Searching journal content for articles similar to Remy et al. 24 (8): 1371.

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  1. Method: Precise and efficient nucleotide substitution near genomic nick via noncanonical homology-directed repair
    • Kazuhiro Nakajima,
    • Yue Zhou,
    • Akiko Tomita,
    • Yoshihiro Hirade,
    • Channabasavaiah B. Gurumurthy,
    • and Shinichiro Nakada
    Genome Res. February 2018 28: 223-230; Published in Advance December 22, 2017, doi:10.1101/gr.226027.117
    ...-sequence homology between the target gene and repair template, but does not require CtIP, RAD51, or RAD52. Thus, it is considered that noncanonical homology-directed repair regulates the SNGD-mediated gene editing. In summary, SNGD promotes precise and efficient gene editing and may be a promising strategy...
  2. Method: Robust and efficient annotation of cell states through gene signature scoring
    • Laure Ciernik,
    • Agnieszka Kraft,
    • Florian Barkmann,
    • Josephine Yates,
    • and Valentina Boeva
    Genome Res. March 2026 36: 630-644; Published in Advance February 18, 2026, doi:10.1101/gr.280926.125
    ...phenotype (Nevins and Potti 2007). One key application of signature scoring is cell annotation, as it offers a highly efficient and reliable method for classifying cells into types and states (Neftel et al. 2019). Notably, the quality of gene signatures plays a critical role in this process, as the accuracy...
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  3. Method: Statistically rigorous and computationally efficient chromatin stripe detection with Quagga
    • Fan Feng,
    • Sean Moran,
    • Anders S. Hansen,
    • Xiaotian Zhang,
    • and Jie Liu
    Genome Res. January 2026 36: 159-168; Published in Advance November 12, 2025, doi:10.1101/gr.280132.124
    ...02139, USA; 3Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02139, USA; 4Koch Institute for Integrative Cancer Research, Cambridge, Massachusetts 02139, USA; 5Department of Biochemistry and Molecular Biology, University of Texas Health Science Center Houston...
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  4. Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
    • Andrew D. Bates,
    • Dawid Grzela,
    • Maciej Studzian,
    • Louise Brennan,
    • Moli Williams,
    • Conor Fawcett,
    • Beth Hammond,
    • Manreen Grewal,
    • Marcin Ratajewski,
    • Lukasz Pulaski,
    • and Urszula L. McClurg
    Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
    ...that balance biological relevance, sensitivity, and interpretability to ultimately answer a deceptively simple question: What TFs directly regulate the expression of my GOI?Cellular processes are regulated by transcription machinery binding the promoters and enhancers of target genes to activate gene...
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  5. Research: Ultraviolet damage and repair maps in Drosophila reveal the impact of domain-specific changes in nucleosome repeat length on repair efficiency
    • Benjamin Morledge-Hampton,
    • Kathiresan Selvam,
    • Manish Chauhan,
    • Alan G. Goodman,
    • and John J. Wyrick
    Genome Res. February 2025 35: 257-267; Published in Advance January 6, 2025, doi:10.1101/gr.279605.124
    ...rapid repair of the TS relative to the NTS. These results are consistent with a previous analysis of these XR-seq data indicating efficient TC-NER of the TS in Drosophila genes (Deger et al. 2019). We then further stratified the repair data by chromatin type. This stratification showed accentuated...
  6. Method: Structure-optimized sgRNA selection with PlatinumCRISPr for efficient Cas9 generation of knockouts
    • Irmgard U. Haussmann,
    • Thomas C. Dix,
    • David W.J. McQuarrie,
    • Veronica Dezi,
    • Abdullah I. Hans,
    • Roland Arnold,
    • and Matthias Soller
    Genome Res. December 2024 34: 2279-2292; Published in Advance December 3, 2024, doi:10.1101/gr.279479.124
    ...@bham.ac.ukAbstractA single guide RNA (sgRNA) directs Cas9 nuclease for gene-specific scission of double-stranded DNA. High Cas9 activity is essential for efficient gene editing to generate gene deletions and gene replacements by homologous recombination. However, cleavage efficiency is below 50...
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  7. Method: Gene duplication is associated with gene diversification and potential neofunctionalization in lung cancer evolution
    • Paul Ashford,
    • Alexander M. Frankell,
    • Zofia Piszka,
    • Camilla S.M. Pang,
    • Mahnaz Abbasian,
    • Maise Al Bakir,
    • Mariam Jamal-Hanjani,
    • Nicholas McGranahan,
    • Charles Swanton,
    • and Christine A. Orengo
    Genome Res. March 2026 36: 561-577; Published in Advance February 19, 2026, doi:10.1101/gr.278663.123
    ...in case studies GOT1, PRDX3, and TALDO1 (for pancancer analysis, see Supplemental Fig. 17) and, additionally, H3C1 in TRACERx LUAD (Supplemental Fig. 18).View larger version: In this window In a new window Figure 4. FIE genes in functionally diverse protein families are targets for discovery of potential...
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  8. Method: ScisTree2 enables large-scale inference of cell lineage trees and genotype calling using efficient local search
    • Haotian Zhang,
    • Yiming Zhang,
    • Teng Gao,
    • and Yufeng Wu
    Genome Res. December 2025 35: 2781-2791; Published in Advance September 3, 2025, doi:10.1101/gr.280542.125
    ...is increasing rapidly. Accurate inference of cell lineage tree from large single-cell data is computationally challenging. In this paper, we present ScisTree2, a fast and accurate cell lineage tree inference and genotype calling approach based on the infinite-sites model. ScisTree2 relies on an efficient local...
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  9. Method: Analysis of coding gene expression from small RNA sequencing
    • Aygun Azadova,
    • Anthonia Ekperuoh,
    • Greg N. Brooke,
    • and Antonio Marco
    Genome Res. March 2026 36: 611-618; Published in Advance February 10, 2026, doi:10.1101/gr.281364.125
    ...-life and the expression of housekeeping or highly abundant genes do not bias the results. Analysis of the expression of both microRNAs and coding genes from the same sRNA-seq experiments demonstrates that known microRNA–target interactions are, as expected, inversely correlated with the expression profiles of these micro...
  10. Method: Efficient integration of spatial omics data for joint domain detection, matching, and alignment with stMSA
    • Han Shu,
    • Jing Chen,
    • Chang Xu,
    • Jialu Hu,
    • Yongtian Wang,
    • Jiajie Peng,
    • Qinghua Jiang,
    • Xuequn Shang,
    • and Tao Wang
    Genome Res. October 2025 35: 2285-2299; Published in Advance August 14, 2025, doi:10.1101/gr.280584.125
    ...consists of a GAT layer and an FCN layer, both designed to reconstruct the input gene expressions. To expedite convergence and enhance efficiency, the decoder layers share the parameters learned from the encoder layers. Specifically, stMSA utilizes the transposed weight matrix of the encoder as the weight...
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