Searching journal content for articles similar to Fungtammasan et al. 22 (6): 993.

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  1. Research: Genome-wide evaluation of the effect of short tandem repeat variation on local DNA methylation
    • Alejandro Martin-Trujillo,
    • Paras Garg,
    • Nihir Patel,
    • Bharati Jadhav,
    • and Andrew J. Sharp
    Genome Res. February 2023 33: 184-196; Published in Advance December 28, 2022, doi:10.1101/gr.277057.122
    ...been extensively assessed, their impact on epigenetics has been poorly studied and limited to specific genomic regions. Here, we investigated the hypothesis that some STRs act as independent regulators of local DNA methylation in the human and modify risk of common human traits. To address...
  2. Research: A novel quantitative trait locus implicates Msh3 in the propensity for genome-wide short tandem repeat expansions in mice
    • Mikhail O. Maksimov,
    • Cynthia Wu,
    • David G. Ashbrook,
    • Flavia Villani,
    • Vincenza Colonna,
    • Nima Mousavi,
    • Nichole Ma,
    • Lu Lu,
    • Jonathan K. Pritchard,
    • Alon Goren,
    • Robert W. Williams,
    • Abraham A. Palmer,
    • and Melissa Gymrek
    Genome Res. May 2023 33: 689-702; Published in Advance May 1, 2023, doi:10.1101/gr.277576.122
    ...-associated loci, we report a novel association between sequence variants in Msh3 and -wide germline mutation patterns at STRs. Our results suggest that in addition to these roles affecting somatic STR instability in disease, common mutations affecting Msh3 may contribute to biases in mutation patterns...
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  3. Corrigendum: Corrigendum: A genome-wide analysis of common fragile sites: What features determine chromosomal instability in the human genome?
    • Arkarachai Fungtammasan,
    • Erin Walsh,
    • Francesca Chiaromonte,
    • Kristin A. Eckert,
    • and Kateryna D. Makova
    Genome Res. October 2016 26: 1451; doi:10.1101/gr.214460.116
    ...chromosomal instability in the human genome? Genome Research 22: 993–1005 (2012) Corrigendum: A -wide analysis of common fragile sites: What features determine chromosomal instability in the human ? Arkarachai Fungtammasan, Erin Walsh, Francesca Chiaromonte, Kristin A. Eckert, and Kateryna D. Makova...
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  4. Research: Genome-wide mapping reveals R-loops associated with centromeric repeats in maize
    • Yang Liu,
    • Qian Liu,
    • Handong Su,
    • Kunpeng Liu,
    • Xue Xiao,
    • Wei Li,
    • Qianwen Sun,
    • James A. Birchler,
    • and Fangpu Han
    Genome Res. August 2021 31: 1409-1418; Published in Advance July 9, 2021, doi:10.1101/gr.275270.121
    ...with tandem repeats in the centromeric regions. For example, in maize, tandemly arranged CentC repeats and interspersed centromeric retrotransposons (CRM) are the major DNA components of maize centromeres (Birchler and Han 2009). One of the common features of centromere sequences is their transcription...
  5. Research: Optical genome mapping enables accurate testing of large repeat expansions
    • Bart van der Sanden,
    • Kornelia Neveling,
    • Syukri Shukor,
    • Michael D. Gallagher,
    • Joyce Lee,
    • Stephanie L. Burke,
    • Maartje Pennings,
    • Ronald van Beek,
    • Michiel Oorsprong,
    • Ellen Kater-Baats,
    • Eveline Kamping,
    • Alide A. Tieleman,
    • Nicol C. Voermans,
    • Ingrid E. Scheffer,
    • Jozef Gecz,
    • Mark A. Corbett,
    • Lisenka E.L.M. Vissers,
    • Andy Wing Chun Pang,
    • Alex Hastie,
    • Erik-Jan Kamsteeg,
    • and Alexander Hoischen
    Genome Res. April 2025 35: 810-823; Published in Advance March 20, 2025, doi:10.1101/gr.279491.124
    ...-wide assay for repeat expansion disorders by measuring exact repeat lengths and somatic instability across multiple loci simultaneously.Short tandem repeats (STRs) are common repeats of a particular k-mer of 1–6 bp in length (Tankard et al. 2018). More than a million cataloged STR loci make up ∼3...
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  6. Mini-Review: The paradox of R-loops: guardians of the genome or drivers of disease?
