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

Cited by (410)

Items 201–300 of 410

  1. An evolutionarily conserved constellation of functional cis-elements programs the virus-responsive fate of the human (epi)genome
    Marianna A. Koutsi, Marialena Pouliou, Dimitris Chatzopoulos, Lydia Champezou, Konstantinos Zagkas, Marili Vasilogianni, Alexandra G. Kouroukli, Marios Agelopoulos · 2025 · Nucleic Acids Research
  2. Confounding factors in profiling of locus-specific human endogenous retrovirus (HERV) transcript signatures in primary T cells using multi-study-derived datasets
    Martin V. Hamann, Maisha Adiba, Ulrike C. Lange · 2023 · BMC Medical Genomics
  3. A method to enrich and purify centromeric DNA from human cells
    Riccardo Gamba, Giulia Mazzucco, Therese Wilhelm, Florian Chardon, Léonid Velikovsky, Julien Picotto, Ylli Doksani, Daniele Fachinetti · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
  4. TandemAligner: a new parameter-free framework for fast sequence alignment
    Andrey V. Bzikadze, Pavel A. Pevzner · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
  5. Complete Reference Genome and Pangenome Expand Biologically Relevant Information for Genome-Wide DNA Methylation Analysis Using Short-Read Sequencing and Array Data
    Zheng Dong, Joanne Whitehead, Maggie Fu, Julia L. MacIsaac, David H. Rehkopf, Luis Rosero‐Bixby, Michael Steffen Kobor, Keegan D. Korthauer · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
  6. Evaluation of Long-Read RNA Sequencing Procedures for Novel Isoform Identification and Quantification in Human Whole Blood
    Hikari Okada, Alessandro Nasti, Yoshio Sakai, Yumie Takeshita, Sadahiro Iwabuchi, Tuyen Thuy Bich Ho, Tomomi Hashiba, Noboru Takata, Takaaki Sato, Takeshi Urabe et al. · 2025 · Genes
  7. Leveraging cfDNA fragmentomic features for the early detection of colorectal cancer
    Lina Shan, Dengyong Xu, Jie Chen, Wenjia Liu, Ji Lin, Juhang Bao, Jianfei Huang, Hanqing Zhang, Hanchen Zhao, Wei Xue et al. · 2026 · Frontiers in Immunology
  8. Loss of SETDB1-mediated H3K9me3 in human neural progenitor cells leads to transcriptional activation of L1 retrotransposons
    Ofelia Karlsson, Ninoslav Pandiloski, Vivien Horváth, Anita Adami, Raquel Garza, Pia Annette Johansson, Jonas Johansson, Christopher H. Douse, Johan Jakobsson · 2026 · Nucleic Acids Research
  9. Multiplexed TrAEL-seq captures DNA replication dynamics in mammalian cells
    Neesha Kara, Laura Biggins, Alex J. Whale, Kieron May, Vera V. Grinkevich, Paola Garran-Garcia, Jhanavi Srinivasan, Peter J. Rugg‐Gunn, Claudia Ribeiro de Almeida, Samantha J. Walker et al. · 2026 · Nucleic Acids Research
  10. Unraveling Non-B DNA Structures in the Era of Telomere-to-Telomere Genomes
    Kateryna D. Makova, Saswat Mohanty, Linnéa Smeds, Jacob P. Sieg, Angelika Lahnsteiner · 2026 · Annual Review of Genomics and Human Genetics
  11. Molecular mechanisms regulating cGAS/STING activation in health and disease
    Min-Guk Cho, Rachel Lee, Jaycee Johnson, Gaorav P. Gupta · 2026 · Journal of Clinical Investigation
  12. Churros: a Docker-based pipeline for large-scale epigenomic analysis
    Jiankang Wang, Ryuichiro Nakato · 2023 · DNA Research
  13. Microsatellite density landscapes illustrate short tandem repeats aggregation in the complete reference human genome
    Yun Xia, Douyue Li, Tingyi Chen, Saichao Pan, Hanrou Huang, Wenxiang Zhang, Yulin Liang, Yongzhuo Fu, Zhuli Peng, Hongxi Zhang et al. · 2024 · BMC Genomics
  14. Leveraging long-read assemblies and machine learning to enhance short-read transposable element detection and genotyping
    Austin Daigle, Logan S. Whitehouse, Roy Zhao, J. J. Emerson, Daniel R. Schrider · 2026 · Genetics
  15. Zygotic activation of transposable elements during zebrafish early embryogenesis
    Bo Li, Ting Li, Dingjie Wang, Ying Yang, Puwen Tan, Yunhao Wang, Yun-Gui Yang, Shunji Jia, Kin Fai Au · 2025 · Nature Communications
  16. Complete reference genome and pangenome improve genome-wide detection and interpretation of DNA methylation using sequencing and array data
    Zheng Dong, Joanne Whitehead, Maggie Fu, Julia L. MacIsaac, David H. Rehkopf, Luis Rosero‐Bixby, Michael Steffen Kobor, Keegan D. Korthauer · 2025 · Cell Reports
