From telomere to telomere: The transcriptional and epigenetic state of human repeat elements

Basic local alignment search tool

Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990) · Journal of Molecular Biology · doi:10.1006/jmbi.1990.9999 · Cited by 98,669 · see citing works

Fast gapped-read alignment with Bowtie 2

Langmead, B., & Salzberg, S. L. (2012) · Nature Methods · doi:10.1038/nmeth.1923 · Cited by 56,400 · see citing works

MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms

Kumar, S., Stecher, G., Li, M., Knyaz, C., & Tamura, K. (2018) · Molecular Biology and Evolution · doi:10.1093/molbev/msy096 · Cited by 37,683 · see citing works

Cutadapt removes adapter sequences from high-throughput sequencing reads

Martin, M. (2011) · EMBnet.journal · doi:10.14806/ej.17.1.200 · Cited by 33,889 · see citing works

A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences

Kimura, M. (1980) · Journal of Molecular Evolution · doi:10.1007/bf01731581 · Cited by 29,778 · see citing works

BEDTools: a flexible suite of utilities for comparing genomic features

Quinlan, A. R., & Hall, I. M. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq033 · Cited by 27,437 · see citing works

MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform

Katoh, K. (2002) · Nucleic Acids Research · doi:10.1093/nar/gkf436 · Cited by 17,027 · see citing works

jModelTest 2: more models, new heuristics and parallel computing

Darriba, D., Taboada, G. L., Doallo, R., & Posada, D. (2012) · Nature Methods · doi:10.1038/nmeth.2109 · Cited by 16,828 · see citing works

Minimap2: Pairwise alignment for nucleotide sequences

Li, H. (2018) · Bioinformatics · doi:10.1093/bioinformatics/bty191 · Cited by 14,807 · see citing works

APE: Analyses of Phylogenetics and Evolution in R language

Paradis, E., Claude, J., & Strimmer, K. (2004) · Bioinformatics · doi:10.1093/bioinformatics/btg412 · Cited by 12,037 · see citing works

Circos: An information aesthetic for comparative genomicsPreprint

Krzywinski, M. I., Schein, J. E., Birol, İ., Connors, J. M., Gascoyne, R. D., Horsman, D. E., Jones, S. J. M., & Marra, M. A. (2009) · Genome Research · doi:10.1101/gr.092759.109 · Cited by 10,838 · see citing works

Tandem repeats finder: a program to analyze DNA sequences

Benson, G. (1999) · Nucleic Acids Research · doi:10.1093/nar/27.2.573 · Cited by 9,374 · see citing works

MUSCLE: a multiple sequence alignment method with reduced time and space complexity

Edgar, R. C. (2004) · BMC Bioinformatics · doi:10.1186/1471-2105-5-113 · Cited by 8,879 · see citing works

deepTools2: a next generation web server for deep-sequencing data analysis

Ramírez, F., Ryan, D. P., Grüning, B., Bhardwaj, V., Kilpert, F., Richter, A. S., Heyne, S., Dündar, F., & Manke, T. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw257 · Cited by 8,096 · see citing works

Molecular Evolution and Phylogenetics

Nei, M., & Kumar, S. (2000) · doi:10.1093/oso/9780195135848.001.0001 · Cited by 8,012 · see citing works

Human DNA methylomes at base resolution show widespread epigenomic differences

Lister, R., Pelizzola, M., Dowen, R. H., Hawkins, R. D., Hon, G., Tonti-Filippini, J., Nery, J. R., Lee, L., Ye, Z., Ngo, Q.-M., et al. (2009) · Nature · doi:10.1038/nature08514 · Cited by 4,673 · see citing works

RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference

Kozlov, A. M., Darriba, D., Flouri, T., Morel, B., & Stamatakis, A. (2019) · Bioinformatics · doi:10.1093/bioinformatics/btz305 · Cited by 4,294 · see citing works

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 · see citing works

Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies

Rhie, A., Walenz, B. P., Koren, S., & Phillippy, A. M. (2020) · Genome Biology · doi:10.1186/s13059-020-02134-9 · Cited by 3,643 · see citing works

The complete sequence of a human genome

Nurk, S., Koren, S., Rhie, A., Rautiainen, M., Bzikadze, A. V., Mikheenko, A., Vollger, M. R., Altemose, N., Uralsky, L., Gershman, A., et al. (2022) · Science · doi:10.1126/science.abj6987 · Cited by 3,136 · see citing works

Shifting the limits in wheat research and breeding using a fully annotated reference genome

Appels, R., Eversole, K., Stein, N., Feuillet, C., Keller, B., Rogers, J., Pozniak, C. J., Choulet, F., Distelfeld, A., Poland, J., et al. (2018) · Science · doi:10.1126/science.aar7191 · Cited by 3,107 · see citing works

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 3,021 · see citing works

mclust 5: Clustering, Classification and Density Estimation Using Gaussian Finite Mixture Models

Scrucca, L., Fop, M., Murphy, T. B., & Adrian, E. R. (2016) · The R Journal · doi:10.32614/rj-2016-021 · Cited by 2,914 · see citing works

Spatial partitioning of the regulatory landscape of the X-inactivation centre

Nora, E. P., Lajoie, B. R., Schulz, E. G., Giorgetti, L., Okamoto, I., Servant, N., Piolot, T., van Berkum, N. L., Meisig, J., Sedat, J., et al. (2012) · Nature · doi:10.1038/nature11049 · Cited by 2,895 · see citing works

Cytosine methylation and the ecology of intragenomic parasites

Yoder, J. A., Walsh, C. P., & Bestor, T. H. (1997) · Trends in Genetics · doi:10.1016/s0168-9525(97)01181-5 · Cited by 1,941 · see citing works

Molecular Evolutionary Genetics Analysis (MEGA) for macOS

Stecher, G., Tamura, K., & Kumar, S. (2019) · Molecular Biology and Evolution · doi:10.1093/molbev/msz312 · Cited by 1,885 · see citing works

The origin and behavior of mutable loci in maize

McClintock, B. (1950) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.36.6.344 · Cited by 1,752 · see citing works

The UCSC Genome Browser Database: update 2006

Hinrichs, A. S. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkj144 · Cited by 1,646 · see citing works

LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons

Ellinghaus, D., Kurtz, S., & Willhoeft, U. (2008) · BMC Bioinformatics · doi:10.1186/1471-2105-9-18 · Cited by 1,623 · see citing works

Identification of Genes Periodically Expressed in the Human Cell Cycle and Their Expression in Tumors

Whitfield, M. L., Sherlock, G., Saldanha, A. J., Murray, J. I., Ball, C. A., Alexander, K. E., Matese, J. C., Perou, C. M., Hurt, M. M., Brown, P. O., et al. (2002) · Molecular Biology of the Cell · doi:10.1091/mbc.02-02-0030 · Cited by 1,527 · see citing works

Regulatory activities of transposable elements: from conflicts to benefits

Chuong, E. B., Elde, N. C., & Feschotte, C. (2016) · Nature Reviews Genetics · doi:10.1038/nrg.2016.139 · Cited by 1,343 · see citing works

Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells

Ball, M. P., Li, J. B., Gao, Y., Lee, J., LeProust, E. M., Park, I., Xie, B., Daley, G. Q., & Church, G. M. (2009) · Nature Biotechnology · doi:10.1038/nbt.1533 · Cited by 1,087 · see citing works

Hot L1s account for the bulk of retrotransposition in the human population

Brouha, B., Schustak, J., Badge, R. M., Lutz-Prigge, S., Farley, A. H., Moran, J. V., & Kazazian, H. H. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0831042100 · Cited by 1,073 · see citing works

Earth BioGenome Project: Sequencing life for the future of life

Lewin, H. A., Robinson, G. E., Kress, W. J., Baker, W. J., Coddington, J., Crandall, K. A., Durbin, R., Edwards, S. V., Forest, F., Gilbert, M. T. P., et al. (2018) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1720115115 · Cited by 962 · see citing works

Precise Maps of RNA Polymerase Reveal How Promoters Direct Initiation and Pausing

Kwak, H., Fuda, N. J., Core, L. J., & Lis, J. T. (2013) · Science · doi:10.1126/science.1229386 · Cited by 849 · see citing works

Resolving the complexity of the human genome using single-molecule sequencing

Chaisson, M., Huddleston, J., Dennis, M. Y., Sudmant, P. H., Malig, M., Hormozdiari, F., Antonacci, F., Surti, U., Sandstrom, R. S., Boitano, M., et al. (2014) · Nature · doi:10.1038/nature13907 · Cited by 783 · see citing works

The Dfam database of repetitive DNA families

Hubley, R. M., Finn, R. D., Clements, J., Eddy, S. R., Jones, T. A., Bao, W., Smit, A. F. A., & Wheeler, T. J. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv1272 · Cited by 768 · see citing works

Telomere-to-telomere assembly of a complete human X chromosome

Miga, K. H., Koren, S., Rhie, A., Vollger, M. R., Gershman, A., Bzikadze, A., Brooks, S., Howe, E., Porubsky, D., Logsdon, G. A., et al. (2020) · Nature · doi:10.1038/s41586-020-2547-7 · Cited by 765 · see citing works

The Dfam community resource of transposable element families, sequence models, and genome annotations

Storer, J. M., Hubley, R. M., Rosen, J. R., Wheeler, T. J., & Smit, A. F. A. (2021) · Mobile DNA · doi:10.1186/s13100-020-00230-y · Cited by 752 · see citing works

KMC 3: counting and manipulating k‐mer statistics

Kokot, M., Dlugosz, M., & Deorowicz, S. (2017) · Bioinform. · doi:10.1093/bioinformatics/btx304 · Cited by 720 · see citing works

Haplotype-resolved diverse human genomes and integrated analysis of structural variation

