From telomere to telomere: The transcriptional and epigenetic state of human repeat elements
Hoyt, Savannah J., Storer, Jessica M., Hartley, Gabrielle A., Grady, Patrick G. S., Gershman, Ariel, de Lima, Leonardo G., Limouse, Charles, Halabian, Reza, Wojenski, Luke, Rodriguez, Matias, Altemose, Nicolas, Rhie, Arang, Core, Leighton J., Gerton, Jennifer L., Makalowski, Wojciech, Olson, Daniel, Rosen, Jeb, Smit, Arian F. A., Straight, Aaron F., Vollger, Mitchell R., Wheeler, Travis J., Schatz, Michael C., Eichler, Evan E., Phillippy, Adam M., Timp, Winston, Miga, Karen H., O’Neill, Rachel J.·2022·Science
Cited by (410)
Items 301–400 of 410
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- Exploring the Expression of the «Dark Matter» of the Genome in Mesothelioma for Potentially Predictive Biomarkers for Prognosis and ImmunotherapyEmanuela Felley‐Bosco · 2023 · Cancers
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- Efficient estimation for large-scale linkage disequilibrium patterns of the human genomeXin Huang, T. J. Zhu, Yingchao Liu, Guo‐An Qi, Jiannan Zhang, Guo‐Bo Chen · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
- Del genoma humano a su pangenoma pasando por los consorcios ENCODE y T2TManuel Gonzalo Claros · 2022 · Encuentros en la Biología
- ProA and ProB repeat sequences shape 3D genome organization in eukaryotesKonstantinn 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)
- Genetic testing in clinical laboratory diagnostics: Present and futureЩербо Сергей Николаевич, Dmitry S. Shcherbo, Alexander A. Novikov, M. I. Savina, Т. И. Туркина · 2023 · Medical alphabet
- Efficient estimation for large-scale linkage disequilibrium patterns of the human genomeXin Huang, T. J. Zhu, Yingchao Liu, Guo‐An Qi, Jiannan Zhang, Guo‐Bo Chen · 2023 · eLife
- Reply from Daniel Phillips and Denis NobleDaniel Phillips, Denis Noble · 2024 · The Journal of Physiology
- Additional file 2 of Characterization of large-scale genomic differences in the first complete human genomeXiangyu 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
- Exploring Alu -Driven DNA Transductions in the Primate GenomesReza 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)
- Isoform and pathway-specific regulation of post-transcriptional RNA processing in human cellsKaran 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)
- Structural Optimization of Azacryptands for Targeting Three‐Way DNA JunctionsAngélique Pipier, Titouan Chetot, Apollonia Kalamatianou, Nicolas Martin, Maëlle Caroff, Sébastien Britton, Nicolas Chéron, Lukáš Trantı́rek, Anton Granzhan, David Monchaud · 2024 · Angewandte Chemie
- Exploring Alu-Driven DNA Transductions in the Primate GenomesReza Halabian, Jessica M. Storer, Savannah J. Hoyt, Gabrielle A. Hartley, Jürgen Brosius, Rachel J. Waugh O'Neill, Wojciech Makałowski · 2024 · Research Square
- Transposable element small and long RNAs in aging brains and implications in Huntington’s and Parkinson’s diseaseGargi Dayama, Shruti Gupta, Brianne K. Connizzo, Adam Thomas Labadorf, Richard H. Myers, Nelson C. Lau · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
- Alu overexpression leads to increased double-stranded RNA in dermatomyositisRayan Najjar, Andrew Lee Mammen, Tomas Mustelin · 2024 · medRxiv
- Evolutionary Biology and Christian ResponsesMichael L. Peterson, Timothy J. Pawl, Ben F. Brammell · 2024 · Cambridge University Press eBooks
- Decoding the Genetic Code: Scientific Exploration of the Telomere-to- Telomere (T2T) GenomeLinjuan Wang, Yujia Li, Zhepei Zhang, Fengcheng Song, Yufei Zan, Ranxi Zheng, Zhengrong Yuan · 2024 · Current Bioinformatics
- Genomic feature of filled regions of telomere-to-telomere genomes in five model speciesChu Xiong, Jun Zheng, Hui Zhang, Yunpeng Zhang, Lihong Hao, Min Wang, Zhen Liang · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
