Adkins CE, Taylor CW. (1999). Lateral inhibition of inositol 1,4,5-trisphosphate receptors by cytosolic Ca(2+). Current biology : CB. 9 [PubMed]
Amari S et al. (2002). Neuroinformatics: the integration of shared databases and tools towards integrative neuroscience. Journal of integrative neuroscience. 1 [PubMed]
Banerjee S, Hasan G. (2005). The InsP3 receptor: its role in neuronal physiology and neurodegeneration. BioEssays : news and reviews in molecular, cellular and developmental biology. 27 [PubMed]
Barbara JG. (2002). IP3-dependent calcium-induced calcium release mediates bidirectional calcium waves in neurones: functional implications for synaptic plasticity. Biochimica et biophysica acta. 1600 [PubMed]
Barrio M, Burrage K, Leier A, Tian T. (2006). Oscillatory regulation of Hes1: Discrete stochastic delay modelling and simulation. PLoS computational biology. 2 [PubMed]
Bezprozvanny I, Ehrlich BE. (1994). Inositol (1,4,5)-trisphosphate (InsP3)-gated Ca channels from cerebellum: conduction properties for divalent cations and regulation by intraluminal calcium. The Journal of general physiology. 104 [PubMed]
Bezprozvanny I, Watras J, Ehrlich BE. (1991). Bell-shaped calcium-response curves of Ins(1,4,5)P3- and calcium-gated channels from endoplasmic reticulum of cerebellum. Nature. 351 [PubMed]
Bliss TV, Collingridge GL. (1993). A synaptic model of memory: long-term potentiation in the hippocampus. Nature. 361 [PubMed]
Cannon RC, Howell FW, Goddard NH, De Schutter E. (2002). Non-curated distributed databases for experimental data and models in neuroscience. Network (Bristol, England). 13 [PubMed]
Cannon RC, O'Donnell C, Nolan MF. (2010). Stochastic ion channel gating in dendritic neurons: morphology dependence and probabilistic synaptic activation of dendritic spikes. PLoS computational biology. 6 [PubMed]
Choi T, Maurya MR, Tartakovsky DM, Subramaniam S. (2010). Stochastic hybrid modeling of intracellular calcium dynamics. The Journal of chemical physics. 133 [PubMed]
Citri A, Malenka RC. (2008). Synaptic plasticity: multiple forms, functions, and mechanisms. Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology. 33 [PubMed]
Collingridge GL, Peineau S, Howland JG, Wang YT. (2010). Long-term depression in the CNS. Nature reviews. Neuroscience. 11 [PubMed]
Dawson AP, Lea EJ, Irvine RF. (2003). Kinetic model of the inositol trisphosphate receptor that shows both steady-state and quantal patterns of Ca2+ release from intracellular stores. The Biochemical journal. 370 [PubMed]
Dawson SP, Fraiman D. (2004). Erratum to "a model of IP3 receptor with a luminal calcium binding site: stochastic simulations and analysis" Cell Calcium. 36
De Schutter E. (2008). Why are computational neuroscience and systems biology so separate? PLoS computational biology. 4 [PubMed]
De Schutter E. (2010). Data publishing and scientific journals: the future of the scientific paper in a world of shared data. Neuroinformatics. 8 [PubMed]
De Young GW, Keizer J. (1992). A single-pool inositol 1,4,5-trisphosphate-receptor-based model for agonist-stimulated oscillations in Ca2+ concentration. Proceedings of the National Academy of Sciences of the United States of America. 89 [PubMed]
Dellis O et al. (2006). Ca2+ entry through plasma membrane IP3 receptors. Science (New York, N.Y.). 313 [PubMed]
Diambra L, Guisoni N. (2005). Modeling stochastic Ca2+ release from a cluster of IP3-sensitive receptors. Cell calcium. 37 [PubMed]
Doi T, Kuroda S, Michikawa T, Kawato M. (2005). Inositol 1,4,5-trisphosphate-dependent Ca2+ threshold dynamics detect spike timing in cerebellar Purkinje cells. The Journal of neuroscience : the official journal of the Society for Neuroscience. 25 [PubMed]
