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Carnevale NT, Hines ML (2006) The NEURON Book

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Acker CD, Antic SD (2009) Quantitative assessment of the distributions of membrane conductances involved in action potential backpropagation along basal dendrites. J Neurophysiol 101:1524-41 [Journal] [PubMed]
  • Excitability of PFC Basal Dendrites (Acker and Antic 2009) [Model]
Aghvami SS, Müller M, Araabi BN, Egger V (2019) Coincidence Detection within the Excitable Rat Olfactory Bulb Granule Cell Spines. J Neurosci 39:584-595 [Journal] [PubMed]
  • Coincident signals in Olfactory Bulb Granule Cell spines (Aghvami et al 2019) [Model]
Ai H, Kai K, Kumaraswamy A, Ikeno H, Wachtler T (2017) Interneurons in the Honeybee Primary Auditory Center Responding to Waggle Dance-Like Vibration Pulses. J Neurosci 37:10624-10635 [Journal] [PubMed]
  • Vibration-sensitive Honeybee interneurons (Ai et al 2017) [Model]
Almog M, Korngreen A (2014) A Quantitative Description of Dendritic Conductances and Its Application to Dendritic Excitation in Layer 5 Pyramidal Neurons J Neurosci 34(1):182-196 [Journal] [PubMed]
  • Ionic mechanisms of dendritic spikes (Almog and Korngreen 2014) [Model]
Amatrudo JM, Weaver CM, Crimins JL, Hof PR, Rosene DL, Luebke JI (2012) Influence of highly distinctive structural properties on the excitability of pyramidal neurons in monkey visual and prefrontal cortices. J Neurosci 32:13644-60 [Journal] [PubMed]
  • Rhesus Monkey Layer 3 Pyramidal Neurons: V1 vs PFC (Amatrudo, Weaver et al. 2012) [Model]
Anderson RW, Farokhniaee A, Gunalan K, Howell B, McIntyre CC (2018) Action potential initiation, propagation, and cortical invasion in the hyperdirect pathway during subthalamic deep brain stimulation Brain Stimulation [Journal]
  • AP initiation, propagation, and cortical invasion in a Layer 5 pyramidal cell (Anderson et 2018) [Model]
Andreozzi E, Carannante I, D'Addio G, Cesarelli M, Balbi P (2019) Phenomenological models of NaV1.5. A side by side, procedural, hands-on comparison between Hodgkin-Huxley and kinetic formalisms Scientific Reports 9:17493 [Journal] [PubMed]
  • Phenomenological models of NaV1.5: Hodgkin-Huxley and kinetic formalisms (Andreozzi et al 2019) [Model]
Anwar H, Roome CJ, Nedelescu H, Chen W, Kuhn B, De Schutter E (2014) Dendritic diameters affect the spatial variability of intracellular calcium dynamics in computer models. Front Cell Neurosci 8:168 [Journal] [PubMed]
  • Calcium dynamics depend on dendritic diameters (Anwar et al. 2014) [Model]
Arsiero M, Lüscher HR, Lundstrom BN, Giugliano M (2007) The impact of input fluctuations on the frequency-current relationships of layer 5 pyramidal neurons in the rat medial prefrontal cortex. J Neurosci 27:3274-84 [Journal] [PubMed]
  • Input Fluctuations effects on f-I curves (Arsiero et al. 2007) [Model]
Ascoli GA, Gasparini S, Medinilla V, Migliore M (2010) Local control of postinhibitory rebound spiking in CA1 pyramidal neuron dendrites. J Neurosci 30:6434-42 [Journal] [PubMed]
  • CA1 pyramidal neuron: rebound spiking (Ascoli et al.2010) [Model]
Bahl A, Stemmler MB, Herz AV, Roth A (2012) Automated optimization of a reduced layer 5 pyramidal cell model based on experimental data. J Neurosci Methods 210:22-34 [Journal] [PubMed]
  • A set of reduced models of layer 5 pyramidal neurons (Bahl et al. 2012) [Model]
Baker JL, Perez-Rosello T, Migliore M, Barrionuevo G, Ascoli GA (2011) A computer model of unitary responses from associational/commissural and perforant path synapses in hippocampal CA3 pyramidal cells. J Comput Neurosci 31:137-58 [Journal] [PubMed]
  • A model of unitary responses from A/C and PP synapses in CA3 pyramidal cells (Baker et al. 2010) [Model]
Balbi P, Martinoia S, Colombo R, Massobrio P (2014) Modelling recurrent discharge in the spinal a-motoneuron: reappraisal of the F wave. Clin Neurophysiol 125:427-9 [Journal] [PubMed]
  • Recurrent discharge in a reduced model of cat spinal motoneuron (Balbi et al, 2013) [Model]
Balbi P, Martinoia S, Massobrio P (2015) Axon-somatic back-propagation in detailed models of spinal alpha motoneurons. Front Comput Neurosci 9:15 [Journal] [PubMed]
  • Axon-somatic back-propagation in a detailed model of cat spinal motoneuron (Balbi et al, 2015) [Model]
Balbi P, Massobrio P, Hellgren Kotaleski J (2017) A single Markov-type kinetic model accounting for the macroscopic currents of all human voltage-gated sodium channel isoforms. PLoS Comput Biol 13:e1005737 [Journal] [PubMed]
  • A single kinetic model for all human voltage-gated sodium channels (Balbi et al, 2017) [Model]
Basak R, Narayanan R (2018) Active dendrites regulate the spatiotemporal spread of signaling microdomains. PLoS Comput Biol 14:e1006485 [Journal] [PubMed]
  • Active dendrites shape signaling microdomains in hippocampal neurons (Basak & Narayanan 2018) [Model]
