Wells, J.N., & Feschotte, C. (2020). A field guide to eukaryotic transposable elements. Annual Review of Genetics, 54, 539-561. https://doi.org/10.1146/annurev-genet-040620-022145

Lander, E. S., Linton, L. M., Birren, B., Nusbaum, C., Zody, M. C., Dewar, K., … International Human Genome Sequencing Consortium. (2001). Initial sequencing and analysis of the human genome. Nature, 409 (6822), 860-921. https://doi.org/10.1038/35057062

Chung, E.B., Elde, N.C., & Feschotte, C. (2017). Regulatory activities of transposable elements: from conflicts to benefits. Nature Reviews Genetics, 18(2), 71-86. https://doi.org/10.1038/nrg.2016.139

McClintock, B. (1956). Controlling elements and the gene. Cold Spring Harbor Symposia on Quantitative Biology, 21, 197-216. https://doi.org/10.1101/SQB.1956.021.01.017

Britten, R.J., & Davidson, E.H. (1971). Repetitive and non-repetitive DNA sequences and a speculation on the origins of evolutionary novelty. The Quarterly Review of Biology, 46(2), 111-138. https://doi.org/10.1016/j.dci.2025.105358

Slotkin, R.K., & Martienssen, R. (2007). Transposable elements and the epigenetic regulation of the genome. Nature Reviews Genetics, 8(4), 272-285. https://doi.org/10.1038/nrg2072

Cosby, R.L., Judd, J., Zhang, R., Zhong, A., Garry, N., Pritham, E.J. and Feschotte, C., (2021). Recurrent evolution of vertebrate transcription factors by transposase capture. Science, 371(6531), eabc6405. https://doi.org/10.1126/science.abc6405

Burns, K.H. (2017). Transposable elements in cancer. Nature Reviews Cancer, 17(7), 415-424. https://doi.org/10.1038/nrc.2017.35

Jang, H. S., Shah, N. M., Du, A. Y., Dailey, Z. Z., Pehrsson, E. C., Godoy, P. M., ... & Wang, T. (2019). Transposable elements drive widespread expression of oncogenes in human cancers. Nature Genetics, 51(4), 611-617. https://doi.org/10.1038/s41588-019-0373-3

Batut, P., & Gingeras, T.R. (2013). RAMPAGE: promoter activity profiling by paired-end sequencing of 5′ complete cDNAs. Current Protocols in Molecular Biology, 104(1), 25B- 11. https://doi.org/10.1002/0471142727.mb25b11s104

Lisch, D. (2013). How important are transposons for plant evolution? Nature Reviews Genetics, 14(1), 49-61. https://doi.org/10.1038/nrg3374

Makarevitch, I., Waters, A. J., West, P. T., Stitzer, M., Hirsch, C. N., Ross-Ibarra, J., & Springer, N. M. (2015). Transposable elements contribute to activation of maize genes in response to abiotic stress. PLoS Genetics, 11(1), e1004915. https://doi.org/10.1371/journal.pgen.1005566

Flemr, M., Malik, R., Franke, V., Nejepinska, J., Sedlacek, R., Vlahovicek, K., & Svoboda, P. (2013). A retrotransposon-driven dicer isoform directs endogenous small interfering RNA production in mouse oocytes. Cell, 155(4), 807-816. https://doi.org/10.1016/j.cell.2013.10.001

Chung, H., Bogwitz, M. R., McCart, C., Andrianopoulos, A., Ffrench-Constant, R. H., Batterham, P., & Daborn, P. J. (2007). Cis-regulatory elements in the Accord retrotransposon result in tissue-specific expression of the Drosophila melanogaster insecticide resistance gene Cyp6g1. Genetics, 175(3), 1071-1077. https://doi.org/10.1534/genetics.106.066597

Studer, A., Zhao, Q., Ross-Ibarra, J., & Doebley, J. (2011). Identification of a functional transposon insertion in the maize domestication gene tb1. Nature Genetics, 43(11), 1160-1163. https://doi.org/10.1038/ng.944

