Hines ML, Morse T, Migliore M, Carnevale NT, Shepherd GM. (2004). ModelDB: A Database to Support Computational Neuroscience. Journal of computational neuroscience. 17 [PubMed]

See more from authors: Hines ML · Morse T · Migliore M · Carnevale NT · Shepherd GM

References and models cited by this paper

Migliore M et al. (2003). ModelDB: making models publicly accessible to support computational neuroscience. Neuroinformatics. 1 [PubMed]

References and models that cite this paper

Amatrudo JM et al. (2012). Influence of highly distinctive structural properties on the excitability of pyramidal neurons in monkey visual and prefrontal cortices. The Journal of neuroscience : the official journal of the Society for Neuroscience. 32 [PubMed]

Anderson WD, Galván EJ, Mauna JC, Thiels E, Barrionuevo G. (2011). Properties and functional implications of I (h) in hippocampal area CA3 interneurons. Pflugers Archiv : European journal of physiology. 462 [PubMed]

Anderson WD et al. (2015). Computational modeling of cytokine signaling in microglia. Molecular bioSystems. 11 [PubMed]

Anderson WD, Makadia HK, Vadigepalli R. (2016). Molecular variability elicits a tunable switch with discrete neuromodulatory response phenotypes. Journal of computational neuroscience. 40 [PubMed]

Bahl A, Stemmler MB, Herz AV, Roth A. (2012). Automated optimization of a reduced layer 5 pyramidal cell model based on experimental data. Journal of neuroscience methods. 210 [PubMed]

Bahmer A, Langner G. (2010). Parameters for a model of an oscillating neuronal network in the cochlear nucleus defined by genetic algorithms. Biological cybernetics. 102 [PubMed]

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. Journal of computational neuroscience. 31 [PubMed]

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. Journal of neurophysiology. 112 [PubMed]

Calin-Jageman RJ, Tunstall MJ, Mensh BD, Katz PS, Frost WN. (2007). Parameter space analysis suggests multi-site plasticity contributes to motor pattern initiation in Tritonia. Journal of neurophysiology. 98 [PubMed]

Canakci S, Toy MF, Inci AF, Liu X, Kuzum D. (2017). Computational analysis of network activity and spatial reach of sharp wave-ripples. PloS one. 12 [PubMed]

Carey RM, Sherwood WE, Shipley MT, Borisyuk A, Wachowiak M. (2015). Role of intraglomerular circuits in shaping temporally structured responses to naturalistic inhalation-driven sensory input to the olfactory bulb. Journal of neurophysiology. 113 [PubMed]

Castro L, Aguiar P. (2012). Phase precession through acceleration of local theta rhythm: a biophysical model for the interaction between place cells and local inhibitory neurons. Journal of computational neuroscience. 33 [PubMed]

Castro L, Aguiar P. (2014). A feedforward model for the formation of a grid field where spatial information is provided solely from place cells. Biological cybernetics. 108 [PubMed]

Cattani A, Solinas S, Canuto C. (2016). A Hybrid Model for the Computationally-Efficient Simulation of the Cerebellar Granular Layer. Frontiers in computational neuroscience. 10 [PubMed]

Coskren PJ et al. (2015). Functional consequences of age-related morphologic changes to pyramidal neurons of the rhesus monkey prefrontal cortex. Journal of computational neuroscience. 38 [PubMed]

Couto J, Linaro D, De Schutter E, Giugliano M. (2015). On the firing rate dependency of the phase response curve of rat Purkinje neurons in vitro. PLoS computational biology. 11 [PubMed]

Devore S, de Almeida L, Linster C. (2014). Distinct roles of bulbar muscarinic and nicotinic receptors in olfactory discrimination learning. The Journal of neuroscience : the official journal of the Society for Neuroscience. 34 [PubMed]

Diamond JS, Polsky A. (2011). Imperfect Space Clamp Permits Electrotonic Interactions between Inhibitory and Excitatory Synaptic Conductances, Distorting Voltage Clamp Recordings. PLoS ONE. 6(4)

Diwakar S, Parasuram H, Nair B, Medini C, Nair M. (2017). Computational Neuroscience of Timing, Plasticity and Function in Cerebellum Microcircuits (Chapter 12) Computational Neurology and Psychiatry, Springer Series in Bio-/Neuroinformatics.