- Genome recombination on demandMarta Seczyńska, Lars Michael Steinmetz · 2025 · Science
- Cytogenomic characterization of karyotypes with additional autosomal materialPriscila Soares Rodrigues, Bruna Burssed, Fernanda Teixeira da Silva Bellucco, Debora Cristina Batista Rosolen, Chong Ae Kim, Maria Isabel Melaragno · 2025 · Scientific Reports
- Nuclear mitochondrial sequences in great ape telomere-to-telomere genomesEdmundo Torres-González, Marzia Angela Cremona, Jessica M. Storer, Mario Ventura, Rachel J. Waugh O'Neill, Kateryna D. Makova · 2026 · Genome Research
- Emerging Functions of the Repeat Genome in Nuclear Structure: A View from the Human KaryotypeLisa L. Hall, Kelly P. Smith, Jeanne Bentley Lawrence · 2025 · Annual Review of Genomics and Human Genetics
- Retrotransposon methylation profiles and survival in Black women with high-grade serous ovarian carcinomaChristelle 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
- El código del genoma humano por fin está completoGabrielle A. Hartley · 2022 · The Conversation
- 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
- Les scientifiques ont complété le casse-tête du génome humainGabrielle A. Hartley · 2022 · The Conversation
- Short tandem repeats and tandem repeat disordersRunze Ma, Tiancheng Liu, Bing Zhu · 2025 · Scientia Sinica Vitae
- Transposable elements as key regulators of placental developmentM. A. Zhilkina, Ekaterina N. Tolmacheva, S. А. Vasilyev · 2025 · Vavilov Journal of Genetics and Breeding
- Activation of transposable elements is linked to a region- and cell type–specific interferon response in Parkinson’s diseaseRaquel 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
- NanoVar: a comprehensive workflow for structural variant detection to uncover the genome’s hidden patternsAsmaa Samy, Cheng Yong Tham, Matthew Dyer, Touati Benoukraf · 2025 · Nature Protocols
- Pan-cancer analysis reveals context-dependent roles of LINE-1 ORF1p in immune regulation and copy number alterationsEfiyenia 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)
- Direct identification of de novo mobile element insertions from single molecule sequencing of human spermStacy 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)
- The Role of Transposable Elements in DevelopmentJohn R. McCoy, Tara T. Doucet-O’Hare · 2025 · Epigenetics and human health
- X-LDR: an atlas of linkage disequilibrium across speciesT. 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. · 2025 · Genome biology
- Flipons: Biological roles of alternative nucleic acid conformationsAlan G. Herbert · 2025 · Elsevier eBooks
- The Relationship between Hereditary Predisposition and Epigenetic Mechanisms of Schizophrenia DevelopmentRustam Nailevich Mustafin · 2025 · OBM Neurobiology
- Additional file 2 of RepEnTools: an automated repeat enrichment analysis package for ChIP-seq data reveals hUHRF1 Tandem-Tudor domain enrichment in young repeatsMichel Choudalakis, Pavel Bashtrykov, Albert Jeltsch · 2024 · Figshare
- Additional file 3 of RepEnTools: an automated repeat enrichment analysis package for ChIP-seq data reveals hUHRF1 Tandem-Tudor domain enrichment in young repeatsMichel Choudalakis, Pavel Bashtrykov, Albert Jeltsch · 2024 · Figshare
- Additional file 1 of Characterization of large-scale genomic differences in the first complete human genomeYang, 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
- Additional file 3 of Characterization of large-scale genomic differences in the first complete human genomeYang, 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
- Additional file 1 of RepEnTools: an automated repeat enrichment analysis package for ChIP-seq data reveals hUHRF1 Tandem-Tudor domain enrichment in young repeatsMichel Choudalakis, Pavel Bashtrykov, Albert Jeltsch · 2024 · Figshare
