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

   Principles of Computational Modelling in Neuroscience (Book) (Sterratt et al. 2011)

References and models cited by this paper

References and models that cite this paper

Abarbanel HD, Gibb L, Huerta R, Rabinovich MI (2003) Biophysical model of synaptic plasticity dynamics. Biol Cybern 89:214-26 [PubMed]

Abbott LF, Marder E (1998) Modeling small networks. Methods in Neuronal Modeling: From Ions to Networks, Second Edition, Koch C:Segev I, ed. pp.361

Abbott LF, Thoroughman KA, Prinz AA, Thirumalai V, Marder E (2003) Activity-dependent modification of intrinsic and synaptic conductances in neurons and rhythmic networks Modeling Neural Development, van_Ooyen A, ed. pp.151

Achard P, De Schutter E (2006) Complex parameter landscape for a complex neuron model. PLoS Comput Biol 2:e94 [PubMed]

Adrian ED (1928) The Basis of Sensation

Aeschlimann M, Tettoni L (2001) Biophysical model of axonal path finding Neurocomputing 38:87-92

Agmon-Snir H, Carr CE, Rinzel J (1998) The role of dendrites in auditory coincidence detection. Nature 393:268-72 [PubMed]

Ajay SM, Bhalla US (2006) Synaptic plasticity in vitro and in silico: insights into an intracellular signaling maze. Physiology (Bethesda) 21:289-96 [PubMed]

Albin RL, Young AB, Penney JB (1989) The functional anatomy of basal ganglia disorders. Trends Neurosci 12:366-75 [PubMed]

Alexander SP, Mathie A, Peters JA (2008) Guide to Receptors and Channels (GRAC), 3rd edition. Br J Pharmacol 153 Suppl 2:S1-209 [PubMed]

Amit D, Brunel N (1997) Dynamics of a recurrent network of spiking neurons before and following learning Network 8:373-404

Amit DJ (1989) Modeling Brain Function: the World of Attractor Neural Networks

Amit DJ, Brunel N (2000) Model of global spontaneous activity and local structured activity during delay periods in the cerebral cortex. Cereb Cortex 7:237-52 [PubMed]

Amit DJ, Fusi S (1994) Learning in neural networks with material synapses Neural Comput 6:957-982

Amit DJ, Gutfreund H, Sompolinsky H (1985) Spin-glass models of neural networks. Phys Rev A 32:1007-1018 [PubMed]

Amit DJ, Tsodyks MV (1991) Quantitative study of attractor neural networks retrieving at low spike rates. II: Low-rate retrieval in symmetric networks Network 2:275-294

Amit DJ, Tsodyks MV (1991) Quantitative study of attractor neural network retrieving at low spike rates I Substrate-spikes, rates, and neuronal gain. Network 2:259-274

Anderson DJ, Rose JE, Hind JE, Brugge JF (1971) Temporal position of discharges in single auditory nerve fibers within the cycle of a sine-wave stimulus: frequency and intensity effects. J Acoust Soc Am 49:Suppl 2:1131+-38 [PubMed]

Aradi I, Erdi P (2006) Computational neuropharmacology: dynamical approaches in drug discovery. Trends Pharmacol Sci 27:240-3 [PubMed]

Aradi I, Santhakumar V, Soltesz I (2004) Impact of heterogeneous perisomatic IPSC populations on pyramidal cell firing rates. J Neurophysiol 91:2849-58 [Journal] [PubMed]

Aradi I, Soltesz I (2002) Modulation of network behaviour by changes in variance in interneuronal properties. J Physiol 538:227-51 [PubMed]

Arisi I, Cattaneo A, Rosato V (2006) Parameter estimate of signal transduction pathways. BMC Neurosci 7 Suppl 1:S6

Armstrong CM, Bezanilla F (1973) Currents related to movement of the gating particles of the sodium channels. Nature 242:459-61 [PubMed]

Arnett DW (1978) Statistical dependence between neighboring retinal ganglion cells in goldfish. Exp Brain Res 32:49-53 [PubMed]

Arrhenius S () Über die Reaktionsgeschwindigkeit bei der Inversion von Rohrzucker in Sauren Z Phys Chem 4:226-248

Ascher P, Nowak L (1988) The role of divalent cations in the N-methyl-D-aspartate responses of mouse central neurones in culture. J Physiol 399:247-66 [PubMed]

Ascoli GA (2002) Neuroanatomical algorithms for dendritic modelling. Network 13:247-60 [PubMed]

Ascoli GA (2006) Mobilizing the base of neuroscience data: the case of neuronal morphologies. Nat Rev Neurosci 7:318-24 [PubMed]

Ascoli GA, Krichmar JL, Nasuto SJ, Senft SL (2001) Generation, description and storage of dendritic morphology data. Philos Trans R Soc Lond B Biol Sci 356:1131-45 [PubMed]

Auer M (2000) Three-dimensional electron cryo-microscopy as a powerful structural tool in molecular medicine. J Mol Med (Berl) 78:191-202 [PubMed]

Auerbach AA, Bennett MV (1969) A rectifying electrotonic synapse in the central nervous system of a vertebrate. J Gen Physiol 53:211-37 [PubMed]

Badoual M, Zou Q, Davison AP, Rudolph M, Bal T, Fregnac Y, Destexhe A (2006) Biophysical and phenomenological models of multiple spike interactions in spike-timing dependent plasticity. Int J Neural Syst 16:79-97 [Journal] [PubMed]

   Biophysical and phenomenological models of spike-timing dependent plasticity (Badoual et al. 2006) [Model]

Baker PF, Hodgkin AL, Ridgway EB (1971) Depolarization and calcium entry in squid giant axons. J Physiol 218:709-55 [PubMed]

Barbour B, Hausser M (1997) Intersynaptic diffusion of neurotransmitter. Trends Neurosci 20:377-84 [PubMed]

Bartos M, Vida I, Jonas P (2007) Synaptic mechanisms of synchronized gamma oscillations in inhibitory interneuron networks. Nat Rev Neurosci 8:45-56 [PubMed]

Bean BP (2007) The action potential in mammalian central neurons. Nat Rev Neurosci 8:451-65 [PubMed]

Bedard C, Kroger H, Destexhe A (2004) Modeling extracellular field potentials and the frequency-filtering properties of extracellular space. Biophys J 86:1829-42 [Journal] [PubMed]

   Modeling local field potentials (Bedard et al. 2004) [Model]

Bell AJ (1992) Self-organisation in real neurons: anti-Hebb in channel space ? Advances In Neural Information Processing Systems, Moody JE:Hanson SJ:Lippmann RP, ed. pp.59

Bennett MR, Farnell L, Gibson WG (2000) The probability of quantal secretion within an array of calcium channels of an active zone. Biophys J 78:2222-40 [PubMed]

Bennett MR, Farnell L, Gibson WG (2000) The probability of quantal secretion near a single calcium channel of an active zone. Biophys J 78:2201-21 [PubMed]

Bennett MR, Gibson WG, Robinson J (1994) Dynamics of the CA3 pyramidal neuron autoassociative memory network in the hippocampus. Philos Trans R Soc Lond B Biol Sci 343:167-87

Bennett MR, Robinson J (1989) Growth and elimination of nerve terminals at synaptic sites during polyneuronal innervation of muscle cells: a trophic hypothesis. Proc R Soc Lond B Biol Sci 235:299-320 [PubMed]

