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• H-currents effect on the fluctuation of gamma/beta oscillations (Avella-Gonzalez et al., 2015) [Model]

Avella Gonzalez OJ et al. (2012). External drive to inhibitory cells induces alternating episodes of high- and low-amplitude oscillations. PLoS computational biology. 8 [PubMed]

• Single E-I oscillating network with amplitude modulation (Avella Gonzalez et al. 2012) [Model]

Bono J, Clopath C. (2017). Modeling somatic and dendritic spike mediated plasticity at the single neuron and network level. Nature communications. 8 [PubMed]

• Modeling dendritic spikes and plasticity (Bono and Clopath 2017) [Model]

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• A detailed and fast model of extracellular recordings (Camunas-Mesa & Qurioga 2013) [Model]

Chrysanthidis N, Fiebig F, Lansner A. (2019). Introducing double bouquet cells into a modular cortical associative memory model Journal of Computational Neuroscience.

• An electrophysiological model of GABAergic double bouquet cells (Chrysanthidis et al. 2019) [Model]

Costa RP et al. (2017). Synaptic Transmission Optimization Predicts Expression Loci of Long-Term Plasticity. Neuron. 96 [PubMed]

• Statistical Long-term Synaptic Plasticity (statLTSP) (Costa et al 2017) [Model]

Costa RP, Sjöström PJ, van Rossum MC. (2013). Probabilistic inference of short-term synaptic plasticity in neocortical microcircuits. Frontiers in computational neuroscience. 7 [PubMed]

• Prob. Inference of Short-Term Synaptic Plasticity in Neocort. Microcircuits (Costa et al. 2013) [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 reports. 21 [PubMed]

• Shaping NMDA spikes by timed synaptic inhibition on L5PC (Doron et al. 2017) [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]

Golomb D et al. (2007). Mechanisms of firing patterns in fast-spiking cortical interneurons. PLoS computational biology. 3 [PubMed]

• Fast-spiking cortical interneuron (Golomb et al. 2007) [Model]

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• CA1 pyr cell: Inhibitory modulation of spatial selectivity+phase precession (Grienberger et al 2017) [Model]

Haeusler S, Maass W. (2007). A statistical analysis of information-processing properties of lamina-specific cortical microcircuit models. Cerebral cortex (New York, N.Y. : 1991). 17 [PubMed]

• Information-processing in lamina-specific cortical microcircuits (Haeusler and Maass 2006) [Model]

Hass J, Hertäg L, Durstewitz D. (2016). A Detailed Data-Driven Network Model of Prefrontal Cortex Reproduces Key Features of In Vivo Activity. PLoS computational biology. 12 [PubMed]

• A detailed data-driven network model of prefrontal cortex (Hass et al 2016) [Model]

Hayut I, Fanselow EE, Connors BW, Golomb D. (2011). LTS and FS inhibitory interneurons, short-term synaptic plasticity, and cortical circuit dynamics. PLoS computational biology. 7 [PubMed]

• Rate model of a cortical RS-FS-LTS network (Hayut et al. 2011) [Model]

Hiratani N, Fukai T. (2017). Detailed Dendritic Excitatory/Inhibitory Balance through Heterosynaptic Spike-Timing-Dependent Plasticity. The Journal of neuroscience : the official journal of the Society for Neuroscience. 37 [PubMed]

• Heterosynaptic Spike-Timing-Dependent Plasticity (Hiratani & Fukai 2017) [Model]

Hoshino O. (2007). Enhanced sound perception by widespread-onset neuronal responses in auditory cortex. Neural computation. 19 [PubMed]

Huang C, Zeldenrust F, Celikel T. (2022). Cortical Representation of Touch in Silico Neuroinformatics. 20 [PubMed]

• Realistic barrel cortical column - Matlab (Huang et al., 2022) [Model]
• Realistic barrel cortical column - NetPyNE (Huang et al., 2022) [Model]

Kim D, Paré D, Nair SS. (2013). Mechanisms contributing to the induction and storage of Pavlovian fear memories in the lateral amygdala. Learning & memory (Cold Spring Harbor, N.Y.). 20 [PubMed]

