Rui Benfeitas

Standard-GEM provides a template for reproducible genome-scale metabolic model development following FAIR principles and software best practices.

The paper identifies three metabolic at-risk profiles in HIV-treated patients using multi-omics integration, highlighting dysregulated metabolism and microbiome interactions.

This study identifies retinoids and sex hormone dysregulation as ageing-related features in Alzheimer's and Parkinson's disease subclasses using transcriptomic and metabolic analyses.

The paper analyzes transcriptomic changes in heart and other metabolically active tissues after myocardial infarction in mice, identifying common and tissue-specific biological responses.

RMetD2 integrates differentially expressed genes into genome-scale metabolic models to reveal metabolic differences between conditions, outperforming existing methods in capturing experimentally observed features.