  17. From Junk DNA to Genomic Treasure: Impacts of Transposable Element DNA , RNA , and Protein in Mammalian Development and Disease
    Ten D. Li, Katelyn Toohill, Andrew J. Modzelewski · 2025 · Wiley Interdisciplinary Reviews - RNA
  18. An allele-resolved nanopore-guided tour of the human placental methylome
    Michaela Kindlova, Hannah Byrne, Jade M Kubler, Sarah Elizabeth Steane, Jessica Whyte, Danielle J. Borg, Vicki Lee Clifton, Adam D. Ewing · 2025 · Nature Communications
  19. STRavinsky STR database and PGTailor PGT tool demonstrate superiority of CHM13-T2T over hg38 and hg19 for STR-based applications
    Noam Hadar, Ginat Narkis, Shirly Amar, Marina Varnavsky, Glenda Calniquer Palti, Amit Safran, Ohad S. Birk · 2023 · European Journal of Human Genetics
  20. Unique repetitive nucleic acid structures mirror switch regions in the human IgH locus
    Ophélie Dézé, Delfina Ordanoska, Delphine Rossille A, Emma Miglierina, Brice Laffleur, Michel Cogné · 2023 · Biochimie
  21. Improving the Completeness of Chromosome-Level Assembly by Recalling Sequences from Lost Contigs
    Junyang Liu, Fang Liu, Weihua Pan · 2023 · Genes
  22. RepEnTools: an automated repeat enrichment analysis package for ChIP-seq data reveals hUHRF1 Tandem-Tudor domain enrichment in young repeats
    Michel Choudalakis, Pavel Bashtrykov, Albert Jeltsch · 2024 · Mobile DNA
  23. Probabilistic and machine-learning methods for predicting local rates of transcription elongation from nascent RNA sequencing data
    Lingjie Liu, Yixin Zhao, Rebecca Hassett, Shushan Toneyan, Peter K. Koo, Adam C. Siepel · 2025 · Nucleic Acids Research
  24. Replicative DNA polymerase epsilon and delta holoenzymes show wide-ranging inhibition at G-quadruplexes in the human genome
    Suzanne E. Hile, Matthias H. Weissensteiner, Kara G Pytko, Joseph M. Dahl, Eduard Kejnovský, Iva Kejnovská, Mark Hedglin, Ilias Georgakopoulos‐Soares, Kateryna D. Makova, Kristin A. Eckert · 2025 · Nucleic Acids Research
  25. Comprehensive fragmentation of cell-free repetitive DNA for enhanced cancer detection in plasma
    Mingguang Zhang, Shuohui Dong, Wei Rao, Shiwen Mei, Gang Hu, Ling Liu, Zhen Wang, Jianqiang Tang · 2025 · Frontiers in Cell and Developmental Biology
  26. The evolutionary entanglement of flipons with zinc fingers and retroelements has engendered a large family of Z-DNA and G-quadruplex binding proteins
    Alan G. Herbert · 2025 · Open Biology
  27. A critique of the hypothesis that CA repeats are primary targets of neuronal MeCP2
    Kashyap Chhatbar, John C. Connelly, Shaun Webb, Skirmantas Kriaučionis, Adrian Peter Bird · 2022 · Life Science Alliance
  28. An Atlas of Linkage Disequilibrium Across Species
    T. J. Zhu, Xing Huang, Mengyuan Yang, Guo‐An Qi, Qi-Xin Zhang, Feng Lin, Wenjing Zhang, Zhe Zhang, Xin Jin, Hou‐Feng Zheng et al. · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
  29. RAmbler resolves complex repeats in human Chromosomes 8, 19, and X
    Sakshar Chakravarty, Glennis A. Logsdon, Stefano Lonardi · 2025 · Genome Research
  30. Birth of protein-coding exons by ancient domestication of LINE-1 retrotransposon
    K. Kitao, Kenji Ichiyanagi, So Nakagawa · 2025 · Genome Research
  31. Characterization of Somatic Mutations in Human tRNA Genes Reveals Tumor-Specific Mutational Loads, and the Generation of tRNA Variants that Alter the Genetic Code
    Marina Murillo-Recio, Marina Salvadores, Adrián Gabriel Torres, Lina Tsapanou, Aina Vaquer Picó, Fran Supek, Lluı́s Ribas de Pouplana · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
  32. Haplotype-Resolved Genomics Reveals Conserved Chromatin Architecture and Epigenetic Constraints of Human Neocentromeres
    Savannah J. Hoyt, Gabrielle A. Hartley, Mariah C. Antopia, Thomas W. Tullius, Dylan J. Taylor, Nicole M Tillquist, Shane J. Neph, Nicole Pauloski, Katherine M. Munson, Kendra Hoekzema et al. · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
  33. Novel Avenues for the Detection of Cancer-Associated Viral Genome Integrations Using Long-Read Sequencing Technologies
    Larissa-Anna Bergmann, Alicja Pacholewska, Michal R. Schweiger · 2025 · Cancers
