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 201–300 of 410
- An evolutionarily conserved constellation of functional cis-elements programs the virus-responsive fate of the human (epi)genomeMarianna A. Koutsi, Marialena Pouliou, Dimitris Chatzopoulos, Lydia Champezou, Konstantinos Zagkas, Marili Vasilogianni, Alexandra G. Kouroukli, Marios Agelopoulos · 2025 · Nucleic Acids Research
- Confounding factors in profiling of locus-specific human endogenous retrovirus (HERV) transcript signatures in primary T cells using multi-study-derived datasetsMartin V. Hamann, Maisha Adiba, Ulrike C. Lange · 2023 · BMC Medical Genomics
- A method to enrich and purify centromeric DNA from human cellsRiccardo Gamba, Giulia Mazzucco, Therese Wilhelm, Florian Chardon, Léonid Velikovsky, Julien Picotto, Ylli Doksani, Daniele Fachinetti · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
- TandemAligner: a new parameter-free framework for fast sequence alignmentAndrey V. Bzikadze, Pavel A. Pevzner · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
- Complete Reference Genome and Pangenome Expand Biologically Relevant Information for Genome-Wide DNA Methylation Analysis Using Short-Read Sequencing and Array DataZheng 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)
- Evaluation of Long-Read RNA Sequencing Procedures for Novel Isoform Identification and Quantification in Human Whole BloodHikari 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
- Leveraging cfDNA fragmentomic features for the early detection of colorectal cancerLina 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
- Loss of SETDB1-mediated H3K9me3 in human neural progenitor cells leads to transcriptional activation of L1 retrotransposonsOfelia Karlsson, Ninoslav Pandiloski, Vivien Horváth, Anita Adami, Raquel Garza, Pia Annette Johansson, Jonas Johansson, Christopher H. Douse, Johan Jakobsson · 2026 · Nucleic Acids Research
- Multiplexed TrAEL-seq captures DNA replication dynamics in mammalian cellsNeesha 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
- Unraveling Non-B DNA Structures in the Era of Telomere-to-Telomere GenomesKateryna D. Makova, Saswat Mohanty, Linnéa Smeds, Jacob P. Sieg, Angelika Lahnsteiner · 2026 · Annual Review of Genomics and Human Genetics
- Molecular mechanisms regulating cGAS/STING activation in health and diseaseMin-Guk Cho, Rachel Lee, Jaycee Johnson, Gaorav P. Gupta · 2026 · Journal of Clinical Investigation
- Churros: a Docker-based pipeline for large-scale epigenomic analysisJiankang Wang, Ryuichiro Nakato · 2023 · DNA Research
- Microsatellite density landscapes illustrate short tandem repeats aggregation in the complete reference human genomeYun Xia, Douyue Li, Tingyi Chen, Saichao Pan, Hanrou Huang, Wenxiang Zhang, Yulin Liang, Yongzhuo Fu, Zhuli Peng, Hongxi Zhang et al. · 2024 · BMC Genomics
- Leveraging long-read assemblies and machine learning to enhance short-read transposable element detection and genotypingAustin Daigle, Logan S. Whitehouse, Roy Zhao, J. J. Emerson, Daniel R. Schrider · 2026 · Genetics
- Zygotic activation of transposable elements during zebrafish early embryogenesisBo Li, Ting Li, Dingjie Wang, Ying Yang, Puwen Tan, Yunhao Wang, Yun-Gui Yang, Shunji Jia, Kin Fai Au · 2025 · Nature Communications
- Complete reference genome and pangenome improve genome-wide detection and interpretation of DNA methylation using sequencing and array dataZheng Dong, Joanne Whitehead, Maggie Fu, Julia L. MacIsaac, David H. Rehkopf, Luis Rosero‐Bixby, Michael Steffen Kobor, Keegan D. Korthauer · 2025 · Cell Reports
- From Junk DNA to Genomic Treasure: Impacts of Transposable Element DNA , RNA , and Protein in Mammalian Development and DiseaseTen D. Li, Katelyn Toohill, Andrew J. Modzelewski · 2025 · Wiley Interdisciplinary Reviews - RNA
- An allele-resolved nanopore-guided tour of the human placental methylomeMichaela Kindlova, Hannah Byrne, Jade M Kubler, Sarah Elizabeth Steane, Jessica Whyte, Danielle J. Borg, Vicki Lee Clifton, Adam D. Ewing · 2025 · Nature Communications