Ebert, P., Audano, P. A., Zhu, Q., Rodriguez-Martin, B., Porubsky, D., Bonder, M. J., Sulovari, A., Ebler, J., Zhou, W., Serra Mari, R., et al. (2021) · Science · doi:10.1126/science.abf7117 · Cited by 702 · see citing works

Chromosome 4q DNA rearrangements associated with facioscapulohumeral muscular dystrophy

Wijmenga, C., Hewitt, J., Sandkuijl, L. A., Clark, L. N., Wright, T. J., Dauwerse, H. G., Gruter, A.-M., Hofker, M. H., Moerer, P., Williamson, R., et al. (1992) · Nature Genetics · doi:10.1038/ng0992-26 · Cited by 689 · see citing works

Roles for retrotransposon insertions in human disease

Hancks, D. C., & Kazazian, H. H. (2016) · Mobile DNA · doi:10.1186/s13100-016-0065-9 · Cited by 670 · see citing works

RNA contributions to the form and function of biomolecular condensates

Roden, C., & Gladfelter, A. S. (2020) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-020-0264-6 · Cited by 668 · see citing works

Propagation of centromeric chromatin requires exit from mitosis

Jansen, L. E. T., Black, B. E., Foltz, D. R., & Cleveland, D. W. (2007) · The Journal of Cell Biology · doi:10.1083/jcb.200701066 · Cited by 630 · see citing works

Exon Shuffling by L1 Retrotransposition

Moran, J. V., DeBerardinis, R. J., & Kazazian, H. H. (1999) · Science · doi:10.1126/science.283.5407.1530 · Cited by 629 · see citing works

Complete genomic and epigenetic maps of human centromeres

Altemose, N., Logsdon, G. A., Bzikadze, A. V., Sidhwani, P., Langley, S. A., Caldas, G. V., Hoyt, S. J., Uralsky, L., Ryabov, F. D., Shew, C. J., et al. (2022) · Science · doi:10.1126/science.abl4178 · Cited by 618 · see citing works

LINE-1 elements in structural variation and disease

Beck, C. R., Garcia-Perez, J. L., Badge, R. M., & Moran, J. V. (2011) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-082509-141802 · Cited by 615 · see citing works

A novel role for Xist RNA in the formation of a repressive nuclear compartment into which genes are recruited when silencedPreprint

Chaumeil, J., Baccon, P. L., Wutz, A., & Heard, É. (2006) · Genes & Development · doi:10.1101/gad.380906 · Cited by 530 · see citing works

RIdeogram : drawing SVG graphics to visualize and map genome-wide data on the idiograms

Hao, Z., Lv, D., Ge, Y., Shi, J., Weijers, D., Yu, G., & Chen, J. (2020) · PeerJ Computer Science · doi:10.7717/peerj-cs.251 · Cited by 529 · see citing works

Gene number, noise reduction and biological complexity.

Bird, A. (1995) · Trends in Genetics · doi:10.1016/s0168-9525(00)89009-5 · Cited by 504 · see citing works

Genomic and Genetic Definition of a Functional Human Centromere

Schueler, M. G., Higgins, A. W., Rudd, M. K., Gustashaw, K. M., & Willard, H. F. (2001) · Science · doi:10.1126/science.1065042 · Cited by 504 · see citing works

A universal classification of eukaryotic transposable elements implemented in Repbase

Kapitonov, V. V., & Jurka, J. (2008) · Nature Reviews Genetics · doi:10.1038/nrg2165-c1 · Cited by 497 · see citing works

Base-pair-resolution genome-wide mapping of active RNA polymerases using precision nuclear run-on (PRO-seq)

Mahat, D. B., Kwak, H., Booth, G. T., Jonkers, I. H., Danko, C. G., Patel, R. K., Waters, C. T., Munson, K. M., Core, L. J., & Lis, J. T. (2016) · Nature Protocols · doi:10.1038/nprot.2016.086 · Cited by 492 · see citing works

X-Chromosome inactivation: a repeat hypothesis

Lyon, M. F. (1998) · Cytogenetic and Genome Research · doi:10.1159/000014969 · Cited by 465 · see citing works

Undermethylation associated with retroelement activation and chromosome remodelling in an interspecific mammalian hybrid

O'Neill, R. J. W., O’Neill, M. J., & Graves, J. A. M. (1998) · Nature · doi:10.1038/29985 · Cited by 457 · see citing works

Functional Rice Centromeres Are Marked by a Satellite Repeat and a Centromere-Specific Retrotransposon

Cheng, Z., Dong, F., Langdon, T., Ouyang, S., Buell, C. R., Gu, M., Blattner, F. R., & Jiang, J. (2002) · The Plant Cell · doi:10.1105/tpc.003079 · Cited by 440 · see citing works

Identification, Characterization, and Cell Specificity of a Human LINE-1 Promoter

Swergold, G. D. (1990) · Molecular and Cellular Biology · doi:10.1128/mcb.10.12.6718 · Cited by 439 · see citing works

Extensive transduction of nonrepetitive DNA mediated by L1 retrotransposition in cancer genomes

Tubio, J. M. C., Li, Y., Ju, Y. S., Martincorena, I., Cooke, S. L., Tojo, M., Gundem, G., Pipinikas, C. P., Zamora, J., Raine, K., et al. (2014) · Science · doi:10.1126/science.1251343 · Cited by 412 · see citing works

Centromeric Retroelements and Satellites Interact with Maize Kinetochore Protein CENH3

Zhong, C. X., Marshall, J. B., Topp, C. N., Mroczek, R. J., Kato, A., Nagaki, K., Birchler, J. A., Jiang, J., & Dawe, R. K. (2002) · The Plant Cell · doi:10.1105/tpc.006106 · Cited by 401 · see citing works

Ancestral, Mammalian-wide Subfamilies of LINE-1 Repetitive Sequences

Smit, A. F. A., Tóth, G. J., Riggs, A. D., & Jurka, J. (1995) · Journal of Molecular Biology · doi:10.1006/jmbi.1994.0095 · Cited by 384 · see citing works

YASS: enhancing the sensitivity of DNA similarity search

Noé, L., & Kucherov, G. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki478 · Cited by 374 · see citing works

Molecular evolution and tempo of amplification of human LINE-1 retrotransposons since the origin of primatesPreprint

Khan, H., Smit, A. F. A., & Boissinot, S. (2005) · Genome Research · doi:10.1101/gr.4001406 · Cited by 369 · see citing works

SVA Elements: A Hominid-specific Retroposon Family

Wang, H., Xing, J., Grover, D., Hedges, D. J., Han, K., Walker, J. A., & Batzer, M. A. (2005) · Journal of Molecular Biology · doi:10.1016/j.jmb.2005.09.085 · Cited by 367 · see citing works

Insertional polymorphisms of full-length endogenous retroviruses in humans

Turner, G., Barbulescu, M., Su, M., Jensen-Seaman, M. I., Kidd, K. K., & Lenz, J. (2001) · Current Biology · doi:10.1016/s0960-9822(01)00455-9 · Cited by 358 · see citing works

The Mobile Element Locator Tool (MELT): population-scale mobile element discovery and biologyPreprint

Gardner, E. J., Lam, V. K. L., Harris, D., Chuang, N. T., Scott, E., Pittard, W. S., Mills, R. E., & Devine, S. E. (2017) · Genome Research · doi:10.1101/gr.218032.116 · Cited by 358 · see citing works

High-resolution comparative analysis of great ape genomes

Kronenberg, Z. N., Fiddes, I. T., Gordon, D., Murali, S., Cantsilieris, S., Meyerson, O. S., Underwood, J. G., Nelson, B. J., Chaisson, M. J. P., Dougherty, M. L., et al. (2018) · Science · doi:10.1126/science.aar6343 · Cited by 350 · see citing works

Segmental duplications and their variation in a complete human genome

Vollger, M. R., Guitart, X., Dishuck, P. C., Mercuri, L., Harvey, W. T., Gershman, A., Diekhans, M., Sulovari, A., Munson, K. M., Lewis, A. P., et al. (2022) · Science · doi:10.1126/science.abj6965 · Cited by 350 · see citing works

Long-read sequence assembly of the gorilla genome

Gordon, D., Huddleston, J., Chaisson, M. J. P., Hill, C. M., Kronenberg, Z. N., Munson, K. M., Malig, M., Raja, A., Fiddes, I., Hillier, L. W., et al. (2016) · Science · doi:10.1126/science.aae0344 · Cited by 333 · see citing works

Analysis of the tandem repeat locus D4Z4 associated with facioscapulohumeral muscular dystropothhy

Hewitt, J., Lyle, R., Clark, L. N., Valleley, E. M. A., Wright, T. J., Wijmenga, C., van Deutekom, J. C. T., Francis, F., Sharpe, P. T., Hofker, M. H., et al. (1994) · Human Molecular Genetics · doi:10.1093/hmg/3.8.1287 · Cited by 332 · see citing works

LINE-1 Activity in Facultative Heterochromatin Formation during X Chromosome Inactivation

Chow, J., Ciaudo, C., Fazzari, M. J., Mise, N., Servant, N., Glass, J. L., Attreed, M., Avner, P. R., Wutz, A., Barillot, E., et al. (2010) · Cell · doi:10.1016/j.cell.2010.04.042 · Cited by 326 · see citing works

The structure, function and evolution of a complete human chromosome 8

Logsdon, G. A., Vollger, M. R., Hsieh, P., Mao, Y., Liskovykh, M. A., Koren, S., Nurk, S., Mercuri, L., Dishuck, P. C., Rhie, A., et al. (2021) · Nature · doi:10.1038/s41586-021-03420-7 · Cited by 326 · see citing works

Mobile elements create structural variation: Analysis of a complete human genomePreprint

