Multi-state Modeling of Biomolecules

Exact Hybrid Particle/Population Simulation of Rule-Based Models of Biochemical Systems

(2014) Justin S. Hogg et al.   PLoS Computational Biology

Modular, rule-based modeling for the design of eukaryotic synthetic gene circuits

(2013) Mario Marchisio et al.   BMC Systems Biology

A rule-based kinetic model of RNA polymerase II C-terminal domain phosphorylation

(2013) S. Aitken et al.   Journal of the Royal Society Interface

Multi-level modelling via stochastic multi-level multiset rewriting

(2013) NICOLAS OURY et al.   MATHEMATICAL STRUCTURES IN COMPUTER SCIENCE

Programming biological models in Python using PySB

(2013) C. F. Lopez et al.   Molecular Systems Biology

Rule-based modeling and simulations of the inner kinetochore structure

(2013) Sergej Tschernyschkow et al.   PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY

Spatial Rule-Based Modeling: A Method and Its Application to the Human Mitotic Kinetochore

(2013) Bashar Ibrahim et al.   Cells

Specification, annotation, visualization and simulation of a large rule-based model for ERBB receptor signaling

(2012) Matthew S Creamer et al.   BMC Systems Biology

Extracellular sheets and tunnels modulate glutamate diffusion in hippocampal neuropil

(2012) Justin P. Kinney et al.   JOURNAL OF COMPARATIVE NEUROLOGY

Computational modeling of cellular signaling processes embedded into dynamic spatial contexts

(2012) Bastian R Angermann et al.   NATURE METHODS

CaMKII activation and dynamics are independent of the holoenzyme structure: an infinite subunit holoenzyme approximation

(2012) P J Michalski et al.   PHYSICAL BIOLOGY

Structural Analysis and Stochastic Modelling Suggest a Mechanism for Calmodulin Trapping by CaMKII

(2012) Melanie I. Stefan et al.   PLoS One

Cell Polarity: Quantitative Modeling as a Tool in Cell Biology

(2012) A. Mogilner et al.   SCIENCE

Rule-based multi-level modeling of cell biological systems

(2011) Carsten Maus et al.   BMC Systems Biology

RuleMonkey: software for stochastic simulation of rule-based models

(2010) Joshua Colvin et al.   BMC BIOINFORMATICS

Rule-based spatial modeling with diffusing, geometrically constrained molecules

(2010) Gerd Gruenert et al.   BMC BIOINFORMATICS

Meredys, a multi-compartment reaction-diffusion simulator using multistate realistic molecular complexes

(2010) Dominic P Tolle et al.   BMC Systems Biology

Rule-based modelling and simulation of biochemical systems with molecular finite automata

(2010) J. Yang et al.   IET Systems Biology

Efficient modeling, simulation and coarse-graining of biological complexity with NFsim

(2010) Michael W Sneddon et al.   NATURE METHODS

CD4 and CD8 binding to MHC molecules primarily acts to enhance Lck delivery

(2010) M. N. Artyomov et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Scalable Rule-Based Modelling of Allosteric Proteins and Biochemical Networks

(2010) Julien F. Ollivier et al.   PLoS Computational Biology

Simulation of large-scale rule-based models

(2009) Joshua Colvin et al.   BIOINFORMATICS

Efficient stochastic simulation of reaction–diffusion processes via direct compilation

(2009) Mieszko Lis et al.   BIOINFORMATICS

ProMoT: modular modeling for systems biology

(2009) Sebastian Mirschel et al.   BIOINFORMATICS

Internal coarse-graining of molecular systems

(2009) J. Feret et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Kinetic Monte Carlo method for rule-based modeling of biochemical networks

(2008) Jin Yang et al.   PHYSICAL REVIEW E

Fast Monte Carlo Simulation Methods for Biological Reaction-Diffusion Systems in Solution and on Surfaces

(2008) Rex A. Kerr et al.   SIAM JOURNAL ON SCIENTIFIC COMPUTING