• A 1000 cell network model for Lateral Amygdala (Kim et al. 2013) [Model]

King PD, Zylberberg J, DeWeese MR. (2013). Inhibitory interneurons decorrelate excitatory cells to drive sparse code formation in a spiking model of V1. The Journal of neuroscience : the official journal of the Society for Neuroscience. 33 [PubMed]

• Inhibitory cells enable sparse coding in V1 model (King et al. 2013) [Model]

Konstantoudaki X, Papoutsi A, Chalkiadaki K, Poirazi P, Sidiropoulou K. (2014). Modulatory effects of inhibition on persistent activity in a cortical microcircuit model. Frontiers in neural circuits. 8 [PubMed]

• Pyramidal neuron, fast, regular, and irregular spiking interneurons (Konstantoudaki et al 2014) [Model]

Kotaleski JH et al. (2011). Striatal fast-spiking interneurons: from firing patterns to postsynaptic impact Front. Syst. Neurosci.. 5:57

• Firing patterns in stuttering fast-spiking interneurons (Klaus et al. 2011) [Model]

Krishnan GP, Filatov G, Shilnikov A, Bazhenov M. (2015). Electrogenic properties of the Na?/K? ATPase control transitions between normal and pathological brain states. Journal of neurophysiology. 113 [PubMed]

• Single cell model with variable ion concentrations and Na+/K+ ATPase (Krishnan et al. 2015) [Model]

Kumar A, Schrader S, Aertsen A, Rotter S. (2008). The high-conductance state of cortical networks. Neural computation. 20 [PubMed]

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• L5 cortical neurons with recreated synaptic inputs in vitro correlation transfer (Linaro et al 2019) [Model]

Lundqvist M, Rehn M, Djurfeldt M, Lansner A. (2006). Attractor dynamics in a modular network model of neocortex. Network (Bristol, England). 17 [PubMed]

Markram H et al. (2015). Reconstruction and Simulation of Neocortical Microcircuitry. Cell. 163 [PubMed]

• The neocortical microcircuit collaboration portal (Markram et al. 2015) [Model]

Mehaffey WH, Doiron B, Maler L, Turner RW. (2005). Deterministic multiplicative gain control with active dendrites. The Journal of neuroscience : the official journal of the Society for Neuroscience. 25 [PubMed]

Mensi S et al. (2012). Parameter extraction and classification of three cortical neuron types reveals two distinct adaptation mechanisms. Journal of neurophysiology. 107 [PubMed]

• Extraction and classification of three cortical neuron types (Mensi et al. 2012) [Model]

Minneci F et al. (2007). Signaling properties of stratum oriens interneurons in the hippocampus of transgenic mice expressing EGFP in a subset of somatostatin-containing cells. Hippocampus. 17 [PubMed]

• CA1 oriens alveus interneurons: signaling properties (Minneci et al. 2007) [Model]

Mondragón-González SL, Burguière E. (2017). Bio-inspired benchmark generator for extracellular multi-unit recordings. Scientific reports. 7 [PubMed]

Morita K. (2008). Possible role of dendritic compartmentalization in the spatial working memory circuit. The Journal of neuroscience : the official journal of the Society for Neuroscience. 28 [PubMed]

• Working memory circuit with branched dendrites (Morita 2008) [Model]

Mosher CP et al. (2020). Cellular Classes in the Human Brain Revealed In Vivo by Heartbeat-Related Modulation of the Extracellular Action Potential Waveform. Cell reports. 30 [PubMed]

• Cellular classes revealed by heartbeat-related modulation of extracellular APs (Mosher et al 2020) [Model]

Neymotin SA, Lee H, Park E, Fenton AA, Lytton WW. (2011). Emergence of physiological oscillation frequencies in a computer model of neocortex. Frontiers in computational neuroscience. 5 [PubMed]

• Emergence of physiological oscillation frequencies in neocortex simulations (Neymotin et al. 2011) [Model]

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

• Mean Field Equations for Two-Dimensional Integrate and Fire Models (Nicola and Campbell, 2013) [Model]