    • Shachinthaka D. Dissanayaka Mudiyanselage,
    • Phillip Wulfridge,
    • and Kavitha Sarma
    Genome Res. September 2025 35: 1919-1928; Published in Advance August 6, 2025, doi:10.1101/gr.278992.124
    ...is unclear.When not properly regulated, R-loops can become a significant source of genomic instability and can activate inflammatory immune responses (Brickner et al. 2022). However, R-loops also play roles in cellular processes, including transcription, DNA replication, DNA repair, and chromosome...
  7. Research: Long-read sequencing technology indicates genome-wide effects of non-B DNA on polymerization speed and error rate
    • Wilfried M. Guiblet,
    • Marzia A. Cremona,
    • Monika Cechova,
    • Robert S. Harris,
    • Iva Kejnovská,
    • Eduard Kejnovsky,
    • Kristin Eckert,
    • Francesca Chiaromonte,
    • and Kateryna D. Makova
    Genome Res. December 2018 28: 1767-1778; Published in Advance November 6, 2018, doi:10.1101/gr.241257.118
    ...to underlie non-B DNA-induced instability, that is, increase in chromosomal rearrangements, including those observed in cancer (Bacolla et al. 2004; Wang et al. 2008). Moreover, the increased occurrence of point mutations at non-B DNA was demonstrated at individual loci in plasmid constructs (for review, see...
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  8. Research: De novo genome assemblies of two cryptodiran turtles with ZZ/ZW and XX/XY sex chromosomes provide insights into patterns of genome reshuffling and uncover novel 3D genome folding in amniotes
    • Basanta Bista,
    • Laura González-Rodelas,
    • Lucía Álvarez-González,
    • Zhi-qiang Wu,
    • Eugenia E. Montiel,
    • Ling Sze Lee,
    • Daleen B. Badenhorst,
    • Srihari Radhakrishnan,
    • Robert Literman,
    • Beatriz Navarro-Dominguez,
    • John B. Iverson,
    • Simon Orozco-Arias,
    • Josefa González,
    • Aurora Ruiz-Herrera,
    • and Nicole Valenzuela
    Genome Res. October 2024 34: 1553-1569; Published in Advance October 16, 2024, doi:10.1101/gr.279443.124
    ...Departament de Biologia Cel·lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain; 3Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain; 4Guangdong Laboratory...
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  9. Research: Rearrangements of viral and human genomes at human papillomavirus integration events and their allele-specific impacts on cancer genome regulation
    • Vanessa L. Porter,
    • Michelle Ng,
    • Kieran O'Neill,
    • Signe MacLennan,
    • Richard D. Corbett,
    • Luka Culibrk,
    • Zeid Hamadeh,
    • Marissa Iden,
    • Rachel Schmidt,
    • Shirng-Wern Tsaih,
    • Carolyn Nakisige,
    • Martin Origa,
    • Jackson Orem,
    • Glenn Chang,
    • Jeremy Fan,
    • Ka Ming Nip,
    • Vahid Akbari,
    • Simon K. Chan,
    • James Hopkins,
    • Richard A. Moore,
    • Eric Chuah,
    • Karen L. Mungall,
    • Andrew J. Mungall,
    • Inanc Birol,
    • Steven J.M. Jones,
    • Janet S. Rader,
    • and Marco A. Marra
    Genome Res. April 2025 35: 653-670; Published in Advance December 5, 2024, doi:10.1101/gr.279041.124
    ...number changes and the proposed structure of an event overlapping MYC. Each color represents a genomic segment on Chromosome 8 in between two human–HPV breakpoints. P-values in B and C were calculated using the Wilcoxon rank-sum test and Spearman's correlation test.We explored how HPV breakpoints were...
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  10. Research: Genome-wide analysis of HPV integration in human cancers reveals recurrent, focal genomic instability
    • Keiko Akagi,
    • Jingfeng Li,
    • Tatevik R. Broutian,
    • Hesed Padilla-Nash,
    • Weihong Xiao,
    • Bo Jiang,
    • James W. Rocco,
    • Theodoros N. Teknos,
    • Bhavna Kumar,
    • Danny Wangsa,
    • Dandan He,
    • Thomas Ried,
    • David E. Symer,
    • and Maura L. Gillison
    Genome Res. February 2014 24: 185-199; Published in Advance November 7, 2013, doi:10.1101/gr.164806.113
    ...Genome-wide analysis of HPV integration in human cancers reveals recurrent, focal genomic instability Keiko Akagi 1 , 2 , 3 , 10 , Jingfeng Li 1 , 2 , 3 , 10 , Tatevik R. Broutian 2 , 4 , Hesed Padilla-Nash 5 , Weihong Xiao 2 , 4...
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