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Opportunities and limits of combining microbiome and genome data for complex trait prediction
(BMC, 2021-08-06)
Background
Analysis and prediction of complex traits using microbiome data combined with host genomic information is a topic of utmost interest. However, numerous questions remain to be answered: how ...
Disentangling the causal relationship between rabbit growth and cecal microbiota through structural equation models
(BMC, 2022-12-19)
Background
The effect of the cecal microbiome on growth of rabbits that were fed under different regimes has been studied previously. However, the term “effect” carries a causal meaning that can be ...
Identification of candidate regulatory genes for intramuscular fatty acid composition in pigs by transcriptome analysis
(BMC, 2024-02-12)
Background
Intramuscular fat (IMF) content and its fatty acid (FA) composition are typically controlled by several genes, each with a small effect. In the current study, to pinpoint candidate genes and ...
On the holobiont ‘predictome’ of immunocompetence in pigs
(BMC, 2023-05-01)
Background
Gut microbial composition plays an important role in numerous traits, including immune response. Integration of host genomic information with microbiome data is a natural step in the prediction ...
Leveraging host-genetics and gut microbiota to determine immunocompetence in pigs
(BMC, 2021-10-24)
Background: The gut microbiota infuences host performance playing a relevant role in homeostasis and function of
the immune system. The aim of the present work was to identify microbial signatures ...
kernInt: A Kernel Framework for Integrating Supervised and Unsupervised Analyses in Spatio-Temporal Metagenomic Datasets
(Frontiers Media, 2021-01-28)
The advent of next-generation sequencing technologies allowed relative quantification of microbiome communities and their spatial and temporal variation. In recent years, supervised learning (i.e., ...
Genetic architecture of innate and adaptive immune cells in pigs
(Frontiers Media, 2023-02-06)
Pig industry is facing new challenges that make necessary to reorient breeding programs to produce more robust and resilient pig populations. The aim of the present work was to study the genetic determinism ...
Identification of transcriptional regulatory variants in pig duodenum, liver, and muscle tissues
(Oxford University Press, 2023-06-24)
Background
In humans and livestock species, genome-wide association studies (GWAS) have been applied to study the association between variants distributed across the genome and a phenotype of interest. ...
Global analysis of the association between pig muscle fatty acid composition and gene expression using RNA-Seq
(Nature Research, 2023-01-11)
Fatty acids (FAs) play an essential role as mediators of cell signaling and signal transduction, affecting metabolic homeostasis and determining meat quality in pigs. However, FAs are transformed by the ...