Searching journal content for articles similar to Taillon-Miller et al. 9 (5): 499.

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  1. 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
    ...transfer) affects stability. Age-matched cohorts of 12 ART-derived and 16 naturally conceived C57BL/6J inbred mice were reared in a controlled setting and whole--sequenced to ∼50× coverage. Using a rigorous pipeline for de novo single-nucleotide variant (dnSNV) discovery, we observe a ∼30% (95% CI: 4...
  2. Method: Multisample motif discovery and visualization for tandem repeats
    • Yaran Zhang,
    • Marc Hulsman,
    • Alex Salazar,
    • Niccolò Tesi,
    • Lydian Knoop,
    • Sven van der Lee,
    • Sanduni Wijesekera,
    • Jana Krizova,
    • Erik-Jan Kamsteeg,
    • and Henne Holstege
    Genome Res. April 2025 35: 850-862; Published in Advance November 13, 2024, doi:10.1101/gr.279278.124
    ...allele sequence individually. Furthermore, these methods are not sensible to small mutations (e.g., single-nucleotide polymorphisms [SNPs]). These small variations can, however, be biologically important, for instance, in clinical settings in which some pure repeats are considered more pathogenic than...
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  3. Research: Single-cell discovery of m6A RNA modifications in the hippocampus
    • Shuangshuang Feng,
    • Maitena Tellaetxe-Abete,
    • Yujie Zhang,
    • Yan Peng,
    • Han Zhou,
    • Mingjie Dong,
    • Erika Larrea,
    • Liang Xue,
    • Li Zhang,
    • and Magdalena J. Koziol
    Genome Res. June 2024 34: 822-836; Published in Advance July 15, 2024, doi:10.1101/gr.278424.123
    ...-to-T mutation/total reads per site) >5% were kept for downstream analyses; (4) C-to-T mutations sites that were found in the single-nucleotide polymorphism (SNP) databases Mouse Genome Project (mgp_REL2021_snps) and Genome Reference Consortium Mouse Build 39 (GCA_000001635.9) were discarded; and (5) only C...
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  4. Method: Secure discovery of genetic relatives across large-scale and distributed genomic data sets
    • Matthew M. Hong,
    • David Froelicher,
    • Ricky Magner,
    • Victoria Popic,
    • Bonnie Berger,
    • and Hyunghoon Cho
    Genome Res. September 2024 34: 1312-1323; Published in Advance August 7, 2024, doi:10.1101/gr.279057.124
    ...to the same bucket index. For this purpose, we devised a novel encoding scheme that splits and subsamples genotypes into k-SNPs (similar to k-mers, but noncontiguous; single-nucleotide polymorphism [SNP]), such that the similarity between k-SNPs reflects extended runs of identical genotypes, typically...
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  5. Mini-Review: Large-scale genomic analysis of the domestic dog informs biological discovery
    • Reuben M. Buckley and
    • Elaine A. Ostrander
    Genome Res. June 2024 34: 811-821; Published in Advance July 2, 2024, doi:10.1101/gr.278569.123
    ...sampling of these populations, along with adequate phenotyping, will likely lead to new genotype–phenotype discoveries (Surbakti et al. 2020).Interpretation of variant effectsIn trait mapping, the single nucleotide polymorphisms (SNPs) with the strongest phenotype association are often within the noncoding...
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  6. Method: An efficient genotyper and star-allele caller for pharmacogenomics
    • Ananth Hari,
    • Qinghui Zhou,
    • Nina Gonzaludo,
    • John Harting,
    • Stuart A. Scott,
    • Xiang Qin,
    • Steve Scherer,
    • S. Cenk Sahinalp,
    • and Ibrahim Numanagić
    Genome Res. January 2023 33: 61-70; Published in Advance January 19, 2023, doi:10.1101/gr.277075.122
    .... 2013). These issues need to be carefully and comprehensively accounted for before the genotyping process in order to obtain accurate results. Lastly, alleles of many pharmacogenes are not defined through a single-nucleotide variant (SNV) but through a complete gene haplotype. Thus, the exact functional...
  7. Method: Efficient and accurate KIR and HLA genotyping with massively parallel sequencing data
    • Li Song,
    • Gali Bai,
    • X. Shirley Liu,
    • Bo Li,
    • and Heng Li
    Genome Res. May 11, 2023 gr.277585.122; Published in Advance May 11, 2023, doi:10.1101/gr.277585.122
    ...to calculate the quality score for each called allele to further filter the false alleles. In addition to genotyping each sample, T1K provides post-processing methods to extend the genotyping results. These include novel single nucleotide polymorphism (SNP) detection on representative alleles and the report...
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  8. Method: Optimized sample selection for cost-efficient long-read population sequencing
    • T. Rhyker Ranallo-Benavidez,
    • Zachary Lemmon,
    • Sebastian Soyk,
    • Sergey Aganezov,
    • William J. Salerno,
    • Rajiv C. McCoy,
    • Zachary B. Lippman,
    • Michael C. Schatz,
    • and Fritz J. Sedlazeck
    Genome Res. May 2021 31: 910-918; Published in Advance April 2, 2021, doi:10.1101/gr.264879.120
    ...diversity are analogous or distinct from those influencing single-nucleotide variants (SNVs). Genome-wide inferences of human evolutionary relationships (The 1000 Genomes Project Consortium 2015) and key population genetic parameters such as θ (Watterson 1975), π (Nei and Li 1979), and Tajima's D (Tajima...
  9. METHODS: Single Nucleotide Polymorphism Mapping Using Genome-Wide Unique Sequences
    • Leslie Y.Y. Chen,
    • Szu-Hsien Lu,
    • Edward S.C. Shih,
    • and Ming-Jing Hwang
    Genome Res. July 1, 2002 12: 1106-1111; Published in Advance June 18, 2002, doi:10.1101/gr.224502
    ...Single Nucleotide Polymorphism Mapping Using Genome-Wide Unique Sequences Leslie Y.Y. Chen , Szu-Hsien Lu , Edward S.C. Shih , and Ming-Jing Hwang 1 Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan Abstract...
  10. METHODS: Polymorphism Ratio Sequencing: A New Approach for Single Nucleotide Polymorphism Discovery and Genotyping
    • Robert G. Blazej,
    • Brian M. Paegel,
    • and Richard A. Mathies
    Genome Res. February 1, 2003 13: 287-293; doi:10.1101/gr.396203
    ...is an internally controlled method for polymorphism discovery, multiplexed allele frequency determination, and genotyping. The compact (16,569 bp) and well-characterized human mitochondrial was selected as a test system for PRS development. Two mitochondrial s from unrelated Centre d'Etude Polymorphisme Humane...
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