Abarbanel HDI, Creveling DR, Kostuk M, Farsian R. (2009). Dynamical state and parameter estimation SIAM J Appl. Dyn. Syst. 8

Abrahao KP, Chancey JH, Chan CS, Lovinger DM. (2017). Ethanol-Sensitive Pacemaker Neurons in the Mouse External Globus Pallidus. Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology. 42 [PubMed]

Bahl A, Stemmler MB, Herz AV, Roth A. (2012). Automated optimization of a reduced layer 5 pyramidal cell model based on experimental data. Journal of neuroscience methods. 210 [PubMed]

• A set of reduced models of layer 5 pyramidal neurons (Bahl et al. 2012) [Model]

Bourquard T et al. (2015). Unraveling the molecular architecture of a G protein-coupled receptor/ß-arrestin/Erk module complex. Scientific reports. 5 [PubMed]

Brookings T, Goeritz ML, Marder E. (2014). Automatic parameter estimation of multicompartmental neuron models via minimization of trace error with control adjustment. Journal of neurophysiology. 112 [PubMed]

Cannon RC et al. (2014). LEMS: a language for expressing complex biological models in concise and hierarchical form and its use in underpinning NeuroML 2. Frontiers in neuroinformatics. 8 [PubMed]

Chan CS et al. (2012). Strain-specific regulation of striatal phenotype in Drd2-eGFP BAC transgenic mice. The Journal of neuroscience : the official journal of the Society for Neuroscience. 32 [PubMed]

Cornelis H et al. (2011). NineML: The network interchange for neuroscience modeling language BMC Neuroscience. 12

Damodaran S, Cressman JR, Jedrzejewski-Szmek Z, Blackwell KT. (2015). Desynchronization of fast-spiking interneurons reduces ß-band oscillations and imbalance in firing in the dopamine-depleted striatum. The Journal of neuroscience : the official journal of the Society for Neuroscience. 35 [PubMed]

• Striatal NN model of MSNs and FSIs investigated effects of dopamine depletion (Damodaran et al 2015) [Model]

Day M, Wokosin D, Plotkin JL, Tian X, Surmeier DJ. (2008). Differential excitability and modulation of striatal medium spiny neuron dendrites. The Journal of neuroscience : the official journal of the Society for Neuroscience. 28 [PubMed]

Dodson PD et al. (2015). Distinct developmental origins manifest in the specialized encoding of movement by adult neurons of the external globus pallidus. Neuron. 86 [PubMed]

Druckmann S et al. (2007). A novel multiple objective optimization framework for constraining conductance-based neuron models by experimental data. Frontiers in neuroscience. 1 [PubMed]

Friedrich P, Vella M, Gulyás AI, Freund TF, Káli S. (2014). A flexible, interactive software tool for fitting the parameters of neuronal models. Frontiers in neuroinformatics. 8 [PubMed]

• Software (called Optimizer) for fitting neuronal models (Friedrich et al. 2014) [Model]

Gewaltig MO, Cannon R. (2014). Current practice in software development for computational neuroscience and how to improve it. PLoS computational biology. 10 [PubMed]

Glajch KE et al. (2016). Npas1+ Pallidal Neurons Target Striatal Projection Neurons. The Journal of neuroscience : the official journal of the Society for Neuroscience. 36 [PubMed]

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]

Golowasch J, Goldman MS, Abbott LF, Marder E. (2002). Failure of averaging in the construction of a conductance-based neuron model. Journal of neurophysiology. 87 [PubMed]

Gurkiewicz M, Korngreen A. (2007). A numerical approach to ion channel modelling using whole-cell voltage-clamp recordings and a genetic algorithm. PLoS computational biology. 3 [PubMed]

• Ion channel modeling with whole cell and a genetic algorithm (Gurkiewicz and Korngreen 2007) [Model]

Günay C, Edgerton JR, Jaeger D. (2008). Channel density distributions explain spiking variability in the globus pallidus: a combined physiology and computer simulation database approach. The Journal of neuroscience : the official journal of the Society for Neuroscience. 28 [PubMed]

• Globus pallidus multi-compartmental model neuron with realistic morphology (Gunay et al. 2008) [Model]

Hansen N, Kern S. (2004). Evaluating the CMA evolution strategy on multimodal test functions Parallel Probl. Solv. Nat. PPSN 2004.

