Isabelle Hautefort

This study develops a method to enrich microeukaryotes in human stool samples for shotgun sequencing, improving their representation and taxonomic diversity in metagenomic libraries.

The paper maps cytokine interaction networks in ulcerative colitis to uncover novel pathogenic mechanisms and therapeutic targets.

SalmoNet2 provides an updated multi-layered network resource for 20 Salmonella strains, enhancing strain comparisons through protein-protein, transcriptional regulatory, and metabolic interactions.

CytokineLink maps cytokine interactions to analyze immune responses in inflammatory and infectious diseases, revealing rewiring in ulcerative colitis and cytokine storm patterns in COVID-19.

ViralLink is a systems biology workflow that reconstructs and analyzes intracellular signaling networks affected by viruses, using transcriptomics data to identify key pathways and proteins in the cellular response to infection.

The paper uses transcriptomics and network analysis to study regulatory networks in Paneth and goblet cell enriched gut organoids, identifying key regulators and their links to inflammatory bowel disease.

The paper integrates proteomic and transcriptomic data from intestinal organoids to identify autophagy-dependent processes in Paneth cells, showing that autophagy impairment affects protein abundance and key cellular functions.