Efficient step size selection for the tau-leaping simulation method.

PubWeight™: 3.71‹?› | Rank: Top 1%

🔗 View Article (PMID 16460151)

Published in J Chem Phys on January 28, 2006

Authors

Yang Cao1, Daniel T Gillespie, Linda R Petzold

Author Affiliations

1: Department of Computer Science, Virginia Tech, Blacksburg, Virginia 24061, USA. ycao@vt.edu

Articles citing this

Networks and the epidemiology of infectious disease. Interdiscip Perspect Infect Dis (2011) 2.00

StochKit2: software for discrete stochastic simulation of biochemical systems with events. Bioinformatics (2011) 1.52

Algorithms and software for stochastic simulation of biochemical reacting systems. Biotechnol Prog (2007) 1.45

Escherichia coli rpoB mutants have increased evolvability in proportion to their fitness defects. Mol Biol Evol (2010) 1.41

Biochemical simulations: stochastic, approximate stochastic and hybrid approaches. Brief Bioinform (2009) 1.31

Lattice Microbes: high-performance stochastic simulation method for the reaction-diffusion master equation. J Comput Chem (2012) 1.30

StochPy: a comprehensive, user-friendly tool for simulating stochastic biological processes. PLoS One (2013) 1.25

Solving the chemical master equation using sliding windows. BMC Syst Biol (2010) 1.24

Global parameter estimation methods for stochastic biochemical systems. BMC Bioinformatics (2010) 1.20

Perspective: Stochastic algorithms for chemical kinetics. J Chem Phys (2013) 1.16

Stochastic ion channel gating in dendritic neurons: morphology dependence and probabilistic synaptic activation of dendritic spikes. PLoS Comput Biol (2010) 1.08

Analytical Derivation of Moment Equations in Stochastic Chemical Kinetics. Chem Eng Sci (2011) 1.03

Systems interface biology. J R Soc Interface (2006) 1.01

Robust stochastic chemical reaction networks and bounded tau-leaping. J Comput Biol (2009) 0.95

Perfect sampling of the master equation for gene regulatory networks. Biophys J (2007) 0.93

An exact accelerated stochastic simulation algorithm. J Chem Phys (2009) 0.92

Stochastic hybrid modeling of intracellular calcium dynamics. J Chem Phys (2010) 0.92

Accurate stochastic simulation via the step anticipation tau-leaping (SAL) algorithm. J Comput Biol (2009) 0.91

Efficient stochastic simulation of chemical kinetics networks using a weighted ensemble of trajectories. J Chem Phys (2013) 0.90

On the precision of quasi steady state assumptions in stochastic dynamics. J Chem Phys (2012) 0.90

Michaelis-Menten speeds up tau-leaping under a wide range of conditions. J Chem Phys (2011) 0.89

New "Tau-Leap" Strategy for Accelerated Stochastic Simulation. Ind Eng Chem Res (2014) 0.89

An accelerated algorithm for discrete stochastic simulation of reaction-diffusion systems using gradient-based diffusion and tau-leaping. J Chem Phys (2011) 0.89

Hybrid approaches for multiple-species stochastic reaction-diffusion models. J Comput Phys (2015) 0.88

TABASCO: A single molecule, base-pair resolved gene expression simulator. BMC Bioinformatics (2007) 0.88

Discrete stochastic simulation methods for chemically reacting systems. Methods Enzymol (2009) 0.88

Kinetic modeling of biological systems. Methods Mol Biol (2009) 0.87

Exact hybrid particle/population simulation of rule-based models of biochemical systems. PLoS Comput Biol (2014) 0.87

Breaking the symmetry: immune enhancement increases persistence of dengue viruses in the presence of asymmetric transmission rates. J Theor Biol (2013) 0.86

Single-cell analysis and stochastic modelling unveil large cell-to-cell variability in influenza A virus infection. Nat Commun (2015) 0.86

FERN - a Java framework for stochastic simulation and evaluation of reaction networks. BMC Bioinformatics (2008) 0.86

