
Gacita, A.2
Wood, L.D.3
Ma, F.4
Xing, D.5
Kim, M.S.6
Manda, S.S.7
Abril, G.8
Pereira, G.9
Makohon-Moore, A.10
-
26
-
-
0042827457
-
Exon skipping caused by an intronic insertion of a young AluYb9 element leads to severe hemophilia A
-
Ganguly A, Dunbar T, Chen P, Godmilow L, Ganguly T. 2003. Exon skipping caused by an intronic insertion of a young AluYb9 element leads to severe hemophilia A. Hum Genet 113: 348–352.
-
(2003)
Hum Genet
, vol.113
, pp. 348-352
-
-
Ganguly, A.1
Dunbar, T.2
Chen, P.3
Godmilow, L.4
Ganguly, T.5
-
27
-
-
84905579746
-
Whole-genome sequence variation, population structure and demographic history of the Dutch population
-
Genome of the Netherlands Consortium. 2014. Whole-genome sequence variation, population structure and demographic history of the Dutch population. Nat Genet 46: 818–825.
-
(2014)
Nat Genet
, vol.46
, pp. 818-825
-
-
-
28
-
-
23844510228
-
Multiple fates of L1 retrotransposition intermediates in cultured human cells
-
Gilbert N, Lutz S, Morrish TA, Moran JV. 2005. Multiple fates of L1 retrotransposition intermediates in cultured human cells. Mol Cell Biol 25: 7780–7795.
-
(2005)
Mol Cell Biol
, vol.25
, pp. 7780-7795
-
-
Gilbert, N.1
Lutz, S.2
Morrish, T.A.3
Moran, J.V.4
-
29
-
-
84929132687
-
Large-scale whole-genome sequencing of the Icelandic population
-
Gudbjartsson DF, Helgason H, Gudjonsson SA, Zink F, Gylfason A, Besenbacher S, Magnusson G, Halldorsson BV, Hjartarson E, Sigurdsson GT, et al. 2015. Large-scale whole-genome sequencing of the Icelandic population. Nat Genet 47: 435–444.
-
(2015)
Nat Genet
, vol.47
, pp. 435-444
-
-
Gudbjartsson, D.F.1
Helgason, H.2
Gudjonsson, S.A.3
Zink, F.4
Gylfason, A.5
Besenbacher, S.6
Magnusson, G.7
Halldorsson, B.V.8
Hjartarson, E.9
Sigurdsson, G.T.10
-
30
-
-
80051702066
-
Retrotransposition of marked SVA elements by human L1s in cultured cells
-
Hancks DC, Goodier JL, Mandal PK, Cheung LE, Kazazian HH Jr. 2011. Retrotransposition of marked SVA elements by human L1s in cultured cells. Hum Mol Genet 20: 3386–3400.
-
(2011)
Hum Mol Genet
, vol.20
, pp. 3386-3400
-
-
Hancks, D.C.1
Goodier, J.L.2
Mandal, P.K.3
Cheung, L.E.4
Jr, K.H.H.5
-
31
-
-
84904247696
-
Somatic retrotransposition in human cancer revealed by whole-genome and whole exome sequencing
-
Helman E, Lawrence MS, Stewart C, Sougnez C, Getz G, Meyerson M. 2014. Somatic retrotransposition in human cancer revealed by whole-genome and whole exome sequencing. Genome Res 24: 1053–1063.
-
(2014)
Genome Res
, vol.24
, pp. 1053-1063
-
-
Helman, E.1
Lawrence, M.S.2
Stewart, C.3
Sougnez, C.4
Getz, G.5
Meyerson, M.6
-
32
-
-
77953892366
-
Mobile interspersed repeats are major structural variants in the human genome
-
Huang CR, Schneider AM, Lu Y, Niranjan T, Shen P, Robinson MA, Steranka JP, Valle D, Civin CI, Wang T, et al. 2010. Mobile interspersed repeats are major structural variants in the human genome. Cell 141: 1171–1182.
