Modelling the molecular mechanisms of synaptic plasticity using systems biology approaches
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[1] W. Rall. Branching dendritic trees and motoneuron membrane resistivity. , 1959, Experimental neurology.
[2] G. Lynch,et al. Intracellular injections of EGTA block induction of hippocampal long-term potentiation , 1983, Nature.
[3] L. Cooper,et al. A physiological basis for a theory of synapse modification. , 1987, Science.
[4] C. Koch,et al. The dynamics of free calcium in dendritic spines in response to repetitive synaptic input. , 1987, Science.
[5] R S Zucker,et al. Postsynaptic calcium is sufficient for potentiation of hippocampal synaptic transmission. , 1988, Science.
[6] J. Lisman,et al. A mechanism for the Hebb and the anti-Hebb processes underlying learning and memory. , 1989, Proceedings of the National Academy of Sciences of the United States of America.
[7] W. Levy,et al. Insights into associative long-term potentiation from computational models of NMDA receptor-mediated calcium influx and intracellular calcium concentration changes. , 1990, Journal of neurophysiology.
[8] T. H. Brown,et al. Biophysical model of a Hebbian synapse. , 1990, Proceedings of the National Academy of Sciences of the United States of America.
[9] A. Hodgkin,et al. A quantitative description of membrane current and its application to conduction and excitation in nerve , 1990 .
[10] Mark F. Bear,et al. Neocortical long-term potentiation , 1993, Current Opinion in Neurobiology.
[11] R. Nicoll,et al. The role of Ca2+ entry via synaptically activated NMDA receptors in the induction of long-term potentiation , 1993, Neuron.
[12] R. Malenka,et al. Involvement of a calcineurin/ inhibitor-1 phosphatase cascade in hippocampal long-term depression , 1994, Nature.
[13] N. Mons,et al. Selective expression of one Ca(2+)-inhibitable adenylyl cyclase in dopaminergically innervated rat brain regions. , 1994, Brain research. Molecular brain research.
[14] J L van Hemmen,et al. Intracellular Ca2+ stores can account for the time course of LTP induction: a model of Ca2+ dynamics in dendritic spines. , 1995, Journal of neurophysiology.
[15] R. Albers,et al. A mechanism for synaptic frequency detection through autophosphorylation of CaM kinase II. , 1996, Biophysical journal.
[16] D. Debanne. Associative Synaptic Plasticity in Hippocampus and Visual Cortex: Cellular Mechanisms and Functional Implications , 1996, Reviews in the neurosciences.
[17] D. Alkon,et al. Pairing-specific long-term depression of Purkinje cell excitatory postsynaptic potentials results from a classical conditioning procedure in the rabbit cerebellar slice. , 1996, Journal of neurophysiology.
[18] P. Greengard,et al. Bidirectional Regulation of DARPP-32 Phosphorylation by Dopamine , 1997, The Journal of Neuroscience.
[19] J. Lisman,et al. Postsynaptic Inhibitors of Calcium/Calmodulin-Dependent Protein Kinase Type II Block Induction But Not Maintenance of Pairing-Induced Long-Term Potentiation , 1997, The Journal of Neuroscience.
[20] E. Kandel,et al. Genetic Demonstration of a Role for PKA in the Late Phase of LTP and in Hippocampus-Based Long-Term Memory , 1997, Cell.
[21] P. De Koninck,et al. Sensitivity of CaM kinase II to the frequency of Ca2+ oscillations. , 1998, Science.
[22] Duncan J. Watts,et al. Collective dynamics of ‘small-world’ networks , 1998, Nature.
[23] Louis J Muglia,et al. Calcium-Stimulated Adenylyl Cyclase Activity Is Critical for Hippocampus-Dependent Long-Term Memory and Late Phase LTP , 1999, Neuron.
[24] U. Bhalla,et al. Emergent properties of networks of biological signaling pathways. , 1999, Science.
[25] Mark C. W. van Rossum,et al. Stable Hebbian Learning from Spike Timing-Dependent Plasticity , 2000, The Journal of Neuroscience.
[26] S. Grant,et al. Proteomic analysis of NMDA receptor–adhesion protein signaling complexes , 2000, Nature Neuroscience.
[27] E. Winzeler,et al. Genomics, gene expression and DNA arrays , 2000, Nature.
