Searching journal content for articles similar to Ong et al. 14 (11): 2295.

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  1. 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
    ...analyses in cancer genomics.The ability of ScisTree2 to analyze a large number of cells may be useful in large-scale cancer genomics analyses. One such analysis is identifying rare cancer subclones, which can drive disease recurrence and therapy resistance. For example, relapse of acute myeloid leukemia...
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  2. Method: Autoencoders for genomic variation analysis
    • Margarita Geleta,
    • Daniel Mas Montserrat,
    • Xavier Giro-i-Nieto,
    • and Alexander G. Ioannidis
    Genome Res. February 2026 36: 348-360; Published in Advance January 20, 2026, doi:10.1101/gr.280086.124
    ...are needed in order to properly capture the genetic composition of populations. Here, we explore deep learning techniques, namely, variational autoencoders (VAEs), to process genomic data from a population perspective. We show the power of VAEs for a variety of tasks relating to the interpretation...
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  3. 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...
  4. 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
    ...(Halo et al. 2021). Eventually, long-read sequencing will become common practice in animal genomics, permanently altering sequencing strategies and analysis techniques while capturing the full spectrum of variation within a single .Large-scale sequencing effortsThe International Dog10K consortium...
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  5. 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
    ...-Relate on the UK Biobank and All of Us data sets. On a data set of 200,000 individuals split between two parties, SF-Relate detects 97% of third-degree or closer relatives within 15 h of runtime. Our work enables secure identification of relatives across large-scale genomic data sets.Collaborative studies that aim...
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  6. 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
    ...prediction. We build on these data, implementing further filtering steps to remove families with homology with other species, to identify putative SSOGs in the gut microbiome and to study them systematically. By looking for patterns in large-scale comparisons, we attempt to disentangle the evolutionary...
  7. 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. April 2026 36: 814-826; Published in Advance March 5, 2026, doi:10.1101/gr.281006.125
    ...models, outperforming both GBLUP and BayesR. These findings demonstrate a favorable trade-off between reduced accuracy (averaging <15%) and substantial computational savings, highlighting the practical value of dimensionality reduction in large-scale genomic analyses.View larger version: In this window...
  8. 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
    .... 2020. Benchmarking principal component analysis for large-scale single-cell RNA-sequencing. Genome Biol 21: 9. doi:10.1186/s13059-019-1900-3 ↵van der Maaten L, Hinton G. 2008. Visualizing data using t-SNE. J Mach Learn Res 9: 2579–2605. ↵van Dijk D, Sharma R, Nainys J, Yim K, Kathail P, Carr AJ...
  9. Method: High-resolution genotype-free mapping of genetic variation with CRI-SPA-Map
    • Sheila Lutz,
    • Megan Lawler,
    • Samuel Amidon,
    • and Frank W Albert
    Genome Res. March 23, 2026 gr.281514.125; Published in Advance March 23, 2026, doi:10.1101/gr.281514.125
    ...strain at defined genomic regions. We applied CRI-SPA-Map to dissect 405 genetic variation on a chromosome arm between a W303-SPA strain and strains from the YKO 406 deletion collection and uncovered a complex pattern of environmentally dependent epistasis at 407 two causal variants. 408 CRI-SPA-Map has...
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  10. 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
    ...Large-scale detection and characterization of interchromosomal rearrangements in normozoospermic bulls using massive genotype and phenotype data sets Jeanlin Jourdain,1,2 Harmonie Barasc,3 Thomas Faraut,3 Anne Calgaro,3 Nathalie Bonnet,3 Camille Marcuzzo,4 Amandine Suin,4 Anne Barbat,2 Chris Hozé,1...
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