Abbott LF, Nelson SB. (2000). Synaptic plasticity: taming the beast. Nature neuroscience. 3 Suppl [PubMed]

Arnold L. (1974). Stochastic Differential Equations: Theory And Applications.

Bhalla US, Iyengar R. (1999). Emergent properties of networks of biological signaling pathways. Science (New York, N.Y.). 283 [PubMed]

• Emergent properties of networks of biological signaling pathways (Bhalla, Iyengar 1999) [Model]

Bower JM, Wilson MA. (1989). The simulation of large-scale neuronal networks Methods In Neuronal Modeling: From Synapses To Networks.

Brette R, Gerstner W. (2005). Adaptive exponential integrate-and-fire model as an effective description of neuronal activity. Journal of neurophysiology. 94 [PubMed]

• Adaptive exponential integrate-and-fire model (Brette & Gerstner 2005) [Model]

Brown R. (1988). Calendar queues: A fast 0(1) priority queue implementation for the simulation event set problem J Commun ACM. 31

Carriero N, Gelernter D. (1989). Linda in context Communications of the ACM, April 1989.

Chad J, Claverol E, Brown A. (2002). Discrete simulation of large aggregates of neurons Neurocomputing. 47

De Schutter E, Bower JM. (1994). An active membrane model of the cerebellar Purkinje cell. I. Simulation of current clamps in slice. Journal of neurophysiology. 71 [PubMed]

• Cerebellar purkinje cell (De Schutter and Bower 1994) [Model]

Destexhe A, Mainen ZF, Sejnowski TJ. (1994). Synthesis of models for excitable membranes, synaptic transmission and neuromodulation using a common kinetic formalism. Journal of computational neuroscience. 1 [PubMed]

• Application of a common kinetic formalism for synaptic models (Destexhe et al 1994) [Model]
• Kinetic synaptic models applicable to building networks (Destexhe et al 1998) [Model]

Diesmann M, Gewaltig MO. (2002). NEST: An environment for neural systemssimulations Forschung und wisschenschaftliches Rechnen.

Drewes R. (2005). Modeling the brain with NCS and Brainlab LINUX Journal online (http:--www.linuxjournal.com-article-8038).

Ermentrout GB. (2002). Simulating, Analyzing, and Animating Dynamical System: A Guide to XPPAUT for Researchers and Students Society for Industrial and Applied Mathematics (SIAM).

Gerstner W, Kistler WM. (2002). Mathematical formulations of Hebbian learning. Biological cybernetics. 87 [PubMed]

Giugliano M. (2000). Synthesis of generalized algorithms for the fast computation of synaptic conductances with Markov kinetic models in large network simulations. Neural computation. 12 [PubMed]

Goodman PH, Drewes R, Maciokas JB, Louis SJ. (2004). An evolutionary autonomous agent with visual cortex and recurrent spiking columnar neural network Lecture Notes In Computer Science. 3102

Gupta A, Wang Y, Markram H. (2000). Organizing principles for a diversity of GABAergic interneurons and synapses in the neocortex. Science (New York, N.Y.). 287 [PubMed]

Gütig R, Aharonov R, Rotter S, Sompolinsky H. (2003). Learning input correlations through nonlinear temporally asymmetric Hebbian plasticity. The Journal of neuroscience : the official journal of the Society for Neuroscience. 23 [PubMed]

Gütig R, Sompolinsky H. (2006). The tempotron: a neuron that learns spike timing-based decisions. Nature neuroscience. 9 [PubMed]

Hammarlund P, Ekeberg O. (1998). Large neural network simulations on multiple hardware platforms. Journal of computational neuroscience. 5 [PubMed]

Hansel D, Mato G, Meunier C, Neltner L. (1998). On numerical simulations of integrate-and-fire neural networks. Neural computation. 10 [PubMed]

Hines ML, Carnevale NT. (1997). The NEURON simulation environment. Neural computation. 9 [PubMed]

Hines ML, Carnevale NT. (2001). NEURON: a tool for neuroscientists. The Neuroscientist : a review journal bringing neurobiology, neurology and psychiatry. 7 [PubMed]

• Spatial gridding and temporal accuracy in NEURON (Hines and Carnevale 2001) [Model]

Hines ML, Carnevale NT. (2006). The NEURON Book.

Houweling AR, Bazhenov M, Timofeev I, Steriade M, Sejnowski TJ. (2005). Homeostatic synaptic plasticity can explain post-traumatic epileptogenesis in chronically isolated neocortex. Cerebral cortex (New York, N.Y. : 1991). 15 [PubMed]

Kanold PO, Manis PB. (2005). Encoding the timing of inhibitory inputs. Journal of neurophysiology. 93 [PubMed]

Kim T, Praehofer H, Zeigler B. (2000). Theory of Modeling and Simulation Integrating Discrete Event and Continuous Complex Dynamic Systems (2nd ed).

