Searching journal content for articles similar to Stewart-Ornstein et al. 35 (9): 2064.

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  1. Method: Global quantification exposes abundant low-level off-target activity by base editors
    • Ilana Buchumenski,
    • Shalom Hillel Roth,
    • Eli Kopel,
    • Efrat Katsman,
    • Ariel Feiglin,
    • Erez Y. Levanon,
    • and Eli Eisenberg
    Genome Res. December 2021 31: 2354-2361; Published in Advance October 19, 2021, doi:10.1101/gr.275770.121
    ..., and is still much higher than the accepted ionizing radiation safety limit. Thus, the mutation load detected in some of the editors calls for a more accurate sequencing and quantification methods to assess the risk due to off-target DNA editing, even if it is too weak a signal to be detected using current...
  2. Research: Transcriptome-wide systematic search does not detect A-to-I RNA editing in cis-antisense RNA duplexes
    • Zohar Rosenwasser,
    • Roni Cohen-Fultheim,
    • Ofir Shliefer,
    • Erez Y. Levanon,
    • and Eli Eisenberg
    Genome Res. March 12, 2026 gr.280820.125; Published in Advance March 12, 2026, doi:10.1101/gr.280820.125
    ...nucleotide type. For paired-end reads, both mates had to map in opposite orientation within 500 kb of each other. To assess the robustness of our detection approach, we performed a sensitivity analysis using more lenient hyperediting detection parameters: mismatch density ≥4% (reduced from ≥5%) and mismatch...
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  3. Research: Strong bias in long-read sequencing prevents assembly of Drosophila melanogaster Y-linked genes
    • A. Bernardo Carvalho,
    • Bernard Y. Kim,
    • and Fabiana Uno
    Genome Res. January 2026 36: 71-82; Published in Advance October 1, 2025, doi:10.1101/gr.280604.125
    .... Hence, although DNA ligase remains a possible explanation for the missing exons, the limited available data do not support it as the primary cause. Perhaps the main difficulty of the T4 ligase hypothesis is that all its known preferences are short range (e.g., blunt end ligation of AT/TA vs. GC/CG ends...
  4. Research: Long-read sequencing reveals HBV integration patterns and oncogenic impact on early-onset hepatocellular carcinoma
    • Yao Wang,
    • Dong Yu,
    • Yue Mei,
    • ZhiDa Fu,
    • Jian Lin,
    • Di Wu,
    • Yuan Yang,
    • and Hongli Yan
    Genome Res. November 2025 35: 2389-2405; Published in Advance September 16, 2025, doi:10.1101/gr.279889.124
    ...randomly to 8 kb using a g-tube. Nick repair (NEB next FFPE DNA repair mix), dA tailing (NEB next Ultra II end repair/dA-tailing module), and adapter ligation (NEB next blunt/TA ligase master mix) were sequentially performed on the sheared gDNA fragments, and DNA purification was performed between each...
  5. Research: Nanopore direct RNA sequencing reveals METTL2A-mediated m3C sites in poly(A) RNA
    • Shuhei Mitsutomi,
    • Anzu Sugawara,
    • Masahide Seki,
    • Yutaka Suzuki,
    • Sotaro Miyao,
    • Haozhe Du,
    • Kenji Takahashi,
    • Yusuke Mizukami,
    • Kenzui Taniue,
    • and Nobuyoshi Akimitsu
    Genome Res. November 2025 35: 2406-2417; Published in Advance October 30, 2025, doi:10.1101/gr.280269.124
    ...I restriction sites of pcDNA3.1 C-FLAG using the Ligation-Convenience kit (Nippon Gene, #315-05963). The base editor construct targeting the S100A4-201 m3C sites was generated by cloning a guide RNA (gRNA) sequence—designed to target the 5′ region of the third exon of S100A4-201—into the BbsI restriction sites...