- STRavinsky STR database and PGTailor PGT tool demonstrate superiority of CHM13-T2T over hg38 and hg19 for STR-based applicationsNoam Hadar, Ginat Narkis, Shirly Amar, Marina Varnavsky, Glenda Calniquer Palti, Amit Safran, Ohad S. Birk · 2023 · European Journal of Human Genetics
- Unique repetitive nucleic acid structures mirror switch regions in the human IgH locusOphélie Dézé, Delfina Ordanoska, Delphine Rossille A, Emma Miglierina, Brice Laffleur, Michel Cogné · 2023 · Biochimie
- Improving the Completeness of Chromosome-Level Assembly by Recalling Sequences from Lost ContigsJunyang Liu, Fang Liu, Weihua Pan · 2023 · Genes
- 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 · Mobile DNA
- Probabilistic and machine-learning methods for predicting local rates of transcription elongation from nascent RNA sequencing dataLingjie Liu, Yixin Zhao, Rebecca Hassett, Shushan Toneyan, Peter K. Koo, Adam C. Siepel · 2025 · Nucleic Acids Research
- Replicative DNA polymerase epsilon and delta holoenzymes show wide-ranging inhibition at G-quadruplexes in the human genomeSuzanne 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
- Comprehensive fragmentation of cell-free repetitive DNA for enhanced cancer detection in plasmaMingguang Zhang, Shuohui Dong, Wei Rao, Shiwen Mei, Gang Hu, Ling Liu, Zhen Wang, Jianqiang Tang · 2025 · Frontiers in Cell and Developmental Biology
- The evolutionary entanglement of flipons with zinc fingers and retroelements has engendered a large family of Z-DNA and G-quadruplex binding proteinsAlan G. Herbert · 2025 · Open Biology
- A critique of the hypothesis that CA repeats are primary targets of neuronal MeCP2Kashyap Chhatbar, John C. Connelly, Shaun Webb, Skirmantas Kriaučionis, Adrian Peter Bird · 2022 · Life Science Alliance
- 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. · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
- RAmbler resolves complex repeats in human Chromosomes 8, 19, and XSakshar Chakravarty, Glennis A. Logsdon, Stefano Lonardi · 2025 · Genome Research
- Birth of protein-coding exons by ancient domestication of LINE-1 retrotransposonK. Kitao, Kenji Ichiyanagi, So Nakagawa · 2025 · Genome Research
- Characterization of Somatic Mutations in Human tRNA Genes Reveals Tumor-Specific Mutational Loads, and the Generation of tRNA Variants that Alter the Genetic CodeMarina Murillo-Recio, Marina Salvadores, Adrián Gabriel Torres, Lina Tsapanou, Aina Vaquer Picó, Fran Supek, Lluı́s Ribas de Pouplana · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
- Haplotype-Resolved Genomics Reveals Conserved Chromatin Architecture and Epigenetic Constraints of Human NeocentromeresSavannah 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)
- Novel Avenues for the Detection of Cancer-Associated Viral Genome Integrations Using Long-Read Sequencing TechnologiesLarissa-Anna Bergmann, Alicja Pacholewska, Michal R. Schweiger · 2025 · Cancers
- Graft-seq precisely maps RNA modifications via site-specific chemical grafting strategyTing 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
- Accurate and Efficient Phylogenetic Inference through End-To-End Deep LearningZhang, Xinru, Ding, Shizhe, Yu, Chungong, Zhao, Jianquan, Bu, Dongbo · 2025 · Molecular Biology and Evolution
- High interferon response signatures in SLE patient leukocytes are associated with increased transposable element expression in gene introns and intergenic regionsLeo J. Arteaga-Vazquez, Hugo Sepúlveda, Bruno Villalobos Reveles, Kazumasa Suzuki, KENNETH C. KALUNIAN, Ferhat Ay, Mark Robin Boothby, Anjana Rao · 2025 · Mobile DNA
- A de novo H3.2K9me2 deposition pathway establishes heterochromatin for suppressing transposon mobilization during fly somatic developmentYi Ni Luo, Yazi Deng, Yu Liang, Wei Wu, Wei Wu, Lu Wang · 2026 · Nucleic Acids Research
