Repbase Update, a database of eukaryotic repetitive elements

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

MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects

Holt, C., & Yandell, M. (2011) · BMC Bioinformatics · doi:10.1186/1471-2105-12-491 · Cited by 2,118

Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture–on-chip (4C)

Simonis, M., Klous, P., Splinter, E., Moshkin, Y., Willemsen, R., de Wit, E., van Steensel, B., & de Laat, W. (2006) · Nature Genetics · doi:10.1038/ng1896 · Cited by 1,386

The sequence and de novo assembly of the giant panda genome

Li, R., Fan, W., Tian, G., Zhu, H., He, L., Cai, J., Huang, Q., Cai, Q., Li, B., Bai, Y., et al. (2010) · Nature · doi:10.1038/nature08696 · Cited by 1,180

A Fine-Scale Map of Recombination Rates and Hotspots Across the Human Genome

Myers, S., Bottolo, L., Freeman, C., McVean, G., & Donnelly, P. (2005) · Science · doi:10.1126/science.1117196 · Cited by 1,134

Genome-Wide Quantitative Enhancer Activity Maps Identified by STARR-seq

Arnold, C. D., Gerlach, D., Stelzer, C., Boryń, Ł. M., Rath, M., & Stark, A. (2013) · Science · doi:10.1126/science.1232542 · Cited by 1,125

The Ensembl gene annotation system

Aken, B. L., Ayling, S., Barrell, D., Clarke, L., Curwen, V., Fairley, S., Fernandez Banet, J., Billis, K., García Girón, C., Hourlier, T., et al. (2016) · Database · doi:10.1093/database/baw093 · Cited by 1,086

The UCSC genome browser and associated tools

Kuhn, R. M., Haussler, D., & Kent, W. J. (2013) · Briefings in Bioinformatics · doi:10.1093/bib/bbs038 · Cited by 883

The complex transcriptional landscape of the anucleate human platelet

Bray, P. F., McKenzie, S. E., Edelstein, L. C., Nagalla, S., Delgrosso, K., Ertel, A., Kupper, J., Jing, Y., Londin, E., Loher, P., et al. (2013) · BMC Genomics · doi:10.1186/1471-2164-14-1 · Cited by 802

Landscape of Somatic Retrotransposition in Human Cancers

Lee, E., Iskow, R., Yang, L., Gokcumen, O., Haseley, P., Luquette, L. J., Lohr, J. G., Harris, C. C., Ding, L., Wilson, R. K., et al. (2012) · Science · doi:10.1126/science.1222077 · Cited by 762

The ctenophore genome and the evolutionary origins of neural systems

Moroz, L. L., Kocot, K. M., Citarella, M. R., Dosung, S., Norekian, T. P., Povolotskaya, I. S., Grigorenko, A. P., Dailey, C., Berezikov, E., Buckley, K. M., et al. (2014) · Nature · doi:10.1038/nature13400 · Cited by 716

Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences

Broad Institute Genome Sequencing Platform, Mikkelsen, T. S., Broad Institute Whole Genome Assembly Team, Wakefield, M. J., Aken, B., Amemiya, C. T., Chang, J. L., Duke, S., Garber, M., Gentles, A. J., et al. (2007) · Nature · doi:10.1038/nature05805 · Cited by 711

Transposable Elements Are Major Contributors to the Origin, Diversification, and Regulation of Vertebrate Long Noncoding RNAs

Kapusta, A., Kronenberg, Z., Lynch, V. J., Zhuo, X., Ramsay, L., Bourque, G., Yandell, M., & Feschotte, C. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003470 · Cited by 687

Active human retrotransposons: variation and disease

Hancks, D. C., & Kazazian, H. H. (2012) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2012.02.006 · Cited by 592

DNA Methylation and SETDB1/H3K9me3 Regulate Predominantly Distinct Sets of Genes, Retroelements, and Chimeric Transcripts in mESCs