Xing, J., Zhang, Y., Han, K., Salem, A. H., Sen, S. K., Huff, C., Zhou, Q., Kirkness, E. F., Levy, S., Batzer, M. A., et al. (2009) · Genome Research · doi:10.1101/gr.091827.109 · Cited by 313 · see citing works

Dfam: a database of repetitive DNA based on profile hidden Markov models

Wheeler, T. J., Clements, J., Eddy, S. R., Hubley, R. M., Jones, T. A., Jurka, J., Smit, A. F. A., & Finn, R. D. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks1265 · Cited by 306 · see citing works

Long Terminal Repeats: From Parasitic Elements to Building Blocks of the Transcriptional Regulatory Repertoire

Thompson, P. J., Macfarlan, T. S., & Lorincz, M. C. (2016) · Molecular Cell · doi:10.1016/j.molcel.2016.03.029 · Cited by 301 · see citing works

Epigenetic patterns in a complete human genome

Gershman, A., Sauria, M. E. G., Guitart, X., Vollger, M. R., Hook, P. W., Hoyt, S. J., Jain, M., Shumate, A., Razaghi, R., Koren, S., et al. (2022) · Science · doi:10.1126/science.abj5089 · Cited by 297 · see citing works

Hominoid-Specific Transposable Elements and KZFPs Facilitate Human Embryonic Genome Activation and Control Transcription in Naive Human ESCs

Pontis, J., Planet, E., Offner, S. E., Turelli, P., Duc, J., Coudray, A., Theunissen, T. W., Jaenisch, R., & Trono, D. (2019) · Cell stem cell · doi:10.1016/j.stem.2019.03.012 · Cited by 293 · see citing works

Frequent Human Genomic DNA Transduction Driven by LINE-1 RetrotranspositionPreprint

Pickeral, O. K., Makałowski, W., Boguski, M. S., & Boeke, J. D. (2000) · Genome Research · doi:10.1101/gr.10.4.411 · Cited by 279 · see citing works

Global DNA demethylation in gastrointestinal cancer is age dependent and precedes genomic damage

Suzuki, K., Suzuki, I., Leodolter, A., Alonso, S., Horiuchi, S., Yamashita, K., & Perucho, M. (2006) · Cancer Cell · doi:10.1016/j.ccr.2006.02.016 · Cited by 267 · see citing works

Transduction of 3'-flanking sequences is common in L1 retrotransposition

Goodier, J. L. (2000) · Human Molecular Genetics · doi:10.1093/hmg/9.4.653 · Cited by 266 · see citing works

Adaptation and conservation insights from the koala genome

Johnson, R. N., O’Meally, D., Chen, Z., Etherington, G., Ho, S. Y. W., Nash, W. J., Grueber, C. E., Cheng, Y., Whittington, C. M., Dennison, S., et al. (2018) · Nature Genetics · doi:10.1038/s41588-018-0153-5 · Cited by 253 · see citing works

Birth of a chimeric primate gene by capture of the transposase gene from a mobile element

Cordaux, R., Udit, S., Batzer, M. A., & Feschotte, C. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0601161103 · Cited by 252 · see citing works

Nascent RNA analyses: tracking transcription and its regulation

Wissink, E. M., Vihervaara, A., Tippens, N. D., & Lis, J. T. (2019) · Nature Reviews Genetics · doi:10.1038/s41576-019-0159-6 · Cited by 247 · see citing works

ATY3/GYPSYretrotransposon‐like sequence localizes to the centromeric regions of cereal chromosomes

Presting, G. G., Malysheva, L., Fuchs, J., & Schubert, I. A. (1998) · The Plant Journal · doi:10.1046/j.1365-313x.1998.00341.x · Cited by 243 · see citing works

Repetitive centromeric satellite RNA is essential for kinetochore formation and cell division

Rošić, S., Köhler, F., & Erhardt, S. (2014) · The Journal of Cell Biology · doi:10.1083/jcb.201404097 · Cited by 242 · see citing works

Human-Specific Integrations of the HERV-K Endogenous Retrovirus Family

Medstrand, P., & Mager, D. L. (1998) · Journal of Virology · doi:10.1128/jvi.72.12.9782-9787.1998 · Cited by 236 · see citing works

The non-autonomous retrotransposon SVA is trans -mobilized by the human LINE-1 protein machinery

Raiz, J., Damert, A., Chira, S., Held, U., Jung‐Klawitter, S., Hamdorf, M., Löwer, J., Strätling, W. H., Löwer, R., & Schumann, G. G. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr863 · Cited by 235 · see citing works

Evolutionary history of 7SL RNA-derived SINEs in Supraprimates

Kriegs, J. O., Churakov, G., Jurka, J., Brosius, J., & Schmitz, J. (2007) · Trends in Genetics · doi:10.1016/j.tig.2007.02.002 · Cited by 234 · see citing works

Transposable elements: genome innovation, chromosome diversity, and centromere conflict

Klein, S. J., & O'Neill, R. J. W. (2018) · Chromosome Research · doi:10.1007/s10577-017-9569-5 · Cited by 222 · see citing works

G4Hunter web application: a web server for G-quadruplex prediction

Brázda, V., Kolomazník, J., Lýsek, J., Bartas, M., Fojta, M., Šťastný, J., & Mergny, J. (2019) · Bioinform. · doi:10.1093/bioinformatics/btz087 · Cited by 202 · see citing works

SVA retrotransposons: Evolution and genetic instability

Hancks, D. C., & Kazazian, H. H. (2010) · Seminars in Cancer Biology · doi:10.1016/j.semcancer.2010.04.001 · Cited by 197 · see citing works

Structure and genetics of the partially duplicated gene RP located immediately upstream of the complement C4A and the C4B genes in the HLA class III region. Molecular cloning, exon-intron structure, composite retroposon, and breakpoint of gene duplication.

Shen, L., Wu, L., Şanlıoğlu, S., Chen, R., Mendoza, A. R., Dangel, A. W., Carroll, M. C., Zipf, W. B., & Yu, C. Y. (1994) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(17)37217-4 · Cited by 196 · see citing works

Repetitive centromeric satellite RNA is essential for kinetochore formation and cell division

Rošić, S., Köhler, F., & Erhardt, S. (2014) · The Journal of Cell Biology · doi:10.1083/jcb.20140409711122014c · Cited by 195 · see citing works

Retrotransposition of marked SVA elements by human L1s in cultured cells

Hancks, D. C., Goodier, J. L., Mandal, P. K., Cheung, L. E., & Kazazian, H. H. (2011) · Human Molecular Genetics · doi:10.1093/hmg/ddr245 · Cited by 191 · see citing works

Human Centromeres Produce Chromosome-Specific and Array-Specific Alpha Satellite Transcripts that Are Complexed with CENP-A and CENP-C

McNulty, S. M., Sullivan, L. L., & Sullivan, B. A. (2017) · Developmental Cell · doi:10.1016/j.devcel.2017.07.001 · Cited by 181 · see citing works

A functional role for Tsix transcription in blocking Xist RNA accumulation but not in X-chromosome choice

Stavropoulos, N., Lu, N., & Lee, J. T. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.171243598 · Cited by 178 · see citing works

Stabilization of quadruplex DNA perturbs telomere replication leading to the activation of an ATR-dependent ATM signaling pathway

Rizzo, A., Salvati, E., Porru, M., D’Angelo, C., Stevens, M. F. G., D’Incalci, M., Leonetti, C., Gilson, É., Zupi, G., & Biroccio, A. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp582 · Cited by 176 · see citing works

Emergence of primate genes by retrotransposon-mediated sequence transduction

Xing, J., Wang, H., Belancio, V. P., Cordaux, R., Deininger, P. L., & Batzer, M. A. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0603224103 · Cited by 170 · see citing works

The complete sequence of a human genomePreprint

Nurk, S., Koren, S., Rhie, A., Rautiainen, M., Bzikadze, A. V., Mikheenko, A., Vollger, M. R., Altemose, N., Uralsky, L. I., Gershman, A., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.05.26.445798 · Cited by 169 · see citing works

LINE Retrotransposon RNA Is an Essential Structural and Functional Epigenetic Component of a Core Neocentromeric Chromatin

Chüeh, A. C., Northrop, E. L., Brettingham‐Moore, K. H., Choo, K. H. A., & Wong, L. H. (2009) · PLoS Genetics · doi:10.1371/journal.pgen.1000354 · Cited by 165 · see citing works

Analysis of the largest tandemly repeated DNA families in the human genome

Warburton, P. E., Hasson, D., Guillem, F., Lescale, C., Jin, X., & Abrusán, G. (2008) · BMC Genomics · doi:10.1186/1471-2164-9-533 · Cited by 164 · see citing works

RNA-dependent stabilization of SUV39H1 at constitutive heterochromatin

Johnson, W. L., Yewdell, W. T., Bell, J. C., McNulty, S. M., Duda, Z., O'Neill, R. J. W., Sullivan, B. A., & Straight, A. F. (2017) · eLife · doi:10.7554/elife.25299 · Cited by 162 · see citing works

Viruses and mobile elements as drivers of evolutionary transitions

Koonin, E. V. (2016) · Philosophical Transactions of the Royal Society B: Biological Sciences · doi:10.1098/rstb.2015.0442 · Cited by 161 · see citing works

StainedGlass: interactive visualization of massive tandem repeat structures with identity heatmaps

Vollger, M. R., Kerpedjiev, P., Phillippy, A. M., & Eichler, E. E. (2022) · Bioinformatics · doi:10.1093/bioinformatics/btac018 · Cited by 161 · see citing works

A survey of transposable element classification systems – A call for a fundamental update to meet the challenge of their diversity and complexity

Piégu, B., Bire, S., Arensburger, P., & Bigot, Y. (2015) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2015.03.009 · Cited by 160 · see citing works

L1 (LINE-1) retrotransposon diversity differs dramatically between mammals and fish