-
(2010)
Cell
, vol.141
, pp. 1171-1182
-
-
Huang, C.R.1
Schneider, A.M.2
Lu, Y.3
Niranjan, T.4
Shen, P.5
Robinson, M.A.6
Steranka, J.P.7
Valle, D.8
Civin, C.I.9
Wang, T.10
-
33
-
-
77953889472
-
Natural mutagenesis of human genomes by endogenous retrotransposons
-
Iskow RC, McCabe MT, Mills RE, Torene S, Pittard WS, Neuwald AF, Van Meir EG, Vertino PM, Devine SE. 2010. Natural mutagenesis of human genomes by endogenous retrotransposons. Cell 141: 1253–1261.
-
(2010)
Cell
, vol.141
, pp. 1253-1261
-
-
Iskow, R.C.1
McCabe, M.T.2
Mills, R.E.3
Torene, S.4
Pittard, W.S.5
Neuwald, A.F.6
Van Meir, E.G.7
Vertino, P.M.8
Devine, S.E.9
-
34
-
-
0028940268
-
2+-sensing receptor gene in familial hypocaliuric hy-percalcemia and neonatal severe hyperparathyroidism
-
2+-sensing receptor gene in familial hypocaliuric hy-percalcemia and neonatal severe hyperparathyroidism. Am J Hum Genet 56: 880–886.
-
(1995)
Am J Hum Genet
, vol.56
, pp. 880-886
-
-
Janicic, N.1
Pausova, Z.2
Cole, D.E.3
Hendy, G.N.4
-
35
-
-
0347755531
-
The UCSC Table Browser data retrieval tool
-
Karolchik D, Hinrichs AS, Furey TS, Roskin KM, Sugnet CW, Haussler D, Kent WJ. 2004. The UCSC Table Browser data retrieval tool. Nucleic Acids Res 32: D493–D496.
-
(2004)
Nucleic Acids Res
, vol.32
, pp. D493-D496
-
-
Karolchik, D.1
Hinrichs, A.S.2
Furey, T.S.3
Roskin, K.M.4
Sugnet, C.W.5
Haussler, D.6
Kent, W.J.7
-
36
-
-
0023867459
-
Haemophilia A resulting from de novo insertion of L1 sequences represents a novel mechanism for mutation in man
-
Kazazian HH, Wong C, Youssoufian H, Scott AF, Phillips DG, Antonarakis SE. 1988. Haemophilia A resulting from de novo insertion of L1 sequences represents a novel mechanism for mutation in man. Nature 332: 164–166.
-
(1988)
Nature
, vol.332
, pp. 164-166
-
-
Kazazian, H.H.1
Wong, C.2
Youssoufian, H.3
Scott, A.F.4
Phillips, D.G.5
Antonarakis, S.E.6
-
37
-
-
84873311500
-
RetroSeq: Transposable element discovery from next-generation sequencing data
-
Keane TM, Wong K, Adams DJ. 2013. RetroSeq: transposable element discovery from next-generation sequencing data. Bioinformatics 29: 389–390.
-
(2013)
Bioinformatics
, vol.29
, pp. 389-390
-
-
Keane, T.M.1
Wong, K.2
Adams, D.J.3
-
38
-
-
0032816281
-
Full-length human L1 insertions retain the capacity for high frequency retrotransposition in cultured cells
-
Kimberland ML, Kivoky V, Prchal J, Schwahn U, Berger W, Kazazian HH Jr. 1999. Full-length human L1 insertions retain the capacity for high frequency retrotransposition in cultured cells. Hum Mol Genet 8: 1557–1560.
-
(1999)
Hum Mol Genet
, vol.8
, pp. 1557-1560
-
-
Kimberland, M.L.1
Kivoky, V.2
Prchal, J.3
Schwahn, U.4
Berger, W.5
Jr, K.H.H.6
-
39
-
-
84959276574
-
Sequence analysis and characterization of active human Alu subfamilies based on the 1000 Genomes Pilot Project
-
Konkel MK, Walker JA, Hotard AB, Ranck MC, Fontenot CC, Storer J, Stewart C, Marth GT, Batzer MA. 2015. Sequence analysis and characterization of active human Alu subfamilies based on the 1000 Genomes Pilot Project. Genome Biol Evol 7: 2608–2622.
