A Field Guide to Eukaryotic Transposable Elements

The zebrafish reference genome sequence and its relationship to the human genome.

Howe, K., Clark, M. D., Torroja, C. F., Torrance, J., Berthelot, C., Muffato, M., Collins, J. E., Humphray, S., McLaren, K., Matthews, L., et al. (2013) · Nature · doi:10.1038/nature12111 · Cited by 5,100

RepeatModeler2 for automated genomic discovery of transposable element families

Flynn, J. M., Hubley, R., Goubert, C., Rosen, J., Clark, A. G., Feschotte, C., & Smit, A. F. (2020) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1921046117 · Cited by 3,848

A unified classification system for eukaryotic transposable elements

Wicker, T., Sabot, F., Hua‐Van, A., Bennetzen, J. L., Capy, P., Chalhoub, B., Flavell, A. J., Leroy, P., Morgante, M., Panaud, O., et al. (2007) · Nature Reviews Genetics · doi:10.1038/nrg2165 · Cited by 3,159

Repeated Sequences in DNA

Britten, R. J., & Kohne, D. E. (1968) · Science · doi:10.1126/science.161.3841.529 · Cited by 2,789

Gene Regulation for Higher Cells: A Theory

Britten, R. J., & Davidson, E. H. (1969) · Science · doi:10.1126/science.165.3891.349 · Cited by 2,078

The origins of genome complexity

Lynch, M., & Conery, J. S. (2003) · Science · doi:10.1126/science.1089370 · Cited by 1,698

Alu repeats and human genomic diversity

Batzer, M., & Deininger, P. (2002) · Nature reviews genetics · doi:10.1038/nrg798 · Cited by 1,522

Benchmarking transposable element annotation methods for creation of a streamlined, comprehensive pipeline

Ou, S., Su, W., Liao, Y., Chougule, K. M., Agda, J. R. A., Hellinga, A. J., Lugo, C. S. B., Elliott, T. A., Ware, D., Peterson, T., et al. (2019) · Genome biology · doi:10.1186/s13059-019-1905-y · Cited by 1,522

Regulatory activities of transposable elements: from conflicts to benefits

Chuong, E. B., Elde, N. C., & Feschotte, C. (2017) · Nature Reviews Genetics · doi:10.1038/nrg.2016.139 · Cited by 1,489

The Norway spruce genome sequence and conifer genome evolution

Nystedt, B., Street, N. R., Wetterbom, A., Zuccolo, A., Lin, Y., Scofield, D. G., Vezzi, F., Delhomme, N., Giacomello, S., Alexeyenko, A., et al. (2013) · Nature · doi:10.1038/nature12211 · Cited by 1,463

Causes and consequences of linkage disequilibrium among transposable elements within eukaryotic genomes

Roze, D. (2023) · Genetics · doi:10.1093/genetics/iyad058 · Cited by 27

Multiple and diversified transposon lineages contribute to early and recent bivalve genome evolution

Martelossi, J., Nicolini, F., Subacchi, S., Pasquale, D., Ghiselli, F., & Luchetti, A. (2023) · BMC Biology · doi:10.1186/s12915-023-01632-z · Cited by 26

Chromatin and gene expression changes during female Drosophila germline stem cell development illuminate the biology of highly potent stem cells

Pang, L.-Y., DeLuca, S. Z., Zhu, H., Urban, J. M., & Spradling, A. C. (2023) · eLife · doi:10.7554/elife.90509 · Cited by 26

Hologenome analysis reveals independent evolution to chemosymbiosis by deep-sea bivalves

Guo, Y., Meng, L., Wang, M., Zhong, Z., Li, D., Zhang, Y., Li, H., Zhang, H., Seim, I., Li, Y., et al. (2023) · BMC Biology · doi:10.1186/s12915-023-01551-z · Cited by 26

Biosynthesis of Haloterpenoids in Red Algae via Microbial-like Type I Terpene Synthases

Steele, T. S., Burkhardt, I., Moore, M. L., de Rond, T., Bone, H. K., Barry, K., Bunting, V. M., Grimwood, J., Handley, L. H., Rajasekar, S., et al. (2023) · ACS Chemical Biology · doi:10.1021/acschembio.3c00627 · Cited by 24

