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

Cited by (410)

Items 301–400 of 410

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  4. Retroviral insertions contributed to the divergence of human and chimpanzee brains
    Patricia Gerdes, Ofelia Karlsson, Raquel Garza, Diahann A. M. Atacho, PingHsun Hsieh, Bharat Prajapati, Chandramouli Muralidharan, Anita Adami, Carrie Davis-Hansson, Emily M. Johansson et al. · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
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    Simona Giunta, Tatsuo Fukagawa, Rachel J. Waugh O'Neill, Bungo Akiyoshi · 2025 · Chromosoma
  7. KaryoScope: rapid, alignment-free sequence annotation for the pangenome era
    T. Rhyker Ranallo-Benavidez, Yi‐An Chen, Tamara Potapova, Jarno Alanko, Hailey Loucks, Julian Lucas, Andrea Guarracino, Simon J. Puglisi, Camille Marchet, Karen H. Miga et al. · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
  8. The human RNA-DNA interactome is cell type-specific and dynamic
    Alice Lambolez, Pelin Sahlén, Wenjing Kang, Xufeng Shu, Jessica Severin, Rodrigo Pracana, Ilyes Abdelhamid, Bhavya Dhaka, Christophe Vroland, Valeria Ranzani et al. · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
  9. Compliant Multi-electrode Micro-channel Array for Recording Afferent Nerve Activity
    Evangelos Delivopoulos, Daniel J. Chew, Ivan Rusev Minev, James W. Fawcett, Stéphanie P. Lacour · 2012
  10. The complete Human Genome sequenced by Telomere to Telomere (T2T) consortium
    Sanjesh Kumar, Aksh Chahal, Mansi Singh · 2022
  11. The future of reproductive medicine with an expanding toolkit: completion of the human reference genome
    David Fred Albertini · 2022 · Journal of Assisted Reproduction and Genetics
  12. Chromosomes: Noncoding DNA (Including Satellite DNA)
    Sierra M Mortimer, Trenton J. Frisbie, John B. Moldovan, Mitsuhiro Nakamura, Siara N. Sandwith, John Yin, John V. Moran · 2022 · Wiley eBooks
  13. EASTR: Correcting systematic alignment errors in multi-exon genes
    Ida Shinder, Richard Hu, Hyun Joo Ji, Kuan-Hao Chao, Mihaela Pertea · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
  14. Exploring the Expression of the «Dark Matter» of the Genome in Mesothelioma for Potentially Predictive Biomarkers for Prognosis and Immunotherapy
    Emanuela Felley‐Bosco · 2023 · Cancers
  15. Human Endogenous Retroviruses in Triple‐Negative Breast Cancer
    Tara Patricia Hurst, Timokratis Karamitros, Gkikas Magiorkinis · 2023 · Wiley eBooks
  16. Efficient estimation for large-scale linkage disequilibrium patterns of the human genome
    Xin Huang, T. J. Zhu, Yingchao Liu, Guo‐An Qi, Jiannan Zhang, Guo‐Bo Chen · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
  17. Del genoma humano a su pangenoma pasando por los consorcios ENCODE y T2T
    Manuel Gonzalo Claros · 2022 · Encuentros en la Biología
  18. ProA and ProB repeat sequences shape 3D genome organization in eukaryotes
    Konstantinn Bonnet, Nicolas Hulo, Raphaël Mourad, Adam D. Ewing, Olivier Croce, Magali Naville, Nikita S. Vassetzky, Éric Gilson, Didier Picard, Geneviève Fourel · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
  19. Genetic testing in clinical laboratory diagnostics: Present and future
    Щербо Сергей Николаевич, Dmitry S. Shcherbo, Alexander A. Novikov, M. I. Savina, Т. И. Туркина · 2023 · Medical alphabet
  20. Efficient estimation for large-scale linkage disequilibrium patterns of the human genome
    Xin Huang, T. J. Zhu, Yingchao Liu, Guo‐An Qi, Jiannan Zhang, Guo‐Bo Chen · 2023 · eLife
  21. Reply from Daniel Phillips and Denis Noble
    Daniel Phillips, Denis Noble · 2024 · The Journal of Physiology
  22. Additional file 2 of Characterization of large-scale genomic differences in the first complete human genome
    Xiangyu Yang, Xuankai Wang, Yawen Zou, Shilong Zhang, Manying Xia, Lianting Fu, Mitchell Robert Vollger, Nae-Chyun Chen, Dylan J. Taylor, William T. Harvey et al. · 2023 · Figshare