-
(2015)
Genome Biol Evol
, vol.7
, pp. 2608-2622
-
-
Konkel, M.K.1
Walker, J.A.2
Hotard, A.B.3
Ranck, M.C.4
Fontenot, C.C.5
Storer, J.6
Stewart, C.7
Marth, G.T.8
Batzer, M.A.9
-
40
-
-
69649109364
-
Circos: An information aesthetic for comparative genomics
-
Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, Horsman D, Jones SJ, Marra MA. 2009. Circos: an information aesthetic for comparative genomics. Genome Res 19: 1639–1645.
-
(2009)
Genome Res
, vol.19
, pp. 1639-1645
-
-
Krzywinski, M.1
Schein, J.2
Birol, I.3
Connors, J.4
Gascoyne, R.5
Horsman, D.6
Jones, S.J.7
Marra, M.A.8
-
41
-
-
84859210032
-
Fast gapped-read alignment with Bowtie 2
-
Langmead B, Salzberg SL. 2012. Fast gapped-read alignment with Bowtie 2. Nat Methods 9: 357–359.
-
(2012)
Nat Methods
, vol.9
, pp. 357-359
-
-
Langmead, B.1
Salzberg, S.L.2
-
42
-
-
84884532166
-
L1 allele
-
L1 allele. Hum Mutat 34: 1361–1365.
-
(2013)
Hum Mutat
, vol.34
, pp. 1361-1365
-
-
Lanikova, L.1
Kucerova, J.2
Indrak, K.3
Divoka, M.4
Issa, J.P.5
Papayannopoulou, T.6
Prchal, J.T.7
Divoky, V.8
-
43
-
-
84865285978
-
Landscape of somatic retrotransposition in human cancers
-
Lee E, Iskow R, Yang L, Gokcumen O, Haseley P, Luquette LJ III, Lohr JG, Harris CC, Ding L, Wilson RK, et al. 2012. Landscape of somatic retrotransposition in human cancers. Science 337: 967–971.
-
(2012)
Science
, vol.337
, pp. 967-971
-
-
Lee, E.1
Iskow, R.2
Yang, L.3
Gokcumen, O.4
Haseley, P.5
Luquette, L.J.6
Lohr, J.G.7
Harris, C.C.8
Ding, L.9
Wilson, R.K.10
-
44
-
-
84897133117
-
MOSAIK: A hash-based algorithm for accurate next-generation sequencing short-read mapping
-
Lee WP, Stromberg MP, Ward A, Stewart C, Garrison EP, Marth GT. 2014. MOSAIK: a hash-based algorithm for accurate next-generation sequencing short-read mapping. PLoS One 9: e90581.
-
(2014)
PLoS One
, vol.9
-
-
Lee, W.P.1
Stromberg, M.P.2
Ward, A.3
Stewart, C.4
Garrison, E.P.5
Marth, G.T.6
-
45
-
-
80054915847
-
A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data
-
Li H. 2011. A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics 27: 2987–2993.
-
(2011)
Bioinformatics
, vol.27
, pp. 2987-2993
-
-
Li, H.1
-
46
-
-
67649884743
-
Fast and accurate short read alignment with Burrows–Wheeler transform
-
Li H, Durbin R. 2009. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25: 1754–1760.
-
(2009)
Bioinformatics
, vol.25
, pp. 1754-1760
-
-
Li, H.1
Durbin, R.2
-
47
-
-
77949587649
-
Fast and accurate long-read alignment with Burrows–Wheeler transform
-
Li H, Durbin R. 2010. Fast and accurate long-read alignment with Burrows–Wheeler transform. Bioinformatics 26: 589–595.
-
(2010)
Bioinformatics
, vol.26
, pp. 589-595
-
-
Li, H.1
Durbin, R.2
-
48
-
-
0035024366
-
Frequency of recent retrotransposition events in the human factor IX gene
-
Li X, Scaringe W, Hill KA, Roberts S, Mengos A, Careri D, Pinto MT, Kasper CK, Sommers SS. 2001. Frequency of recent retrotransposition events in the human factor IX gene. Hum Mutat 17: 511–519.