Bennett MV, Zukin RS (2004) Electrical coupling and neuronal synchronization in the Mammalian brain. Neuron 41:495-511 [PubMed]

Benzi R, Sutera A, Vulpiani A (1983) The mechanism of stochastic resonance` J Phys A Math Gen 14:L453-L457

Berridge MJ (1998) Neuronal calcium signaling. Neuron 21:13-26 [PubMed]

Berridge MJ, Bootman MD, Roderick HL (2003) Calcium signalling: dynamics, homeostasis and remodelling. Nat Rev Mol Cell Biol 4:517-29 [PubMed]

Berry M, Bradley PM (1976) The application of network analysis to the study of branching patterns of large dendritic fields. Brain Res 109:111-32 [PubMed]

Bertram R, Sherman A, Stanley EF (1996) Single-domain/bound calcium hypothesis of transmitter release and facilitation. J Neurophysiol 75:1919-31 [Journal] [PubMed]

Betz WJ (1970) Depression of transmitter release at the neuromuscular junction of the frog. J Physiol 206:629-44 [PubMed]

Betz WJ, Caldwell JH, Ribchester RR (1980) The effects of partial denervation at birth on the development of muscle fibres and motor units in rat lumbrical muscle. J Physiol 303:265-79 [PubMed]

Beurle RL (1956) Properties of a mass of cells capable of regenerating pulses. Philos Trans R Soc Lond B Biol Sci 240:55-94

Bezanilla F, Armstrong CM (1977) Inactivation of the sodium channel. I. Sodium current experiments. J Gen Physiol 70:549-66 [PubMed]

Bhalla US (1998) The network within: signaling pathways The Book of GENESIS: Exploring Realistic Neural Models with the General Neural Simulation System, Bower J:Beeman D, ed. pp.169

Bhalla US (2001) Modeling networks of signaling pathways Computational Neuroscience: Realistic Modeling for Experimentalists, De_Schutter E, ed. pp.25

Bhalla US (2004) Signaling in small subcellular volumes. I. Stochastic and diffusion effects on individual pathways. Biophys J 87:733-44 [PubMed]

Bhalla US (2004) Models of cell signaling pathways. Curr Opin Genet Dev 14:375-81 [PubMed]

Bhalla US (2004) Signaling in small subcellular volumes. II. Stochastic and diffusion effects on synaptic network properties. Biophys J 87:745-53 [PubMed]

Bhalla US, Bower JM (1993) Exploring parameter space in detailed single neuron models: simulations of the mitral and granule cells of the olfactory bulb. J Neurophysiol 69:1948-65 [Journal] [PubMed]

   Granule Cells of the Olfactory Bulb (Simoes_De_Souza et al. 2014) [Model]
   Olfactory Mitral Cell (Bhalla, Bower 1993) [Model]

Bhalla US, Iyengar R (1999) Emergent properties of networks of biological signaling pathways. Science 283:381-7 [PubMed]

   Emergent properties of networks of biological signaling pathways (Bhalla, Iyengar 1999) [Model]

Bi GQ, Poo MM (1998) Synaptic modifications in cultured hippocampal neurons: dependence on spike timing, synaptic strength, and postsynaptic cell type. J Neurosci 18:10464-72 [PubMed]

Bienenstock EL, Cooper LN, Munro PW (1982) Theory for the development of neuron selectivity: orientation specificity and binocular interaction in visual cortex. J Neurosci 2:32-48 [PubMed]

Billups B, Graham BP, Wong AY, Forsythe ID (2005) Unmasking group III metabotropic glutamate autoreceptor function at excitatory synapses in the rat CNS. J Physiol 565:885-96 [PubMed]

Blackwell KT (2006) An efficient stochastic diffusion algorithm for modeling second messengers in dendrites and spines. J Neurosci Methods 157:142-53 [PubMed]

Blackwell KT, Hellgren-kotaleski J (2002) Modeling the dynamicsof second messenger pathways Neuroscience Databases, Kotter R, ed. pp.63

Blaustein MP, Hodgkin AL (1969) The effect of cyanide on the efflux of calcium from squid axons. J Physiol 200:497-527 [PubMed]

Bliss TV, Lomo T (1973) Long-lasting potentiation of synaptic transmission in the dentate area of the anaesthetized rabbit following stimulation of the perforant path. J Physiol 232:331-56 [PubMed]

Block H (1962) The perceptron: A model for brain functioning Rev Mod Phys 34:123-135

Bloomfield SA, Hamos JE, Sherman SM (1987) Passive cable properties and morphological correlates of neurones in the lateral geniculate nucleus of the cat. J Physiol 383:653-92 [PubMed]

Booth V, Rinzel J (1995) A minimal, compartmental model for a dendritic origin of bistability of motoneuron firing patterns. J Comput Neurosci 2:299-312 [Journal] [PubMed]

Borg-graham L (1999) Interpretations of data and mechanisms for hippocampal pyramidal cell models Cerebral Cortex cortical Models, Jones E:Ulinski P:Peters A, ed. pp.19

Borg-Graham LJ (1989) Modelling the somatic electrical response of hippocampal pyramidal neurons Technical Report AITR-1161

Bormann G, Brosens F, De_schutter E (2001) Diffusion Computational Modeling of Genetic and Biochemical Networks, Bower JM:Bolouri H, ed. pp.189

Bower JM, Beeman D (1998) The Book Of Genesis: Exploring Realistic Neural Models With The General Neural Simulation System

Brenner S (2010) Sequences and consequences Philos Trans R Soc Lond B 365:207-212

Brette R (2006) Exact simulation of integrate-and-fire models with synaptic conductances. Neural Comput 18:2004-27 [PubMed]

Brette R, Piwkowska Z, Monier C, Rudolph-Lilith M, Fournier J, Levy M, Fregnac Y, Bal T, Dest (2008) High-resolution intracellular recordings using a real-time computational model of the electrode. Neuron 59:379-91 [PubMed]

   High-Res. Recordings Using a Real-Time Computational Model of the Electrode (Brette et al. 2008) [Model]

Brette R, Rudolph M, Carnevale T, Hines M, Beeman D, Bower JM, Diesmann M, Morrison A, et al. (2007) Simulation of networks of spiking neurons: A review of tools and strategies. J Comp Neurosci 23:349-98 [Journal] [PubMed]

   Networks of spiking neurons: a review of tools and strategies (Brette et al. 2007) [Model]

Brown A, Yates PA, Burrola P, Ortuño D, Vaidya A, Jessell TM, Pfaff SL, O'Leary DD, Lemke G (2000) Topographic mapping from the retina to the midbrain is controlled by relative but not absolute levels of EphA receptor signaling. Cell 102:77-88 [PubMed]

Brown AM, Schwindt PC, Crill WE (1993) Voltage dependence and activation kinetics of pharmacologically defined components of the high-threshold calcium current in rat neocortical neurons. J Neurophysiol 70:1530-43 [Journal] [PubMed]

Brown DA, Griffith WH (1983) Calcium-activated outward current in voltage-clamped hippocampal neurones of the guinea-pig. J Physiol 337:287-301 [PubMed]

Brown MC, Jansen JK, Van Essen D (1976) Polyneuronal innervation of skeletal muscle in new-born rats and its elimination during maturation. J Physiol 261:387-422 [PubMed]