  23. Exploring Alu -Driven DNA Transductions in the Primate Genomes
    Reza Halabian, Jessica M. Storer, Savannah J. Hoyt, Gabrielle A. Hartley, Juergen Brosius, Rachel J. Waugh O'Neill, Wojciech Makałowski · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
  24. Isoform and pathway-specific regulation of post-transcriptional RNA processing in human cells
    Karan Bedi, Brian Magnuson, Ishwarya Venkata Narayanan, Ariel McShane, Mario Ashaka, Michelle T. Paulsen, Thomas E. Wilson, Mats E. Ljungman · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
  25. Structural Optimization of Azacryptands for Targeting Three‐Way DNA Junctions
    Angélique Pipier, Titouan Chetot, Apollonia Kalamatianou, Nicolas Martin, Maëlle Caroff, Sébastien Britton, Nicolas Chéron, Lukáš Trantı́rek, Anton Granzhan, David Monchaud · 2024 · Angewandte Chemie
  26. Exploring Alu-Driven DNA Transductions in the Primate Genomes
    Reza Halabian, Jessica M. Storer, Savannah J. Hoyt, Gabrielle A. Hartley, Jürgen Brosius, Rachel J. Waugh O'Neill, Wojciech Makałowski · 2024 · Research Square
  27. Transposable element small and long RNAs in aging brains and implications in Huntington’s and Parkinson’s disease
    Gargi Dayama, Shruti Gupta, Brianne K. Connizzo, Adam Thomas Labadorf, Richard H. Myers, Nelson C. Lau · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
  28. Alu overexpression leads to increased double-stranded RNA in dermatomyositis
    Rayan Najjar, Andrew Lee Mammen, Tomas Mustelin · 2024 · medRxiv
  29. Evolutionary Biology and Christian Responses
    Michael L. Peterson, Timothy J. Pawl, Ben F. Brammell · 2024 · Cambridge University Press eBooks
  30. Decoding the Genetic Code: Scientific Exploration of the Telomere-to- Telomere (T2T) Genome
    Linjuan Wang, Yujia Li, Zhepei Zhang, Fengcheng Song, Yufei Zan, Ranxi Zheng, Zhengrong Yuan · 2024 · Current Bioinformatics
  31. Genomic feature of filled regions of telomere-to-telomere genomes in five model species
    Chu Xiong, Jun Zheng, Hui Zhang, Yunpeng Zhang, Lihong Hao, Min Wang, Zhen Liang · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
  32. Genome recombination on demand
    Marta Seczyńska, Lars Michael Steinmetz · 2025 · Science
  33. Cytogenomic characterization of karyotypes with additional autosomal material
    Priscila Soares Rodrigues, Bruna Burssed, Fernanda Teixeira da Silva Bellucco, Debora Cristina Batista Rosolen, Chong Ae Kim, Maria Isabel Melaragno · 2025 · Scientific Reports
  34. Nuclear mitochondrial sequences in great ape telomere-to-telomere genomes
    Edmundo Torres-González, Marzia Angela Cremona, Jessica M. Storer, Mario Ventura, Rachel J. Waugh O'Neill, Kateryna D. Makova · 2026 · Genome Research
  35. Emerging Functions of the Repeat Genome in Nuclear Structure: A View from the Human Karyotype
    Lisa L. Hall, Kelly P. Smith, Jeanne Bentley Lawrence · 2025 · Annual Review of Genomics and Human Genetics
  36. Retrotransposon methylation profiles and survival in Black women with high-grade serous ovarian carcinoma
    Christelle Colin, Katherine A. Lawson‐Michod, Courtney E. Johnson, Irma Vlasac, Sean Yoder, Tania Mesa, Dana Roeber, Chad Daniel Huff, Michelle A.T. Hildebrandt, Kristin Haller et al. · 2025 · Clinical Epigenetics
  37. El código del genoma humano por fin está completo
    Gabrielle A. Hartley · 2022 · The Conversation
  38. The Human Genome Project pieced together only 92% of the DNA – now scientists have finally filled in the remaining 8%
    Gabrielle A. Hartley · 2022 · The Conversation
  39. Les scientifiques ont complété le casse-tête du génome humain
    Gabrielle A. Hartley · 2022 · The Conversation
  40. Short tandem repeats and tandem repeat disorders
    Runze Ma, Tiancheng Liu, Bing Zhu · 2025 · Scientia Sinica Vitae
  41. Transposable elements as key regulators of placental development
    M. A. Zhilkina, Ekaterina N. Tolmacheva, S. А. Vasilyev · 2025 · Vavilov Journal of Genetics and Breeding
  42. Activation of transposable elements is linked to a region- and cell type–specific interferon response in Parkinson’s disease