Epigenetic variation as a new plant breeding tool: A review

Alfalahi, A. O., Hussein, Z. T., Khalofah, A., Sadder, M. T., Qasem, J. R., Al-Khayri, J. M., Jain, S. M., & Almehemdi, A. F. (2022) · Journal of King Saud University - Science · doi:10.1016/j.jksus.2022.102302 · Cited by 23

Retrotransposon LINE-1 bodies in the cytoplasm of piRNA-deficient mouse spermatocytes: Ribonucleoproteins overcoming the integrated stress response

Luca, C. D., Gupta, A. K., & Bortvin, A. L. (2023) · PLoS Genetics · doi:10.1371/journal.pgen.1010797 · Cited by 25

Programmed DNA elimination: silencing genes and repetitive sequences in somatic cells

Zagoskin, M. V., & Wang, J. (2021) · Biochemical Society Transactions · doi:10.1042/bst20190951 · Cited by 23

Discovery of numerous novel Helitron -like elements in eukaryote genomes using HELIANO

Li, Z., Gilbert, C., Peng, H., & Pollet, N. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkae679 · Cited by 25

An Ancient Clade of Penelope -Like Retroelements with Permuted Domains Is Present in the Green Lineage and Protists, and Dominates Many Invertebrate Genomes

Craig, R. J., Yushenova, I. A., Rodríguez, F., & Arkhipova, I. R. (2021) · Molecular Biology and Evolution · doi:10.1093/molbev/msab225 · Cited by 25

On the Base Composition of Transposable Elements

Boissinot, S. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms23094755 · Cited by 23

Repeat turnover meets stable chromosomes: repetitive DNA sequences mark speciation and gene pool boundaries in sugar beet and wild beets

Schmidt, N., Sielemann, K., Breitenbach, S., Fuchs, J., Pucker, B., Weißhaar, B., Holtgräwe, D., & Heitkam, T. (2023) · The Plant Journal · doi:10.1111/tpj.16599 · Cited by 21

The good, the bad and the ugly of transposable elements annotation tools

Loreto, É. L. S., de Melo, E. S., Wallau, G. L., & Gomes, T. M. F. D. F. (2023) · Genetics and Molecular Biology · doi:10.1590/1678-4685-gmb-2023-0138 · Cited by 26

Intraspecific Variation of Transposable Elements Reveals Differences in the Evolutionary History of Fungal Phytopathogen Pathotypes

Nakamoto, A., Joubert, P. M., & Krasileva, K. V. (2023) · Genome Biology and Evolution · doi:10.1093/gbe/evad206 · Cited by 21

Chiropterans Are a Hotspot for Horizontal Transfer of DNA Transposons in Mammalia

Paulat, N. S., Storer, J. M., Moreno-Santillán, D. D., Osmanski, A. B., Sullivan, K. A. M., Grimshaw, J., Korstian, J. M., Halsey, M. K., Garcia, C. J., Crookshanks, C., et al. (2023) · Molecular Biology and Evolution · doi:10.1093/molbev/msad092 · Cited by 20

The large bat Helitron DNA transposase forms a compact monomeric assembly that buries and protects its covalently bound 5′-transposon end

Košek, D., Grabundžija, I., Lei, H., Bilić, I., Wang, H., Jin, Y., Peaslee, G. F., Hickman, A. B., & Dyda, F. (2021) · Molecular Cell · doi:10.1016/j.molcel.2021.07.028 · Cited by 21

Polymorphic transposable elements contribute to variation in recombination landscapes

Huang, Y., Gao, Z. Y., Ly, K., Lin, L., Lambooij, J.-P., King, E. G., Janssen, A., Wei, K. H.-C., & Lee, Y. C. G. (2025) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2427312122 · Cited by 22

Silencing by the HUSH Epigenetic Transcriptional Repressor Complex

Lehner, P. J. (2025) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-020425-045352 · Cited by 20

Transcription of Endogenous Retroviruses: Broad and Precise Mechanisms of Control