Kopell N, Ermentrout GB. (1986). Parabolic bursting in an excitable system coupled with a slow oscillation. Siam J Appl Math. 46

Köhn J, Wörgötter F. (1998). Employing the zeta-transform to optimize the calculation of the synaptic conductance of NMDA and other synaptic channels in network simulations. Neural computation. 10 [PubMed]

Lansner A et al. (2005). Massively parallel simulationof brain-scale neuronal network models Technical Report TRITA-NA-P0513, School of Computer Science and Communication, Stockholm.

Lee G, Farhat NH. (2001). The double queue method: a numerical method for integrate-and-fire neuron networks. Neural networks : the official journal of the International Neural Network Society. 14 [PubMed]

Lytton WW. (1996). Optimizing synaptic conductance calculation for network simulations. Neural computation. 8 [PubMed]

Lytton WW, Hines ML. (2005). Independent variable time-step integration of individual neurons for network simulations. Neural computation. 17 [PubMed]

• Local variable time step method (Lytton, Hines 2005) [Model]

Markram H, Goodman PH, Wiebers JL. (2000). Blockade of A-type potassium channels recovers memory impairment caused by synaptic loss: Implications for Alzheimers dementia J Investig Med. 48

Markram H, Lübke J, Frotscher M, Roth A, Sakmann B. (1997). Physiology and anatomy of synaptic connections between thick tufted pyramidal neurones in the developing rat neocortex. The Journal of physiology. 500 ( Pt 2) [PubMed]

Markram H, Lübke J, Frotscher M, Sakmann B. (1997). Regulation of synaptic efficacy by coincidence of postsynaptic APs and EPSPs. Science (New York, N.Y.). 275 [PubMed]

Markram H, Pikus D, Gupta A, Tsodyks M. (1998). Potential for multiple mechanisms, phenomena and algorithms for synaptic plasticity at single synapses. Neuropharmacology. 37 [PubMed]

Markram H, Wang Y, Tsodyks M. (1998). Differential signaling via the same axon of neocortical pyramidal neurons. Proceedings of the National Academy of Sciences of the United States of America. 95 [PubMed]

Mattia M, Del Giudice P. (2000). Efficient event-driven simulation of large networks of spiking neurons and dynamical synapses. Neural computation. 12 [PubMed]

Moffitt MA, McIntyre CC. (2005). Model-based analysis of cortical recording with silicon microelectrodes. Clinical neurophysiology : official journal of the International Federation of Clinical Neurophysiology. 116 [PubMed]

Morrison A, Mehring C, Geisel T, Aertsen AD, Diesmann M. (2005). Advancing the boundaries of high-connectivity network simulation with distributed computing. Neural computation. 17 [PubMed]

Nenadic Z, Ghosh BK, Ulinski P. (2003). Propagating waves in visual cortex: a large-scale model of turtle visual cortex. Journal of computational neuroscience. 14 [PubMed]

• Turtle visual cortex model (Nenadic et al. 2003, Wang et al. 2005, Wang et al. 2006) [Model]

Prescott SA, De Koninck Y. (2005). Integration time in a subset of spinal lamina I neurons is lengthened by sodium and calcium currents acting synergistically to prolong subthreshold depolarization. The Journal of neuroscience : the official journal of the Society for Neuroscience. 25 [PubMed]

• Tonic neuron in spinal lamina I: prolongation of subthreshold depol. (Prescott and De Koninck 2005) [Model]

Reutimann J, Giugliano M, Fusi S. (2003). Event-driven simulation of spiking neurons with stochastic dynamics. Neural computation. 15 [PubMed]

Rochel O, Martinez D. (2003). An event-driven framework for the simulation of networks of spiking neurons Proc. 11th European Symposium on Artificial Neural Networks .

Rotter S, Diesmann M. (1999). Exact digital simulation of time-invariant linear systems with applications to neuronal modeling. Biological cybernetics. 81 [PubMed]

Rudolph M, Destexhe A. (2006). Analytical integrate-and-fire neuron models with conductance-based dynamics for event-driven simulation strategies. Neural computation. 18 [PubMed]

Saghatelyan A et al. (2005). Activity-dependent adjustments of the inhibitory network in the olfactory bulb following early postnatal deprivation. Neuron. 46 [PubMed]

• Olfactory bulb granule cell: effects of odor deprivation (Saghatelyan et al 2005) [Model]

Sejnowski TJ, Destexhe A. (2001). Thalamocortical Assemblies-How Ion Channels, Single Neurons and large-Scale Networks Organize Sleep.