Behabadi BF, Polsky A, Jadi M, Schiller J, Mel BW (2012) Location-dependent excitatory synaptic interactions in pyramidal neuron dendrites. PLoS Comput Biol 8:e1002599 [Journal] [PubMed]
  • Excitatory synaptic interactions in pyramidal neuron dendrites (Behabadi et al. 2012) [Model]
Beining M, Mongiat LA, Schwarzacher SW, Cuntz H, Jedlicka P (2017) T2N as a new tool for robust electrophysiological modeling demonstrated for mature and adult-born dentate granule cells eLife [Journal]
  • Mature and young adult-born dentate granule cell models (T2N interface) (Beining et al. 2017) [Model]
  • GC model (Beining et al 2017) [Model]
Berzhanskaya J, Chernyy N, Gluckman BJ, Schiff SJ, Ascoli GA (2013) Modulation of hippocampal rhythms by subthreshold electric fields and network topology. J Comput Neurosci 34:369-89 [Journal] [PubMed]
  • Modulation of hippocampal rhythms by electric fields and network topology (Berzhanskaya et al. 2013) [Model]
Bezaire M, Raikov I, Burk K, Armstrong C, Soltesz I (2016) SimTracker tool and code template to design, manage and analyze neural network model simulations in parallel NEURON bioRxiv [Journal]
  • Hippocampal CA1 NN with spontaneous theta, gamma: full scale & network clamp (Bezaire et al 2016) [Model]
Bezaire MJ, Raikov I, Burk K, Vyas D, Soltesz I (2016) Interneuronal mechanisms of hippocampal theta oscillations in a full-scale model of the rodent CA1 circuit. Elife [Journal] [PubMed]
  • Hippocampal CA1 NN with spontaneous theta, gamma: full scale & network clamp (Bezaire et al 2016) [Model]
Brette R, Goodman DF (2011) Vectorized algorithms for spiking neural network simulation. Neural Comput 23:1503-35 [Journal] [PubMed]
  • Vectorized algorithms for spiking neural network simulation (Brette and Goodman 2011) [Model]
Briant LJ, Stalbovskiy AO, Nolan MF, Champneys AR, Pickering AE (2014) Increased intrinsic excitability of muscle vasoconstrictor preganglionic neurons may contribute to the elevated sympathetic activity in hypertensive rats. J Neurophysiol 112:2756-78 [Journal] [PubMed]
  • Sympathetic Preganglionic Neurone (Briant et al. 2014) [Model]
Calì C, Berger TK, Pignatelli M, Carleton A, Markram H, Giugliano M (2008) Inferring connection proximity in networks of electrically coupled cells by subthreshold frequency response analysis. J Comput Neurosci 24:330-45 [Journal] [PubMed]
  • Inferring connection proximity in electrically coupled networks (Cali et al. 2007) [Model]
Carnevale NT, Morse TM (1996-2009) Research reports that have used NEURON Web published citations at the NEURON website [Journal]
Casale AE, McCormick DA (2011) Active action potential propagation but not initiation in thalamic interneuron dendrites. J Neurosci 31:18289-302 [Journal] [PubMed]
  • Active dendritic action potential propagation (Casale & McCormick 2011) [Model]
Cattani A, Solinas S, Canuto C (2016) A Hybrid Model for the Computationally-Efficient Simulation of the Cerebellar Granular Layer. Front Comput Neurosci 10:30 [Journal] [PubMed]
Chadderdon GL, Neymotin SA, Kerr CC, Lytton WW (2012) Reinforcement learning of targeted movement in a spiking neuronal model of motor cortex. PLoS One 7:e47251 [Journal] [PubMed]
  • Reinforcement learning of targeted movement (Chadderdon et al. 2012) [Model]
Chambers JD, Bethwaite B, Diamond NT, Peachey T, Abramson D, Petrou S, Thomas EA (2012) Parametric computation predicts a multiplicative interaction between synaptic strength parameters that control gamma oscillations. Front Comput Neurosci 6:53 [Journal] [PubMed]
  • Parametric computation and persistent gamma in a cortical model (Chambers et al. 2012) [Model]
Chen W, De Schutter E (2014) Python-based geometry preparation and simulation visualization toolkits for STEPS. Front Neuroinform 8:37 [Journal] [PubMed]
  • Python-based toolkits for STEPS (Chen and De Schutter 2014) [Model]
Cisi RR, Kohn AF (2008) Simulation system of spinal cord motor nuclei and associated nerves and muscles, in a Web-based architecture. J Comput Neurosci 25:520-42 [Journal] [PubMed]
  • Simulation system of spinal cord motor nuclei and assoc. nerves and muscles (Cisi and Kohn 2008) [Model]
Connelly WM, Crunelli V, Errington AC (2015) The Global Spike: Conserved Dendritic Properties Enable Unique Ca2+ Spike Generation in Low-Threshold Spiking Neurons. J Neurosci 35:15505-22 [Journal] [PubMed]
  • Rat LGN Thalamocortical Neuron (Connelly et al 2015, 2016) [Model]
Coskren PJ, Luebke JI, Kabaso D, Wearne SL, Yadav A, Rumbell T, Hof PR, Weaver CM (2015) Functional consequences of age-related morphologic changes to pyramidal neurons of the rhesus monkey prefrontal cortex. J Comput Neurosci 38:263-83 [Journal] [PubMed]
  • Rhesus Monkey Layer 3 Pyramidal Neurons: Young vs aged PFC (Coskren et al. 2015) [Model]
Deitcher Y, Eyal G, Kanari L, Verhoog MB, Atenekeng Kahou GA, Mansvelder HD, de Kock CPJ, Segev I (2017) Comprehensive Morpho-Electrotonic Analysis Shows 2 Distinct Classes of L2 and L3 Pyramidal Neurons in Human Temporal Cortex. Cereb Cortex 27:5398-5414 [Journal] [PubMed]
