A list of bioinformatics and computational biology tools with papers that have used them.
MICOM is a customisable metabolic model of the human gut microbiome that simulates microbial growth rates and metabolic interactions, providing insights into how diet and microbiome composition affect community function, with applications in health and disease contexts.
- Longitudinal flux balance analyses of a patient with episodic colonic inflammation reveals microbiome metabolic dynamics - Basile et al., 2023, Gut Microbes
- Metatranscriptomics-guided genome-scale metabolic modeling of microbial communities - Zapieri et al. 2023, Cell Reports Methods
- Microbiome community-scale metabolic modelling predicts personalised short-chain fatty acid production profiles in the human gut