TY - STD TI - Hasler J, Strub K. Alu elements as regulators of gene expression. Nucleic Acids Res. 2006;34:5491–7. ID - ref1 ER - TY - STD TI - The International Human Genome Mapping Consortium. A physical map of the human genome. Nature 2001;409:934–41. ID - ref2 ER - TY - STD TI - The 1000 Genomes Project Consortium. A global reference for human genetic variation. Nature. 2015;526:68–74. ID - ref3 ER - TY - STD TI - Dewannieux M, Esnault C, Heidmann T. LINE-mediated retrotransposition of marked Alu sequences. Nat Genet. 2003;35:41–8. ID - ref4 ER - TY - STD TI - Christensen SM, Eickbush TH. R2 target-primed reverse transcription: ordered cleavage and polymerization steps by protein subunits asymmetrically bound to the target DNA. Mol Cell Biol. 2005;25:6617–28. ID - ref5 ER - TY - STD TI - Konkel MK, Walker JA, Hotard AB, Ranck MC, Fontenot CC, Storer J, et al. Sequence Analysis and Characterization of Active Human Alu Subfamilies Based on the 1000 Genomes Pilot Project. Genome Biol Evol. 2015;7:2608–22. ID - ref6 ER - TY - STD TI - Batzer MA, Deininger PL. Alu Repeats and Human Genomic Diversity. Nat Rev Genet. 2002;3:370–9. ID - ref7 ER - TY - STD TI - Han K, Xing J, Wang H, Hedges DJ, Garber RK, Cordaux R, et al. Under the genomic radar: The Stealth model of Alu amplification. Genome Res. 2005;15:655–64. ID - ref8 ER - TY - STD TI - Xing J, Hedges DJ, Han K, Wang H, Cordaux R, Batzer M A Alu element mutation spectra: molecular clocks and the effect of DNA methylation. J Mol Biol. 2004;344:675–82. ID - ref9 ER - TY - STD TI - Mills RE, Bennett EA, Iskow RC, Devine SE. Which transposable elements are active in the human genome? Trends Genet. 2007;23:183–91. ID - ref10 ER - TY - STD TI - Bennett EA, Keller H, Mills RE, Schmidt S, Moran JV, Weichenrieder O, et al. Active Alu retrotransposons in the human genome. Genome Res. 2008;18:1875–83. ID - ref11 ER - TY - STD TI - Dewannieux M, Heidmann T. Role of poly(A) tail length in Alu retrotransposition. Genomics. 2005;86:378–81. ID - ref12 ER - TY - STD TI - Wildschutte JH, Baron AA, Diroff NM, Kidd JM. Discovery and characterization of Alu repeat sequences via precise local read assembly. Nucleic Acids Res. 2015;43:10292–307. ID - ref13 ER - TY - STD TI - Tajnik M, Vigilante A, Braun S, Hänel H, Luscombe NM, Ule J, et al. Intergenic Alu exonisation facilitates the evolution of tissue-specific transcript ends. Nucleic Acids Res. 2015;43:gkv956. ID - ref14 ER - TY - STD TI - Hormozdiari F, Alkan C, Ventura M, Hajirasouliha I, Malig M, Hach F, et al. Alu repeat discovery and characterization within human genomes. Genome Res. 2011:840–9. ID - ref15 ER - TY - STD TI - Rishishwar L, Tellez Villa CE, Jordan IK. Transposable element polymorphisms recapitulate human evolution. Mobile DNA. 2015;6:21. ID - ref16 ER - TY - STD TI - Salem AH, Kilroy GE, Watkins WS, Jorde LB, Batzer MA. Recently integrated Alu elements and human genomic diversity. Mol Biol Evol. 2003;20:1349–61. ID - ref17 ER - TY - STD TI - Sudmant PH, Rausch T, Gardner EJ, Handsaker RE, Abyzov A, Huddleston J, et al. An integrated map of structural variation in 2,504 human genomes. Nature. 2015;526:75–81. ID - ref18 ER - TY - STD TI - Gu Z, Jin K, Crabbe MJC, Zhang Y, Liu X, Huang Y, et al. Enrichment analysis of Alu elements with different spatial chromatin proximity in the human genome. Protein Cell. Higher Education Press. 2016;7:250–66. ID - ref19 ER - TY - STD TI - Wang L, Rishishwar L, Mariño-Ramírez L, Jordan IK. Human population-specific gene expression and transcriptional network modification with polymorphic transposable elements. Nucleic Acids Res. 2017;45:2318–28. ID - ref20 ER - TY - STD TI - Stewart C, Kural D, Strömberg MP, Walker JA, Konkel MK, Stütz AM, et al. A comprehensive map of mobile element insertion polymorphisms in humans. PLoS Genet. 