  6. Method: Verkko2 integrates proximity-ligation data with long-read De Bruijn graphs for efficient telomere-to-telomere genome assembly, phasing, and scaffolding
    • Dmitry Antipov,
    • Mikko Rautiainen,
    • Sergey Nurk,
    • Brian P. Walenz,
    • Steven J. Solar,
    • Adam M. Phillippy,
    • and Sergey Koren
    Genome Res. July 2025 35: 1583-1594; Published in Advance May 19, 2025, doi:10.1101/gr.280383.124
    ...ultralong sequencing reads. Thus, correctly resolving the acrocentrics in a diploid requires differentiating between 10 similar short arms and scaffolding across each rDNA array gap. Doing so is necessary for understanding variation within these important regions of the and better detecting abnormalities...
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  7. Method: DIG-seq: a genome-wide CRISPR off-target profiling method using chromatin DNA
    • Daesik Kim and
    • Jin-Soo Kim
    Genome Res. December 2018 28: 1894-1900; Published in Advance November 9, 2018, doi:10.1101/gr.236620.118
    ...v. 1.0) to identify potential off-target sites, and no DNA resection in vitro by cellular repair enzymes, making it possible to pinpoint DSB ends precisely.Cell-free methods provide a list of potential off-target sites that are cleaved in vitro. No mutations are, however, detectably induced at most...
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  8. Method: An optimized toolkit for high-molecular-weight DNA extraction and ultra-long-read nanopore sequencing using glass beads and hexamminecobalt(III) chloride
    • Inswasti Cahyani,
    • John Tyson,
    • Nadine Holmes,
    • Josh Quick,
    • Chris Moore,
    • Nick Loman,
    • and Matthew Loose
    Genome Res. May 2025 35: 1154-1166; Published in Advance March 24, 2025, doi:10.1101/gr.279943.124
    ...24385 and GM24631 ligation-based libraries (Supplemental Fig. S1A). We hypothesized that this was most likely due to suboptimal pore occupancy (i.e., the number of available pores sequencing at any time), resulting from the reduced number of adapted DNA ends available for sequencing because of the lower...
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  9. Method: Deep structural clustering reveals hidden systematic biases in RNA sequencing data
    • Qiang Su,
    • Yi Long,
    • Deming Gou,
    • Junmin Quan,
    • Xiaoming Zhou,
    • and Qizhou Lian
    Genome Res. November 2025 35: 2563-2577; Published in Advance September 19, 2025, doi:10.1101/gr.280713.125
    ...spike-ins of equal length but varying GC-content, MFE, and tertiary structure. Although an RNA of length k can form 4k sequences (Supplemental Fig. S1A), we constrained the design to eight variable sites within a 50-nt core, flanked by 8-nt poly(A) tails at each end. This yielded 48 spike-in variants...
  10. Method: Nanopore-based consensus sequencing enables accurate multimodal tumor cell-free DNA profiling
    • Li-Ting Chen,
    • Myrthe Jager,
    • Dàmi Rebergen,
    • Geertruid J. Brink,
    • Tom van den Ende,
    • Willem Vanderlinden,
    • Pauline Kolbeck,
    • Marc Pagès-Gallego,
    • Ymke van der Pol,
    • Nicolle Besselink,
    • Norbert Moldovan,
    • Nizar Hami,
    • Wigard P. Kloosterman,
    • Hanneke van Laarhoven,
    • Florent Mouliere,
    • Ronald Zweemer,
    • Jan Lipfert,
    • Sarah Derks,
    • Alessio Marcozzi,
    • and Jeroen de Ridder
    Genome Res. April 2025 35: 886-899; Published in Advance January 13, 2025, doi:10.1101/gr.279144.124
    ...features, such as fragment length and end-motifs (van der Pol and Mouliere 2019; Lo et al. 2021; Liu 2022). Simultaneously evaluating mutational and fragmentomic features in -wide cfDNA through a multimodal approach maximizes the capacity to detect ctDNA (Peneder et al. 2021; Moldovan et al. 2024).A number...
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