  34. Graft-seq precisely maps RNA modifications via site-specific chemical grafting strategy
    Ting Li, Ke Ding, Ziming Bao, Quan Ma, Chenyang Huang, Jie Cao, Xiao Shu, Minsong Gao, Zisheng Luo, Xushen Xiong et al. · 2025 · Cell Reports Methods
  35. Accurate and Efficient Phylogenetic Inference through End-To-End Deep Learning
    Zhang, Xinru, Ding, Shizhe, Yu, Chungong, Zhao, Jianquan, Bu, Dongbo · 2025 · Molecular Biology and Evolution
  36. High interferon response signatures in SLE patient leukocytes are associated with increased transposable element expression in gene introns and intergenic regions
    Leo J. Arteaga-Vazquez, Hugo Sepúlveda, Bruno Villalobos Reveles, Kazumasa Suzuki, KENNETH C. KALUNIAN, Ferhat Ay, Mark Robin Boothby, Anjana Rao · 2025 · Mobile DNA
  37. A de novo H3.2K9me2 deposition pathway establishes heterochromatin for suppressing transposon mobilization during fly somatic development
    Yi Ni Luo, Yazi Deng, Yu Liang, Wei Wu, Wei Wu, Lu Wang · 2026 · Nucleic Acids Research
  38. Tracking mobilization uncovers an evolutionarily conserved mechanism in suppressing mobile genetic elements
    Lu Wang, Yu Liang, Shuheng Wu, Yazi Deng, Wei Wu, Z.Z. Zhao Zhang, Wei Wu, Lu Wang · 2026 · Molecular Cell
  39. AniAnn’s: alignment-free annotation of tandem repeat arrays using fast average nucleotide identity estimates
    Alexander P. Sweeten, Michael C. Schatz, Adam M. Phillippy · 2026 · Bioinformatics
  40. Recent insights into crosstalk between genetic parasites and their host genome
    Amit Kumar Mandal · 2022 · Briefings in Functional Genomics
  41. Grand challenge in chromatin epigenomics: everything, everywhere, all at once
    Sharon Dent · 2023 · Frontiers in Epigenetics and Epigenomics
  42. Repetitive Sequence Stability in Embryonic Stem Cells
    Guang W. Shi, Qianwen Pang, Zhancheng Lin, Xinyi Zhang, Kaimeng Huang · 2024 · International Journal of Molecular Sciences
  43. Cytogenetic bands and sharp peaks of Alu underlie large-scale segmental regulation of nuclear genome architecture
    Lisa L. Hall, Kevin M. Creamer, Meg Byron, Jeanne Bentley Lawrence · 2024 · Nucleus
  44. Transposable element expression is associated with sex chromosome number in humans
    Jordan Teoli, Miriam Merenciano, Marie Fablet, Anamaria Necşulea, Daniel Siqueira de Oliveira, Alessandro Brandulas Cammarata, Audrey Labalme, Hervé Lejeune, Jean‐François Lemaître, François Gueyffier et al. · 2025 · PLoS Genetics
  45. Human acrocentric chromosome short-arm de novo mutation and recombination
    Jiadong Lin, Francesco Kumara Mastrorosa, Michelle D. Noyes, DongAhn Yoo, Arang Rhie, David Porubskỳ, Kendra Hoekzema, Katherine M. Munson, Nidhi Koundinya, W. Scott Watkins et al. · 2026 · Cell
  46. Information: Its Role and Meaning in Organisms
    Leszek Konieczny, Irena Roterman‐Konieczna, Paweł Spólnik · 2023 · Springer eBooks
  47. The final pieces of the human genome
    Michael Attwaters · 2022 · Nature Reviews Genetics
  48. A refined characterization of large-scale genomic differences in the first complete human genome
    Xiangyu Yang, Xuankai Wang, Yawen Zou, Shilong Zhang, Manying Xia, Mitchell Robert Vollger, Nae-Chyun Chen, Dylan J. Taylor, William T. Harvey, Glennis A. Logsdon et al. · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
  49. Mini-heterochromatin domains constrain the cis -regulatory impact of SVA transposons in human brain development and disease
    Vivien Horváth, Raquel Garza, Marie E. Jönsson, Pia Annette Johansson, Anita Adami, Georgia Christoforidou, Ofelia Karlsson, Laura Castilla‐Vallmanya, Patricia Gerdes, Ninoslav Pandiloski et al. · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
  50. Cryptic endogenous retrovirus subfamilies in the primate lineage
    Xun Chen, Zicong Zhang, Yi-Zhi Yan, Clément Goubert, Guillaume Bourque, Fumitaka Inoue · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
  51. DNA-sequence and epigenomic determinants of local rates of transcription elongation
    Lingjie Liu, Yixin Zhao, Adam C. Siepel · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
  52. Genome-wide maps of highly-similar intrachromosomal repeats that mediate ectopic recombination in three human genome assemblies