Karimi, M. M., Goyal, P., Maksakova, I. A., Bilenky, M., Leung, D., Tang, J. X., Shinkai, Y., Mager, D. L., Jones, S., Hirst, M., et al. (2011) · Cell Stem Cell · doi:10.1016/j.stem.2011.04.004 · Cited by 535

Transposable elements reveal a stem cell-specific class of long noncoding RNAs

Kelley, D., & Rinn, J. (2012) · Genome Biology · doi:10.1186/gb-2012-13-11-r107 · Cited by 531

Aberrant Overexpression of Satellite Repeats in Pancreatic and Other Epithelial Cancers

Ting, D. T., Lipson, D., Paul, S., Brannigan, B. W., Akhavanfard, S., Coffman, E. J., Contino, G., Deshpande, V., Iafrate, A. J., Letovsky, S., et al. (2011) · Science · doi:10.1126/science.1200801 · Cited by 540

Widespread contribution of transposable elements to the innovation of gene regulatory networks

Sundaram, V., Cheng, Y., Ma, Z., Li, D., Xing, X., Edge, P., Snyder, M. P., & Wang, T. (2014) · Genome Research · doi:10.1101/gr.168872.113 · Cited by 529

Effects of Retroviruses on Host Genome Function

Jern, P., & Coffin, J. M. (2008) · Annual Review of Genetics · doi:10.1146/annurev.genet.42.110807.091501 · Cited by 499

Tracing the evolutionary history and global expansion of Candida auris using population genomic analyses

Chow, N. A., Muñoz, J. F., Gade, L., Berkow, E., Li, X., Welsh, R. M., Forsberg, K., Lockhart, S. R., Adam, R., Alanio, A., et al. (2020) · doi:10.1101/2020.01.06.896548 · Cited by 463

The genomic and transcriptomic landscape of a HeLa cell line

Landry, J. J. M., Pyl, P. T., Rausch, T., Zichner, T., Tekkedil, M. M., Stütz, A. M., Jauch, A., Aiyar, R. S., Pau, G., Delhomme, N., et al. (2013) · G3 Genes|Genomes|Genetics · doi:10.1534/g3.113.005777 · Cited by 416

Population genomics reveal recent speciation and rapid evolutionary adaptation in polar bears

Liu, S., Lorenzen, E. D., Fumagalli, M., Li, B., Harris, K., Xiong, Z., Zhou, L., Korneliussen, T. S., Somel, M., Babbitt, C., et al. (2014) · Cell · doi:10.1016/j.cell.2014.03.054 · Cited by 411

Genomic signatures of evolutionary transitions from solitary to group living

Kapheim, K. M., Pan, H., Li, C., Salzberg, S. L., Puiu, D., Magoc, T., Robertson, H. M., Hudson, M. E., Venkat, A., Fischman, B. J., et al. (2015) · Science · doi:10.1126/science.aaa4788 · Cited by 409

Suv39h-Dependent H3K9me3 Marks Intact Retrotransposons and Silences LINE Elements in Mouse Embryonic Stem Cells

Bulut-Karslioglu, A., De La Rosa-Velázquez, I. A., Ramirez, F., Barenboim, M., Onishi-Seebacher, M., Arand, J., Galán, C., Winter, G. E., Engist, B., Gerle, B., et al. (2014) · Molecular Cell · doi:10.1016/j.molcel.2014.05.029 · Cited by 368

Repetitive sequences in complex genomes: Structure and evolution

Jurka, J., Kapitonov, V. V., Kohany, O., & Jurka, M. V. (2007) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev.genom.8.080706.092416 · Cited by 331

Highly multiplexed simultaneous detection of RNAs and proteins in single cells

Frei, A. P., Bava, F.-A., Zunder, E. R., Hsieh, E. W. Y., Chen, S.-Y., Nolan, G. P., & Gherardini, P. F. (2016) · Nature Methods · doi:10.1038/nmeth.3742 · Cited by 330

