Yunfan Bai

The paper introduces FICUS, a framework that integrates omics data with logic models to identify shared signaling mechanisms across patient subgroups.

OmniPath Metabo integrates metabolomics data with prior knowledge to enable mechanistic analysis of the metabolome through harmonized databases and network construction.

This study shows that different modes of macrophage cell death affect wound healing outcomes, with necroptosis impairing repair and apoptosis promoting better tissue recovery.

OmniPath integrates molecular knowledge from 168 resources to support multi-omics analysis, offering curated data, predictions, and tools for causal modeling across bulk, single-cell, and spatial data.

The paper introduces COSMOS+ to integrate mechanistic prior knowledge with multi-omics data analysis to generate mechanistic hypotheses about disease resistance mechanisms.

The paper compares metabolic dysregulation in obese mice during feeding and fasting using multi-omics data, revealing opposite metabolic shifts linked to obesity.

iTraNet is a web tool for visualizing and analyzing trans-omics networks, revealing differences in hub molecule responses to glucose between wild-type and ob/ob mice.

This study uses multiomic analysis of skeletal muscle in obese and healthy mice to reveal differences in metabolic regulation by metabolites and genes after glucose administration.