Thomas Faraut

The paper integrates long-read, short-read, and SNP data using a pangenome and imputation framework to identify structural variants associated with stature and milk traits in dairy cattle.

The paper identifies 440 parent-of-origin expressed genes in pigs, revealing weak conservation of genomic imprinting across species and tissues.

The paper detects structural variants in French cattle using long and short-read data, identifying 25,191 deletions and 30,118 insertions across 14 breeds.

This study evaluates TE polymorphic detection tools using simulated data based on real genomes, finding that few tools perform well and all are sensitive to genomic and TE characteristics.

The paper introduces a method to measure differences between pangenome graphs using pairwise graph edit distance and applies it to yeast and human datasets.

This study identifies two active endogenous retrovirus families in goats, revealing distinct evolutionary dynamics among ruminants.

The paper evaluates two functional link methods for identifying enhancer/gene relationships using benchmark data and finds neither performs best, highlighting the need for reliable genome-wide reference data.

The paper describes a method to order and orient sequence scaffolds into chromosome-scale assemblies using RH mapping and sequencing in ducks.