Donohue DE, Ascoli GA. (2008). A comparative computer simulation of dendritic morphology. PLoS computational biology. 4 [PubMed]

Eglen SJ et al. (2017). Toward standard practices for sharing computer code and programs in neuroscience. Nature neuroscience. 20 [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 Frontiers in neural circuits. 8 [PubMed]

Esposito U, Giugliano M, van Rossum M, Vasilaki E. (2014). Measuring symmetry, asymmetry and randomness in neural network connectivity. PloS one. 9 [PubMed]

Fink CG, Gliske S, Catoni N, Stacey WC. (2015). Network Mechanisms Generating Abnormal and Normal Hippocampal High-Frequency Oscillations: A Computational Analysis. eNeuro. 2 [PubMed]

Forrest MD. (2015). Simulation of alcohol action upon a detailed Purkinje neuron model and a simpler surrogate model that runs >400 times faster. BMC neuroscience. 16 [PubMed]

Giugliano M, Gambazzi L, Ballerini L, Prato M, Campidelli S. (2012). Carbon nanotubes as electrical interfaces to neurons Nanotechnology for Biology and Medicine.

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]

Gleeson P, Steuber V, Silver RA. (2007). neuroConstruct: a tool for modeling networks of neurons in 3D space. Neuron. 54 [PubMed]

Goldwyn JH, Shea-Brown E. (2011). The what and where of adding channel noise to the Hodgkin-Huxley equations. PLoS computational biology. 7 [PubMed]

Goodliffe JW et al. (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 [PubMed]

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. 3 [PubMed]

Handy G, Taheri M, White JA, Borisyuk A. (2017). Mathematical investigation of IP3-dependent calcium dynamics in astrocytes. Journal of computational neuroscience. 42 [PubMed]

Harris JJ, Engl E, Attwell D, Jolivet RB. (2019). Energy-efficient information transfer at thalamocortical synapses. PLoS computational biology. 15 [PubMed]

Hay E, Hill S, Schürmann F, Markram H, Segev I. (2011). Models of neocortical layer 5b pyramidal cells capturing a wide range of dendritic and perisomatic active properties. PLoS computational biology. 7 [PubMed]

Hay E, Schürmann F, Markram H, Segev I. (2013). Preserving axosomatic spiking features despite diverse dendritic morphology. Journal of neurophysiology. 109 [PubMed]

Hay E, Segev I. (2015). Dendritic Excitability and Gain Control in Recurrent Cortical Microcircuits. Cerebral cortex (New York, N.Y. : 1991). 25 [PubMed]

Hossain WA, Antic SD, Yang Y, Rasband MN, Morest DK. (2005). Where is the spike generator of the cochlear nerve? Voltage-gated sodium channels in the mouse cochlea. The Journal of neuroscience : the official journal of the Society for Neuroscience. 25 [PubMed]

Huys QJ, Paninski L. (2009). Smoothing of, and parameter estimation from, noisy biophysical recordings. PLoS computational biology. 5 [PubMed]

Hübel N, Andrew RD, Ullah G. (2016). Large extracellular space leads to neuronal susceptibility to ischemic injury in a Na+/K+ pumps-dependent manner. Journal of computational neuroscience. 40 [PubMed]

Hübel N, Hosseini-Zare MS, Žiburkus J, Ullah G. (2017). The role of glutamate in neuronal ion homeostasis: A case study of spreading depolarization. PLoS computational biology. 13 [PubMed]

Hübel N, Ullah G. (2016). Anions Govern Cell Volume: A Case Study of Relative Astrocytic and Neuronal Swelling in Spreading Depolarization. PloS one. 11 [PubMed]

Jedlicka P et al. (2011). Increased dentate gyrus excitability in neuroligin-2-deficient mice in vivo. Cerebral cortex (New York, N.Y. : 1991). 21 [PubMed]

Kim JK, Forger DB. (2012). A mechanism for robust circadian timekeeping via stoichiometric balance. Molecular systems biology. 8 [PubMed]

Komendantov AO, Ascoli GA. (2009). Dendritic excitability and neuronal morphology as determinants of synaptic efficacy. Journal of neurophysiology. 101 [PubMed]

Lazar AA, Liu T, Turkcan MK, Zhou Y. (2021). Accelerating with FlyBrainLab the discovery of the functional logic of the Drosophila brain in the connectomic and synaptomic era eLife. 10 [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. Journal of neurophysiology. 104 [PubMed]

Lee S, Jones SR. (2013). Distinguishing mechanisms of gamma frequency oscillations in human current source signals using a computational model of a laminar neocortical network. Frontiers in human neuroscience. 7 [PubMed]

Linaro D, Storace M, Giugliano M. (2011). Accurate and fast simulation of channel noise in conductance-based model neurons by diffusion approximation. PLoS computational biology. 7 [PubMed]

Lytton WW. (2006). Neural Query System: Data-mining from within the NEURON simulator. Neuroinformatics. 4 [PubMed]

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

Makadia HK et al. (2015). Multiscale model of dynamic neuromodulation integrating neuropeptide-induced signaling pathway activity with membrane electrophysiology. Biophysical journal. 108 [PubMed]

Makadia HK, Schwaber JS, Vadigepalli R. (2015). Intracellular Information Processing through Encoding and Decoding of Dynamic Signaling Features. PLoS computational biology. 11 [PubMed]

Manninen T, Havela R, Linne M-L. (2017). Reproducibility and comparability of computational models for astrocyte calcium excitability Front. Neuroinform..