Brunel N, van Rossum MC (2007) Lapicque's 1907 paper: from frogs to integrate-and-fire. Biol Cybern 97:337-9 [PubMed]

Buckingham J (1991) Delicate nets, faint recollections: a study of partially connected associative network memories

Buckingham J, Willshaw D (1993) On setting unit thresholds in an incompletely connected associative net Network 4:441-459

Buice MA, Cowan JD (2009) Statistical mechanics of the neocortex. Prog Biophys Mol Biol 99:53-86 [PubMed]

Burgoyne RD (2007) Neuronal calcium sensor proteins: generating diversity in neuronal Ca2+ signalling. Nat Rev Neurosci 8:182-93 [PubMed]

Burke RE, Marks WB (2002) Some approaches to quantitative dendritic morphology Computational Neuroanatomy: Principles and Methods, Ascoli GA, ed. pp.27

Burke RE, Marks WB, Ulfhake B (1992) A parsimonious description of motoneuron dendritic morphology using computer simulation. J Neurosci 12:2403-16 [PubMed]

Butson CR, McIntyre CC (2005) Tissue and electrode capacitance reduce neural activation volumes during deep brain stimulation. Clin Neurophysiol 116:2490-500 [PubMed]

Cannon RC, D'Alessandro G (2006) The ion channel inverse problem: neuroinformatics meets biophysics. PLoS Comput Biol 2:e91-506 [PubMed]

Cannon RC, Gewaltig MO, Gleeson P, Bhalla US, Cornelis H, Hines ML, Howell FW, Muller E, Stil (2007) Interoperability of neuroscience modeling software: current status and future directions. Neuroinformatics 5:127-38 [Journal] [PubMed]

Cannon RC, Turner DA, Pyapali GK, Wheal HV (1998) An on-line archive of reconstructed hippocampal neurons. J Neurosci Methods 84:49-54 [PubMed]

Cannon SC, Robinson DA, Shamma S (1983) A proposed neural network for the integrator of the oculomotor system. Biol Cybern 49:127-36 [PubMed]

Carnevale NT, Hines ML (2006) The NEURON Book

Carriquiry AL, Ireland WP, Kliemann W, Uemura E (1991) Statistical evaluation of dendritic growth models. Bull Math Biol 53:579-89 [PubMed]

Castellani GC, Quinlan EM, Bersani F, Cooper LN, Shouval HZ (2007) A model of bidirectional synaptic plasticity: from signaling network to channel conductance. Learn Mem 12:423-32 [PubMed]

Catterall WA, Dib-Hajj S, Meisler MH, Pietrobon D (2008) Inherited neuronal ion channelopathies: new windows on complex neurological diseases. J Neurosci 28:11768-77

Catterall WA, Goldin AL, Waxman SG (2005) International Union of Pharmacology. XLVII. Nomenclature and structure-function relationships of voltage-gated sodium channels. Pharmacol Rev 57:397-409 [PubMed]

Catterall WA, Gutman G (2005) Introduction to the IUPHAR compendium of voltage-gated ion channels Pharmacol Rev 57:385

Catterall WA, Perez-Reyes E, Snutch TP, Striessnig J (2005) International Union of Pharmacology. XLVIII. Nomenclature and structure-function relationships of voltage-gated calcium channels. Pharmacol Rev 57:411-25 [PubMed]

Cellerino A, Novelli E, Galli-Resta L (2000) Retinal ganglion cells with NADPH-diaphorase activity in the chick form a regular mosaic with a strong dorsoventral asymmetry that can be modelled by a minimal spacing rule. Eur J Neurosci 12:613-20 [PubMed]

Chalfie M, Tu Y, Euskirchen G, Ward WW, Prasher DC (1994) Green fluorescent protein as a marker for gene expression. Science 263:802-5 [PubMed]

Cherniak C, Changizi M, Kang D (1999) Large-scale optimization of neuron arbors. Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics 59:6001-9

Cherniak C, Mokhtarzada Z, Nodelman U (2002) Optimal-wiring models of neuroanatomy Computational Neuroanatomy: Principles and Methods, Ascoli GA, ed. pp.71

Chow CC, White JA (1996) Spontaneous action potentials due to channel fluctuations. Biophys J 71:3013-21 [PubMed]

   Spontaneous firing caused by stochastic channel gating (Chow, White 1996) [Model]

Chung SH (1974) In search of the rules for nerve connections. Cell 3:201-5 [PubMed]

Churchland PS, Sejnowski TJ (1992) The Computational Brain

Clapham DE, Julius D, Montell C, Schultz G (2005) International Union of Pharmacology. XLIX. Nomenclature and structure-function relationships of transient receptor potential channels. Pharmacol Rev 57:427-50 [PubMed]

Clements JD, Lester RA, Tong G, Jahr CE, Westbrook GL (1992) The time course of glutamate in the synaptic cleft. Science 258:1498-501 [PubMed]

Coggan JS, Bartol TM, Esquenazi E, Stiles JR, Lamont S, Martone ME, Berg DK, Ellisman MH, Sej (2005) Evidence for ectopic neurotransmission at a neuronal synapse. Science 309:446-51 [PubMed]

Cole KS (1968) Membrane, Ions And Impulses

Collier JR, Monk NA, Maini PK, Lewis JH (1996) Pattern formation by lateral inhibition with feedback: a mathematical model of delta-notch intercellular signalling. J Theor Biol 183:429-46 [PubMed]

Colquhoun D, Hawkes AG, Srodzinski K (1996) Joint distributions of apparent open times and shut times of single ion channels and the maximum likelihood fitting of mechanisms Philos Trans R Soc Lond 354:2555-2590

Connor JA, Stevens CF (1971) Inward and delayed outward membrane currents in isolated neural somata under voltage clamp. J Physiol 213:1-19 [PubMed]

Connor JA, Stevens CF (1971) Voltage clamp studies of a transient outward membrane current in gastropod neural somata. J Physiol 213:21-30 [PubMed]

Connor JA, Walter D, McKown R (1977) Neural repetitive firing: modifications of the Hodgkin-Huxley axon suggested by experimental results from crustacean axons. Biophys J 18:81-102 [PubMed]

Connors BW, Long MA (2004) Electrical synapses in the mammalian brain. Annu Rev Neurosci 27:393-418 [PubMed]

Cook JE, Chalupa LM (2000) Retinal mosaics: new insights into an old concept. Trends Neurosci 23:26-34 [PubMed]

Cook JE, Rankin EC (1986) Impaired refinement of the regenerated retinotectal projection of the goldfish in stroboscopic light: a quantitative WGA-HRP study. Exp Brain Res 63:421-30 [PubMed]

COOMBS JS, CURTIS DR, ECCLES JC (1956) Time courses of motoneuronal responses. Nature 178:1049-50 [PubMed]

Cowan JD, Sharp DH (1988) Neural nets. Q Rev Biophys 21:365-427

Crank J, Nicolson P (1947) A practical method for numerical evaluation of solutions for partial differential equations of the heat conduction type Proc Camb Philos Sco 43:50-67

Crepel F, Delhaye-Bouchaud N, Guastavino JM, Sampaio I (1980) Multiple innervation of cerebellar Purkinje cells by climbing fibres in staggerer mutant mouse. Nature 283:483-4 [PubMed]

