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• CA1 pyramidal neuron: rebound spiking (Ascoli et al.2010) [Model]

Ashhad S, Narayanan R. (2013). Quantitative interactions between the A-type K+ current and inositol trisphosphate receptors regulate intraneuronal Ca2+ waves and synaptic plasticity. The Journal of physiology. 591 [PubMed]

• Calcium waves and mGluR-dependent synaptic plasticity in CA1 pyr. neurons (Ashhad & Narayanan 2013) [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. Journal of computational neuroscience. 31 [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, Massobrio P. (2015). Axon-somatic back-propagation in detailed models of spinal alpha motoneurons. Frontiers in computational neuroscience. 9 [PubMed]

• Axon-somatic back-propagation in a detailed model of cat spinal motoneuron (Balbi et al, 2015) [Model]

Basak R, Narayanan R. (2018). Active dendrites regulate the spatiotemporal spread of signaling microdomains. PLoS computational biology. 14 [PubMed]

• Active dendrites shape signaling microdomains in hippocampal neurons (Basak & Narayanan 2018) [Model]

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• NeuroGPU example on L5_TTPC1_cADpyr232_1 (Ben-Shalom 2022)(Ramaswamy et al., 2015) [Model]

Berzhanskaya J, Chernyy N, Gluckman BJ, Schiff SJ, Ascoli GA. (2013). Modulation of hippocampal rhythms by subthreshold electric fields and network topology. Journal of computational neuroscience. 34 [PubMed]

• Modulation of hippocampal rhythms by electric fields and network topology (Berzhanskaya et al. 2013) [Model]

Bhalla US. (2017). Synaptic input sequence discrimination on behavioral timescales mediated by reaction-diffusion chemistry in dendrites. eLife. 6 [PubMed]

• Discrimination on behavioral time-scales mediated by reaction-diffusion in dendrites (Bhalla 2017) [Model]

Cannon RC, O'Donnell C, Nolan MF. (2010). Stochastic ion channel gating in dendritic neurons: morphology dependence and probabilistic synaptic activation of dendritic spikes. PLoS computational biology. 6 [PubMed]

• Stochastic ion channels and neuronal morphology (Cannon et al. 2010) [Model]

Dan O, Hopp E, Borst A, Segev I. (2018). Non-uniform weighting of local motion inputs underlies dendritic computation in the fly visual system. Scientific reports. 8 [PubMed]

• Vertical system (VS) fly cells with biophysics (Dan et al 2018) [Model]

Das A, Narayanan R. (2015). Active dendrites mediate stratified gamma-range coincidence detection in hippocampal model neurons. The Journal of physiology. 593 [PubMed]

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

• A comparative computer simulation of dendritic morphology (Donohue and Ascoli 2008) [Model]

Du K et al. (2017). Cell-type-specific inhibition of the dendritic plateau potential in striatal spiny projection neurons. Proceedings of the National Academy of Sciences of the United States of America. 114 [PubMed]

• Specific inhibition of dendritic plateau potential in striatal projection neurons (Du et al 2017) [Model]

Ferrante M, Ascoli GA. (2015). Distinct and synergistic feedforward inhibition of pyramidal cells by basket and bistratified interneurons. Frontiers in cellular neuroscience. 9 [PubMed]

• Feedforward inhibition in pyramidal cells (Ferrante & Ascoli 2015) [Model]

Ferrante M, Blackwell KT, Migliore M, Ascoli GA. (2008). Computational models of neuronal biophysics and the characterization of potential neuropharmacological targets. Current medicinal chemistry. 15 [PubMed]

• Computational neuropharmacology of CA1 pyramidal neuron (Ferrante et al. 2008) [Model]

Gidon A, Segev I. (2012). Principles governing the operation of synaptic inhibition in dendrites. Neuron. 75 [PubMed]

• Principles governing the operation of synaptic inhibition in dendrites (Gidon & Segev 2012) [Model]

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]

Hagen E et al. (2017). Focal Local Field Potential Signature of the Single-Axon Monosynaptic Thalamocortical Connection. The Journal of neuroscience : the official journal of the Society for Neuroscience. 37 [PubMed]

