Fabien Degalez
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View article: Long-read transcriptomics of a diverse human cohort reveals widespread ancestry bias in gene annotation
Long-read transcriptomics of a diverse human cohort reveals widespread ancestry bias in gene annotation Open
Accurate gene annotations are fundamental for interpreting genetic variation, cellular function, and disease mechanisms. However, current human gene annotations are largely derived from transcriptomic data of individuals with European ance…
View article: Variant calling and genotyping accuracy of ddRAD-seq: Comparison with 20X WGS in layers
Variant calling and genotyping accuracy of ddRAD-seq: Comparison with 20X WGS in layers Open
Whole Genome Sequencing (WGS) remains a costly or unsuitable method for routine genotyping of laying hens. Until now, breeding companies have been using or developing SNP chips. Nevertheless, alternatives methods based on sequencing have b…
View article: GEGA (Gallus Enriched Gene Annotation): an online tool providing genomics and functional information across 47 tissues for a chicken gene-enriched atlas gathering Ensembl and Refseq genome annotations
GEGA (Gallus Enriched Gene Annotation): an online tool providing genomics and functional information across 47 tissues for a chicken gene-enriched atlas gathering Ensembl and Refseq genome annotations Open
GEGA is a user-friendly tool designed to navigate through various genomic and functional information related to an enriched gene atlas in chicken that integrates the gene catalogues from the two reference databases, NCBI-RefSeq and EMBL-En…
View article: Impact of genome build on RNA-seq interpretation and diagnostics
Impact of genome build on RNA-seq interpretation and diagnostics Open
View article: Enriched atlas of lncRNA and protein-coding genes for the GRCg7b chicken assembly and its functional annotation across 47 tissues
Enriched atlas of lncRNA and protein-coding genes for the GRCg7b chicken assembly and its functional annotation across 47 tissues Open
View article: GEGA (Gallus Enriched Gene Annotation): an online tool providing genomics and functional information across 47 tissues for a chicken gene-enriched atlas gathering Ensembl & Refseq genome annotations
GEGA (Gallus Enriched Gene Annotation): an online tool providing genomics and functional information across 47 tissues for a chicken gene-enriched atlas gathering Ensembl & Refseq genome annotations Open
GEGA is a user-friendly tool to navigate through different genomics and functional information related to an enriched gene atlas in chicken that unifies the gene catalogues from the two reference databases, NCBI-RefSeq & EMBL-Ensembl/GENCO…
View article: Variant calling and genotyping accuracy of ddRAD-seq: comparison with 20X WGS in layers
Variant calling and genotyping accuracy of ddRAD-seq: comparison with 20X WGS in layers Open
Whole Genome Sequencing (WGS) remains a costly or unsuitable method for routine genotyping of laying hens methods, thus alternatives have been developed. Among these, reduced representation sequencing approaches can offer both sequencing q…
View article: Impact of genome build on RNA-seq interpretation and diagnostics
Impact of genome build on RNA-seq interpretation and diagnostics Open
Summary Transcriptomics is a powerful tool for unraveling the molecular effects of genetic variants and disease diagnosis. Prior studies have demonstrated that choice of genome build impacts variant interpretation and diagnostic yield for …
View article: Régulation des transcrits, phénotypes intermédiaires entre génotype et phénotype : Focus sur les gènes à ARN longs non-codants (ARNlnc) chez la poule et les phénotypes liés aux lipides
Régulation des transcrits, phénotypes intermédiaires entre génotype et phénotype : Focus sur les gènes à ARN longs non-codants (ARNlnc) chez la poule et les phénotypes liés aux lipides Open
La thèse s’articulait autour de l'annotation du génome de la poule et de l'identification de variants génétiques pour aboutir à des GWAS pour des phénotypes macroscopiques ou expressionnels.Le premier objectif a été d'enrichir l'annotation…
View article: The ChickenGTEx atlas: the genetic regulation of multi-tissue and single-cell transcriptome signatures in chickens
The ChickenGTEx atlas: the genetic regulation of multi-tissue and single-cell transcriptome signatures in chickens Open
Chicken is a valuable model for understanding fundamental biology and vertebrate evolution, as well as a major source of nutrient-dense and lean-protein-enriched food globally. Although it is the first non-mammalian amniote genome to be se…
View article: Enriched atlas of lncRNA and protein-coding genes for the GRCg7b chicken assembly and its functional annotation across 47 tissues
Enriched atlas of lncRNA and protein-coding genes for the GRCg7b chicken assembly and its functional annotation across 47 tissues Open
Gene atlases for livestock are steadily improving thanks to new genome assemblies and new expression data improving the gene annotation. However, gene content varies across databases due to differences in RNA sequencing data and bioinforma…
View article: The ChickenGTEx pilot analysis: a reference of regulatory variants across 28 chicken tissues
The ChickenGTEx pilot analysis: a reference of regulatory variants across 28 chicken tissues Open
Chicken is a valuable model for understanding fundamental biology, vertebrate evolution and diseases, as well as a major source of nutrient-dense and lean-protein-enriched food globally. Although it is the first non-mammalian amniote genom…
View article: Supplementary Material for: Fourth Report on Chicken Genes and Chromosomes 2022
Supplementary Material for: Fourth Report on Chicken Genes and Chromosomes 2022 Open
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View article: Fourth Report on Chicken Genes and Chromosomes 2022
Fourth Report on Chicken Genes and Chromosomes 2022 Open
International audience
View article: LncRNAs in domesticated animals: from dog to livestock species
LncRNAs in domesticated animals: from dog to livestock species Open
View article: Watch Out for a Second SNP: Focus on Multi-Nucleotide Variants in Coding Regions and Rescued Stop-Gained
Watch Out for a Second SNP: Focus on Multi-Nucleotide Variants in Coding Regions and Rescued Stop-Gained Open
Most single-nucleotide polymorphisms (SNPs) are located in non-coding regions, but the fraction usually studied is harbored in protein-coding regions because potential impacts on proteins are relatively easy to predict by popular tools suc…
View article: RNA-Seq Data for Reliable SNP Detection and Genotype Calling: Interest for Coding Variant Characterization and Cis-Regulation Analysis by Allele-Specific Expression in Livestock Species
RNA-Seq Data for Reliable SNP Detection and Genotype Calling: Interest for Coding Variant Characterization and Cis-Regulation Analysis by Allele-Specific Expression in Livestock Species Open
In addition to their common usages to study gene expression, RNA-seq data accumulated over the last 10 years are a yet-unexploited resource of SNPs in numerous individuals from different populations. SNP detection by RNA-seq is particularl…