- Tracking mobilization uncovers an evolutionarily conserved mechanism in suppressing mobile genetic elementsLu Wang, Yu Liang, Shuheng Wu, Yazi Deng, Wei Wu, Z.Z. Zhao Zhang, Wei Wu, Lu Wang · 2026 · Molecular Cell
- AniAnn’s: alignment-free annotation of tandem repeat arrays using fast average nucleotide identity estimatesAlexander P. Sweeten, Michael C. Schatz, Adam M. Phillippy · 2026 · Bioinformatics
- Recent insights into crosstalk between genetic parasites and their host genomeAmit Kumar Mandal · 2022 · Briefings in Functional Genomics
- Grand challenge in chromatin epigenomics: everything, everywhere, all at onceSharon Dent · 2023 · Frontiers in Epigenetics and Epigenomics
- Repetitive Sequence Stability in Embryonic Stem CellsGuang W. Shi, Qianwen Pang, Zhancheng Lin, Xinyi Zhang, Kaimeng Huang · 2024 · International Journal of Molecular Sciences
- Cytogenetic bands and sharp peaks of Alu underlie large-scale segmental regulation of nuclear genome architectureLisa L. Hall, Kevin M. Creamer, Meg Byron, Jeanne Bentley Lawrence · 2024 · Nucleus
- Transposable element expression is associated with sex chromosome number in humansJordan 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
- Human acrocentric chromosome short-arm de novo mutation and recombinationJiadong 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
- Information: Its Role and Meaning in OrganismsLeszek Konieczny, Irena Roterman‐Konieczna, Paweł Spólnik · 2023 · Springer eBooks
- The final pieces of the human genomeMichael Attwaters · 2022 · Nature Reviews Genetics
- A refined characterization of large-scale genomic differences in the first complete human genomeXiangyu 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)
- Mini-heterochromatin domains constrain the cis -regulatory impact of SVA transposons in human brain development and diseaseVivien 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)
- Cryptic endogenous retrovirus subfamilies in the primate lineageXun Chen, Zicong Zhang, Yi-Zhi Yan, Clément Goubert, Guillaume Bourque, Fumitaka Inoue · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
- DNA-sequence and epigenomic determinants of local rates of transcription elongationLingjie Liu, Yixin Zhao, Adam C. Siepel · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
- Genome-wide maps of highly-similar intrachromosomal repeats that mediate ectopic recombination in three human genome assembliesLuis 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)
- RT2T: A Global Collaborative Project to Study Chromosomal Evolution in the Suborder RuminantiaTed 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
- RetroTest unravels LINE-1 retrotransposition in Head and Neck Squamous Cell CarcinomaJenifer 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
- Distinct interferon response patterns link to increased transposable element expression in leukocytes of systemic lupus erythematosus patientsLeo 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)
- Identification of chromatin-associated RNAs at human centromeresKelsey A. Fryer, Charles Limouse, Aaron F. Straight · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
- NANOME: A Nextflow pipeline for haplotype-aware allele-specific consensus DNA methylation detection by nanopore long-read sequencingYang 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)
- DNA methylation dysregulation patterns in the 1p36 region instabilityJoanna Swierkowska, Michał Kabza, Małgorzata Rydzanicz, Maciej Giefing, Rafał Płoski, Lisa G. Shaffer, Marzena Gajęcka · 2024 · Journal of Applied Genetics
- Genome-wide maps of highly-similar intrachromosomal repeats that can mediate ectopic recombination in three human genome assembliesLuis 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
- Unraveling LINE ‐1 retrotransposition in head and neck squamous cell carcinomaJenifer 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
- ZNF280AY: a pseudogene on the ovine Y chromosome and its copy number variation associated with testicular size in Hu sheepYangkai Liu, Li Wang, Jialei Chen, Tajmal Hussain Solangi, Ran Li, Mengzhen Le, Xiangpeng Yue · 2025 · Journal of Animal Science
