Articles citing this article

The Citing articles tool gives a list of articles citing the current article.
The citing articles come from EDP Sciences database, as well as other publishers participating in CrossRef Cited-by Linking Program. You can set up your personal account to receive an email alert each time this article is cited by a new article (see the menu on the right-hand side of the abstract page).

Cited article:

This article has been cited by the following article(s):

Superresolution Modeling of Calcium Release in the Heart

Mark A. Walker, George S.B. Williams, Tobias Kohl, et al.
Biophysical Journal 107 (12) 3018 (2014)
DOI: 10.1016/j.bpj.2014.11.003
See this article

Solution of the chemical master equation by radial basis functions approximation with interface tracking

Ivan Kryven, Susanna Röblitz and Christof Schütte
BMC Systems Biology 9 (1) (2015)
DOI: 10.1186/s12918-015-0210-y
See this article

Reference Module in Biomedical Sciences

K.S. Ramos, M. Martin, I.N. Ramos and G.A. Rempala
Reference Module in Biomedical Sciences (2016)
DOI: 10.1016/B978-0-12-801238-3.99176-1
See this article

The Interplay of Intrinsic and Extrinsic Bounded Noises in Biomolecular Networks

Giulio Caravagna, Giancarlo Mauri, Alberto d'Onofrio and Bin Xue
PLoS ONE 8 (2) e51174 (2013)
DOI: 10.1371/journal.pone.0051174
See this article

Hybrid stochastic simulations of intracellular reaction–diffusion systems

Georgios Kalantzis
Computational Biology and Chemistry 33 (3) 205 (2009)
DOI: 10.1016/j.compbiolchem.2009.03.002
See this article

Modeling and Simulation of Low-Frequency Noise in Nano Devices: Stochastically Correct and Carefully Crafted Numerical Techniques

A. Gokcen Mahmutoglu and Alper Demir
IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems 34 (5) 794 (2015)
DOI: 10.1109/TCAD.2014.2376985
See this article

The interplay of climate, intervention and imported cases as determinants of the 2014 dengue outbreak in Guangzhou

Qu Cheng, Qinlong Jing, Robert C. Spear, et al.
PLOS Neglected Tropical Diseases 11 (6) e0005701 (2017)
DOI: 10.1371/journal.pntd.0005701
See this article

Stochasticity of Intranuclear Biochemical Reaction Processes Controls the Final Decision of Cell Fate Associated with DNA Damage

Kazunari Iwamoto, Hiroyuki Hamada, Yukihiro Eguchi, Masahiro Okamoto and Thomas G. Hofmann
PLoS ONE 9 (7) e101333 (2014)
DOI: 10.1371/journal.pone.0101333
See this article

Estimating HIV-1 Fitness Characteristics from Cross-Sectional Genotype Data

Sathej Gopalakrishnan, Hesam Montazeri, Stephan Menz, et al.
PLoS Computational Biology 10 (11) e1003886 (2014)
DOI: 10.1371/journal.pcbi.1003886
See this article

Hybrid Stochastic and Deterministic Simulations of Calcium Blips

S. Rüdiger, J.W. Shuai, W. Huisinga, et al.
Biophysical Journal 93 (6) 1847 (2007)
DOI: 10.1529/biophysj.106.099879
See this article

Hybrid Systems Biology

Mostafa Herajy and Monika Heiner
Lecture Notes in Computer Science, Hybrid Systems Biology 9957 20 (2016)
DOI: 10.1007/978-3-319-47151-8_2
See this article

Microdomain [Ca2+] Fluctuations Alter Temporal Dynamics in Models of Ca2+-Dependent Signaling Cascades and Synaptic Vesicle Release

Seth H. Weinberg
Neural Computation 28 (3) 493 (2016)
DOI: 10.1162/NECO_a_00811
See this article

Almost sure convergence of numerical approximations for Piecewise Deterministic Markov Processes

Martin G. Riedler
Journal of Computational and Applied Mathematics 239 50 (2013)
DOI: 10.1016/
See this article

Hybrid deterministic/stochastic algorithm for large sets of rate equations

M. Gherardi, T. Jourdan, S. Le Bourdiec and G. Bencteux
Computer Physics Communications 183 (9) 1966 (2012)
DOI: 10.1016/j.cpc.2012.04.020
See this article

Hybrid representation and simulation of stiff biochemical networks

Mostafa Herajy and Monika Heiner
Nonlinear Analysis: Hybrid Systems 6 (4) 942 (2012)
DOI: 10.1016/j.nahs.2012.05.004
See this article