Cui J, Cox DH, Aldrich RW (1997) Intrinsic voltage dependence and Ca2+ regulation of mslo large conductance Ca-activated K+ channels. J Gen Physiol 109:647-73 [PubMed]

Davis GW (2006) Homeostatic control of neural activity: from phenomenology to molecular design. Annu Rev Neurosci 29:307-23 [PubMed]

Day M, Wang Z, Ding J, An X, Ingham CA, Shering AF, Wokosin D, Ilijic E, Sun Z, Sampson AR, M (2006) Selective elimination of glutamatergic synapses on striatopallidal neurons in Parkinson disease models. Nat Neurosci 9:251-9 [PubMed]

Dayan P, Abbott LF (2001) Theoretical Neuroscience. Computational and Mathematical Modeling of Neural Systems

Dayan P, Willshaw DJ (1991) Optimising synaptic learning rules in linear associative memories. Biol Cybern 65:253-65 [PubMed]

De Schutter E, Bower JM (1994) An active membrane model of the cerebellar Purkinje cell II. Simulation of synaptic responses. J Neurophysiol 71:401-19 [Journal] [PubMed]

   Cerebellar purkinje cell (De Schutter and Bower 1994) [Model]

De Schutter E, Bower JM (1994) An active membrane model of the cerebellar Purkinje cell. I. Simulation of current clamps in slice. J Neurophysiol 71:375-400 [Journal] [PubMed]

   Cerebellar purkinje cell (De Schutter and Bower 1994) [Model]

De Schutter E, Smolen P (1998) Calcium dynamics in large neuronal models Methods In Neuronal Modeling: From Ions To Networks, Koch C:Segev I, ed. pp.211

De Young GW, Keizer J (1992) A single-pool inositol 1,4,5-trisphosphate-receptor-based model for agonist-stimulated oscillations in Ca2+ concentration. Proc Natl Acad Sci U S A 89:9895-9 [PubMed]

Dejean C, Hyland B, Arbuthnott G (2009) Cortical effects of subthalamic stimulation correlate with behavioral recovery from dopamine antagonist induced akinesia. Cereb Cortex 19:1055-63 [PubMed]

DEL CASTILLO J, KATZ B (1954) Statistical factors involved in neuromuscular facilitation and depression. J Physiol 124:574-85 [PubMed]

DEL CASTILLO J, KATZ B (1954) Quantal components of the end-plate potential. J Physiol 124:560-73 [PubMed]

Destexhe A, Bal T (2009) Dynamic-Clamp from Principles to Applications, Destexhe A:Bal T, ed.

Destexhe A, Huguenard JR (2000) Nonlinear thermodynamic models of voltage-dependent currents. J Comput Neurosci 9:259-70 [Journal] [PubMed]

Destexhe A, Mainen Z, Sejnowski TJ (1994) An efficient method for computing synaptic conductances based on a kinetic model of receptor binding Neural Comput 6:14-18 [Journal]

   Efficient Method for Computing Synaptic Conductance (Destexhe et al 1994) [Model]
   Kinetic synaptic models applicable to building networks (Destexhe et al 1998) [Model]
   Application of a common kinetic formalism for synaptic models (Destexhe et al 1994) [Model]

Destexhe A, Mainen ZF, Sejnowski TJ (1994) Synthesis of models for excitable membranes, synaptic transmission and neuromodulation using a common kinetic formalism. J Comput Neurosci 1:195-230 [Journal] [PubMed]

   Application of a common kinetic formalism for synaptic models (Destexhe et al 1994) [Model]
   Kinetic synaptic models applicable to building networks (Destexhe et al 1998) [Model]

Destexhe A, Mainen ZF, Sejnowski TJ (1998) Kinetic models of synaptic transmission Methods In Neuronal Modeling, Koch C:Segev I, ed. pp.1

   Kinetic synaptic models applicable to building networks (Destexhe et al 1998) [Model]

Destexhe A, Sejnowski TJ (1995) G protein activation kinetics and spillover of gamma-aminobutyric acid may account for differences between inhibitory responses in the hippocampus and thalamus. Proc Natl Acad Sci U S A 92:9515-9 [PubMed]

Dittman JS, Kreitzer AC, Regehr WG (2000) Interplay between facilitation, depression, and residual calcium at three presynaptic terminals. J Neurosci 20:1374-85 [PubMed]

Dittman JS, Regehr WG (1998) Calcium dependence and recovery kinetics of presynaptic depression at the climbing fiber to Purkinje cell synapse. J Neurosci 18:6147-62 [PubMed]

Doi T, Kuroda S, Michikawa T, Kawato M (2005) Inositol 1,4,5-trisphosphate-dependent Ca2+ threshold dynamics detect spike timing in cerebellar Purkinje cells. J Neurosci 25:950-61 [Journal] [PubMed]

   Spike timing detection in different forms of LTD (Doi et al 2005) [Model]

Donohue DE, Ascoli GA (2005) Local Diameter Fully Constrains Dendritic Size in Basal but not Apical Trees of CA1 Pyramidal Neurons J Comp Neurosci 19:223-238 [Journal]

Donohue DE, Scorcioni R, Ascoli GA (2002) Generation and description of neuronal morphology using L-Neuron: A case study Computational Neuroanatomy: Principles and Methods, Ascoli G, ed. pp.49

Douglass JK, Wilkens L, Pantazelou E, Moss F (1993) Noise enhancement of information transfer in crayfish mechanoreceptors by stochastic resonance. Nature 365:337-40 [PubMed]

Doyle DA, Morais Cabral J, Pfuetzner RA, Kuo A, Gulbis JM, Cohen SL, Chait BT, MacKinnon R (1998) The structure of the potassium channel: molecular basis of K+ conduction and selectivity. Science 280:69-77 [PubMed]

Eccles JC, Ito M, Szentagothai J (1967) The Cerebellum as a Neuronal Machine

Economo MN, Fernandez FR, White JA (2010) Dynamic clamp: alteration of response properties and creation of virtual realities in neurophysiology. J Neurosci 30:2407-13 [PubMed]

Edelstein-keshet L (1988) Mathematical Models In Biology

Eglen SJ, Willshaw DJ (2002) Influence of cell fate mechanisms upon retinal mosaic formation: a modelling study. Development 129:5399-408 [PubMed]

Einstein A (1905) Über die von der molekulartheoretischen Theorie der Warme geforderte Bewegung von in ruhenden Flussigkeiten suspendierten Teilchen Ann Phys Leipzig 17:549

Elmqvist D, Quastel DM (1965) A quantitative study of end-plate potentials in isolated human muscle. J Physiol 178:505-29 [PubMed]

Ermentrout GB (2002) Simulating, Analyzing, and Animating Dynamical System: A Guide to XPPAUT for Researchers and Students Society for Industrial and Applied Mathematics (SIAM)

Evers JF, Schmitt S, Sibila M, Duch C (2005) Progress in functional neuroanatomy: precise automatic geometric reconstruction of neuronal morphology from confocal image stacks. J Neurophysiol 93:2331-42 [PubMed]

Eyring H (1935) The activated complex in chemical reactions J Chem Physiol 3:107-115

Feldheim DA, Kim YI, Bergemann AD, Frisen J, Barbacid M, Flanagan JG (2000) Genetic analysis of ephrin-A2 and ephrin-A5 shows their requirement in multiple aspects of retinocollicular mapping. Neuron 25:563-74 [PubMed]

