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. J Comput Neurosci 31:137-58 [Journal] [PubMed]

•	A model of unitary responses from A/C and PP synapses in CA3 pyramidal cells (Baker et al. 2010) [Model]

Barreto E, Cressman JR (2011) Ion concentration dynamics as a mechanism for neuronal bursting. J Biol Phys 37:361-73 [Journal] [PubMed]

•	Ion concentration dynamics as a mechanism for neuronal bursting (Barreto & Cressman 2011) [Model]

Beck JM, Pouget A (2007) Exact inferences in a neural implementation of a hidden Markov model. Neural Comput 19:1344-61 [Journal] [PubMed]

Bittner KC, Milstein AD, Grienberger C, Romani S, Magee JC (2017) Behavioral time scale synaptic plasticity underlies CA1 place fields. Science 357:1033-1036 [Journal] [PubMed]

•	Behavioral time scale synaptic plasticity underlies CA1 place fields (Bittner et al. 2017) [Model]

Booth V, Xique I, Diniz Behn C (2017) One-Dimensional Map for the Circadian Modulation of Sleep in a Sleep-Wake Regulatory Network Model for Human Sleep SIAM Journal on Applied Dynamical Systems 16:1089-1112 [Journal]

•	Human sleep-wake regulatory network model (Gleit et al 2013, Booth et al 2017) [Model]

Calì C, Berger TK, Pignatelli M, Carleton A, Markram H, Giugliano M (2008) Inferring connection proximity in networks of electrically coupled cells by subthreshold frequency response analysis. J Comput Neurosci 24:330-45 [Journal] [PubMed]

•	Inferring connection proximity in electrically coupled networks (Cali et al. 2007) [Model]

Caplan JS, Williams AH, Marder E (2014) Many parameter sets in a multicompartment model oscillator are robust to temperature perturbations. J Neurosci 34:4963-75 [Journal] [PubMed]

•	Temperature-Dependent Pyloric Pacemaker Kernel (Caplan JS et al., 2014) [Model]

Dudman JT, Nolan MF (2009) Stochastically gating ion channels enable patterned spike firing through activity-dependent modulation of spike probability. PLoS Comput Biol 5:e1000290 [Journal] [PubMed]

Ermentrout GB, Terman DH (2010) Mathematical Foundations of Neuroscience Interdisciplinary Applied Mathematics, Antman SS:Marsden JE:Sirovich L:Wiggins, ed. pp.1 [Journal]

•	Mathematical Foundations of Neuroscience (Ermentrout and Terman 2010) [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]

Földy C, Aradi I, Howard A, Soltesz I (2004) Diversity beyond variance: modulation of firing rates and network coherence by GABAergic subpopulations. Eur J Neurosci 19:119-30 [PubMed]

Fountas Z, Shanahan M (2017) The role of cortical oscillations in a spiking neural network model of the basal ganglia. PLoS One 12:e0189109 [Journal] [PubMed]

•	Cortical oscillations and the basal ganglia (Fountas & Shanahan 2017) [Model]

Girard B, Tabareau N, Pham QC, Berthoz A, Slotine JJ (2008) Where neuroscience and dynamic system theory meet autonomous robotics: a contracting basal ganglia model for action selection. Neural Netw 21:628-41 [Journal] [PubMed]

•	A contracting model of the basal ganglia (Girard et al. 2008) [Model]

Giugliano M, Gambazzi L, Ballerini L, Prato M, Campidelli S (2012) Carbon nanotubes as electrical interfaces to neurons Nanotechnology for Biology and Medicine, Parpura V, Silva GA, ed. pp.187 [Journal]

•	Carbon nanotubes as electrical interfaces to neurons (Giugliano et al. 2008) [Model]

Gloveli T, Dugladze T, Rotstein HG, Traub RD, Monyer H, Heinemann U, Whittington MA, Kopell NJ (2005) Orthogonal arrangement of rhythm-generating microcircuits in the hippocampus. Proc Natl Acad Sci U S A 102:13295-300 [Journal] [PubMed]

•	Gamma and theta rythms in biophysical models of hippocampus circuits (Kopell et al. 2011) [Model]

Goldberg DH, Andreou AG (2007) Distortion of neural signals by spike coding. Neural Comput 19:2797-839 [Journal] [PubMed]

Goldwyn JH, Imennov NS, Famulare M, Shea-Brown E (2011) Stochastic differential equation models for ion channel noise in Hodgkin-Huxley neurons. Phys Rev E Stat Nonlin Soft Matter Phys 83:041908 [Journal] [PubMed]

•	On stochastic diff. eq. models for ion channel noise in Hodgkin-Huxley neurons (Goldwyn et al. 2010) [Model]