Jarosz, A. S., & Halo, J. V. (2024) · Viruses · doi:10.3390/v16081312 · Cited by 20

Rapid evolution of piRNA clusters in the Drosophila melanogaster ovaryPreprint

Srivastav, S. P., Feschotte, C., & Clark, A. G. (2024) · Genome Research · doi:10.1101/gr.278062.123 · Cited by 22

All Quiet on the TE Front? The Role of Chromatin in Transposable Element Silencing

Di Stefano, L. (2022) · Cells · doi:10.3390/cells11162501 · Cited by 18

Direct Regulation of DNA Repair by E2F and RB in Mammals and Plants: Core Function or Convergent Evolution?

Manickavinayaham, S., Dennehey, B. K., & Johnson, D. G. (2021) · Cancers · doi:10.3390/cancers13050934 · Cited by 21

Plants acquired a major retrotransposon horizontally from fungi during the conquest of land

Wang, Q., Wang, Y., Wang, J., Gong, Z. H., & Han, G. (2021) · New Phytologist · doi:10.1111/nph.17568 · Cited by 18

Comparative Methylome Analysis Reveals Epigenetic Signatures Associated with Growth and Shell Color in the Pacific Oyster, Crassostrea gigas

Tan, C., Shi, C., Li, Y., Teng, W., Li, Y., Fu, H., Ren, L., Yu, H., Li, Q., & Liu, S. (2022) · Marine Biotechnology · doi:10.1007/s10126-022-10154-8 · Cited by 18

Regulation and function of R-loops at repetitive elements

Gambelli, A., Ferrando, A., Boncristiani, C., & Schoeftner, S. (2023) · Biochimie · doi:10.1016/j.biochi.2023.08.013 · Cited by 18

Deciphering recent transposition patterns in plants through comparison of 811 genome assemblies

Huang, Y., Sahu, S. K., & Liu, X. (2025) · Plant Biotechnology Journal · doi:10.1111/pbi.14570 · Cited by 19

TE Density: a tool to investigate the biology of transposable elements

Teresi, S. J., Teresi, M. B., & Edger, P. P. (2022) · Mobile DNA · doi:10.1186/s13100-022-00264-4 · Cited by 19

Population-level transposable element expression dynamics influence trait evolution in a fungal crop pathogen

Abraham, L., Oggenfuss, U., & Croll, D. (2024) · mBio · doi:10.1128/mbio.02840-23 · Cited by 17

Adaptation in the face of internal conflict: the paradox of the organism revisited

Patten, M. M., Schenkel, M. A., & Ågren, J. A. (2023) · Biological reviews/Biological reviews of the Cambridge Philosophical Society · doi:10.1111/brv.12983 · Cited by 17

Intercellular bridges are essential for transposon repression and meiosis in the male germline

Sorkin, J., Tilton, K., Lawlor, M. A., Sarathy, S. N., Liang, S., Albanese, A., Rabbani, M., Hammoud, S. S., Ellison, C. E., Pratto, F., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-56742-9 · Cited by 16

Integration of TE Induces Cancer Specific Alternative Splicing Events

Kim, W. R., Park, E. G., Lee, Y. J., Bae, W. H., Lee, D. H., & Kim, H. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms231810918 · Cited by 16

Adaptations of Pseudoxylaria towards a comb-associated lifestyle in fungus-farming termite colonies

Fricke, J., Schalk, F., Kreuzenbeck, N. B., Seibel, E., Hoffmann, J., Dittmann, G., Conlon, B. H., Guo, H., de Beer, Z. W., Vassão, D. G., et al. (2023) · The ISME Journal · doi:10.1038/s41396-023-01374-4 · Cited by 16

A BrLINE1-RUP insertion in BrCER2 alters cuticular wax biosynthesis in Chinese cabbage (Brassica rapa L. ssp. pekinensis)

Li, B., Yue, Z., Ding, X., Zhao, Y., Lei, J., Zang, Y., Hu, Q., & Tao, P. (2023) · Frontiers in Plant Science · doi:10.3389/fpls.2023.1212528 · Cited by 16