Drug-Class Specific Impact of Antivirals on the Reproductive Capacity of HIV

Max von Kleist, Stephan Menz, Wilhelm Huisinga and Niko Beerenwinkel
PLoS Computational Biology 6 (3) e1000720 (2010)
DOI: 10.1371/journal.pcbi.1000720
See this article

A Hybrid of the Chemical Master Equation and the Gillespie Algorithm for Efficient Stochastic Simulations of Sub-Networks

Jaroslav Albert and Ramon Grima
PLOS ONE 11 (3) e0149909 (2016)
DOI: 10.1371/journal.pone.0149909
See this article

Quantitative spatial analysis of transcripts in multinucleate cells using single-molecule FISH

ChangHwan Lee, Samantha E. Roberts and Amy S. Gladfelter
Methods 98 124 (2016)
DOI: 10.1016/j.ymeth.2015.12.007
See this article

The Digital Patient

Seth H. Weinberg
The Digital Patient 85 (2016)
DOI: 10.1002/9781118952788.ch8
See this article

Stochastic models of intracellular calcium signals

Sten Rüdiger
Physics Reports 534 (2) 39 (2014)
DOI: 10.1016/j.physrep.2013.09.002
See this article

Adaptive Discrete Galerkin Methods Applied to the Chemical Master Equation

P. Deuflhard, W. Huisinga, T. Jahnke and M. Wulkow
SIAM Journal on Scientific Computing 30 (6) 2990 (2008)
DOI: 10.1137/070689759
See this article

Numerical Approach to Spatial Deterministic-Stochastic Models Arising in Cell Biology

James C. Schaff, Fei Gao, Ye Li, et al.
PLOS Computational Biology 12 (12) e1005236 (2016)
DOI: 10.1371/journal.pcbi.1005236
See this article

HIV Quasispecies Dynamics during Pro-Active Treatment Switching: Impact on Multi-Drug Resistance and Resistance Archiving in Latent Reservoirs

Max von Kleist, Stephan Menz, Hartmut Stocker, et al.
PLoS ONE 6 (3) e18204 (2011)
DOI: 10.1371/journal.pone.0018204
See this article

Modeling cellular compartmentation in one-carbon metabolism

Marco Scotti, Lorenzo Stella, Emily J. Shearer and Patrick J. Stover
Wiley Interdisciplinary Reviews: Systems Biology and Medicine 5 (3) 343 (2013)
DOI: 10.1002/wsbm.1209
See this article

Mechanotransduction Dynamics at the Cell-Matrix Interface

Seth H. Weinberg, Devin B. Mair and Christopher A. Lemmon
Biophysical Journal 112 (9) 1962 (2017)
DOI: 10.1016/j.bpj.2017.02.027
See this article

Hybrid semantics for Bio-PEPA

Vashti Galpin
Information and Computation 236 122 (2014)
DOI: 10.1016/j.ic.2014.01.016
See this article

Approaches to in vitro tissue regeneration with application for human disease modeling and drug development

Mohammad R. Ebrahimkhani, Carissa L. Young, Douglas A. Lauffenburger, Linda G. Griffith and Jeffrey T. Borenstein
Drug Discovery Today 19 (6) 754 (2014)
DOI: 10.1016/j.drudis.2014.04.017
See this article

Stefanie Winkelmann and Christof Schütte
37 (2020)
DOI: 10.1007/978-3-030-62387-6_2
See this article

Alexander Andreychenko, Thilo Krüger and David Spieler
8453 1 (2014)
DOI: 10.1007/978-3-662-45489-3_1
See this article

Stochastic Hybrid Automata with delayed transitions to model biochemical systems with delays

Giulio Caravagna, Alberto d'Onofrio, Marco Antoniotti and Giancarlo Mauri
Information and Computation 236 19 (2014)
DOI: 10.1016/j.ic.2014.01.010
See this article

Exact Simulation of the Jump Times of a Class of Piecewise Deterministic Markov Processes

Vincent Lemaire, Michèle Thieullen and Nicolas Thomas
Journal of Scientific Computing 75 (3) 1776 (2018)
DOI: 10.1007/s10915-017-0607-4
See this article

Origin of Self-Replicating Biopolymers: Autocatalytic Feedback Can Jump-Start the RNA World

Meng Wu and Paul G. Higgs
Journal of Molecular Evolution 69 (5) 541 (2009)
DOI: 10.1007/s00239-009-9276-8
See this article