- Expression of LTR and LINE1 transposable elements defines atypical teratoid/rhabdoid tumor subtypesMartin 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
- Repeats Influence Structural DNA Properties Around Functional Annotations Associated with 3D Organization and TranscriptionAaron Sievers, Michael Hausmann, Georg Lars Hildenbrand · 2025 · Genes
- A new era of bioinformaticsAnna Yu. Aksenova, Anna S. Zhuk, Elena Igorevna Stepchenkova, Viacheslav A. Semenikhin, Mikhail Langovoy · 2025 · Ecological genetics
- Prospects for epigenetic research in neurofibromatosis type 1Rustam Nailevich Mustafin · 2025 · Siberian Journal of Oncology
- Coexistence of virome-encoded health-associated genes and pathogenic genes in global habitatsMin Qian, Dong Zhu, Keyu Yao, Shu-yue Liu, Ming Li, Mao Ye, Yong‐Guan Zhu · 2025 · Applied and Environmental Microbiology
- Cis-regulatory co-option of a transposon family reinforces cell identity across the immune systemJason D. Chobirko, Cedric Feschotte, Andrew Grimson · 2026 · The EMBO Journal
- DNA repeats: origins, conservation, and role in human diseaseAjay Kumar Rana · 2026 · Genome Instability & Disease
- Dark and camouflaged genomic regions remain challenging in CHM13Mark E. Wadsworth, Madeline L. Page, Bernardo Aguzzoli Heberle, Justin B. Miller, Cody J. Steely, Mark Ebbert · 2026 · Scientific Reports
- Protocol for efficient CRISPRi-mediated silencing of retrotransposons in human pluripotent stem cellsAnita Adami, Raquel Garza, Fereshteh Dorazehi, Christopher H. Douse, Johan Jakobsson · 2026 · STAR Protocols
- Centromere evolution in annual and perennial soybeans and its implication for hybridization in cultivated speciesJiamin Hou, Yanni Wei, Hui Liu, Boran Zhuang, Zhengkun Chen, Xinyu Zhu, Jing Han, Weifeng Su, Hui Tan, Wannan Xu et al. · 2026 · Genome biology
- Superabundant microRNAs are transcribed from human rDNA spacer promoters insulated by CTCFSteven Henikoff, Jorja G. Henikoff · 2026 · Science Advances
- Human endogenous retrovirus profiling reveals heterogenous expression in cutaneous melanomaTongyi Fei, Bhavya Singh, Nicholas Dopkins, Jez Lim Marston, Jasmine H. Francis, Douglas F. Nixon, Alexander Noor Shoushtari, Matthew L. Bendall · 2026 · Frontiers in Oncology
- Polymorphic CGG repeats in gene regulation and diseaseYijing Zhao, Dale John Annear, Emily Graves Allen, R. Frank Kooy, David Lee Nelson, Peng Jin · 2026 · The American Journal of Human Genetics
- Human Alu loci gain enhancer-type epigenetic modifications in monocytes during response to bacterial LPSYonghao Pan, Kenji Ichiyanagi · 2026 · Epigenetics & Chromatin
- Neocentromeres fail to maintain DNA methylation boundaries, driving CENP-A drift, instability, and chromosome missegregationMegan A. Mahlke, Angela Enriquez, Lior Lumerman, Poulomi Nath, Cy Chittenden, Savannah J. Hoyt, Jonas Koeppel, Yuan Xu, Rebecca Raphael, Kylie Zaffina et al. · 2026 · Cell Reports
- Decoding the power of the microbiome in human healthManoj Kumar, Noora Almohannadi, Souhaila Al Khodor · 2026 · Frontiers in Cellular and Infection Microbiology
- T2T-CHM13 reference genome reduces mapping bias and enhances alignment accuracy at disease-associated variantsIlaria Cherchi, Francesco Orlando, Orsetta Quaini, Marta Paoli, Yari Ciani, Francesca Demichelis · 2026 · iScience
- Assessing Hardy-Weinberg equilibrium in T2T-aligned 1000 genomes projectElika Garg, Jaffa Romain, Lei Sun, Andrew D. Paterson · 2026 · PLoS Genetics
- Epigenetics and genotypic variationMiriam Merenciano, Anaïs E. A. Larue, Cristian Groza, Cristina P Vieira, Rita Rebollo, Clément Goubert · 2024 · Elsevier eBooks
- Hétérochromatine et contrôle épigénétique des séquences répétéesConstance Kleijwegt, Jérôme Déjardin · 2024 · médecine/sciences