Feng N, Yang Y, Zheng X (2005) Spatiotemporal neuronal signaling by nitric oxide: diffusion-reaction modeling and analysis. Conf Proc IEEE Eng Med Biol Soc 6:6085-8 [PubMed]

Fenwick EM, Marty A, Neher E (1982) Sodium and calcium channels in bovine chromaffin cells. J Physiol 331:599-635 [PubMed]

Fick A (1855) Über Diffusion Ann Phys Chem 94:59-86

Firth CA, Bray D (2001) Stochastic simulation of cell signaling pathways Computational Modeling of Genetic and Biochemical Networks, Bower JM:Bolouri H, ed. pp.263

Fitzhugh R (1961) Impulses and Physiological States in Theoretical Models of Nerve Membrane. Biophys J 1:445-66 [PubMed]

Fladby T, Jansen JK (1987) Postnatal loss of synaptic terminals in the partially denervated mouse soleus muscle. Acta Physiol Scand 129:239-46 [PubMed]

Flanagan JG, Vanderhaeghen P (1998) The ephrins and Eph receptors in neural development. Annu Rev Neurosci 21:309-45 [PubMed]

Foldy 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 [Journal] [PubMed]

Foldy C, Dyhrfjeld-Johnsen J, Soltesz I (2005) Structure of cortical microcircuit theory. J Physiol 562:47-54

Forsythe ID, Tsujimoto T, Barnes-Davies M, Cuttle MF, Takahashi T (1998) Inactivation of presynaptic calcium current contributes to synaptic depression at a fast central synapse. Neuron 20:797-807 [PubMed]

Fourcaud-Trocme N, Hansel D, van Vreeswijk C, Brunel N (2003) How spike generation mechanisms determine the neuronal response to fluctuating inputs. J Neurosci 23:11628-40 [PubMed]

Fox AP, Nowycky MC, Tsien RW (1987) Kinetic and pharmacological properties distinguishing three types of calcium currents in chick sensory neurones. J Physiol 394:149-72 [PubMed]

Fraiman D, Dawson SP (2004) A model of IP3 receptor with a luminal calcium binding site: stochastic simulations and analysis. Cell Calcium 35:403-13 [PubMed]

Franks KM, Bartol TM, Sejnowski TJ (2002) A Monte Carlo model reveals independent signaling at central glutamatergic synapses. Biophys J 83:2333-48 [PubMed]

Fraser SE (1980) Differential adhesion approach to the patterning of nerve connections. Dev Biol 79:453-64

Froemke RC, Dan Y (2002) Spike-timing-dependent synaptic modification induced by natural spike trains. Nature 416:433-8 [PubMed]

Fuhrmann G, Segev I, Markram H, Tsodyks M (2002) Coding of temporal information by activity-dependent synapses. J Neurophysiol 87:140-8 [Journal] [PubMed]

FURSHPAN EJ, POTTER DD (1959) Transmission at the giant motor synapses of the crayfish. J Physiol 145:289-325 [PubMed]

Fusi S, Drew PJ, Abbott LF (2005) Cascade models of synaptically stored memories. Neuron 45:599-611 [PubMed]

Gabbiani F, Koch C (1998) Principles of spike train analysis Methods In Neuronal Modeling: From Ions To Networks, Segev I, ed. pp.313

Gabbiani F, Midtgaard J, Knopfel T (1994) Synaptic integration in a model of cerebellar granule cells. J Neurophysiol 72:999-1009 [Journal] [PubMed]

   Synaptic integration in a model of granule cells (Gabbiani et al 1994) [Model]

Galli-Resta L, Resta G, Tan SS, Reese BE (1997) Mosaics of islet-1-expressing amacrine cells assembled by short-range cellular interactions. J Neurosci 17:7831-8 [PubMed]

Gardner-Medwin AR (1976) The recall of events through the learning of associations between their parts. Proc R Soc Lond B Biol Sci 194:375-402 [PubMed]

Garofalo L, Ribeiro-da-Silva A, Cuello AC (1992) Nerve growth factor-induced synaptogenesis and hypertrophy of cortical cholinergic terminals. Proc Natl Acad Sci U S A 89:2639-43 [PubMed]

Gaze RM, Feldman JD, Cooke J, Chung SH (1979) The orientation of the visuotectal map in Xenopus: developmental aspects. J Embryol Exp Morphol 53:39-66

Gaze RM, Hope RA (1983) The visuotectal projection following translocation of grafts within an optic tectum in the goldfish. J Physiol 344:257-75 [PubMed]

Gaze RM, Keating MJ (1972) The visual system and "neuronal specificity". Nature 237:375-8 [PubMed]

Gaze RM, Keating MJ, Chung SH (1974) The evolution of the retinotectal map during development in Xenopus. Proc R Soc Lond B Biol Sci 185:301-30 [PubMed]

Gaze RM, Sharma SC (1970) Axial differences in the reinnervation of the goldfish optic tectum by regenerating optic nerve fibres. Exp Brain Res 10:171-81 [PubMed]

Geisler CD, Goldberg JM (1966) A stochastic model of the repetitive activity of neurons. Biophys J 6:53-69 [PubMed]

Gentet LJ, Stuart GJ, Clements JD (2000) Direct measurement of specific membrane capacitance in neurons. Biophys J 79:314-20 [PubMed]

Gerstner W (2000) Population dynamics of spiking neurons: fast transients, asynchronous states, and locking. Neural Comput 12:43-89 [PubMed]

Gerstner W, Kistler WM (2002) Spiking neuron models

Gierer A (1983) Model for the retino-tectal projection. Proc R Soc Lond B Biol Sci 218:77-93 [PubMed]

Gierer A, Meinhardt H (1972) A theory of biological pattern formation. Kybernetik 12:30-9 [PubMed]

Gillespie DT (1977) Exact stochastic simulation of coupled chemical reactions. Journal Of Physical Chemistry 81:2340-2361

Gillespie DT (2001) Approximate accelerated stochastic simulation of chemically reacting systems The Journal Of Chemical Physics 115:1716-1733

Gillies A, Willshaw D (2006) Membrane channel interactions underlying rat subthalamic projection neuron rhythmic and bursting activity. J Neurophysiol 95:2352-65 [Journal] [PubMed]

   Rat subthalamic projection neuron (Gillies and Willshaw 2006) [Model]

Gin E, Kirk V, Sneyd J (2006) A bifurcation analysis of calcium buffering. J Theor Biol 242:1-15 [PubMed]

Gingrich KJ, Byrne JH (1985) Simulation of synaptic depression, posttetanic potentiation, and presynaptic facilitation of synaptic potentials from sensory neurons mediating gill-withdrawal reflex in Aplysia. J Neurophysiol 53:652-69 [Journal] [PubMed]

   SN-MN neurons of Aplysia (Zhou et al. 2014) [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]

Goddard NH, Hood G (1998) Large-scale simulation using parallel genesis The Book of GENESIS, 2nd Edn, Bower JM:Beeman D, ed. pp.349

Goldbeter A, Dupont G, Berridge MJ (1990) Minimal model for signal-induced Ca2+ oscillations and for their frequency encoding through protein phosphorylation. Proc Natl Acad Sci U S A 87:1461-5 [PubMed]

