Gholamreza Bidkhori

The paper introduces MIGRENE, a computational framework for constructing personalized microbiome metabolism models using metagenomic data.

This study uses metabolic modeling of gut microbiome data from type 2 diabetes patients to show how metformin treatment alters microbial growth rates and metabolic pathways.

The paper introduces the reactobiome, a stratification method for the human gut microbiome, identifying five reactotypes with distinct metabolic features and validating them in a longitudinal cohort.

This study compares mucosal microbiota composition and function along the intestine using shotgun metagenomics, highlighting functional enrichments and antimicrobial resistance patterns.

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