Searching journal content for articles similar to Agudelo et al. 30 (1): 107.

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  1. Method: Highly efficient and scarless genome editing via essential gene-coupled homology-directed repair
    • Joo Hye Yeo,
    • Hyongbum Henry Kim,
    • Sang Ho Oh,
    • and Jinu Lee
    Genome Res. April 15, 2026 gr.281194.125; Published in Advance April 15, 2026, doi:10.1101/gr.281194.125
    ...strategies, including small-molecule treatments and marker-based 32 selection, are constrained by cytotoxicity, genomic scarring, and inconsistent 33 performance. Here, we present ESS-HDR (essential gene–supported scarless HDR), a 34 robust, drug- and marker-free platform that selectively enriches HDR...
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  2. 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
    ...RNAs, influencing their stability, and therefore represents a robust and versatile tool for mRNA epitranscriptomics.Another key feature of the presented approach is the choice of the restriction enzyme used for golden gate cloning of gRNAs into Dem6A-Vec. The developed approach involves the utilization...
  3. Research: A 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 ; Published in Advance March 12, 2026, doi:10.1101/gr.280820.125
    ...source of dsRNA is cotranscription of sense and antisense strands of the same genomic region. Binding of these complementary, naturally occurring, antisense transcripts (NATs) results in a perfect RNA duplex, which may be targeted by ADARs. To explore the scope of ADAR editing of NAT-derived dsRNA, we...
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  4. Method: Enabling efficient and robust analysis of tandem repeats in genomic data using wavefront-based string decomposer
    • Junhai Qi,
    • Zhidong Yang,
    • Ting Yu,
    • and Guojun Li
    Genome Res. April 8, 2026 gr.281346.125; Published in Advance April 8, 2026, doi:10.1101/gr.281346.125
    ...16 TRs are genomic sequences composed of tandemly arranged DNA repeat units. TRs are broadly categorized into short17 tandem repeats (STRs) and long tandem repeats (LTRs) based on repeat unit length. STRs typically consist of 1–6 base18 pair (bp) repeat units, whereas LTRs can span hundreds of base...
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  5. Research: Dynamic A-to-I RNA editing in response to gut microbiome in honeybees
    • Yuange Duan,
    • Min Huang,
    • Lin Ye,
    • Ling Ma,
    • Yashuai Wu,
    • Yating Du,
    • Jiyao Liu,
    • Fan Song,
    • Li Tian,
    • Wanzhi Cai,
    • Hu Li,
    • Xin Zhou,
    • and Shiqi Luo
    Genome Res. March 4, 2026 ; Published in Advance March 4, 2026, doi:10.1101/gr.280291.124
    ...the transcriptome (Eisenberg and Levanon 2018; Duan 2025). Editing events taking place in coding sequences (CDSs)might alter the genomically encoded amino acid and lead to nonsynonymous changes, namely, “recoding” (Alon et al. 2015). Genome-wide profiling of RNA editing sites has been performed in several metazoans...
  6. Method: Robust 16S rRNA classification based on a compressed LCA index
    • Omar Ahmed,
    • Christina Boucher,
    • and Ben Langmead
    Genome Res. December 2025 35: 2650-2660; Published in Advance August 25, 2025, doi:10.1101/gr.279846.124
    ...was by O.A. Reviewing and editing were by O.A., C.B., and B.L. Supervision was by C.B. and B.L. All author approved the final version.Footnotes [Supplemental material is available for this article.] Article published online before print. Article, supplemental material, and publication date are at https...
  7. Research: Loss of multilevel 3D genome organization during breast cancer progression
    • Roberto Rossini,
    • Saleh Oshaghi,
    • Maxim Nekrasov,
    • Aurélie Bellanger,
    • Renae Domaschenz,
    • Yasmin Dijkwel,
    • Mohamed Abdelhalim,
    • Rahul Agrawal,
    • Marit Ledsaak,
    • Philippe Collas,
    • Ragnhild Eskeland,
    • David Tremethick,
    • and Jonas Paulsen
    Genome Res. January 2026 36: 20-37; Published in Advance October 9, 2025, doi:10.1101/gr.280791.125
    ...editing efficiency, we amplified genomic DNA from puromycin-selected, doubly transfected C1 cells using primers targeting regions surrounding sites recognized by sgRNAs in RE1, -2, or -3 (Supplemental Fig. S49A). PCR products were analyzed by gel electrophoresis, purified, and sequenced (Supplemental Fig...
  8. 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
    ...editing efficiency. This approach led to the successful generation of xenotransplantation pigs with multiple homozygously edited genes in a much shorter time frame than previously achievable.ResultsSurrogate reporters for genomic targetingEfficient selection methods are essential for enhancing multiplex...
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  9. Method: Pangenome-based genome inference using integer programming
    • Ghanshyam Chandra,
    • Md Helal Hossen,
    • Stephan Scholz,
    • Alexander T. Dilthey,
    • Daniel Gibney,
    • and Chirag Jain
    Genome Res. December 2025 35: 2661-2670; Published in Advance August 21, 2025, doi:10.1101/gr.280567.125
    ...: chirag@iisc.ac.inAbstractAffordable genotyping methods are essential in genomics. Commonly used genotyping methods primarily support single-nucleotide variants and short indels but neglect structural variants. Additionally, accuracy of read alignments to a reference is unreliable in highly polymorphic...
  10. Method: Robust chromatin state annotation
    • Mehdi Foroozandeh Shahraki,
    • Marjan Farahbod,
    • and Maxwell W. Libbrecht
    Genome Res. March 2024 34: 469-483; Published in Advance March 21, 2024, doi:10.1101/gr.278343.123
    ...assignment at every genomic position. We hypothesized that these posterior probabilities indicate reliability, such that confidently annotated positions are robust. However, these probability values are often vastly too confident; most positions receive >0.99 posterior probability (Libbrecht et al. 2021).We...
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