Furano, A. V. (2003) · Trends in Genetics · doi:10.1016/j.tig.2003.11.006 · Cited by 157 · see citing works

ALU ternative Regulation for Gene Expression

Chen, L., & Yang, L. C. (2017) · Trends in Cell Biology · doi:10.1016/j.tcb.2017.01.002 · Cited by 152 · see citing works

Independent amylase gene copy number bursts correlate with dietary preferences in mammals

Pajic, P., Pavlidis, P., Dean, K., Neznanova, L., Daugherity, E. K., Romano, R.-A., Garneau, D., Globig, A., Rühl, S., & Gökçümen, Ö. (2019) · eLife · doi:10.7554/elife.44628 · Cited by 138 · see citing works

Patterns of Segmental Duplication in the Human Genome

Zhang, L. (2004) · Molecular Biology and Evolution · doi:10.1093/molbev/msh262 · Cited by 129 · see citing works

Centromere transcription allows CENP-A to transit from chromatin association to stable incorporation

Bobkov, G. O. M., Gilbert, N., & Heun, P. (2018) · The Journal of Cell Biology · doi:10.1083/jcb.201611087 · Cited by 125 · see citing works

Chasing perfection: validation and polishing strategies for telomere-to-telomere genome assemblies

Cartney, A. M. M., Shafin, K., Alonge, M., Bzikadze, A. V., Formenti, G., Fungtammasan, A., Howe, K., Jain, C., Koren, S., Logsdon, G. A., et al. (2022) · Nature Methods · doi:10.1038/s41592-022-01440-3 · Cited by 124 · see citing works

Establishment of Centromeric Chromatin by the CENP-A Assembly Factor CAL1 Requires FACT-Mediated Transcription

Chen, C.-C., Bowers, S. R., Lipinszki, Z., Palladino, J., Trusiak, S., Bettini, E., Rosin, L. F., Przewloka, M. R., Glover, D. M., O'Neill, R. J. W., et al. (2015) · Developmental Cell · doi:10.1016/j.devcel.2015.05.012 · Cited by 120 · see citing works

5′-Transducing SVA retrotransposon groups spread efficiently throughout the human genomePreprint

Damert, A., Raiz, J., Horn, A. V., Löwer, J., Wang, H., Xing, J., Batzer, M. A., Löwer, R., & Schumann, G. G. (2009) · Genome Research · doi:10.1101/gr.093435.109 · Cited by 117 · see citing works

Islands of retroelements are major components of Drosophila centromeres

Chang, C.-H., Chavan, A., Palladino, J., Wei, X.-L., Martins, N. M. C., Santinello, B., Chen, C.-C., Erceg, J., Beliveau, B. J., Wu, C.-T., et al. (2019) · PLoS Biology · doi:10.1371/journal.pbio.3000241 · Cited by 117 · see citing works

LINEs and SINEs of primate evolution

Konkel, M. K., Walker, J. A., & Batzer, M. A. (2010) · Evolutionary Anthropology Issues News and Reviews · doi:10.1002/evan.20283 · Cited by 110 · see citing works

High variability of genomic instability and gene expression profiling in different HeLa clones

Frattini, A., Fabbri, M., Valli, R., De Paoli, E., Montalbano, G., Gribaldo, L., Pasquali, F., & Maserati, E. (2015) · Scientific Reports · doi:10.1038/srep15377 · Cited by 109 · see citing works

A Novel Correlation between LINE-1 Hypomethylation and the Malignancy of Gastrointestinal Stromal Tumors

Igarashi, S., Suzuki, H., Niinuma, T., Shimizu, H., Nojima, M., Iwaki, H., Nobuoka, T., Nishida, T., Miyazaki, Y., Takamaru, H., et al. (2010) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-10-0581 · Cited by 92 · see citing works

How independent are the appearances of n-mers in different genomes?

Fofanov, Y., Luo, Y., Katili, C., Wang, J. J., Belosludtsev, Y. Y., Powdrill, T. F., Belapurkar, C., Fofanov, V. Y., Li, T.-B., Chumakov, S. M., et al. (2004) · Bioinformatics · doi:10.1093/bioinformatics/bth266 · Cited by 92 · see citing works

Sequence Features and Transcriptional Stalling within Centromere DNA Promote Establishment of CENP-A Chromatin

Catania, S., Pidoux, A. L., & Allshire, R. C. (2015) · PLoS Genetics · doi:10.1371/journal.pgen.1004986 · Cited by 91 · see citing works

FlexiDot: highly customizable, ambiguity-aware dotplots for visual sequence analyses

Seibt, K. M., Schmidt, T., & Heitkam, T. (2018) · Bioinformatics · doi:10.1093/bioinformatics/bty395 · Cited by 87 · see citing works

Variable and hierarchical size distribution of L1-retroelement-enriched CENP-A clusters within a functional human neocentromere

Chüeh, A. C., Wong, L. H., Wong, N. C., & Choo, K. H. A. (2004) · Human Molecular Genetics · doi:10.1093/hmg/ddi008 · Cited by 85 · see citing works

Identification, Characterization, and Cell Specificity of a Human LINE-1 Promoter

Swergold, G. D. (1990) · Molecular and Cellular Biology · doi:10.1128/mcb.10.12.6718-6729.1990 · Cited by 80 · see citing works

Species-specific shifts in centromere sequence composition are coincident with breakpoint reuse in karyotypically divergent lineages

Bulazel, K. V., Ferreri, G. C., Eldridge, M. D. B., & O'Neill, R. J. W. (2007) · Genome biology · doi:10.1186/gb-2007-8-8-r170 · Cited by 79 · see citing works

Ancient exapted transposable elements promote nuclear enrichment of human long noncoding RNAsPreprint

Carlevaro-Fita, J., Polidori, T., Das, M., Navarro, C., Zoller, T. I., & Johnson, R. (2018) · Genome Research · doi:10.1101/gr.229922.117 · Cited by 78 · see citing works

Hybrid de novo genome assembly and centromere characterization of the gray mouse lemur (Microcebus murinus)

Larsen, P. A., Harris, R. A., Liu, Y., Murali, S. C., Campbell, C. R., Brown, A., Sullivan, B. A., Shelton, J. M., Brown, S. J., Raveendran, M., et al. (2017) · BMC Biology · doi:10.1186/s12915-017-0439-6 · Cited by 72 · see citing works

The bipartite TAD organization of the X-inactivation center ensures opposing developmental regulation of Tsix and Xist

van Bemmel, J. V., Galupa, R., Gard, C., Servant, N., Picard, C., Davies, J., Szempruch, A., Zhan, Y., Żylicz, J. J., Nora, E. P., et al. (2019) · Nature Genetics · doi:10.1038/s41588-019-0412-0 · Cited by 71 · see citing works

Different evolutionary fates of recently integrated human and chimpanzee LINE-1 retrotransposons

Lee, J., Cordaux, R., Han, K., Wang, J., Hedges, D. J., Liang, P., & Batzer, M. A. (2006) · Gene · doi:10.1016/j.gene.2006.08.029 · Cited by 70 · see citing works

Long-read assembly of the Chinese rhesus macaque genome and identification of ape-specific structural variants

He, Y.-X., Luo, X., Zhou, B., Hu, T., Meng, X., Audano, P., Kronenberg, Z., Eichler, E., Jin, J., Guo, Y., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-12174-w · Cited by 70 · see citing works

A rapid, sensitive, scalable method for Precision Run-On sequencing (PRO-seq)Preprint

Judd, J., Wojenski, L., Wainman, L. M., Tippens, N. D., Rice, E. J., Dziubek, A., Villafano, G. J., Wissink, E. M., Versluis, P. P., Bagepalli, L., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.05.18.102277 · Cited by 69 · see citing works

Identification and characterization of satellite III subfamilies to the acrocentric chromosomes

Bandyopadhyay, R., McQuillan, C. I., Page, S. L., Choo, K. H. A., & Shaffer, L. G. (2001) · Chromosome Research · doi:10.1023/a:1016648404388 · Cited by 68 · see citing works

Centromere Remodeling in Hoolock leuconedys (Hylobatidae) by a New Transposable Element Unique to the Gibbons

Carbone, L., Harris, R. A., Mootnick, A. R., Milosavljevic, A., Martin, D. I. K., Rocchi, M., Capozzi, O., Archidiacono, N., Konkel, M. K., Walker, J. A., et al. (2012) · Genome Biology and Evolution · doi:10.1093/gbe/evs048 · Cited by 64 · see citing works

Human Endogenous Retrovirus K106 (HERV-K106) Was Infectious after the Emergence of Anatomically Modern Humans

Jha, A. R., Nixon, D. F., Rosenberg, M. G., Martin, J. N., Deeks, S. G., Hudson, R. R., Garrison, K. E., & Pillai, S. K. (2011) · PLoS ONE · doi:10.1371/journal.pone.0020234 · Cited by 48 · see citing works

Human Megasatellite DNA RS447: Copy-Number Polymorphisms and Interspecies Conservation

Gondo, Y., Okada, T., Matsuyama, N., Saitoh, Y., Yanagisawa, Y., & Ikeda, J. (1998) · Genomics · doi:10.1006/geno.1998.5545 · Cited by 47 · see citing works

Expression, tandem repeat copy number variation and stability of four macrosatellite arrays in the human genome

Tremblay, D. C., Alexander, G. C., Moseley, S. C., & Chadwick, B. P. (2010) · BMC Genomics · doi:10.1186/1471-2164-11-632 · Cited by 47 · see citing works

The UCSC repeat browser allows discovery and visualization of evolutionary conflict across repeat families

Fernandes, J. D., Zamudio-Hurtado, A., Clawson, H., Kent, W. J., Haussler, D. H., Salama, S. R., & Haeussler, M. (2020) · Mobile DNA · doi:10.1186/s13100-020-00208-w · Cited by 46 · see citing works