Hay E, Hill S, Schürmann F, Markram H, Segev I. (2011). Models of neocortical layer 5b pyramidal cells capturing a wide range of dendritic and perisomatic active properties. PLoS computational biology. 7 [PubMed]

• L5b PC model constrained for BAC firing and perisomatic current step firing (Hay et al., 2011) [Model]
• Layer V pyramidal cell model with reduced morphology (Mäki-Marttunen et al 2018) [Model]
• Cortical Layer 5b pyr. cell with [Na+]i mechanisms, from Hay et al 2011 (Zylbertal et al 2017) [Model]

Hendrickson EB, Edgerton JR, Jaeger D. (2011). The capabilities and limitations of conductance-based compartmental neuron models with reduced branched or unbranched morphologies and active dendrites. Journal of computational neuroscience. 30 [PubMed]

• Comparison of full and reduced globus pallidus models (Hendrickson 2010) [Model]

Hendrickson EB, Edgerton JR, Jaeger D. (2011). The use of automated parameter searches to improve ion channel kinetics for neural modeling. Journal of computational neuroscience. 31 [PubMed]

Hernández VM et al. (2015). Parvalbumin+ Neurons and Npas1+ Neurons Are Distinct Neuron Classes in the Mouse External Globus Pallidus. The Journal of neuroscience : the official journal of the Society for Neuroscience. 35 [PubMed]

Holmes WR, Ambros-Ingerson J, Grover LM. (2006). Fitting experimental data to models that use morphological data from public databases. Journal of computational neuroscience. 20 [PubMed]

Johenning FW et al. (2015). Ryanodine Receptor Activation Induces Long-Term Plasticity of Spine Calcium Dynamics. PLoS biology. 13 [PubMed]

Jędrzejewska-Szmek J, Damodaran S, Dorman DB, Blackwell KT. (2017). Calcium dynamics predict direction of synaptic plasticity in striatal spiny projection neurons. The European journal of neuroscience. 45 [PubMed]

• Striatal Spiny Projection Neuron (SPN) plasticity rule (Jedrzejewska-Szmek et al 2016) [Model]

Keren N, Bar-Yehuda D, Korngreen A. (2009). Experimentally guided modelling of dendritic excitability in rat neocortical pyramidal neurones. The Journal of physiology. 587 [PubMed]

Keren N, Peled N, Korngreen A. (2005). Constraining compartmental models using multiple voltage recordings and genetic algorithms. Journal of neurophysiology. 94 [PubMed]

Lee SH, Schwaller B, Neher E. (2000). Kinetics of Ca2+ binding to parvalbumin in bovine chromaffin cells: implications for [Ca2+] transients of neuronal dendrites. The Journal of physiology. 525 Pt 2 [PubMed]

Marder E, Goaillard JM. (2006). Variability, compensation and homeostasis in neuron and network function. Nature reviews. Neuroscience. 7 [PubMed]

Martínez-Álvarez A et al. (2016). Automatic Tuning of a Retina Model for a Cortical Visual Neuroprosthesis Using a Multi-Objective Optimization Genetic Algorithm. International journal of neural systems. 26 [PubMed]

Mastro KJ, Bouchard RS, Holt HA, Gittis AH. (2014). Transgenic mouse lines subdivide external segment of the globus pallidus (GPe) neurons and reveal distinct GPe output pathways. The Journal of neuroscience : the official journal of the Society for Neuroscience. 34 [PubMed]

Meza RC, López-Jury L, Canavier CC, Henny P. (2018). Role of the Axon Initial Segment in the Control of Spontaneous Frequency of Nigral Dopaminergic Neurons In Vivo. The Journal of neuroscience : the official journal of the Society for Neuroscience. 38 [PubMed]

• Role of the AIS in the control of spontaneous frequency of dopaminergic neurons (Meza et al 2017) [Model]

Nevian T, Sakmann B. (2004). Single spine Ca2+ signals evoked by coincident EPSPs and backpropagating action potentials in spiny stellate cells of layer 4 in the juvenile rat somatosensory barrel cortex. The Journal of neuroscience : the official journal of the Society for Neuroscience. 24 [PubMed]

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]

Olypher AV, Calabrese RL. (2007). Using constraints on neuronal activity to reveal compensatory changes in neuronal parameters. Journal of neurophysiology. 98 [PubMed]

