Akin M, Onderdonk A, Guo Y (2017) Effects of local network topology on the functional reconstruction of spiking neural network models. Appl Netw Sci 2:22 [Journal] [PubMed]

Beverlin B, Kakalios J, Nykamp D, Netoff TI (2012) Dynamical changes in neurons during seizures determine tonic to clonic shift. J Comput Neurosci 33:41-51 [Journal] [PubMed]

•	Epileptic seizure model with Morris-Lecar neurons (Beverlin and Netoff 2011) [Model]

Bohte SM, Mozer MC (2007) Reducing the variability of neural responses: a computational theory of spike-timing-dependent plasticity. Neural Comput 19:371-403 [Journal] [PubMed]

Clopath C, Büsing L, Vasilaki E, Gerstner W (2010) Connectivity reflects coding: a model of voltage-based STDP with homeostasis. Nat Neurosci 13:344-52 [Journal] [PubMed]

•	Voltage-based STDP synapse (Clopath et al. 2010) [Model]

Droste F, Lindner B (2017) Exact analytical results for integrate-and-fire neurons driven by excitatory shot noise J. Comp. Neurosci. [Journal]

•	Theory and simulation of integrate-and-fire neurons driven by shot noise (Droste & Lindner 2017) [Model]

Dyhrfjeld-Johnsen J, Santhakumar V, Morgan RJ, Huerta R, Tsimring L, Soltesz I (2007) Topological determinants of epileptogenesis in large-scale structural and functional models of the dentate gyrus derived from experimental data. J Neurophysiol 97:1566-87 [Journal] [PubMed]

•	Dentate gyrus (Morgan et al. 2007, 2008, Santhakumar et al. 2005, Dyhrfjeld-Johnsen et al. 2007) [Model]

Egger R, Narayanan RT, Guest JM, Bast A, Udvary D, Messore LF, Das S, de Kock CP, Oberlaender M (2020) Cortical Output Is Gated by Horizontally Projecting Neurons in the Deep Layers Neuron [Journal]

•	Sensory-evoked responses of L5 pyramidal tract neurons (Egger et al 2020) [Model]

Esposito U, Giugliano M, van Rossum M, Vasilaki E (2014) Measuring symmetry, asymmetry and randomness in neural network connectivity. PLoS One 9:e100805 [Journal] [PubMed]

•	Statistics of symmetry measure for networks of neurons (Esposito et al. 2014) [Model]

Esposito U, Giugliano M, Vasilaki E (2014) Adaptation of short-term plasticity parameters via error-driven learning may explain the correlation between activity-dependent synaptic properties, connectivity motifs and target specificity. Front Comput Neurosci 8:175 [Journal] [PubMed]

•	Adaptation of Short-Term Plasticity parameters (Esposito et al. 2015) [Model]

Gal E, London M, Globerson A, Ramaswamy S, Reimann MW, Muller E, Markram H, Segev I (2017) Rich cell-type-specific network topology in neocortical microcircuitry. Nat Neurosci 20:1004-1013 [Journal] [PubMed]

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

Gilra A, Bhalla US (2015) Bulbar microcircuit model predicts connectivity and roles of interneurons in odor coding. PLoS One 10:e0098045 [Journal] [PubMed]

•	Olfactory bulb microcircuits model with dual-layer inhibition (Gilra & Bhalla 2015) [Model]

Gleeson P, Steuber V, Silver RA (2007) neuroConstruct: a tool for modeling networks of neurons in 3D space. Neuron 54:219-35 [Journal] [PubMed]

Gourévitch B, Eggermont JJ (2007) Evaluating information transfer between auditory cortical neurons. J Neurophysiol 97:2533-43 [Journal] [PubMed]

Gutnisky DA, Yu J, Hires SA, To MS, Bale M, Svoboda K, Golomb D (2017) Mechanisms underlying a thalamocortical transformation during active tactile sensation PLoS Comput Biol 13(6):e1005576 [Journal]

•	L4 cortical barrel NN model receiving thalamic input during whisking or touch (Gutnisky et al. 2017) [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 Comput Biol 12:e1004930 [Journal] [PubMed]

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

Hay E, Segev I (2015) Dendritic Excitability and Gain Control in Recurrent Cortical Microcircuits. Cereb Cortex 25:3561-71 [Journal] [PubMed]

•	Layer V pyramidal cell model with reduced morphology (Mäki-Marttunen et al 2018) [Model]
•	Microcircuits of L5 thick tufted pyramidal cells (Hay & Segev 2015) [Model]

