Akin M, Onderdonk A, Guo Y. (2017). Effects of local network topology on the functional reconstruction of spiking neural network models. Applied network science. 2 [PubMed]

Beverlin B, Kakalios J, Nykamp D, Netoff TI. (2012). Dynamical changes in neurons during seizures determine tonic to clonic shift. Journal of computational neuroscience. 33 [PubMed]

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

Bogaard A, Parent J, Zochowski M, Booth V. (2009). Interaction of cellular and network mechanisms in spatiotemporal pattern formation in neuronal networks. The Journal of neuroscience : the official journal of the Society for Neuroscience. 29 [PubMed]

• Small world networks of Type I and Type II Excitable Neurons (Bogaard et al. 2009) [Model]

Dominguez D, Koroutchev K, Serrano E, Rodríguez FB. (2007). Information and topology in attractor neural networks. Neural computation. 19 [PubMed]

Dyhrfjeld-Johnsen J et al. (2007). Topological determinants of epileptogenesis in large-scale structural and functional models of the dentate gyrus derived from experimental data. Journal of neurophysiology. 97 [PubMed]

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

French DA, Gruenstein EI. (2006). An integrate-and-fire model for synchronized bursting in a network of cultured cortical neurons. Journal of computational neuroscience. 21 [PubMed]

Gal E et al. (2017). Rich cell-type-specific network topology in neocortical microcircuitry. Nature neuroscience. 20 [PubMed]

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

Giacopelli G, Tegolo D, Spera E, Migliore M. (2021). On the structural connectivity of large-scale models of brain networks at cellular level. Scientific reports. 11 [PubMed]

• On the structural connectivity of large-scale models of brain networks (Giacopelli et al 2021) [Model]

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

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]

Hilgetag CC, Kaiser M. (2010). Optimal hierarchical modular topologies for producing limited sustained activation of neural networks Front. Neuroinform.. 4(8)

• Network topologies for producing limited sustained activation (Kaiser and Hilgetag 2010) [Model]

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]

Humphries MD, Gurney K, Prescott TJ. (2006). The brainstem reticular formation is a small-world, not scale-free, network. Proceedings. Biological sciences. 273 [PubMed]

• Medial reticular formation of the brainstem: anatomy and dynamics (Humphries et al. 2006, 2007) [Model]

Humphries MD, Wood R, Gurney K. (2009). Dopamine-modulated dynamic cell assemblies generated by the GABAergic striatal microcircuit. Neural networks : the official journal of the International Neural Network Society. 22 [PubMed]

• Striatal GABAergic microcircuit, dopamine-modulated cell assemblies (Humphries et al. 2009) [Model]

Jacob T et al. (2019). A Proposed Mechanism for Spontaneous Transitions between Interictal and Ictal Activity. The Journal of neuroscience : the official journal of the Society for Neuroscience. 39 [PubMed]

• A NN with synaptic depression for testing the effects of connectivity on dynamics (Jacob et al 2019) [Model]

Kitano K, Fukai T. (2007). Variability v.s. synchronicity of neuronal activity in local cortical network models with different wiring topologies. Journal of computational neuroscience. 23 [PubMed]

Mirzakhalili E, Gourgou E, Booth V, Epureanu B. (2017). Synaptic Impairment and Robustness of Excitatory Neuronal Networks with Different Topologies. Frontiers in neural circuits. 11 [PubMed]

• Synaptic Impairment, Robustness of Excitatory NNs w/ Different Topologies (Mirzakhalili et al 2017) [Model]

Morgan RJ, Santhakumar V, Soltesz I. (2007). Modeling the dentate gyrus. Progress in brain research. 163 [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. Proceedings of the National Academy of Sciences of the United States of America. 105 [PubMed]

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

Mäki-Marttunen T, Aćimović J, Ruohonen K, Linne ML. (2013). Structure-dynamics relationships in bursting neuronal networks revealed using a prediction framework. PloS one. 8 [PubMed]

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

Mäki-Marttunen T et al. (2018). A stepwise neuron model fitting procedure designed for recordings with high spatial resolution: Application to layer 5 pyramidal cells. Journal of neuroscience methods. 293 [PubMed]

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

Psujek S, Ames J, Beer RD. (2006). Connection and coordination: the interplay between architecture and dynamics in evolved model pattern generators. Neural computation. 18 [PubMed]

Reimann MW, Horlemann AL, Ramaswamy S, Muller EB, Markram H. (2017). Morphological Diversity Strongly Constrains Synaptic Connectivity and Plasticity. Cerebral cortex (New York, N.Y. : 1991). 27 [PubMed]

• The neocortical microcircuit collaboration portal (Markram 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. Journal of neurophysiology. 112 [PubMed]

Voigt T, Herzog A, Michaelis B, Kube K, De_lima AD. (2007). Displaced strategies optimize connectivity in neocortical networks Neurocomputing. 70

Zang Y, Hong S, De Schutter E. (2020). Firing rate-dependent phase responses of Purkinje cells support transient oscillations. eLife. 9 [PubMed]

• Purkinje neuron network (Zang et al. 2020) [Model]

van Ooyen A et al. (2014). Independently outgrowing neurons and geometry-based synapse formation produce networks with realistic synaptic connectivity. PloS one. 9 [PubMed]

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