Bai, L., & Brutnell, T.P. (2011). The Activator/Dissociation transposable elements comprise a two-component gene regulatory switch that controls endogenous gene expression in maize. Genetics, 187(3), 749-759. https://doi.org/10.1534/genetics.110.124149

Rebollo, R., Karimi, M. M., Bilenky, M., Gagnier, L., Miceli-Royer, K., Zhang, Y., ... & Mager, D. L. (2011). Retrotransposon-induced heterochromatin spreading in the mouse revealed by insertional polymorphisms. PLoS Genetics, 7(9), e1002301. https://doi.org/10.1371/journal.pgen.1002301

Ma, G., Babarinde, I. A., Zhou, X., & Hutchins, A. P. (2022). Transposable elements in pluripotent stem cells and human disease. Frontiers in Genetics, 13, 902541. https://doi.org/10.3389/fgene.2022.902541.

Cordaux, R., Udit, S., Batzer, M.A., & Feschotte, C. (2006). Birth of a chimeric primate gene by capture of the transposase gene from a mobile element. Proceedings of the National Academy of Sciences, 103(21), 8101-8106. https://doi.org/10.1073/pnas.0601161103

Modzelewski, A. J., Shao, W., Chen, J., Lee, A., Qi, X., Noon, M., ... & He, L. (2021). A mouse-specific retrotransposon drives a conserved Cdk2ap1 isoform essential for development. Cell, 184(22), 5541-5558. https://doi.org/10.1016/j.cell.2021.09.021

Salvi, S., Sponza, G., Morgante, M., Tomes, D., Niu, X., Fengler, K. A., ... & Tuberosa, R. (2007). Conserved noncoding genomic sequences associated with a flowering-time quantitative trait locus in maize. Proceedings of the National Academy of Sciences, 104(27), 11376-11381. https://doi.org/10.1073/pnas.0704145104

Babaian, A., & Mager, D. L. (2016a). Endogenous retroviral promoter exaptation in human cancer. Mobile DNA, 7 (1), 24. https://doi.org/10.1186/s13100-016-0081-9

Babaian, A., & Mager, D. L. (2016b). Endogenous retroviruses in development and disease. Genome Biology, 17 (1), 258. https://doi.org/10.1186/s13059-016-1124-8

Reilly, M. T., Faulkner, G. J., Dubnau, J., Ponomarev, I., & Gage, F. H. (2013). The role of transposable elements in health and diseases of the central nervous system. Journal of Neuroscience, 33 (45), 17577–17586. https://doi.org/10.1523/JNEUROSCI.3964-13.2013

Saleh, A., Macia, A., & Muotri, A. R. (2019). Transposable elements, inflammation, and neurological disease. Frontiers in Nneurology, 10, 894. https://doi.org/10.3389/fneur.2019.00894

Crow, Y. J., & Rehwinkel, J. (2009). Aicardi-Goutieres syndrome and related phenotypes: linking nucleic acid metabolism with autoimmunity. Human Molecular Genetics, 18(R2), R130-R136. https://doi.org/10.1093/hmg/ddp293

Payer, L. M., & Burns, K. H. (2019). Transposable elements in human genetic disease. Nature Reviews Genetics, 20(12), 760-772. https://doi.org/10.1038/s41576-019-0165-8.

De Cecco, M., Ito, T., Petrashen, A. P., Elias, A. E., Skvir, N. J., Criscione, S. W., … Sedivy, J. M. (2019). LINE-1 derepression in senescent cells triggers interferon and inflammaging. Nature, 568 (7752), 405-409. https://doi.org/10.1038/s41586-019-1087-5

Lipatov, M., Lenkov, K., Petrov, D. A., & Bergman, C. M. (2005). Paucity of chimeric gene-transposable element transcripts in the Drosophila melanogaster genome. BMC Biology, 3, 1-18. https://doi.org/10.1186/1741-7007-3-24.