Hazan L, Ziv NE (2020) Activity dependent and independent determinants of synaptic size diversity. J Neurosci [Journal] [PubMed]

•	Mesoscopic model of spontaneous synaptic size fluctuations (Hazan & Ziv 2020) [Model]
•	Kesten and Langevin synaptic size fluctuation simulator (Hazan & Ziv 2020) [Model]

Hooks BM, Hires SA, Zhang YX, Huber D, Petreanu L, Svoboda K, Shepherd GM (2011) Laminar analysis of excitatory local circuits in vibrissal motor and sensory cortical areas. PLoS Biol 9:e1000572 [Journal] [PubMed]

•	Laminar analysis of excitatory circuits in vibrissal motor and sensory cortex (Hooks et al. 2011) [Model]

Humphries MD, Wood R, Gurney K (2010) Reconstructing the three-dimensional GABAergic microcircuit of the striatum. PLoS Comput Biol 6:e1001011 [Journal] [PubMed]

•	Striatal GABAergic microcircuit, spatial scales of dynamics (Humphries et al, 2010) [Model]

Keane A, Henderson JA, Gong P (2018) Dynamical patterns underlying response properties of cortical circuits. J R Soc Interface [Journal] [PubMed]

•	Dynamical patterns underlying response properties of cortical circuits (Keane et al 2018) [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]

Kitano K, Fukai T (2007) Variability v.s. synchronicity of neuronal activity in local cortical network models with different wiring topologies. J Comput Neurosci 23:237-50 [Journal] [PubMed]

Kobayashi R, Kurita S, Kurth A, Kitano K, Mizuseki K, Diesmann M, Richmond BJ, Shinomoto S (2019) Reconstructing neuronal circuitry from parallel spike trains. Nat Commun 10:4468 [Journal] [PubMed]

•	GLMCC validation neural network model (Kobayashi et al. 2019) [Model]

Litwin-Kumar A, Doiron B (2012) Slow dynamics and high variability in balanced cortical networks with clustered connections. Nat Neurosci 15:1498-505 [Journal] [PubMed]

•	Excitatory and inhibitory population activity (Bittner et al 2017) (Litwin-Kumar & Doiron 2017) [Model]

London M, Roth A, Beeren L, Häusser M, Latham PE (2010) Sensitivity to perturbations in vivo implies high noise and suggests rate coding in cortex. Nature 466:123-7 [Journal] [PubMed]

•	Perturbation sensitivity implies high noise and suggests rate coding in cortex (London et al. 2010) [Model]

Mäki-Marttunen T, Acimovic J, Ruohonen K, Linne ML (2013) Structure-dynamics relationships in bursting neuronal networks revealed using a prediction framework. PLoS One 8:e69373 [Journal] [PubMed]

•	Structure-dynamics relationships in bursting neuronal networks revealed (Mäki-Marttunen et al. 2013) [Model]

Mäki-Marttunen T, Halnes G, Devor A, Metzner C, Dale AM, Andreassen OA, Einevoll GT (2018) A stepwise neuron model fitting procedure designed for recordings with high spatial resolution: Application to layer 5 pyramidal cells. J Neurosci Methods 293:264-283 [Journal] [PubMed]

•	Layer V pyramidal cell model with reduced morphology (Mäki-Marttunen et al 2018) [Model]

Matsubara T, Torikai H (2016) An Asynchronous Recurrent Network of Cellular Automaton-Based Neurons and Its Reproduction of Spiking Neural Network Activities. IEEE Trans Neural Netw Learn Syst 27:836-52 [Journal] [PubMed]

Morgan RJ, Santhakumar V, Soltesz I (2007) Modeling the dentate gyrus. Prog Brain Res 163:639-58 [Journal] [PubMed]

•	Dentate gyrus (Morgan et al. 2007, 2008, Santhakumar et al. 2005, Dyhrfjeld-Johnsen et al. 2007) [Model]

Morgan RJ, Soltesz I (2008) Nonrandom connectivity of the epileptic dentate gyrus predicts a major role for neuronal hubs in seizures. Proc Natl Acad Sci U S A 105:6179-84 [Journal] [PubMed]

•	Dentate gyrus (Morgan et al. 2007, 2008, Santhakumar et al. 2005, Dyhrfjeld-Johnsen et al. 2007) [Model]

