Citation Relationships

Legends: Link to a Model Reference cited by multiple papers


Mattioni M, Le Novère N (2013) Integration of biochemical and electrical signaling-multiscale model of the medium spiny neuron of the striatum. PLoS One 8:e66811 [PubMed]

   Multiscale simulation of the striatal medium spiny neuron (Mattioni & Le Novere 2013)

References and models cited by this paper

References and models that cite this paper

Allbritton NL, Meyer T, Stryer L (1992) Range of messenger action of calcium ion and inositol 1,4,5-trisphosphate. Science 258:1812-5 [PubMed]
Araya R, Eisenthal KB, Yuste R (2006) Dendritic spines linearize the summation of excitatory potentials. Proc Natl Acad Sci U S A 103:18799-804 [Journal] [PubMed]
Araya R, Jiang J, Eisenthal KB, Yuste R (2006) The spine neck filters membrane potentials. Proc Natl Acad Sci U S A 103:17961-6 [Journal] [PubMed]
Araya R, Nikolenko V, Eisenthal KB, Yuste R (2007) Sodium channels amplify spine potentials. Proc Natl Acad Sci U S A 104:12347-52 [Journal] [PubMed]
Arellano JI, Benavides-Piccione R, Defelipe J, Yuste R (2007) Ultrastructure of dendritic spines: correlation between synaptic and spine morphologies. Front Neurosci 1:131-43 [Journal] [PubMed]
Arendt KL, Royo M, Fernández-Monreal M, Knafo S, Petrok CN, Martens JR, Esteban JA (2010) PIP3 controls synaptic function by maintaining AMPA receptor clustering at the postsynaptic membrane. Nat Neurosci 13:36-44 [Journal] [PubMed]
Bacskai BJ, Hochner B, Mahaut-Smith M, Adams SR, Kaang BK, Kandel ER, Tsien RY (1993) Spatially resolved dynamics of cAMP and protein kinase A subunits in Aplysia sensory neurons. Science 260:222-6 [PubMed]
Bhalla US (2011) Multiscale interactions between chemical and electric signaling in LTP induction, LTP reversal and dendritic excitability. Neural Netw 24:943-9 [Journal] [PubMed]
   Multiscale interactions between chemical and electric signaling in LTP (Bhalla 2011) [Model]
Bloodgood BL, Giessel AJ, Sabatini BL (2009) Biphasic synaptic Ca influx arising from compartmentalized electrical signals in dendritic spines. PLoS Biol 7:e1000190 [Journal] [PubMed]
Bloodgood BL, Sabatini BL (2007) Ca(2+) signaling in dendritic spines. Curr Opin Neurobiol 17:345-51 [Journal] [PubMed]
Bower JM, Beeman D (1998) The Book Of Genesis: Exploring Realistic Neural Models With The General Neural Simulation System
Brunel N, van Rossum MC (2007) Lapicque's 1907 paper: from frogs to integrate-and-fire. Biol Cybern 97:337-9 [Journal] [PubMed]
Burger SK, Thompson DC, Ayers PW (2011) Quantum mechanics/molecular mechanics strategies for docking pose refinement: distinguishing between binders and decoys in cytochrome C peroxidase. J Chem Inf Model 51:93-101 [Journal] [PubMed]
Cao Y, Wang P, Jin X, Wang J, Yang Y (2012) Tunnel structure analysis using the multi-scale modeling method Tunnelling And Underground Space Technology 28:124-134
Carter AG, Sabatini BL (2004) State-dependent calcium signaling in dendritic spines of striatal medium spiny neurons. Neuron 44:483-93 [Journal] [PubMed]
Catterall WA (2000) Structure and regulation of voltage-gated Ca2+ channels. Annu Rev Cell Dev Biol 16:521-55 [Journal] [PubMed]
Citri A, Malenka RC (2008) Synaptic plasticity: multiple forms, functions, and mechanisms. Neuropsychopharmacology 33:18-41 [Journal] [PubMed]