Manninen T, Hituri K, Kotaleski JH, Blackwell KT, Linne ML. (2010). Postsynaptic signal transduction models for long-term potentiation and depression. Frontiers in computational neuroscience. 4 [PubMed]

Masquelier T. (2018). STDP Allows Close-to-Optimal Spatiotemporal Spike Pattern Detection by Single Coincidence Detector Neurons. Neuroscience. 389 [PubMed]

Masquelier T, Deco G. (2013). Network bursting dynamics in excitatory cortical neuron cultures results from the combination of different adaptive mechanisms. PloS one. 8 [PubMed]

Masquelier T, Portelli G, Kornprobst P. (2016). Microsaccades enable efficient synchrony-based coding in the retina: a simulation study. Scientific reports. 6 [PubMed]

Masquelier T, Saeed Reza. (2018). Optimal localist and distributed coding of spatiotemporal spike patterns through STDP and coincidence detection Front. Comput. Neurosci..

Mattioni M, Cohen U, Le Novère N. (2012). Neuronvisio: A Graphical User Interface with 3D Capabilities for NEURON. Frontiers in neuroinformatics. 6 [PubMed]

Matveev V, Bose A, Nadim F. (2007). Capturing the bursting dynamics of a two-cell inhibitory network using a one-dimensional map. Journal of computational neuroscience. 23 [PubMed]

McColgan T et al. (2017). Dipolar extracellular potentials generated by axonal projections. eLife. 6 [PubMed]

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

McDougal RA, Shepherd GM. (2015). 3D-printer visualization of neuron models. Frontiers in neuroinformatics. 9 [PubMed]

McKinnon ML et al. (2019). Dramatically Amplified Thoracic Sympathetic Postganglionic Excitability and Integrative Capacity Revealed with Whole-Cell Patch-Clamp Recordings. eNeuro. 6 [PubMed]

McTavish TS, Migliore M, Shepherd GM, Hines ML. (2012). Mitral cell spike synchrony modulated by dendrodendritic synapse location. Frontiers in computational neuroscience. 6 [PubMed]

Moroni M et al. (2011). Chloride ions in the pore of glycine and GABA channels shape the time course and voltage dependence of agonist currents. The Journal of neuroscience : the official journal of the Society for Neuroscience. 31 [PubMed]

Morse TM. (2008). ModelDB in computational neuroscience education - a research tool as interactive educational media. Brains, minds & media : journal of new media in neural and cognitive science and education. 3 [PubMed]

Muller W, Waltemath D, Henkel R, Lange M, Weise S. (2014). Chapter 3 Information Retrieval in Life Sciences: A Programmatic Survey Approaches in Integrative Bioinformatics: Towards the Virtual Cell.

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. Journal of neurophysiology. 107 [PubMed]

Ness TV, Remme MW, Einevoll GT. (2016). Active subthreshold dendritic conductances shape the local field potential. The Journal of physiology. 594 [PubMed]

Neymotin SA et al. (2015). Neuronal calcium wave propagation varies with changes in endoplasmic reticulum parameters: a computer model. Neural computation. 27 [PubMed]

Neymotin SA et al. (2017). Optimizing computer models of corticospinal neurons to replicate in vitro dynamics. Journal of neurophysiology. 117 [PubMed]

Nicola W, Campbell SA. (2013). Bifurcations of large networks of two-dimensional integrate and fire neurons. Journal of computational neuroscience. 35 [PubMed]

Osinski BL, Kay LM. (2016). Granule cell excitability regulates gamma and beta oscillations in a model of the olfactory bulb dendrodendritic microcircuit. Journal of neurophysiology. 116 [PubMed]

Parasuram H et al. (2016). Computational Modeling of Single Neuron Extracellular Electric Potentials and Network Local Field Potentials using LFPsim. Frontiers in computational neuroscience. 10 [PubMed]

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

Poleg-Polsky A. (2015). Effects of Neural Morphology and Input Distribution on Synaptic Processing by Global and Focal NMDA-Spikes. PloS one. 10 [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. Cerebral cortex (New York, N.Y. : 1991). 24 [PubMed]

Pouille F, McTavish TS, Hunter LE, Restrepo D, Schoppa NE. (2017). Intraglomerular gap junctions enhance interglomerular synchrony in a sparsely connected olfactory bulb network. The Journal of physiology. 595 [PubMed]

