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Keyword

Gillespie algorithm

Description: The Gillespie algorithm is a stochastic simulation method for modeling discrete events, especially chemical reactions and other systems of interacting processes.
Wikidata ID: wiki/Q5562121
OpenAlex ID: keywords/gillespie-algorithm
Exact stochastic simulation of coupled chemical reactions
1977 · Daniel T. Gillespie · The Journal of Physical Chemistry · 10,150
DifferentialEquations.jl – A Performant and Feature-Rich Ecosystem for Solving Differential Equations in Julia
2017 · Christopher Rackauckas, Qing Nie · Journal of Open Research Software · 1,630
Stochastic chemical kinetics and the quasi-steady-state assumption: Application to the Gillespie algorithm
2003 · Christopher V. Rao, Adam P. Arkin · The Journal of Chemical Physics · 657
Efficient formulation of the stochastic simulation algorithm for chemically reacting systems
2004 · Yang Cao, Hong Li, et al. · The Journal of Chemical Physics · 421
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A modified next reaction method for simulating chemical systems with time dependent propensities and delays
2007 · David F. Anderson · The Journal of Chemical Physics · 352
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Binomial distribution based τ-leap accelerated stochastic simulation
2004 · Abhijit Chatterjee, Dionisios G. Vlachos, et al. · The Journal of Chemical Physics · 233
Multiscale stochastic simulation algorithm with stochastic partial equilibrium assumption for chemically reacting systems
2005 · Yang Cao, Dan Gillespie, et al. · Journal of Computational Physics · 212
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The Stochastic Evolution of a Protocell: The Gillespie Algorithm in a Dynamically Varying Volume
2012 · T. Carletti, A. Filisetti · Computational and Mathematical Methods in Medicine · 207
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Nested stochastic simulation algorithm for chemical kinetic systems with disparate rates
2005 · Weinan E, Di Liu, et al. · The Journal of Chemical Physics · 191
Exact stochastic simulation of coupled chemical reactions with delays
2007 · Xiaodong Cai · The Journal of Chemical Physics · 184
The sorting direct method for stochastic simulation of biochemical systems with varying reaction execution behavior
2005 · James M. McCollum, Gregory D. Peterson, et al. · Computational Biology and Chemistry · 182
Proceedings of the 2006 ACM symposium on Applied computing
2006 · Lecca, Paola · 174
The Effect of Transcription and Translation Initiation Frequencies on the Stochastic Fluctuations in Prokaryotic Gene Expression
2001 · Andrzej M. Kierzek, Jolanta Zaim, et al. · Journal of Biological Chemistry · 165
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A multi-algorithm, multi-timescale method for cell simulation
2004 · Kouichi Takahashi, Kazunari Kaizu, et al. · Bioinformatics · 164
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Incorporating Diffusion in Complex Geometries into Stochastic Chemical Kinetics Simulations
2006 · Samuel A. Isaacson, Charles S. Peskin · SIAM Journal on Scientific Computing · 156
A practical guide to stochastic simulations of reaction-diffusion processes
2007 · Erban, Radek, Chapman, Jonathan, et al. · arXiv (Cornell University) · 154
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STEPS: efficient simulation of stochastic reaction–diffusion models in realistic morphologies
2012 · Iain Hepburn, Weiliang Chen, et al. · BMC Systems Biology · 150
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Biochemical Network Stochastic Simulator (BioNetS): software for stochastic modeling of biochemical networks
2004 · David Adalsteinsson, David McMillen, et al. · BMC Bioinformatics · 147
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STOCKS: STOChastic Kinetic Simulations of biochemical systems with Gillespie algorithm
2002 · Andrzej M. Kierzek · Bioinformatics · 145
StochKit2: software for discrete stochastic simulation of biochemical systems with events
2011 · Kevin R. Sanft, Sheng Wu, et al. · Bioinformatics · 144
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Simulating mesoscopic reaction-diffusion systems using the Gillespie algorithm
2005 · David Bernstein · Physical Review E · 140
Continuous time boolean modeling for biological signaling: application of Gillespie algorithm
2012 · Gautier Stoll, Eric Viara, et al. · BMC Systems Biology · 134
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A General Modeling Strategy for Gene Regulatory Networks with Stochastic Dynamics
2006 · Andre Ribeiro, Rui Zhu, et al. · Journal of Computational Biology · 126
Nested stochastic simulation algorithms for chemical kinetic systems with multiple time scales
2006 · Weinan E, Di Liu, et al. · Journal of Computational Physics · 126
Modeling and Simulation of Intracellular Dynamics: Choosing an Appropriate Framework
2004 · O. Wolkenhauer, M. Ullah, et al. · IEEE Transactions on NanoBioscience · 125
Works count: 1,152
Citation count: 24,070
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