Goldwyn JH, Shea-Brown E (2011) The what and where of adding channel noise to the Hodgkin-Huxley equations. PLoS Comput Biol 7:e1002247 [Journal] [PubMed]

•	Stochastic versions of the Hodgkin-Huxley equations (Goldwyn, Shea-Brown 2011) (pylab) [Model]
•	Stochastic versions of the Hodgkin-Huxley equations (Goldwyn, Shea-Brown 2011) [Model]

Humphries MD, Gurney K (2007) Solution methods for a new class of simple model neurons. Neural Comput 19:3216-25 [Journal] [PubMed]

Huys QJ, Paninski L (2009) Smoothing of, and parameter estimation from, noisy biophysical recordings. PLoS Comput Biol 5:e1000379 [Journal] [PubMed]

•	Smoothing of, and parameter estimation from, noisy biophysical recordings (Huys & Paninski 2009) [Model]

Jolivet R, Lewis TJ, Gerstner W (2004) Generalized integrate-and-fire models of neuronal activity approximate spike trains of a detailed model to a high degree of accuracy. J Neurophysiol 92:959-76 [Journal] [PubMed]

•	Spike Response Model simulator (Jolivet et al. 2004, 2006, 2008) [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]

Kilinc D, Demir A (2017) Noise in Neuronal and Electronic Circuits: A General Modeling Framework and Non-Monte Carlo Simulation Techniques. IEEE Trans Biomed Circuits Syst 11:958-974 [Journal] [PubMed]

•	A neuronal circuit simulator for non Monte Carlo analysis of neuronal noise (Kilinc & Demir 2018) [Model]

Kilinc D, Demir A (2018) Spike timing precision of neuronal circuits. J Comput Neurosci 44:341-362 [Journal] [PubMed]

•	A neuronal circuit simulator for non Monte Carlo analysis of neuronal noise (Kilinc & Demir 2018) [Model]

Kilinc D,Demir A (2015) Simulation of noise in neurons and neuronal circuits Proceedings of the IEEE/ACM international conference on computer-aided design (ICCAD) :589-596 [Journal]

•	A neuronal circuit simulator for non Monte Carlo analysis of neuronal noise (Kilinc & Demir 2018) [Model]

Kim H, Bao S (2008) Distributed representation of perceptual categories in the auditory cortex. J Comput Neurosci 24:277-90 [Journal] [PubMed]

•	Distributed representation of perceptual categories in the auditory cortex (Kim and Bao 2008) [Model]

Kumar A, Schrader S, Aertsen A, Rotter S (2008) The high-conductance state of cortical networks. Neural Comput 20:1-43 [Journal] [PubMed]

Laing CR, Longtin A (2003) Dynamics of deterministic and stochastic paired excitatory-inhibitory delayed feedback. Neural Comput 15:2779-822 [Journal] [PubMed]

Lian Y, Grayden DB, Kameneva T, Meffin H, Burkitt AN (2019) Toward a Biologically Plausible Model of LGN-V1 Pathways Based on Efficient Coding Frontiers in Neural Circuits 13:13 [Journal]

•	Towards a biologically plausible model of LGN-V1 pathways (Lian et al 2019) [Model]

Linaro D, Storace M, Giugliano M (2011) Accurate and fast simulation of channel noise in conductance-based model neurons by diffusion approximation. PLoS Comput Biol 7:e1001102 [Journal] [PubMed]

•	Accurate and fast simulation of channel noise in conductance-based model neurons (Linaro et al 2011) [Model]

Lundstrom BN, Famulare M, Sorensen LB, Spain WJ, Fairhall AL (2009) Sensitivity of firing rate to input fluctuations depends on time scale separation between fast and slow variables in single neurons J Comput Neurosci [Journal]

•	Hodgkin-Huxley simplifed 2D and 3D models (Lundstrom et al. 2009) [Model]

Machens CK, Brody CD (2008) Design of continuous attractor networks with monotonic tuning using a symmetry principle. Neural Comput 20:452-85 [Journal] [PubMed]

Maia PD, Kutz JN (2014) Compromised axonal functionality after neurodegeneration, concussion and/or traumatic brain injury. J Comput Neurosci 37:317-32 [Journal] [PubMed]

Masuda N, Okada M, Aihara K (2007) Filtering of spatial bias and noise inputs by spatially structured neural networks. Neural Comput 19:1854-70 [Journal] [PubMed]

Monaco JD, Knierim JJ, Zhang K (2011) Sensory feedback, error correction, and remapping in a multiple oscillator model of place cell activity Frontiers in Computational Neuroscience 5(0):39 [Journal]

•	Sensory feedback in an oscillatory interference model of place cell activity (Monaco et al. 2011) [Model]

Moradi K, Moradi K, Ganjkhani M, Hajihasani M, Gharibzadeh S, Kaka G (2013) A fast model of voltage-dependent NMDA receptors. J Comput Neurosci 34:521-31 [Journal] [PubMed]