Dufour JF, Arias IM, Turner TJ. (1997). Inositol 1,4,5-trisphosphate and calcium regulate the calcium channel function of the hepatic inositol 1,4,5-trisphosphate receptor. The Journal of biological chemistry. 272 [PubMed]
Ehrlich BE, Watras J. (1988). Inositol 1,4,5-trisphosphate activates a channel from smooth muscle sarcoplasmic reticulum. Nature. 336 [PubMed]
Eungdamrong NJ, Iyengar R. (2004). Modeling cell signaling networks. Biology of the cell. 96 [PubMed]
Faisal AA, Laughlin SB. (2007). Stochastic simulations on the reliability of action potential propagation in thin axons. PLoS computational biology. 3 [PubMed]
Falcke M. (2003). On the role of stochastic channel behavior in intracellular Ca2+ dynamics. Biophysical journal. 84 [PubMed]
Foskett JK. (2010). Inositol trisphosphate receptor Ca2+ release channels in neurological diseases. Pflugers Archiv : European journal of physiology. 460 [PubMed]
Foskett JK, White C, Cheung KH, Mak DO. (2007). Inositol trisphosphate receptor Ca2+ release channels. Physiological reviews. 87 [PubMed]
Fraiman D, Dawson SP. (2004). A model of IP3 receptor with a luminal calcium binding site: stochastic simulations and analysis. Cell calcium. 35 [PubMed]
Franks KM, Sejnowski TJ. (2002). Complexity of calcium signaling in synaptic spines. BioEssays : news and reviews in molecular, cellular and developmental biology. 24 [PubMed]
Fujiwara A, Hirose K, Yamazawa T, Iino M. (2001). Reduced IP3 sensitivity of IP3 receptor in Purkinje neurons. Neuroreport. 12 [PubMed]
Gillespie DT. (1976). A General method for numerically simulating the stochastic time evolution of coupledchemical reactions J Comput Phys. 22
Gillespie DT. (1977). Exact stochastic simulation of coupled chemical reactions. Journal Of Physical Chemistry. 81
Gin E, Falcke M, Wagner LE, Yule DI, Sneyd J. (2009). Markov chain Monte Carlo fitting of single-channel data from inositol trisphosphate receptors. Journal of theoretical biology. 257 [PubMed]
Gin E, Falcke M, Wagner LE, Yule DI, Sneyd J. (2009). A kinetic model of the inositol trisphosphate receptor based on single-channel data. Biophysical journal. 96 [PubMed]
Gin E, Wagner LE, Yule DI, Sneyd J. (2009). Inositol trisphosphate receptor and ion channel models based on single-channel data. Chaos (Woodbury, N.Y.). 19 [PubMed]
Girolami M. (2008). Bayesian inference for differential equations Theor Comput Sci. 408
Haeri HH, Hashemianzadeh SM, Monajjemi M. (2007). A kinetic Monte Carlo simulation study of inositol 1,4,5-trisphosphate receptor (IP3R) calcium release channel. Computational biology and chemistry. 31 [PubMed]
Hepburn I, Chen W, Wils S, De Schutter E. (2012). STEPS: efficient simulation of stochastic reaction-diffusion models in realistic morphologies. BMC systems biology. 6 [PubMed]
Ito M. (2002). The molecular organization of cerebellar long-term depression. Nature reviews. Neuroscience. 3 [PubMed]
Kaftan EJ, Ehrlich BE, Watras J. (1997). Inositol 1,4,5-trisphosphate (InsP3) and calcium interact to increase the dynamic range of InsP3 receptor-dependent calcium signaling. The Journal of general physiology. 110 [PubMed]
Kaznacheyeva E, Lupu VD, Bezprozvanny I. (1998). Single-channel properties of inositol (1,4,5)-trisphosphate receptor heterologously expressed in HEK-293 cells. The Journal of general physiology. 111 [PubMed]
Kettenmann H, Falcke M, Skupin A. (2010). Calcium signals driven by single channel noise. PLoS Comput Biol. 6
Khodakhah K, Ogden D. (1995). Fast activation and inactivation of inositol trisphosphate-evoked Ca2+ release in rat cerebellar Purkinje neurones. The Journal of physiology. 487 ( Pt 2) [PubMed]
