Searching journal content for articles similar to Goodman 8 (3): 159.

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  1. Editorial: Scope note Genome Res. May 2018 28: x; Published in Advance April 12, 2018, doi:10.1101/gr.236893.118
    ...novel computational algorithms that provide insight into biological processes editing and engineering Genome Research is cross-disciplinary, publishing studies that reflect aspects of the above areas in disease and medicine, neuroscience, microbiology, and human, animal, and plant biology.The Editors...
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  2. Editorial: Scope note Genome Res. May 2011 21: xi
    ...genome;21/5/xi 1088-9051 Scope note Editorial Scope note The broader goal of Genome Research is to publish research findings that offer novel insights into the structure, function, and biology of s and the biology of diseases. Specific areas of interest include proteomics, systems biology, single...
  3. Method: 3′-end ligation sequencing is a sensitive method to detect DNA nicks at potential sites of off-target activity induced by prime editors
    • Jacob Stewart-Ornstein,
    • Matthew J. Irby,
    • Marina K. Lilieholm,
    • Dylan Laprise,
    • Maria D. Collier,
    • Thomas Aunins,
    • Dewi Harjanto,
    • Aaron N. Chang,
    • Deepak Reyon,
    • and Jeremy S. Duffield
    Genome Res. September 2025 35: 2064-2075; Published in Advance August 5, 2025, doi:10.1101/gr.280164.124
    ..., in vitro approaches, in which the editor is combined with human genomic DNA and sites where editing may occur are identified biochemically, are important tools. Existing biochemical approaches for off-target discovery recognize double-stranded breaks generated by nuclease-based gene editors such as SpCas9...
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  4. 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
    .... 2014). Only a small fraction of these were previously identified for the same samples (Supplemental Fig. S2B), indicating that the classical SNV detection schemes may overlook a large fraction of sites (see also Supplemental Table S6). Note that, for some editors, no excess of hyperediting sites...
  5. Method: Minimizing reference bias with an imputed personalized reference
    • Kavya Vaddadi,
    • Mao-Jan Lin,
    • Sina Majidian,
    • Taher Mun,
    • and Ben Langmead
    Genome Res. March 5, 2026 gr.280989.125; Published in Advance March 5, 2026, doi:10.1101/gr.280989.125
    ...through an expensive iterative alignment process, also focusing on monoploids. MMSEQ (Turro et al. 2011) performs variant calling on an input BAM file to construct a personalized diploid transcriptome, but does not perform imputation. RefEditor (Yuan et al. 2015) uses genotype imputation to obtain phased...
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  6. Method: Homozygous editing of multiple genes for accelerated generation of xenotransplantation pigs
    • Xiaoyue Duan,
    • Chaolei Chen,
    • Chang Du,
    • Liang Guo,
    • Jun Liu,
    • Naipeng Hou,
    • Pan Li,
    • Xiaolan Qi,
    • Fei Gao,
    • Xuguang Du,
    • Jiangping Song,
    • and Sen Wu
    Genome Res. May 2025 35: 1167-1178; Published in Advance March 5, 2025, doi:10.1101/gr.279709.124
    ...for Cas9-based editing (Kim et al. 2011; Ramakrishna et al. 2014), “TREE” reporters for base editors (Standage-Beier et al. 2019), “fluoPEER” reporters for prime editors (Schene et al. 2022), and CRISPRa selection for gain of function (Heidersbach et al. 2023). For these methods, the gene of interest...
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  7. Method: Quantifying pathological progression from single-cell transcriptomic data with scPSS
    • Samin Rahman Khan,
    • M Saifur Rahman,
    • M. Sohel Rahman,
    • and Md Abul Hassan Samee
    Genome Res. February 2026 36: 375-386; Published in Advance January 14, 2026, doi:10.1101/gr.280411.125
    ...healthy versus IPF condition of individuals based on the proportion of pathological cells of each cell group and all cells together. (E) With cells from both healthy and diseased individuals in the reference data set, we see an increase in predictive accuracy for the same experiment. (Note...
  8. 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...
  9. Research: The role of transposon activity in shaping cis-regulatory element evolution after whole-genome duplication
    • Øystein Monsen,
    • Lars Grønvold,
    • Alex Datsomor,
    • Thomas Harvey,
    • James Kijas,
    • Alexander Suh,
    • Torgeir R. Hvidsten,
    • and Simen Rød Sandve
    Genome Res. March 2025 35: 475-488; Published in Advance February 12, 2025, doi:10.1101/gr.278931.124
    ...chromatin resulted in a slightly different superfamily list than the initial machine-predicted annotations presented in Figure 1. Note also that only TE subfamily sequences with more than 500 insertions have been included. The percentage of enriched TE subfamilies per superfamily are indicated above bars...
  10. Method: A versatile type VI CRISPR-based approach for targeted m6A demethylation in mRNAs
    • Panagiotis G. Adamopoulos,
    • Konstantina Athanasopoulou,
    • and Andreas Scorilas
    Genome Res. January 2026 36: 169-182; Published in Advance December 11, 2025, doi:10.1101/gr.280476.125
    ...region for the incorporation of any gRNA sequence through the golden gate cloning method (Ran et al. 2013). Of note, the designed plasmid contains a gRNA cloning site that encompasses two cleavage sites for the type IIS PaqCI restriction endonuclease (Kennedy et al. 2023), thus enabling the scarless...
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