    Luis Fernandez-Luna, Carlos Aguilar-Perez, Christopher M. Grochowski, Michele G. Mehaffey, Claudia M.B. Carvalho, Claudia G. Gonzaga-Jauregui · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
  53. RT2T: A Global Collaborative Project to Study Chromosomal Evolution in the Suborder Ruminantia
    Ted Kalbfleisch, Stephanie McKay, Brenda M. Murdoch, David L. Adelson, Diego Almansa-Villa, Gabrielle M. Becker, Linda M. Beckett, María José Benítez-Galeano, Fernando H. Biase, Theresa Casey et al. · 2024 · Research Square
  54. RetroTest unravels LINE-1 retrotransposition in Head and Neck Squamous Cell Carcinoma
    Jenifer Brea Iglesias, Ana Oitabén, Sonia Zumalave, Bernardo Rodríguez–Martín, María Gallardo‐Gómez, Martín Santamarina, Ana Pequeño‐Valtierra, Laura Juaneda‐Magdalena, Ramón García‐Escudero, José Luis López-Cedrún et al. · 2024 · medRxiv
  55. Distinct interferon response patterns link to increased transposable element expression in leukocytes of systemic lupus erythematosus patients
    Leo J. Arteaga-Vazquez, Hugo Sepúlveda, Bruno Villalobos Reveles, Kazumasa Suzuki, KENNETH C. KALUNIAN, Ferhat Ay, Mark Robin Boothby, Anjana Rao · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
  56. Identification of chromatin-associated RNAs at human centromeres
    Kelsey A. Fryer, Charles Limouse, Aaron F. Straight · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
  57. NANOME: A Nextflow pipeline for haplotype-aware allele-specific consensus DNA methylation detection by nanopore long-read sequencing
    Yang Liu, Hash Brown Taha, Qiuyang Zhang, Ziwei Pan, Christina Chatzipantsiou, Emma Wade, Thatcher Slocum, Lasya Karuturi, Yue Zhao, Shilpita Karmakar et al. · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
  58. DNA methylation dysregulation patterns in the 1p36 region instability
    Joanna Swierkowska, Michał Kabza, Małgorzata Rydzanicz, Maciej Giefing, Rafał Płoski, Lisa G. Shaffer, Marzena Gajęcka · 2024 · Journal of Applied Genetics
  59. Genome-wide maps of highly-similar intrachromosomal repeats that can mediate ectopic recombination in three human genome assemblies
    Luis Fernandez-Luna, Carlos Aguilar-Perez, Christopher M. Grochowski, Michele G. Mehaffey, Claudia M.B. Carvalho, Claudia G. Gonzaga-Jauregui · 2024 · Human Genetics and Genomics Advances
  60. Unraveling LINE ‐1 retrotransposition in head and neck squamous cell carcinoma
    Jenifer Brea Iglesias, Ana Oitabén, Sonia Zumalave, Bernardo Rodríguez–Martín, María Gallardo‐Gómez, Martín Santamarina, Ana Pequeño‐Valtierra, Laura Juaneda‐Magdalena, Ramón García‐Escudero, José Luis López-Cedrún et al. · 2025 · Molecular Oncology
  61. ZNF280AY: a pseudogene on the ovine Y chromosome and its copy number variation associated with testicular size in Hu sheep
    Yangkai Liu, Li Wang, Jialei Chen, Tajmal Hussain Solangi, Ran Li, Mengzhen Le, Xiangpeng Yue · 2025 · Journal of Animal Science
  62. Expression of LTR and LINE1 transposable elements defines atypical teratoid/rhabdoid tumor subtypes
    Martin V. Hamann, Shweta Godbole, Maisha Adiba, Sabrina M. Leddy, Jelena Navolić, Ghazaleh Tabatabai, Daniel J. Merk, Ulrike C. Lange, Julia E. Neumann · 2025 · Acta Neuropathologica Communications
  63. Repeats Influence Structural DNA Properties Around Functional Annotations Associated with 3D Organization and Transcription
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  64. A new era of bioinformatics
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  66. Coexistence of virome-encoded health-associated genes and pathogenic genes in global habitats
    Min Qian, Dong Zhu, Keyu Yao, Shu-yue Liu, Ming Li, Mao Ye, Yong‐Guan Zhu · 2025 · Applied and Environmental Microbiology
  67. Cis-regulatory co-option of a transposon family reinforces cell identity across the immune system
    Jason D. Chobirko, Cedric Feschotte, Andrew Grimson · 2026 · The EMBO Journal
  68. DNA repeats: origins, conservation, and role in human disease
    Ajay Kumar Rana · 2026 · Genome Instability & Disease
  69. Dark and camouflaged genomic regions remain challenging in CHM13
    Mark E. Wadsworth, Madeline L. Page, Bernardo Aguzzoli Heberle, Justin B. Miller, Cody J. Steely, Mark Ebbert · 2026 · Scientific Reports
