Adrien Rougny

User-driven development and evaluation of an agentic framework for analysis of large pathway diagrams

The paper describes the development and evaluation of an agentic framework using LLMs to explore molecular interaction maps through user-driven prototyping and testing.

Deciphering shared molecular dysregulation across Parkinson's disease variants using a multi-modal network-based data integration and analysis

The paper integrates multi-modal data to identify shared molecular dysregulation across Parkinson's disease variants, finding common transcriptomic features in glial cells and potential involvement of ROBO signalling.

FAIRification of computational models in biology

The paper proposes adapting FAIR indicators to assess and improve the quality and transparency of computational models in biology.

FAIR assessment of MINERVA as an opportunity to foster open science and scientific crowdsourcing in systems biomedicine

The paper assesses the FAIRness of the MINERVA platform using the RDA FAIR Data Maturity Model, focusing on the Parkinson's Disease Map and the COVID-19 Disease Map.

A versatile and interoperable computational framework for the analysis and modeling of COVID-19 disease mechanisms

The paper presents a computational framework for analyzing SARS-CoV-2-host interactions to identify drug targets and model disease mechanisms.

A Detailed Map of Coupled Circadian Clock and Cell Cycle with Qualitative Dynamics Validation

The paper creates a merged SBGN PD map of the circadian clock and cell cycle, validates its dynamics, and identifies NR1D1's role in regulating cell cycle progression.

Reusability and composability in process description maps: RAS-RAF-MEK-ERK signalling

The paper evaluates the reusability and composability of manually-built RAS-RAF-MEK-ERK signaling pathway maps from three databases to improve disease model assembly.

SBGN Bricks Ontology as a tool to describe recurring concepts in molecular networks

The paper introduces SBGN bricks and their ontology to provide structured semantics for recurring molecular network concepts, enabling better annotation and construction of molecular maps.