104 citations · 105 across the 7 of their papers we have counts for
9 papers
PhysiBoSS-Models: A database for multiscale models
Vincent Noel, Marco Ruscone, Randy Heiland +5
PhysiBoSS is an open-source platform that integrates agent-based modeling of cell populations with intracellular stochastic Boolean networks, enabling multiscale simulations of com…
Building multiscale models with PhysiBoSS, an agent-based modeling tool
Marco Ruscone, Andrea Checcoli, Randy Heiland +4
Multiscale models provide a unique tool for studying complex processes that study events occurring at different scales across space and time. In the context of biological systems,…
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…
Predicting genetic interactions from Boolean models of biological networks
Laurence Calzone, Emmanuel Barillot, Andrei Zinovyev
Genetic interaction can be defined as a deviation of the phenotypic quantitative effect of a double gene mutation from the effect predicted from single mutations using a simple (e.…
DeDaL: Cytoscape 3.0 app for producing and morphing data-driven and structure-driven network layouts
Urszula Czerwinska, Laurence Calzone, Emmanuel Barillot +1
Visualization and analysis of molecular profiling data together with biological networks are able to provide new mechanistical insights into biological functions. Currently, high-t…
Integrative multi-omics module network inference with Lemon-Tree
Eric Bonnet, Laurence Calzone, Tom Michoel
Module network inference is an established statistical method to reconstruct co-expression modules and their upstream regulatory programs from integrated multi-omics datasets measu…
NaviCell: a web-based environment for navigation, curation and maintenance of large molecular interaction maps
Inna Kuperstein, David PA Cohen, Stuart Pook +3
Molecular biology knowledge can be systematically represented in a computer-readable form as a comprehensive map of molecular interactions. There exist a number of maps of molecula…
Cell death and life in cancer: mathematical modeling of cell fate decisions
Andrei Zinovyev, Simon Fourquet, Laurent Tournier +2
Tumor development is characterized by a compromised balance between cell life and death decision mechanisms, which are tighly regulated in normal cells. Understanding this process…
Continuous time Boolean modeling for biological signaling: application of Gillespie algorithm
Gautier Stoll, Eric Viara, Emmanuel Barillot +1
This article presents an algorithm that allows modeling of biological networks in a qualitative framework with continuous time. Mathematical modeling is used as a systems biology t…