Eradication-resolution dynamics with stochastic flare-ups

Hugo A. van den Berg and Zoe A. Duncombe
Journal of Theoretical Biology 264 (3) 962 (2010)
DOI: 10.1016/j.jtbi.2010.03.010
See this article

Tumour suppression by immune system through stochastic oscillations

Giulio Caravagna, Alberto d’Onofrio, Paolo Milazzo and Roberto Barbuti
Journal of Theoretical Biology 265 (3) 336 (2010)
DOI: 10.1016/j.jtbi.2010.05.013
See this article

Convergence of stochastic gene networks to hybrid piecewise deterministic processes

A. Crudu, A. Debussche, A. Muller and O. Radulescu
The Annals of Applied Probability 22 (5) (2012)
DOI: 10.1214/11-AAP814
See this article

Bayesian inference for hybrid discrete-continuous stochastic kinetic models

Chris Sherlock, Andrew Golightly and Colin S Gillespie
Inverse Problems 30 (11) 114005 (2014)
DOI: 10.1088/0266-5611/30/11/114005
See this article

T.S. Kalbfleisch, G.A. Rempala and K.S. Ramos
641 (2010)
DOI: 10.1016/B978-0-08-046884-6.00236-0
See this article

Hybrid models for chemical reaction networks: Multiscale theory and application to gene regulatory systems

Stefanie Winkelmann and Christof Schütte
The Journal of Chemical Physics 147 (11) 114115 (2017)
DOI: 10.1063/1.4986560
See this article

Efficient simulation of discrete stochastic reaction systems with a splitting method

Tobias Jahnke and Derya Altıntan
BIT Numerical Mathematics 50 (4) 797 (2010)
DOI: 10.1007/s10543-010-0286-0
See this article

Katherine Chiang, François Fages, Jie-Hong Jiang and Sylvain Soliman
8130 192 (2013)
DOI: 10.1007/978-3-642-40708-6_15
See this article

Giulio Caravagna, Giancarlo Mauri and Alberto d’Onofrio
201 (2013)
DOI: 10.1007/978-1-4614-7385-5_13
See this article

Information transfer in signaling pathways: A study using coupled simulated and experimental data

Jürgen Pahle, Anne K Green, C Jane Dixon and Ursula Kummer
BMC Bioinformatics 9 (1) (2008)
DOI: 10.1186/1471-2105-9-139
See this article

Modeling of Chemical Reaction Systems with Detailed Balance Using Gradient Structures

Jan Maas and Alexander Mielke
Journal of Statistical Physics 181 (6) 2257 (2020)
DOI: 10.1007/s10955-020-02663-4
See this article

A Dynamical Low-Rank Approach to the Chemical Master Equation

Tobias Jahnke and Wilhelm Huisinga
Bulletin of Mathematical Biology 70 (8) 2283 (2008)
DOI: 10.1007/s11538-008-9346-x
See this article

Stochastic modelling for quantitative description of heterogeneous biological systems

Darren J. Wilkinson
Nature Reviews Genetics 10 (2) 122 (2009)
DOI: 10.1038/nrg2509
See this article

Andrew Golightly and Colin S. Gillespie
1021 169 (2013)
DOI: 10.1007/978-1-62703-450-0_9
See this article

Sven Sahle, Ralph Gauges, Jurgen Pahle, Natalia Simus, Ursula Kummer, Stefan Hoops, Christine Lee, Mudita Singhal, Liang Xu and Pedro Mendes
1698 (2006)
DOI: 10.1109/WSC.2006.322945
See this article

Arnab Ganguly, Derya Altintan and Heinz Koeppl
787 (2015)
DOI: 10.1109/ACC.2015.7170830
See this article

From in vivo to in silico biology and back

Barbara Di Ventura, Caroline Lemerle, Konstantinos Michalodimitrakis and Luis Serrano
Nature 443 (7111) 527 (2006)
DOI: 10.1038/nature05127
See this article

Stochastic representations of ion channel kinetics and exact stochastic simulation of neuronal dynamics

David F. Anderson, Bard Ermentrout and Peter J. Thomas
Journal of Computational Neuroscience 38 (1) 67 (2015)
DOI: 10.1007/s10827-014-0528-2
See this article

Stochastic simulation algorithms for computational systems biology: Exact, approximate, and hybrid methods

Giulia Simoni, Federico Reali, Corrado Priami and Luca Marchetti
Wiley Interdisciplinary Reviews: Systems Biology and Medicine 11 (6) (2019)
DOI: 10.1002/wsbm.1459
See this article