    Raquel Garza, Anita Adami, Arun Thiruvalluvan, Sasvi S. Wijesinghe, Annabel J. Curle, Oliver H. Tam, Talitha Forcier, Danai A Lagka, Nina-Lydia Kazakou, Diahann A. M. Atacho et al. · 2026 · Science Advances
  43. NanoVar: a comprehensive workflow for structural variant detection to uncover the genome’s hidden patterns
    Asmaa Samy, Cheng Yong Tham, Matthew Dyer, Touati Benoukraf · 2025 · Nature Protocols
  44. Pan-cancer analysis reveals context-dependent roles of LINE-1 ORF1p in immune regulation and copy number alterations
    Efiyenia Ismini Kaparos, Wenjing Zhang, Ryusei Miyanaga, Wilson McKerrow, Jef D. Boeke, Teresa Davoli, Paolo Mita, Kelly V. Ruggles, David Fenyö · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
  45. Direct identification of de novo mobile element insertions from single molecule sequencing of human sperm
    Stacy Li, Landen Gozashti, Caitlin Connelly, Clément Goubert, Kenneth Aston, Joseph G. Gleeson, Aaron R. Quinlan, Xiaoxu Yang, Peter H. Sudmant · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
  46. The Role of Transposable Elements in Development
    John R. McCoy, Tara T. Doucet-O’Hare · 2025 · Epigenetics and human health
  47. X-LDR: an atlas of linkage disequilibrium across species
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  48. Flipons: Biological roles of alternative nucleic acid conformations
    Alan G. Herbert · 2025 · Elsevier eBooks
  49. The Relationship between Hereditary Predisposition and Epigenetic Mechanisms of Schizophrenia Development
    Rustam Nailevich Mustafin · 2025 · OBM Neurobiology
  50. Additional file 2 of 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 · Figshare
  51. Additional file 3 of 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 · Figshare
  52. Additional file 1 of Characterization of large-scale genomic differences in the first complete human genome
    Yang, Xiangyu, Wang, Xuankai, Zou, Yawen, Zhang, Shilong, Manying Xia, Lianting Fu, Mitchell Robert Vollger, Chen, Nae-Chyun, Dylan J. Taylor, William T. Harvey et al. · 2023 · Figshare
  53. Additional file 3 of Characterization of large-scale genomic differences in the first complete human genome
    Yang, Xiangyu, Wang, Xuankai, Zou, Yawen, Zhang, Shilong, Manying Xia, Lianting Fu, Mitchell Robert Vollger, Chen, Nae-Chyun, Dylan J. Taylor, Harvey, William T. et al. · 2023 · Figshare
  54. Additional file 1 of 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 · Figshare
  55. Origin and evolution of acrocentric chromosomes in human and great apes
    Steven J. Solar, Prajna Hebbar, Leonardo Gomes de Lima, Alexander P. Sweeten, Arang Rhie, Tamara Potapova, Luciana de Gennaro, Andrea Guarracino, Juhyun Kim, Brandon D. Pickett et al. · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
  56. Genome-wide analysis of FSHD cell lines using Nanopore sequencing reveals allele-specific differences at DUX4 target genes and complex repeats
    Jasmine Sakr, Xiangduo Kong, Negar Mojgani, Erisa Taghizadeh, Elnaz Abdollahzadeh, Kyoko Yokomori, Ali Mortazavi · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
  57. Chromosome-naïve global networks of initiators of hybrid assembly pathways of endogenous multiprotein complexes
    Gennadi V. Glinsky · 2026 · Research Square
  58. Synthetic rewriting technologies in mammalian cells
    Yuqi Wang, Yali Cui, Guang-Rong Zhao, Yi Wu, Ying‐Jin Yuan · 2026 · Nature Communications
  59. Parallel profiling of genome mutations and multiple chromatin modalities in single cells by scNanoCT&ATAC-seq
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  60. XhetRel: a pipeline for X heterozygosity and relatedness analysis of sequencing data
    Barış Salman, Nerses Bebek, Sibel Uğur İşeri · 2026 · Bioinformatics Advances
  61. Unraveling novel transposable elements (TEs)-driven gene dysregulation in non-small cell lung cancer (NSCLC) by integrated transcriptomic and TEs analysis