Golding NL, Kath WL, Spruston N (2001) Dichotomy of action-potential backpropagation in CA1 pyramidal neuron dendrites. J Neurophysiol 86:2998-3010 [Journal] [PubMed]

   Dichotomy of action-potential backpropagation in CA1 pyramidal neuron dendrites (Golding et al 2001) [Model]

Goldman DE (1943) POTENTIAL, IMPEDANCE, AND RECTIFICATION IN MEMBRANES. J Gen Physiol 27:37-60 [PubMed]

Goldman L, Schauf CL (1972) Inactivation of the sodium current in Myxicola giant axons. Evidence for coupling to the activation process. J Gen Physiol 59:659-75 [PubMed]

Goldman MS, Golowasch J, Marder E, Abbott LF (2001) Global structure, robustness, and modulation of neuronal models. J Neurosci 21:5229-38 [Journal] [PubMed]

   Global structure, robustness, and modulation of neuronal models (Goldman et al. 2001) [Model]

Goldstein SA, Bayliss DA, Kim D, Lesage F, Plant LD, Rajan S (2005) International Union of Pharmacology. LV. Nomenclature and molecular relationships of two-P potassium channels. Pharmacol Rev 57:527-40 [PubMed]

Goodhill G, Urbach J (2003) Axon guidance and gradient detection by growth cones Modeling Neural Development, van_Ooyen A, ed. pp.95

Goodhill GJ (2007) Contributions of theoretical modeling to the understanding of neural map development. Neuron 56:301-11 [PubMed]

Gouze JL, Lasry JM, Changeux JP (1983) Selective stabilization of muscle innervation during development: a mathematical model. Biol Cybern 46:207-15 [PubMed]

Gradinaru V, Mogri M, Thompson KR, Henderson JM, Deisseroth K (2009) Optical deconstruction of parkinsonian neural circuitry. Science 324:354-9 [PubMed]

Graham B, Redman S (1994) A simulation of action potentials in synaptic boutons during presynaptic inhibition. J Neurophysiol 71:538-49 [Journal] [PubMed]

Graham B, Willshaw D (1995) Improving recall from an associative memory Biol Cybern 72:337-346

Graham B, Willshaw D (1999) Probabilistic synaptic transmission in the associative net. Neural Comput 11:117-37 [PubMed]

Graham BP, Lauchlan K, McLean DR (2006) Dynamics of outgrowth in a continuum model of neurite elongation. J Comput Neurosci 20:43-60 [Journal] [PubMed]

   Continuum model of tubulin-driven neurite elongation (Graham et al 2006) [Model]

Graham BP, van Ooyen A (2004) Transport limited effects in a model of dendritic branching. J Theor Biol 230:421-32 [PubMed]

   Compartmental models of growing neurites (Graham and van Ooyen 2004) [Model]

Graham BP, van Ooyen A (2006) Mathematical modelling and numerical simulation of the morphological development of neurons. BMC Neurosci 7 Suppl 1:S9 [PubMed]

   Continuum model of tubulin-driven neurite elongation (Graham et al 2006) [Model]
   Compartmental models of growing neurites (Graham and van Ooyen 2004) [Model]

Gutman GA, Chandy KG, Grissmer S, Lazdunski M, McKinnon D, Pardo LA, Robertson GA, Rudy B, Sa (2005) International Union of Pharmacology. LIII. Nomenclature and molecular relationships of voltage-gated potassium channels. Pharmacol Rev 57:473-508 [PubMed]

HAGIWARA S, SAITO N (1959) Voltage-current relations in nerve cell membrane of Onchidium verruculatum. J Physiol 148:161-79 [PubMed]

Hale J, Kocak H (1991) Dynamics and Bifurcations

Halliwell JV, Adams PR (1982) Voltage-clamp analysis of muscarinic excitation in hippocampal neurons. Brain Res 250:71-92 [PubMed]

Hamill OP, Marty A, Neher E, Sakmann B, Sigworth FJ (1981) Improved patch-clamp techniques for high-resolution current recording from cells and cell-free membrane patches. Pflugers Arch 391:85-100 [PubMed]

Hansel D, Mato G, Meunier C, Neltner L (1998) On numerical simulations of integrate-and-fire neural networks. Neural Comput 10:467-83 [PubMed]

Hashimoto T, Elder CM, Okun MS, Patrick SK, Vitek JL (2003) Stimulation of the subthalamic nucleus changes the firing pattern of pallidal neurons. J Neurosci 23:1916-23 [PubMed]

Hayer A, Bhalla US (2005) Molecular switches at the synapse emerge from receptor and kinase traffic. PLoS Comput Biol 1:137-54 [PubMed]

Hebb DO (1949) The Organization Of Behavior

Heinemann C, von Ruden L, Chow RH, Neher E (1993) A two-step model of secretion control in neuroendocrine cells. Pflugers Arch 424:105-12 [PubMed]

Heinemann SH, Rettig J, Graack HR, Pongs O (1996) Functional characterization of Kv channel beta-subunits from rat brain. J Physiol 493 ( Pt 3):625-33

Hely TA, Graham B, Ooyen AV (2001) A computational model of dendrite elongation and branching based on MAP2 phosphorylation. J Theor Biol 210:375-84 [PubMed]

Hentschel HG, van Ooyen A (1999) Models of axon guidance and bundling during development. Proc Biol Sci 266:2231-8 [PubMed]

Hertz J, Krogh A, Palmer RG (1991) Introduction to the Theory of Neural Computation.

Herz AV, Gollisch T, Machens CK, Jaeger D (2006) Modeling single-neuron dynamics and computations: a balance of detail and abstraction. Science 314:80-5 [PubMed]

Hill AV (1936) Excitation and accomodation in nerve Proc Roy Soc 119:305-355

Hill TL, Chen Y (1972) On the theory of ion transport across the nerve membrane. VI. Free energy and activation free energies of conformational change. Proc Natl Acad Sci U S A 69:1723-6 [PubMed]

Hille B (2001) Ionic Channels of Excitable Membranes

Hillman DE (1979) Neuronal shape parameters and substructures as a basis of neuronal form. The Neurosciences (4th Study Program), F O Schmitt and F G Worden, ed. pp.477

Hines ML, Carnevale NT (1997) The NEURON simulation environment. Neural Comput 9:1179-209 [PubMed]

Hines ML, Carnevale NT (2008) Translating network models to parallel hardware in NEURON J. Neurosci. Meth. 169:425-455 [Journal] [PubMed]

   Translating network models to parallel hardware in NEURON (Hines and Carnevale 2008) [Model]

Hines ML, Markram H, Schuermann F (2008) Fully Implicit Parallel Simulation of Single Neurons J Comp Neurosci 25:439-448 [Journal] [PubMed]

   Fully Implicit Parallel Simulation of Single Neurons (Hines et al. 2008) [Model]

Hirschberg B, Maylie J, Adelman JP, Marrion NV (1998) Gating of recombinant small-conductance Ca-activated K+ channels by calcium. J Gen Physiol 111:565-81 [PubMed]

Hodgkin AL (1948) The local electric changes associated with repetitive action in a non-medullated axon. J Physiol 107:165-81 [PubMed]

HODGKIN AL, HUXLEY AF (1952) Currents carried by sodium and potassium ions through the membrane of the giant axon of Loligo. J Physiol 116:449-72 [PubMed]