Sten Rüdiger and Jianwei Shuai
91 (2019)
DOI: 10.1007/978-3-030-00817-8_4
See this article

COPASI--a COmplex PAthway SImulator

S. Hoops, S. Sahle, R. Gauges, C. Lee, J. Pahle, N. Simus, M. Singhal, L. Xu, P. Mendes and U. Kummer
Bioinformatics 22 (24) 3067 (2006)
DOI: 10.1093/bioinformatics/btl485
See this article

Biochemical simulations: stochastic, approximate stochastic and hybrid approaches

J. Pahle
Briefings in Bioinformatics 10 (1) 53 (2008)
DOI: 10.1093/bib/bbn050
See this article

A. Gokcen Mahmutoglu, Alper Demir and Jaijeet Roychowdhury
500 (2013)
DOI: 10.1109/ICCAD.2013.6691163
See this article

Stochastic simulation of calcium microdomains in the vicinity of an L-type calcium channel

Frederic von Wegner and R. H. A. Fink
European Biophysics Journal 39 (7) 1079 (2010)
DOI: 10.1007/s00249-009-0504-3
See this article

Simulating biological processes: stochastic physics from whole cells to colonies

Tyler M Earnest, John A Cole and Zaida Luthey-Schulten
Reports on Progress in Physics 81 (5) 052601 (2018)
DOI: 10.1088/1361-6633/aaae2c
See this article

Stochastic Simulation of Imperfect Mixing in Free Radical Polymerization

Hugo F. Hernandez and Klaus Tauer
Macromolecular Symposia 271 (1) 64 (2008)
DOI: 10.1002/masy.200851107
See this article

Hybrid Simulations of Heterogeneous Biochemical Models in SBML

Hui Ju K. Chiang, François Fages, Jie Hong R. Jiang and Sylvain Soliman
ACM Transactions on Modeling and Computer Simulation 25 (2) 1 (2015)
DOI: 10.1145/2742545
See this article

Modeling the evolution of a classic genetic switch

Christos Josephides and Alan M Moses
BMC Systems Biology 5 (1) (2011)
DOI: 10.1186/1752-0509-5-24
See this article

Adaptive space and time numerical simulation of reaction–diffusion models for intracellular calcium dynamics

Ch. Nagaiah, S. Rüdiger, G. Warnecke and M. Falcke
Applied Mathematics and Computation 218 (20) 10194 (2012)
DOI: 10.1016/j.amc.2012.03.100
See this article

Model reduction for stochastic chemical systems with abundant species

Stephen Smith, Claudia Cianci and Ramon Grima
The Journal of Chemical Physics 143 (21) 214105 (2015)
DOI: 10.1063/1.4936394
See this article

Hybrid CME–ODE method for efficient simulation of the galactose switch in yeast

David M. Bianchi, Joseph R. Peterson, Tyler M. Earnest, Michael J. Hallock and Zaida Luthey‐Schulten
IET Systems Biology 12 (4) 170 (2018)
DOI: 10.1049/iet-syb.2017.0070
See this article

Regularity and stability for the semigroup of jump diffusions with state-dependent intensity

Vlad Bally, Dan Goreac and Victor Rabiet
The Annals of Applied Probability 28 (5) (2018)
DOI: 10.1214/18-AAP1382
See this article

Solving the chemical master equation for monomolecular reaction systems analytically

Tobias Jahnke and Wilhelm Huisinga
Journal of Mathematical Biology 54 (1) 1 (2006)
DOI: 10.1007/s00285-006-0034-x
See this article

Hybrid and Hybrid Adaptive Petri Nets: On the computation of a Reachability Graph

Estíbaliz Fraca, Jorge Júlvez and Manuel Silva
Nonlinear Analysis: Hybrid Systems 16 24 (2015)
DOI: 10.1016/j.nahs.2014.11.005
See this article

Path integral approach to generating functions for multistep post-transcription and post-translation processes and arbitrary initial conditions

Jaroslav Albert
Journal of Mathematical Biology 79 (6-7) 2211 (2019)
DOI: 10.1007/s00285-019-01426-4
See this article

Human mobility and innovation spreading in ancient times: a stochastic agent-based simulation approach

Nataša Djurdjevac Conrad, Luzie Helfmann, Johannes Zonker, Stefanie Winkelmann and Christof Schütte
EPJ Data Science 7 (1) (2018)
DOI: 10.1140/epjds/s13688-018-0153-9
See this article