Overstreet CK, Klein JD, Helms Tillery SI. (2013). Computational modeling of direct neuronal recruitment during intracortical microstimulation in somatosensory cortex. Journal of neural engineering. 10 [PubMed]

• Direct recruitment of S1 pyramidal cells and interneurons via ICMS (Overstreet et al., 2013) [Model]

Pashut T et al. (2011). Mechanisms of magnetic stimulation of central nervous system neurons. PLoS computational biology. 7 [PubMed]

• Mechanisms of magnetic stimulation of central nervous system neurons (Pashut et al. 2011) [Model]

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Ramaswamy S et al. (2015). The neocortical microcircuit collaboration portal: a resource for rat somatosensory cortex. Frontiers in neural circuits. 9 [PubMed]

• The neocortical microcircuit collaboration portal (Markram et al. 2015) [Model]

Reimann MW, King JG, Muller EB, Ramaswamy S, Markram H. (2015). An algorithm to predict the connectome of neural microcircuits. Frontiers in computational neuroscience. 9 [PubMed]

• The neocortical microcircuit collaboration portal (Markram et al. 2015) [Model]

Richardson MJ, Melamed O, Silberberg G, Gerstner W, Markram H. (2005). Short-term synaptic plasticity orchestrates the response of pyramidal cells and interneurons to population bursts. Journal of computational neuroscience. 18 [PubMed]

Rowat P. (2007). Interspike interval statistics in the stochastic Hodgkin-Huxley model: coexistence of gamma frequency bursts and highly irregular firing. Neural computation. 19 [PubMed]

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Sudhakar SK, Choi TJ, Ahmed OJ. (2019). Biophysical Modeling Suggests Optimal Drug Combinations for Improving the Efficacy of GABA Agonists after Traumatic Brain Injuries. Journal of neurotrauma. 36 [PubMed]

• Biophysical modeling of pathological brain states (Sudhakar et al 2019) [Model]

Touboul J, Brette R. (2008). Dynamics and bifurcations of the adaptive exponential integrate-and-fire model. Biological cybernetics. 99 [PubMed]

• Brette-Gerstner model (Touboul and Brette 2008) [Model]

Upchurch CM, Knowlton CJ, Chamberland S, Canavier CC. (2024). Persistent Interruption in Parvalbumin-Positive Inhibitory Interneurons: Biophysical and Mathematical Mechanisms. eNeuro. 11 [PubMed]

• Persistent Interruption in Parvalbumin-Positive Inhibitory Interneurons: Biophysical and Mathematical Mechanisms (Upchurch et al., 2024) [Model]

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• Engaging distinct oscillatory neocortical circuits (Vierling-Claassen et al. 2010) [Model]

Vinci G, Ventura V, Smith MA, Kass RE. (2018). Adjusted regularization of cortical covariance. Journal of computational neuroscience. 45 [PubMed]

• Adjusted regularization of cortical covariance (Vinci et al 2018) [Model]

Wilmes KA, Sprekeler H, Schreiber S. (2016). Inhibition as a Binary Switch for Excitatory Plasticity in Pyramidal Neurons. PLoS computational biology. 12 [PubMed]

• Inhibition of bAPs and Ca2+ spikes in a multi-compartment pyramidal neuron model (Wilmes et al 2016) [Model]

Yang GR, Murray JD, Wang XJ. (2016). A dendritic disinhibitory circuit mechanism for pathway-specific gating. Nature communications. 7 [PubMed]

• A dendritic disinhibitory circuit mechanism for pathway-specific gating (Yang et al. 2016) [Model]

Zerlaut Y, Chemla S, Chavane F, Destexhe A. (2018). Modeling mesoscopic cortical dynamics using a mean-field model of conductance-based networks of adaptive exponential integrate-and-fire neurons. Journal of computational neuroscience. 44 [PubMed]

• Mesoscopic dynamics from AdEx recurrent networks (Zerlaut et al JCNS 2018) [Model]
• Mesoscopic dynamics from AdEx recurrent networks (Zerlaut et al JCNS 2018) (PyNN) [Model]