Cvijovic M, Soueidan H, Sherman DJ, Klipp E, Nikolski M (2008) Exploratory simulation of cell ageing using hierarchical models. Genome Inform 21:114-25 [PubMed]
Davison A (2012) Automated capture of experiment context for easier reproducibility in computational research Computing In Science And Engineering 14:48-56
Day M, Wang Z, Ding J, An X, Ingham CA, Shering AF, Wokosin D, Ilijic E, Sun Z, Sampson AR, Mugnaini E, Deutch AY, Sesack SR, Arbuthnott GW, Surmeier DJ (2006) Selective elimination of glutamatergic synapses on striatopallidal neurons in Parkinson disease models. Nat Neurosci 9:251-9 [Journal] [PubMed]
Day M, Wokosin D, Plotkin JL, Tian X, Surmeier DJ (2008) Differential excitability and modulation of striatal medium spiny neuron dendrites. J Neurosci 28:11603-14 [Journal] [PubMed]
Desdouits F, Cheetham JJ, Huang HB, Kwon YG, da Cruz e Silva EF, Denefle P, Ehrlich ME, Nairn AC, Greengard P, Girault JA (1995) Mechanism of inhibition of protein phosphatase 1 by DARPP-32: studies with recombinant DARPP-32 and synthetic peptides. Biochem Biophys Res Commun 206:652-8 [PubMed]
Destexhe A, Babloyantz A, Sejnowski TJ (1993) Ionic mechanisms for intrinsic slow oscillations in thalamic relay neurons. Biophys J 65:1538-52 [Journal] [PubMed]
   Thalamocortical Relay cell under current clamp in high-conductance state (Zeldenrust et al 2018) [Model]
Djurfeldt M, Hjorth J, Eppler JM, Dudani N, Helias M, Potjans TC, Bhalla US, Diesmann M, Kotaleski JH, Ekeberg O (2010) Run-time interoperability between neuronal network simulators based on the MUSIC framework. Neuroinformatics 8:43-60 [Journal] [PubMed]
Ekeberg O, Djurfeldt M (2008) MUSIC multisimulation coordinator: Request for comments Nat Preced.
Fernandez E, Schiappa R, Girault JA, Le Novère N (2006) DARPP-32 is a robust integrator of dopamine and glutamate signals. PLoS Comput Biol 2:e176 [Journal] [PubMed]
Frey U, Morris RG (1997) Synaptic tagging and long-term potentiation. Nature 385:533-6 [Journal] [PubMed]
Gabriel E, Fagg GE, Bosilca G, Angskun T, Dongarra JJ, Squyres JM, Sahay V, Kambadur P, Barre (2004) Open MPI: goals, concept, and design of a next generation MPI implementation Proceedings, 11th European PVM-MPI Users' Group Meeting, Kranzlmuller D:Kacsuk P:Dongara J, ed. pp.97
Gasparini S, Magee JC (2006) State-dependent dendritic computation in hippocampal CA1 pyramidal neurons. J Neurosci 26:2088-100 [Journal] [PubMed]
Gewaltig M-O, Diesmann M (2007) NEST (Neural Simulation Tool) Scholarpedia 2:1430
Goto S, Matsukado Y, Mihara Y, Inoue N, Miyamoto E (1986) The distribution of calcineurin in rat brain by light and electron microscopic immunohistochemistry and enzyme-immunoassay. Brain Res 397:161-72 [PubMed]
Govindarajan A, Israely I, Huang SY, Tonegawa S (2011) The dendritic branch is the preferred integrative unit for protein synthesis-dependent LTP. Neuron 69:132-46 [Journal] [PubMed]
Govindarajan A, Kelleher RJ, Tonegawa S (2006) A clustered plasticity model of long-term memory engrams. Nat Rev Neurosci 7:575-83 [Journal] [PubMed]
Gropp W (2002) MPICH2: a new start for MPI implementations Proceedings of the 9th European PVM-MPI Users' Group Meeting on Recent Advances in Parallel Virtual Machine and Message Passing Interface, Kranzlmuller D:Kacsuk P:Dongara J:Volkert J, ed. pp.7
Gruber AJ, O'Donnell P (2009) Bursting activation of prefrontal cortex drives sustained up states in nucleus accumbens spiny neurons in vivo. Synapse 63:173-80 [Journal] [PubMed]