  • 2 Distinct Classes of L2 and L3 Pyramidal Neurons in Human Temporal Cortex (Deitcher et al 2017) [Model]
Doron M, Chindemi G, Muller E, Markram H, Segev I (2017) Timed Synaptic Inhibition Shapes NMDA Spikes, Influencing Local Dendritic Processing and Global I/O Properties of Cortical Neurons. Cell Rep 21:1550-1561 [Journal] [PubMed]
  • Shaping NMDA spikes by timed synaptic inhibition on L5PC (Doron et al. 2017) [Model]
Dover K, Marra C, Solinas S, Popovic M, Subramaniyam S, Zecevic D, D'Angelo E, Goldfarb M (2016) FHF-independent conduction of action potentials along the leak-resistant cerebellar granule cell axon. Nat Commun 7:12895 [Journal] [PubMed]
  • Cerebellum granule cell FHF (Dover et al. 2016) [Model]
Doyon N, Prescott SA, Castonguay A, Godin AG, Kröger H, De Koninck Y (2011) Efficacy of synaptic inhibition depends on multiple, dynamically interacting mechanisms implicated in chloride homeostasis. PLoS Comput Biol 7:e1002149 [Journal] [PubMed]
Eguchi A, Neymotin SA, Stringer SM (2014) Color opponent receptive fields self-organize in a biophysical model of visual cortex via spike-timing dependent plasticity Front. Neural Circuits 8:16 [Journal] [PubMed]
  • Simulated cortical color opponent receptive fields self-organize via STDP (Eguchi et al., 2014) [Model]
Ermentrout GB, Terman DH (2010) Mathematical Foundations of Neuroscience Interdisciplinary Applied Mathematics, Antman SS:Marsden JE:Sirovich L:Wiggins, ed. pp.1 [Journal]
  • Mathematical Foundations of Neuroscience (Ermentrout and Terman 2010) [Model]
Ferguson KA, Huh CY, Amilhon B, Manseau F, Williams S, Skinner FK (2015) Network models provide insights into how oriens-lacunosum-moleculare and bistratified cell interactions influence the power of local hippocampal CA1 theta oscillations. Front Syst Neurosci 9:110 [Journal] [PubMed]
  • CA1 SOM+ (OLM) hippocampal interneuron (Ferguson et al. 2015) [Model]
Ferrario A, Merrison-Hort R, Soffe SR, Borisyuk R (2018) Structural and functional properties of a probabilistic model of neuronal connectivity in a simple locomotor network. Elife [Journal] [PubMed]
  • Model of the Xenopus tadpole swimming spinal network (Roberts et al. 2014) [Model]
Forrest MD (2015) Simulation of alcohol action upon a detailed Purkinje neuron model and a simpler surrogate model that runs >400 times faster. BMC Neurosci 16:27 [Journal] [PubMed]
  • Alcohol action in a detailed Purkinje neuron model and an efficient simplified model (Forrest 2015) [Model]
Foutz TJ, Arlow RL, McIntyre CC (2012) Theoretical principles underlying optical stimulation of a channelrhodopsin-2 positive pyramidal neuron. J Neurophysiol 107:3235-45 [Journal] [PubMed]
  • Optical stimulation of a channelrhodopsin-2 positive pyramidal neuron model (Foutz et al 2012) [Model]
Friedrich P, Vella M, Gulyás AI, Freund TF, Káli S (2014) A flexible, interactive software tool for fitting the parameters of neuronal models. Front Neuroinform 8:63 [Journal] [PubMed]
  • Software (called Optimizer) for fitting neuronal models (Friedrich et al. 2014) [Model]
Giugliano M, Gambazzi L, Ballerini L, Prato M, Campidelli S (2012) Carbon nanotubes as electrical interfaces to neurons Nanotechnology for Biology and Medicine, Parpura V, Silva GA, ed. pp.187 [Journal]
  • Carbon nanotubes as electrical interfaces to neurons (Giugliano et al. 2008) [Model]
Gleeson P, Crook S, Cannon RC, Hines ML, Billings GO, Farinella M, Morse TM, Davison AP, Ray S, Bhalla US, Barnes SR, Dimitrova YD, Silver RA (2010) NeuroML: a language for describing data driven models of neurons and networks with a high degree of biological detail. PLoS Comput Biol 6:e1000815 [Journal] [PubMed]
Goodliffe JW, Song H, Rubakovic A, Chang W, Medalla M, Weaver CM, Luebke JI (2018) Differential changes to D1 and D2 medium spiny neurons in the 12-month-old Q175+/- mouse model of Huntington's Disease. PLoS One 13:e0200626 [Journal] [PubMed]
  • Electrotonic transform and EPSCs for WT and Q175+/- spiny projection neurons (Goodliffe et al 2018) [Model]
Graham BP, Saudargiene A, Cobb S (2014) Spine head calcium as a measure of summed postsynaptic activity for driving synaptic plasticity. Neural Comput 26:2194-222 [Journal] [PubMed]
  • Spine head calcium in a CA1 pyramidal cell model (Graham et al. 2014) [Model]
Grein S, Stepniewski M, Reiter S, Knodel MM, Queisser G (2014) 1D-3D hybrid modeling-from multi-compartment models to full resolution models in space and time. Front Neuroinform 8:68 [Journal] [PubMed]
Grossman N, Simiaki V, Martinet C, Toumazou C, Schultz SR, Nikolic K (2013) The spatial pattern of light determines the kinetics and modulates backpropagation of optogenetic action potentials. J Comput Neurosci 34:477-88 [Journal] [PubMed]
Grunditz A, Holbro N, Tian L, Zuo Y, Oertner TG (2008s) Supplementary data to Spine Neck Plasticity Controls Postsynaptic Calcium Signals through Electrical Compartmentalization J Neurosci 28(50):13457-13466 [Journal]