HODGKIN AL, HUXLEY AF (1952) The components of membrane conductance in the giant axon of Loligo. J Physiol 116:473-96 [PubMed]

HODGKIN AL, HUXLEY AF (1952) The dual effect of membrane potential on sodium conductance in the giant axon of Loligo. J Physiol 116:497-506 [PubMed]

Hodgkin AL, Huxley AF (1952) A quantitative description of membrane current and its application to conduction and excitation in nerve. J Physiol 117:500-44 [Journal] [PubMed]

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

HODGKIN AL, HUXLEY AF, KATZ B (1952) Measurement of current-voltage relations in the membrane of the giant axon of Loligo. J Physiol 116:424-48 [PubMed]

HODGKIN AL, KATZ B (1949) The effect of sodium ions on the electrical activity of giant axon of the squid. J Physiol 108:37-77 [PubMed]

Hoffman DA, Magee JC, Colbert CM, Johnston D (1997) K+ channel regulation of signal propagation in dendrites of hippocampal pyramidal neurons. Nature 387:869-75 [PubMed]

Hofmann F, Biel M, Kaupp UB (2005) International Union of Pharmacology. LI. Nomenclature and structure-function relationships of cyclic nucleotide-regulated channels. Pharmacol Rev 57:455-62 [PubMed]

Holmes WR, Rall W (1992) Estimating the electrotonic structure of neurons with compartmental models. J Neurophysiol 68:1438-52 [Journal] [PubMed]

Holmes WR, Rall W (1992) Electrotonic length estimates in neurons with dendritic tapering or somatic shunt. J Neurophysiol 68:1421-37 [Journal] [PubMed]

Holmes WR, Segev I, Rall W (1992) Interpretation of time constant and electrotonic length estimates in multicylinder or branched neuronal structures. J Neurophysiol 68:1401-20 [Journal] [PubMed]

Holtzman DM, Li Y, Parada LF, Kinsman S, Chen CK, Valletta JS, Zhou J, Long JB, Mobley WC (1992) p140trk mRNA marks NGF-responsive forebrain neurons: evidence that trk gene expression is induced by NGF. Neuron 9:465-78 [PubMed]

Honda H (1998) Topographic mapping in the retinotectal projection by means of complementary ligand and receptor gradients: a computer simulation study. J Theor Biol 192:235-46 [PubMed]

Honda H (2003) Competition between retinal ganglion axons for targets under the servomechanism model explains abnormal retinocollicular projection of Eph receptor-overexpressing or ephrin-lacking mice. J Neurosci 23:10368-77 [PubMed]

Hoops S, Sahle S, Gauges R, Lee C, Pahle J, Simus N, Singhal M, Xu L, Mendes P, Kummer U (2006) COPASI--a COmplex PAthway SImulator. Bioinformatics 22:3067-74 [PubMed]

Hope RA, Hammond BJ, Gaze RM (1976) The arrow model: retinotectal specificity and map formation in the goldfish visual system. Proc R Soc Lond B Biol Sci 194:447-66 [PubMed]

Hopfield JJ (1982) Neural networks and physical systems with emergent collective computational abilities. Proc Natl Acad Sci U S A 79:2554-8 [PubMed]

Hopfield JJ (1984) Neurons with graded response have collective computational properties like those of two-state neurons. Proc Natl Acad Sci U S A 81:3088-92 [PubMed]

Horsfield K, Woldenberg MJ, Bowes CL (1987) Sequential and synchronous growth models related to vertex analysis and branching ratios. Bull Math Biol 49:413-29 [PubMed]

Hospedales TM, van Rossum MC, Graham BP, Dutia MB (2008) Implications of noise and neural heterogeneity for vestibulo-ocular reflex fidelity. Neural Comput 20:756-78 [PubMed]

Hoyt RC (1968) Sodium inactivation in nerve fibers. Biophys J 8:1074-97 [PubMed]

HUBEL DH, WIESEL TN (1963) RECEPTIVE FIELDS OF CELLS IN STRIATE CORTEX OF VERY YOUNG, VISUALLY INEXPERIENCED KITTENS. J Neurophysiol 26:994-1002 [Journal] [PubMed]

Huguenard JR, McCormick DA (1992) Simulation of the currents involved in rhythmic oscillations in thalamic relay neurons. J Neurophysiol 68:1373-83 [Journal] [PubMed]

Huys QJ, Ahrens MB, Paninski L (2006) Efficient estimation of detailed single-neuron models. J Neurophysiol 96:872-90 [Journal] [PubMed]

   Efficient estimation of detailed single-neuron models (Huys et al. 2006) [Model]

Ireland W, Heidel J, Uemura E (1985) A mathematical model for the growth of dendritic trees. Neurosci Lett 54:243-9 [PubMed]

Irvine LA, Jafri MS, Winslow RL (1999) Cardiac sodium channel Markov model with temperature dependence and recovery from inactivation. Biophys J 76:1868-85 [PubMed]

Izhikevich EM (2003) Simple model of spiking neurons. IEEE Trans Neural Netw 14:1569-72 [Journal] [PubMed]

   Artificial neuron model (Izhikevich 2003, 2004, 2007) [Model]

Izhikevich EM (2004) Which model to use for cortical spiking neurons? IEEE Trans Neural Netw 15:1063-70 [Journal] [PubMed]

   Artificial neuron model (Izhikevich 2003, 2004, 2007) [Model]

Izhikevich EM, Edelman GM (2008) Large-scale model of mammalian thalamocortical systems. Proc Natl Acad Sci U S A 105:3593-8 [PubMed]

Jacobson M, Levine RL (1975) Plasticity in the adult frog brain: filling the visual scotoma after excision or translocation of parts of the optic tectum. Brain Res 88:339-45 [PubMed]

Jaeger D, Bower JM (1999) Synaptic control of spiking in cerebellar Purkinje cells: dynamic current clamp based on model conductances. J Neurosci 19:6090-101 [PubMed]

Jaffe DB, Ross WN, Lisman JE, Lasser-Ross N, Miyakawa H, Johnston D (1994) A model for dendritic Ca2+ accumulation in hippocampal pyramidal neurons based on fluorescence imaging measurements. J Neurophysiol 71:1065-77 [Journal] [PubMed]

Jahr CE, Stevens CF (1990) A quantitative description of NMDA receptor-channel kinetic behavior. J Neurosci 10:1830-7 [PubMed]

Jahr CE, Stevens CF (1990) Voltage dependence of NMDA-activated macroscopic conductances predicted by single-channel kinetics. J Neurosci 10:3178-82 [PubMed]

Jansen JK, Fladby T (1990) The perinatal reorganization of the innervation of skeletal muscle in mammals. Prog Neurobiol 34:39-90 [PubMed]

Jentsch TJ (2000) Neuronal KCNQ potassium channels: physiology and role in disease. Nat Rev Neurosci 1:21-30 [PubMed]

Jentsch TJ, Neagoe I, Scheel O (2005) CLC chloride channels and transporters. Curr Opin Neurobiol 15:319-25 [PubMed]

Jiang Y, Lee A, Chen J, Ruta V, Cadene M, Chait BT, MacKinnon R (2003) X-ray structure of a voltage-dependent K+ channel. Nature 423:33-41 [PubMed]

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]

Jolivet R, Schurmann F, Berger TK, Naud R, Gerstner W, Roth A (2008) The quantitative single-neuron modeling competition. Biol Cybern 99:417-26 [PubMed]