• Activity constraints on stable neuronal or network parameters (Olypher and Calabrese 2007) [Model]

Plesser HE, Morillas C, Martínez-Cañada P, Pelayo F, Romero S. (2017). Genetic algorithm for optimization of models of the early stages in the visual system Neurocomputing. 250

Prinz AA, Billimoria CP, Marder E. (2003). Alternative to hand-tuning conductance-based models: construction and analysis of databases of model neurons. Journal of neurophysiology. 90 [PubMed]

Prinz AA, Bucher D, Marder E. (2004). Similar network activity from disparate circuit parameters. Nature neuroscience. 7 [PubMed]

• Lobster STG pyloric network model with calcium sensor (Gunay & Prinz 2010) (Prinz et al. 2004) [Model]

Prinz AA, Thirumalai V, Marder E. (2003). The functional consequences of changes in the strength and duration of synaptic inputs to oscillatory neurons. The Journal of neuroscience : the official journal of the Society for Neuroscience. 23 [PubMed]

Qian K, Yu N, Tucker KR, Levitan ES, Canavier CC. (2014). Mathematical analysis of depolarization block mediated by slow inactivation of fast sodium channels in midbrain dopamine neurons. Journal of neurophysiology. 112 [PubMed]

Ray S, Bhalla US. (2008). PyMOOSE: Interoperable Scripting in Python for MOOSE. Frontiers in neuroinformatics. 2 [PubMed]

• Moose/PyMOOSE: interoperable scripting in Python for MOOSE (Ray and Bhalla 2008) [Model]

Richmond P, Cope A, Gurney K, Allerton DJ. (2014). From model specification to simulation of biologically constrained networks of spiking neurons. Neuroinformatics. 12 [PubMed]

Rossant C et al. (2011). Fitting neuron models to spike trains. Frontiers in neuroscience. 5 [PubMed]

Rumbell TH et al. (2016). Automated evolutionary optimization of ion channel conductances and kinetics in models of young and aged rhesus monkey pyramidal neurons. Journal of computational neuroscience. 41 [PubMed]

• Rhesus Monkey Young and Aged L3 PFC Pyramidal Neurons (Rumbell et al. 2016) [Model]

Ryu C et al. (2017). STIM1 Regulates Somatic Ca2+ Signals and Intrinsic Firing Properties of Cerebellar Purkinje Neurons. The Journal of neuroscience : the official journal of the Society for Neuroscience. 37 [PubMed]

Schaefer AT, Larkum ME, Sakmann B, Roth A. (2003). Coincidence detection in pyramidal neurons is tuned by their dendritic branching pattern. Journal of neurophysiology. 89 [PubMed]

• Pyramidal neuron coincidence detection tuned by dendritic branching pattern (Schaefer et al 2003) [Model]

Segev I, London M. (2000). Untangling dendrites with quantitative models. Science (New York, N.Y.). 290 [PubMed]

Taylor AL, Goaillard JM, Marder E. (2009). How multiple conductances determine electrophysiological properties in a multicompartment model. The Journal of neuroscience : the official journal of the Society for Neuroscience. 29 [PubMed]

Tucker KR, Huertas MA, Horn JP, Canavier CC, Levitan ES. (2012). Pacemaker rate and depolarization block in nigral dopamine neurons: a somatic sodium channel balancing act. The Journal of neuroscience : the official journal of the Society for Neuroscience. 32 [PubMed]

Van Geit W, De Schutter E, Achard P. (2008). Automated neuron model optimization techniques: a review. Biological cybernetics. 99 [PubMed]

Van Geit W et al. (2016). BluePyOpt: Leveraging Open Source Software and Cloud Infrastructure to Optimise Model Parameters in Neuroscience. Frontiers in neuroinformatics. 10 [PubMed]

Vanier MC, Bower JM. (1999). A comparative survey of automated parameter-search methods for compartmental neural models. Journal of computational neuroscience. 7 [PubMed]

van Ooyen A, Duijnhouwer J, Remme MW, van Pelt J. (2002). The effect of dendritic topology on firing patterns in model neurons. Network (Bristol, England). 13 [PubMed]

Rumbell T, Kozloski J. (2019). Dimensions of control for subthreshold oscillations and spontaneous firing in dopamine neurons PLOS Computational Biology. 15

• Control of oscillations and spontaneous firing in dopamine neurons (Rumbell & Kozloski 2019) [Model]