John P. Thomas

This paper identifies a microbiota-responsive polyfunctional cytotoxic CD4⁺ T-cell state linked to mucosal inflammation and treatment resistance in ulcerative colitis.

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.

The paper identifies cytokine interaction networks, not individual cytokines, as the driver of anti-TNF non-response in Crohn's disease using single-cell RNA sequencing data.

This paper identifies non-coding SNPs affecting epithelial regulatory networks in UC and links them to clinical outcomes using iSNP analysis.

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

The paper models the impact of non-coding SNPs on gene regulatory networks in IBD to stratify patients based on gene dysregulation and therapeutic response.

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.