Grunditz A, Holbro N, Tian L, Zuo Y, Oertner TG (2008) Spine neck plasticity controls postsynaptic calcium signals through electrical compartmentalization. J Neurosci 28:13457-66 [Journal] [PubMed]
   Spine neck plasticity controls postsynaptic calcium signals (Grunditz et al. 2008) [Model]
Harvey CD, Yasuda R, Zhong H, Svoboda K (2008) The spread of Ras activity triggered by activation of a single dendritic spine. Science 321:136-40 [Journal] [PubMed]
Hayer A, Bhalla US (2005) Molecular switches at the synapse emerge from receptor and kinase traffic. PLoS Comput Biol 1:137-54 [Journal] [PubMed]
Hemmings HC, Nairn AC, Greengard P (1984) DARPP-32, a dopamine- and adenosine 3':5'-monophosphate-regulated neuronal phosphoprotein. II. Comparison of the kinetics of phosphorylation of DARPP-32 and phosphatase inhibitor 1. J Biol Chem 259:14491-7 [PubMed]
Holbro N, Grunditz A, Wiegert JS, Oertner TG (2010) AMPA receptors gate spine Ca(2+) transients and spike-timing-dependent potentiation. Proc Natl Acad Sci U S A 107:15975-80 [Journal] [PubMed]
Ingebritsen TS, Stewart AA, Cohen P (1983) The protein phosphatases involved in cellular regulation. 6. Measurement of type-1 and type-2 protein phosphatases in extracts of mammalian tissues; an assessment of their physiological roles. Eur J Biochem 132:297-307 [PubMed]
Ingram G, Cameron I, Hangos K (2004) Classification and analysis of integrating frameworks in multiscale modelling Chemical Engineering Science 59:2171-2187
Izhikevich EM (2003) Simple model of spiking neurons. IEEE Trans Neural Netw 14:1569-72 [Journal] [PubMed]
   Artificial neuron model (Izhikevich 2003, 2004, 2007) [Model]
Izhikevich EM, Edelman GM (2008) Large-scale model of mammalian thalamocortical systems. Proc Natl Acad Sci U S A 105:3593-8 [Journal] [PubMed]
Jackson MB, Redman SJ (2003) Calcium dynamics, buffering, and buffer saturation in the boutons of dentate granule-cell axons in the hilus. J Neurosci 23:1612-21 [PubMed]
Karr JR, Sanghvi JC, Macklin DN, Gutschow MV, Jacobs JM, Bolival B, Assad-Garcia N, Glass JI, Covert MW (2012) A whole-cell computational model predicts phenotype from genotype. Cell 150:389-401 [Journal] [PubMed]
Kessels HW, Malinow R (2009) Synaptic AMPA receptor plasticity and behavior. Neuron 61:340-50 [Journal] [PubMed]
King MM, Huang CY, Chock PB, Nairn AC, Hemmings HC, Chan KF, Greengard P (1984) Mammalian brain phosphoproteins as substrates for calcineurin. J Biol Chem 259:8080-3 [PubMed]
Kotaleski JH, Blackwell KT (2010) Modelling the molecular mechanisms of synaptic plasticity using systems biology approaches. Nat Rev Neurosci 11:239-51 [Journal] [PubMed]
Le Novère N (2006) Model storage, exchange and integration. BMC Neurosci 7 Suppl 1:S11 [Journal] [PubMed]
Lee SJ, Yasuda R (2009) Spatiotemporal Regulation of Signaling in and out of Dendritic Spines: CaMKII and Ras. Open Neurosci J 3:117-127 [Journal] [PubMed]
Li L, Stefan MI, Le Novère N (2012) Calcium input frequency, duration and amplitude differentially modulate the relative activation of calcineurin and CaMKII. PLoS One 7:e43810 [Journal] [PubMed]
Lisman JE, Raghavachari S, Tsien RW (2007) The sequence of events that underlie quantal transmission at central glutamatergic synapses. Nat Rev Neurosci 8:597-609 [Journal] [PubMed]