2011;7:e1002236. ID - ref21 ER - TY - STD TI - Witherspoon DJ, Watkins WS, Zhang Y, Xing J, Tolpinrud WL, Hedges DJ, et al. Alu repeats increase local recombination rates. BMC Genomics. 2009;10:530. ID - ref22 ER - TY - STD TI - Xing J, Zhang Y, Han K, Xing J, Zhang Y, Han K, et al. Mobile elements create structural variation: Analysis of a complete human genome. Genome Res. 2009:1516–26. ID - ref23 ER - TY - STD TI - Thung DT, de Ligt J, Vissers LEM, Steehouwer M, Kroon M, de Vries P, et al. Mobster: accurate detection of mobile element insertions in next generation sequencing data. Genome Biol. 2014;15:488. ID - ref24 ER - TY - STD TI - Wu J, Lee W-P, Ward A, Walker JA, Konkel MK, Batzer MA, et al. Tangram: a comprehensive toolbox for mobile element insertion detection. BMC Genomics. 2014;15:795. ID - ref25 ER - TY - STD TI - Ewing AD. Transposable element detection from whole genome sequence data. Mobile DNA. 2015;6:24. ID - ref26 ER - TY - STD TI - Rishishwar L, Mariño-Ramírez L, Jordan IK. Benchmarking computational tools for polymorphic transposable element detection. Brief Bioinform. 2016;bbw072:1–11. ID - ref27 ER - TY - STD TI - Witherspoon DJ, Zhang YH, Xing JC, Watkins WS, Ha H, Batzer MA, et al. Mobile element scanning (ME-Scan) identifies thousands of novel Alu insertions in diverse human populations. Genome Res. 2013;23:1170–81. ID - ref28 ER - TY - STD TI - Witherspoon DJ, Xing J, Zhang Y, Watkins WS, Batzer MA, Jorde LB. Mobile element scanning (ME-Scan) by targeted high-throughput sequencing. BMC Genomics. 2010;11:410. ID - ref29 ER - TY - STD TI - Platt RN, Zhang Y, Witherspoon DJ, Xing J, Suh A, Keith MS, et al. Targeted Capture of Phylogenetically Informative Ves SINE Insertions in Genus Myotis. Genome Biol Evol. 2015;7:1664–75. ID - ref30 ER - TY - STD TI - Ha H, Loh JW, Xing J. Identification of polymorphic SVA retrotransposons using a mobile element scanning method for SVA (ME-Scan-SVA). Mobile DNA. 2016;7:15. ID - ref31 ER - TY - STD TI - Xing J, Witherspoon DJ, Jorde LB. Mobile element biology: new possibilities with high-throughput sequencing. Trends Genet Elsevier Ltd. 2013;29:280–9. ID - ref32 ER - TY - STD TI - Ha H, Wang N, Xing J. Library Construction for High-Throughput Mobile Element Identification and Genotyping. Methods Mol Biol. Totowa, NJ: Humana Press; 2015. p. 1–15. ID - ref33 ER - TY - STD TI - Carter AB, Salem A, Hedges DJ, Keegan CN, Kimball B, Walker JA, et al. Genome-wide analysis of the human Yb-lineage. Hum Genomics. 2004;1:167–78. ID - ref34 ER - TY - STD TI - Ahmed M, Li W, Liang P. Identification of three new Alu Yb subfamilies by source tracking of recently integrated Alu Yb elements. Mobile DNA. 2013;4:25. ID - ref35 ER - TY - STD TI - Hancks DC, Kazazian HH. Roles for retrotransposon insertions in human disease. Mobile DNA. 2016;7:9. ID - ref36 ER - TY - STD TI - Jurka J, Kapitonov VV, Pavlicek A, Klonowski P, Kohany O, Walichiewicz J. Repbase Update, a database of eukaryotic repetitive elements. Cytogenet Genome Res. 2005;110:462–7. ID - ref37 ER - TY - STD TI - Smit A, Hubley R, Green P. RepeatMasker Open-3.0. 2010. ID - ref38 ER - TY - STD TI - Stewart C, Kural D, Strömberg MP, Walker JA, Konkel MK, Stütz AM, et al. A comprehensive map of mobile element insertion polymorphisms in humans. PLoS Genet. 2011;7 ID - ref39 ER - TY - STD TI - Wang J, Song L, Grover D, Azrak S, Batzer MA, Liang P. dbRIP: A Highly Integrated Database of Retrotransposon Insertion Polymorphisms in Humans. Hum Mutat. 2006;27:323–9. ID - ref40 ER - TY - STD TI - Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010;26:841–2. ID - ref41 ER - TY - STD TI - Cloutier P, Lavallée-Adam M, Faubert D, Blanchette M, Coulombe B. A Newly Uncovered Group of Distantly Related Lysine Methyltransferases Preferentially Interact with Molecular Chaperones to Regulate Their Activity. PLoS Genet. 