Searching journal content for articles similar to Carlson et al. 15 (11): 1553.

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  1. 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
    ...and consequently, yielding better visualizations.View larger version: In this window In a new window Figure 5. Metrics for assessing LD structure and inter-SNP correlation. (A) Average correlation versus genomic distance for real (blue) and simulated (orange) genotypes. We select multiple reference SNPs and plot...
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  2. 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
    ...several key advantages. First, using CRI-SPA-Map to target an ORF that 409 had been deleted with a selectable marker cassette guarantees that this ORF is replaced with 410 donor DNA. This property enables mapping without genotyping, as the known position of the 411 deleted ORF specifies the genomic...
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  3. Method: Automated interpretable artificial intelligence genomic prediction with AlGP
    • Lei Wei,
    • Ziqin Jiang,
    • Baoliang Fan,
    • Yidan Yan,
    • Zhenqiang Xu,
    • Xiaoxiang Hu,
    • and Yuzhe Wang
    Genome Res. March 5, 2026 ; Published in Advance March 5, 2026, doi:10.1101/gr.281006.125
    ..., China; 3College of Animal Science and Technology, Hebei Agricultural University, Baoding 071001, China; 4National Research Facility for Phenotypic and Genotypic Analysis of Model Animals (Beijing), China Agricultural University, Beijing 100193, China Predicting phenotypes from genomic mutations remains...
  4. Research: MHC in newts illuminates the evolutionary dynamics of complex regions in giant genomes
    • Wiesław Babik,
    • Katarzyna Dudek,
    • Gemma Palomar,
    • Marzena Marszałek,
    • Grzegorz Dubin,
    • Maximina H. Yun,
    • and Magdalena Migalska
    Genome Res. February 2026 36: 303-317; Published in Advance January 12, 2026, doi:10.1101/gr.281127.125
    ...understood. Here, we use comparative genomics, expression across multiple ontogenetic stages and tissues, as well as polymorphism data to investigate MHC evolution in newts. Contrary to earlier suggestions of a massively expanded MHC in salamanders, we find that the core MHC region remains relatively compact...
  5. Research: Genotype imputation from low-coverage data for medical and population genetic analyses
    • Simone Andrea Biagini,
    • Sara Becelaere,
    • Mio Aerden,
    • Tatjana Jatsenko,
    • Laurens Hannes,
    • Philip Van Damme,
    • Jeroen Breckpot,
    • Koenraad Devriendt,
    • Bernard Thienpont,
    • Joris Robert Vermeesch,
    • Isabelle Cleynen,
    • and Toomas Kivisild
    Genome Res. September 2025 35: 1929-1941; Published in Advance July 22, 2025, doi:10.1101/gr.280175.124
    ...of Leuven, Leuven 3000, Belgium; 5Laboratory of Neurobiology, Neuroscience Department, KU Leuven, Leuven 3000, Belgium; 6Neurology Department, University Hospitals Leuven, Leuven 3000, Belgium; 7Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia Corresponding author: toomas.kivisild@kuleuven.beAbstractGenotype...
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  6. Method: Proxy panels enable privacy-aware outsourcing of genotype imputation
    • Degui Zhi,
    • Xiaoqian Jiang,
    • and Arif Harmanci
    Genome Res. February 2025 35: 326-339; Published in Advance January 10, 2025, doi:10.1101/gr.278934.124
    ...in The 1000 Genomes Project (Supplemental Methods).We found that the allele and haplotype frequencies exhibit very little resemblance to the original and local haplotype frequencies (Supplemental Fig. S5A–C). Next, we calculated the genotype correlations (Pearson R2 between alleles of variants) to quantify...
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  7. Research: Genetic variation in recalcitrant repetitive regions of the Drosophila melanogaster genome
    • Harsh G. Shukla,
    • Mahul Chakraborty,
    • and J.J. Emerson
    Genome Res. September 2025 35: 2023-2040; Published in Advance July 16, 2025, doi:10.1101/gr.280728.125
    ...@tamu.edu, jje@uci.eduAbstractMany essential functions of organisms are encoded in highly repetitive genomic regions, including histones involved in DNA packaging, centromeres that are core components of chromosome segregation, ribosomal RNA comprising the protein translation machinery, telomeres that ensure...
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  8. Research: Pangenome analysis reveals families of ubiquitin-ligase adaptors as key genomic divergence drivers that lead to hybrid incompatibility
    • Dongying Xie,
    • Pohao Ye,
    • Yiming Ma,
    • and Zhongying Zhao
    Genome Res. March 2026 36: 506-521; Published in Advance February 17, 2026, doi:10.1101/gr.280885.125
    ...and the translocation of one of its members, Cni-neib-1, to the center of Chr IV (Xie et al. 2024), we initially anticipated that the genomic region encompassing Cni-neib-1 would also exhibit rapid evolution. Unexpectedly, the ∼40 kb region surrounding Cni-neib-1 is invariant (>99% sequence identity) across both the c...
  9. Method: A spectral component approach leveraging identity-by-descent graphs to address recent population structure in genomic analysis
    • Ruhollah Shemirani,
    • Gillian M. Belbin,
    • Sinead Cullina,
    • Christa Caggiano,
    • Christopher R. Gignoux,
    • Noah Zaitlen,
    • and Eimear E. Kenny
    Genome Res. March 2026 36: 534-546; Published in Advance December 23, 2025, doi:10.1101/gr.280659.125
    ...using imputed genotype data, using BOLT-LMM. Looking exclusively at the imputed rare variants (MAF < 0.01), we observed lower genomic inflation factor values for both models in all three phenotypes along with similar patterns as the nonimputed GWAS, with SPCs having a lower inflation factor (1...
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  10. Research: Adaptation of centromeres to breakage through local genomic and epigenomic remodeling in wheat
    • Jingwei Zhou,
    • Yuhong Huang,
    • Huan Ma,
    • Yiqian Chen,
    • Chuanye Chen,
    • Fangpu Han,
    • and Handong Su
    Genome Res. November 2025 35: 2461-2471; Published in Advance September 30, 2025, doi:10.1101/gr.280913.125
    ...structures (Birchler and Han 2018). The details become murky after that, with few resolved instances of centromere breakage and subsequent repair events to maintain genomic structure and function.Allohexaploid wheat exhibits remarkable tolerance to chromosome restructuring (Levy and Feldman 2022). Recent...
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