Endogenous retroviral LTRs as promoters for human genes: A critical assessment

Cohen, C. J., Lock, W. M., & Mager, D. L. (2009) · Gene · doi:10.1016/j.gene.2009.06.020 · Cited by 314

A comprehensive map of mobile element insertion polymorphisms in humans

Stewart, C., Kural, D., Strömberg, M. P., Walker, J. A., Konkel, M. K., Stütz, A. M., Urban, A. E., Grubert, F., Lam, H. Y. K., Lee, W.-P., et al. (2011) · PLoS Genetics · doi:10.1371/journal.pgen.1002236 · Cited by 307

Comparative 454 pyrosequencing of transcripts from two olive genotypes during fruit development

Alagna, F., D'Agostino, N., Torchia, L., Servili, M., Rao, R., Pietrella, M., Giuliano, G., Chiusano, M. L., Baldoni, L., & Perrotta, G. (2009) · BMC Genomics · doi:10.1186/1471-2164-10-399 · Cited by 263

Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories

The GEUVADIS Consortium, 't Hoen, P. A. C., Friedländer, M. R., Almlöf, J., Sammeth, M., Pulyakhina, I., Anvar, S. Y., Laros, J. F. J., Buermans, H. P. J., Karlberg, O., et al. (2013) · Nature Biotechnology · doi:10.1038/nbt.2702 · Cited by 250

Histone H3K9 methylation is dispensable for Caenorhabditis elegans development but suppresses RNA:DNA hybrid-associated repeat instability

Zeller, P., Padeken, J., van Schendel, R., Kalck, V., Tijsterman, M., & Gasser, S. M. (2016) · Nature Genetics · doi:10.1038/ng.3672 · Cited by 204

Epigenomic consequences of immortalized plant cell suspension culture

Tanurdzic, M., Vaughn, M. W., Jiang, H., Lee, T.-J., Slotkin, R. K., Sosinski, B., Thompson, W. F., Doerge, R. W., & Martienssen, R. A. (2008) · PLoS Biology · doi:10.1371/journal.pbio.0060302 · Cited by 218

Transcriptome characterization by RNA sequencing identifies a major molecular and clinical subdivision in chronic lymphocytic leukemia

Ferreira, P. G., Jares, P., Rico, D., Gómez-López, G., Martínez-Trillos, A., Villamor, N., Ecker, S., González-Pérez, A., Knowles, D. G., Monlong, J., et al. (2014) · Genome Research · doi:10.1101/gr.152132.112 · Cited by 214

Resurrection of endogenous retroviruses in antibody-deficient mice

Young, G. R., Eksmond, U., Salcedo, R., Alexopoulou, L., Stoye, J. P., & Kassiotis, G. (2012) · Nature · doi:10.1038/nature11599 · Cited by 215

Genomic legacy of the African cheetah, Acinonyx jubatus

Dobrynin, P., Liu, S., Tamazian, G., Xiong, Z., Yurchenko, A. A., Krasheninnikova, K., Kliver, S., Schmidt-Küntzel, A., Koepfli, K.-P., Johnson, W., et al. (2015) · Genome Biology · doi:10.1186/s13059-015-0837-4 · Cited by 204

Transposable Elements in TDP-43-Mediated Neurodegenerative Disorders

Li, W., Jin, Y., Prazak, L., Hammell, M., & Dubnau, J. (2012) · PLoS ONE · doi:10.1371/journal.pone.0044099 · Cited by 195

African lungfish genome sheds light on the vertebrate water-to-land transition

Wang, K., Wang, J., Zhu, C., Yang, L., Ren, Y., Ruan, J., Fan, G., Hu, J., Xu, W., Bi, X., et al. (2021) · Cell · doi:10.1016/j.cell.2021.01.047 · Cited by 192

