Ion channel modeling with whole cell and a genetic algorithm (Gurkiewicz and Korngreen 2007)

Akaike H. (1974). A new look at the statistical model identification IEEE Trans Appl Comp. 19

Aldrich RW, Getting PA, Thompson SH. (1979). Inactivation of delayed outward current in molluscan neurone somata. The Journal of physiology. 291 [PubMed]

Armstrong CM, Bezanilla F. (1977). Inactivation of the sodium channel. II. Gating current experiments. The Journal of general physiology. 70 [PubMed]

Baranauskas G, Martina M. (2006). Sodium currents activate without a Hodgkin-and-Huxley-type delay in central mammalian neurons. The Journal of neuroscience : the official journal of the Society for Neuroscience. 26 [PubMed]

• Sodium currents activate without a delay (Baranauskas and Martina 2006) [Model]

Bean BP. (2007). The action potential in mammalian central neurons. Nature reviews. Neuroscience. 8 [PubMed]

Bekkers JM. (2000). Properties of voltage-gated potassium currents in nucleated patches from large layer 5 cortical pyramidal neurons of the rat. The Journal of physiology. 525 Pt 3 [PubMed]

Benison G, Keizer J, Chalupa LM, Robinson DW. (2001). Modeling temporal behavior of postnatal cat retinal ganglion cells. Journal of theoretical biology. 210 [PubMed]

• Retinal Ganglion Cell: I-CaN and I-CaL (Benison et al. 2001) [Model]
• Retinal Ganglion Cell: I-Na,t (Benison et al 2001) [Model]
• Retinal Ganglion Cell: I-A (Benison et al 2001) [Model]

Bezanilla F, Armstrong CM. (1977). Inactivation of the sodium channel. I. Sodium current experiments. The Journal of general physiology. 70 [PubMed]

Cannon RC, D'Alessandro G. (2006). The ion channel inverse problem: neuroinformatics meets biophysics. PLoS computational biology. 2 [PubMed]

Goldman L, Schauf CL. (1972). Inactivation of the sodium current in Myxicola giant axons. Evidence for coupling to the activation process. The Journal of general physiology. 59 [PubMed]

Gurkiewicz M, Korngreen A. (2006). Recording, analysis, and function of dendritic voltage-gated channels. Pflugers Archiv : European journal of physiology. 453 [PubMed]

HODGKIN AL, HUXLEY AF. (1952). A quantitative description of membrane current and its application to conduction and excitation in nerve. The Journal of physiology. 117 [PubMed]

• Squid axon (Hodgkin, Huxley 1952) (NEURON) [Model]
• Squid axon (Hodgkin, Huxley 1952) (SNNAP) [Model]
• Squid axon (Hodgkin, Huxley 1952) (LabAXON) [Model]
• Squid axon (Hodgkin, Huxley 1952) (SBML, XPP, other) [Model]
• Squid axon (Hodgkin, Huxley 1952) used in (Chen et al 2010) (R language) [Model]

HODGKIN AL, HUXLEY AF. (1952). Currents carried by sodium and potassium ions through the membrane of the giant axon of Loligo. The Journal of physiology. 116 [PubMed]

HODGKIN AL, HUXLEY AF. (1952). The components of membrane conductance in the giant axon of Loligo. The Journal of physiology. 116 [PubMed]

HODGKIN AL, HUXLEY AF. (1952). The dual effect of membrane potential on sodium conductance in the giant axon of Loligo. The Journal of physiology. 116 [PubMed]

HODGKIN AL, HUXLEY AF. (1952). Movement of sodium and potassium ions during nervous activity. Cold Spring Harbor symposia on quantitative biology. 17 [PubMed]

HODGKIN AL, HUXLEY AF, KATZ B. (1952). Measurement of current-voltage relations in the membrane of the giant axon of Loligo. The Journal of physiology. 116 [PubMed]

Hering J, Feltz A, Lambert RC. (2004). Slow inactivation of the Ca(V)3.1 isotype of T-type calcium channels. The Journal of physiology. 555 [PubMed]

Hines ML, Carnevale NT. (1997). The NEURON simulation environment. Neural computation. 9 [PubMed]

Hines ML, Carnevale NT. (2000). Expanding NEURON's repertoire of mechanisms with NMODL. Neural computation. 12 [PubMed]

Horn R. (1987). Statistical methods for model discrimination. Applications to gating kinetics and permeation of the acetylcholine receptor channel. Biophysical journal. 51 [PubMed]

Korngreen A, Kaiser KM, Zilberter Y. (2005). Subthreshold inactivation of voltage-gated K+ channels modulates action potentials in neocortical bitufted interneurones from rats. The Journal of physiology. 562 [PubMed]

• Subthreshold inact. of K channels modulates APs in bitufted interneurons (Korngreen et al 2005) [Model]

Korngreen A, Sakmann B. (2000). Voltage-gated K+ channels in layer 5 neocortical pyramidal neurones from young rats: subtypes and gradients. The Journal of physiology. 525 Pt 3 [PubMed]

• Pyramidal Neuron Deep: K+ kinetics (Korngreen, Sakmann 2000) [Model]

Levy DI, Deutsch C. (1996). Recovery from C-type inactivation is modulated by extracellular potassium. Biophysical journal. 70 [PubMed]

Llinás RR. (1988). The intrinsic electrophysiological properties of mammalian neurons: insights into central nervous system function. Science (New York, N.Y.). 242 [PubMed]

Magleby KL. (1992). Ion channels. Preventing artifacts and reducing errors in single-channel analysis. Methods in enzymology. 207 [PubMed]

Marom S, Levitan IB. (1994). State-dependent inactivation of the Kv3 potassium channel. Biophysical journal. 67 [PubMed]

Milescu LS, Akk G, Sachs F. (2005). Maximum likelihood estimation of ion channel kinetics from macroscopic currents. Biophysical journal. 88 [PubMed]

Mitchell M. (1996). An Introduction to Genetic Algorithms.