A DNA repeat, NBL2, is hypermethylated in some cancers but hypomethylated in others

Nishiyama, R., Qi, L., Tsumagari, K., Weissbecker, K., Dubeau, L., Champagne, M. A., Sikka, S. C., Nagai, H., & Ehrlich, M. (2005) · Cancer Biology & Therapy · doi:10.4161/cbt.4.4.1622 · Cited by 45 · see citing works

Identifying related L1 retrotransposons by analyzing 3' transduced sequences

Szak, S. T., Pickeral, O. K., Landsman, D., & Boeke, J. D. (2003) · Genome biology · doi:10.1186/gb-2003-4-5-r30 · Cited by 43 · see citing works

Selection and thermostability suggest G-quadruplexes are novel functional elements of the human genomePreprint

Guiblet, W. M., DeGiorgio, M., Cheng, X., Chiaromonte, F., Eckert, K. A., Huang, Y.-F., & Makova, K. D. (2021) · Genome Research · doi:10.1101/gr.269589.120 · Cited by 43 · see citing works

Molecular organization and chromosomal location of human GC-rich heterochromatic blocks

Meneveri, R., Agresti, A., Marozzi, A., Saccone, S., Rocchi, M., Archidiacono, N., Corneo, G. M., Valle, G. D., & Ginelli, E. (1993) · Gene · doi:10.1016/0378-1119(93)90128-p · Cited by 42 · see citing works

Recent Amplification of the Kangaroo Endogenous Retrovirus, KERV, Limited to the Centromere

Ferreri, G. C., Brown, J. D., Obergfell, C. J., Jue, N. K., Finn, C., O’Neill, M. J., & O'Neill, R. J. W. (2011) · Journal of Virology · doi:10.1128/jvi.01604-10 · Cited by 41 · see citing works

Hypermorphic expression of centromeric retroelement-encoded small RNAs impairs CENP-A loading

Carone, D. M., Zhang, C., Hall, L. E., Obergfell, C. J., Carone, B. R., O’Neill, M. J., & O'Neill, R. J. W. (2013) · Chromosome Research · doi:10.1007/s10577-013-9337-0 · Cited by 38 · see citing works

A new moderately repetitive DNa sequence family of movel organization

Epstein, N. D., Karlsson, S., O’Brien, S. J., Modi, W. S., Moulton, A. D., & Niehuis, A. W. (1987) · Nucleic Acids Research · doi:10.1093/nar/15.5.2327 · Cited by 37 · see citing works

A novel long non-coding RNA from NBL2 pericentromeric macrosatellite forms a perinucleolar aggregate structure in colon cancer

Dumbović, G., Biayna, J., Banús, J., Samuelsson, J., Roth, A., Diederichs, S., Alonso, S., Buschbeck, M., Perucho, M., & Forcales, S. V. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky263 · Cited by 37 · see citing works

Discovering Transcriptional Regulatory Elements From Run‐On and Sequencing Data Using the Web‐Based dREG Gateway

Chu, T., Wang, Z., Chou, S., & Danko, C. G. (2018) · Current Protocols in Bioinformatics · doi:10.1002/cpbi.70 · Cited by 37 · see citing works

A novel sperm-specific hypomethylation sequence is a demethylation hotspot in human hepatocellular carcinomas

Nagai, H., Kim, Y. S., Yasuda, T., Ohmachi, Y., Yokouchi, H., Monden, M., Emi, M., Konishi, N., Nogami, M., Okumura, K., et al. (1999) · Gene · doi:10.1016/s0378-1119(99)00322-4 · Cited by 35 · see citing works

Truncated ORF1 proteins can suppress LINE-1 retrotransposition in trans

Sokolowski, M. J., Chynces, M., deHaro, D. L., Christian, C. M., & Belancio, V. P. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx211 · Cited by 32 · see citing works

ULTRA

Olson, D. R., & Wheeler, T. J. (2018) · ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB) · doi:10.1145/3233547.3233604 · Cited by 32 · see citing works

Detection of subclonal L1 transductions in colorectal cancer by long-distance inverse-PCR and Nanopore sequencing

Pradhan, B., Cajuso, T., Katainen, R., Sulo, P., Tanskanen, T. J., Kilpivaara, O., Pitkänen, E., Aaltonen, L. A., Kauppi, L., & Palin, K. (2017) · Scientific Reports · doi:10.1038/s41598-017-15076-3 · Cited by 31 · see citing works

Construction of a reporter vector for analysis of bidirectional transcriptional activity of retrovirus LTR

André‐Arpin, C., Laverdure, S., Barbeau, B., Gross, A., & Mesnard, J.-M. (2014) · Plasmid · doi:10.1016/j.plasmid.2014.06.001 · Cited by 30 · see citing works

Helicase Lymphoid-Specific Enzyme Contributes to the Maintenance of Methylation of SST1 Pericentromeric Repeats That Are Frequently Demethylated in Colon Cancer and Associate with Genomic Damage

Samuelsson, J., Dumbović, G., Rivera, C. P., Moreta-Moraleda, C., Alibés, A., Ruiz‐Larroya, T., Gimenez‐Bonafé, P., Alonso, S., Forcales, S. V., & Perucho, M. (2016) · Epigenomes · doi:10.3390/epigenomes1010002 · Cited by 25 · see citing works

A high-quality genome assembly for the endangered golden snub-nosed monkey (Rhinopithecus roxellana)

Wang, L., Wu, J., Liu, X., Di, D., Liang, Y., Feng, Y., Zhang, S., Li, B., & Qi, X. (2019) · GigaScience · doi:10.1093/gigascience/giz098 · Cited by 23 · see citing works

Transposable element subfamily annotation has a reproducibility problem

Carey, K. M., Patterson, G., & Wheeler, T. J. (2021) · Mobile DNA · doi:10.1186/s13100-021-00232-4 · Cited by 21 · see citing works

A common 1.6 mb Y-chromosomal inversion predisposes to subsequent deletions and severe spermatogenic failure in humans

Hallast, P., Kibena, L., Punab, M., Arciero, E., Rootsi, S., Grigorova, M., Flores, R., Jobling, M. A., Poolamets, O., Pomm, K., et al. (2021) · eLife · doi:10.7554/elife.65420 · Cited by 21 · see citing works

Comparative Analyses of Gibbon Centromeres Reveal Dynamic Genus-Specific Shifts in Repeat Composition

Hartley, G. A., Okhovat, M., O'Neill, R. J. W., & Carbone, L. (2021) · Molecular Biology and Evolution · doi:10.1093/molbev/msab148 · Cited by 19 · see citing works

Chromatin regulatory dynamics of early human small intestinal development using a directed differentiation model

Hung, Y.-H., Huang, S., Dame, M. K., Yu, Q., Yu, Q. C., Zeng, Y. A., Camp, J. G., Spence, J. R., & Sethupathy, P. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa1204 · Cited by 18 · see citing works

An improved de novo genome assembly of the common marmoset genome yields improved contiguity and increased mapping rates of sequence data

Jayakumar, V., Ishii, H., Seki, M., Kumita, W., Inoue, T., Hase, S., Sato, K., Okano, H., Sasaki, E., & Sakakibara, Y. (2020) · BMC Genomics · doi:10.1186/s12864-020-6657-2 · Cited by 13 · see citing works

Chasing perfection: validation and polishing strategies for telomere-to-telomere genome assembliesPreprint

Cartney, A. M. M., Shafin, K., Alonge, M., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.07.02.450803 · Cited by 13 · see citing works

Co-Opted Megasatellite DNA Drives Evolution of Secondary Night Vision in Azara's Owl Monkey

Koga, A., Tanabe, H., Hirai, Y., Imai, H., Imamura, M., Oishi, T., Stanyon, R., & Hirai, H. (2017) · Genome Biology and Evolution · doi:10.1093/gbe/evx142 · Cited by 12 · see citing works

Somatic Hypomethylation of Pericentromeric SST1 Repeats and Tetraploidization in Human Colorectal Cancer Cells

González, B., Navarro-Jiménez, M., Gennaro, M. J. A.-D., Jansen, S. M., Granada, I., Perucho, M., & Alonso, S. (2021) · Cancers · doi:10.3390/cancers13215353 · Cited by 10 · see citing works

Next-generation sequencing-based detection of germline L1-mediated transductions

Tica, J., Lee, E., Untergasser, A., Meiers, S., Garfield, D. A., Gökçümen, Ö., Furlong, E. E. M., Park, P. J., Stütz, A. M., & Korbel, J. O. (2016) · BMC Genomics · doi:10.1186/s12864-016-2670-x · Cited by 8 · see citing works

Mer22-related sequence elements form pericentric repetitive DNA families in primates

Fátyol, K., Illies, K., Szalay, A. A., Diamond, D. C., & Janish, C. (2000) · Molecular and General Genetics MGG · doi:10.1007/pl00008661 · Cited by 6 · see citing works

Loss of X Chromosome Inactivation in Androgenetic Complete Hydatidiform Moles With 46, XX Karyotype

Chen, X., Ma, Y., Wang, L., Zhang, X., Yu, Y. P., Lü, W., Xie, X., & Cheng, X. (2020) · International Journal of Gynecological Pathology · doi:10.1097/pgp.0000000000000697 · Cited by 3 · see citing works

Repetitive Elements and Human Disorders

El‐Sawy, M., & Deininger, P. L. (2006) · Encyclopedia of Life Sciences · doi:10.1038/npg.els.0005493 · Cited by 1 · see citing works

Untitled work

Berner (1996) · doi:10.1002/(sici)1098-2264(199612)17:4

The complete sequence of a human genome

Nurk, S., Koren, S., Rhie, A., Rautiainen, M., Bzikadze, A. V., Mikheenko, A., Vollger, M. R., Altemose, N., Uralsky, L., Gershman, A., et al. (2022) · Science · doi:10.1126/science.abj6987 · Cited by 3,136 · see citing works