Post-transcriptional and translational regulation of plant gene expression by transposons

Kan, Q., & Li, Q. (2023) · Current Opinion in Plant Biology · doi:10.1016/j.pbi.2023.102438 · Cited by 16

Spoink, a LTR retrotransposon, invaded D. melanogaster populations in the 1990s

Pianezza, R., Scarpa, A., Narayanan, P., Signor, S. A., & Kofler, R. (2024) · PLoS Genetics · doi:10.1371/journal.pgen.1011201 · Cited by 16

Harbinger transposon insertion in ethylene signaling gene leads to emergence of new sexual forms in cucurbits

Huang, H.-Y., Zhang, S., Abou-Choucha, F., Verdenaud, M., Tan, F., Pichot, C., Parsa, H. S., Slavković, F., Chen, Q., Troadec, C., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-49250-9 · Cited by 16

Centrophilic Retrotransposons of Plant Genomes

Bousios, A., Kakutani, T., & Henderson, I. R. (2025) · Annual Review of Plant Biology · doi:10.1146/annurev-arplant-083123-082220 · Cited by 16

Disruption of HaVipR1 confers Vip3Aa resistance in the moth crop pest Helicoverpa armigera

Bachler, A., Padovan, A., Anderson, C. J., Wei, Y., Wu, Y., Pearce, S. L., Downes, S. J., James, B., Tessnow, A. E., Sword, G. A., et al. (2025) · PLoS Biology · doi:10.1371/journal.pbio.3003165 · Cited by 16

Transposons and accessory genes drive adaptation in a clonally evolving fungal pathogen

López‐Díaz, C., Ayhan, D. H., López, A. R., Gómez-Gil, L., Ma, L., & Pietro, A. D. (2025) · Nature Communications · doi:10.1038/s41467-025-62213-y · Cited by 18

Evolution of antiviral host defenses against a backdrop of endogenous retroelements

Kassiotis, G., & Stoye, J. P. (2025) · Science · doi:10.1126/science.adx4379 · Cited by 15

Transposon control as a checkpoint for tissue regeneration

Angileri, K. M., Bagia, N. A., & Feschotte, C. (2022) · Development · doi:10.1242/dev.191957 · Cited by 15

Large effective population size masks population genetic structure in Hirondellea amphipods within the deepest marine ecosystem, the Mariana Trench

Piertney, S. B., Wenzel, M. A., & Jamieson, A. J. (2023) · Molecular Ecology · doi:10.1111/mec.16887 · Cited by 15

Genomic Instability Evolutionary Footprints on Human Health: Driving Forces or Side Effects?

Veschetti, L., Treccani, M., Tomi, E. D., & Malerba, G. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms241411437 · Cited by 16

TopoQual polishes circular consensus sequencing data and accurately predicts quality scores

Weerakoon, M., Lee, S., Mitchell, E., & Heaton, H. (2025) · BMC Bioinformatics · doi:10.1186/s12859-024-06020-0 · Cited by 15

Blessing or curse: how the epigenetic resolution of host-transposable element conflicts shapes their evolutionary dynamics

Huang, Y., & Lee, Y. C. G. (2024) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2023.2775 · Cited by 15

Orphan genes are not a distinct biological entity

Pereira, A. B., Marano, M., Bathala, R., Zaragoza, R. A., Neira, A., Samano, A., Owoyemi, A. O., & Casola, C. (2024) · BioEssays · doi:10.1002/bies.202400146 · Cited by 15

Locus-specific chromatin profiling of evolutionarily young transposable elements

Taylor, D., Lowe, R., Philippe, C., Cheng, K. C. L., Grant, O. A., Zabet, N. R., Cristofari, G., & Branco, M. R. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab1232 · Cited by 15

The Role of Transposable Elements in Sexual Development

Chiang, V. S., DeRosa, H., Park, J., & Hunter, R. G. (2022) · Frontiers in Behavioral Neuroscience · doi:10.3389/fnbeh.2022.923732 · Cited by 13

