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Biophys J. Nov 1996; 71(5): 2404–2412.
PMCID: PMC1233730

A hidden Markov model approach to neuron firing patterns.


Analysis and characterization of neuronal discharge patterns are of interest to neurophysiologists and neuropharmacologists. In this paper we present a hidden Markov model approach to modeling single neuron electrical activity. Basically the model assumes that each interspike interval corresponds to one of several possible states of the neuron. Fitting the model to experimental series of interspike intervals by maximum likelihood allows estimation of the number of possible underlying neuron states, the probability density functions of interspike intervals corresponding to each state, and the transition probabilities between states. We present an application to the analysis of recordings of a locus coeruleus neuron under three pharmacological conditions. The model distinguishes two states during halothane anesthesia and during recovery from halothane anesthesia, and four states after administration of clonidine. The transition probabilities yield additional insights into the mechanisms of neuron firing.

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Selected References

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  • Aghajanian GK, Cedarbaum JM, Wang RY. Evidence for norepinephrine-mediated collateral inhibition of locus coeruleus neurons. Brain Res. 1977 Nov 18;136(3):570–577. [PubMed]
  • Albert PS. A two-state Markov mixture model for a time series of epileptic seizure counts. Biometrics. 1991 Dec;47(4):1371–1381. [PubMed]
  • Aston-Jones G, Shipley MT, Chouvet G, Ennis M, van Bockstaele E, Pieribone V, Shiekhattar R, Akaoka H, Drolet G, Astier B, et al. Afferent regulation of locus coeruleus neurons: anatomy, physiology and pharmacology. Prog Brain Res. 1991;88:47–75. [PubMed]
  • Carlson JH, Foote SL. Oscillation of interspike interval length in substantia nigra dopamine neurons: effects of nicotine and the dopaminergic D2 agonist LY 163502 on electrophysiological activity. Synapse. 1992 Jul;11(3):229–248. [PubMed]
  • Charlety PJ, Grenhoff J, Chergui K, De la Chapelle B, Buda M, Svensson TH, Chouvet G. Burst firing of mesencephalic dopamine neurons is inhibited by somatodendritic application of kynurenate. Acta Physiol Scand. 1991 May;142(1):105–112. [PubMed]
  • Chergui K, Akaoka H, Charléty PJ, Saunier CF, Buda M, Chouvet G. Subthalamic nucleus modulates burst firing of nigral dopamine neurones via NMDA receptors. Neuroreport. 1994 Jun 2;5(10):1185–1188. [PubMed]
  • Chergui K, Charléty PJ, Akaoka H, Saunier CF, Brunet JL, Buda M, Svensson TH, Chouvet G. Tonic activation of NMDA receptors causes spontaneous burst discharge of rat midbrain dopamine neurons in vivo. Eur J Neurosci. 1993 Feb 1;5(2):137–144. [PubMed]
  • Coast DA, Cano GG, Briller SA. Use of hidden Markov models for electrocardiographic signal analysis. J Electrocardiol. 1990;23 (Suppl):184–191. [PubMed]
  • Ennis M, Aston-Jones G. Evidence for self- and neighbor-mediated postactivation inhibition of locus coeruleus neurons. Brain Res. 1986 May 28;374(2):299–305. [PubMed]
  • Gonon FG. Nonlinear relationship between impulse flow and dopamine released by rat midbrain dopaminergic neurons as studied by in vivo electrochemistry. Neuroscience. 1988 Jan;24(1):19–28. [PubMed]
  • Grace AA, Bunney BS. The control of firing pattern in nigral dopamine neurons: burst firing. J Neurosci. 1984 Nov;4(11):2877–2890. [PubMed]
  • Hoffman RE, Shi WX, Bunney BS. Nonlinear sequence-dependent structure of nigral dopamine neuron interspike interval firing patterns. Biophys J. 1995 Jul;69(1):128–137. [PMC free article] [PubMed]
  • Johnson SW, Seutin V, North RA. Burst firing in dopamine neurons induced by N-methyl-D-aspartate: role of electrogenic sodium pump. Science. 1992 Oct 23;258(5082):665–667. [PubMed]
  • Krogh A, Brown M, Mian IS, Sjölander K, Haussler D. Hidden Markov models in computational biology. Applications to protein modeling. J Mol Biol. 1994 Feb 4;235(5):1501–1531. [PubMed]
  • Morier N, Sauvé R. Analysis of a novel double-barreled anion channel from rat liver rough endoplasmic reticulum. Biophys J. 1994 Aug;67(2):590–602. [PMC free article] [PubMed]
  • Saunier CF, Akaoka H, de La Chapelle B, Charléty PJ, Chergui K, Chouvet G, Buda M, Quintin L. Activation of brain noradrenergic neurons during recovery from halothane anesthesia. Persistence of phasic activation after clonidine. Anesthesiology. 1993 Nov;79(5):1072–1082. [PubMed]
  • Segundo JP, Perkel DH, Moore GP. Spike probability in neurones: influence of temporal structure in the train of synaptic events. Kybernetik. 1966 May;3(2):67–82. [PubMed]
  • Segundo JP, Vibert JF, Stiber M, Hanneton S. Periodically modulated inhibition and its postsynaptic consequences--I. General features. Influence of modulation frequency. Neuroscience. 1995 Oct;68(3):657–692. [PubMed]
  • Seidemann E, Meilijson I, Abeles M, Bergman H, Vaadia E. Simultaneously recorded single units in the frontal cortex go through sequences of discrete and stable states in monkeys performing a delayed localization task. J Neurosci. 1996 Jan 15;16(2):752–768. [PubMed]
  • Shepard PD, German DC. Electrophysiological and pharmacological evidence for the existence of distinct subpopulations of nigrostriatal dopaminergic neuron in the rat. Neuroscience. 1988 Nov;27(2):537–546. [PubMed]
  • Svensson TH, Bunney BS, Aghajanian GK. Inhibition of both noradrenergic and serotonergic neurons in brain by the alpha-adrenergic agonist clonidine. Brain Res. 1975 Jul 11;92(2):291–306. [PubMed]

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