- Origin and evolution of acrocentric chromosomes in human and great apesSteven 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)
- Genome-wide analysis of FSHD cell lines using Nanopore sequencing reveals allele-specific differences at DUX4 target genes and complex repeatsJasmine Sakr, Xiangduo Kong, Negar Mojgani, Erisa Taghizadeh, Elnaz Abdollahzadeh, Kyoko Yokomori, Ali Mortazavi · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
- Chromosome-naïve global networks of initiators of hybrid assembly pathways of endogenous multiprotein complexesGennadi V. Glinsky · 2026 · Research Square
- Synthetic rewriting technologies in mammalian cellsYuqi Wang, Yali Cui, Guang-Rong Zhao, Yi Wu, Ying‐Jin Yuan · 2026 · Nature Communications
- Parallel profiling of genome mutations and multiple chromatin modalities in single cells by scNanoCT&ATAC-seqXiaoying Fan, Dan Su, Zhuobin Lin, Lin Guang Luo, Enze Deng, Qingpei Huang, Wenxin Xu, Zhihua Guo, Zhixiang Zuo · 2026 · Research Square
- XhetRel: a pipeline for X heterozygosity and relatedness analysis of sequencing dataBarış Salman, Nerses Bebek, Sibel Uğur İşeri · 2026 · Bioinformatics Advances
- Unraveling novel transposable elements (TEs)-driven gene dysregulation in non-small cell lung cancer (NSCLC) by integrated transcriptomic and TEs analysisS Shrinidhi, R. Sagaya Jansi, Ameer Khusro · 2026 · Computational Biology and Chemistry
- Evolution and Comparative Analysis of Sheep Reference Genomes: From Fragmented Assemblies to Telomere-to-Telomere GenomicsDan Yue, Ying Lu, Yuqing Chong, Jiao Wu, Zhendong Gao, Ruoshan Ma, Keyu Li, Weidong Deng, Bo Wang · 2026 · Biology
- The Role of Transposable Elements in the Development of Aggressive Behavior in PigsRustam Nailevich Mustafin, А В Казанцева, I. R. Gilyazova, T. V. Leonova, E. K. Khusnutdinova, O. G. Gusev · 2026 · Russian Journal of Genetics
- Resolving repetitive and telomeric regions through a high-contiguity genome assembly of the African Turquoise killifishNagyeong Kim, Chang-Myung Oh, Yumi Kim, Jun Ho Kim · 2026 · Genes & Genomics
- Mechanisms of Interactions of Circular RNAs with Mobile Elements and MicroRNAs in the Development of Breast CancerRustam Nailevich Mustafin · 2026 · Molecular Biology
- Protocol to identify SINE-VNTR-Alu regulators using genome-wide screening in human K562 cellsZiqiang Zhou, Shicong Zhu, Deng Pan, Hsiang‐Ying Lee, Nian Liu · 2026 · STAR Protocols
- Epigenomic methylome landscape of promoters in vertebrate genomesYoung Ho Lee, Chul Min Lee, Erich D. Jarvis, Heebal Kim · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
- CRISPR-mediated regulation of apoptosis in cancer: Molecular targets, mechanisms, and translational challengesQian Tang, Xun-Huan Song, An-Ni Guo, Yuan Chen, Jing-Wei Shao · 2026 · Biochemical and Biophysical Research Communications
- Dynamics of H3.1 and H3.3 histone variants at mouse chromocenters during cell cycle and differentiationStefano Arfè · 2022 · theses.fr (ABES)
- Investigating the role of the centromeric histone variant CENP-A in cancerCharlène Renaud-Pageot · 2024 · theses.fr (ABES)
- PERREO: An integrated pipeline for repetitive elements analysis enables the repeatome expression profiling in cancerFrancisco J. Rodríguez-Martín, Mario Masero-Leon, Daniel Gómez-Cabello · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
- Diploid telomere-to-telomere assemblies reveal hierarchical satellite architectures and heritable MHC structural diversity in macaquesSeiya Imoto, Takuya Yamamoto, Yusuke Nakamura, Shokichi Takahama, Kazuma Kiyotani, Toyomasa Katagiri, Emiko Urano, Nobuhiro Shimozawa, Naohide Ageyama, Yasuhiro Yasutomi et al. · 2026 · Research Square
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