[28] L. Abbott,et al. Competitive Hebbian learning through spike-timing-dependent synaptic plasticity , 2000, Nature Neuroscience.
[29] P. Greengard,et al. Amplification of dopaminergic signaling by a positive feedback loop. , 2000, Proceedings of the National Academy of Sciences of the United States of America.
[30] B. Kholodenko,et al. Negative feedback and ultrasensitivity can bring about oscillations in the mitogen-activated protein kinase cascades. , 2000, European journal of biochemistry.
[31] R. Albert,et al. The large-scale organization of metabolic networks , 2000, Nature.
[32] Dennis Bray,et al. Molecular model of a lattice of signalling proteins involved in bacterial chemotaxis , 2000, Nature Cell Biology.
[33] D. A. Baxter,et al. Modeling transcriptional control in gene networks—methods, recent results, and future directions , 2000, Bulletin of mathematical biology.
[34] J. Lisman,et al. A Model of Synaptic Memory A CaMKII/PP1 Switch that Potentiates Transmission by Organizing an AMPA Receptor Anchoring Assembly , 2001, Neuron.
[35] M. Kawato,et al. Exploration of Signal Transduction Pathways in Cerebellar Long-Term Depression by Kinetic Simulation , 2001, The Journal of Neuroscience.
[36] J. Sweatt,et al. The neuronal MAP kinase cascade: a biochemical signal integration system subserving synaptic plasticity and memory , 2001, Journal of neurochemistry.
[37] J. Lisman,et al. The molecular basis of CaMKII function in synaptic and behavioural memory , 2002, Nature Reviews Neuroscience.
[38] J. Ferrell. Self-perpetuating states in signal transduction: positive feedback, double-negative feedback and bistability. , 2002, Current opinion in cell biology.
[39] Reinhart Heinrich,et al. Mathematical models of protein kinase signal transduction. , 2002, Molecular cell.
[40] Upinder S Bhalla,et al. Mechanisms for temporal tuning and filtering by postsynaptic signaling pathways. , 2002, Biophysical journal.
[41] L. Cooper,et al. A unified model of NMDA receptor-dependent bidirectional synaptic plasticity , 2002, Proceedings of the National Academy of Sciences of the United States of America.
[42] P. Greengard,et al. Regulation of DARPP‐32 dephosphorylation at PKA‐ and Cdk5‐sites by NMDA and AMPA receptors: distinct roles of calcineurin and protein phosphatase‐2A , 2002, Journal of neurochemistry.
[43] J. Kotaleski,et al. Subcellular interactions between parallel fibre and climbing fibre signals in purkinje cells predict sensitivity of classical conditioning to interstimulus interval , 2002, Integrative physiological and behavioral science : the official journal of the Pavlovian Society.
[44] H. Kitano. Systems Biology: A Brief Overview , 2002, Science.
[45] Masao Ito. The molecular organization of cerebellar long-term depression , 2002, Nature Reviews Neuroscience.
[46] D. Debanne,et al. Long-term plasticity of intrinsic excitability: learning rules and mechanisms. , 2003, Learning & memory.
[47] P. Greengard,et al. Regulation of AMPA receptor dephosphorylation by glutamate receptor agonists , 2003, Neuropharmacology.
[48] M. Tyers,et al. From genomics to proteomics , 2003, Nature.
[49] A. Arkin,et al. Motifs, modules and games in bacteria. , 2003, Current opinion in microbiology.
[50] Peter J Woolf,et al. A Spatial Focusing Model for G Protein Signals , 2003, The Journal of Biological Chemistry.
[51] J. Lippincott-Schwartz,et al. Development and Use of Fluorescent Protein Markers in Living Cells , 2003, Science.
[52] U. Bhalla. Signaling in small subcellular volumes. II. Stochastic and diffusion effects on synaptic network properties. , 2004, Biophysical journal.
[53] H. Sauro,et al. Quantitative analysis of signaling networks. , 2004, Progress in biophysics and molecular biology.
[54] D. Bray,et al. Stochastic simulation of chemical reactions with spatial resolution and single molecule detail , 2004, Physical biology.
[55] Hyejin Kang,et al. Translational Control by MAPK Signaling in Long-Term Synaptic Plasticity and Memory , 2004, Cell.
[56] U. Bhalla,et al. A role for ERKII in synaptic pattern selectivity on the time‐scale of minutes , 2004, The European journal of neuroscience.