-
(2001)
Hum Mutat
, vol.17
, pp. 511-519
-
-
Li, X.1
Scaringe, W.2
Hill, K.A.3
Roberts, S.4
Mengos, A.5
Careri, D.6
Pinto, M.T.7
Kasper, C.K.8
Sommers, S.S.9
-
49
-
-
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
-
50
-
-
84879375056
-
Transduction-specific ATLAS reveals a cohort of highly active L1 retrotransposons in human populations
-
Macfarlane CM, Collier P, Rahbari R, Beck CR, Wagstaff JF, Igoe S, Moran JV, Badge RM. 2013. Transduction-specific ATLAS reveals a cohort of highly active L1 retrotransposons in human populations. Hum Mutat 34: 974–985.
-
(2013)
Hum Mutat
, vol.34
, pp. 974-985
-
-
Macfarlane, C.M.1
Collier, P.2
Rahbari, R.3
Beck, C.R.4
Wagstaff, J.F.5
Igoe, S.6
Moran, J.V.7
Badge, R.M.8
-
51
-
-
0026503996
-
Disruption of the APC gene by a retrotransposal insertion of L1 sequence in a colon cancer
-
Miki Y, Nishisho I, Horii A, Miyoshi Y, Utsunomiya J, Kinzler KW, Vogelstein B, Nakamura Y. 1992. Disruption of the APC gene by a retrotransposal insertion of L1 sequence in a colon cancer. Cancer Res 52: 643–645.
-
(1992)
Cancer Res
, vol.52
, pp. 643-645
-
-
Miki, Y.1
Nishisho, I.2
Horii, A.3
Miyoshi, Y.4
Utsunomiya, J.5
Kinzler, K.W.6
Vogelstein, B.7
Nakamura, Y.8
-
52
-
-
0030058209
-
Mutation analysis in the BRCA2 gene in primary breast cancers
-
Miki Y, Katagiri T, Kasumi F, Yoshimot T, Nakamura Y. 1996. Mutation analysis in the BRCA2 gene in primary breast cancers. Nat Genet 13: 245–247.
-
(1996)
Nat Genet
, vol.13
, pp. 245-247
-
-
Miki, Y.1
Katagiri, T.2
Kasumi, F.3
Yoshimot, T.4
Nakamura, Y.5
-
54
-
-
0030606320
-
High frequency retrotransposition in cultured mammalian cells
-
Moran JV, Holmes SE, Naas TP, DeBerardinis RJ, Boeke JD, Kazazian HH Jr. 1996. High frequency retrotransposition in cultured mammalian cells. Cell 87: 917–927.
-
(1996)
Cell
, vol.87
, pp. 917-927
-
-
Moran, J.V.1
Holmes, S.E.2
Naas, T.P.3
DeBerardinis, R.J.4
Boeke, J.D.5
Jr, K.H.H.6
-
55
-
-
0033525586
-
Exon shuffling by L1 retrotransposition
-
Moran JV, DeBerardinis RJ, Kazazian HH Jr. 1999. Exon shuffling by L1 retrotransposition. Science 283: 1530–1534.
-
(1999)
Science
, vol.283
, pp. 1530-1534
-
-
Moran, J.V.1
DeBerardinis, R.J.2
Jr, K.H.H.3
-
56
-
-
2342562448
-
Molecular pathology of haemophilia B, identification of five novel mutations including a LINE 1 insertion in Indian patients
-
Mukherjee S, Mukhopadhyay A, Banerjee D, Chandak GR, Ray K. 2004. Molecular pathology of haemophilia B, identification of five novel mutations including a LINE 1 insertion in Indian patients. Haemophilia 10: 259–263.
-
(2004)
Haemophilia
, vol.10
, pp. 259-263
-
-
Mukherjee, S.1
Mukhopadhyay, A.2
Banerjee, D.3
Chandak, G.R.4
Ray, K.5
-
57
-
-
20544466648
-
Somatic mosaicism in neuronal precursor cells mediated by L1 retrotransposition
-
Muotri AR, Chu VT, Marchetto MC, Deng W, Moran JV, Gage FH. 2005. Somatic mosaicism in neuronal precursor cells mediated by L1 retrotransposition. Nature 435: 903–910.
-
(2005)
Nature
, vol.435
, pp. 903-910
-
-
Muotri, A.R.1
Chu, V.T.2
Marchetto, M.C.3
Deng, W.4
Moran, J.V.5
Gage, F.H.6
-
58
-
-
84937516456
-
SVA retrotransposition in exon 6 of the coagulation factor IX gene causing severe hemophilia B
-
Nakamura Y, Murata M, Takagi Y, Kozuka Y, Hasebe R, Takagi A, Kitazawa J, Shima M, Kojima T. 2015. SVA retrotransposition in exon 6 of the coagulation factor IX gene causing severe hemophilia B. Int J Hematol 102: 134–139.