- YHSeqY3000 panel captures all founding lineages in the Chinese paternal genomic diversity databaseMengge Wang, Shuhan Duan, Qiuxia Sun, Kaijun Liu, Yan Liu, Zhiyong Wang, Xiangping Li, Lan‐Hai Wei, Yunhui Liu, Shengjie Nie et al. · 2025 · BMC Biology
- REPrise: de novo interspersed repeat detection using inexact seedingAtsushi Takeda, Daisuke Nonaka, Yuta Imazu, Tsukasa Fukunaga, Michiaki Hamada · 2025 · Mobile DNA
- Cap Analysis of Gene Expression Clarifies Transcriptomic Divergence Within Monozygotic Twin PairsHirokazu Katoh, Hiroaki Asai, Keiko Takemoto, Rie Tomizawa, Chika Honda, Mikio Watanabe, Tomoyuki Honda · 2023 · Twin Research and Human Genetics
- A computational model of the line-1 retrotransposon life cycle and visualization of metabolic networks in 3-dimensions.Michael Martin · 2022
- Allele pairing at Sun1-enriched domains at the nuclear periphery via T 1 A 3 tandem DNA repeatsGayan I. Balasooriya, David L. Spector · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
- Telomere-to-Telomere Assembly Improves Host Reads Removal in Metagenomic High-Throughput Sequencing of Human SamplesLei Wang, Guoning Xing · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
- RAmbler: de novo genome assembly of complex repetitive regionsSakshar Chakravarty, Glennis A. Logsdon, Stefano Lonardi · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
- Efficient estimation for large-scale linkage disequilibrium patterns of the human genomeXin Huang, T. J. Zhu, Yingchao Liu, Jiannan Zhang, Guo‐Bo Chen · 2023 · eLife
- Evolutionary Tinkering Enriches the Hierarchical and Interlaced Structures in Amino Acid SequencesZecheng Zhang, Chunxiuzi Liu, Yingjun Zhu, Peng Lu, Weiyi Qiu, Qian-Yuan Tang, Liu He, Ke Zhang, Zengru Di, Yu Liu · 2023 · Research Square
- Differences in Alu vs L1-rich chromosome bands underpin architectural reorganization of the inactive-X chromosome and SAHFsLisa L. Hall, Kevin M. Creamer, Meg Byron, Jeanne Bentley Lawrence · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
- REPrise: de novo interspersed repeat detection using inexact seedingAtsushi Takeda, Daisuke Nonaka, Yuta Imazu, Tsukasa Fukunaga, Michiaki Hamada · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
- RT2T: A Global Collaborative Project to Study Chromosomal Evolution in the Suborder RuminantiaTed 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
- Birth of protein-coding exons by ancient domestication of LINE retrotransposonK. Kitao, Kenji Ichiyanagi, So Nakagawa · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
- TAD hierarchy restricts poised LTR activation and loss of TAD hierarchy promotes LTR co-option in cancerElissa W.P. Wong, Merve Şahin, Rui Yang, UkJin Lee, Yingqian Ada Zhan, Rohan Misra, Fanny V. Tomas, Nawaf Alomran, Alexander Polyzos, Cindy J. Lee et al. · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
- Mobile element insertions affect human pigmentation and skin cancer riskJeffrey M. Kidd · 2024 · Nature Genetics
- Tracking mobilization uncovers an evolutionarily conserved mechanism in suppressing transpositions during somatic developmentYi Ni Luo, Yu Liang, Shuheng Wu, Yazi Deng, Wei Wu, ZZ Zhao Zhang, Wei Wu, Lu Wang · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
- Sequencing the gaps: dark genomic regions persist in CHM13 despite long-read advancesMark E. Wadsworth, Madeline L. Page, Bernardo Aguzzoli Heberle, Justin B. Miller, Cody J. Steely, Mark Ebbert · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
- TrAEL-seq captures DNA replication dynamics in mammalian cellsNeesha Kara, Laura Biggins, Vera V. Grinkevich, Alex J. Whale, Paola Garran-Garcia, Jhanavi Srinivasan, Peter J. Rugg‐Gunn, Simon Andrews, Aled Parry, Helen M.R. Robinson et al. · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
- A complete and near-perfect rhesus macaque reference genome: lessons from subtelomeric repeats and sequencing biasShilong Zhang, Ning Xu, Yong Lu, Yanhong Nie, Zhengtong Li, Luciana de Gennaro, Lianting Fu, Zhendong Zhang, Jieyi Chen, Kaiyue Ma et al. · 2025 · bioRxiv (Cold Spring Harbor Laboratory)