Océane Cassan

A genome-wide, machine learning-guided exploration of the cis-regulatory code involved in neuronal differentiation

The paper develops a machine learning method to identify cis-regulatory element profiles and their sequence features during neuronal differentiation using single-cell ATAC-seq and RNA-seq data.

Optimizing data integration improves Gene Regulatory Network inference in Arabidopsis thaliana

The paper optimizes data integration for GRN inference in Arabidopsis thaliana by introducing DIOgene, which improves prediction accuracy and identifies gene-specific integration intensities.

Probing transcription factor combinatorics in different promoter classes and in enhancers

The paper introduces TFcoop, a method to infer TF combinations involved in target TF binding, and shows it outperforms PWM methods while revealing cell-type-specific and promoter-class-specific TF interactions.