Searching journal content for articles similar to Maruya et al. 6 (1): 51.

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  1. Method: High-resolution genotype-free mapping of genetic variation with CRI-SPA-Map
    • Sheila Lutz,
    • Megan Lawler,
    • Samuel Amidon,
    • and Frank W Albert
    Genome Res. March 23, 2026 gr.281514.125; Published in Advance March 23, 2026, doi:10.1101/gr.281514.125
    ...isolates carry tracts of W303 alleles extending from the targeted ORF to the telomere. A 276 causal W303 allele is included in a distal isolate if the causal variant is located either in the 277 targeted ORF or between the targeted ORF and the telomere (Supplemental Fig. S8 A–C). The 278 causal allele can...
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  2. Method: Early feature extraction drives model performance in high-resolution chromatin accessibility prediction
    • Aayush Grover,
    • Till Muser,
    • Liine Kasak,
    • Lin Zhang,
    • Ekaterina Krymova,
    • and Valentina Boeva
    Genome Res. March 2026 36: 619-629; Published in Advance January 12, 2026, doi:10.1101/gr.281042.125
    ...of noncoding genetic variants and the decoding of regulatory element architecture (Zhou and Troyanskaya 2015; Kelley et al. 2018; Avsec et al. 2021a; Pampari et al. 2024). Accurate, high-resolution maps of chromatin accessibility are essential for downstream tasks such as identifying regulatory elements...
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  3. Method: High-resolution spatial transcriptomics in fixed tissue using a cost-effective PCL-seq workflow
    • Xue Dong,
    • Mengzhu Hu,
    • Xiaonan Cui,
    • Wenjian Zhou,
    • Jingtao Cai,
    • Guangyao Mao,
    • and Weiyang Shi
    Genome Res. September 2025 35: 2052-2063; Published in Advance August 5, 2025, doi:10.1101/gr.279906.124
    ...) (Supplemental Fig. 1A–C). The final condition selected was 10 sec at 100% intensity, as it achieved efficient PC linker cleavage in illuminated regions while maintaining sharp boundaries. This was confirmed by fluorescence signal loss in the illuminated areas.Second, during the in situ tissue reactions phase...
  4. Method: Simultaneous modeling of chromatin conformation changes from multiple single-cell interaction maps with ChromMovie
    • Krzysztof H. Banecki,
    • Haoxi Chai,
    • Yijun Ruan,
    • and Dariusz Plewczynski
    Genome Res. April 8, 2026 ; Published in Advance April 8, 2026, doi:10.1101/gr.280985.125
    ...an important distinction. In contrast to averaged Hi-C modeling strategies, which rely heavily on distribution estimation and ensemble sampling, ChromMovie emphasizes the reconstruction of individual chromatin conformations. Figure 5. Benchmarking of ChromMovie computational time on a single NVIDIA A100 GPU...
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  5. Method: Tn5 tagments and transposes oligos to single-stranded DNA for strand-specific RNA sequencing
    • Yanjun Zhang,
    • Yin Tang,
    • Zhongxing Sun,
    • Junqi Jia,
    • Yuan Fang,
    • Xinyi Wan,
    • and Dong Fang
    Genome Res. March 2023 33: 412-426; Published in Advance March 23, 2023, doi:10.1101/gr.277213.122
    ...while constructing the RNA sequencing library (Fig. 3A). In addition, we used RNase A and RNase H to digest RNA and denatured the reverse-transcribed cDNA by heat to prevent the potential contamination of the RNA/DNA hybrid. The resulting single-strand cDNA was subjected to TABLE-seq, respectively...
  6. Method: Long-read RNA sequencing reveals allele-specific N6-methyladenosine modifications
    • Dayea Park and
    • Can Cenik
    Genome Res. April 2025 35: 999-1011; Published in Advance October 29, 2024, doi:10.1101/gr.279270.124
    ...In a new window Figure 2. Comparative analysis of allelic modifications in wild-type (WT) and Mettl3 knockout mESCs. (A) Allelic impartiality while allelic read assignment and m6A detection. The left panels outline the schematic of the data procedural steps for ASMs analysis. The right panels display...
  7. Method: KAS-ATAC reveals the genome-wide single-stranded accessible chromatin landscape of the human genome
    • Samuel H. Kim,
    • Georgi K. Marinov,
    • and William J. Greenleaf
    Genome Res. January 2025 35: 124-134; Published in Advance November 21, 2024, doi:10.1101/gr.279621.124
    ...on the highly specific covalent labeling of unpaired single-stranded guanine residues with N3-kethoxal (Fig. 1A); N3-kethoxal adducts can subsequently be subjected to a click reaction and the addition of biotin, which is then used to specifically pull-down labeled DNA fragments. Most ssDNA in the is found...
  8. Research: Mitotic chromosomes harbor cell type– and species-specific structural features within a universal loop array conformation
    • Marlies E. Oomen,
    • A. Nicole Fox,
    • Inma Gonzalez,
    • Amandine Molliex,
    • Thaleia Papadopoulou,
    • Pablo Navarro,
    • and Job Dekker
    Genome Res. August 2025 35: 1733-1744; Published in Advance June 6, 2025, doi:10.1101/gr.280648.125
    ...type–dependent differences in CTCF retention and that mitotic chromosome conformation is adaptable through modulation of loop sizes to generate chromosomes of appropriate dimensions.ResultsA subset of CTCF sites remains bound in mitotic mESCsIn recent years, several genomics studies have reported...
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  9. Research: High resolution genomes of multiple Xiphophorus species provide new insights into microevolution, hybrid incompatibility, and epistasis
    • Yuan Lu,
    • Edward Rice,
    • Kang Du,
    • Susanne Kneitz,
    • Magali Naville,
    • Corentin Dechaud,
    • Jean-Nicolas Volff,
    • Mikki Boswell,
    • William Boswell,
    • LaDeana Hillier,
    • Chad Tomlinson,
    • Kremitzki Milin,
    • Ronald B. Walter,
    • Manfred Schartl,
    • and Wesley C. Warren
    Genome Res. April 2023 33: 557-571; Published in Advance May 5, 2023, doi:10.1101/gr.277434.122
    ...allele inheritance, it is possible to identify, via genetic mapping, loci linked to traits (Wittbrodt et al. 1989; Lu et al. 2017a, 2020b; Powell et al. 2020, 2021; Schartl et al. 2021). Using interspecies hybridization coupled with gene mapping strategies, the X. maculatus and X. birchmanni alleles...
  10. Resource: A high-resolution map of small-scale inversions in the gibbon genome
    • Ludovica Mercuri,
    • Donato Palmisano,
    • Alberto L'Abbate,
    • Pietro D'Addabbo,
    • Francesco Montinaro,
    • Claudia Rita Catacchio,
    • Patrick Hasenfeld,
    • Mario Ventura,
    • Jan O. Korbel,
    • Ashley D. Sanders,
    • Flavia Angela Maria Maggiolini,
    • and Francesca Antonacci
    Genome Res. October 2022 32: 1941-1951; Published in Advance September 30, 2022, doi:10.1101/gr.276960.122
    ...(Supplemental Fig. S3A).Validation of simple inversionsWe selected nine inversions >500 kbp and tested them by FISH in the same NSI for which Strand-seq was generated. In detail, eight out of nine were tested in interphase nuclei by three-color FISH, whereas one larger inversion (Chr2_inv16) was tested...
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