Searching journal content for articles similar to Garimella et al. 30 (8): 1154.

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Method: Reference-informed prediction of alternative splicing and splicing-altering mutations from sequences
- Chencheng Xu,
- Suying Bao,
- Ye Wang,
- Wenxing Li,
- Hao Chen,
- Yufeng Shen,
- Tao Jiang,
- and Chaolin Zhang
Genome Res. July 2024 34: 1052-1065; Published in Advance July 26, 2024, doi:10.1101/gr.279044.124
...genes. The model architecture enables DeltaSplice to perform “reference-informed prediction” by incorporating the known splice site usage of a reference gene sequence to improve its prediction on splicing-altering mutations. We benchmarked DeltaSplice and several other state-of-the-art methods...
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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
...of the mammalian . We use whole- sequencing to identify de novo mutations in cohorts of age-matched ART-derived and naturally conceived mice. Our reliance on mice of a single inbred strain background allows us to rigorously control for potential genetic influences and environmental exposures on mutation rates...
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Method: k-mer manifold approximation and projection for visualizing DNA sequences
- Chengbo Fu,
- Einari A. Niskanen,
- Gong-Hong Wei,
- Zhirong Yang,
- Marta Sanvicente-García,
- Marc Güell,
- and Lu Cheng
Genome Res. May 2025 35: 1234-1246; Published in Advance April 10, 2025, doi:10.1101/gr.279458.124
...that are easier to interpret and locate on a reference sequence. For instance, locating a consensus sequence with up to two mutations on the reference sequence is more straightforward than evaluating PWM-derived P-values. Additionally, KMAP provides an intuitive 2D visualization of the k-mer manifold, displaying...
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Research: Leveraging the T2T assembly to resolve rare and pathogenic inversions in reference genome gaps
- Kristine Bilgrav Saether,
- Jesper Eisfeldt,
- Jesse D. Bengtsson,
- Ming Yin Lun,
- Christopher M. Grochowski,
- Medhat Mahmoud,
- Hsiao-Tuan Chao,
- Jill A. Rosenfeld,
- Pengfei Liu,
- Marlene Ek,
- Jakob Schuy,
- Adam Ameur,
- Hongzheng Dai,
- Undiagnosed Diseases Network,
- James Paul Hwang,
- Fritz J. Sedlazeck,
- Weimin Bi,
- Ronit Marom,
- Josephine Wincent,
- Ann Nordgren,
- Claudia M.B. Carvalho,
- and Anna Lindstrand
Genome Res. November 2024 34: 1785-1797; Published in Advance November 1, 2024, doi:10.1101/gr.279346.124
...in inversion detection due to its increased resolution across repetitive sequences (Nurk et al. 2022; Porubsky et al. 2023a). This reference is the first complete reference, adding over 200 megabase pairs (Mbp) of sequence compared to GRCh38 (Nurk et al. 2022). In fact, both GRCh37 and GRCh38 lack information...
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Research: Rates and spectra of de novo structural mutations in Chlamydomonas reinhardtii
- Eugenio López-Cortegano,
- Rory J. Craig,
- Jobran Chebib,
- Eniolaye J. Balogun,
- and Peter D. Keightley
Genome Res. January 2023 33: 45-60; Published in Advance December 12, 2022, doi:10.1101/gr.276957.122
...-read sequencing technology that has been applied reliably detects only single-nucleotide mutations (SNMs) and short insertions and deletions (indels), and little is known about the rates at which SMs occur de novo.SMs include larger indels (often defined as those >50 bp), duplications, transposable element (TE...
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Resource: Chromosome-level subgenome-aware de novo assembly provides insight into Saccharomyces bayanus genome divergence after hybridization
- Cory Gardner,
- Junhao Chen,
- Christina Hadfield,
- Zhaolian Lu,
- David Debruin,
- Yu Zhan,
- Maureen J. Donlin,
- Tae-Hyuk Ahn,
- and Zhenguo Lin
Genome Res. November 2024 34: 2133-2146; Published in Advance September 17, 2024, doi:10.1101/gr.279364.124
...and mitigated the maladaptive effect of hybridization. This paper describes the first in-depth study using long-read sequencing technology of an S. bayanus hybrid , which may serve as an excellent reference for future studies of this important yeast and other yeast strains.It has generally been believed...
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Research: The rate and spectrum of new mutations in mice inferred by long-read sequencing
- Eugenio López-Cortegano,
- Jobran Chebib,
- Anika Jonas,
- Anastasia Vock,
- Sven Künzel,
- Peter D. Keightley,
- and Diethard Tautz
Genome Res. January 2025 35: 43-54; Published in Advance December 2, 2024, doi:10.1101/gr.279982.124
...of de novo structural variation in mammals (e.g., Kloosterman et al. 2015; Belyeu et al. 2021; Steensma et al. 2023), but these studies have employed short-read technology, which limits the SMs detected primarily to copy-number variants and hinders the discovery of mutations within repetitive sequences...
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Research: Global characterization of somatic mutations and DNA methylation changes during vegetative propagation in strawberries
- Shaoqiang Hu,
- Xiangguo Zeng,
- Yuguo Liu,
- Yongping Li,
- Minghao Qu,
- Wen-Biao Jiao,
- Yongchao Han,
- and Chunying Kang
Genome Res. October 2024 34: 1582-1594; Published in Advance October 15, 2024, doi:10.1101/gr.279378.124
...version 4 (Edger et al. 2018). During the analysis, the low-quality mutation sites and the mutation sites close to the simple sequence repeats were filtered out (see “Methods”). The mutations present in the regenerated plants (with a percentage of ≥30% reads in each site) but absent in the control plants...
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Method: Aligning distant sequences to graphs using long seed sketches
- Amir Joudaki,
- Alexandru Meterez,
- Harun Mustafa,
- Ragnar Groot Koerkamp,
- André Kahles,
- and Gunnar Rätsch
Genome Res. July 2023 33: 1208-1217; Published in Advance April 18, 2023, doi:10.1101/gr.277659.123
...sequence of length |π(wi)| = 80 + 250 = 330. Because of the size of the graphs and number of branches in our experiments, it is highly unlikely that the same path will be sampled multiple times. The query sequences qi are obtained by applying mutations with rates of 5%, 10%, 15%, 20%, and 25...
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Method: Discovery of an unusually high number of de novo mutations in sperm of older men using duplex sequencing
- Renato Salazar,
- Barbara Arbeithuber,
- Maja Ivankovic,
- Monika Heinzl,
- Sofia Moura,
- Ingrid Hartl,
- Theresa Mair,
- Angelika Lahnsteiner,
- Thomas Ebner,
- Omar Shebl,
- Johannes Pröll,
- and Irene Tiemann-Boege
Genome Res. March 2022 32: 499-511; Published in Advance February 24, 2022, doi:10.1101/gr.275695.121
...and high oncogenic score (Tomasetti and Vogelstein 2015).ResultsDS detects ultra-low-mutation frequenciesHigh-throughput sequencing is a widely used method for prospective screening of mutations, but given its high error rate of ∼0.1%–2%, it cannot be used for detecting low or ultra-low-frequency variants...
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