Searching journal content for articles similar to Georgakopoulos-Soares et al. 28 (9): 1264.

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  1. Method: Accurate sequencing of DNA motifs able to form alternative (non-B) structures
    • Matthias H. Weissensteiner,
    • Marzia A. Cremona,
    • Wilfried M. Guiblet,
    • Nicholas Stoler,
    • Robert S. Harris,
    • Monika Cechova,
    • Kristin A. Eckert,
    • Francesca Chiaromonte,
    • Yi-Fei Huang,
    • and Kateryna D. Makova
    Genome Res. July 11, 2023 ; Published in Advance July 11, 2023, doi:10.1101/gr.277490.122
    ...and L’EMbeDS, Sant’Anna School of Advanced Studies, Pisa 56127, Italy Approximately 13% of the human at certain motifs have the potential to form noncanonical (non-B) DNA structures (e.g., G-quadruplexes, cruciforms, and Z-DNA), which regulate many cellular processes but also affect the activity...
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  2. 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
    ...of non-B DNA motifs to form noncanonical structures regulates many cellular processes (Zhao et al. 2010), these structures can also affect DNA synthesis and lead to instability, and thus can be viewed as both a blessing and a curse (Valton and Prioleau 2016). In vitro and ex vivo studies of individual...
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  3. 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
    ...(SNVs), ignoring low-frequency SNVs or other relevant sources of genetic variation such as tandem repeats (TRs).Short tandem repeats (STRs), also known as microsatellites, are stretches of repeated units of DNA with motifs 2–6 bp in size that are distributed broadly across the and, in total, make up ∼3...
  4. Resource: Quadrupia provides a comprehensive catalog of G-quadruplexes across genomes from the tree of life
    • Nikol Chantzi,
    • Akshatha Nayak,
    • Fotis A. Baltoumas,
    • Eleni Aplakidou,
    • Shiau Wei Liew,
    • Jesslyn Elvaretta Galuh,
    • Michail Patsakis,
    • Austin Montgomery,
    • Camille Moeckel,
    • Ioannis Mouratidis,
    • Saiful Arefeen Sazed,
    • Wilfried Guiblet,
    • Panagiotis Karmiris-Obratański,
    • Guliang Wang,
    • Apostolos Zaravinos,
    • Karen M. Vasquez,
    • Chun Kit Kwok,
    • Georgios A. Pavlopoulos,
    • and Ilias Georgakopoulos-Soares
    Genome Res. November 2025 35: 2578-2600; Published in Advance August 26, 2025, doi:10.1101/gr.279790.124
    ...) are one of the most thoroughly studied non-B DNA structures. G4s are commonly found in GC-rich areas of a and are characterized by Hoogsteen base pairs, in which hydrogen bonds link four guanine bases into a square planar formation known as a G-quartet. Multiple G-quartets, stacked on top of each other...
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  5. Method: Identification of the shortest species-specific oligonucleotide sequences
    • Ioannis Mouratidis,
    • Maxwell A. Konnaris,
    • Nikol Chantzi,
    • Candace S.Y. Chan,
    • Michail Patsakis,
    • Kimonas Provatas,
    • Austin Montgomery,
    • Fotis A. Baltoumas,
    • Congzhou M. Sha,
    • Manvita Mareboina,
    • Georgios A. Pavlopoulos,
    • Dionysios V. Chartoumpekis,
    • and Ilias Georgakopoulos-Soares
    Genome Res. February 2025 35: 279-295; Published in Advance January 2, 2025, doi:10.1101/gr.280070.124
    ...contributed equally to this work. Corresponding authors: ipm5219@psu.edu, izg5139@psu.eduAbstractDespite the exponential increase in sequencing information driven by massively parallel DNA sequencing technologies, universal and succinct genomic fingerprints for each organism are still missing. Identifying...
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  6. Research: Selection and thermostability suggest G-quadruplexes are novel functional elements of the human genome
    • Wilfried M. Guiblet,
    • Michael DeGiorgio,
    • Xiaoheng Cheng,
    • Francesca Chiaromonte,
    • Kristin A. Eckert,
    • Yi-Fei Huang,
    • and Kateryna D. Makova
    Genome Res. July 2021 31: 1136-1149; Published in Advance June 29, 2021, doi:10.1101/gr.269589.120
    ...SNPs with low minor allele frequencies (MAFs) was found at non-B DNA loci, which include G4 loci, supporting their evolution under purifying selection (Du et al. 2014). Fewer polymorphic SNPs and fixed differences were found at structure-disruptive than other motif positions for G4 loci located in both...
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