Complete genomic and epigenetic maps of human centromeres

Altemose, N., Logsdon, G. A., Bzikadze, A. V., Sidhwani, P., Langley, S. A., Caldas, G. V., Hoyt, S. J., Uralsky, L., Ryabov, F. D., Shew, C. J., et al. (2022) · Science · doi:10.1126/science.abl4178 · Cited by 618 · see citing works

The complete sequence of a human Y chromosome

Rhie, A., Nurk, S., Cechova, M., Hoyt, S. J., Taylor, D. J., Altemose, N., Hook, P. W., Koren, S., Rautiainen, M., Alexandrov, I. A., et al. (2023) · Nature · doi:10.1038/s41586-023-06457-y · Cited by 471 · see citing works

A complete reference genome improves analysis of human genetic variation

Aganezov, S., Yan, S. M., Soto, D. C., Kirsche, M., Zarate, S., Avdeyev, P., Taylor, D. J., Shafin, K., Shumate, A., Xiao, C., et al. (2022) · Science · doi:10.1126/science.abl3533 · Cited by 441 · see citing works

Epigenetic patterns in a complete human genome

Gershman, A., Sauria, M. E. G., Guitart, X., Vollger, M. R., Hook, P. W., Hoyt, S. J., Jain, M., Shumate, A., Razaghi, R., Koren, S., et al. (2022) · Science · doi:10.1126/science.abj5089 · Cited by 297 · see citing works

A systematic framework for understanding the microbiome in human health and disease: from basic principles to clinical translation

Ma, Z., Zuo, T., Frey, N., & Rangrez, A. Y. (2024) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-024-01946-6 · Cited by 297 · see citing works

The complete sequence of a human genomePreprint

Nurk, S., Koren, S., Rhie, A., Rautiainen, M., Bzikadze, A. V., Mikheenko, A., Vollger, M. R., Altemose, N., Uralsky, L. I., Gershman, A., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.05.26.445798 · Cited by 169 · see citing works

Long-Read DNA Sequencing: Recent Advances and Remaining Challenges

Warburton, P. E., & Sebra, R. P. (2023) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-101722-103045 · Cited by 163 · see citing works

Complete sequencing of ape genomes

Yoo, D., Rhie, A., Hebbar, P., Antonacci, F., Logsdon, G. A., Solar, S. J., Antipov, D., Pickett, B. D., Safonova, Y., Montinaro, F., et al. (2025) · Nature · doi:10.1038/s41586-025-08816-3 · Cited by 157 · see citing works

Taming transposable elements in vertebrates: from epigenetic silencing to domestication

Almeida, M. V., Vernaz, G., Putman, A. L. K., & Miska, E. A. (2022) · Trends in Genetics · doi:10.1016/j.tig.2022.02.009 · Cited by 145 · see citing works

Transposable elements as essential elements in the control of gene expression

Gebrie, A. (2023) · Mobile DNA · doi:10.1186/s13100-023-00297-3 · Cited by 146 · see citing works

Recombination between heterologous human acrocentric chromosomes

Guarracino, A., Buonaiuto, S., de Lima, L. G., Potapova, T., Rhie, A., Koren, S., Rubinstein, B., Fischer, C., Human Pangenome Reference Consortium, Abel, H. J., et al. (2023) · Nature · doi:10.1038/s41586-023-05976-y · Cited by 134 · see citing works

Genomics in the long-read sequencing era

van Dijk, E., Naquin, D., Gorrichon, K., Jaszczyszyn, Y., Ouazahrou, R., Thermes, C., & Hernandez, C. (2023) · Trends in Genetics · doi:10.1016/j.tig.2023.04.006 · Cited by 134 · see citing works

Assembly of 43 human Y chromosomes reveals extensive complexity and variation

Hallast, P., Ebert, P., Loftus, M. G., Yilmaz, F., Audano, P. A., Logsdon, G. A., Bonder, M. J., Zhou, W., Höps, W., Kim, K., et al. (2023) · Nature · doi:10.1038/s41586-023-06425-6 · Cited by 123 · see citing works

The complete sequence and comparative analysis of ape sex chromosomes

Makova, K. D., Pickett, B. D., Harris, R. S., Hartley, G. A., Čechová, M., Pál, K., Nurk, S., Yoo, D., Li, Q., Hebbar, P., et al. (2024) · Nature · doi:10.1038/s41586-024-07473-2 · Cited by 122 · see citing works

Transposable elements in mammalian chromatin organization

Lawson, H. A., Liang, Y., & Wang, T. (2023) · Nature Reviews Genetics · doi:10.1038/s41576-023-00609-6 · Cited by 121 · see citing works

Co‐based Nanozymatic Profiling: Advances Spanning Chemistry, Biomedical, and Environmental Sciences

Li, J., Cai, X., Jiang, P., Wang, H., Zhang, S., Sun, T., Chen, C., & Fan, K. (2023) · Advanced Materials · doi:10.1002/adma.202307337 · Cited by 115 · see citing works

Sequencing and characterizing short tandem repeats in the human genome

Tanudisastro, H., Deveson, I. W., Dashnow, H., & MacArthur, D. G. (2024) · Nature reviews genetics · doi:10.1038/s41576-024-00692-3 · Cited by 108 · see citing works

DNA 5-methylcytosine detection and methylation phasing using PacBio circular consensus sequencing

Ni, P., Nie, F., Zhong, Z., Xu, J., Huang, N., Zhang, J., Zhao, H., Zou, Y. F., Huang, Y., Li, J., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-39784-9 · Cited by 114 · see citing works

LINE-1 retrotransposition and its deregulation in cancers: implications for therapeutic opportunitiesPreprint

Mendez‐Dorantes, C., & Burns, K. H. (2023) · Genes & Development · doi:10.1101/gad.351051.123 · Cited by 106 · see citing works

PBSIM3: a simulator for all types of PacBio and ONT long reads

Ono, Y., Hamada, M., & Asai, K. (2022) · NAR Genomics and Bioinformatics · doi:10.1093/nargab/lqac092 · Cited by 101 · see citing works

Noncanonical DNA structures are drivers of genome evolution

Makova, K. D., & Weissensteiner, M. H. (2023) · Trends in Genetics · doi:10.1016/j.tig.2022.11.005 · Cited by 94 · see citing works

TRASH: Tandem Repeat Annotation and Structural Hierarchy

Włodzimierz, P., Hong, M., & Henderson, I. R. (2023) · Bioinformatics · doi:10.1093/bioinformatics/btad308 · Cited by 92 · see citing works

The structure, function, and evolution of plant centromeresPreprint

Naish, M., & Henderson, I. R. (2024) · Genome Research · doi:10.1101/gr.278409.123 · Cited by 86 · see citing works

LINE-1 retrotransposons drive human neuronal transcriptome complexity and functional diversification

Garza, R., Atacho, D. A. M., Adami, A., Gerdes, P., Vinod, M., Hsieh, P., Karlsson, O., Horváth, V., Johansson, P. A., Pandiloski, N., et al. (2023) · Science Advances · doi:10.1126/sciadv.adh9543 · Cited by 83 · see citing works

Advancing genomic technologies and clinical awareness accelerates discovery of disease-associated tandem repeat sequencesPreprint

Gall-Duncan, T., Sato, N. J., Yuen, R. K. C., & Pearson, C. E. (2021) · Genome Research · doi:10.1101/gr.269530.120 · Cited by 82 · see citing works

Variation and Evolution of Human Centromeres: A Field Guide and Perspective

Miga, K. H., & Alexandrov, I. A. (2021) · Annual Review of Genetics · doi:10.1146/annurev-genet-071719-020519 · Cited by 80 · see citing works

Diverse mechanisms of centromere specification

Mellone, B. G., & Fachinetti, D. (2021) · Current Biology · doi:10.1016/j.cub.2021.09.083 · Cited by 77 · see citing works

Differences in activity and stability drive transposable element variation in tropical and temperate maizePreprint

Ou, S., Scheben, A., Collins, T. C., Qiu, Y., Seetharam, A. S., Menard, C. C., Manchanda, N., Gent, J. I., Schatz, M. C., Anderson, S. N., et al. (2024) · Genome Research · doi:10.1101/gr.278131.123 · Cited by 74 · see citing works

Epigenomic signatures reveal mechanistic clues and predictive markers for autism spectrum disorder

LaSalle, J. M. (2023) · Molecular Psychiatry · doi:10.1038/s41380-022-01917-9 · Cited by 79 · see citing works

Immune targeting of HIV-1 reservoir cells: a path to elimination strategies and cure

Armani-Tourret, M., Bone, B., Tan, T. S., Sun, W., Bellefroid, M., Struyve, T., Louella, M., Yu, X. G., & Lichterfeld, M. (2024) · Nature Reviews Microbiology · doi:10.1038/s41579-024-01010-8 · Cited by 67 · see citing works

T2T-YAO: A Telomere-to-Telomere Assembled Diploid Reference Genome for Han Chinese

He, Y., Chu, Y., Guo, S., Hu, J. Y., Li, R., Zheng, Y., Ma, X., Du, Z., Zhao, L., Yu, W., et al. (2023) · Genomics Proteomics & Bioinformatics · doi:10.1016/j.gpb.2023.08.001 · Cited by 61 · see citing works

A proposed metric set for evaluation of genome assembly quality

Wang, P., & Wang, F. (2022) · Trends in Genetics · doi:10.1016/j.tig.2022.10.005 · Cited by 56 · see citing works

Genome-wide repeat landscapes in cancer and cell-free DNA

Annapragada, A. V., Niknafs, N., White, J. R., Bruhm, D. C., Cherry, C., Medina, J. E., Adleff, V., Hruban, C., Mathios, D., Foda, Z. H., et al. (2024) · Science Translational Medicine · doi:10.1126/scitranslmed.adj9283 · Cited by 54 · see citing works