  70. Protocol for efficient CRISPRi-mediated silencing of retrotransposons in human pluripotent stem cells
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  71. Centromere evolution in annual and perennial soybeans and its implication for hybridization in cultivated species
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  72. Superabundant microRNAs are transcribed from human rDNA spacer promoters insulated by CTCF
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  73. Human endogenous retrovirus profiling reveals heterogenous expression in cutaneous melanoma
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  74. Polymorphic CGG repeats in gene regulation and disease
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  75. Human Alu loci gain enhancer-type epigenetic modifications in monocytes during response to bacterial LPS
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  76. Neocentromeres fail to maintain DNA methylation boundaries, driving CENP-A drift, instability, and chromosome missegregation
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  77. Decoding the power of the microbiome in human health
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  78. T2T-CHM13 reference genome reduces mapping bias and enhances alignment accuracy at disease-associated variants
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  79. Assessing Hardy-Weinberg equilibrium in T2T-aligned 1000 genomes project
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  80. Epigenetics and genotypic variation
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  81. Hétérochromatine et contrôle épigénétique des séquences répétées
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  83. REPrise: de novo interspersed repeat detection using inexact seeding
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  84. Cap Analysis of Gene Expression Clarifies Transcriptomic Divergence Within Monozygotic Twin Pairs
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  85. A computational model of the line-1 retrotransposon life cycle and visualization of metabolic networks in 3-dimensions.
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  86. Allele pairing at Sun1-enriched domains at the nuclear periphery via T 1 A 3 tandem DNA repeats
    Gayan I. Balasooriya, David L. Spector · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
  87. Telomere-to-Telomere Assembly Improves Host Reads Removal in Metagenomic High-Throughput Sequencing of Human Samples
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  88. RAmbler: de novo genome assembly of complex repetitive regions
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  89. Efficient estimation for large-scale linkage disequilibrium patterns of the human genome
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  92. REPrise: de novo interspersed repeat detection using inexact seeding
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  93. RT2T: A Global Collaborative Project to Study Chromosomal Evolution in the Suborder Ruminantia
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  94. Birth of protein-coding exons by ancient domestication of LINE retrotransposon
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  95. TAD hierarchy restricts poised LTR activation and loss of TAD hierarchy promotes LTR co-option in cancer
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  96. Mobile element insertions affect human pigmentation and skin cancer risk
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  97. Tracking mobilization uncovers an evolutionarily conserved mechanism in suppressing transpositions during somatic development
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  98. Sequencing the gaps: dark genomic regions persist in CHM13 despite long-read advances
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  99. TrAEL-seq captures DNA replication dynamics in mammalian cells
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  100. A complete and near-perfect rhesus macaque reference genome: lessons from subtelomeric repeats and sequencing bias
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