Lejla Gul

The paper identifies a stromal remodelling programme in ulcerative colitis patients who failed prior anti-TNF therapy, linking it to MAPK/EGFR signalling and suggesting MEK/EGFR inhibitors as potential treatments.

OmniPath Metabo integrates metabolomics data with prior knowledge to enable mechanistic analysis of the metabolome through harmonized databases and network construction.

AutophagyNet is an updated database providing curated interactions and annotations for autophagy proteins, enabling analysis of autophagy regulation across different contexts.

This study shows that extracellular vesicles from Bacteroides thetaiotaomicron affect host immune pathways differently in various cell types and disease states, with implications for IBD therapy.

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.

The paper integrates intra- and intercellular signaling knowledge into a database for multicellular omics analysis, demonstrating its application to SARS-CoV-2 infection and ulcerative colitis.

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 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.