Resolving rates of mutation in the brain using single-neuron genomics

Evrony, G. D., Lee, E., Park, P. J., & Walsh, C. A. (2016) · eLife · doi:10.7554/elife.12966 · Cited by 163

Oil accumulation mechanisms of the oleaginous microalga Chlorella protothecoides revealed through its genome, transcriptomes, and proteomes

Gao, C., Wang, Y., Shen, Y., Yan, D., He, X., Dai, J., & Wu, Q. (2014) · BMC Genomics · doi:10.1186/1471-2164-15-582 · Cited by 175

piRNA-mediated transgenerational inheritance of an acquired trait

Grentzinger, T., Armenise, C., Brun, C., Mugat, B., Serrano, V., Pelisson, A., & Chambeyron, S. (2012) · Genome Research · doi:10.1101/gr.136614.111 · Cited by 162

Evolutionary dynamics of transposable elements in the short-tailed opossum Monodelphis domestica

Gentles, A. J., Wakefield, M. J., Kohany, O., Gu, W., Batzer, M. A., Pollock, D. D., & Jurka, J. (2007) · Genome Research · doi:10.1101/gr.6070707 · Cited by 156

The goose genome sequence leads to insights into the evolution of waterfowl and susceptibility to fatty liver

Lu, L., Chen, Y., Wang, Z., Li, X., Chen, W., Tao, Z., Shen, J., Tian, Y., Wang, D., Li, G., et al. (2015) · Genome biology · doi:10.1186/s13059-015-0652-y · Cited by 137

Our Conflict with Transposable Elements and Its Implications for Human Disease

Burns, K. H. (2020) · Annual Review of Pathology: Mechanisms of Disease · doi:10.1146/annurev-pathmechdis-012419-032633 · Cited by 137

An improved genome assembly uncovers prolific tandem repeats in Atlantic cod

Tørresen, O. K., Star, B., Jentoft, S., Reinar, W. B., Grove, H., Miller, J. R., Walenz, B. P., Knight, J., Ekholm, J. M., Peluso, P., et al. (2017) · BMC Genomics · doi:10.1186/s12864-016-3448-x · Cited by 137

Widespread selection and gene flow shape the genomic landscape during a radiation of monkeyflowers

Stankowski, S., Chase, M. A., Fuiten, A. M., Rodrigues, M. F., Ralph, P. L., & Streisfeld, M. A. (2019) · PLOS Biology · doi:10.1371/journal.pbio.3000391 · Cited by 134

Reference-assisted chromosome assembly

Kim, J., Larkin, D. M., Cai, Q., Asan, Zhang, Y., Ge, R.-L., Auvil, L., Capitanu, B., Zhang, G., Lewin, H. A., et al. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1220349110 · Cited by 128

Onco-exaptation of an endogenous retroviral LTR drives IRF5 expression in Hodgkin lymphoma

Babaian, A., Romanish, M. T., Gagnier, L., Kuo, L. Y., Karimi, M. M., Steidl, C., & Mager, D. L. (2016) · Oncogene · doi:10.1038/onc.2015.308 · Cited by 121

The Asian arowana (Scleropages formosus) genome provides new insights into the evolution of an early lineage of teleosts

Bian, C., Hu, Y., Ravi, V., Kuznetsova, I. S., Shen, X., Mu, X., Sun, Y., You, X., Li, J., Li, X., et al. (2016) · Scientific Reports · doi:10.1038/srep24501 · Cited by 107

The contribution of transposable elements to size variations between four teleost genomes

Gao, B., Shen, D., Xue, S., Chen, C., Cui, H., & Song, C. (2016) · Mobile DNA · doi:10.1186/s13100-016-0059-7 · Cited by 100

Miniature inverted-repeat transposable elements: discovery, distribution, and activity

Fattash, I., Rooke, R., Wong, A., Hui, C., Luu, T., Bhardwaj, P., & Yang, G. (2013) · Genome · doi:10.1139/gen-2012-0174 · Cited by 99