• Pyramidal Neuron: Deep, Thalamic Relay and Reticular, Interneuron (Destexhe et al 1998, 2001) [Model]

Shelley MJ, Tao L. (2001). Efficient and accurate time-stepping schemes for integrate-and-fire neuronal networks. Journal of computational neuroscience. 11 [PubMed]

Sleator D, Tarjan R. (1983). Self adjusting binary trees Proc ACM SIGACT Symposium on Theory of Computing.

Song S, Miller KD, Abbott LF. (2000). Competitive Hebbian learning through spike-timing-dependent synaptic plasticity. Nature neuroscience. 3 [PubMed]

Traub RD et al. (2005). Single-column thalamocortical network model exhibiting gamma oscillations, sleep spindles, and epileptogenic bursts. Journal of neurophysiology. 93 [PubMed]

• A single column thalamocortical network model (Traub et al 2005) [Model]
• Collection of simulated data from a thalamocortical network model (Glabska, Chintaluri, Wojcik 2017) [Model]

Tsodyks M, Pawelzik K, Markram H. (1998). Neural networks with dynamic synapses. Neural computation. 10 [PubMed]

• Synaptic plasticity: pyramid->pyr and pyr->interneuron (Tsodyks et al 1998) [Model]

Vitko I et al. (2005). Functional characterization and neuronal modeling of the effects of childhood absence epilepsy variants of CACNA1H, a T-type calcium channel. The Journal of neuroscience : the official journal of the Society for Neuroscience. 25 [PubMed]

• T channel currents (Vitko et al 2005) [Model]

Vogels TP, Abbott LF. (2005). Signal propagation and logic gating in networks of integrate-and-fire neurons. The Journal of neuroscience : the official journal of the Society for Neuroscience. 25 [PubMed]

• Networks of spiking neurons: a review of tools and strategies (Brette et al. 2007) [Model]
• Thalamocortical Relay cell under current clamp in high-conductance state (Zeldenrust et al 2018) [Model]

Wang Y et al. (2006). Heterogeneity in the pyramidal network of the medial prefrontal cortex. Nature neuroscience. 9 [PubMed]

Watts L. (1994). Event-driven simulation of networks of spiking neurons Advances in Neural Information Processing Systems. 6

Wolf JA et al. (2005). NMDA/AMPA ratio impacts state transitions and entrainment to oscillations in a computational model of the nucleus accumbens medium spiny projection neuron. The Journal of neuroscience : the official journal of the Society for Neuroscience. 25 [PubMed]

• Afferent Integration in the NAcb MSP Cell (Wolf et al. 2005) [Model]

Zeigler BP, Vahie S. (1993). DEVS formalism and methodology: unity of conception-diversity of application Proceedings of the 1993 Winter Simulation Conference.

Aisa B, Mingus B, O'Reilly R. (2008). The emergent neural modeling system. Neural networks : the official journal of the International Neural Network Society. 21 [PubMed]

Brette R, Goodman DF. (2011). Vectorized algorithms for spiking neural network simulation. Neural computation. 23 [PubMed]

• Vectorized algorithms for spiking neural network simulation (Brette and Goodman 2011) [Model]

Bédard C, Destexhe A. (2008). A modified cable formalism for modeling neuronal membranes at high frequencies. Biophysical journal. 94 [PubMed]

Carnevale NT, Morse TM. (1996). Research reports that have used NEURON Web published citations at the NEURON website.

Gleeson P et al. (2010). NeuroML: a language for describing data driven models of neurons and networks with a high degree of biological detail. PLoS computational biology. 6 [PubMed]

Huang CW, Cheng JT, Tsai JJ, Wu SN, Huang CC. (2009). Diabetic hyperglycemia aggravates seizures and status epilepticus-induced hippocampal damage. Neurotoxicity research. 15 [PubMed]

• Contribution of ATP-sensitive potassium channels in the neuronal network (Huang et al. 2009) [Model]

Huang CW, Huang CC, Lin MW, Tsai JJ, Wu SN. (2008). The synergistic inhibitory actions of oxcarbazepine on voltage-gated sodium and potassium currents in differentiated NG108-15 neuronal cells and model neurons. The international journal of neuropsychopharmacology. 11 [PubMed]

• Synergistic inhibitory action of oxcarbazepine on INa and IK (Huang et al. 2008) [Model]

Huang CW, Tsai JJ, Huang CC, Wu SN. (2009). Experimental and simulation studies on the mechanisms of levetiracetam-mediated inhibition of delayed-rectifier potassium current (KV3.1): contribution to the firing of action potentials. Journal of physiology and pharmacology : an official journal of the Polish Physiological Society. 60 [PubMed]

• Simulation studies on mechanisms of levetiracetam-mediated inhibition of IK(DR) (Huang et al. 2009) [Model]

