Domenico Cozzetto

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 shows NOX4 induces Warburg-type metabolic reprogramming in the healthy adult heart, balancing energy and anabolic demands through transcriptional and epigenetic mechanisms.

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.

The paper identifies pQTLs for 91 plasma proteins, finds novel associations, and uses MR to uncover causal roles in immune-mediated diseases, suggesting new therapeutic targets.

The paper evaluates 43 methods for predicting intrinsically disordered regions and binding regions in proteins, finding that deep learning methods outperform older physicochemical approaches but binding prediction remains challenging.

The paper reports results from the CAFA3 challenge, showing improved computational protein function prediction and new annotations for over 1000 genes through experimental screens in C. albicans, P. aureginosa, and Drosophila.

STRING2GO uses deep maxout neural networks to improve protein function prediction from interaction networks, outperforming existing methods in accuracy.

This paper introduces a multi-task deep neural network for protein function prediction, showing improved accuracy over baseline methods and single-task predictors.