Guet-McCreight A, Camiré O, Topolnik L, Skinner FK (2016) Using a Semi-Automated Strategy to Develop Multi-Compartment Models That Predict Biophysical Properties of Interneuron-Specific 3 (IS3) Cells in Hippocampus. eNeuro [Journal] [PubMed]
  • Interneuron Specific 3 Interneuron Model (Guet-McCreight et al, 2016) [Model]
Gulledge AT, Carnevale NT, Stuart GJ (2012) Electrical advantages of dendritic spines. PLoS One 7:e36007 [Journal] [PubMed]
Günay C, Sieling FH, Dharmar L, Lin WH, Wolfram V, Marley R, Baines RA, Prinz AA (2015) Distal spike initiation zone location estimation by morphological simulation of ionic current filtering demonstrated in a novel model of an identified Drosophila motoneuron. PLoS Comput Biol 11:e1004189 [Journal] [PubMed]
  • Drosophila 3rd instar larval aCC motoneuron (Gunay et al. 2015) [Model]
Hagen E, Fossum JC, Pettersen KH, Alonso JM, Swadlow HA, Einevoll GT (2017) Focal Local Field Potential Signature of the Single-Axon Monosynaptic Thalamocortical Connection. J Neurosci 37:5123-5143 [Journal] [PubMed]
  • LFP signature of monosynaptic thalamocortical connection (Hagen et al 2017) [Model]
Hahn PJ, McIntyre CC (2010) Modeling shifts in the rate and pattern of subthalamopallidal network activity during deep brain stimulation. J Comput Neurosci 28:425-41 [Journal] [PubMed]
  • Basal ganglia network model of subthalamic deep brain stimulation (Hahn and McIntyre 2010) [Model]
Hallermann S, de Kock CP, Stuart GJ, Kole MH (2012) State and location dependence of action potential metabolic cost in cortical pyramidal neurons. Nat Neurosci 15:1007-14 [Journal] [PubMed]
  • State and location dependence of action potential metabolic cost (Hallermann et al., 2012) [Model]
Hay E, Schürmann F, Markram H, Segev I (2013) Preserving axosomatic spiking features despite diverse dendritic morphology. J Neurophysiol 109:2972-81 [Journal] [PubMed]
  • Preserving axosomatic spiking features despite diverse dendritic morphology (Hay et al., 2013) [Model]
Heitmann S, Breakspear M (2018) Chapter 1 Handbook for the Brain Dynamics Toolbox: Version 2018a :1-88 [Journal]
  • Brain Dynamics Toolbox (Heitmann & Breakspear 2016, 2017, 2018) [Model]
Hernández OE, Zurek EE (2013) Teaching and learning the Hodgkin-Huxley model based on software developed in NEURON's programming language hoc. BMC Med Educ 13:70 [Journal] [PubMed]
  • Software for teaching the Hodgkin-Huxley model (Hernandez & Zurek 2013) (SENB written in NEURON hoc) [Model]
Holmes WR, Huwe JA, Williams B, Rowe MH, Peterson EH (2017) Models of utricular bouton afferents: role of afferent-hair cell connectivity in determining spike train regularity. J Neurophysiol 117:1969-1986 [Journal] [PubMed]
  • Role of afferent-hair cell connectivity in determining spike train regularity (Holmes et al 2017) [Model]
Huang S, Hong S, De Schutter E (2015) Non-linear leak currents affect mammalian neuron physiology. Front Cell Neurosci 9:432 [Journal] [PubMed]
  • Concentration dependent nonlinear K+ and Cl- leak current (Huang et al. 2015) [Model]
Hummos A, Franklin CC, Nair SS (2014) Intrinsic mechanisms stabilize encoding and retrieval circuits differentially in a hippocampal network model. Hippocampus 24:1430-48 [Journal] [PubMed]
  • Role for short term plasticity and OLM cells in containing spread of excitation (Hummos et al 2014) [Model]
Hummos A, Nair SS (2017) An integrative model of the intrinsic hippocampal theta rhythm. PLoS One 12:e0182648 [Journal] [PubMed]
  • Role for short term plasticity and OLM cells in containing spread of excitation (Hummos et al 2014) [Model]
Kerr CC, Neymotin SA, Chadderdon GL, Fietkiewicz CT, Francis JT, Lytton WW (2012) Electrostimulation as a prosthesis for repair of information flow in a computer model of neocortex. IEEE Trans Neural Syst Rehabil Eng 20:153-60 [Journal] [PubMed]
  • Prosthetic electrostimulation for information flow repair in a neocortical simulation (Kerr 2012) [Model]
Kerr CC, Van Albada SJ, Neymotin SA, Chadderdon GL, Robinson PA, Lytton WW (2013) Cortical information flow in Parkinson's disease: a composite network/field model. Front Comput Neurosci 7:39 [Journal] [PubMed]
  • Composite spiking network/neural field model of Parkinsons (Kerr et al 2013) [Model]
Kim D, Paré D, Nair SS (2013) Mechanisms contributing to the induction and storage of Pavlovian fear memories in the lateral amygdala. Learn Mem 20:421-30 [Journal] [PubMed]
  • A 1000 cell network model for Lateral Amygdala (Kim et al. 2013) [Model]
Kim H (2017) Impact of the localization of dendritic calcium persistent inward current on the input-output properties of spinal motoneuron pool: a computational study. J Appl Physiol (1985) 123:1166-1187 [Journal] [PubMed]
  • Locational influence of dendritic PIC on input-output properties of spinal motoneurons (Kim 2017) [Model]
Kole MH, Ilschner SU, Kampa BM, Williams SR, Ruben PC, Stuart GJ (2008) Action potential generation requires a high sodium channel density in the axon initial segment. Nat Neurosci 11:178-86 [Journal] [PubMed]
