Searching journal content for articles similar to Xuan et al. 12 (7): 1142.

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  1. 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
    ...on both strands. In addition, the GENCODE database, a well-regarded repository of gene annotations, was utilized to search for cis-NAT regions. We identified 12,793 genomic regions annotated as being expressed from both the positive and negative DNA strands (regardless of whether they are expressed...
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  2. Method: Automated interpretable artificial intelligence genomic prediction with AlGP
    • Lei Wei,
    • Ziqin Jiang,
    • Baoliang Fan,
    • Yidan Yan,
    • Zhenqiang Xu,
    • Xiaoxiang Hu,
    • and Yuzhe Wang
    Genome Res. March 5, 2026 ; Published in Advance March 5, 2026, doi:10.1101/gr.281006.125
    ...DNA variants to phenotypes, spans the entire central dogma of molecular biology; incorporates various nongenetic factors, such as environmental influences (Yao et al. 2025); and is one of the most challenging tasks in biological prediction. Genomic selection (GS) is the most advanced methodology...
  3. 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
    ....Reconstructing cell lineage trees from noisy single-cell DNA data has been actively studied in recent literature. Existing methods differ in their modeling assumptions and also in computational approaches. First, mutational models are essential for single-cell DNA data analysis, as mutations give rise to genomic...
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  4. Method: Autoencoders for genomic variation analysis
    • Margarita Geleta,
    • Daniel Mas Montserrat,
    • Xavier Giro-i-Nieto,
    • and Alexander G. Ioannidis
    Genome Res. February 2026 36: 348-360; Published in Advance January 20, 2026, doi:10.1101/gr.280086.124
    ...“logistic mixing,” a neural network without hidden layers that uses a simple update rule to adjust the output probabilities for better bitstream coding. This idea has been brought to genomic compression of sequencing reads with GeCo3 (Silva et al. 2020). Another recent use of neural networks for DNA...
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  5. Resource: A systems view on DNA damage response kinetics in Tetrahymena
    • Emily Nischwitz,
    • Vivien A.C. Schoonenberg,
    • Rachel Mullner,
    • Albert Fradera-Sola,
    • Susanne Zimbelmann,
    • Joshua J. Smith,
    • and Falk Butter
    Genome Res. January 28, 2026 ; Published in Advance January 28, 2026, doi:10.1101/gr.281000.125
    ...; Scully et al. 2019), ICL (Lehoczký et al. 2007), and general DDR (Ciccia and Elledge 2010; Pizzul et al. 2022). Our list of these factors, containing 173 DNA repair genes, is not intended to be comprehensive but highlights established key genes in the different DNA repair pathways as well as non...
  6. 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
    ...studies have sought to catalog driver events occurring in hundreds of cancer genes across different tumor types (Martincorena and Campbell 2015; Chung et al. 2016; Tokheim and Karchin 2019; Dietlein et al. 2020; Kumar et al. 2020; The ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium 2020...
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  7. Research: Genomic regulatory landscape underlying the antiviral response of Atlantic salmon
    • Shahmir Naseer,
    • Thomas C Clark,
    • Bertrand Collet,
    • Pooran Dewari,
    • Damir Baranasic,
    • Daniel J Macqueen,
    • Pierre Boudinot,
    • and Samuel A.M. Martin
    Genome Res. October 22, 2025 gr.280579.125; Published in Advance October 22, 2025, doi:10.1101/gr.280579.125
    ...for resolving how specific cell types 469 contribute to the epigenomic regulation of the interferon response in salmonid immunity. 470 ISREs are DNA sequence motifs responsible for the regulation of immune genes (Au et al., 471 1995), which serve as recognition sites for transcription factors integral...
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  8. Research: Pangenome analysis reveals families of ubiquitin-ligase adaptors as key genomic divergence drivers that lead to hybrid incompatibility
    • Dongying Xie,
    • Pohao Ye,
    • Yiming Ma,
    • and Zhongying Zhao
    Genome Res. March 2026 36: 506-521; Published in Advance February 17, 2026, doi:10.1101/gr.280885.125
    ...method. (Right) Comparative genomic features between interspecific and intraspecific strains, including sizes (A), gene numbers (B), repeat content as a percentage of the (C), proportions of repeat types among total repeats (D), gene length distributions (E), and coding DNA sequence (CDS) length...
  9. Method: A scalable computational framework for predicting gene expression from candidate cis-regulatory elements
    • Qinhu Zhang,
    • Siguo Wang,
    • Zhipeng Li,
    • Wenzheng Bao,
    • Wenjian Liu,
    • and De-Shuang Huang
    Genome Res. February 2026 36: 361-374; Published in Advance January 16, 2026, doi:10.1101/gr.281219.125
    ...for predicting gene expression (ScPGE) from discrete candidate CREs (cCREs). ScPGE assembles DNA sequences, transcription factor (TF) binding scores, and epigenomic tracks from discrete cCREs into three-dimensional tensors, and then models the relationships between cCREs and genes by combining convolutional...
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  10. 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
    ...genomics. Early works in molecular biology on gene expression were limited, because purified RNA is unstable and difficult to work with. However, the discovery (and use in the laboratory) of reverse transcriptase, permitting the controlled synthesis of RNAs into cDNAs (Maniatis et al. 1976...
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