• LFP signature of monosynaptic thalamocortical connection (Hagen et al 2017) [Model]

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

• Preserving axosomatic spiking features despite diverse dendritic morphology (Hay et al., 2013) [Model]

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]

• An ion-based model for swelling of neurons and astrocytes (Hubel & Ullah 2016) [Model]

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

• Accelerating with FlyBrainLab discovery of the functional logic of Drosophila brain (Lazar et al 21) [Model]

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

McDougal RA, Hines ML, Lytton WW. (2013). Water-tight membranes from neuronal morphology files. Journal of neuroscience methods. 220 [PubMed]

• Constructed Tessellated Neuronal Geometries (CTNG) (McDougal et al. 2013) [Model]

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

• 3D-printer visualization of NEURON models (McDougal and Shepherd, 2015) [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. Journal of neurophysiology. 107 [PubMed]

• Neocort. pyramidal cells subthreshold somatic voltage controls spike propagation (Munro Kopell 2012) [Model]

Nanda S, Das R, Bhattacharjee S, Cox DN, Ascoli GA. (2018). Morphological determinants of dendritic arborization neurons in Drosophila larva. Brain structure & function. 223 [PubMed]

• Morphological determinants of dendritic arborization neurons in Drosophila larva (Nanda et al 2018) [Model]

Newton AJH, McDougal RA, Hines ML, Lytton WW. (2018). Using NEURON for Reaction-Diffusion Modeling of Extracellular Dynamics. Frontiers in neuroinformatics. 12 [PubMed]

• Using NEURON for reaction-diffusion modeling of extracellular dynamics (Newton et al 2018) [Model]

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

• Computer models of corticospinal neurons replicate in vitro dynamics (Neymotin et al. 2017) [Model]

Schmidt M, Bakker R, Hilgetag CC, Diesmann M, van Albada SJ. (2018). Multi-scale account of the network structure of macaque visual cortex. Brain structure & function. 223 [PubMed]

• Multi-area layer-resolved spiking network model of resting-state dynamics in macaque visual cortex [Model]

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

• Generation of granule cell dendritic morphology (Schneider et al. 2014) [Model]

Schwarzacher SW, Cuntz H, Jedlicka P, Beining M, Mongiat LA. (2017). T2N as a new tool for robust electrophysiological modeling demonstrated for mature and adult-born dentate granule cells eLife.

• GC model (Beining et al 2017) [Model]
• Mature and young adult-born dentate granule cell models (T2N interface) (Beining et al. 2017) [Model]

Sinha M, Narayanan R. (2015). HCN channels enhance spike phase coherence and regulate the phase of spikes and LFPs in the theta-frequency range. Proceedings of the National Academy of Sciences of the United States of America. 112 [PubMed]

• Subthreshold conductances regulate theta-frequency LFPs and spike phase (Sinha and Narayanan, 2015) [Model]

Tejada J, Arisi GM, García-Cairasco N, Roque AC. (2012). Morphological alterations in newly born dentate gyrus granule cells that emerge after status epilepticus contribute to make them less excitable. PloS one. 7 [PubMed]

• Dentate gyrus network model (Tejada et al 2014) [Model]

Tomsett RJ et al. (2015). Virtual Electrode Recording Tool for EXtracellular potentials (VERTEX): comparing multi-electrode recordings from simulated and biological mammalian cortical tissue. Brain structure & function. 220 [PubMed]

• Large-scale model of neocortical slice in vitro exhibiting persistent gamma (Tomsett et al. 2014) [Model]

Venkadesh S et al. (2018). Evolving Simple Models of Diverse Intrinsic Dynamics in Hippocampal Neuron Types. Frontiers in neuroinformatics. 12 [PubMed]

• Evolving simple models of diverse dynamics in hippocampal neuron types (Venkadesh et al 2018) [Model]

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

Wu T, Fan J, Lee KS, Li X. (2016). Cortical neuron activation induced by electromagnetic stimulation: a quantitative analysis via modelling and simulation. Journal of computational neuroscience. 40 [PubMed]