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MIRs are classic, tRNA-derived SINEs that amplified before the mammalian radiation.
Smit AF, Riggs AD. Smit AF, et al. Nucleic Acids Res. 1995 Jan 11;23(1):98-102. doi: 10.1093/nar/23.1.98. Nucleic Acids Res. 1995. PMID: 7870595 Free PMC article.
Functional noncoding sequences derived from SINEs in the mammalian genome.
Nishihara H, Smit AF, Okada N. Nishihara H, et al. Among authors: smit af. Genome Res. 2006 Jul;16(7):864-74. doi: 10.1101/gr.5255506. Epub 2006 May 22. Genome Res. 2006. PMID: 16717141 Free PMC article.
The Dfam database of repetitive DNA families.
Hubley R, Finn RD, Clements J, Eddy SR, Jones TA, Bao W, Smit AF, Wheeler TJ. Hubley R, et al. Among authors: smit af. Nucleic Acids Res. 2016 Jan 4;44(D1):D81-9. doi: 10.1093/nar/gkv1272. Epub 2015 Nov 26. Nucleic Acids Res. 2016. PMID: 26612867 Free PMC article.
The UCSC Genome Browser database: 2015 update.
Rosenbloom KR, Armstrong J, Barber GP, Casper J, Clawson H, Diekhans M, Dreszer TR, Fujita PA, Guruvadoo L, Haeussler M, Harte RA, Heitner S, Hickey G, Hinrichs AS, Hubley R, Karolchik D, Learned K, Lee BT, Li CH, Miga KH, Nguyen N, Paten B, Raney BJ, Smit AF, Speir ML, Zweig AS, Haussler D, Kuhn RM, Kent WJ. Rosenbloom KR, et al. Among authors: smit af. Nucleic Acids Res. 2015 Jan;43(Database issue):D670-81. doi: 10.1093/nar/gku1177. Epub 2014 Nov 26. Nucleic Acids Res. 2015. PMID: 25428374 Free PMC article.
Realistic artificial DNA sequences as negative controls for computational genomics.
Caballero J, Smit AF, Hood L, Glusman G. Caballero J, et al. Among authors: smit af. Nucleic Acids Res. 2014 Jul;42(12):e99. doi: 10.1093/nar/gku356. Epub 2014 May 6. Nucleic Acids Res. 2014. PMID: 24803667 Free PMC article.
A novel abundant family of retroposed elements (DAS-SINEs) in the nine-banded armadillo (Dasypus novemcinctus).
Churakov G, Smit AF, Brosius J, Schmitz J. Churakov G, et al. Among authors: smit af. Mol Biol Evol. 2005 Apr;22(4):886-93. doi: 10.1093/molbev/msi071. Epub 2004 Dec 22. Mol Biol Evol. 2005. PMID: 15616140
Identification of new medium reiteration frequency repeats in the genomes of Primates, Rodentia and Lagomorpha.
Jurka J, Kapitonov VV, Klonowski P, Walichiewicz J, Smit AF. Jurka J, et al. Among authors: smit af. Genetica. 1996-1997;98(3):235-47. doi: 10.1007/BF00057588. Genetica. 1996. PMID: 9204548
Tiggers and DNA transposon fossils in the human genome.
Smit AF, Riggs AD. Smit AF, et al. Proc Natl Acad Sci U S A. 1996 Feb 20;93(4):1443-8. doi: 10.1073/pnas.93.4.1443. Proc Natl Acad Sci U S A. 1996. PMID: 8643651 Free PMC article.
Identification of a new, abundant superfamily of mammalian LTR-transposons.
Smit AF. Smit AF. Nucleic Acids Res. 1993 Apr 25;21(8):1863-72. doi: 10.1093/nar/21.8.1863. Nucleic Acids Res. 1993. PMID: 8388099 Free PMC article.
Ancestral, mammalian-wide subfamilies of LINE-1 repetitive sequences.
Smit AF, Tóth G, Riggs AD, Jurka J. Smit AF, et al. J Mol Biol. 1995 Feb 24;246(3):401-417. doi: 10.1006/jmbi.1994.0095. J Mol Biol. 1995. PMID: 7877164
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