From logical modelling to transcriptomic data analysis – A systems biology perspective
Date(s) : 07/05/2025 iCal
9h00 - 11h00
Abstract:
Biological systems are inherently complex. They are composed of numerous elements whose interactions give rise to emergent properties. The study of these systems often relies on holistic approaches that account for both the entire system and the interactions among its various components. In particular, mathematical modelling is a powerful tool for simulating and analysing the behaviour of biological systems. Among the existing mathematical models, logical models (both Boolean and multivalued) distinguish themselves by their minimal reliance on quantitative data.
My thesis focuses on studying biological systems using logical models. After introducing systems biology and logical modelling, I present my main contribution: a method for refining Boolean models, termed “Multivalued Refinements of Boolean Models” (MRBM). Boolean models use binary variables to represent the activity of biological components, but this simplification can lead to an incomplete representation of a system’s dynamics. Multivalued models can overcome this limitation by allowing components to adopt more than two activity levels. However, determining which components should be modelled as multivalued remains a challenge. The MRBM method addresses this challenge by leveraging a new updating strategy, called “partial most permissive” updating, which is based on the classical “most permissive” scheme.
This thesis also includes a collaborative study on RNA sequencing data from mice affected by Hutchinson-Gilford Progeria syndrome. This study illustrates a different approach to studying biological systems — other than logical modelling.
The Jury:
Mme Laurence Calzone, Institut Curie — Rapportrice
Mme Madalena Chaves, INRIA — Rapportrice
M. Paul Ruet, CNRS — Examinateur
M. Elias Ventre, INRIA — Examinateur
M. Denis Thieffry, IBENS — Examinateur
M. Jacques Van Helden, AMU — Président du jury
Mme Anaïs Baudot, MMG — Directrice de thèse
Mme Élisabeth Rémy, I2M — Directrice de thèse
Emplacement
Luminy - Auditorium de l'Hexagone
Catégories
