Searching journal content for articles similar to Inazuka et al. 7 (11): 1094.

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Research: Modest increase in the de novo single-nucleotide mutation rate in house mice born by assisted reproduction
- Laura Blanco-Berdugo,
- Alexis Garretson,
- and Beth L. Dumont
Genome Res. January 2026 36: 50-60; Published in Advance November 13, 2025, doi:10.1101/gr.281180.125
...estimates indicate that our study design has 80% power to detect a ∼35% increase in the dnSNV rate between the ART and naturally conceived cohorts, assuming a baseline mutation rate equivalent to that previously reported for C57BL/6J mice (Lindsay et al. 2019; Supplemental Fig. 3).View larger version...
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Method: DENT-seq for genome-wide strand-specific identification of DNA single-strand break sites with single-nucleotide resolution
- Juniper J. Elacqua,
- Navpreet Ranu,
- Sarah E. DiIorio,
- and Paul C. Blainey
Genome Res. January 2021 31: 75-87; Published in Advance December 21, 2020, doi:10.1101/gr.265223.120
...) and N6-methoxy-2,6-diaminopurine (K) act as a universal pyrimidine and purine, respectively (Fig. 1A; Hill et al. 1998). dPTP and dKTP can be incorporated into a DNA molecule at the site of a single-strand break via nick translation (Fig. 1B) and generate readily detectable transition mutations when...
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Resource: Streamlined spatial and environmental expression signatures characterize the minimalist duckweed Wolffia australiana
- Tom Denyer,
- Pin-Jou Wu,
- Kelly Colt,
- Bradley W. Abramson,
- Zhili Pang,
- Pavel Solansky,
- Allen Mamerto,
- Tatsuya Nobori,
- Joseph R. Ecker,
- Eric Lam,
- Todd P. Michael,
- and Marja C.P. Timmermans
Genome Res. July 2024 34: 1106-1120; Published in Advance July 1, 2024, doi:10.1101/gr.279091.124
...to a very streamlined system with the majority of genes dedicated to basic cellular processes. The detection of 92% of all annotated genes in the single-cell transcriptome data sets corroborates this idea.Wolffia, similar to other duckweeds, has a compact with fewer protein-coding genes than most other...
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Method: Accurate detection of tandem repeats from error-prone sequences with EquiRep
- Zhezheng Song,
- Tasfia Zahin,
- Xiang Li,
- and Mingfu Shao
Genome Res. December 2025 35: 2714-2721; Published in Advance August 21, 2025, doi:10.1101/gr.280750.125
...the sequence of the underlying repeat unit. Although several methods exist, they often exhibit low accuracy when the repeat unit length increases or the number of copies is low. Furthermore, methods capable of handling highly mutated sequences remain scarce, highlighting a significant opportunity...
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Research: T2T-CHM13 improves read mapping and detection of clinically relevant genetic variation in the Swedish population
- Daniel Schmitz,
- Adam Ameur,
- and Åsa Johansson
Genome Res. November 2025 35: 2377-2388; Published in Advance September 16, 2025, doi:10.1101/gr.279320.124
...for the detection of many novel variants, especially in the previously unresolved regions. They also found that their novel reference reduces the number of false-positive calls mainly in protein-coding genes, and they highlight the increased sensitivity for detection of rare variants and singletons (Aganezov et al...
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Method: De novo detection of somatic variants in high-quality long-read single-cell RNA sequencing data
- Arthur Dondi,
- Nico Borgsmüller,
- Pedro F. Ferreira,
- Brian J. Haas,
- Francis Jacob,
- Viola Heinzelmann-Schwarz,
- Tumor Profiler Consortium,
- and Niko Beerenwinkel
Genome Res. April 2025 35: 900-913; Published in Advance March 19, 2025, doi:10.1101/gr.279281.124
...using cell mutational profiles. LongSom distinguishes somatic SNVs from noise and germline polymorphisms by applying an extensive set of hard filters and statistical tests. Applying LongSom to human ovarian cancer samples, we detected clinically relevant somatic SNVs that were validated against matched...
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Research: Assessing DNA methylation detection for primary human tissue using Nanopore sequencing
- Rylee Genner,
- Stuart Akeson,
- Melissa Meredith,
- Pilar Alvarez Jerez,
- Laksh Malik,
- Breeana Baker,
- Abigail Miano-Burkhardt,
- CARD-long-read Team,
- Benedict Paten,
- Kimberley J. Billingsley,
- Cornelis Blauwendraat,
- and Miten Jain
Genome Res. April 2025 35: 632-643; Published in Advance March 7, 2025, doi:10.1101/gr.279159.124
...accuracy and sequencing throughput. However, the effects on methylation detection have not yet been documented. Here, we performed a series of computational analyses to characterize differences in Nanopore-based 5mC detection between the ONT R9 and R10 chemistries. We compared 5mC calls in R9 and R10...
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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
...determination. Therefore, integrated analysis of stripes with genomic and epigenomic features at a -wide scale shows vast potential in understanding the cooperation between regulatory elements in 3D nucleome. To this end, we present Quagga, a computational tool for detection and statistical verification...
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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
...framework for multiple ST analysis tasks, including spatial domain detection and cell cycle identification. Although these methods have successfully analyzed individual slices, they remain limited to two-dimensional (2D) analyses owing to their single-slice focus.As the availability of SO data derived from...
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Research: Colibactin leads to a bacteria-specific mutation pattern and self-inflicted DNA damage
- Emily Lowry,
- Yiqing Wang,
- Tal Dagan,
- and Amir Mitchell
Genome Res. August 2024 34: 1154-1164; Published in Advance August 16, 2024, doi:10.1101/gr.279517.124
...; Pleguezuelos-Manzano et al. 2020). This enrichment is attributed to the particularly narrow minor groove of these sequences, which promotes colibactin binding (Dziubańska-Kusibab et al. 2020). Recent work has found that a colibactin-associated mutational signature is detected in 5%–10% of colorectal cancers...
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