Towards a New Method for Perturbation Analysis in Biochemical Pathways Based on Network Propagation

Niccolò De Paolis, Paolo Milazzo

2025

Abstract

We introduce a preliminary definition of a network propagation approach to tackle the problem of investigating the spread of mutation-induced perturbations in biochemical pathways relying on network topology alone, without the need for quantitative details such as species concentrations and kinetic constants of reactions required to model the trajectory of species concentrations using stochastic and deterministic algorithms. These details are not always available, hence our goal is to provide insights regarding the impact of perturbations even when lacking such information. We further describe the definition of a synthetic dataset the algorithm has been tested on and provide the results obtained in terms of accuracy in identifying the effect of the perturbation on each species. Finally, a real world scenario is presented in order to show the potential of the proposed solution and spot its possible limitations.

Paper Citation

in Harvard Style

De Paolis N. and Milazzo P. (2025). Towards a New Method for Perturbation Analysis in Biochemical Pathways Based on Network Propagation. In Proceedings of the 18th International Joint Conference on Biomedical Engineering Systems and Technologies - Volume 1: BIOINFORMATICS; ISBN 978-989-758-731-3, SciTePress, pages 684-691. DOI: 10.5220/0013384200003911

in Bibtex Style

@conference{bioinformatics25,
author={Niccolò De Paolis and Paolo Milazzo},
title={Towards a New Method for Perturbation Analysis in Biochemical Pathways Based on Network Propagation},
booktitle={Proceedings of the 18th International Joint Conference on Biomedical Engineering Systems and Technologies - Volume 1: BIOINFORMATICS},
year={2025},
pages={684-691},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0013384200003911},
isbn={978-989-758-731-3},
}

in EndNote Style

TY - CONF

JO - Proceedings of the 18th International Joint Conference on Biomedical Engineering Systems and Technologies - Volume 1: BIOINFORMATICS
TI - Towards a New Method for Perturbation Analysis in Biochemical Pathways Based on Network Propagation
SN - 978-989-758-731-3
AU - De Paolis N.
AU - Milazzo P.
PY - 2025
SP - 684
EP - 691
DO - 10.5220/0013384200003911
PB - SciTePress