Limit cycle analysis of a class of hybrid gene regulatory networks

Sun, Honglu; Folschette, Maxime; Magnin, Morgan

Document type :

Communication dans un congrès avec actes

Title :

Limit cycle analysis of a class of hybrid gene regulatory networks

Author(s) :

Sun, Honglu [Auteur]
Méthodes Formelles pour la Bioinformatique [LS2N - équipe MéForBio]
Folschette, Maxime [Auteur]

BioComputing
Magnin, Morgan [Auteur]
Méthodes Formelles pour la Bioinformatique [LS2N - équipe MéForBio]

Conference title :

20th International Conference on Computational Methods in Systems Biology (CMSB 2022)

City :

Bucharest

Country :

Roumanie

Start date of the conference :

2022-09-14

Journal title :

Lecture Notes in Computer Science

Publisher :

Springer

English keyword(s) :

Hybrid modeling
Celerity
Transition matrix
Limit cycle
Gene regulatory networks
Poincaré map

HAL domain(s) :

Informatique [cs]/Bio-informatique [q-bio.QM]

English abstract : [en]

Many gene regulatory networks have periodic behavior, for instance the cell cycle or the circadian clock. Therefore, the study of formal methods to analyze limit cycles in mathematical models of gene regulatory networks ...
Show more >Many gene regulatory networks have periodic behavior, for instance the cell cycle or the circadian clock. Therefore, the study of formal methods to analyze limit cycles in mathematical models of gene regulatory networks is of interest. In this work, we study a pre-existing hybrid modeling framework (HGRN) which extends René Thomas' widespread discrete modeling. We propose a new formal method to nd all limit cycles that are simple and deterministic, and analyze their stability, that is, the ability of the model to converge back to the cycle after a small perturbation. Up to now, only limit cycles in two dimensions (with two genes) have been studied; our work lls this gap by proposing a generic approach applicable in higher dimensions. For this, the hybrid states are abstracted to consider only their borders, in order to enumerate all simple abstract cycles containing possible concrete trajectories. Then, a Poincaré map is used, based on the notion of transition matrix of the concrete continuous dynamics inside these abstract paths. We successfully applied this method on existing models: three HGRNs of negative feedback loops with 3 components, and a HGRN of the cell cycle with 5 components.Show less >

Language :

Anglais

Peer reviewed article :

Oui

Audience :

Internationale

Popular science :

Non

Collections :

Centre de Recherche en Informatique, Signal et Automatique de Lille (CRIStAL) - UMR 9189

Source :

Harvested from HAL

Files

https://hal.archives-ouvertes.fr/hal-03700025v2/document
Open access
Access the document

https://hal.archives-ouvertes.fr/hal-03700025v2/document
Open access
Access the document

https://hal.archives-ouvertes.fr/hal-03700025v2/document
Open access
Access the document

https://hal.archives-ouvertes.fr/hal-03700025v2/document
Open access
Access the document

document
Open access
Access the document

Limit_cycle_analysis_of_a_class_of_hybrid_gene_regulatory_networks%20-%202022-08-01.pdf
Open access
Access the document

Limit cycle analysis of a class of hybrid ... BibTeX CSV Excel RIS

Files

Limit cycle analysis of a class of hybrid ...

BibTeX

CSV

Excel

RIS