Kotaleski JH, Blackwell KT. (2010). Modelling the molecular mechanisms of synaptic plasticity using systems biology approaches. Nature reviews. Neuroscience. 11 [PubMed]
LeBeau AP, Yule DI, Groblewski GE, Sneyd J. (1999). Agonist-dependent phosphorylation of the inositol 1,4,5-trisphosphate receptor: A possible mechanism for agonist-specific calcium oscillations in pancreatic acinar cells. The Journal of general physiology. 113 [PubMed]
Libersat F, Duch C. (2004). Mechanisms of dendritic maturation. Molecular neurobiology. 29 [PubMed]
Linne ML, De_schutter E, Achard P, Wils S, Hituri K. (2008). Stochastic modeling of inositol-1,4,5- trisphophate receptors in Purkinje cell spine Proceedings of the 5th TICSP Workshop on Computation Systems Biology (WCSB 2008). 4
Llano I, DiPolo R, Marty A. (1994). Calcium-induced calcium release in cerebellar Purkinje cells. Neuron. 12 [PubMed]
Maeda N et al. (1991). Structural and functional characterization of inositol 1,4,5-trisphosphate receptor channel from mouse cerebellum. The Journal of biological chemistry. 266 [PubMed]
Mak DO, Foskett JK. (1994). Single-channel inositol 1,4,5-trisphosphate receptor currents revealed by patch clamp of isolated Xenopus oocyte nuclei. The Journal of biological chemistry. 269 [PubMed]
Mak DO, McBride S, Foskett JK. (2001). ATP regulation of recombinant type 3 inositol 1,4,5-trisphosphate receptor gating. The Journal of general physiology. 117 [PubMed]
Mak DO, McBride SM, Foskett JK. (2003). Spontaneous channel activity of the inositol 1,4,5-trisphosphate (InsP3) receptor (InsP3R). Application of allosteric modeling to calcium and InsP3 regulation of InsP3R single-channel gating. The Journal of general physiology. 122 [PubMed]
Marchant JS, Taylor CW. (1997). Cooperative activation of IP3 receptors by sequential binding of IP3 and Ca2+ safeguards against spontaneous activity. Current biology : CB. 7 [PubMed]
Marchenko SM, Thomas RC. (2006). Nuclear Ca2+ signalling in cerebellar Purkinje neurons. Cerebellum (London, England). 5 [PubMed]
Marchenko SM, Yarotskyy VV, Kovalenko TN, Kostyuk PG, Thomas RC. (2005). Spontaneously active and InsP3-activated ion channels in cell nuclei from rat cerebellar Purkinje and granule neurones. The Journal of physiology. 565 [PubMed]
Mathworks The. (2011). MATLAB (2011) version 7.13.0.564 (R2011b).
Michaelsen K, Lohmann C. (2010). Calcium dynamics at developing synapses: mechanisms and functions. The European journal of neuroscience. 32 [PubMed]
Mishra J, Bhalla US. (2002). Simulations of inositol phosphate metabolism and its interaction with InsP(3)-mediated calcium release. Biophysical journal. 83 [PubMed]
Moraru II, Kaftan EJ, Ehrlich BE, Watras J. (1999). Regulation of type 1 inositol 1,4,5-trisphosphate-gated calcium channels by InsP3 and calcium: Simulation of single channel kinetics based on ligand binding and electrophysiological analysis. The Journal of general physiology. 113 [PubMed]
Ogasawara H, Doi T, Kawato M. (2008). Systems biology perspectives on cerebellar long-term depression. Neuro-Signals. 16 [PubMed]
Penny WD et al. (2010). Comparing families of dynamic causal models. PLoS computational biology. 6 [PubMed]
Ranjan R et al. (2011). Channelpedia: an integrative and interactive database for ion channels. Frontiers in neuroinformatics. 5 [PubMed]
Saarinen A, Linne ML, Yli-Harja O. (2008). Stochastic differential equation model for cerebellar granule cell excitability. PLoS computational biology. 4 [PubMed]
Sachs F, Qin F, Palade P. (1995). Models of Ca2+ release channel adaptation. Science (New York, N.Y.). 267 [PubMed]
Schuster S, Marhl M, Höfer T. (2002). Modelling of simple and complex calcium oscillations. From single-cell responses to intercellular signalling. European journal of biochemistry. 269 [PubMed]