Genome-wide methylation patterns from canine nanopore assemblies

Schall, P. Z., Winkler, P. A., Petersen‐Jones, S. M., Yuzbasiyan‐Gurkan, V., & Kidd, J. M. (2023) · G3 Genes Genomes Genetics · doi:10.1093/g3journal/jkad203 · Cited by 14

Insight on ecDNA-mediated tumorigenesis and drug resistance

Huang, Q., Zhang, S., Wang, G., & Han, J. (2024) · Heliyon · doi:10.1016/j.heliyon.2024.e27733 · Cited by 14

Transactivation of Human Endogenous Retroviruses by Viruses

Evans, E., Saraph, A., & Tokuyama, M. (2024) · Viruses · doi:10.3390/v16111649 · Cited by 15

RNA binding by Periphilin plays an essential role in initiating silencing by the HUSH complex

Bloor, S., Wit, N., & Lehner, P. J. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkae1165 · Cited by 14

The dynamic genomes of Hydra and the anciently active repeat complement of animal chromosomes

Kon‐Nanjo, K., Kon, T., Koubková-Yu, T. C.-T., Rodriguez‐Terrones, D., Falcon, F., Martínez, D. E., Steele, R. E., Tanaka, E. M., Holstein, T. W., & Simakov, O. (2025) · Genome biology · doi:10.1186/s13059-025-03653-z · Cited by 17

Biallelic and gene-wide genomic substitution for endogenous intron and retroelement mutagenesis in human cells

Ohno, T., Akase, T., Kono, S., Kurasawa, H., Takashima, T., Kaneko, S., & Aizawa, Y. (2022) · Nature Communications · doi:10.1038/s41467-022-31982-1 · Cited by 14

Transposon dynamics in the emerging oilseed crop Thlaspi arvense

Contreras‐Garrido, A., Galanti, D., Movilli, A., Becker, C., Bossdorf, O., Drost, H., & Weigel, D. (2024) · PLoS Genetics · doi:10.1371/journal.pgen.1011141 · Cited by 14

Atypical epigenetic and small RNA control of degenerated transposons and their fragments in clonally reproducing Spirodela polyrhizaPreprint

Dombey, R., Buendía-Ávila, D., Barragán‐Borrero, V., Diezma‐Navas, L., Ponce-Mañe, A., Vargas-Guerrero, J. M., Elias, R., & Marí‐Ordóñez, A. (2025) · Genome Research · doi:10.1101/gr.279532.124 · Cited by 17

Evolution of Repetitive Elements, Their Roles in Homeostasis and Human Disease, and Potential Therapeutic Applications

Snowbarger, J. M., Koganti, P., & Spruck, C. (2024) · Biomolecules · doi:10.3390/biom14101250 · Cited by 14

Unveiling the hidden players: The crucial role of transposable elements in the placenta and their potential contribution to pre-eclampsia

Keighley, L. M., Lynch‐Sutherland, C. F., Almomani, S. N., Eccles, M. R., & Macaulay, E. C. (2023) · Placenta · doi:10.1016/j.placenta.2023.05.017 · Cited by 13

Genome-Wide Association Analysis of Freezing Tolerance and Winter Hardiness in Winter Wheat of Nordic Origin

Vaitkevičiūtė, G., Chawade, A., Lillemo, M., Liatukas, Ž., Aleliūnas, A., & Armonienė, R. (2023) · Plants · doi:10.3390/plants12234014 · Cited by 13

Lifestyles shape genome size and gene content in fungal pathogens

Fijarczyk, A., Hessenauer, P., Hamelin, R. C., & Landry, C. R. (2025) · eLife · doi:10.7554/elife.104975.4 · Cited by 13

Massive invasion of organellar DNA drives nuclear genome evolution in Toxoplasma

Namasivayam, S., Sun, C., Bah, A., Oberstaller, J., Pierre-Louis, E., Etheridge, R. D., Feschotte, C., Pritham, E. J., & Kissinger, J. C. (2023) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2308569120 · Cited by 13

Transposon accumulation at xenobiotic gene family loci in aphidsPreprint

Baril, T., Pym, A., Bass, C., & Hayward, A. (2023) · Genome Research · doi:10.1101/gr.277820.123 · Cited by 14