[57] B. Kholodenko,et al. Signaling switches and bistability arising from multisite phosphorylation in protein kinase cascades , 2004, The Journal of cell biology.
[58] William Holmes,et al. Models of Calmodulin Trapping and CaM Kinase II Activation in a Dendritic Spine , 2004, Journal of Computational Neuroscience.
[59] Kim T. Blackwell,et al. Paired Turbulence and Light do not Produce a Supralinear Calcium Increase in Hermissenda , 2004, Journal of Computational Neuroscience.
[60] Angus C Nairn,et al. DARPP-32: an integrator of neurotransmission. , 2004, Annual review of pharmacology and toxicology.
[61] F. Crépel,et al. Coactivation of metabotropic glutamate receptors and of voltage-gated calcium channels induces long-term depression in cerebellar Purkinje cells in vitro , 2004, Experimental Brain Research.
[62] James M. Bower,et al. Transient Versus Asymptotic Dynamics of CaM Kinase II: Possible Roles of Phosphatase , 2001, Journal of Computational Neuroscience.
[63] Masaru Tomita,et al. A multi-algorithm, multi-timescale method for cell simulation , 2004, Bioinform..
[64] Upinder S. Bhalla,et al. Molecular Switches at the Synapse Emerge from Receptor and Kinase Traffic , 2005, PLoS Comput. Biol..
[65] Maryann E Martone,et al. Evidence for Ectopic Neurotransmission at a Neuronal Synapse , 2005, Science.
[66] J. Stark,et al. Network motifs: structure does not determine function , 2006, BMC Genomics.
[67] D. Bray,et al. Simulated Diffusion of Phosphorylated CheY through the Cytoplasm of Escherichia coli , 2005, Journal of bacteriology.
[68] Masaru Tomita,et al. Space in systems biology of signaling pathways – towards intracellular molecular crowding in silico , 2005, FEBS letters.
[69] Markus R. Wenk,et al. The emerging field of lipidomics , 2005 .
[70] Joseph E LeDoux,et al. Auditory Fear Conditioning and Long-Term Potentiation in the Lateral Amygdala Require ERK/MAP Kinase Signaling in the Auditory Thalamus: A Role for Presynaptic Plasticity in the Fear System , 2005, The Journal of Neuroscience.
[71] Iain D G Campuzano,et al. Proteomic Analysis of in Vivo Phosphorylated Synaptic Proteins* , 2005, Journal of Biological Chemistry.
[72] Johan Hattne,et al. Stochastic reaction-diffusion simulation with MesoRD , 2005, Bioinform..
[73] J. Ferrell,et al. Interlinked Fast and Slow Positive Feedback Loops Drive Reliable Cell Decisions , 2005, Science.
[74] Xiao-Jing Wang,et al. The Stability of a Stochastic CaMKII Switch: Dependence on the Number of Enzyme Molecules and Protein Turnover , 2005, PLoS biology.
[75] Jan Lankelma,et al. Principles behind the multifarious control of signal transduction , 2004, The FEBS journal.
[76] Muffy Calder,et al. When kinases meet mathematics: the systems biology of MAPK signalling , 2005, FEBS letters.
[77] S. L. Wong,et al. Towards a proteome-scale map of the human protein–protein interaction network , 2005, Nature.
[78] R. Tsien,et al. The Fluorescent Toolbox for Assessing Protein Location and Function , 2006, Science.
[79] Jeanette Kotaleski,et al. Transient Calcium and Dopamine Increase PKA Activity and DARPP-32 Phosphorylation , 2006, PLoS Comput. Biol..
[80] Nicola Elvassore,et al. PGE1 stimulation of HEK293 cells generates multiple contiguous domains with different [cAMP]: role of compartmentalized phosphodiesterases , 2006, The Journal of cell biology.
[81] Kim T. Blackwell,et al. An efficient stochastic diffusion algorithm for modeling second messengers in dendrites and spines , 2006, Journal of Neuroscience Methods.
[82] B. Sakmann,et al. Spine Ca2+ Signaling in Spike-Timing-Dependent Plasticity , 2006, The Journal of Neuroscience.
[83] J. Girault,et al. DARPP-32 is a robust integrator of dopamine and glutamate signals , 2006 .
[84] Rebecca C Wade,et al. Bridging from molecular simulation to biochemical networks. , 2007, Current opinion in structural biology.
