Quantitative and logic modelling of molecular and gene networks
N Le Novere - Nature Reviews Genetics, 2015 - nature.com
Behaviours of complex biomolecular systems are often irreducible to the elementary
properties of their individual components. Explanatory and predictive mathematical models …
properties of their individual components. Explanatory and predictive mathematical models …
Structure and dynamics of molecular networks: a novel paradigm of drug discovery: a comprehensive review
P Csermely, T Korcsmáros, HJM Kiss, G London… - Pharmacology & …, 2013 - Elsevier
Despite considerable progress in genome-and proteome-based high-throughput screening
methods and in rational drug design, the increase in approved drugs in the past decade did …
methods and in rational drug design, the increase in approved drugs in the past decade did …
Robust satisfaction of temporal logic over real-valued signals
We consider temporal logic formulae specifying constraints in continuous time and space on
the behaviors of continuous and hybrid dynamical system admitting uncertain parameters …
the behaviors of continuous and hybrid dynamical system admitting uncertain parameters …
Computational modeling, formal analysis, and tools for systems biology
E Bartocci, P Lió - PLoS computational biology, 2016 - journals.plos.org
As the amount of biological data in the public domain grows, so does the range of modeling
and analysis techniques employed in systems biology. In recent years, a number of …
and analysis techniques employed in systems biology. In recent years, a number of …
Modeling formalisms in systems biology
Abstract Systems Biology has taken advantage of computational tools and high-throughput
experimental data to model several biological processes. These include signaling, gene …
experimental data to model several biological processes. These include signaling, gene …
Rule-based multi-level modeling of cell biological systems
Background Proteins, individual cells, and cell populations denote different levels of an
organizational hierarchy, each of which with its own dynamics. Multi-level modeling is …
organizational hierarchy, each of which with its own dynamics. Multi-level modeling is …
A cell-based simulation software for multi-cellular systems
CellSys is a modular software tool for efficient off-lattice simulation of growth and
organization processes in multi-cellular systems in 2D and 3D. It implements an agent …
organization processes in multi-cellular systems in 2D and 3D. It implements an agent …
[HTML][HTML] System design of stochastic models using robustness of temporal properties
Stochastic models such as Continuous-Time Markov Chains (CTMC) and Stochastic Hybrid
Automata (SHA) are powerful formalisms to model and to reason about the dynamics of …
Automata (SHA) are powerful formalisms to model and to reason about the dynamics of …
A general computational method for robustness analysis with applications to synthetic gene networks
Motivation: Robustness is the capacity of a system to maintain a function in the face of
perturbations. It is essential for the correct functioning of natural and engineered biological …
perturbations. It is essential for the correct functioning of natural and engineered biological …
Tellurium notebooks—an environment for reproducible dynamical modeling in systems biology
The considerable difficulty encountered in reproducing the results of published dynamical
models limits validation, exploration and reuse of this increasingly large biomedical …
models limits validation, exploration and reuse of this increasingly large biomedical …