The potential role of the mobile and non-coding genomes in adaptive response

Godden, A. M., & Immler, S. (2022) · Trends in Genetics · doi:10.1016/j.tig.2022.08.006 · Cited by 12

Navigating the brain and aging: exploring the impact of transposable elements from health to disease

Breton, A. L., Bettencourt, M. P., & Gendrel, A.-V. (2024) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2024.1357576 · Cited by 12

Exploring the Relationship of Transposable Elements and Ageing: Causes and Consequences

Merenciano, M., Larue, A. E. A., Garambois, C., Nunes, W. V. B., & Vieira, C. P. (2025) · Genome Biology and Evolution · doi:10.1093/gbe/evaf088 · Cited by 15

Stage-specific transposon activity in the life cycle of the fairy-ring mushroom Marasmius oreades

Hiltunen, M., Ament‐Velásquez, S. L., Ryberg, M. K., & Johannesson, H. (2022) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2208575119 · Cited by 12

Replitrons: A major group of eukaryotic transposons encoding HUH endonuclease

Craig, R. J. (2023) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2301424120 · Cited by 13

Interplay between epigenome and 3D chromatin structure

Han, M.-H., Issagulova, D., & Park, M. (2023) · BMB Reports · doi:10.5483/bmbrep.2023-0197 · Cited by 13

Comprehensive identification of onco-exaptation events in bladder cancer cell lines revealed L1PA2-SYT1 as a prognosis-relevant event

Wang, Z., Ying, Y., Wang, M., Chen, Q., Wang, Y., Yu, X., He, W. A., Li, J., Zeng, S., & Xu, C. (2023) · iScience · doi:10.1016/j.isci.2023.108482 · Cited by 11

Combining EHMT and PARP Inhibition: A Strategy to Diminish Therapy-Resistant Ovarian Cancer Tumor Growth while Stimulating Immune Activation

Nguyen, L. L., Watson, Z. L., Ortega, R., Woodruff, E. R., Jordan, K. R., Iwanaga, R., Yamamoto, T. M., Bailey, C. A., To, F., Jeong, A. D., et al. (2024) · Molecular Cancer Therapeutics · doi:10.1158/1535-7163.mct-23-0613 · Cited by 11

IRescue: uncertainty-aware quantification of transposable elements expression at single cell level

Polimeni, B., Marasca, F., Ranzani, V., & Bodega, B. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkae793 · Cited by 11

LINE1 modulate human T cell function by regulating protein synthesis during the life span

Burattin, F. V., Vadalà, R., Panepuccia, M., Ranzani, V., Crosti, M., Colombo, F. A., Ruberti, C., Erba, E., Prati, D., Nittoli, T., et al. (2024) · Science Advances · doi:10.1126/sciadv.ado2134 · Cited by 12

Allotetraploid nature of a wild potato species, Solanum stoloniferum Schlechtd. et Bché., as revealed by whole‐genome sequencing

Hosaka, A., Sanetomo, R., & Hosaka, K. (2024) · The Plant Journal · doi:10.1111/tpj.17158 · Cited by 11

The reverse transcriptase domain of prime editors contributes to DNA repair in mammalian cells

Zheng, C., Zhang, G., Dean, L. J., Sontheimer, E. J., & Xue, W. (2025) · Nature Biotechnology · doi:10.1038/s41587-025-02568-1 · Cited by 14

Genetic basis of camouflage in an alpine plant and its long-term co-evolution with an insect herbivore

Zhang, H., Zhang, P., Niu, Y., Tao, T., Liu, G., Dong, C., Zheng, Z., Zhang, Z., Li, Y., Niu, Z., et al. (2025) · Nature Ecology & Evolution · doi:10.1038/s41559-025-02653-3 · Cited by 11

Taxonomy, Phylogeny, Genomes, and Repeatomes in the Subgenera Salvia, Sclarea, and Glutinaria (Salvia, Lamiaceae)

