341 citations · 1.7k across the 37 of their papers we have counts for
12 papers · 1 filter
Model Reduction for the Chemical Master Equation: an Information-Theoretic Approach
K. Öcal, G. Sanguinetti, R. Grima
The complexity of mathematical models in biology has rendered model reduction an essential tool in the quantitative biologist's toolkit. For stochastic reaction networks described…
Bayesian learning of effective chemical master equations in crowded intracellular conditions
Svitlana Braichenko, Ramon Grima, Guido Sanguinetti
Biochemical reactions inside living cells often occur in the presence of crowders -- molecules that do not participate in the reactions but influence the reaction rates through exc…
Parameter estimation for biochemical reaction networks using Wasserstein distances
Kaan Öcal, Ramon Grima, Guido Sanguinetti
We present a method for estimating parameters in stochastic models of biochemical reaction networks by fitting steady-state distributions using Wasserstein distances. We simulate a…
Approximation and inference methods for stochastic biochemical kinetics - a tutorial review
David Schnoerr, Guido Sanguinetti, Ramon Grima
Stochastic fluctuations of molecule numbers are ubiquitous in biological systems. Important examples include gene expression and enzymatic processes in living cells. Such systems a…
Stochastic Simulation of Biomolecular Networks in Dynamic Environments
Margaritis Voliotis, Philipp Thomas, Ramon Grima +1
Simulation of biomolecular networks is now indispensable for studying biological systems, from small reaction networks to large ensembles of cells. Here we present a novel approach…
Model reduction for stochastic chemical systems with abundant species
Stephen Smith, Claudia Cianci, Ramon Grima
Biochemical processes typically involve many chemical species, some in abundance and some in low molecule numbers. Here we first identify the rate constant limits under which the c…