-
(2015)
Int J Hematol
, vol.102
, pp. 134-139
-
-
Nakamura, Y.1
Murata, M.2
Takagi, Y.3
Kozuka, Y.4
Hasebe, R.5
Takagi, A.6
Kitazawa, J.7
Shima, M.8
Kojima, T.9
-
59
-
-
0027258342
-
′ end of exon 44 of the dystrophin gene resulted in skipping of the exon during splicing in a case of Duchenne muscular dystrophy
-
′ end of exon 44 of the dystrophin gene resulted in skipping of the exon during splicing in a case of Duchenne muscular dystrophy. J Clin Invest 91: 1862–1867.
-
(1993)
J Clin Invest
, vol.91
, pp. 1862-1867
-
-
Narita, N.1
Nisho, H.2
Kitoh, Y.3
Ishikawa, Y.4
Ishikawa, Y.5
Minami, R.6
Nakamura, H.7
Matsuo, M.8
-
60
-
-
0035208118
-
Twin priming: A proposed mechanism for the creation of inversions in L1 retrotransposition
-
Ostertag EA, Kazazian HH Jr. 2001. Twin priming: a proposed mechanism for the creation of inversions in L1 retrotransposition. Genome Res 11: 2059–2065.
-
(2001)
Genome Res
, vol.11
, pp. 2059-2065
-
-
Ostertag, E.A.1
Jr, K.H.H.2
-
61
-
-
84881159598
-
Great ape genetic diversity and population history
-
Prado-Martinez J, Sudmant PH, Kidd JM, Li H, Kelley JL, Lorente-Galdos B, Veeramah KR, Woerner AE, O’Connor TD, Santpere G, et al. 2013. Great ape genetic diversity and population history. Nature 499: 471–475.
-
(2013)
Nature
, vol.499
, pp. 471-475
-
-
Prado-Martinez, J.1
Sudmant, P.H.2
Kidd, J.M.3
Li, H.4
Kelley, J.L.5
Lorente-Galdos, B.6
Veeramah, K.R.7
Woerner, A.E.8
O’Connor, T.D.9
Santpere, G.10
-
62
-
-
84949227547
-
BEDTools: The Swiss-Army tool for genome feature analysis
-
Quinlan AR. 2014. BEDTools: The Swiss-Army tool for genome feature analysis. Curr Protoc Bioinformatics 47: 11.12.11–11.12.34.
-
(2014)
Curr Protoc Bioinformatics
, vol.47
-
-
Quinlan, A.R.1
-
63
-
-
84857888415
-
The non-autonomous retrotransposon SVA is trans-mobilized by the human LINE-1 protein machinery
-
Raiz J, Damert A, Chira S, Held U, Klawitter S, Hamdorf M, Lower J, Stratling WH, Lower R, Schumann GG. 2012. The non-autonomous retrotransposon SVA is trans-mobilized by the human LINE-1 protein machinery. Nucleic Acids Res 40: 1666–1683.
-
(2012)
Nucleic Acids Res
, vol.40
, pp. 1666-1683
-
-
Raiz, J.1
Damert, A.2
Chira, S.3
Held, U.4
Klawitter, S.5
Hamdorf, M.6
Lower, J.7
Stratling, W.H.8
Lower, R.9
Schumann, G.G.10
-
64
-
-
84941024427
-
Retrotransposon insertions in the clonal evolution of pancreatic ductal adenocarcinoma
-
Rodic N, Steranka JP, Makohon-Moore A, Moyer A, Shen P, Sharma R, Kohutek ZA, Huang CR, Ahn D, Mita P, et al. 2015. Retrotransposon insertions in the clonal evolution of pancreatic ductal adenocarcinoma. Nat Med 21: 1060–1064.