Lu Li (2010) Modelling Dopamine and Glutamate Signal Integration Inuence on Neuronadaptation Ph.D. thesis, University of Cambridge
Lucic V, Greif GJ, Kennedy MB (2008) Detailed state model of CaMKII activation and autophosphorylation. Eur Biophys J 38:83-98 [Journal] [PubMed]
Machné R, Finney A, Müller S, Lu J, Widder S, Flamm C (2006) The SBML ODE Solver Library: a native API for symbolic and fast numerical analysis of reaction networks. Bioinformatics 22:1406-7 [Journal] [PubMed]
Majda AJ (2000) Real world turbulence and modern applied mathematics Mathematics: Frontiers and Perspectives. American Mathematical Society
Malenka RC, Bear MF (2004) LTP and LTD: an embarrassment of riches. Neuron 44:5-21 [Journal] [PubMed]
Malinow R, Malenka RC (2002) AMPA receptor trafficking and synaptic plasticity. Annu Rev Neurosci 25:103-26 [Journal] [PubMed]
Markram H (2006) The blue brain project. Nat Rev Neurosci 7:153-60 [Journal] [PubMed]
Markram H, Roth A, Helmchen F (1998) Competitive calcium binding: implications for dendritic calcium signaling. J Comput Neurosci 5:331-48 [PubMed]
Matsuzaki M, Honkura N, Ellis-Davies GC, Kasai H (2004) Structural basis of long-term potentiation in single dendritic spines. Nature 429:761-6 [Journal] [PubMed]
Mattioni M, Cohen U, Le Novère N (2012) Neuronvisio: A Graphical User Interface with 3D Capabilities for NEURON. Front Neuroinform 6:20 [Journal] [PubMed]
   Neuronvisio: a gui with 3D capabilities for NEURON (Mattioni et al. 2012) [Model]
Meyer T, Hanson PI, Stryer L, Schulman H (1992) Calmodulin trapping by calcium-calmodulin-dependent protein kinase. Science 256:1199-202 [PubMed]
Moyer JT, Wolf JA, Finkel LH (2007) Effects of dopaminergic modulation on the integrative properties of the ventral striatal medium spiny neuron. J Neurophysiol 98:3731-48 [Journal] [PubMed]
Olivier BG, Rohwer JM, Hofmeyr JH (2005) Modelling cellular systems with PySCeS. Bioinformatics 21:560-1 [Journal] [PubMed]
Palmer LM, Stuart GJ (2009) Membrane potential changes in dendritic spines during action potentials and synaptic input. J Neurosci 29:6897-903 [Journal] [PubMed]
   Membrane potential changes in dendritic spines during APs and synaptic input (Palmer & Stuart 2009) [Model]
Perrino BA, Wilson AJ, Ellison P, Clapp LH (2002) Substrate selectivity and sensitivity to inhibition by FK506 and cyclosporin A of calcineurin heterodimers composed of the alpha or beta catalytic subunit. Eur J Biochem 269:3540-8 [PubMed]
Petersen JD, Chen X, Vinade L, Dosemeci A, Lisman JE, Reese TS (2003) Distribution of postsynaptic density (PSD)-95 and Ca2+/calmodulin-dependent protein kinase II at the PSD. J Neurosci 23:11270-8 [PubMed]
Pitt-francis J, Et_al (2009) Chaste: a test-driven approach to software development for biological modelling Comput Phys Commun 180:2452-2471
Pjesivac-Grbovic J, Angskun T, Bosilca G, Fagg GE, Gabriel E, Dongarra JJ (2007) Performance analysis of MPI collective operations Cluster Computing 10:127-143
Quintana AR, Wang D, Forbes JE, Waxham MN (2005) Kinetics of calmodulin binding to calcineurin. Biochem Biophys Res Commun 334:674-80 [Journal] [PubMed]
Ray S, Bhalla US (2008) PyMOOSE: Interoperable Scripting in Python for MOOSE. Front Neuroinform 2:6 [Journal] [PubMed]
   Moose/PyMOOSE: interoperable scripting in Python for MOOSE (Ray and Bhalla 2008) [Model]
