5 citations · 5 across the 5 of their papers we have counts for
6 papers
A Boolean encoding of the Most Permissive semantics for Boolean networks
Laure de Chancel, Brigitte Mossé, Aurélien Naldi +1
Boolean networks are widely used to model biological regulatory networks and study their dynamics. Classical semantics, such as the asynchronous semantics, do not always accurately…
BioSimulators: a central registry of simulation engines and services for recommending specific tools
Bilal Shaikh, Lucian P. Smith, Dan Vasilescu +68
Computational models have great potential to accelerate bioscience, bioengineering, and medicine. However, it remains challenging to reproduce and reuse simulations, in part, becau…
Linear cuts in Boolean networks
Aurélien Naldi, Adrien Richard, Elisa Tonello
Boolean networks are popular tools for the exploration of qualitative dynamical properties of biological systems. Several dynamical interpretations have been proposed based on the…
Geometric analysis of pathways dynamics: application to versatility of TGF-β receptors
Satya Swarup Samal, Aurélien Naldi, Dima Grigoriev +3
We propose a new geometric approach to describe the qualitative dynamics of chemical reactions networks. By this method we identify metastable regimes, defined as low dimensional r…
Symbolic dynamics of biochemical pathways as finite states machines
Ovidiu Radulescu, Satya Swarup Samal, Aurélien Naldi +2
We discuss the symbolic dynamics of biochemical networks with separate timescales. We show that symbolic dynamics of monomolecular reaction networks with separated rate constants c…
SBML Qualitative Models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools
Claudine Chaouiya, Duncan Berenguier, Sarah M Keating +21
Background: Qualitative frameworks, especially those based on the logical discrete formalism, are increasingly used to model regulatory and signalling networks. A major advantage o…