Stochastic simulation in systems biology. Comput Struct Biotechnol J (2014) 0.85

Extinction models for cancer stem cell therapy. Math Biosci (2011) 0.85

Slow Scale Tau-leaping Method. Comput Methods Appl Mech Eng (2008) 0.83

Accelerating the Gillespie τ-Leaping Method using graphics processing units. PLoS One (2012) 0.83

A hybrid multiscale Monte Carlo algorithm (HyMSMC) to cope with disparity in time scales and species populations in intracellular networks. BMC Bioinformatics (2007) 0.82

Simulation methods with extended stability for stiff biochemical Kinetics. BMC Syst Biol (2010) 0.82

The role of feedback control mechanisms on the establishment of oscillatory regimes in the Ras/cAMP/PKA pathway in S. cerevisiae. EURASIP J Bioinform Syst Biol (2012) 0.82

Fast stochastic algorithm for simulating evolutionary population dynamics. Bioinformatics (2012) 0.81

Modeling delay in genetic networks: from delay birth-death processes to delay stochastic differential equations. J Chem Phys (2014) 0.81

Exact and approximate stochastic simulation of intracellular calcium dynamics. J Biomed Biotechnol (2011) 0.81

cuTauLeaping: a GPU-powered tau-leaping stochastic simulator for massive parallel analyses of biological systems. PLoS One (2014) 0.81

Stochastic dynamics of interacting haematopoietic stem cell niche lineages. PLoS Comput Biol (2014) 0.80

Stiffness detection and reduction in discrete stochastic simulation of biochemical systems. J Chem Phys (2011) 0.80

Role of intracellular stochasticity in biofilm growth. Insights from population balance modeling. PLoS One (2013) 0.79

Stochastic reaction-diffusion processes with embedded lower-dimensional structures. Bull Math Biol (2013) 0.79

A higher-order numerical framework for stochastic simulation of chemical reaction systems. BMC Syst Biol (2012) 0.79

Parallel solutions for voxel-based simulations of reaction-diffusion systems. Biomed Res Int (2014) 0.79

In vivo and in silico analysis of PCNA ubiquitylation in the activation of the Post Replication Repair pathway in S. cerevisiae. BMC Syst Biol (2013) 0.78

On speeding up stochastic simulations by parallelization of random number generation. Chem Eng Sci (2015) 0.78

Stochastic operator-splitting method for reaction-diffusion systems. J Chem Phys (2012) 0.78

Improved spatial direct method with gradient-based diffusion to retain full diffusive fluctuations. J Chem Phys (2012) 0.77

Stochasticity in Ca2+ increase in spines enables robust and sensitive information coding. PLoS One (2014) 0.77

Noise propagation with interlinked feed-forward pathways. Sci Rep (2016) 0.77

Efficient simulation of stochastic chemical kinetics with the Stochastic Bulirsch-Stoer extrapolation method. BMC Syst Biol (2014) 0.77

Lazy Updating of hubs can enable more realistic models by speeding up stochastic simulations. J Chem Phys (2014) 0.76

Parametric sensitivity analysis for biochemical reaction networks based on pathwise information theory. BMC Bioinformatics (2013) 0.76

The emergence of resistance to fungicides. PLoS One (2014) 0.76

Discrete-continuous reaction-diffusion model with mobile point-like sources and sinks. Eur Phys J E Soft Matter (2016) 0.76

A Hybrid of the Chemical Master Equation and the Gillespie Algorithm for Efficient Stochastic Simulations of Sub-Networks. PLoS One (2016) 0.76

BCG-mediated bladder cancer immunotherapy: identifying determinants of treatment response using a calibrated mathematical model. PLoS One (2013) 0.76

Asynchronous τ-leaping. J Chem Phys (2016) 0.76

Adaptive deployment of model reductions for tau-leaping simulation. J Chem Phys (2015) 0.75

Small-Volume Effect Enables Robust, Sensitive, and Efficient Information Transfer in the Spine. Biophys J (2017) 0.75