2013;9:e1003210. ID - ref42 ER - TY - STD TI - Małecki J, Ho AYY, Moen A, Dahl H-A, Falnes PØ. Human METTL20 is a mitochondrial lysine methyltransferase that targets the β subunit of electron transfer flavoprotein (ETFβ) and modulates its activity. J Biol Chem. 2015;290:423–34. ID - ref43 ER - TY - STD TI - The 1000 Genomes Project Consortium. A map of human genome variation from population-scale sequencing. Nature. 2010;467:1061–73. ID - ref44 ER - TY - STD TI - Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, et al. BLAST+: architecture and applications. BMC Bioinformatics. 2009;10:421. ID - ref45 ER - TY - STD TI - Comeaux MS, Roy-Engel AM, Hedges DJ, Deininger PL. Diverse cis factors controlling Alu retrotransposition: what causes Alu elements to die? Genome Res. 2009;19:545–55. ID - ref46 ER - TY - STD TI - Parekh RB, Dwek R, Sutton B. Upstream sequences modulate the internal promoter of the human 7SL RNA gene. Nature. 1985;318:452–7. ID - ref47 ER - TY - STD TI - Chesnokov I, Schmid CW. Flanking sequences of an Alu source stimulate transcription in vitro by interacting with sequence-specific transcription factors. J Mol Evol. 1996;42:30–6. ID - ref48 ER - TY - STD TI - Cordaux R, Hedges DJ, Herke SW, Batzer MA. Estimating the retrotransposition rate of human Alu elements. Gene. 2006;373:134–7. ID - ref49 ER - TY - STD TI - Batzer MA, Kilroy GE, Richard PE, Shaikh TH, Desselle TD, Hoppens CL, et al. Structure and variability of recently inserted Alu family members.[erratum appears in Nucleic Acids Res 1991 Feb 11;19(3):698–9]. Nucleic Acids Res. 1990;18:6793–8. ID - ref50 ER - TY - STD TI - Labuda D, Striker G. Sequence conservation in Alu evolution. Nucleic Acids Res. 1989;17:2477–91. ID - ref51 ER - TY - STD TI - Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009;25:1754–60. ID - ref52 ER - TY - STD TI - The International HapMap 3 Consortium, Principal investigators, Altshuler DM, Gibbs RA, Peltonen L, Project coordination leaders, et al. Integrating common and rare genetic variation in diverse human populations. Nature. 2010;467:52–8. ID - ref53 ER - TY - STD TI - Bamshad MJ, Watkins WS, Dixon ME, Jorde LB, Rao BB, Naidu JM, et al. Female gene flow stratifies Hindu castes. Nature. 1998;395:651. ID - ref54 ER - TY - STD TI - Jorde LB, Bamshad MJ, Watkins WS, Zenger R, Fraley AE, Krakowiak PA, et al. Origins and affinities of modern humans: a comparison of mitochondrial and nuclear genetic data. Am J Hum Genet. 1995;57:523–38. ID - ref55 ER - TY - STD TI - Watkins WS, Bamshad M, Dixon ME, Bhaskara Rao B, Naidu JM, Reddy PG, et al. Multiple Origins of the mtDNA 9-bp Deletion in Populations of South India. Am J Phys Anthropol. 1999;109(147–15):147–58. ID - ref56 ER - TY - STD TI - Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, et al. The Human Genome Browser at UCSC The Human Genome Browser at UCSC. Genome Res. 2002;12:996–1006. ID - ref57 ER - TY - STD TI - Ye J, Coulouris G, Zaretskaya I, Cutcutache I, Rozen S, Madden TL. Primer-BLAST: A tool to design target-specific primers for polymerase chain reaction. BMC Bioinformatics. 2012;13:134. ID - ref58 ER - TY - STD TI - Untergasser A, Cutcutache I, Koressaar T, Ye J, Faircloth BC, Remm M, et al. Primer3-new capabilities and interfaces. Nucleic Acids Res. 2012;40:1–12. ID - ref59 ER - TY - STD TI - Corporation GC. Sequencher. Ann Arbor: Gene Codes Corporation; 2015. ID - ref60 ER - TY - STD TI - David M, Mustafa H, Brudno M. Detecting Alu insertions from high-throughput sequencing data. Nucleic Acids Res. 2013;41:1–13. ID - ref61 ER - TY - STD TI - Durbin RM, Altshuler DL, Durbin RM, Abecasis GR, Bentley DR, Chakravarti A, et al. A map of human genome variation from population-scale sequencing. Nature. 2010;467:1061–73. ID - ref62 ER -