Pastoll H, Solanka L, van Rossum MC, Nolan MF (2013) Feedback inhibition enables theta-nested gamma oscillations and grid firing fields. Neuron 77:141-54 [Journal] [PubMed]

•	An attractor network model of grid cells and theta-nested gamma oscillations (Pastoll et al 2013) [Model]

Polsky A, Mel B, Schiller J (2009) Encoding and decoding bursts by NMDA spikes in basal dendrites of layer 5 pyramidal neurons. J Neurosci 29:11891-903 [Journal] [PubMed]

•	NMDA spikes in basal dendrites of L5 pyramidal neurons (Polsky et al. 2009) [Model]

Potjans TC, Diesmann M (2014) The cell-type specific cortical microcircuit: relating structure and activity in a full-scale spiking network model. Cereb Cortex 24:785-806 [Journal] [PubMed]

•	A full-scale cortical microcircuit spiking network model (Shimoura et al 2018) [Model]

Ray S, Aldworth ZN, Stopfer MA (2020) Feedback inhibition and its control in an insect olfactory circuit. Elife [Journal] [PubMed]

•	Locust olfactory network with GGN and full KC population in the mushroom body (Ray et al 2020) [Model]

Reimann MW, Horlemann AL, Ramaswamy S, Muller EB, Markram H (2017) Morphological Diversity Strongly Constrains Synaptic Connectivity and Plasticity. Cereb Cortex 27:4570-4585 [Journal] [PubMed]

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

Reimann MW, Nolte M, Scolamiero M, Turner K, Perin R, Chindemi G, Dlotko P, Levi R, Hess K, Markram H (2017) Cliques of Neurons Bound into Cavities Provide a Missing Link between Structure and Function. Front Comput Neurosci 11:48 [Journal] [PubMed]

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

Sadeh S, Clopath C, Rotter S (2015) Emergence of Functional Specificity in Balanced Networks with Synaptic Plasticity. PLoS Comput Biol 11:e1004307 [Journal] [PubMed]

•	Functional balanced networks with synaptic plasticity (Sadeh et al, 2015) [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 Struct Funct 223:1409-1435 [Journal] [PubMed]

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

Schmidt M, Bakker R, Shen K, Bezgin G, Diesmann M, van Albada SJ (2018) A multi-scale layer-resolved spiking network model of resting-state dynamics in macaque visual cortical areas. PLoS Comput Biol 14:e1006359 [Journal] [PubMed]

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

Smolen P (2015) Modeling maintenance of long-term potentiation in clustered synapses: long-term memory without bistability. Neural Plast 2015:185410 [Journal] [PubMed]

•	Modeling maintenance of Long-Term Potentiation in clustered synapses (Smolen 2015) [Model]

Soudry D, Meir R (2014) The neuronal response at extended timescales: a linearized spiking input-output relation. Front Comput Neurosci 8:29 [Journal] [PubMed]

•	Method for deriving general HH neuron model`s spiking input-output relation (Soudry & Meir 2014) [Model]

Tikidji-Hamburyan RA, Martínez JJ, White JA, Canavier CC (2015) Resonant Interneurons Can Increase Robustness of Gamma Oscillations. J Neurosci 35:15682-95 [Journal] [PubMed]

•	PIR gamma oscillations in network of resonators (Tikidji-Hamburyan et al. 2015) [Model]

Tomm C, Avermann M, Petersen C, Gerstner W, Vogels TP (2014) Connection-type-specific biases make uniform random network models consistent with cortical recordings. J Neurophysiol 112:1801-14 [Journal] [PubMed]

van Ooyen A, Carnell A, de Ridder S, Tarigan B, Mansvelder HD, Bijma F, de Gunst M, van Pelt J (2014) Independently outgrowing neurons and geometry-based synapse formation produce networks with realistic synaptic connectivity. PLoS One 9:e85858 [Journal] [PubMed]

•	NETMORPH: creates NNs with realistic neuron morphologies (Koene et al. 2009, van Ooyen et al. 2014) [Model]

Vasilaki E, Giugliano M (2014) Emergence of connectivity motifs in networks of model neurons with short- and long-term plastic synapses. PLoS One 9:e84626 [Journal] [PubMed]

•	Emergence of Connectivity Motifs in Networks of Model Neurons (Vasilaki, Giugliano 2014) [Model]

Vogels TP, Abbott LF (2005) Signal propagation and logic gating in networks of integrate-and-fire neurons. J Neurosci 25:10786-95 [Journal] [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]