  • Na+ channel dependence of AP initiation in cortical pyramidal neuron (Kole et al. 2008) [Model]
Kuck A, Stegeman DF, van Asseldonk EHF (2017) Modeling trans-spinal direct current stimulation for the modulation of the lumbar spinal motor pathways J Neural Eng. 14(5):056014 [Journal] [PubMed]
Le Franc Y, Le Masson G (2010) Multiple firing patterns in deep dorsal horn neurons of the spinal cord: computational analysis of mechanisms and functional implications. J Neurophysiol 104:1978-96 [Journal] [PubMed]
Li G, Cleland TA (2013) A two-layer biophysical model of cholinergic neuromodulation in olfactory bulb. J Neurosci 33:3037-58 [Journal] [PubMed]
  • A two-layer biophysical olfactory bulb model of cholinergic neuromodulation (Li and Cleland 2013) [Model]
Li G, Cleland TA (2017) A coupled-oscillator model of olfactory bulb gamma oscillations. PLoS Comput Biol 13:e1005760 [Journal] [PubMed]
  • 2D model of olfactory bulb gamma oscillations (Li and Cleland 2017) [Model]
Linaro D, Storace M, Giugliano M (2011) Accurate and fast simulation of channel noise in conductance-based model neurons by diffusion approximation. PLoS Comput Biol 7:e1001102 [Journal] [PubMed]
  • Accurate and fast simulation of channel noise in conductance-based model neurons (Linaro et al 2011) [Model]
Lonardoni D, Amin H, Di Marco S, Maccione A, Berdondini L, Nieus T (2017) Recurrently connected and localized neuronal communities initiate coordinated spontaneous activity in neuronal networks. PLoS Comput Biol 13:e1005672 [Journal] [PubMed]
Lytton WW, Neymotin SA, Wester JC, Contreras D (2011) Neocortical simulation for epilepsy surgery guidance: Localization and intervention Computational Surgery and Dual Training [Journal]
  • Computational Surgery (Lytton et al. 2011) [Model]
Lytton WW, Orman R, Stewart M (2008) Broadening of activity with flow across neural structures. Perception 37:401-7 [Journal] [PubMed]
  • Broadening of activity with flow across neural structures (Lytton et al. 2008) [Model]
Lytton WW, Seidenstein AH, Dura-Bernal S, McDougal RA, Schürmann F, Hines ML (2016) Simulation Neurotechnologies for Advancing Brain Research: Parallelizing Large Networks in NEURON. Neural Comput 28:2063-90 [Journal] [PubMed]
  • Parallelizing large networks in NEURON (Lytton et al. 2016) [Model]
Major G, Polsky A, Denk W, Schiller J, Tank DW (2008) Spatiotemporally graded NMDA spike/plateau potentials in basal dendrites of neocortical pyramidal neurons. J Neurophysiol 99:2584-601 [Journal] [PubMed]
Mandge D, Manchanda R (2018) A biophysically detailed computational model of urinary bladder small DRG neuron soma. PLoS Comput Biol 14:e1006293 [Journal] [PubMed]
  • Computational model of bladder small DRG neuron soma (Mandge & Manchanda 2018) [Model]
Manninen T, Hituri K, Kotaleski JH, Blackwell KT, Linne ML (2010) Postsynaptic signal transduction models for long-term potentiation and depression. Front Comput Neurosci 4:152 [Journal] [PubMed]
Markram H, Muller E, Ramaswamy S, Reimann MW, Abdellah M, Sanchez CA, Ailamaki A, Alonso-Nanclares L, Antille N, Arsever S, Kahou GA, Berger TK, Bilgili A, Buncic N, Chalimourda A, Chindemi G, Courcol JD, Delalondre F, Delattre V, Druckmann S, Dumusc R, Dynes J, Eilemann S, Gal E, Gevaert ME, Ghobril JP, Gidon A, Graham JW, Gupta A, Haenel V, Hay E, Heinis T, Hernando JB, Hines M, Kanari L, Keller D, Kenyon J, Khazen G, Kim Y, King JG, Kisvarday Z, Kumbhar P, Lasserre S, Le Bé JV, Magalhães BR, Merchán-Pérez A, Meystre J, Morrice BR, Muller J, Muñoz-Céspedes A, Muralidhar S, Muthurasa K, Nachbaur D, Newton TH, Nolte M, Ovcharenko A, Palacios J, Pastor L, Perin R, Ranjan R, Riachi I, Rodríguez JR, Riquelme JL, Rössert C, Sfyrakis K, Shi Y, Shillcock JC, Silberberg G, Silva R, Tauheed F, Telefont M, Toledo-Rodriguez M, Tränkler T, Van Geit W, Díaz JV, Walker R, Wang Y, Zaninetta SM (2015) Reconstruction and Simulation of Neocortical Microcircuitry. Cell 163:456-92 [Journal] [PubMed]
  • The neocortical microcircuit collaboration portal (Markram et al. 2015) [Model]
Mateos-Aparicio P, Murphy R, Storm JF (2014) Complementary functions of SK and Kv7/M potassium channels in excitability control and synaptic integration in rat hippocampal dentate granule cells. J Physiol 592:669-93 [Journal] [PubMed]
  • Dentate granule cell: mAHP & sAHP; SK & Kv7/M channels (Mateos-Aparicio et al., 2014) [Model]
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]
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 [Journal] [PubMed]
  • Multiscale simulation of the striatal medium spiny neuron (Mattioni & Le Novere 2013) [Model]
Medan V, Mäki-Marttunen T, Sztarker J, Preuss T (2018) Differential processing in modality-specific Mauthner cell dendrites. J Physiol 596:667-689 [Journal] [PubMed]
  • Goldfish Mauthner cell (Medan et al 2017) [Model]
Miceli S, Ness TV, Einevoll GT, Schubert D (2017) Impedance Spectrum in Cortical Tissue: Implications for Propagation of LFP Signals on the Microscopic Level Eneuro 4:1-15 [Journal]
