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Browsing Tag

Plant Genetics and Genomics

33 posts
GGenetics
SPAmix: a scalable, accurate, and universal analysis framework for large-scale genetic association studies in admixed populations | Genome Biology
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SPAmix: a scalable, accurate, and universal analysis framework for large-scale genetic association studies in admixed populations | Genome Biology

  • October 16, 2025
Model residuals of linear regression and logistic regression Linear regression and logistic regression are regular models to fit…
GGenetics
Genetic variation and genome-enabled selection of white lupin for key seed quality traits | BMC Genomics
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Genetic variation and genome-enabled selection of white lupin for key seed quality traits | BMC Genomics

  • October 16, 2025
Foyer CH, Lam H-M, Nguyen HT, Siddique KHM, Varshney RK, Colmer TD, et al. Neglecting legumes has compromised…
GGenetics
A novel gene expression stability metric to unveil homeostasis and regulation | Genome Biology
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A novel gene expression stability metric to unveil homeostasis and regulation | Genome Biology

  • October 10, 2025
K-proportion and gene homeostasis Z-Index identify regulatory genes As cells of the same type and in the same…
TTechnology
The genetic influence of sex on gene expression for blood in pigs | BMC Genomics
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The genetic influence of sex on gene expression for blood in pigs | BMC Genomics

  • October 9, 2025
Data summary We collected 386 blood samples with matched genotype and gene expression data from the PigGTEx project…
GGenetics
Genomic predictions for growth and feed efficiency traits in a duck breeding population | BMC Genomics
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Genomic predictions for growth and feed efficiency traits in a duck breeding population | BMC Genomics

  • October 8, 2025
Animal population and phenotype data This study used a breeding population of Zhongxin white duck (a commercial breed…
BBusiness
Structural and evolutionary features of red algal UV sex chromosomes | Genome Biology
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Structural and evolutionary features of red algal UV sex chromosomes | Genome Biology

  • October 7, 2025
To define the male and female haplotypes of the sex-determining locus in Gracilaria species, we leveraged male reference…
BBusiness
Computational investigation of the sequence context of arginine/glycine-rich motifs in the human proteome | BMC Genomics
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Computational investigation of the sequence context of arginine/glycine-rich motifs in the human proteome | BMC Genomics

  • October 6, 2025
Human RG motif statistical comparisons reveal significant differences in physicochemical properties To understand important characteristics or properties of…
BBusiness
SpatPPI: a geometric deep learning model for predicting protein–protein interactions involving intrinsically disordered regions | Genome Biology
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SpatPPI: a geometric deep learning model for predicting protein–protein interactions involving intrinsically disordered regions | Genome Biology

  • October 6, 2025
Data preparation In this section, we introduce the details of the datasets used in this study, including the…
GGenetics
Incorporating additive genetic effects and linkage disequilibrium information to discover gene-environment interactions using BV-LDER-GE | Genome Biology
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Incorporating additive genetic effects and linkage disequilibrium information to discover gene-environment interactions using BV-LDER-GE | Genome Biology

  • October 3, 2025
Model overview We consider the following model to incorporate both additive and interaction effects: $${Y}_{i}={\sum }_{j=1}^{M}{G}_{ji}{\beta }_{j}+{\sum }_{j=1}^{M}{S}_{ji}{\gamma…
GGenetics
Exploring the genetic basis of heterosis in eucalypt growth based on transcriptome analysis | BMC Genomics
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Exploring the genetic basis of heterosis in eucalypt growth based on transcriptome analysis | BMC Genomics

  • October 3, 2025
Preparation of preliminary data In all samples, the proportion of clean reads was higher than 99.5% (Table S2),…
BBusiness
A closed-loop method for precise genome size estimation using HiFi reads | BMC Genomics
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A closed-loop method for precise genome size estimation using HiFi reads | BMC Genomics

  • September 29, 2025
Blommaert J. Genome size evolution: towards new model systems for old questions. Proc Biol Sci. 2020;287(1933): 20201441. PubMed …
TTechnology
Variable efficiency of nonsense-mediated mRNA decay across human tissues, tumors and individuals | Genome Biology
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Variable efficiency of nonsense-mediated mRNA decay across human tissues, tumors and individuals | Genome Biology

  • September 29, 2025
Individual-level quantification of NMD efficiency We quantified the individual-level NMD efficiency (iNMDeff) by utilizing matched RNA-seq and whole-exome…
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