Kalnyuk, J. V., Yurkevich, O. Y., Дмитриевна, Б. Е., Semenov, A. R., Zoshchuk, S. A., Amosova, А. V., & Muravenko, O. V. (2025) · International Journal of Molecular Sciences · doi:10.3390/ijms26136436 · Cited by 11

Long-read detection of transposable element mobilization in the soma of hypomethylated Arabidopsis thaliana individuals

Movilli, A., Sushko, S., Rabanal, F. A., & Weigel, D. (2025) · Genome biology · doi:10.1186/s13059-025-03691-7 · Cited by 12

Synergistic epistasis of the deleterious effects of transposable elements

Lee, Y. C. G. (2021) · Genetics · doi:10.1093/genetics/iyab211 · Cited by 11

Comprehensive Analysis and Drug Modulation of Human Endogenous Retrovirus in Hepatocellular Carcinomas

Chang, Y., Hsu, M.-H., Chung, C., Chen, H.-D., Tu, S.-J., Lee, Y.-T., Yen, J.-C., Liu, T., & Chang, J. (2023) · Cancers · doi:10.3390/cancers15143664 · Cited by 12

A Quantitative, Genome-Wide Analysis in Drosophila Reveals Transposable Elements’ Influence on Gene Expression Is Species-Specific

Fablet, M., Salces-Ortiz, J., Jacquet, A., Menezes, B. F., Dechaud, C., Veber, P., Rebollo, R., & Vieira, C. P. (2023) · Genome Biology and Evolution · doi:10.1093/gbe/evad160 · Cited by 11

Accounting for diverse transposable element landscapes is key to developing and evaluating accurate de novo annotation strategies

Gozashti, L., & Hoekstra, H. E. (2024) · Genome biology · doi:10.1186/s13059-023-03118-1 · Cited by 12

AFM-based force spectroscopy unravels stepwise formation of the DNA transposition complex in the widespread Tn3 family mobile genetic elements

Fernandez, M., Shkumatov, A. V., Liu, Y., Stulemeijer, C., Derclaye, S., Efremov, R. G., Hallet, B., & Alsteens, D. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad241 · Cited by 10

Schistosome Transgenesis: The Long Road to Success

Kalinna, B. H., Ross, A. G., & Walduck, A. K. (2024) · Biology · doi:10.3390/biology13010048 · Cited by 10

Enhancer adoption by an LTR retrotransposon generates viral-like particles, causing developmental limb phenotypes

Glaser, J., Cova, G., Fauler, B., Prada‐Medina, C. A., Stanislas, V., Phan, M. H. Q., Schöpflin, R., Aktas, Y., Franke, M., Andrey, G., et al. (2025) · Nature Genetics · doi:10.1038/s41588-025-02248-5 · Cited by 11

Human Endogenous Retroviruses and Diseases

Chen, C., Cui, Y., Wang, S., Yang, Y., Liu, Z., Jin, S., Shen, F., Gaipl, U. S., Ma, H., & Zhou, J. (2025) · MedComm · doi:10.1002/mco2.70452 · Cited by 10

Extensive horizontal transfer of transposable elements shapes fungal mobilomes

Romeijn, J., Bañales, I., & Seidl, M. F. (2025) · Current Biology · doi:10.1016/j.cub.2025.11.012 · Cited by 10

Optimized R2 retroelement complexes for DNA insertion into plant genomes

Muchenje, K. T., McCombe, C. L., Wang, Y., Öz, M. T., Li, E., Saffron, A., & Demirer, G. S. (2026) · Nature Biotechnology · doi:10.1038/s41587-026-03197-y · Cited by 10

Shining Light on the Dark Side of the Genome

Wallrath, L. L., Rodríguez, F., & Geyer, P. (2022) · Cells · doi:10.3390/cells11030330 · Cited by 10

Temporal changes in transcripts of miniature inverted‐repeat transposable elements during rice endosperm development

Nagata, H., Ono, A., Tonosaki, K., Kawakatsu, T., Sato, Y., Yano, K., Kishima, Y., & Kinoshita, T. (2022) · The Plant Journal · doi:10.1111/tpj.15698 · Cited by 10

