Searching journal content for articles similar to Kofler et al. 28 (6): 824.

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  1. Resource: Charting the regulatory landscape of TP53 on transposable elements in cancer
    • Xuan Qu,
    • Yonghao Liang,
    • Colin McCornack,
    • Xiaoyun Xing,
    • Heather Schmidt,
    • Chad Tomlinson,
    • Catrina Fronick,
    • Edward A. Belter, Jr.,
    • Juan F. Macias-Velasco,
    • and Ting Wang
    Genome Res. June 2025 35: 1456-1471; Published in Advance May 13, 2025, doi:10.1101/gr.279398.124
    ...author: twang@wustl.eduAbstractThe relationship between TP53 and transposable elements (TEs) has been obscure. Given the important role of TEs in oncogenesis, a comprehensive profiling of TE expression dynamics under the regulation of TP53 provides valuable resources for more clarity in TP53's roles...
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  2. Research: Rapid evolution of piRNA-mediated silencing of an invading transposable element was driven by abundant de novo mutations
    • Shuo Zhang,
    • Beverly Pointer,
    • and Erin S. Kelleher
    Genome Res. April 2020 30: 566-575; Published in Advance April 1, 2020, doi:10.1101/gr.251546.119
    ...(Supplemental Table S1), which were isolated from nature before P-element invasion and are therefore devoid of genomic P-elements. We annotated piRNA clusters based on the density of mapped piRNAs using proTRAC (Rosenkranz and Zischler 2012). We varied the stringency of piRNA cluster identification to generate...
  3. Resource: High-quality assembly of the Chinese white truffle genome and recalibrated divergence time estimate provide insight into the evolutionary dynamics of Tuberaceae
    • Jacopo Martelossi,
    • Jacopo Vujovic,
    • Yue Huang,
    • Alessia Tatti,
    • Kaiwei Xu,
    • Federico Puliga,
    • Yuanxue Chen,
    • Omar Rota Stabelli,
    • Fabrizio Ghiselli,
    • Xiaoping Zhang,
    • and Alessandra Zambonelli
    Genome Res. November 2025 35: 2601-2616; Published in Advance August 21, 2025, doi:10.1101/gr.280368.124
    ....zambonelli@unibo.itAbstractThe genus Tuber (family: Tuberaceae) includes the most economically valuable ectomycorrhizal (ECM), truffle-forming fungi. Previous genomic analyses revealed that massive transposable element (TE) proliferation represents a convergent genomic feature of ECM fungi, including Tuberaceae. Repetitive sequences...
  4. Research: Experimentally evolving Drosophila erecta populations may fail to establish an effective piRNA-based host defense against invading P-elements
    • Divya Selvaraju,
    • Filip Wierzbicki,
    • and Robert Kofler
    Genome Res. March 2024 34: 410-425; Published in Advance March 15, 2024, doi:10.1101/gr.278706.123
    ...of transposable elements (TEs), hosts have developed sophisticated defense mechanisms. In mammals and invertebrates, a major defense mechanism operates through PIWI-interacting RNAs (piRNAs). To investigate the establishment of the host defense, we introduced the P-element, one of the most widely studied...
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  5. Research: Atypical epigenetic and small RNA control of degenerated transposons and their fragments in clonally reproducing Spirodela polyrhiza
    • Rodolphe Dombey,
    • Daniel Buendía-Ávila,
    • Verónica Barragán-Borrero,
    • Laura Diezma-Navas,
    • Arturo Ponce-Mañe,
    • José Mario Vargas-Guerrero,
    • Rana Elias,
    • and Arturo Marí-Ordóñez
    Genome Res. March 2025 35: 522-544; Published in Advance March 4, 2025, doi:10.1101/gr.279532.124
    ...: arturo.mari-ordonez@gmi.oeaw.ac.atAbstractA handful of model plants have provided insight into silencing of transposable elements (TEs) through RNA-directed DNA methylation (RdDM). Guided by 24 nt long small-interfering RNAs (siRNAs), this epigenetic regulation installs DNA methylation and histone...
