Natural genetic variation caused by transposable elements in humans.

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Published in Genetics on October 01, 2004

Authors

E Andrew Bennett1, Laura E Coleman, Circe Tsui, W Stephen Pittard, Scott E Devine

Author Affiliations

1: Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322, USA.

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Sources and evolution of human Alu repeated sequences. Proc Natl Acad Sci U S A (1988) 3.95

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MaskerAid: a performance enhancement to RepeatMasker. Bioinformatics (2000) 3.66

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A genome-wide screen for normally methylated human CpG islands that can identify novel imprinted genes. Genome Res (2002) 3.50

Cytoplasmic ribonucleoprotein complexes containing human LINE-1 protein and RNA. EMBO J (1996) 3.34

Master genes in mammalian repetitive DNA amplification. Trends Genet (1992) 3.11

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Nucleic acid chaperone activity of the ORF1 protein from the mouse LINE-1 retrotransposon. Mol Cell Biol (2001) 2.98

Tiggers and DNA transposon fossils in the human genome. Proc Natl Acad Sci U S A (1996) 2.89

Insertional mutagenesis of the myc locus by a LINE-1 sequence in a human breast carcinoma. Nature (1988) 2.69

LINEs and Alus--the polyA connection. Nat Genet (1997) 2.58

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Clustering and subfamily relationships of the Alu family in the human genome. Mol Biol Evol (1987) 2.23

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Tracing the LINEs of human evolution. Proc Natl Acad Sci U S A (2002) 1.58

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Free left arms as precursor molecules in the evolution of Alu sequences. J Mol Evol (1991) 1.46

Trimeric structure for an essential protein in L1 retrotransposition. Proc Natl Acad Sci U S A (2003) 1.43

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Human L1 retrotransposition: insights and peculiarities learned from a cultured cell retrotransposition assay. Genetica (1999) 0.93

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