Faulkner, G. J., Kimura, Y., Daub, C. O., Wani, S., Plessy, C., Irvine, K. M., ... & Carninci, P. (2009). The regulated retrotransposon transcriptome of mammalian cells. Nature Genetics, 41(5), 563-571. https://doi.org/10.1038/ng.368

Pinson, M.E., Pogorelcnik, R., Court, F., Arnaud, P. and Vaurs-Barrière, C., (2018). CLIFinder: identification of LINE-1 chimeric transcripts in RNA-seq data. Bioinformatics, 34(4), 688-690. https://doi.org/10.1093/bioinformatics/btx671

Babaian, A., Thompson, I. R., Lever, J., Gagnier, L., Karimi, M. M., & Mager, D. L. (2019). LIONS: analysis suite for detecting and quantifying transposable element initiated transcription from RNA-seq. Bioinformatics, 35(19), 3839-3841. https://doi.org/10.1093/bioinformatics/btz130

Treiber, C. D., & Waddell, S. (2020). Transposon expression in the Drosophila brain is driven by neighboring genes and diversifies the neural transcriptome. Genome Research, 30 (11), 1559-1569. https://doi.org/10.1101/gr.265938.120

Oliveira, D. S., Fablet, M., Larue, A., Vallier, A., Carareto, C. M., Rebollo, R., & Vieira, C. (2023). ChimeraTE: a pipeline to detect chimeric transcripts derived from genes and transposable elements. Nucleic Acids Research, 51(18), 9764-9784. https://doi.org/10.1093/nar/gkad671

Wang, S., Wang, M., Ichino, L., Boone, B. A., Zhong, Z., Papareddy, R. K., ... & Jacobsen, S. E. (2024). MBD2 couples DNA methylation to transposable element silencing during male gametogenesis. Nature Plants, 10, 13-24. https://doi.org/10.1038/s41477-023-01599-3

Guo, W., Wang, D., & Lisch, D. (2021). RNA-directed DNA methylation prevents rapid and heritable reversal of transposon silencing under heat stress in Zea mays. PLoS Genetics, 17(6), e1009326. https://doi.org/10.1371/journal.pgen.1009326

Liu, S., De Jonge, J., Trejo-Arellano, M., Santos-González, J., Köhler, C., & Hennig, L. (2020). Role of H1 and DNA methylation in selective regulation of transposable elements during heat stress. New Phytologist, 229(4), 2238-2250. https://doi.org/10.1111/nph.17018

Colonna Romano, N., & Fanti, L. (2022). Transposable elements: major players in shaping genomic and evolutionary patterns. Cells, 11(6), 1048. https://doi.org/10.3390/cells11061048

Niu, X. M., Xu, Y. C., Li, Z. W., Bian, Y. T., Hou, X. H., Chen, J. F., ... & Guo, Y. L. (2019). Transposable elements drive rapid phenotypic variation in Capsella rubella. Proceedings of the National Academy of Sciences, 116(14), 6908-6913. https://doi.org/10.1073/pnas.1811498116

Song, X., & Cao, X. (2017). Transposon-mediated epigenetic regulation contributes to phenotypic diversity and environmental adaptation in rice. Current Opinion in Plant Biology, 36, 111-118. https://doi.org/10.1016/j.pbi.2017.02.004

VandenDriessche, T., Ivics, Z., Izsvák, Z., & Chuah, M. K. (2009). Emerging potential of transposons for gene therapy and generation of induced pluripotent stem cells. Blood, 114(8), 1461-1468. https://doi.org/10.1182/blood-2009-04-210427

Deniger, D. C., Pasetto, A., Tran, E., Parkhurst, M. R., Cohen, C. J., Robbins, P. F., … Rosenberg, S. A. (2016). Stable, nonviral expression of mutated tumor neoantigen-specific T-cell receptors using the Sleeping Beauty transposon/transposase system. The Journal of the American Society of Gene Therapy, 24 (6), 1078-1089. https://doi.org/10.1038/mt.2016.6