Human cancer-associated mutations in the Aα subunit of protein phosphatase 2A increase lung cancer incidence in Aα knock-in and knockout mice

Ruediger, R., Ruiz, J., & Walter, G. (2011) · Molecular and Cellular Biology · doi:10.1128/mcb.05744-11 · Cited by 98

SIRT7 mediates L1 elements transcriptional repression and their association with the nuclear lamina

Vazquez, B. N., Thackray, J. K., Simonet, N. G., Chahar, S., Kane-Goldsmith, N., Newkirk, S. J., Lee, S., Xing, J., Verzi, M. P., An, W., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz519 · Cited by 79

Distinguishing the immunostimulatory properties of noncoding RNAs expressed in cancer cells

Tanne, A., Muniz, L. R., Puzio-Kuter, A., Leonova, K. I., Gudkov, A. V., Ting, D. T., Monasson, R., Cocco, S., Levine, A. J., Bhardwaj, N., et al. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1517584112 · Cited by 74

Non-targeted transcription factors motifs are a systemic component of ChIP-seq datasets

Worsley Hunt, R., & Wasserman, W. W. (2014) · Genome Biology · doi:10.1186/s13059-014-0412-4 · Cited by 73

Formation and Longevity of Chimeric and Duplicate Genes in Drosophila melanogaster

Rogers, R. L., Bedford, T., & Hartl, D. L. (2009) · Genetics · doi:10.1534/genetics.108.091538 · Cited by 71

R2D2 Organizes Small Regulatory RNA Pathways in Drosophila∇†

Okamura, K., Robine, N., Liu, Y., Liu, Q., & Lai, E. C. (2011) · Molecular and Cellular Biology · doi:10.1128/mcb.01141-10 · Cited by 70

A family of conserved noncoding elements derived from an ancient transposable element

Xie, X., Kamal, M., & Lander, E. S. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0604768103 · Cited by 66

Single nucleotide differences (SNDs) in the dbSNP database may lead to errors in genotyping and haplotyping studies

Musumeci, L., Arthur, J. W., Cheung, F. S. G., Hoque, A., Lippman, S., & Reichardt, J. K. V. (2010) · Human Mutation · doi:10.1002/humu.21137 · Cited by 62

CAGE profiling of ncRNAs in hepatocellular carcinoma reveals widespread activation of retroviral LTR promoters in virus-induced tumors

Hashimoto, K., Suzuki, A. M., Dos Santos, A., Desterke, C., Collino, A., Ghisletti, S., Braun, E., Bonetti, A., Fort, A., Qin, X.-Y., et al. (2015) · Genome Research · doi:10.1101/gr.191031.115 · Cited by 64

euL1db: the European database of L1HS retrotransposon insertions in humans

Mir, A. A., Philippe, C., & Cristofari, G. (2015) · Nucleic Acids Research · doi:10.1093/nar/gku1043 · Cited by 62

A multi-omic characterization of temperature stress in a halotolerant Scenedesmus strain for algal biotechnology

Calhoun, S., Bell, T. A. S., Dahlin, L. R., Kunde, Y., LaButti, K., Louie, K. B., Kuftin, A., Treen, D., Dilworth, D., Mihaltcheva, S., et al. (2021) · Communications Biology · doi:10.1038/s42003-021-01859-y · Cited by 60

Highly conserved gene order and numerous novel repetitive elements in genomic regions linked to wing pattern variation in Heliconius butterflies

Papa, R., Morrison, C. M., Walters, J. R., Counterman, B. A., Chen, R., Halder, G., Ferguson, L., Chamberlain, N., ffrench-Constant, R., Kapan, D. D., et al. (2008) · BMC Genomics · doi:10.1186/1471-2164-9-345 · Cited by 50

Genomic architecture of haddock (Melanogrammus aeglefinus) shows expansions of innate immune genes and short tandem repeats

