Continuous time boolean modeling for biological signaling: application of Gillespie algorithm
Gautier Stoll,Gautier Stoll,Gautier Stoll,Eric Viara,Emmanuel Barillot,Emmanuel Barillot,Emmanuel Barillot,Laurence Calzone,Laurence Calzone,Laurence Calzone +9 more
TLDR
An algorithm for modeling biological networks in a discrete framework with continuous time based on continuous time Markov process applied on a Boolean state space, which allows to describe kinetic phenomena which were difficult to handle in the original models.Abstract:
Mathematical modeling is used as a Systems Biology tool to answer biological questions, and more precisely, to validate a network that describes biological observations and predict the effect of perturbations. This article presents an algorithm for modeling biological networks in a discrete framework with continuous time.read more
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Logical Modeling and Dynamical Analysis of Cellular Networks.
Wassim Abou-Jaoudé,Pauline Traynard,Pedro T. Monteiro,Pedro T. Monteiro,Julio Saez-Rodriguez,Tomáš Helikar,Denis Thieffry,Claudine Chaouiya +7 more
TL;DR: A number of recent methodological advances to ease the analysis of large and intricate networks are reviewed, including approaches to determine model attractors and their reachability properties, to assess the dynamical impact of variations of external signals, and to consistently reduce large models.
Journal ArticleDOI
Integrative modelling of the influence of MAPK network on cancer cell fate decision.
Luca Grieco,Laurence Calzone,Isabelle Bernard-Pierrot,François Radvanyi,Brigitte Kahn-Perlès,Denis Thieffry +5 more
TL;DR: A comprehensive and generic reaction map for the MAPK signalling network is built, using CellDesigner software, and tentative proliferative or anti-proliferative mechanisms can be connected with established bladder cancer deregulations, namely Epidermal Growth Factor Receptor over-expression and Fibroblast Growth factor Receptor 3 activating mutations.
Journal ArticleDOI
Mathematical Modelling of Molecular Pathways Enabling Tumour Cell Invasion and Migration.
David P. A. Cohen,Loredana Martignetti,Sylvie Robine,Emmanuel Barillot,Andrei Zinovyev,Laurence Calzone +5 more
TL;DR: A logical model has been constructed that recapitulates published experimental results of known gene perturbations on local invasion and migration processes, and is focused on several unexpected synergistic genetic interactions leading to theoretically very high metastasis probability.
Journal ArticleDOI
Logical modeling of lymphoid and myeloid cell specification and transdifferentiation.
Samuel Collombet,Chris van Oevelen,Jose Luis Sardina Ortega,Wassim Abou-Jaoudé,Bruno Di Stefano,Morgane Thomas-Chollier,Thomas Graf,Denis Thieffry +7 more
TL;DR: Focusing on B-cell and macrophage development, a qualitative dynamical model recapitulating cytokine-induced differentiation of common progenitors, the effect of various reported gene knockdowns, and the reprogramming of pre-B cells into macrophages induced by the ectopic expression of specific transcription factors is defined.
Journal ArticleDOI
A Modeling Approach to Explain Mutually Exclusive and Co-Occurring Genetic Alterations in Bladder Tumorigenesis
Elisabeth Remy,Sandra Rebouissou,Sandra Rebouissou,Claudine Chaouiya,Andrei Zinovyev,Andrei Zinovyev,Andrei Zinovyev,François Radvanyi,François Radvanyi,Laurence Calzone,Laurence Calzone,Laurence Calzone +11 more
TL;DR: Overall, this work shows how to predict combinations of the major gene alterations leading to invasiveness through two main progression pathways in bladder cancer.
References
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Book
Stochastic processes in physics and chemistry
TL;DR: In this article, the authors introduce the Fokker-planck equation, the Langevin approach, and the diffusion type of the master equation, as well as the statistics of jump events.
Journal ArticleDOI
A General Method for Numerically Simulating the Stochastic Time Evolution of Coupled Chemical Reactions
TL;DR: In this paper, an exact method is presented for numerically calculating, within the framework of the stochastic formulation of chemical kinetics, the time evolution of any spatially homogeneous mixture of molecular species which interreact through a specified set of coupled chemical reaction channels.
Journal ArticleDOI
Probabilistic Boolean networks: a rule-based uncertainty model for gene regulatory networks
TL;DR: Probabilistic Boolean Networks (PBN) are introduced that share the appealing rule-based properties of Boolean networks, but are robust in the face of uncertainty.
Journal ArticleDOI
Homeostasis and differentiation in random genetic control networks.
TL;DR: This work has found what seems to be a new class of dynamically stable systems, which suggests that even haphazardly constructed control nets of high molecular specificity undergo homeostasis and differentiation.
Journal ArticleDOI
Dynamical analysis of a generic Boolean model for the control of the mammalian cell cycle
TL;DR: This work compares the respective advantages and limits of synchronous versus asynchronous updating assumptions to delineate the asymptotical behaviour of regulatory networks and proposes several intermediate strategies to optimize the computation of asymPTotical properties depending on available knowledge.