  • Impedance spectrum in cortical tissue: implications for LFP signal propagation (Miceli et al. 2017) [Model]
Moriyoshi Y, Takeuchi T (1991) [Exocrine pancreatic function tests]. Rinsho Byori Suppl 89:49-57 [PubMed]
Mukunda CL, Narayanan R (2017) Degeneracy in the regulation of short-term plasticity and synaptic filtering by presynaptic mechanisms. J Physiol 595:2611-2637 [Journal] [PubMed]
  • Conductance based model for short term plasticity at CA3-CA1 synapses (Mukunda & Narayanan 2017) [Model]
Munro E, Kopell N (2012) Subthreshold somatic voltage in neocortical pyramidal cells can control whether spikes propagate from the axonal plexus to axon terminals: a model study. J Neurophysiol 107:2833-52 [Journal] [PubMed]
  • Neocort. pyramidal cells subthreshold somatic voltage controls spike propagation (Munro Kopell 2012) [Model]
Narayanan R, Johnston D (2007) Long-term potentiation in rat hippocampal neurons is accompanied by spatially widespread changes in intrinsic oscillatory dynamics and excitability. Neuron 56:1061-75 [Journal] [PubMed]
  • Resonance properties through Chirp stimulus responses (Narayanan Johnston 2007, 2008) [Model]
  • Chirp stimulus responses in a morphologically realistic model (Narayanan and Johnston, 2007) [Model]
Narayanan R, Johnston D (2008) The h channel mediates location dependence and plasticity of intrinsic phase response in rat hippocampal neurons. J Neurosci 28:5846-60 [Journal] [PubMed]
  • Resonance properties through Chirp stimulus responses (Narayanan Johnston 2007, 2008) [Model]
Narayanan R, Johnston D (2010) The h current is a candidate mechanism for regulating the sliding modification threshold in a BCM-like synaptic learning rule. J Neurophysiol 104:1020-33 [Journal] [PubMed]
  • BCM-like synaptic plasticity with conductance-based models (Narayanan Johnston, 2010) [Model]
Ness TV, Remme MW, Einevoll GT (2016) Active subthreshold dendritic conductances shape the local field potential. J Physiol 594:3809-25 [Journal] [PubMed]
Neymotin S, Uhlrich DJ, Manning KA, Lytton WW (2008) Data mining of time-domain features from neural extracellular field data Applic. of Comput. Intel. in Bioinf. and Biomed.: Current Trends and Open Problems 151:119-140 [Journal]
  • NEURON interfaces to MySQL and the SPUD feature extraction algorithm (Neymotin et al. 2008) [Model]
Neymotin SA, Chadderdon GL, Kerr CC, Francis JT, Lytton WW (2013) Reinforcement learning of two-joint virtual arm reaching in a computer model of sensorimotor cortex. Neural Comput 25:3263-93 [Journal] [PubMed]
  • Sensorimotor cortex reinforcement learning of 2-joint virtual arm reaching (Neymotin et al. 2013) [Model]
Neymotin SA, Dura-Bernal S, Lakatos P, Sanger TD, Lytton WW (2016) Multitarget Multiscale Simulation for Pharmacological Treatment of Dystonia in Motor Cortex. Front Pharmacol 7:157 [Journal] [PubMed]
  • Multitarget pharmacology for Dystonia in M1 (Neymotin et al 2016) [Model]
Neymotin SA, Hilscher MM, Moulin TC, Skolnick Y, Lazarewicz MT, Lytton WW (2013) Ih tunes theta/gamma oscillations and cross-frequency coupling in an in silico CA3 model. PLoS One 8:e76285 [Journal] [PubMed]
  • Ih tunes oscillations in an In Silico CA3 model (Neymotin et al. 2013) [Model]
Neymotin SA, Jacobs KM, Fenton AA, Lytton WW (2011) Synaptic information transfer in computer models of neocortical columns. J Comput Neurosci 30:69-84 [Journal] [PubMed]
  • Synaptic information transfer in computer models of neocortical columns (Neymotin et al. 2010) [Model]
Neymotin SA, Lee H, Fenton AA, Lytton WW (2010) Interictal EEG discoordination in a rat seizure model. J Clin Neurophysiol 27:438-44 [Journal] [PubMed]
Neymotin SA, Lee H, Park E, Fenton AA, Lytton WW (2011) Emergence of physiological oscillation frequencies in a computer model of neocortex. Front Comput Neurosci 5:19 [Journal] [PubMed]
  • Emergence of physiological oscillation frequencies in neocortex simulations (Neymotin et al. 2011) [Model]
Neymotin SA, McDougal RA, Sherif MA, Fall CP, Hines ML, Lytton WW (2015) Neuronal calcium wave propagation varies with changes in endoplasmic reticulum parameters: a computer model. Neural Comput 27:898-924 [Journal] [PubMed]
  • Neuronal dendrite calcium wave model (Neymotin et al, 2015) [Model]
Nichols EJ, Hutt A (2015) Neural field simulator: two-dimensional spatio-temporal dynamics involving finite transmission speed. Front Neuroinform 9:25 [Journal] [PubMed]
  • Neural Field Simulator (Nichols & Hutt 2012-2015) [Model]
Oltedal L, Mørkve SH, Veruki ML, Hartveit E (2007) Patch-clamp investigations and compartmental modeling of rod bipolar axon terminals in an in vitro thin-slice preparation of the mammalian retina. J Neurophysiol 97:1171-87 [Journal] [PubMed]
  • Recording from rod bipolar axon terminals in situ (Oltedal et al 2007) [Model]
Omurtag A, Lytton WW (2010) Spectral method and high-order finite differences for the nonlinear cable equation. Neural Comput 22:2113-36 [Journal] [PubMed]