    S Shrinidhi, R. Sagaya Jansi, Ameer Khusro · 2026 · Computational Biology and Chemistry
  62. Evolution and Comparative Analysis of Sheep Reference Genomes: From Fragmented Assemblies to Telomere-to-Telomere Genomics
    Dan Yue, Ying Lu, Yuqing Chong, Jiao Wu, Zhendong Gao, Ruoshan Ma, Keyu Li, Weidong Deng, Bo Wang · 2026 · Biology
  63. The Role of Transposable Elements in the Development of Aggressive Behavior in Pigs
    Rustam Nailevich Mustafin, А В Казанцева, I. R. Gilyazova, T. V. Leonova, E. K. Khusnutdinova, O. G. Gusev · 2026 · Russian Journal of Genetics
  64. Resolving repetitive and telomeric regions through a high-contiguity genome assembly of the African Turquoise killifish
    Nagyeong Kim, Chang-Myung Oh, Yumi Kim, Jun Ho Kim · 2026 · Genes & Genomics
  65. Mechanisms of Interactions of Circular RNAs with Mobile Elements and MicroRNAs in the Development of Breast Cancer
    Rustam Nailevich Mustafin · 2026 · Molecular Biology
  66. Protocol to identify SINE-VNTR-Alu regulators using genome-wide screening in human K562 cells
    Ziqiang Zhou, Shicong Zhu, Deng Pan, Hsiang‐Ying Lee, Nian Liu · 2026 · STAR Protocols
  67. Epigenomic methylome landscape of promoters in vertebrate genomes
    Young Ho Lee, Chul Min Lee, Erich D. Jarvis, Heebal Kim · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
  68. CRISPR-mediated regulation of apoptosis in cancer: Molecular targets, mechanisms, and translational challenges
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  69. Dynamics of H3.1 and H3.3 histone variants at mouse chromocenters during cell cycle and differentiation
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  70. Investigating the role of the centromeric histone variant CENP-A in cancer
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  71. PERREO: An integrated pipeline for repetitive elements analysis enables the repeatome expression profiling in cancer
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  72. Diploid telomere-to-telomere assemblies reveal hierarchical satellite architectures and heritable MHC structural diversity in macaques
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  74. 1950–2000: five decades of curiosity-driven discovery in alternative DNA structures
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  76. Repetitive DNA-resolved epigenomics maps chromatin rewiring during aging and malignant transformation
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  77. Retroelement Hypomethylation Links Hypoxia Signaling, Immune Phenotypes, and Survival in Clear Cell Renal Cell Carcinoma
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  78. Prospects for retroelement-targeted therapy of schizophrenia
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  79. A long-read human pangenome initiative for comprehensive interpretation of nuclear-embedded mitochondrial DNA
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  83. Transposable element small RNAs and large RNAs in aging brains and implications in Huntington's and Parkinson's disease
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  87. De novo missense variants in TRIM28 identified in individuals with neurodevelopmental delay show features of transposable element activation
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  88. ONT-only genome assembly of a Korean male individual using a semen sample
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  92. Cooperation of transposable elements to endow global networks of initiators of hybrid assembly pathways of endogenous multiprotein complexes
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  93. Complex subtelomeric architectures in a complete rhesus macaque reference genome
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  100. Telomere-to-telomere co-mapping of transposable elements and human genes identifies a cluster of young L1 elements in the interferon-alpha domain with potential evolutionary arms-race
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