Searching journal content for articles similar to Ghosh et al. 7 (2): 165.

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  1. Method: High-fidelity, large-scale targeted profiling of microsatellites
    • Caitlin A. Loh,
    • Danielle A. Shields,
    • Adam Schwing,
    • and Gilad D. Evrony
    Genome Res. July 2024 34: 1008-1026; Published in Advance July 16, 2024, doi:10.1101/gr.278785.123
    ...tools enables high-fidelity, large-scale profiling of microsatellites, which may find utility in diverse applications such as lineage tracing, population genetics, ecology, and forensics.Microsatellites, also known as short tandem repeats, are genomic sequences composed of tandem repeats of short (1...
  2. Method: ScisTree2 enables large-scale inference of cell lineage trees and genotype calling using efficient local search
    • Haotian Zhang,
    • Yiming Zhang,
    • Teng Gao,
    • and Yufeng Wu
    Genome Res. December 2025 35: 2781-2791; Published in Advance September 3, 2025, doi:10.1101/gr.280542.125
    ...the genetic variants from the single-cell sequence reads. Most genotype callers output a discrete probability distribution over possible genotypes for each cell and variant site. For simplicity, ScisTree2 only considers two genotype states: wild type (allele 0) and mutant (allele 1). ScisTree2 takes...
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  3. Research: Large-scale investigation of species-specific orphan genes in the human gut microbiome elucidates their evolutionary origins
    • Nikolaos Vakirlis and
    • Anne Kupczok
    Genome Res. June 2024 34: 888-903; Published in Advance July 8, 2024, doi:10.1101/gr.278977.124
    ...de novo origination (Karlowski et al. 2023). Furthermore, a recent study of E. coli showed that “remodeling events,” that is, fusions of alternative reading-frames of segments of existing genes, are a potent source of entirely new protein sequences (Watson et al. 2022).Finally, SSOGs can also result...
  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
    ...large-scale data setsWe summarize our results on the AoU and UKB data sets in Tables 1 and 2. Across all three data sets (AoU-20K, UKB-100K, and UKB-200K), SF-Relate obtains near-perfect recall and precision (both exceeding 97% in all cases) for detecting the presence of third-degree or closer...
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  5. Method: Automated interpretable artificial intelligence genomic prediction with AIGP
    • Lei Wei,
    • Ziqin Jiang,
    • Baoliang Fan,
    • Yidan Yan,
    • Zhenqiang Xu,
    • Xiaoxiang Hu,
    • and Yuzhe Wang
    Genome Res. March 5, 2026 gr.281006.125; Published in Advance March 5, 2026, doi:10.1101/gr.281006.125
    ...as a prominent tool for explaining multiple 86 biological features. However, it has not been used to elucidate allele substitution effects, 87 revealing various distribution patterns of non-additive genetic variances. 88 This study used real genotype-phenotypic data from different species alongside a series 89...
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  6. 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
    ...% of variance in dog breed body size is explained by association at seven genetic markers. The figure shows several combinations of small and large body-size alleles contributing to the heights of different breeds. Raw data provided by Rimbault et al. (2013). (B) Recurrent mutations in FBXW7 are a feature...
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  7. Method: Large-scale detection and characterization of inter-chromosomal rearrangements in normozoospermic bulls using massive genotype and phenotype data sets
    • Jeanlin Jourdain,
    • Harmonie Barasc,
    • Thomas Faraut,
    • Anne Calgaro,
    • Nathalie Bonnet,
    • Camille Marcuzzo,
    • Amandine Suin,
    • Anne Barbat,
    • Chris Hozé,
    • Florian Besnard,
    • Sébastien Taussat,
    • Cécile Grohs,
    • Claire Kuchly,
    • Carole Iampietro,
    • Cécile Donnadieu,
    • Alain Pinton,
    • Didier Boichard,
    • and Aurélien Capitan
    Genome Res. July 6, 2023 ; Published in Advance July 6, 2023, doi:10.1101/gr.277787.123
    ...directly on the sires, when they were still alive (applicable for one bull), or on a selection of their progeny representing each of the genotype combinations observed around putative chromosomal fusion points (sons and daughters for 10 bulls, granddaughters for two bulls). Analysis of blood lymphocytes...
  8. Method: Read-level genotyping of short tandem repeats using long reads and single-nucleotide variation with STRkit
    • David R. Lougheed,
    • Tomi Pastinen,
    • and Guillaume Bourque
    Genome Res. March 2026 36: 578-588; Published in Advance January 15, 2026, doi:10.1101/gr.280766.125
    ...within reads (Narzisi and Schatz 2015; Mousavi et al. 2019), affecting mappability to a reference . Some SRS STR genotyping tools can estimate larger-than-read-length allele sizes (Dolzhenko et al. 2017; Dolzhenko et al. 2019; Mousavi et al. 2019) but cannot capture variation in motif structure nor...
  9. Research: Accurate genotyping of three major respiratory bacterial pathogens with ONT R10.4.1 long-read sequencing
    • Nora Zidane,
    • Carla Rodrigues,
    • Valérie Bouchez,
    • Martin Rethoret-Pasty,
    • Virginie Passet,
    • Sylvain Brisse,
    • and Chiara Crestani
    Genome Res. August 2025 35: 1758-1766; Published in Advance June 2, 2025, doi:10.1101/gr.279829.124
    ..., as these may strongly impact gene-by-gene approaches like cgMLST. In fact, spurious SNPs introduced by sequencing errors can create artificial alleles, increasing allelic distances between isolates. As a result, most public bacterial genotyping databases, such as BIGSdb-Pasteur, do not currently accept ONT...
  10. Method: Fast and accurate out-of-core PCA framework for large scale biobank data
    • Zilong Li,
    • Jonas Meisner,
    • and Anders Albrechtsen
    Genome Res. September 2023 33: 1599-1608; Published in Advance August 24, 2023, doi:10.1101/gr.277525.122
    ..., PCAoneArnoldi) alongside various other software packages widely used for large-scale PCA in genetics. These packages include FlashPCA2, PLINK2 (a faster reimplementation of FastPCA, Chang et al. 2015), TeraPCA and ProPCA. To assess the overall accuracy of all estimated PCs, we computed the mean explained...
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