Pascal Croiseau
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View article: Guiding eQTL mapping and genomic prediction of gene expression in three pig breeds with tissue-specific epigenetic annotations from early development
Guiding eQTL mapping and genomic prediction of gene expression in three pig breeds with tissue-specific epigenetic annotations from early development Open
Gene expression is a dynamic phenotype influenced by tissue-specific regulatory mechanisms, which can modulate expression directly or indirectly through cis or trans factors. Identifying genetic variants in these regulatory regions can imp…
View article: Genomic evaluation for juvenile mortality including causal variants in French Holstein and Montbéliarde cattle breeds
Genomic evaluation for juvenile mortality including causal variants in French Holstein and Montbéliarde cattle breeds Open
Juvenile mortality is a major concern for the dairy cattle industry because of its wide-ranging economic, environmental, and ethical effects. Over the last few years, an increased number of genetic defects associated with juvenile mortalit…
View article: Impact of genomic selection on genetic diversity in five local European cattle breeds
Impact of genomic selection on genetic diversity in five local European cattle breeds Open
Genomic selection (GS) has revolutionised animal breeding and accelerated genetic gains in breeding programs. While GS has become common in major dairy cattle breeds, its implementation in local breeds has begun only more recently or is st…
View article: Trajectories of genetic correlations in populations under selection: from theory to a case-study
Trajectories of genetic correlations in populations under selection: from theory to a case-study Open
Background Breeding programs select for multiple commercial traits, aiming to achieve genetic progress for all. Often, selection is based on a selection index, i . e . a linear combination of traits with weights defined by, among other inf…
View article: Guiding eQTL mapping and genomic prediction of gene expression in three pig breeds with tissue-specific epigenetic annotations from early development
Guiding eQTL mapping and genomic prediction of gene expression in three pig breeds with tissue-specific epigenetic annotations from early development Open
Gene expression is a dynamic phenotype influenced by tissue-specific regulatory mechanisms, which can modulate expression directly or indirectly through cis or trans factors. Identifying genetic variants in these regulatory regions can imp…
View article: The fecal microbiota of Holstein cows is heritable and genetically correlated to dairy performances
The fecal microbiota of Holstein cows is heritable and genetically correlated to dairy performances Open
The fecal microbiota of ruminants constitutes a diversified community that has been phenotypically associated with a variety of host phenotypes, such as production and health. To gain a better understanding of the complex and interconnecte…
View article: Genomic prediction using functional annotations and QTL features in dairy and beef cattle.breeds
Genomic prediction using functional annotations and QTL features in dairy and beef cattle.breeds Open
Session 15. Role of bioinformatics applied to livestock data - Exploitingstructural variation and pangenome-based techniques for livestock
View article: Characterization of bovine vaginal microbiota using 16S rRNA sequencing: associations with host fertility, longevity, health, and production
Characterization of bovine vaginal microbiota using 16S rRNA sequencing: associations with host fertility, longevity, health, and production Open
Due to their potential impact on the host's phenotype, organ-specific microbiotas are receiving increasing attention in several animal species, including cattle. Specifically, the vaginal microbiota of ruminants is attracting growing inter…
View article: Deep Learning and GBLUP Integration: An Approach that Identifies Nonlinear Genetic Relationships Between Traits
Deep Learning and GBLUP Integration: An Approach that Identifies Nonlinear Genetic Relationships Between Traits Open
Background Genomic prediction aims to predict the breeding values of multiple complex traits, usually assumed to be normally distributed by the largely used statistical methods, thus imposing linear genetic correlations between traits. Whi…
View article: Benchmarking predictive models: evaluating parametric, ensemble, and deep learning approaches for animal phenotype prediction from genotypes.
Benchmarking predictive models: evaluating parametric, ensemble, and deep learning approaches for animal phenotype prediction from genotypes. Open
International audience
View article: Host genes shape the lower gut microbiota of Holstein cows: evidence from sequence-based GWAS
Host genes shape the lower gut microbiota of Holstein cows: evidence from sequence-based GWAS Open
International audience
View article: Characterization of bovine vaginal microbiota and its relationship with host fertility, health, and production
Characterization of bovine vaginal microbiota and its relationship with host fertility, health, and production Open
Background Because of its potential influence on the host’s phenotype, increasing attention is paid to organ-specific microbiota in several animal species, including cattle. However, ecosystems other than those related to the digestive tra…
View article: Sequence-based GWAS meta-analyses for beef production traits
Sequence-based GWAS meta-analyses for beef production traits Open
Background Combining the results of within-population genome-wide association studies (GWAS) based on whole-genome sequences into a single meta-analysis (MA) is an accurate and powerful method for identifying variants associated with compl…
View article: Methods to Estimate Erosion Factors of Genomic Breeding Values of Candidates due to Long-Distance Linkage Disequilibrium
Methods to Estimate Erosion Factors of Genomic Breeding Values of Candidates due to Long-Distance Linkage Disequilibrium Open
International audience
View article: Exploring Non-Linear Genetic Relationships Between Correlated Traits
Exploring Non-Linear Genetic Relationships Between Correlated Traits Open
International audience
View article: Incorporating biological information into genomic prediction models
Incorporating biological information into genomic prediction models Open
International audience
View article: Additional file 1 of Sequence-based GWAS meta-analyses for beef production traits
Additional file 1 of Sequence-based GWAS meta-analyses for beef production traits Open
Additional file 1: Table S1. QTL detected in within-population GWAS and fixed-effects and z-score meta-analyses.
View article: Capitalizing on complex annotations in Bayesian genomic prediction for a backcross population of growing pigs
Capitalizing on complex annotations in Bayesian genomic prediction for a backcross population of growing pigs Open
International audience
View article: Accounting for overlapping annotations in genomic prediction models of complex traits
Accounting for overlapping annotations in genomic prediction models of complex traits Open
Background: It is now widespread in livestock and plant breeding to use genotyping data to predict phenotypes with genomic prediction models. In parallel, genomic annotations related to a variety of traits are increasing in number and gran…
View article: The Use of A Priori Biological Information to Evaluate the Ability of BayesRC Model in Genomic Prediction
The Use of A Priori Biological Information to Evaluate the Ability of BayesRC Model in Genomic Prediction Open
International audience
View article: An evaluation of the predictive performance and mapping power of the BayesR model for genomic prediction
An evaluation of the predictive performance and mapping power of the BayesR model for genomic prediction Open
Technological advances and decreasing costs have led to the rise of increasingly dense genotyping data, making feasible the identification of potential causal markers. Custom genotyping chips, which combine medium-density genotypes with a …
View article: Sequence -based GWAS for milk production traits, udder health and morphology in French dairy cattle
Sequence -based GWAS for milk production traits, udder health and morphology in French dairy cattle Open
International audience
View article: An evaluation of the interpretability and predictive performance of the BayesR model for genomic prediction
An evaluation of the interpretability and predictive performance of the BayesR model for genomic prediction Open
Background: Technological advances and decreasing costs have led to the rise of increasingly dense genotyping data, making feasible the identification of potential causal or candidate markers. Custom genotyping chips, which represent a cos…
View article: An evaluation of the interpretability and predictive performance of the BayesR model for genomic prediction
An evaluation of the interpretability and predictive performance of the BayesR model for genomic prediction Open
Technological advances and decreasing costs have led to the rise of increasingly dense genotyping data, making feasible the identification of potential causal markers. Custom genotyping chips, which combine medium-density genotypes with a …