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  6. LETTER: Evolutionary dynamics of transposable elements in the short-tailed opossum Monodelphis domestica
    • Andrew J. Gentles,
    • Matthew J. Wakefield,
    • Oleksiy Kohany,
    • Wanjun Gu,
    • Mark A. Batzer,
    • David D. Pollock,
    • and Jerzy Jurka
    Genome Res. July 2007 17: 992-1004; Published in Advance May 10, 2007, doi:10.1101/gr.6070707
    ...Evolutionary dynamics of transposable elements in the short-tailed opossum Monodelphis domestica Andrew J. Gentles 1 , 2 , 6 , Matthew J. Wakefield 3 , Oleksiy Kohany 2 , Wanjun Gu 4 , Mark A. Batzer 5 , David D. Pollock 4...
  7. Research: Timescale and genetic linkage explain the variable impact of defense systems on horizontal gene transfer
    • Yang Liu,
    • João Botelho,
    • and Jaime Iranzo
    Genome Res. February 2025 35: 268-278; Published in Advance January 10, 2025, doi:10.1101/gr.279300.124
    ..., Spain; 3Institute for Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, 50018, Zaragoza, Spain Corresponding author: jaime.iranzo@cab.inta-csic.esAbstractProkaryotes have evolved a wide repertoire of defense systems to prevent invasion by mobile genetic elements (MGEs...
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  8. Mini-Review: The additional diagnostic yield of long-read sequencing in undiagnosed rare diseases
    • Giulia F. Del Gobbo and
    • Kym M. Boycott
    Genome Res. April 2025 35: 559-571; Published in Advance February 3, 2025, doi:10.1101/gr.279970.124
    ...for variants of uncertain significance (VUSs), variants residing in novel disease genes, and complex genetic and/or environmental causes of disease. Additionally, inherent limitations to SRS technology may be a significant contributor. Given the nature of the short reads, SRS struggles in alignment...
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  9. Resource: Dynamic regulation of gonadal transposon control across the lifespan of the naturally short-lived African turquoise killifish
    • Bryan B. Teefy,
    • Ari Adler,
    • Alan Xu,
    • Katelyn Hsu,
    • Param Priya Singh,
    • and Bérénice A. Benayoun
    Genome Res. January 2023 33: 141-153; Published in Advance December 28, 2022, doi:10.1101/gr.277301.122
    ...of the gonadal transcriptome throughout the lifespan in the naturally short-lived African turquoise killifish (Nothobranchius furzeri). By combining mRNA-seq and small RNA-seq from 26 individuals, we characterize the aging gonads of young-adult, middle-aged, and old female and male fish. We analyze changes...
  10. Resource: A mosquito small RNA genomics resource reveals dynamic evolution and host responses to viruses and transposons
    • Qicheng Ma,
    • Satyam P. Srivastav,
    • Stephanie Gamez,
    • Gargi Dayama,
    • Fabiana Feitosa-Suntheimer,
    • Edward I. Patterson,
    • Rebecca M. Johnson,
    • Erik M. Matson,
    • Alexander S. Gold,
    • Douglas E. Brackney,
    • John H. Connor,
    • Tonya M. Colpitts,
    • Grant L. Hughes,
    • Jason L. Rasgon,
    • Tony Nolan,
    • Omar S. Akbari,
    • and Nelson C. Lau
    Genome Res. March 2021 31: 512-528; Published in Advance January 8, 2021, doi:10.1101/gr.265157.120
    ...infection. The MSRG resource will aid efforts to dissect and combat the capacity of mosquitoes to tolerate and spread arboviruses.Mosquitoes are one of the most prevalent vectors of human pathogens, yet they have wide variability to vector different pathogens. For example, human malaria parasites...
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