•	A fast model of voltage-dependent NMDA Receptors (Moradi et al. 2013) [Model]

Muller E, Buesing L, Schemmel J, Meier K (2007) Spike-frequency adapting neural ensembles: beyond mean adaptation and renewal theories. Neural Comput 19:2958-3010 [Journal] [PubMed]

Muresan RC, Savin C (2007) Resonance or integration? Self-sustained dynamics and excitability of neural microcircuits. J Neurophysiol 97:1911-30 [Journal] [PubMed]

Norheim ES, Wyller J, Nordlie E, Einevoll GT (2012) A minimal mechanistic model for temporal signal processing in the lateral geniculate nucleus. Cogn Neurodyn 6:259-81 [Journal] [PubMed]

•	LGNcircuit: Minimal LGN network model of temporal processing of visual input (Norheim et al. 2012) [Model]

Paninski L (2006) The spike-triggered average of the integrate-and-fire cell driven by gaussian white noise. Neural Comput 18:2592-616 [Journal] [PubMed]

Paninski L, Pillow JW, Simoncelli EP (2004) Maximum likelihood estimation of a stochastic integrate-and-fire neural encoding model. Neural Comput 16:2533-61 [Journal] [PubMed]

Rakowski F, Karbowski J (2017) Optimal synaptic signaling connectome for locomotory behavior in Caenorhabditis elegans: Design minimizing energy cost. PLoS Comput Biol 13:e1005834 [Journal] [PubMed]

•	Optimal synaptic assignment for locomotory behavior in C. elegans (Rakowski & Karbowski 2017) [Model]

Rössert C, Moore LE, Straka H, Glasauer S (2011) Cellular and network contributions to vestibular signal processing: impact of ion conductances, synaptic inhibition, and noise. J Neurosci 31:8359-72 [Journal] [PubMed]

•	Frog second-order vestibular neuron models (Rossert et al. 2011) [Model]

Rössert C, Solinas S, D'Angelo E, Dean P, Porrill J (2014) Model cerebellar granule cells can faithfully transmit modulated firing rate signals. Front Cell Neurosci 8:304 [Journal] [PubMed]

•	Information transmission in cerebellar granule cell models (Rossert et al. 2014) [Model]

Sakai Y, Fukai T (2008) The actor-critic learning is behind the matching law: matching versus optimal behaviors. Neural Comput 20:227-51 [Journal] [PubMed]

Salazar-Gatzimas E, Chen J, Creamer MS, Mano O, Mandel HB, Matulis CA, Pottackal J, Clark DA (2016) Direct Measurement of Correlation Responses in Drosophila Elementary Motion Detectors Reveals Fast Timescale Tuning. Neuron 92:227-239 [Journal] [PubMed]

•	Comparing correlation responses to motion estimation models (Salazar-Gatzimas et al. 2016) [Model]

Shimazaki H, Shinomoto S (2007) A method for selecting the bin size of a time histogram. Neural Comput 19:1503-27 [Journal] [PubMed]

Sterratt D, Graham B, Gillies A, Willshaw D (2011) Principles of Computational Modelling in Neuroscience, Cambridge University Press :1-401 [Journal]

•	Principles of Computational Modelling in Neuroscience (Book) (Sterratt et al. 2011) [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:e40726 [Journal] [PubMed]

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

Teka W, Marinov TM, Santamaria F (2014) Neuronal spike timing adaptation described with a fractional leaky integrate-and-fire model. PLoS Comput Biol 10:e1003526 [Journal] [PubMed]

•	Fractional leaky integrate-and-fire model (Teka et al. 2014) [Model]

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

•	Brain networks simulators - a comparative study (Tikidji-Hamburyan et al 2017) [Model]

Toyoizumi T, Pfister JP, Aihara K, Gerstner W (2007) Optimality model of unsupervised spike-timing-dependent plasticity: synaptic memory and weight distribution. Neural Comput 19:639-71 [Journal] [PubMed]

Triesch J (2007) Synergies between intrinsic and synaptic plasticity mechanisms. Neural Comput 19:885-909 [Journal] [PubMed]

van Elburg RA, van Ooyen A (2010) Impact of dendritic size and dendritic topology on burst firing in pyramidal cells. PLoS Comput Biol 6:e1000781 [Journal] [PubMed]

•	Impact of dendritic size and topology on pyramidal cell burst firing (van Elburg and van Ooyen 2010) [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]

Vogelstein RJ, Mallik U, Culurciello E, Cauwenberghs G, Etienne-Cummings R (2007) A multichip neuromorphic system for spike-based visual information processing. Neural Comput 19:2281-300 [Journal] [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:e58926 [Journal] [PubMed]