Gapless assembly of complete human and plant chromosomes using only nanopore sequencingPreprint

Koren, S., Bao, Z., Guarracino, A., Ou, S., Goodwin, S., Jenike, K. M., Lucas, J., McNulty, B., Park, J., Rautiainen, M., et al. (2024) · Genome Research · doi:10.1101/gr.279334.124 · Cited by 52 · see citing works

3D genome, on repeat: Higher-order folding principles of the heterochromatinized repetitive genome

Haws, S. A., Simándi, Z., Barnett, R. J., & Phillips‐Cremins, J. E. (2022) · Cell · doi:10.1016/j.cell.2022.06.052 · Cited by 51 · see citing works

A classical revival: Human satellite DNAs enter the genomics era

Altemose, N. (2022) · Seminars in Cell and Developmental Biology · doi:10.1016/j.semcdb.2022.04.012 · Cited by 51 · see citing works

Integrating evolutionary genomics of forest trees to inform future tree breeding amid rapid climate change

Feng, J., Dan, X., Cui, Y., Gong, Y., Peng, M., Sang, Y., Ingvarsson, P. K., & Wang, J. (2024) · Plant Communications · doi:10.1016/j.xplc.2024.101044 · Cited by 53 · see citing works

Fourth Report on Chicken Genes and Chromosomes 2022

Smith, J., Alfieri, J. M., Anthony, N., Arensburger, P., Athrey, G., Balacco, J., Balic, A., Bardou, P., Barela, P., Bigot, Y., et al. (2022) · Cytogenetic and Genome Research · doi:10.1159/000529376 · Cited by 52 · see citing works

Phased gap-free genome assembly of octoploid cultivated strawberry illustrates the genetic and epigenetic divergence among subgenomes

Song, Y., Peng, Y., Liu, L., Li, G., Zhao, X., Wang, X., Cao, S., Muyle, A., Zhou, Y., & Zhou, H. (2023) · Horticulture Research · doi:10.1093/hr/uhad252 · Cited by 47 · see citing works

Centromere Identity and the Regulation of Chromosome Segregation

Sundararajan, K., & Straight, A. F. (2022) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2022.914249 · Cited by 42 · see citing works

Genome stability from the perspective of telomere length

Lu, X., & Liu, L. (2023) · Trends in Genetics · doi:10.1016/j.tig.2023.10.013 · Cited by 41 · see citing works

Computational analysis of DNA methylation from long-read sequencing

Fu, Y., Timp, W., & Sedlazeck, F. J. (2025) · Nature Reviews Genetics · doi:10.1038/s41576-025-00822-5 · Cited by 42 · see citing works

A complete diploid human genome benchmark for personalized genomics

Hansen, N. F., Dwarshuis, N., Ji, H. J., Rhie, A., Loucks, H., Logsdon, G., Vollger, M., Storer, J. M., Kim, J., Adam, E., et al. (2026) · Cell · doi:10.1016/j.cell.2026.06.016 · Cited by 11 · see citing works

Causes and Consequences of Varying Transposable Element Activity: An Evolutionary Perspective

Betancourt, A. J., Wei, K. H.-C., Huang, Y., & Lee, Y. C. G. (2024) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-120822-105708 · Cited by 40 · see citing works

A retrotransposon storm marks clinical phenoconversion to late-onset Alzheimer’s disease

Macciardi, F., Giulia Bacalini, M., Miramontes, R., Boattini, A., Taccioli, C., Modenini, G., Malhas, R., Anderlucci, L., Gusev, Y., Gross, T. J., et al. (2022) · GeroScience · doi:10.1007/s11357-022-00580-w · Cited by 37 · see citing works

Multimodal Omics Approaches to Aging and Age-Related Diseases

Ji, Q.-Z., Jiang, X.-Y., Wang, M.-X., Xin, Z.-J., Zhang, W.-Q., Qu, J., & Liu, G.-H. (2024) · Phenomics · doi:10.1007/s43657-023-00125-x · Cited by 32 · see citing works

Nanopore sequencing of 1000 Genomes Project samples to build a comprehensive catalog of human genetic variationPreprint

Gustafson, J. A., Gibson, S. B., Damaraju, N., Zalusky, M. P., Hoekzema, K., Twesigomwe, D., Yang, L., Snead, A. A., Richmond, P. A., Coster, W. D., et al. (2024) · medRxiv · doi:10.1101/2024.03.05.24303792 · Cited by 33 · see citing works

MCHelper automatically curates transposable element libraries across eukaryotic speciesPreprint

Orozco-Arias, S., Sierra, P., Durbin, R. M., & González, J. (2024) · Genome Research · doi:10.1101/gr.278821.123 · Cited by 37 · see citing works

Conserved and divergent mechanisms of inner kinetochore assembly onto centromeric chromatin

Yatskevich, S., Barford, D., & Muir, K. (2023) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2023.102638 · Cited by 36 · see citing works

Randomizing the human genome by engineering recombination between repeat elements

Koeppel, J., Ferreira, R., Vanderstichele, T., Riedmayr, L. M., Peets, E. M., Girling, G., Weller, J., Murat, P., Liberante, F. G., Ellis, T., et al. (2025) · Science · doi:10.1126/science.ado3979 · Cited by 37 · see citing works

Evolutionary dynamics between transposable elements and their host genomes: mechanisms of suppression and escape

Lawlor, M. A., & Ellison, C. E. (2023) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2023.102092 · Cited by 33 · see citing works

Cancer cells restrict immunogenicity of retrotransposon expression via distinct mechanisms

Sun, S., You, E., Hong, J., Hoyos, D., Priore, I. S. D., Tsanov, K. M., Mattagajasingh, O., Gioacchino, A. D., Marhon, S. A., Chacon-Barahona, J. A., et al. (2024) · Immunity · doi:10.1016/j.immuni.2024.10.015 · Cited by 35 · see citing works

The formation and propagation of human Robertsonian chromosomes

de Lima, L. G., Guarracino, A., Koren, S., Potapova, T., McKinney, S., Rhie, A., Solar, S. J., Seidel, C. W., Fagen, B. L., Walenz, B. P., et al. (2025) · Nature · doi:10.1038/s41586-025-09540-8 · Cited by 34 · see citing works

Satellite DNAs in Health and Disease

Ugarković, Đ., Sermek, A., Ljubić, S., & Feliciello, I. (2022) · Genes · doi:10.3390/genes13071154 · Cited by 34 · see citing works

RNA Sequencing in Disease Diagnosis

Smail, C., & Montgomery, S. B. (2024) · Annual review of genomics and human genetics (Print) · doi:10.1146/annurev-genom-021623-121812 · Cited by 31 · see citing works

Mammalian DNA methylome dynamics: mechanisms, functions and new frontiers

Wei, A., & Wu, H. (2022) · Development · doi:10.1242/dev.182683 · Cited by 33 · see citing works

Leveraging the power of long reads for targeted sequencingPreprint

Iyer, S. V., Goodwin, S., & McCombie, W. R. (2024) · Genome Research · doi:10.1101/gr.279168.124 · Cited by 34 · see citing works

Epigenomic insights into common human disease pathology

Bell, C. G. (2024) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-024-05206-2 · Cited by 32 · see citing works

The Ruminant Telomere-to-Telomere (RT2T) Consortium

Kalbfleisch, T., McKay, S., Murdoch, B. M., Adelson, D. L., Almansa-Villa, D., Becker, G. M., Beckett, L. M., Benítez-Galeano, M. J., Biase, F. H., Casey, T., et al. (2024) · Nature Genetics · doi:10.1038/s41588-024-01835-2 · Cited by 32 · see citing works

Topoisomerase-modulated genome-wide DNA supercoiling domains colocalize with nuclear compartments and regulate human gene expression

Yao, Q., Zhu, L., Shi, Z., Banerjee, S., & Chen, C. (2024) · Nature Structural & Molecular Biology · doi:10.1038/s41594-024-01377-5 · Cited by 32 · see citing works

Interaction of Proteins with Inverted Repeats and Cruciform Structures in Nucleic Acids

Bowater, R. P., Bohálová, N., & Brázda, V. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms23116171 · Cited by 32 · see citing works

Deciphering D4Z4 CpG methylation gradients in fascioscapulohumeral muscular dystrophy using nanopore sequencingPreprint

Butterfield, R. J., Dunn, D. M., Duval, B., Moldt, S., & Weiss, R. B. (2023) · Genome Research · doi:10.1101/gr.277871.123 · Cited by 32 · see citing works

Fragile sites, chromosomal lesions, tandem repeats, and disease

Mirceta, M., Shum, N., Schmidt, M. H. M., & Pearson, C. E. (2022) · Frontiers in Genetics · doi:10.3389/fgene.2022.985975 · Cited by 30 · see citing works

Software evaluation for de novo detection of transposons

Rodriguez, M., & Makałowski, W. (2022) · Mobile DNA · doi:10.1186/s13100-022-00266-2 · Cited by 30 · see citing works

Transposable elements in early human embryo development and embryo models

DiRusso, J., & Clark, A. T. (2023) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2023.102086 · Cited by 29 · see citing works

A working model for the formation of Robertsonian chromosomes

Gerton, J. L. (2024) · Journal of Cell Science · doi:10.1242/jcs.261912 · Cited by 29 · see citing works

Global mapping of RNA-chromatin contacts reveals a proximity-dominated connectivity model for ncRNA-gene interactions

Limouse, C., Smith, O. K., Jukam, D., Fryer, K. A., Greenleaf, W. J., & Straight, A. F. (2023) · Nature Communications · doi:10.1038/s41467-023-41848-9 · Cited by 30 · see citing works

Efficient estimation for large-scale linkage disequilibrium patterns of the human genome

