Hybrid modelling and dynamical analysis of gene regulatory networks with delays

J Ahmad, G Bernot, JP Comet, D Lime, O Roux - ComPlexUs, 2007 - karger.com
René Thomas' discrete modelling of gene regulatory networks (GRN) is a well-known
approach to study the dynamics resulting from a set of interacting genes. It deals with some …

Simplified models for the mammalian circadian clock

JP Comet, G Bernot, A Das, F Diener, C Massot… - Procedia Computer …, 2012 - Elsevier
Numerous biological mechanisms are synchronized by the circadian rhythm in species so
diverse as mushrooms, drosophiles or mammals. Because of its ubiquity and of its …

Boolean networks and their dynamics: the impact of updates

L Paulevé, S Sené - Systems Biology Modelling and Analysis …, 2022 - Wiley Online Library
Boolean networks are a mathematical model that has been widely used since decades in
the context of biological regulation networks' qualitative modelling. They consist in …

On the modelling and analysis of the regulatory network of dengue virus pathogenesis and clearance

B Aslam, J Ahmad, A Ali, RZ Paracha… - … Biology and Chemistry, 2014 - Elsevier
Dengue virus can ignite both protective and pathogenic responses in human. The
pathogenesis is related with modified functioning of our immune system during infection …

Formal modeling and analysis of the mal-associated biological regulatory network: insight into cerebral malaria

J Ahmad, U Niazi, S Mansoor, U Siddique, J Bibby - PloS one, 2012 - journals.plos.org
The discrete modeling formalism of René Thomas is a well known approach for the
modeling and analysis of Biological Regulatory Networks (BRNs). This formalism uses a set …

Attractor landscapes in Boolean networks with firing memory: a theoretical study applied to genetic networks

E Goles, F Lobos, GA Ruz, S Sené - Natural Computing, 2020 - Springer
In this paper we study the dynamical behavior of Boolean networks with firing memory,
namely Boolean networks whose vertices are updated synchronously depending on their …

On the effects of firing memory in the dynamics of conjunctive networks

E Goles, P Montealegre, M Ríos-Wilson - Cellular Automata and Discrete …, 2019 - Springer
Boolean networks are one of the most studied discrete models in the context of the study of
gene expression. In order to define the dynamics associated to a Boolean network, there are …

Concretizing the process hitting into biological regulatory networks

M Folschette, L Paulevé, K Inoue, M Magnin… - … Methods in Systems …, 2012 - Springer
Abstract The Process Hitting (PH) is a recently introduced framework to model concurrent
processes. Its major originality lies in a specific restriction on the causality of actions, which …

[HTML][HTML] Identification of biological regulatory networks from process hitting models

M Folschette, L Paulevé, K Inoue, M Magnin… - Theoretical Computer …, 2015 - Elsevier
Qualitative formalisms offer a well-established alternative to the more traditionally used
differential equation models of Biological Regulatory Networks (BRNs). These formalisms …

Formal modeling of mTOR associated biological regulatory network reveals novel therapeutic strategy for the treatment of cancer

Z Bibi, J Ahmad, A Siddiqa, RZ Paracha… - Frontiers in …, 2017 - frontiersin.org
Cellular homeostasis is a continuous phenomenon that if compromised can lead to several
disorders including cancer. There is a need to understand the dynamics of cellular …