[85] Scott E. Fraser,et al. Imaging in Systems Biology , 2007, Cell.
[86] D. Lovinger,et al. Retrograde endocannabinoid signaling at striatal synapses requires a regulated postsynaptic release step , 2007, Proceedings of the National Academy of Sciences.
[87] Nicolas Brunel,et al. STDP in a Bistable Synapse Model Based on CaMKII and Associated Signaling Pathways , 2007, PLoS Comput. Biol..
[88] Angus C Nairn,et al. The B″/PR72 subunit mediates Ca2+-dependent dephosphorylation of DARPP-32 by protein phosphatase 2A , 2007, Proceedings of the National Academy of Sciences.
[89] Daniel T Gillespie,et al. Stochastic simulation of chemical kinetics. , 2007, Annual review of physical chemistry.
[90] Upinder S. Bhalla,et al. A propagating ERKII switch forms zones of elevated dendritic activation correlated with plasticity. , 2007 .
[91] Upinder S. Bhalla,et al. PyMOOSE: Interoperable Scripting in Python for MOOSE , 2008, Frontiers in neuroinformatics.
[92] P. Serrano,et al. PKMζ Maintains Late Long-Term Potentiation by N-Ethylmaleimide-Sensitive Factor/GluR2-Dependent Trafficking of Postsynaptic AMPA Receptors , 2008, The Journal of Neuroscience.
[93] Susana R. Neves,et al. Design Logic of a Cannabinoid Receptor Signaling Network That Triggers Neurite Outgrowth , 2008, Science.
[94] The Spread of Ras Activity Triggered by Activation of a Single Dendritic Spine , 2008, Science.
[95] Ravi Iyengar,et al. Cell Shape and Negative Links in Regulatory Motifs Together Control Spatial Information Flow in Signaling Networks , 2008, Cell.
[96] T. Sejnowski,et al. Calmodulin Activation by Calcium Transients in the Postsynaptic Density of Dendritic Spines , 2008, PloS one.
[97] R. Malenka,et al. Synaptic Plasticity: Multiple Forms, Functions, and Mechanisms , 2008, Neuropsychopharmacology.
[98] J. Tyson,et al. Design principles of biochemical oscillators , 2008, Nature Reviews Molecular Cell Biology.
[99] Wulfram Gerstner,et al. Phenomenological models of synaptic plasticity based on spike timing , 2008, Biological Cybernetics.
[100] S. Jager,et al. Rapid Erasure of Long-Term Memory Associations in the Cortex by an Inhibitor of PKM z , 2009 .
[101] D. Feldman. Synaptic mechanisms for plasticity in neocortex. , 2009, Annual review of neuroscience.
[102] H. Shouval,et al. Translational switch for long-term maintenance of synaptic plasticity , 2009, Molecular systems biology.
[103] Christopher M. Overall,et al. Deciphering complex mechanisms in neurodegenerative diseases: the advent of systems biology , 2009, Trends in Neurosciences.
[104] Seok-Jin R. Lee,et al. Activation of CaMKII in single dendritic spines during long-term potentiation , 2009, Nature.
[105] Robert E Campbell,et al. Genetically encoded FRET-based biosensors for multiparameter fluorescence imaging. , 2009, Current opinion in biotechnology.
[106] S. Swamy,et al. Neurotransmitters Drive Combinatorial Multistate Postsynaptic Density Networks , 2009, Science Signaling.
[107] S. Grant,et al. The origin and evolution of synapses , 2009, Nature Reviews Neuroscience.
[108] O. Sporns,et al. Complex brain networks: graph theoretical analysis of structural and functional systems , 2009, Nature Reviews Neuroscience.
[109] D. A. Baxter,et al. Interlinked dual-time feedback loops can enhance robustness to stochasticity and persistence of memory. , 2009, Physical review. E, Statistical, nonlinear, and soft matter physics.
[110] David Warde-Farley,et al. Dynamic modularity in protein interaction networks predicts breast cancer outcome , 2009, Nature Biotechnology.
[111] Avi Ma’ayan. Insights into the Organization of Biochemical Regulatory Networks Using Graph Theory Analyses* , 2009, Journal of Biological Chemistry.
[112] M. Zaccolo,et al. The Role of Type 4 Phosphodiesterases in Generating Microdomains of cAMP: Large Scale Stochastic Simulations , 2010, PloS one.