Schulz M, Uhlendorf J, Klipp E, Liebermeister W (2006) SBMLmerge, a system for combining biochemical network models. Genome Inform 17:62-71 [PubMed]
Segev I, Fleshman JW, Burke RE (1998) Compartmental models of complex neurons Methods in Neuronal Modeling, Koch C:Segev I, ed. pp.93
Shen H, Sesack SR, Toda S, Kalivas PW (2008) Automated quantification of dendritic spine density and spine head diameter in medium spiny neurons of the nucleus accumbens. Brain Struct Funct 213:149-57 [Journal] [PubMed]
Stefan MI, Edelstein SJ, Le Novère N (2008) An allosteric model of calmodulin explains differential activation of PP2B and CaMKII. Proc Natl Acad Sci U S A 105:10768-73 [Journal] [PubMed]
Surmeier DJ, Ding J, Day M, Wang Z, Shen W (2007) D1 and D2 dopamine-receptor modulation of striatal glutamatergic signaling in striatal medium spiny neurons. Trends Neurosci 30:228-35 [Journal] [PubMed]
Surmeier DJ, Shen W, Day M, Gertler T, Chan S, Tian X, Plotkin JL (2010) The role of dopamine in modulating the structure and function of striatal circuits. Prog Brain Res 183:149-67 [Journal] [PubMed]
Takahashi K, Kaizu K, Hu B, Tomita M (2004) A multi-algorithm, multi-timescale method for cell simulation. Bioinformatics 20:538-46 [Journal] [PubMed]
Tolle DP, Le Novère N (2010) Brownian diffusion of AMPA receptors is sufficient to explain fast onset of LTP. BMC Syst Biol 4:25 [Journal] [PubMed]
Tzortzopoulos A, Best SL, Kalamida D, Török K (2004) Ca2+/calmodulin-dependent activation and inactivation mechanisms of alphaCaMKII and phospho-Thr286-alphaCaMKII. Biochemistry 43:6270-80 [Journal] [PubMed]
Vayttaden SJ, Bhalla US (2004) Developing complex signaling models using GENESIS/Kinetikit. Sci STKE 2004:pl4 [Journal] [PubMed]
Vervaeke K, Lorincz A, Gleeson P, Farinella M, Nusser Z, Silver RA (2010) Rapid desynchronization of an electrically coupled interneuron network with sparse excitatory synaptic input. Neuron 67:435-51 [Journal] [PubMed]
   Rapid desynchronization of an electrically coupled Golgi cell network (Vervaeke et al. 2010) [Model]
Weinan E, Engquist B (2003) Multiscale modeling and computation Notices Of American Mathematical Society 50:1062
Wils S, De Schutter E (2009) STEPS: Modeling and Simulating Complex Reaction-Diffusion Systems with Python. Front Neuroinform 3:15 [Journal] [PubMed]
Wilson JC (1992) Dendritic morphology, inward rectification, and the functional properties of neostriatal neurons Single neuron computation :141-171
Wolf JA, Moyer JT, Lazarewicz MT, Contreras D, Benoit-Marand M, O'Donnell P, Finkel LH (2005) NMDA/AMPA ratio impacts state transitions and entrainment to oscillations in a computational model of the nucleus accumbens medium spiny projection neuron. J Neurosci 25:9080-95 [Journal] [PubMed]
   Afferent Integration in the NAcb MSP Cell (Wolf et al. 2005) [Model]
Yasuda R, Harvey CD, Zhong H, Sobczyk A, van Aelst L, Svoboda K (2006) Supersensitive Ras activation in dendrites and spines revealed by two-photon fluorescence lifetime imaging. Nat Neurosci 9:283-91 [Journal] [PubMed]
Zhabotinsky AM (2000) Bistability in the Ca(2+)/calmodulin-dependent protein kinase-phosphatase system. Biophys J 79:2211-21 [Journal] [PubMed]
McDougal RA, Bulanova AS, Lytton WW (2016) Reproducibility in Computational Neuroscience Models and Simulations. IEEE Trans Biomed Eng 63:2021-35 [Journal] [PubMed]
(96 refs)