Sharp AH et al. (1999). Differential cellular expression of isoforms of inositol 1,4,5-triphosphate receptors in neurons and glia in brain. The Journal of comparative neurology. 406 [PubMed]
Shuai JW, Yang DP, Pearson JE, Rüdiger S. (2009). An investigation of models of the IP3R channel in Xenopus oocyte. Chaos (Woodbury, N.Y.). 19 [PubMed]
Siekmann I et al. (2011). MCMC estimation of Markov models for ion channels. Biophysical journal. 100 [PubMed]
Sneyd J, Dufour JF. (2002). A dynamic model of the type-2 inositol trisphosphate receptor. Proceedings of the National Academy of Sciences of the United States of America. 99 [PubMed]
Sneyd J, Falcke M. (2005). Models of the inositol trisphosphate receptor. Progress in biophysics and molecular biology. 89 [PubMed]
Sneyd J, Falcke M, Dufour JF, Fox C. (2004). A comparison of three models of the inositol trisphosphate receptor. Progress in biophysics and molecular biology. 85 [PubMed]
Steinmetz PN, Manwani A, Koch C, London M, Segev I. (2000). Subthreshold voltage noise due to channel fluctuations in active neuronal membranes. Journal of computational neuroscience. 9 [PubMed]
Swillens S, Champeil P, Combettes L, Dupont G. (1998). Stochastic simulation of a single inositol 1,4,5-trisphosphate-sensitive Ca2+ channel reveals repetitive openings during 'blip-like' Ca2+ transients. Cell calcium. 23 [PubMed]
Tang Y, Othmer HG. (1993). Oscillations and waves in a model of InsP3-controlled calcium dynamics Experimental and Theoretical Advances in Biological Pattern Formation. 259
Tang Y, Stephenson JL, Othmer HG. (1996). Simplification and analysis of models of calcium dynamics based on IP3-sensitive calcium channel kinetics. Biophysical journal. 70 [PubMed]
Taufiq-Ur-Rahman, Skupin A, Falcke M, Taylor CW. (2009). Clustering of InsP3 receptors by InsP3 retunes their regulation by InsP3 and Ca2+. Nature. 458 [PubMed]
Taylor CW, da Fonseca PC, Morris EP. (2004). IP(3) receptors: the search for structure. Trends in biochemical sciences. 29 [PubMed]
Turner TE, Schnell S, Burrage K. (2004). Stochastic approaches for modelling in vivo reactions. Computational biology and chemistry. 28 [PubMed]
Wagner LE, Joseph SK, Yule DI. (2008). Regulation of single inositol 1,4,5-trisphosphate receptor channel activity by protein kinase A phosphorylation. The Journal of physiology. 586 [PubMed]
Wagner LE, Yule DI. (2012). Differential regulation of the InsP3 receptor type-1 and -2 single channel properties by InsP3, Ca²? and ATP. The Journal of physiology. 590 [PubMed]
Watras J, Bezprozvanny I, Ehrlich BE. (1991). Inositol 1,4,5-trisphosphate-gated channels in cerebellum: presence of multiple conductance states. The Journal of neuroscience : the official journal of the Society for Neuroscience. 11 [PubMed]
White JA, Klink R, Alonso A, Kay AR. (1998). Noise from voltage-gated ion channels may influence neuronal dynamics in the entorhinal cortex. Journal of neurophysiology. 80 [PubMed]
Wilkinson DJ. (2007). Bayesian methods in bioinformatics and computational systems biology. Briefings in bioinformatics. 8 [PubMed]
Wils S, De Schutter E. (2009). STEPS: Modeling and Simulating Complex Reaction-Diffusion Systems with Python. Frontiers in neuroinformatics. 3 [PubMed]
Denizot A, Arizono M, Nägerl UV, Soula H, Berry H. (2019). Simulation of calcium signaling in fine astrocytic processes: Effect of spatial properties on spontaneous activity. PLoS computational biology. 15 [PubMed]
Manninen T, Havela R, Linne M-L. (2017). Reproducibility and comparability of computational models for astrocyte calcium excitability Front. Neuroinform..