Boyang Ji

AlphaGEM Enables Precise Genome-Scale Metabolic Modelling by Integrating Protein Structure Alignment with deep-learning-based Dark Metabolism Mining

AlphaGEM constructs genome-scale metabolic models using structural alignment and deep learning, improving accuracy over existing methods for diverse species.

Euktect: Enhanced Eukaryotic Sequence Detection and Classification in Metagenomes via the DNA Language Model

Euktect improves eukaryotic sequence detection and classification in metagenomes using a deep-learning model, enhancing the identification of fungal species and linking eukaryotic sequences to clinical phenotypes.

Systems analysis of metabolic responses to a mixed meal test in an obese cohort reveals links between tissue metabolism and the gut microbiota

The paper analyzes metabolic responses to a mixed meal test in an obese cohort, linking tissue metabolism with gut microbiota changes and identifying potential biomarkers for T2DM.

Bayesian genome scale modelling identifies thermal determinants of yeast metabolism

This paper uses Bayesian modeling to identify temperature-dependent enzymes in yeast metabolism, revealing squalene epoxidase as a key rate-limiting enzyme and demonstrating its role in thermotolerance.

Compositional and functional differences of the mucosal microbiota along the intestine of healthy individuals

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

Integrated metabolic modeling, culturing and transcriptomics explains enhanced virulence of V. cholerae during co-infection with ETEC

This study uses genome-scale metabolic models and co-culture experiments to show that V. cholerae grows better and is more virulent during co-infection with ETEC due to metabolic cross-feeding.

Reconstruction and Analysis of a Kluyveromyces marxianus Genome-scale Metabolic Model

The paper presents a genome-scale metabolic model for Kluyveromyces marxianus, iSM996, which predicts carbon source utilization and growth under different temperatures.