Olivier Dameron

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.

BioPAX-Explorer simplifies querying and analyzing BioPAX biological pathway data by providing an object-oriented Python framework with query capabilities and tools for data extraction and workflow development.

Regulus infers signed transcriptional regulatory networks from few samples by integrating TF binding, gene expression, and regulatory region data with biological constraints.

The paper analyzes reproducibility issues in the Regulatory Circuits project and proposes solutions for improving reusability and reproducibility of its data integration pipeline.