  • Spectral method and high-order finite differences for nonlinear cable (Omurtag and Lytton 2010) [Model]
Ona-Jodar T, Gerkau NJ, Sara Aghvami S, Rose CR, Egger V (2017) Two-Photon Na+ Imaging Reports Somatically Evoked Action Potentials in Rat Olfactory Bulb Mitral and Granule Cell Neurites. Front Cell Neurosci 11:50 [Journal] [PubMed]
  • Na+ Signals in olfactory bulb neurons (granule cell model) (Ona-Jodar et al. 2017) [Model]
Parekh R, Ascoli GA (2013) Neuronal morphology goes digital: a research hub for cellular and system neuroscience. Neuron 77:1017-38 [Journal] [PubMed]
  • Neuronal morphology goes digital ... (Parekh & Ascoli 2013) [Model]
Pelot NA, Behrend CE, Grill WM (2017) Modeling the response of small myelinated axons in a compound nerve to kilohertz frequency signals. J Neural Eng 14:046022 [Journal] [PubMed]
Podlaski WF, Seeholzer A, Groschner LN, Miesenböck G, Ranjan R, Vogels TP (2017) Mapping the function of neuronal ion channels in model and experiment. Elife [Journal] [PubMed]
Popovic MA, Gao X, Carnevale NT, Zecevic D (2014) Cortical dendritic spine heads are not electrically isolated by the spine neck from membrane potential signals in parent dendrites. Cereb Cortex 24:385-95 [Journal] [PubMed]
Publio R, Oliveira RF, Roque AC (2009) A computational study on the role of gap junctions and rod Ih conductance in the enhancement of the dynamic range of the retina. PLoS One 4:e6970 [Journal] [PubMed]
  • A network model of the vertebrate retina (Publio et al. 2009) [Model]
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]
Reetz O, Stadler K, Strauss U (2014) Protein kinase C activation mediates interferon-ß-induced neuronal excitability changes in neocortical pyramidal neurons. J Neuroinflammation 11:185 [Journal] [PubMed]
  • Firing neocortical layer V pyramidal neuron (Reetz et al. 2014; Stadler et al. 2014) [Model]
Reilly JP (2016) Survey of numerical electrostimulation models. Phys Med Biol 61:4346-63 [Journal] [PubMed]
  • Extracellular stimulation of myelinated axon (Reilly 2016) [Model]
Rössert C, Moore LE, Straka H, Glasauer S (2011) Cellular and network contributions to vestibular signal processing: impact of ion conductances, synaptic inhibition, and noise. J Neurosci 31:8359-72 [Journal] [PubMed]
  • Frog second-order vestibular neuron models (Rossert et al. 2011) [Model]
Rowan MS, Neymotin SA (2013) Synaptic Scaling Balances Learning in a Spiking Model of Neocortex Adaptive and Natural Computing Algorithms, Tomassini M, Antonioni A, Daolio F, Buesser P, ed. pp.20 [Journal]
  • Synaptic scaling balances learning in a spiking model of neocortex (Rowan & Neymotin 2013) [Model]
Rowan MS, Neymotin SA, Lytton WW (2014) Electrostimulation to reduce synaptic scaling driven progression of Alzheimer's disease. Front Comput Neurosci 8:39 [Journal] [PubMed]
  • Electrostimulation to reduce synaptic scaling driven progression of Alzheimers (Rowan et al. 2014) [Model]
Royeck M, Horstmann MT, Remy S, Reitze M, Yaari Y, Beck H (2008) Role of axonal NaV1.6 sodium channels in action potential initiation of CA1 pyramidal neurons. J Neurophysiol 100:2361-80 [Journal] [PubMed]
  • Axonal NaV1.6 Sodium Channels in AP Initiation of CA1 Pyramidal Neurons (Royeck et al. 2008) [Model]
Rubin DB, Cleland TA (2006) Dynamical mechanisms of odor processing in olfactory bulb mitral cells. J Neurophysiol 96:555-68 [Journal] [PubMed]
  • Dynamical model of olfactory bulb mitral cell (Rubin, Cleland 2006) [Model]
Rudnicki M, Hemmert W (2017) High Entrainment Constrains Synaptic Depression Levels of an In vivo Globular Bushy Cell Model. Front Comput Neurosci 11:16 [Journal] [PubMed]
  • High entrainment constrains synaptic depression in a globular bushy cell (Rudnicki & Hemmert 2017) [Model]
Rumbell T, Kozloski J (2019) Dimensions of control for subthreshold oscillations and spontaneous firing in dopamine neurons PLOS Computational Biology 15:1-34 [Journal]
  • Control of oscillations and spontaneous firing in dopamine neurons (Rumbell & Kozloski 2019) [Model]
Rumbell TH, Draguljic D, Yadav A, Hof PR, Luebke JI, Weaver CM (2016) Automated evolutionary optimization of ion channel conductances and kinetics in models of young and aged rhesus monkey pyramidal neurons. J Comput Neurosci 41:65-90 [Journal] [PubMed]
  • Rhesus Monkey Young and Aged L3 PFC Pyramidal Neurons (Rumbell et al. 2016) [Model]
Sailamul P, Jang J, Paik SB (2017) Synaptic convergence regulates synchronization-dependent spike transfer in feedforward neural networks. J Comput Neurosci 43:189-202 [Journal] [PubMed]
  • Convergence regulates synchronization-dependent AP transfer in feedforward NNs (Sailamul et al 2017) [Model]
Sanjay M, Neymotin SA, Krothapalli SB (2015) Impaired dendritic inhibition leads to epileptic activity in a computer model of CA3. Hippocampus 25:1336-50 [Journal] [PubMed]
  • CA3 Network Model of Epileptic Activity (Sanjay et. al, 2015) [Model]
