Sylvain Foissac

The paper studies the evolution of regulatory chromatin contacts in duplicated genes using Hi-C data, finding faster divergence in chromatin contacts compared to expression patterns.

The paper integrates tissue-specific epigenetic annotations into genomic predictions of gene expression in three pig breeds, improving eQTL mapping interpretability but facing challenges in cross-breed predictions.

HiCDOC predicts and differentially analyzes chromatin compartments from Hi-C data with replicates, identifying biologically relevant compartment changes supported by transcriptional differences.

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

The paper analyzes single-cell transcriptomic and epigenomic data from porcine blastocysts to identify gene regulatory dynamics in embryonic and extra-embryonic lineages during development.

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.

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.

The paper uses single-cell RNA sequencing and proteomics to analyze pig blastocyst development, identifying new cell subpopulations and regulatory networks.

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 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.