Philippe Bardou

Pan1c : a pipeline to easily build chromosome-level pangenome graphs

Pan1C is a pipeline that builds chromosome-level pangenome graphs, improving alignment and variant calling by integrating multiple strategies and benchmarked across different species.

Inferring domestic goat demographic history through ancient genome imputation

This paper uses genotype imputation to analyze low coverage ancient goat genomes, revealing demographic patterns and genetic consequences of domestication.

A tailored variant filtering procedure for multi-breed and multi-species unbalanced animal SNP collections

The paper develops a tailored variant filtering method for multi-breed and multi-species SNP datasets to reduce bias from standard approaches.

The variability of goat microRNA genes is strongly shaped by functional constraints

The study identifies miRNA polymorphisms in goats, finding low variation in seed regions due to purifying selection and higher variation in regulatory regions of isolated populations.

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.

A single base pair duplication in SLC33A1 gene causes fetal losses and neonatal lethality in Manech Tete Rousse dairy sheep

The paper identifies a single base pair duplication in SLC33A1 causing fetal losses and neonatal lethality in MTR sheep through whole genome sequencing and breeding studies.

Homozygous haplotype deficiency in Manech Tete Rousse dairy sheep revealed a nonsense variant in MMUT gene affecting newborn lamb viability

The paper identifies recessive deleterious variants in Manech Tete Rousse dairy sheep using genome scans, finds a nonsense mutation in MMUT causing lamb mortality, and links other haplotypes to morphological traits.

Analysis Of Polycerate Mutants Reveals The Evolutionary Co-Option Of HOXD1 To Determine The Number And Topology Of Horns In Bovidae

The paper identifies POLYCERATE alleles in sheep and goats linked to defective HOXD1 function, showing haploinsufficiency causes horn bud splitting and highlights HOXD1's role in headgear patterning in Bovidae.

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.

RumimiR: a detailed microRNA database focused on ruminant species

RumimiR is a database of microRNAs for ruminant species, providing detailed information on sequences, tissue origins, and experimental conditions.