-
(2015)
Nat Med
, vol.21
, pp. 1060-1064
-
-
Rodic, N.1
Steranka, J.P.2
Makohon-Moore, A.3
Moyer, A.4
Shen, P.5
Sharma, R.6
Kohutek, Z.A.7
Huang, C.R.8
Ahn, D.9
Mita, P.10
-
65
-
-
84897025665
-
The genomic landscape of Neanderthal ancestry in present-day humans
-
Sankararaman S, Mallick S, Dannemann M, Prufer K, Kelso J, Paabo S, Patterson N, Reich D. 2014. The genomic landscape of Neanderthal ancestry in present-day humans. Nature 507: 354–357.
-
(2014)
Nature
, vol.507
, pp. 354-357
-
-
Sankararaman, S.1
Mallick, S.2
Dannemann, M.3
Prufer, K.4
Kelso, J.5
Paabo, S.6
Patterson, N.7
Reich, D.8
-
66
-
-
17344363489
-
Positional cloning of the gene for X-linked retinitis pigmentosa 2
-
Schwahn U, Lenzner S, Dong J, Feil S, Hinzmann B, van Duijnhoven G, Kirschner R, Hemberger M, Bergen AA, Rosenberg T, et al. 1998. Positional cloning of the gene for X-linked retinitis pigmentosa 2. Nat Genet 19: 327–332.
-
(1998)
Nat Genet
, vol.19
, pp. 327-332
-
-
Schwahn, U.1
Lenzner, S.2
Dong, J.3
Feil, S.4
Hinzmann, B.5
van Duijnhoven, G.6
Kirschner, R.7
Hemberger, M.8
Bergen, A.A.9
Rosenberg, T.10
-
67
-
-
84973358479
-
A hot L1 retrotransposon evades somatic repression and initiates human colorectal cancer
-
Scott EC, Gardner EJ, Masood A, Chuang NT, Vertino PM, Devine SE. 2016. A hot L1 retrotransposon evades somatic repression and initiates human colorectal cancer. Genome Res 26: 745–755.
-
(2016)
Genome Res
, vol.26
, pp. 745-755
-
-
Scott, E.C.1
Gardner, E.J.2
Masood, A.3
Chuang, N.T.4
Vertino, P.M.5
Devine, S.E.6
-
68
-
-
33646256347
-
Extensive individual variation in L1 retrotransposition capability contributes to human genetic diversity
-
Seleme MC, Vetter MR, Cordaux R, Bastone L, Batzer MA, Kazazian HH Jr. 2006. Extensive individual variation in L1 retrotransposition capability contributes to human genetic diversity. Proc Natl Acad Sci 103: 6611–6616.
-
(2006)
Proc Natl Acad Sci
, vol.103
, pp. 6611-6616
-
-
Seleme, M.C.1
Vetter, M.R.2
Cordaux, R.3
Bastone, L.4
Batzer, M.A.5
Jr, K.H.H.6
-
69
-
-
84875698271
-
Endogenous retrotransposition activates oncogenic pathways in hepatocellular carcinoma
-
Shukla R, Upton KR, Munoz-Lopez M, Gearhardt DJ, Fisher ME, Nguyen T, Brennan PM, Baillie JK, Collino A, Ghisletti S, et al. 2013. Endogenous retrotransposition activates oncogenic pathways in hepatocellular carcinoma. Cell 153: 101–111.
-
(2013)
Cell
, vol.153
, pp. 101-111
-
-
Shukla, R.1
Upton, K.R.2
Munoz-Lopez, M.3
Gearhardt, D.J.4
Fisher, M.E.5
Nguyen, T.6
Brennan, P.M.7
Baillie, J.K.8
Collino, A.9
Ghisletti, S.10
-
71
-
-
84870482898
-
Extensive somatic L1 retrotransposition in colorectal tumors
-
Solyom S, Ewing AD, Rahrmann EP, Doucet T, Nelson HH, Burns MB, Harris RS, Sigmon DF, Casella A, Erlanger B,, et al. 2012. Extensive somatic L1 retrotransposition in colorectal tumors. Genome Res 22: 2328–2338.
