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List of works by Linda Petzold

A framework for discrete stochastic simulation on 3D moving boundary domains

scientific article

A neuropeptide speeds circadian entrainment by reducing intercellular synchrony.

scientific article published on 28 October 2013

A top-down approach to mechanistic biological modeling: application to the single-chain antibody folding pathway

scientific article published on 18 July 2008

Accelerated maximum likelihood parameter estimation for stochastic biochemical systems

scientific article

Accelerated stochastic simulation of the stiff enzyme-substrate reaction

scientific article

Accuracy of the Michaelis-Menten approximation when analysing effects of molecular noise

scientific article published on May 2015

Adaptive deployment of model reductions for tau-leaping simulation

scientific article published on May 2015

Adaptive explicit-implicit tau-leaping method with automatic tau selection

scientific article

Algorithms and software for stochastic simulation of biochemical reacting systems

scientific article published on 26 September 2007

Automated estimation of rare event probabilities in biochemical systems

scientific article

Automatic and portable cloud deployment for scientific simulations

Automatic identification of model reductions for discrete stochastic simulation

scientific article published in July 2012

Avoiding negative populations in explicit Poisson tau-leaping

scientific article

BiP clustering facilitates protein folding in the endoplasmic reticulum

scientific article

Computational model of tranexamic acid on urokinase mediated fibrinolysis

scientific article published on 26 May 2020

Confidence from uncertainty--a multi-target drug screening method from robust control theory

scientific article

Control over single-cell distribution of G1 lengths by WNT governs pluripotency

scientific article published on 26 September 2019

Core modular blood and brain biomarkers in social defeat mouse model for post traumatic stress disorder

scientific article

Core module biomarker identification with network exploration for breast cancer metastasis

scientific article

Effect of reactant size on discrete stochastic chemical kinetics

scientific article published in January 2007

Efficient formulation of the stochastic simulation algorithm for chemically reacting systems

scientific article

Efficient step size selection for the tau-leaping simulation method

scientific article

Functional network inference of the suprachiasmatic nucleus

scientific article published on 4 April 2016

GillesPy: A Python Package for Stochastic Model Building and Simulation

scientific article

Identification of dynamic mass-action biochemical reaction networks using sparse Bayesian methods

scientific article published on 31 January 2022

Local error estimates for adaptive simulation of the Reaction-Diffusion Master Equation via operator splitting

scientific article published on June 2014

MOLNs: A CLOUD PLATFORM FOR INTERACTIVE, REPRODUCIBLE, AND SCALABLE SPATIAL STOCHASTIC COMPUTATIONAL EXPERIMENTS IN SYSTEMS BIOLOGY USING PyURDME.

scientific article published on June 2016

Macromolecular Crowding Regulates the Gene Expression Profile by Limiting Diffusion

scientific article

Mechanical feedback coordinates cell wall expansion and assembly in yeast mating morphogenesis.

scientific article published on 18 January 2018

Mesoscopic-microscopic spatial stochastic simulation with automatic system partitioning.

scientific article

Michaelis-Menten speeds up tau-leaping under a wide range of conditions

scientific article

On the Inference of Functional Circadian Networks Using Granger Causality

scientific article published on 28 September 2015

Ontogeny of circadian rhythms and synchrony in the suprachiasmatic nucleus

scientific article published on 20 October 2017

Oscillator model reduction preserving the phase response: application to the circadian clock

scientific article published on 16 May 2008

Perspective: Stochastic algorithms for chemical kinetics

scientific article published on May 2013

Reaction rates for a generalized reaction-diffusion master equation ⬇️

scientific article published on 19 January 2016

Reaction rates for mesoscopic reaction-diffusion kinetics ⬇️

scientific article published on 23 February 2015

Reaction rates for reaction-diffusion kinetics on unstructured meshes ⬇️

scientific article

Reaction-diffusion master equation in the microscopic limit

scientific article published on 03 April 2012

Reducing Complexity in Management of eScience Computations

Refining the weighted stochastic simulation algorithm

scientific article

Sensitivity Measures for Oscillating Systems: Application to Mammalian Circadian Gene Network

scientific article published on January 2008

Sensitivity analysis of discrete stochastic systems

scientific article published on 4 February 2005

Spatial stochastic dynamics enable robust cell polarization

scientific article

State-dependent biasing method for importance sampling in the weighted stochastic simulation algorithm. ⬇️

scientific article

State-dependent doubly weighted stochastic simulation algorithm for automatic characterization of stochastic biochemical rare events.

scientific article published on December 2011

Stiffness in stochastic chemically reacting systems: The implicit tau-leaping method

article by Muruhan Rathinam et al published 22 December 2003 in Journal of Chemical Physics

StochKit2: software for discrete stochastic simulation of biochemical systems with events

scientific article

Stochastic Simulation Service: Bridging the Gap between the Computational Expert and the Biologist

scientific article

Synchrony and entrainment properties of robust circadian oscillators

scientific article published on August 2008

Systems biology approach to understanding post-traumatic stress disorder

scientific article

The Role of Chromatin Density in Cell Population Heterogeneity during Stem Cell Differentiation

scientific article published on 17 October 2017

The Time Dependent Propensity Function for Acceleration of Spatial Stochastic Simulation of Reaction-Diffusion Systems.

scientific article published in October 2014

The diffusive finite state projection algorithm for efficient simulation of the stochastic reaction-diffusion master equation

scientific article

The effect of cell geometry on polarization in budding yeast.

scientific article published on 11 June 2018

The multinomial simulation algorithm for discrete stochastic simulation of reaction-diffusion systems

scientific article published on March 2009

The numerical stability of leaping methods for stochastic simulation of chemically reacting systems

scientific article published in December 2004

The role of dimerisation and nuclear transport in the Hes1 gene regulatory network

scientific article published on 18 May 2013

The slow-scale stochastic simulation algorithm.

scientific article published in January 2005

The subtle business of model reduction for stochastic chemical kinetics

scientific article published on February 2009

Using stochastic epidemiological models to evaluate conservation strategies for endangered amphibians

scientific article published on August 2017

Validation data for a hybrid smoothed dissipative particle dynamics (SDPD) spatial stochastic simulation algorithm (sSSA) method

Validity conditions for stochastic chemical kinetics in diffusion-limited systems

scientific article published on February 2014

Velocity response curves support the role of continuous entrainment in circadian clocks

scientific article published in April 2010

WAVOS: a MATLAB toolkit for wavelet analysis and visualization of oscillatory systems

scientific article published on 26 March 2012

Wavelet measurement suggests cause of period instability in mammalian circadian neurons

scientific article published on August 2011

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