Richmond P, Buesing L, Giugliano M, Vasilaki E. (2011). Democratic population decisions result in robust policy-gradient learning: a parametric study with GPU simulations. PloS one. 6 [PubMed]

Savtchenko LP et al. (2018). Disentangling astroglial physiology with a realistic cell model in silico. Nature communications. 9 [PubMed]

Schneider CJ, Cuntz H, Soltesz I. (2014). Linking macroscopic with microscopic neuroanatomy using synthetic neuronal populations. PLoS computational biology. 10 [PubMed]

Scuri R, Lombardo P, Cataldo E, Ristori C, Brunelli M. (2007). Inhibition of Na+/K+ ATPase potentiates synaptic transmission in tactile sensory neurons of the leech. The European journal of neuroscience. 25 [PubMed]

Short SM, Morse TM, McTavish TS, Shepherd GM, Verhagen JV. (2016). Respiration Gates Sensory Input Responses in the Mitral Cell Layer of the Olfactory Bulb. PloS one. 11 [PubMed]

Singh C, Levy WB. (2017). A consensus layer V pyramidal neuron can sustain interpulse-interval coding. PloS one. 12 [PubMed]

Stacey WC, Krieger A, Litt B. (2011). Network recruitment to coherent oscillations in a hippocampal computer model. Journal of neurophysiology. 105 [PubMed]

Stanley DA et al. (2013). Phase shift in the 24-hour rhythm of hippocampal EEG spiking activity in a rat model of temporal lobe epilepsy. Journal of neurophysiology. 110 [PubMed]

Stockton DB, Santamaria F. (2015). NeuroManager: a workflow analysis based simulation management engine for computational neuroscience. Frontiers in neuroinformatics. 9 [PubMed]

Testa-Silva G et al. (2012). Hyperconnectivity and slow synapses during early development of medial prefrontal cortex in a mouse model for mental retardation and autism. Cerebral cortex (New York, N.Y. : 1991). 22 [PubMed]

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

Vasilaki E, Giugliano M. (2014). Emergence of connectivity motifs in networks of model neurons with short- and long-term plastic synapses. PloS one. 9 [PubMed]

Waltemath D, Wolkenhauer O. (2016). How Modeling Standards, Software, and Initiatives Support Reproducibility in Systems Biology and Systems Medicine. IEEE transactions on bio-medical engineering. 63 [PubMed]

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. The Journal of neuroscience : the official journal of the Society for Neuroscience. 31 [PubMed]

Williams AH, O'Donnell C, Sejnowski TJ, O'Leary T. (2016). Dendritic trafficking faces physiologically critical speed-precision tradeoffs. eLife. 5 [PubMed]

Yamazaki T et al. (2011). Simulation Platform: a cloud-based online simulation environment. Neural networks : the official journal of the International Neural Network Society. 24 [PubMed]

Zachariou M, Alexander SP, Coombes S, Christodoulou C. (2013). A biophysical model of endocannabinoid-mediated short term depression in hippocampal inhibition. PloS one. 8 [PubMed]

Zandt BJ, Visser S, van Putten MJ, Ten Haken B. (2014). A neural mass model based on single cell dynamics to model pathophysiology. Journal of computational neuroscience. 37 [PubMed]

Zandt BJ, ten Haken B, van Dijk JG, van Putten MJ. (2011). Neural dynamics during anoxia and the "wave of death". PloS one. 6 [PubMed]

Zhang YH, Ji Y, Zheng WM. (2016). Modelling Spiking Neural Network from the Architecture Evaluation Perspective Journal of Computer Science and Technology. 31

Zhou L, Baxter DA, Byrne JH. (2014). Contribution of PKC to the maintenance of 5-HT-induced short-term facilitation at sensorimotor synapses of Aplysia. Journal of neurophysiology. 112 [PubMed]

Zylbertal A, Kahan A, Ben-Shaul Y, Yarom Y, Wagner S. (2015). Prolonged Intracellular Na+ Dynamics Govern Electrical Activity in Accessory Olfactory Bulb Mitral Cells. PLoS biology. 13 [PubMed]

Zylbertal A, Yarom Y, Wagner S. (2017). The Slow Dynamics of Intracellular Sodium Concentration Increase the Time Window of Neuronal Integration: A Simulation Study Frontiers in computational neuroscience. 11 [PubMed]

de Almeida L, Idiart M, Linster C. (2013). A model of cholinergic modulation in olfactory bulb and piriform cortex. Journal of neurophysiology. 109 [PubMed]

This website requires cookies and limited processing of your personal data in order to function. By continuing to browse or otherwise use this site, you are agreeing to this use. See our Privacy policy and how to cite and terms of use.