-
(2012)
Genome Res
, vol.22
, pp. 2328-2338
-
-
Solyom, S.1
Ewing, A.D.2
Rahrmann, E.P.3
Doucet, T.4
Nelson, H.H.5
Burns, M.B.6
Harris, R.S.7
Sigmon, D.F.8
Casella, A.9
Erlanger, B.10
-
72
-
-
80052318161
-
A comprehensive map of mobile element insertion polymorphisms in humans
-
Stewart C, Kural D, Stromberg MP, Walker JA, Konkel MK, Stutz AM, Urban AE, Grubert F, Lam HY, Lee WP, 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
Kural, D.2
Stromberg, M.P.3
Walker, J.A.4
Konkel, M.K.5
Stutz, A.M.6
Urban, A.E.7
Grubert, F.8
Lam, H.Y.9
Lee, W.P.10
-
73
-
-
84943182461
-
An integrated map of structural variation in 2504 human genomes
-
Sudmant PH, Rausch T, Gardner EJ, Handsaker RE, Abyzov A, Huddleston J, Zhang Y, Ye K, Jun G, Fritz MHY, et al. 2015. An integrated map of structural variation in 2504 human genomes. Nature 526: 75–81.
-
(2015)
Nature
, vol.526
, pp. 75-81
-
-
Sudmant, P.H.1
Rausch, T.2
Gardner, E.J.3
Handsaker, R.E.4
Abyzov, A.5
Huddleston, J.6
Zhang, Y.7
Ye, K.8
Jun, G.9
Fritz, M.H.Y.10
-
74
-
-
0035171986
-
An Alu insert as the cause of a severe form of hemophilia A
-
Sukarova E, Dimovski AJ, Tchacarova P, Petkov GH, Efremov GD. 2001. An Alu insert as the cause of a severe form of hemophilia A. Acta Haematol. 106: 126–129.
-
(2001)
Acta Haematol
, vol.106
, pp. 126-129
-
-
Sukarova, E.1
Dimovski, A.J.2
Tchacarova, P.3
Petkov, G.H.4
Efremov, G.D.5
-
75
-
-
0003308786
-
Molecular archeology of L1 insertions in the human genome
-
research0052
-
Szak ST, Pickeral OK, Makalowski W, Boguski MS, Landsman D, Boeke JD. 2002. Molecular archeology of L1 insertions in the human genome. Genome Biol 3: research0052.
-
(2002)
Genome Biol
, vol.3
-
-
Szak, S.T.1
Pickeral, O.K.2
Makalowski, W.3
Boguski, M.S.4
Landsman, D.5
Boeke, J.D.6
-
76
-
-
84991628639
-
Deep sequencing of 10,000 human genomes
-
Telenti A, Pierce LC, Biggs WH, di lulio J, Wong EHM, Fabiani MM, Kirkness EF, Moustafa A, Shah N, Xie C, et al. 2016. Deep sequencing of 10,000 human genomes. Proc Natl Acad Sci 113: 11901–11906.
-
(2016)
Proc Natl Acad Sci
, vol.113
, pp. 11901-11906
-
-
Telenti, A.1
Pierce, L.C.2
Biggs, W.H.3
Di lulio, J.4
Wong, E.H.M.5
Fabiani, M.M.6
Kirkness, E.F.7
Moustafa, A.8
Shah, N.9
Xie, C.10
-
77
-
-
33646035105
-
De novo Alu element insertions targeted to a sequence common to the BRCA1 and BRCA2 genes
-
Teugels E, De Brakeleer S, Goelen G, Lissens W, Sermijn E, De Greve J. 2005. De novo Alu element insertions targeted to a sequence common to the BRCA1 and BRCA2 genes. Hum Mutat 26: 284.
-
(2005)
Hum Mutat
, vol.26
, pp. 284
-
-
Teugels, E.1
De Brakeleer, S.2
Goelen, G.3
Lissens, W.4
Sermijn, E.5
De Greve, J.6
-
78
-
-
85047841580
-
Mobster: Accurate
-
Thung DT, de Ligt J, Vissers LE, Steehouwer M, Kroon M, de Vries P, Slagboom EP, Ye K, Veltman JA, Hehir-Dwa JY. 2014. Mobster: accurate
-
(2014)
-
-
Thung, D.T.1
De Ligt, J.2
Vissers, L.E.3
Steehouwer, M.4
Kroon, M.5
De Vries, P.6
Slagboom, E.P.7
Ye, K.8
Veltman, J.A.9
Hehir-Dwa, J.Y.10
|