Siu Hung Joshua Chan

ADToolbox: Incorporating Metagenomics Data for Improved Prediction of Anaerobic Digestion Dynamics

ADToolbox integrates metagenomics data into an enhanced ADM model to improve prediction of anaerobic digestion dynamics and VFA production.

Microbial Interactions from a New Perspective: Reinforcement Learning Reveals New Insights into Microbiome Evolution

This paper introduces a reinforcement learning algorithm to model microbial metabolism and evolution, showing improved prediction of stable metabolic strategies in heterogeneous communities.

kb_DRAM: Annotating and functional profiling of genomes with DRAM in KBase

kb_DRAM integrates DRAM tools into KBase for microbial and viral genome annotation and metabolic modeling through a user-friendly interface.

A comprehensive genome-scale model for Rhodosporidium toruloides IFO0880 accounting for functional genomics and phenotypic data

The paper constructs a genome-scale metabolic model for Rhodosporidium toruloides IFO0880, integrating functional genomics and phenotypic data to improve predictions of gene essentiality and metabolic capabilities.

Bridging evolutionary game theory and metabolic models for predicting microbial metabolic interactions

This paper develops NECom, a bi-level optimization framework integrating evolutionary game theory and metabolic models to predict microbial interactions with improved accuracy.