The widespread nature of Pack-TYPE transposons reveals their importance for plant genome evolution

Gisby, J., & Catoni, M. (2022) · PLoS Genetics · doi:10.1371/journal.pgen.1010078 · Cited by 10

Transposable Element Diversity Remains High in Gigantic Genomes

Haley, A., & Mueller, R. L. (2022) · Journal of Molecular Evolution · doi:10.1007/s00239-022-10063-3 · Cited by 10

Repeat-Induced Point Mutation and Gene Conversion Coinciding with Heterochromatin Shape the Genome of a Plant-Pathogenic Fungus

Komluski, J., Habig, M., & Stukenbrock, E. H. (2023) · mBio · doi:10.1128/mbio.03290-22 · Cited by 10

Retrotransposons and Telomeres

Kalmykova, A. I., & Sokolova, O. A. (2023) · Biochemistry (Moscow) · doi:10.1134/s0006297923110068 · Cited by 10

FHY3/FAR1 transposable elements generate adaptive genetic variation in the Bassia scoparia genome

Hall, N. D., Montgomery, J. S., Chen, J., Saski, C. A., Matzrafi, M., Westra, P. H., Gaines, T. A., & Patterson, E. L. (2025) · Pest Management Science · doi:10.1002/ps.8798 · Cited by 11

Locus-specific human endogenous retroviruses reveal lymphoma subtypes

Singh, B., Dopkins, N., Fei, T., Marston, J. L., Michael, S., Reyes-Gopar, H., Curty, G., Heymann, J. J., Chadburn, A., Martin, P., et al. (2025) · iScience · doi:10.1016/j.isci.2025.112541 · Cited by 11

Improved DNA-Versus-Protein Homology Search for Protein Fossils

Yin, Y., & Frith, M. C. (2022) · IEEE Transactions on Computational Biology and Bioinformatics · doi:10.1109/tcbb.2022.3177855 · Cited by 10

Dynamic co-evolution of transposable elements and the piRNA pathway in African cichlid fishes

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Developmental regulators moonlighting as transposons defense factors

Tan, K., & Wilkinson, M. (2023) · Andrology · doi:10.1111/andr.13427 · Cited by 9

Unraveling the role of satellite DNAs in the evolution of the giant XY sex chromosomes of the flea beetle Omophoita octoguttata (Coleoptera, Chrysomelidae)

Vidal, J. A. D., Charlesworth, D., Utsunomia, R., Garrido-Ramos, M. A., dos Santos, R. Z., Porto‐Foresti, F., Artoni, R. F., Liehr, T., Almeida, M. C., & Cioffi, M. D. B. (2025) · BMC Biology · doi:10.1186/s12915-025-02155-5 · Cited by 9

Satellite DNAs rising from the transposon graveyards

Šatović-Vukšić, E., Majcen, P., & Plohl, M. (2025) · DNA Research · doi:10.1093/dnares/dsaf026 · Cited by 9

Transposable Elements

KIDWELL, M. G. (2005) · Elsevier eBooks · doi:10.1016/b978-012301463-4/50005-x · Cited by 60

Conceptual and Empirical Investigations of Eukaryotic Transposable Element Evolution

Elliott, T. A. (2017) · The Atrium (University of Guelph) · doi:10.13140/rg.2.2.16651.49446 · Cited by 3

The Structural, Functional and Evolutionary Impact of Transposable Elements in Eukaryotes

Almojil, D., Bourgeois, Y., Falis, M., Hariyani, I. E., Wilcox, J. J. S., & Boissinot, S. (2021) · Genes · doi:10.3390/genes12060918 · Cited by 80

The genomes and transposable elements in plants: are they friends or foes?

Kim, N. (2017) · Genes & Genomics · doi:10.1007/s13258-017-0522-y · Cited by 23

Ten things you should know about transposable elements

Bourque, G., Burns, K. H., Gehring, M. A., Gorbunova, V., Seluanov, A., Hammell, M., Imbeault, M., Izsvák, Z., Levin, H. L., Macfarlan, T. S., et al. (2018) · Open Collections · doi:10.14288/1.0374202