An efficient and unbiased method for sensitivity analysis of stochastic reaction networks. J R Soc Interface (2014) 0.75

A hierarchical exact accelerated stochastic simulation algorithm. J Chem Phys (2012) 0.75

Stochastic chemical kinetics : A review of the modelling and simulation approaches. Biophys Rev (2013) 0.75

Weighted next reaction method and parameter selection for efficient simulation of rare events in biochemical reaction systems. EURASIP J Bioinform Syst Biol (2011) 0.75

Using model-based proposals for fast parameter inference on discrete state space, continuous-time Markov processes. J R Soc Interface (2015) 0.75

Massive exploration of perturbed conditions of the blood coagulation cascade through GPU parallelization. Biomed Res Int (2014) 0.75

Stochastic representations of ion channel kinetics and exact stochastic simulation of neuronal dynamics. J Comput Neurosci (2014) 0.75

COPASI and its Applications in Biotechnology. J Biotechnol (2017) 0.75

Articles by these authors

The slow-scale stochastic simulation algorithm. J Chem Phys (2005) 2.68

Avoiding negative populations in explicit Poisson tau-leaping. J Chem Phys (2005) 2.22

Refining the weighted stochastic simulation algorithm. J Chem Phys (2009) 1.58

StochKit2: software for discrete stochastic simulation of biochemical systems with events. Bioinformatics (2011) 1.52

Adaptive explicit-implicit tau-leaping method with automatic tau selection. J Chem Phys (2007) 1.48

Algorithms and software for stochastic simulation of biochemical reacting systems. Biotechnol Prog (2007) 1.45

The multinomial simulation algorithm for discrete stochastic simulation of reaction-diffusion systems. J Chem Phys (2009) 1.38

Automated estimation of rare event probabilities in biochemical systems. J Chem Phys (2011) 1.28

Effect of reactant size on discrete stochastic chemical kinetics. J Chem Phys (2007) 1.23

The subtle business of model reduction for stochastic chemical kinetics. J Chem Phys (2009) 1.21

A neuropeptide speeds circadian entrainment by reducing intercellular synchrony. Proc Natl Acad Sci U S A (2013) 1.19

Accelerated stochastic simulation of the stiff enzyme-substrate reaction. J Chem Phys (2005) 1.17

Perspective: Stochastic algorithms for chemical kinetics. J Chem Phys (2013) 1.16

The numerical stability of leaping methods for stochastic simulation of chemically reacting systems. J Chem Phys (2004) 1.09

Wavelet measurement suggests cause of period instability in mammalian circadian neurons. J Biol Rhythms (2011) 1.04

State-dependent biasing method for importance sampling in the weighted stochastic simulation algorithm. J Chem Phys (2010) 1.03

Accelerated maximum likelihood parameter estimation for stochastic biochemical systems. BMC Bioinformatics (2012) 1.02

Synchrony and entrainment properties of robust circadian oscillators. J R Soc Interface (2008) 0.99

Sensitivity Measures for Oscillating Systems: Application to Mammalian Circadian Gene Network. IEEE Trans Automat Contr (2008) 0.98

Effect of excluded volume on 2D discrete stochastic chemical kinetics. J Comput Phys (2009) 0.96

State-dependent doubly weighted stochastic simulation algorithm for automatic characterization of stochastic biochemical rare events. J Chem Phys (2011) 0.91

Velocity response curves support the role of continuous entrainment in circadian clocks. J Biol Rhythms (2010) 0.88

WAVOS: a MATLAB toolkit for wavelet analysis and visualization of oscillatory systems. BMC Res Notes (2012) 0.86

Oscillator model reduction preserving the phase response: application to the circadian clock. Biophys J (2008) 0.84

Core module biomarker identification with network exploration for breast cancer metastasis. BMC Bioinformatics (2012) 0.84

Confidence from uncertainty--a multi-target drug screening method from robust control theory. BMC Syst Biol (2010) 0.79

Systems biology approach to understanding post-traumatic stress disorder. Mol Biosyst (2015) 0.75