Schmidt-Hieber C, Bischofberger J (2010) Fast sodium channel gating supports localized and efficient axonal action potential initiation. J Neurosci 30:10233-42 [Journal] [PubMed]
  • Fast sodium channel gating in mossy fiber axons (Schmidt-Hieber et al. 2010) [Model]
Schmidt-Hieber C, Häusser M (2013) Cellular mechanisms of spatial navigation in the medial entorhinal cortex. Nat Neurosci 16:325-31 [Journal] [PubMed]
  • MEC layer II stellate cell: Synaptic mechanisms of grid cells (Schmidt-Hieber & Hausser 2013) [Model]
Schmidt-Hieber C, Jonas P, Bischofberger J (2007) Subthreshold dendritic signal processing and coincidence detection in dentate gyrus granule cells. J Neurosci 27:8430-41 [Journal] [PubMed]
  • Dentate gyrus granule cell: subthreshold signal processing (Schmidt-Hieber et al. 2007) [Model]
Sekulic V, Chen TC, Lawrence JJ, Skinner FK (2015) Dendritic distributions of I h channels in experimentally-derived multi-compartment models of oriens-lacunosum/moleculare (O-LM) hippocampal interneurons. Front Synaptic Neurosci 7:2 [Journal] [PubMed]
  • Multi-comp. CA1 O-LM interneuron model with varying dendritic Ih distributions (Sekulic et al 2015) [Model]
Singh C, Levy WB (2017) A consensus layer V pyramidal neuron can sustain interpulse-interval coding. PLoS One 12:e0180839 [Journal] [PubMed]
  • Stochastic layer V pyramidal neuron: interpulse interval coding and noise (Singh & Levy 2017) [Model]
Solinas SMG, Edelmann E, Leßmann V, Migliore M (2019) A kinetic model for Brain-Derived Neurotrophic Factor mediated spike timing-dependent LTP. PLoS Comput Biol 15:e1006975 [Journal] [PubMed]
  • STDP and BDNF in CA1 spines (Solinas et al. 2019) [Model]
Steephen JE, Manchanda R (2009) Differences in biophysical properties of nucleus accumbens medium spiny neurons emerging from inactivation of inward rectifying potassium currents. J Comput Neurosci 27:453-70 [Journal] [PubMed]
  • Effects of KIR current inactivation in NAc Medium Spiny Neurons (Steephen and Manchanda 2009) [Model]
Sterratt D, Graham B, Gillies A, Willshaw D (2011) Principles of Computational Modelling in Neuroscience, Cambridge University Press :1-401 [Journal]
  • Principles of Computational Modelling in Neuroscience (Book) (Sterratt et al. 2011) [Model]
Stiefel KM, Englitz B, Sejnowski TJ (2013) Origin of intrinsic irregular firing in cortical interneurons. Proc Natl Acad Sci U S A 110:7886-91 [Journal] [PubMed]
Thomas EA, Petrou S (2013) Network-specific mechanisms may explain the paradoxical effects of carbamazepine and phenytoin. Epilepsia 54:1195-202 [Journal] [PubMed]
  • State dependent drug binding to sodium channels in the dentate gyrus (Thomas & Petrou 2013) [Model]
van der Velden L, van Hooft JA, Chameau P (2012) Altered dendritic complexity affects firing properties of cortical layer 2/3 pyramidal neurons in mice lacking the 5-HT3A receptor. J Neurophysiol 108:1521-8 [Journal] [PubMed]
  • Altered complexity in layer 2/3 pyramidal neurons (Luuk van der Velden et al. 2012) [Model]
van Elburg RA, van Ooyen A (2009) Generalization of the event-based Carnevale-Hines integration scheme for integrate-and-fire models. Neural Comput 21:1913-30 [Journal] [PubMed]
  • Generalized Carnevale-Hines algorithm (van Elburg and van Ooyen 2009) [Model]
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]
Wang XD, Hao J, Poo MM, Zhang XH (2006) How does a neuron perform subtraction? - Arithmetic rules of synaptic integration of excitation and inhibition Advances in Neural Networks-ISNN 2006 3971:7-14
Welday AC, Shlifer IG, Bloom ML, Zhang K, Blair HT (2011) Cosine directional tuning of theta cell burst frequencies: evidence for spatial coding by oscillatory interference. J Neurosci 31:16157-76 [Journal] [PubMed]
  • Synthesis of spatial tuning functions from theta cell spike trains (Welday et al., 2011) [Model]
Yamazaki T, Ikeno H, Okumura Y, Satoh S, Kamiyama Y, Hirata Y, Inagaki K, Ishihara A, Kannon T, Usui S (2011) Simulation Platform: a cloud-based online simulation environment. Neural Netw 24:693-8 [Journal] [PubMed]
Young RG, Castelfranco AM, Hartline DK (2013) The "Lillie transition": models of the onset of saltatory conduction in myelinating axons. J Comput Neurosci 34:533-46 [Journal] [PubMed]
  • Lillie Transition: onset of saltatory conduction in myelinating axons (Young et al. 2013) [Model]
Yu N, Canavier CC (2015) A Mathematical Model of a Midbrain Dopamine Neuron Identifies Two Slow Variables Likely Responsible for Bursts Evoked by SK Channel Antagonists and Terminated by Depolarization Block. J Math Neurosci 5:5 [Journal] [PubMed]
  • Phase plane reveals two slow variables in midbrain dopamine neuron bursts (Yu and Canavier, 2015) [Model]
Zhang X, Santaniello S (2019) Role of cerebellar GABAergic dysfunctions in the origins of essential tremor Proceedings of the National Academy of Sciences [Journal]
  • A cortico-cerebello-thalamo-cortical loop model under essential tremor (Zhang & Santaniello 2019) [Model]
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