Nakamura T, Oyama A, Obayashi S. (2001). Real-coded adaptive range genetic algorithm applied to transonic wing optimization Appl Soft Comp. 1

Neher E. (1992). Correction for liquid junction potentials in patch clamp experiments. Methods in enzymology. 207 [PubMed]

Patlak J. (1991). Molecular kinetics of voltage-dependent Na+ channels. Physiological reviews. 71 [PubMed]

Press WH, Teukolsky SA, Flannery BP, Vellerling WT. (1992). Numerical Recipes In C: The Art Of Scientific Computing.

Sakmann B, Neher E. (1995). Single-channel Recording. 2

Sather W, Dieudonné S, MacDonald JF, Ascher P. (1992). Activation and desensitization of N-methyl-D-aspartate receptors in nucleated outside-out patches from mouse neurones. The Journal of physiology. 450 [PubMed]

Sigworth FJ, Zhou J. (1992). Ion channels. Analysis of nonstationary single-channel currents. Methods in enzymology. 207 [PubMed]

Starkus JG, Kuschel L, Rayner MD, Heinemann SH. (1997). Ion conduction through C-type inactivated Shaker channels. The Journal of general physiology. 110 [PubMed]

Stuart GJ, Dodt HU, Sakmann B. (1993). Patch-clamp recordings from the soma and dendrites of neurons in brain slices using infrared video microscopy. Pflugers Archiv : European journal of physiology. 423 [PubMed]

Willms AR. (2002). NEUROFIT: software for fitting Hodgkin-Huxley models to voltage-clamp data. Journal of neuroscience methods. 121 [PubMed]

• NEUROFIT: fitting HH models to voltage clamp data (Willms 2002) [Model]

Willms AR, Baro DJ, Harris-Warrick RM, Guckenheimer J. (1999). An improved parameter estimation method for Hodgkin-Huxley models. Journal of computational neuroscience. 6 [PubMed]

• NEUROFIT: fitting HH models to voltage clamp data (Willms 2002) [Model]

Almog M, Korngreen A. (2014). A Quantitative Description of Dendritic Conductances and Its Application to Dendritic Excitation in Layer 5 Pyramidal Neurons The Journal of neuroscience : the official journal of the Society for Neuroscience. 34 [PubMed]

• Ionic mechanisms of dendritic spikes (Almog and Korngreen 2014) [Model]

Andreozzi E, Carannante I, D'Addio G, Cesarelli M, Balbi P. (2019). Phenomenological models of NaV1.5. A side by side, procedural, hands-on comparison between Hodgkin-Huxley and kinetic formalisms Scientific reports. 9 [PubMed]

• Phenomenological models of NaV1.5: Hodgkin-Huxley and kinetic formalisms (Andreozzi et al 2019) [Model]

Ben-Shalom R et al. (2022). NeuroGPU: Accelerating multi-compartment, biophysically detailed neuron simulations on GPUs Journal of neuroscience methods. 366 [PubMed]

• NeuroGPU example on L5_TTPC1_cADpyr232_1 (Ben-Shalom 2022)(Ramaswamy et al., 2015) [Model]

Carnevale NT, Morse TM. (1996). Research reports that have used NEURON Web published citations at the NEURON website.

Ferneyhough GB, Thibealut CM, Dascalu SM, Harris FC. (2016). ModFossa: A library for modeling ion channels using Python. Journal of bioinformatics and computational biology. 14 [PubMed]

• ModFossa: a library for modeling ion channels using Python (Ferneyhough et al 2016) [Model]

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]

Gurkiewicz M, Korngreen A, Waxman SG, Lampert A. (2011). Kinetic modeling of Nav1.7 provides insight into erythromelalgia-associated F1449V mutation. Journal of neurophysiology. 105 [PubMed]

• HMM of Nav1.7 WT and F1449V (Gurkiewicz et al. 2011) [Model]

Jȩdrzejewski-Szmek Z, Abrahao KP, Jȩdrzejewska-Szmek J, Lovinger DM, Blackwell KT. (2018). Parameter Optimization Using Covariance Matrix Adaptation-Evolutionary Strategy (CMA-ES), an Approach to Investigate Differences in Channel Properties Between Neuron Subtypes. Frontiers in neuroinformatics. 12 [PubMed]

• Parameter optimization using CMA-ES (Jedrzejewski-Szmek et al 2018) [Model]

Menon V, Spruston N, Kath WL. (2009). A state-mutating genetic algorithm to design ion-channel models. Proceedings of the National Academy of Sciences of the United States of America. 106 [PubMed]

• Hippocampus CA1 pyramidal model with Na channel exhibiting slow inactivation (Menon et al. 2009) [Model]

Nowotny T, Levi R, Selverston AI. (2008). Probing the dynamics of identified neurons with a data-driven modeling approach. PloS one. 3 [PubMed]

• Data-driven, HH-type model of the lateral pyloric (LP) cell in the STG (Nowotny et al. 2008) [Model]