Huang, X., Zhu, T.-N., Liu, Y., Qi, G., Zhang, J., & Chen, G. (2023) · eLife · doi:10.7554/elife.90636 · Cited by 28 · see citing works

Non-canonical DNA in human and other ape telomere-to-telomere genomes

Smeds, L., Kamali, K., Kejnovská, I., Kejnovský, E., Chiaromonte, F., & Makova, K. D. (2025) · Nucleic Acids Research · doi:10.1093/nar/gkaf298 · Cited by 28 · see citing works

Earth Biogenome Project: present status and future plans

Gupta, P. K. (2022) · Trends in Genetics · doi:10.1016/j.tig.2022.04.008 · Cited by 27 · see citing works

Advances in the discovery and analyses of human tandem repeats

Chaisson, M., Sulovari, A., Valdmanis, P. N., Miller, D. E., & Eichler, E. E. (2023) · Emerging Topics in Life Sciences · doi:10.1042/etls20230074 · Cited by 27 · see citing works

A telomere-to-telomere genome assembly of Zhonghuang 13, a widely-grown soybean variety from the original center of Glycine max

Zhang, A., Kong, T., Sun, B., Qiu, S., Guo, J., Ruan, S., Guo, Y., Guo, J., Zhang, Z., Liu, Y., et al. (2023) · The Crop Journal · doi:10.1016/j.cj.2023.10.003 · Cited by 25 · see citing works

Long-read sequencing: An effective method for genetic analysis of CYP21A2 variation in congenital adrenal hyperplasia

Li, H., Zhu, X., Yang, Y., Wang, W., Mao, A., Li, J., Bao, S., & Li, J. (2023) · Clinica Chimica Acta · doi:10.1016/j.cca.2023.117419 · Cited by 23 · see citing works

Mini-heterochromatin domains constrain the cis-regulatory impact of SVA transposons in human brain development and disease

Horváth, V., Garza, R., Jönsson, M. E., Johansson, P. A., Adami, A., Christoforidou, G., Karlsson, O., Castilla‐Vallmanya, L., Koutounidou, S., Gerdes, P., et al. (2024) · Nature Structural & Molecular Biology · doi:10.1038/s41594-024-01320-8 · Cited by 23 · see citing works

Proximal telomeric decompaction due to telomere shortening drives FOXC1-dependent myocardial senescence

Li, B., Xiong, W., Zuo, W., Shi, Y., Wang, T., Chang, L., Wu, Y., Ma, H., Bian, Q., & Chang, A. C. Y. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkae274 · Cited by 22 · see citing works

Resolution of ring chromosomes, Robertsonian translocations, and complex structural variants from long-read sequencing and telomere-to-telomere assembly

Mostovoy, Y., Boone, P. M., Huang, Y., Garimella, K. V., Tan, K., Russell, B. E., Salani, M., de Esch, C. E. F., Lemanski, J. M., Currall, B., et al. (2024) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2024.10.006 · Cited by 22 · see citing works

LINE-1 retrotransposons mediate cis-acting transcriptional control in human pluripotent stem cells and regulate early brain development

Adami, A., Garza, R., Gerdes, P., Johansson, P. A., Dorazehi, F., Koutounidou, S., Castilla‐Vallmanya, L., Atacho, D. A. M., Sharma, Y., Johansson, J., et al. (2025) · Cell Genomics · doi:10.1016/j.xgen.2025.100979 · Cited by 22 · see citing works

A human-specific regulatory mechanism revealed in a pre-implantation model

Fueyo, R., Wang, S., Crocker, O. J., Swigut, T., Nakauchi, H., & Wysocka, J. (2025) · Nature · doi:10.1038/s41586-025-09571-1 · Cited by 25 · see citing works

The influence of transposable elements on animal colouration

Galbraith, J. D., & Hayward, A. (2023) · Trends in Genetics · doi:10.1016/j.tig.2023.04.005 · Cited by 22 · see citing works

Characterization of large-scale genomic differences in the first complete human genome

Yang, X., Wang, X., Zou, Y., Zhang, S., Xia, M., Fu, L., Vollger, M. R., Chen, N.-C., Taylor, D. J., Harvey, W. T., et al. (2023) · Genome biology · doi:10.1186/s13059-023-02995-w · Cited by 22 · see citing works

When synthetic biology meets medicine

Feng, Y., Su, C., Mao, G., Sun, B., Cai, Y., Dai, J., & Ma, Y. (2024) · Life Medicine · doi:10.1093/lifemedi/lnae010 · Cited by 21 · see citing works

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 23 · see citing works

UniAligner: a parameter-free framework for fast sequence alignment

Bzikadze, A. V., & Pevzner, P. A. (2023) · Nature Methods · doi:10.1038/s41592-023-01970-4 · Cited by 19 · see citing works

scNanoSeq-CUT&Tag: a single-cell long-read CUT&Tag sequencing method for efficient chromatin modification profiling within individual cells

Li, Q., Guo, Y., Wu, Z., Xu, X., Zhen-huan, J., Qi, S., Liu, Z., Wen, L., & Tang, F. (2024) · Nature Methods · doi:10.1038/s41592-024-02453-w · Cited by 20 · see citing works

HSF1-Activated Non-Coding Stress Response: Satellite lncRNAs and Beyond, an Emerging Story with a Complex Scenario

Vourc’h, C., Dufour, S., Timcheva, K., Seigneurin‐Berny, D., & Verdel, A. (2022) · Genes · doi:10.3390/genes13040597 · Cited by 22 · see citing works

Locus specific endogenous retroviral expression associated with Alzheimer’s disease

Dawson, T., Rentia, U., Sanford, J., Cruchaga, C., Kauwe, J. S. K., & Crandall, K. A. (2023) · Frontiers in Aging Neuroscience · doi:10.3389/fnagi.2023.1186470 · Cited by 20 · see citing works

The haplotype-resolved telomere-to-telomere carnation (Dianthus caryophyllus) genome reveals the correlation between genome architecture and gene expression

Lan, L., Leng, L., Liu, W., Ren, Y., Reeve, W. G., Fu, X., Wu, Z., & Zhang, X. (2023) · Horticulture Research · doi:10.1093/hr/uhad244 · Cited by 19 · see citing works

Evolutionary dynamics of predicted G-quadruplexes in human and other great apes

Mohanty, S. K., Chiaromonte, F., & Makova, K. D. (2025) · Genome biology · doi:10.1186/s13059-025-03635-1 · Cited by 18 · see citing works

Long-read sequencing and genome assembly of natural history collection samples and challenging specimens

Bein, B., Chrysostomakis, I., Arantes, L. S., Brown, T., Gerheim, C., Schell, T., Schneider, C., Leushkin, E. V., Chen, Z., Sigwart, J. D., et al. (2025) · Genome biology · doi:10.1186/s13059-025-03487-9 · Cited by 18 · see citing works

Pan-cancer multi-omic model of LINE-1 activity reveals locus heterogeneity of retrotransposition efficiency

Solovyov, A., Behr, J. M., Hoyos, D., Banks, E., Drong, A., Thornlow, B. P., Zhong, J. Z., Garcia-Rivera, E., McKerrow, W., Chu, C., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-57271-1 · Cited by 20 · see citing works

Single-cell omics sequencing technologies: the long-read generation

Wen, L., & Tang, F. (2025) · Trends in Genetics · doi:10.1016/j.tig.2025.07.012 · Cited by 17 · see citing works

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 · see citing works

Defining a core configuration for human centromeres during mitosis

Gupta, A. S., Seidel, C. W., Tsuchiya, D., McKinney, S., Yu, Z., Smith, S. E., Unruh, J. R., & Gerton, J. L. (2023) · Nature Communications · doi:10.1038/s41467-023-42980-2 · Cited by 16 · see citing works

Using long-read CAGE sequencing to profile cryptic-promoter-derived transcripts and their contribution to the immunopeptidomePreprint

Maeng, J. H., Jang, H. J., Du, A. Y., Tzeng, S., & Wang, T. (2023) · Genome Research · doi:10.1101/gr.277061.122 · Cited by 16 · see citing works

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 · see citing works

Lactylation in CNS disorders: mechanisms, cellular function, and disease relevance

Tian, J., Zhang, T., Zhang, R., Hao, S., Dong, J., Chen, Y., Zhou, J., & Tian, Y. (2025) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2025.1566921 · Cited by 15 · see citing works

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 · see citing works

A single-cell transposable element atlas of human cell identity

Reyes-Gopar, H., Marston, J. L., Singh, B., Greenig, M., Lin, J., Ostrowski, M., Randall, K. N., Sandoval‐Motta, S., Dopkins, N., Lawrence, E., et al. (2025) · Cell Reports Methods · doi:10.1016/j.crmeth.2025.101086 · Cited by 13 · see citing works

Transformer-Based Classification of Transposable Element Consensus Sequences with TEclass2

Bickmann, L., Rodriguez, M., Jiang, X., & Makałowski, W. (2025) · Biology · doi:10.3390/biology15010059 · Cited by 16 · see citing works

Chromosomes: Noncoding DNA (Including Satellite DNA)

Mortimer, S. M., Frisbie, T. J., Moldovan, J. B., Nakamura, M., Sandwith, S. N., Yin, J., & Moran, J. V. (2022) · Encyclopedia of Life Sciences · doi:10.1002/9780470015902.a0025409

Identification and annotation of recombinant repeats in mammals indicates they are experimental products for creating novel transposable element families.

Lim, S. L. (2014) · Adelaide Research & Scholarship (AR&S) (University of Adelaide)

Human transposable elements in Repbase: genomic footprints from fish to humans

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Transposable Elements Are a Significant Contributor to Tandem Repeats in the Human Genome

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Research Article Transposable Elements Are a Significant Contributor to Tandem

Genome, R. I. T. H., Ahmed, M., & Liang, P. (2016)