Sandrine Lagarrigue

Genetic determinism and inheritance of differential DNA methylation profiles across three successive generations in quail.

This study examines how DNA methylation profiles change across three generations in quails exposed to genistein, finding that while methylation differences accumulate, genetic factors largely explain these changes.

Transmission of an environmental modification in quails across three generations: changes in the contribution to phenotypic variability

The paper examines phenotypic variability across three generations of quails subjected to an initial environmental modification, finding increased epiline contribution to traits like body weight.

A single-nucleus atlas of the adult laying hen liver reveals metabolic specialization and improved cellular resolution through enhanced genome annotation

The paper creates a single-nucleus RNA sequencing atlas of the adult chicken liver, revealing cellular composition and showing improved resolution through enhanced genome annotation.

Empowering bioinformatics communities with Nextflow and nf-core

This paper discusses the adoption of Nextflow and nf-core frameworks to standardize bioinformatics pipelines, improving collaboration and interoperability across research communities.

The ChickenGTEx pilot analysis: a reference of regulatory variants across 28 chicken tissues

The ChickenGTEx project provides a multi-tissue reference of regulatory variants in chicken, analyzing their functional impacts and utility in genetics, genomics, and evolutionary studies.

Unravelling the genetic architecture of persistence in production, quality, and efficiency traits in laying hens at late production stages

The paper analyzes trait persistence in laying hens from 70 to 92 weeks, identifying traits with stable genetic variance and those requiring alternative selection strategies.

Molecular responses of chicken embryos to maternal heat stress through DNA methylation and gene expression

This study investigates how maternal heat stress affects DNA methylation and gene expression in chicken embryos, identifying key genes and methylation sites associated with heat tolerance.

Cross-species orthology detection of long non-coding RNAs (lncRNA) through 13 species using genomic and functional annotations.

The paper develops a workflow to detect cross-species orthology of lncRNAs across 13 vertebrate species using syntenic methods and motif analysis, revealing conserved lncRNAs and functional motifs.

Variant calling and genotyping accuracy of ddRAD-seq: comparison with 20X WGS in layers

This study compares ddRAD-seq and 20X WGS for variant calling and genotyping in laying hens, showing ddRAD-seq can retain 40% of SNPs with 98% reliability after quality control.

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 provides a comprehensive chicken gene atlas with genomics and functional data across 47 tissues, integrating multiple databases and offering tools for gene analysis and visualization.

Enriched atlas of lncRNA and protein-coding genes for the GRCg7b chicken assembly and its functional annotation across 47 tissues.

The paper creates an enriched gene atlas for the GRCg7b chicken assembly, increasing the number of annotated lncRNAs and PCGs and providing functional annotations across 47 tissues.

Transcriptome and chromatin structure annotation of liver, CD4+ and CD8+ T cells from four livestock species.

The paper annotates transcriptomes and chromatin structures in liver and T cells from four livestock species using RNA-seq, ATAC-seq, and Hi-C, revealing conserved regulatory elements and genome organization patterns.

Muscle transcriptome analysis reveals molecular pathways and biomarkers involved in extreme ultimate pH and meat defect occurrence in chicken

The paper identifies genes and pathways associated with extreme pHu in chicken breast meat and finds 20 predictive genes for meat quality defects.

Genome-wide characterization of RNA editing in chicken: lack of evidence for non-A-to-I events

The paper characterizes RNA editing in chicken, finding limited non-A-to-I events and highlighting evolutionary conservation of A-to-I editing.