Khalil R, Moftah MZ, Moustafa AA. (2017). The effects of dynamical synapses on firing rate activity: a spiking neural network model. The European journal of neuroscience. 46 [PubMed]

Kim H, Kim M. (2018). PyMUS: Python-Based Simulation Software for Virtual Experiments on Motor Unit System. Frontiers in neuroinformatics. 12 [PubMed]

• PyMUS: A Python based Motor Unit Simulator (Kim & Kim 2018) [Model]

Kobayashi R, Tsubo Y, Shinomoto S. (2009). Made-to-order spiking neuron model equipped with a multi-timescale adaptive threshold. Frontiers in computational neuroscience. 3 [PubMed]

• Multi-timescale adaptive threshold model (Kobayashi et al 2009) (NEURON) [Model]
• Multi-timescale adaptive threshold model (Kobayashi et al 2009) [Model]

Kozloski J, Wagner J. (2011). An Ultrascalable Solution to Large-scale Neural Tissue Simulation. Frontiers in neuroinformatics. 5 [PubMed]

Lytton WW et al. (2016). Simulation Neurotechnologies for Advancing Brain Research: Parallelizing Large Networks in NEURON. Neural computation. 28 [PubMed]

• Parallelizing large networks in NEURON (Lytton et al. 2016) [Model]

Magalhães B, Hines M, Sterling T, Schüermann F. (2019). Exploiting Flow Graph of System of ODEs to Accelerate the Simulation of Biologically-Detailed Neural Networks 2019 IEEE International Parallel and Distributed Processing Symposium (IPDPS).

• Fully-Asynchronous Cache-Efficient Simulation of Detailed Neural Networks (Magalhaes et al 2019) [Model]

McDougal RA, Bulanova AS, Lytton WW. (2016). Reproducibility in Computational Neuroscience Models and Simulations. IEEE transactions on bio-medical engineering. 63 [PubMed]

Podlaski WF et al. (2017). Mapping the function of neuronal ion channels in model and experiment. eLife. 6 [PubMed]

Richert M, Nageswaran JM, Dutt N, Krichmar JL. (2011). An efficient simulation environment for modeling large-scale cortical processing. Frontiers in neuroinformatics. 5 [PubMed]

• Efficient simulation environment for modeling large-scale cortical processing (Richert et al. 2011) [Model]

Sherfey JS et al. (2018). DynaSim: A MATLAB Toolbox for Neural Modeling and Simulation. Frontiers in neuroinformatics. 12 [PubMed]

• DynaSim: a MATLAB toolbox for neural modeling and simulation (Sherfey et al 2018) [Model]

Sterratt DC, Graham B, Gillies A, Willshaw D. (2011). Principles of Computational Modelling in Neuroscience, Cambridge University Press.

• Principles of Computational Modelling in Neuroscience (Book) (Sterratt et al. 2011) [Model]

Stewart RD, Bair W. (2009). Spiking neural network simulation: numerical integration with the Parker-Sochacki method. Journal of computational neuroscience. 27 [PubMed]

• Numerical Integration of Izhikevich and HH model neurons (Stewart and Bair 2009) [Model]

Susi G et al. (2021). FNS allows efficient event-driven spiking neural network simulations based on a neuron model supporting spike latency Scientific reports. 11 [PubMed]

• FNS spiking neural simulator; LIFL neuron model, event-driven simulation (Susi et al 2021) [Model]

Tikidji-Hamburyan RA, El-Ghazawi TA, Narayana V, Bozkus Z. (2017). Software for Brain Network Simulations: A Comparative Study Front. Neuroinform..

• Brain networks simulators - a comparative study (Tikidji-Hamburyan et al 2017) [Model]

Versace M, Ames H, Léveillé J, Fortenberry B, Gorchetchnikov A. (2008). KInNeSS: a modular framework for computational neuroscience. Neuroinformatics. 6 [PubMed]

• KInNeSS : a modular framework for computational neuroscience (Versace et al. 2008) [Model]

Zeldenrust F, Chameau P, Wadman WJ. (2018). Spike and burst coding in thalamocortical relay cells. PLoS computational biology. 14 [PubMed]

• Thalamocortical Relay cell under current clamp in high-conductance state (Zeldenrust et al 2018) [Model]

van Elburg RA, van Ooyen A. (2009). Generalization of the event-based Carnevale-Hines integration scheme for integrate-and-fire models. Neural computation. 21 [PubMed]

• Generalized Carnevale-Hines algorithm (van Elburg and van Ooyen 2009) [Model]

Świetlik D, Białowąs J, Kusiak A, Cichońska D. (2018). Memory and forgetting processes with the firing neuron model. Folia morphologica. 77 [PubMed]