Tørresen, O. K., Brieuc, M. S. O., Solbakken, M. H., Sørhus, E., Nederbragt, A. J., Jakobsen, K. S., Meier, S., Edvardsen, R. B., & Jentoft, S. (2018) · BMC Genomics · doi:10.1186/s12864-018-4616-y · Cited by 46

Low Levels of LTR Retrotransposon Deletion by Ectopic Recombination in the Gigantic Genomes of Salamanders

Frahry, M. B., Sun, C., Chong, R. A., & Mueller, R. L. (2015) · Journal of Molecular Evolution · doi:10.1007/s00239-014-9663-7 · Cited by 44

Realistic artificial DNA sequences as negative controls for computational genomics

Caballero, J., Smit, A. F. A., Hood, L., & Glusman, G. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku356 · Cited by 35

Reaching the depth of the Chinese hamster ovary cell transcriptome

Jacob, N. M., Kantardjieff, A., Yusufi, F. N. K., Retzel, E. F., Mulukutla, B. C., Chuah, S. H., Yap, M., & Hu, W. (2010) · Biotechnology and Bioengineering · doi:10.1002/bit.22588 · Cited by 33

Comparative Analysis of Teleost Genome Sequences Reveals an Ancient Intron Size Expansion in the Zebrafish Lineage

Moss, S. P., Joyce, D. A., Humphries, S., Tindall, K. J., & Lunt, D. H. (2011) · Genome Biology and Evolution · doi:10.1093/gbe/evr090 · Cited by 28

Repression of interrupted and intact rDNA by the SUMO pathway in drosophila melanogaster

Luo, Y., Fefelova, E., Ninova, M., Chen, Y.-C. A., & Aravin, A. A. (2020) · eLife · doi:10.7554/elife.52416 · Cited by 19

SINEs, evolution and genome structure in the opossum

Gu, W., Ray, D. A., Walker, J. A., Barnes, E. W., Gentles, A. J., Samollow, P. B., Jurka, J., Batzer, M. A., & Pollock, D. D. (2007) · Gene · doi:10.1016/j.gene.2007.02.028 · Cited by 18

DNA Polymerase Diversity Reveals Multiple Incursions of Polintons During Nematode Evolution

(2023) · doi:10.1093/molbev/msad274 · Cited by 12

Chromosome-level genome assembly of the glass catfish (Kryptopterus vitreolus) reveals molecular clues to its transparent phenotype

Bian, C., 深圳大学生命与海洋科学学院水产基因组学实验室, 广. 深. 5., Laboratory of Aquatic Genomics, C. O. L. S. A. O., Li, R.-H., Ruan, Z.-Q., Chen, W.-T., Huang, Y., Liu, L.-Y., Zhou, H.-L., Chong, C.-M., et al. (2024) · Zoological Research · doi:10.24272/j.issn.2095-8137.2023.396 · Cited by 4

Patterns and Processes of Genomic Evolution Inferred From the Ten Smallest Vertebrate Genomes

Liu, K., Wang, Q., Wang, N., Meng, L., Li, S., Wang, H., Liu, Y., Liu, Q., Zhang, Y., Doretto, L. B., et al. (2025) · Advanced Science · doi:10.1002/advs.202417251 · Cited by 3

A telomere-to-telomere chromosome-scale genome assembly of glass catfish (Kryptopterus vitreolus)

Bian, C., Li, D., Wang, Y., He, Z., Chen, W.-T., Chong, C.-M., Zhou, H., & Shi, Q. (2025) · Scientific Data · doi:10.1038/s41597-025-04841-z · Cited by 2

A complete telomere-to-telomere chromosome-level genome assembly of X-ray tetra (Pristella maxillaris)

Bian, C., Hu, C., He, Z., Li, Z., & Shi, Q. (2025) · Scientific Data · doi:10.1038/s41597-025-04824-0 · Cited by 2