Searching journal content for articles similar to Tian et al. 10 (9): 1403.

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  1. Research: Chimeric mitochondrial RNA transcripts predict mitochondrial genome deletion mutations in mitochondrial genetic diseases and aging
    • Amy R. Vandiver,
    • Allen Herbst,
    • Paul Stothard,
    • and Jonathan Wanagat
    Genome Res. January 2025 35: 55-65; Published in Advance November 27, 2024, doi:10.1101/gr.279072.124
    ...tools to correct or modulate mtDNA deletion mutations and a lack of understanding regarding the mechanisms of mutation accumulation are driving research in mitochondrial genetics to reveal new opportunities for treatment or prevention.Current methods for mtDNA deletion mutation detection, mapping...
  2. Method: Single-cell Rapid Capture Hybridization sequencing reliably detects isoform usage and coding mutations in targeted genes
    • Hongke Peng,
    • Jafar S. Jabbari,
    • Luyi Tian,
    • Changqing Wang,
    • Yupei You,
    • Chong Chyn Chua,
    • Natasha S. Anstee,
    • Noorul Amin,
    • Andrew H. Wei,
    • Nadia M. Davidson,
    • Andrew W. Roberts,
    • David C.S. Huang,
    • Matthew E. Ritchie,
    • and Rachel Thijssen
    Genome Res. April 2025 35: 942-955; Published in Advance January 10, 2025, doi:10.1101/gr.279322.124
    ...in insufficient read coverage, thereby limiting our ability to perform mutation calling for specific genes. Here, we developed a single-cell Rapid Capture Hybridization sequencing (scRaCH-seq) method that demonstrates high specificity and efficiency in capturing targeted transcripts using long-read sequencing...
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  3. Research: Transcriptomic and proteomic effects of gene deletion are not evolutionarily conserved
    • Yang Li and
    • Jianzhi Zhang
    Genome Res. March 2025 35: 512-521; Published in Advance February 18, 2025, doi:10.1101/gr.280008.124
    ...in the same S. cerevisiae strain by different laboratories, our observation cannot be explained by rapid evolution or large measurement error of gene expression. Analysis of transcriptomic and proteomic effects of gene deletions in multiple S. cerevisiae strains by the same laboratory reveals a high...
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  4. 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
    ...sequence, with the frequency (number of copies) of the unit being three, five, 10, and 20; (3) introduce random errors—insertions, deletions, and substitutions at equal probabilities—at the rates of 10%, 15% and 20% into the concatenated string to simulate real-world sequencing errors and mutations; and (4...
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  5. Research: Multiple paralogs and recombination mechanisms contribute to the high incidence of 22q11.2 deletion syndrome
    • Lisanne Vervoort,
    • Nicolas Dierckxsens,
    • Marta Sousa Santos,
    • Senne Meynants,
    • Erika Souche,
    • Ruben Cools,
    • Tracy Heung,
    • Koen Devriendt,
    • Hilde Peeters,
    • Donna M. McDonald-McGinn,
    • Ann Swillen,
    • Jeroen Breckpot,
    • Beverly S. Emanuel,
    • Hilde Van Esch,
    • Anne S. Bassett,
    • and Joris R. Vermeesch
    Genome Res. April 2025 35: 786-797; Published in Advance November 13, 2024, doi:10.1101/gr.279331.124
    ...Biosciences). The RS_Long_Amplicon_Analysis.1 pipeline was used for analysis.Low-pass sequencingThe mosaic LCR22-A/B (AB002) deletion was detected in the context of noninvasive prenatal testing of the pregnant patient JV2001. Procedures for noninvasive prenatal testing were followed as described (Bayindir et...
  6. 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
    ...and models will continue as long as data generation schemas are expensive and experimentally challenging. Quagga is an important, rapid, and cost-effective solution for identifying architectural stripes at the scale when lacking ChIP-seq or other sequencing data for which only Hi-C or another 3C family data...
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  7. Research: Rapid evolution of piRNA clusters in the Drosophila melanogaster ovary
    • Satyam P. Srivastav,
    • Cédric Feschotte,
    • and Andrew G. Clark
    Genome Res. May 2024 34: 711-724; Published in Advance May 15, 2024, doi:10.1101/gr.278062.123
    ...heterochromatin. Overall, we conclude that piCs are subject to a high rate of structural genomic change relative to the rest of the , which likely contributes to their rapid evolutionary turnover. Additionally, we find that common piCs are enriched for both insertions and deletions, which is consistent...
  8. Research: Xist upstream deletion leads to dysregulation of Xist and autosomal gene expression
    • Sudeshna Majumdar,
    • Lakshmi Sowjanya Bammidi,
    • Hemant C. Naik,
    • Avinchal Manhas,
    • Runumi Baro,
    • Akash Kalita,
    • Amlan Jyoti Naskar,
    • Sundarraj Nidharshan,
    • Girija S. Bariha,
    • Dimple Notani,
    • and Srimonta Gayen
    Genome Res. September 2025 35: 1992-2010; Published in Advance August 6, 2025, doi:10.1101/gr.279822.124
    ...representing IF-RNA-FISH for CIZ1 (red) and Xist (green) in WT and D1 deleted lines. Bottom: Quantification of enrichment of CIZ1 on the inactive X in compact versus dispersed Xist nuclei. n = 128, 111, 120, 114 (for each data point from left to right). A single-stranded RNA probe was used to detect Xist...
  9. Research: Long-read transcriptome sequencing of CLL and MDS patients uncovers molecular effects of SF3B1 mutations
    • Alicja Pacholewska,
    • Matthias Lienhard,
    • Mirko Brüggemann,
    • Heike Hänel,
    • Lorina Bilalli,
    • Anja Königs,
    • Felix Heß,
    • Kerstin Becker,
    • Karl Köhrer,
    • Jesko Kaiser,
    • Holger Gohlke,
    • Norbert Gattermann,
    • Michael Hallek,
    • Carmen D. Herling,
    • Julian König,
    • Christina Grimm,
    • Ralf Herwig,
    • Kathi Zarnack,
    • and Michal R. Schweiger
    Genome Res. November 2024 34: 1832-1848; Published in Advance September 13, 2024, doi:10.1101/gr.279327.124
    ..., and short (15–20 nt) AG–AG′ inserts from nondifferentially alternatively spliced 3′AS events. The chosen events without differential splicing detected with SF3B1 mutation were from PAPCL1, USP1, and ZNF124 (AG′–AG distance >50 nt) as well as GPR98B, UROD, and CELF2 (AG′–AG distance <20 nt). (C) Table...
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  10. 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
    ...and increased to higher levels after prolonged culture time, suggesting a rapid loss and gain of DNA methylation during callus induction (Wang et al. 2022). In woodland strawberry (Fragaria vesca), slight increases in CG and CHG methylation and decreases in CHH methylation were observed in callus tissue...
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