Katz B, Miledi R (1968) The role of calcium in neuromuscular facilitation. J Physiol 195:481-92 [PubMed]

Keizer J, Levine L (1996) Ryanodine receptor adaptation and Ca2+(-)induced Ca2+ release-dependent Ca2+ oscillations. Biophys J 71:3477-87 [PubMed]

Kepler TB, Abbott LF, Marder E (1992) Reduction of conductance-based neuron models. Biol Cybern 66:381-7 [PubMed]

Kiddie G, Mclean D, Van_Ooyen A, Graham B (2005) Biologically plausible models of neurite outgrowth Development, dynamics and pathology of neuronal networks: from molecules to functional circuits, Progress in Brain Research, van Pelt J: Kamermans M: Levelt C: van Ooyen A: Ramakers G: Roelfsema P, ed. pp.67

Kirkpatrick S, Gelatt CD, Vecchi MP (1983) Optimization by Simulated Annealing. Science 220:671-680 [PubMed]

Klee R, Ficker E, Heinemann U (1995) Comparison of voltage-dependent potassium currents in rat pyramidal neurons acutely isolated from hippocampal regions CA1 and CA3. J Neurophysiol 74:1982-95 [Journal] [PubMed]

Kliemann W (1987) A stochastic dynamical model for the characterization of the geometrical structure of dendritic processes. Bull Math Biol 49:135-52 [PubMed]

Knight BW (1972) Dynamics of encoding in a population of neurons. J Gen Physiol 59:734-66 [PubMed]

Koene RA, Tijms B, van Hees P, Postma F, de Ridder A, Ramakers GJ, van Pelt J, van Ooyen A (2009) NETMORPH: a framework for the stochastic generation of large scale neuronal networks with realistic neuron morphologies. Neuroinformatics 7:195-210 [Journal] [PubMed]

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

Kohling R (2002) Voltage-gated sodium channels in epilepsy. Epilepsia 43:1278-95 [PubMed]

Koulakov AA, Tsigankov DN (2004) A stochastic model for retinocollicular map development. BMC Neurosci 5:30-210 [PubMed]

Krottje JK, van Ooyen A (2007) A mathematical framework for modeling axon guidance. Bull Math Biol 69:3-31 [PubMed]

Kubo Y, Adelman JP, Clapham DE, Jan LY, Karschin A, Kurachi Y, Lazdunski M, Nichols CG, Seino (2005) International Union of Pharmacology. LIV. Nomenclature and molecular relationships of inwardly rectifying potassium channels. Pharmacol Rev 57:509-26 [PubMed]

Kuroda S, Schweighofer N, Kawato M (2001) Exploration of signal transduction pathways in cerebellar long-term depression by kinetic simulation. J Neurosci 21:5693-702 [PubMed]

Kusano K, Landau EM (1975) Depression and recovery of transmission at the squid giant synapse. J Physiol 245:13-22 [PubMed]

Larkman A, Mason A (1990) Correlations between morphology and electrophysiology of pyramidal neurons in slices of rat visual cortex. I. Establishment of cell classes. J Neurosci 10:1407-14 [PubMed]

Larkman A, Stratford K, Jack J (1991) Quantal analysis of excitatory synaptic action and depression in hippocampal slices. Nature 350:344-7 [PubMed]

Laurent G (1996) Dynamical representation of odors by oscillating and evolving neural assemblies. Trends Neurosci 19:489-96 [PubMed]

Le Novere N, Shimizu TS (2001) STOCHSIM: modelling of stochastic biomolecular processes. Bioinformatics 17:575-6 [PubMed]

Lebedev MA, Nicolelis MA (2006) Brain-machine interfaces: past, present and future. Trends Neurosci 29:536-46 [PubMed]

LeVay S, Wiesel TN, Hubel DH (1980) The development of ocular dominance columns in normal and visually deprived monkeys. J Comp Neurol 191:1-51 [PubMed]

Levine R, Jacobson M (1974) Deployment of optic nerve fibers is determined by positional markers in the frog's tectum. Exp Neurol 43:527-38 [PubMed]

Levy WB, Steward O (1979) Synapses as associative memory elements in the hippocampal formation. Brain Res 175:233-45 [PubMed]

Levy WB, Steward O (1983) Temporal contiguity requirements for long-term associative potentiation/depression in the hippocampus. Neuroscience 8:791-7 [PubMed]

Li GH, Qin CD, Li MH (1994) On the mechanisms of growth cone locomotion: modeling and computer simulation. J Theor Biol 169:355-62 [PubMed]

Li GH, Qin CD, Wang ZS (1992) Neurite branching pattern formation: modeling and computer simulation. J Theor Biol 157:463-86 [PubMed]

Li WC, Soffe SR, Roberts A (2004) A direct comparison of whole cell patch and sharp electrodes by simultaneous recording from single spinal neurons in frog tadpoles. J Neurophysiol 92:380-6 [PubMed]

Li YX, Rinzel J (1994) Equations for InsP3 receptor-mediated [Ca2+]i oscillations derived from a detailed kinetic model: a Hodgkin-Huxley like formalism. J Theor Biol 166:461-73 [PubMed]

Liley AW, North KAK (1952) An electrical investigation of effects of repetitive stimulation on mammalian neuromuscular junction J Neurophysiol 16:509-527 [Journal]

Lima PA, Marrion NV (2007) Mechanisms underlying activation of the slow AHP in rat hippocampal neurons. Brain Res 1150:74-82 [PubMed]

Lindsay KA, Maxwell DJ, Rosenberg JR, Tucker G (2007) A new approach to reconstruction models of dendritic branching patterns. Math Biosci 205:271-96 [PubMed]

Lisman JE, Idiart MA (1995) Storage of 7 +/- 2 short-term memories in oscillatory subcycles. Science 267:1512-5 [PubMed]

Liu Z, Golowasch J, Marder E, Abbott LF (1998) A model neuron with activity-dependent conductances regulated by multiple calcium sensors. J Neurosci 18:2309-20 [PubMed]

   Activity dependent conductances in a neuron model (Liu et al. 1998) [Model]

Long SB, Campbell EB, Mackinnon R (2005) Crystal structure of a mammalian voltage-dependent Shaker family K+ channel. Science 309:897-903 [PubMed]

Vilela Filho O, Silva DJ, Souza HA, Cavalcante JE, Sousa JT, Ferraz FP, Silva LG, Santos LF (2001) Stereotactic subthalamic nucleus lesioning for the treatment of Parkinson's disease. Stereotact Funct Neurosurg 77:79-86 [PubMed]

Dragly SA, Hobbi Mobarhan M, Våvang Solbrå A, Tennøe S, Hafreager A, Malthe-Sørenssen A, Fyhn M, Hafting T, Einevoll GT (2017) Neuronify: An Educational Simulator for Neural Circuits. eNeuro [Journal] [PubMed]

   Neuronify: An Educational Simulator for Neural Circuits (Dragly et al 2017) [Model]

Martinez-Canada P, Morillas C, Pino B, Ros E, Pelayo F (2016) A Computational Framework for Realistic Retina Modeling. Int J Neural Syst 26:1650030 [Journal] [PubMed]

   COREM: configurable retina simulator (Martínez-Cañada et al., 2016) [Model]

(317 refs)