Nathalie Théret

Refining Protein Co-Membership in Reactome: A Weighted Scoring Approach Based on Hierarchy and Sequences of Patwhays

The paper introduces a weighted pathway co-membership method for Reactome pathways, improving gene prioritization in cancer hallmarks by incorporating biological distances and hierarchical structure.

FUSE-PhyloTree: Linking functions and sequence conservation modules of a protein family through phylogenomic analysis

A rule-based multiscale model of hepatic stellate cell plasticity: critical role of the inactivation loop in fibrosis progression

This paper develops a rule-based model of hepatic stellate cell dynamics in fibrosis, showing the critical role of inactivation loops in fibrosis progression and identifying inactivated HSCs as markers of fibrosis.

A pipeline to create predictive functional networks: application to the tumor progression of hepatocellular carcinoma

The paper introduces a pipeline to generate predictive functional networks using gene expression data and pathway databases, applied to hepatocellular carcinoma progression to identify regulatory biomolecules.