Reading Lists

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The main target region in the brain we focus on is the hippocampal formation and the para-hippocampal regions (such as the entorhinal cortex). Our main approach is electrophysiology, as well as computational modeling and simulations of neuronal network.

These papers are categorized here to facilitate reading but the contents in them may not be limited to the category name.

Potential Lab meeting papers

Many books are available through the University in electronic format via SciWeb website. All books by Springer and CRC are available.


Basic Anatomy of Hippocampus


  • [, Axon Guide]
  • An EEG primer


Computational Models of Epilepsy

  • Traub: On the structure of ictal events in vitro.Epilepsia. 1996 Sep;37(9):879-91
  • PA Robinson: Steady states and global dynamics of electrical activity in the cerebral cortex. Physical Review E, Vol.58, No.3, 1998
  • Farley BG, A neuronal network model and the "slow potentials" of electro-physiolgy," Comp. in Biomed Res. 2, 265-294

Oscillatory neuronal activity

Normal Physiology

Information processing in hippocampus

  • Harris KD, Henze DA, Hirase H, Leinekugel X, Dragoi G, Czurko A, et al. Spike train dynamics predicts theta-related phase precession in hippocampal pyramidal

cells. Nature. 2002;417:738{741. 444

  • Hirase H, Czurko A, Csicsvari J, Buzsaki G. Firing rate and theta-phase coding by hippocampal pyramidal neurons during 'space clamping'. Eur J Neurosci.


  • Kamondi A, Acsady L, J WX, Buzsaki G. Theta oscillations in somata and dendrites of hippocampal pyramidal cells in vivo: activity-dependent phase-precession of action potentials. Hippocampus. 1998;8:244{261.
  • Colgin LL, Denninger T, Fyhn M, Hafting T, Bonnevie T, Jensen O, et al. Frequency of gamma oscillations routes flow of information in the hippocampus. Nature. 2009;462:353{357.
  • Colgin LL. Theta-gamma coupling in the entorhinal-hippocampal system. Current opinion in neurobiology. 2015;31:45{50. doi:doi:10.1016/j.conb.2014.08.001.
  • Oscillatory dynamics in the hippocampus support dentate gyrus–CA3 coupling

Visual Binding

  • Busch NA, Herrmann CS, Muller MM, Lenz D, Gruber T. A cross-laboratory study of event-related gamma activity in a standard object recognition paradigm. Neuroimage. 2006;33:1169{1177.

Learning and memory

  • Kendrick KM, Zhan Y, Fischer H, Nicol AU, Zhang X, J F. Learning alters theta amplitude, theta-gamma coupling and neuronal synchronization in inferotemporal cortex. BMC Neuroscience. 2011;12:471{2202.
  • Tort ABL, Komorowski R, Eichenbaum H, Kopell N. Measuring Phase-Amplitude Coupling Between Neuronal Oscillations of Different Frequencies. J Neurophysiol. 2010;104:1195{1210.
  • Stujenske JM, Likhtik E, Topiwala MA, Gordon JA. Fear and safety engage competing patterns of theta-gamma coupling in the basolateral amygdala. Neuron. 2014;83:919{933.


  • Karalis N, Dejean C, Chaudun F, Khoder S, Rozeske RR, Wurtz H, et al. 4-Hz oscillations synchronize prefrontal{amygdala circuits during fear behavior. Nature Neuroscience. 2016;19:605{612.
  • Stujenske JM, Likhtik E, Topiwala MA, Gordon JA. Fear and safety engage competing patterns of theta-gamma coupling in the basolateral amygdala. Neuron. 2014;83:919{933.
  • Giraud AL, Poeppel D. Cortical oscillations and speech processing: emerging computational principles and operations. Nat Neurosci. 2012;15:511{514.
  • Herrmann CS, Knight RT. Mechanisms of human attention: event-related potentials and oscillations. Neuroscience and Biobehavioral Reviews. 2001;25(6):465 { 476. doi:
  • Lakatos P, Karmos G, Mehta AD, Ulbert I, Schroeder CE. Entrainment of Neuronal Oscillations as a Mechanism of Attentional Selection. Science. 2008;320(5872):110{113. doi:10.1126/science.1154735.

Task dependent oscillation example:

  • Lee et al., 2005,
  • Liebe etal, 2012,
  • Thut et al. 2012,
  • Polania et al., 2012

Pathological Physiological activity

Ih Channels

Phase Locking

  • Matias FS, Carelli PV, R MC, M C. Self-Organized Near-Zero-Lag Synchronization Induced by Spike-Timing Dependent Plasticity in Cortical Populations. PLoS ONE. 2015;10:e0140504. doi:10.1371/journal.pone.0140504.
  • Oprisan SA. Stability of Synchronous Oscillations in a Periodic Network. International Journal of Neuroscience. 2009;(4):482{491. doi:10.1080/00207450802336766.
  • Oprisan SA. Existence and Stability Criteria for Phase-Locked Modes in Ring Networks Using Phase-Resetting Curves and Spike Time Resetting Curves. In: Schultheiss NW, Prinz AA, Butera RJ, editors. Phase Response Curves in Neuroscience. vol. 6. New York: Springer; 2012. p. 131{162.

Phase Locking and synaptic plasticity

  • Matias FS, Carelli PV, Mirasso CR, Copelli M. Anticipated synchronization in a biologically plausible model of neuronal motifs. Phys Rev E. 2011;84:021922. doi:10.1103/PhysRevE.84.021922.
  • Matias FS, Gollo LL, Carelli PV, Bressler SL, Copelli M, Mirasso CR. Modeling positive Granger causality and negative phase lag between cortical areas. NeuroImage. 2014;99:411 { 418. doi:10.1016/j.neuroimage.2014.05.063.

Phase Resetting

  • Rizzuto DS, Madsen JR, Bromfield EB, Schulze-Bonhage A, Seelig D, Aschenbrenner-Scheibe R, et al. Reset of human neocortical oscillations during a working memory task. Proc Natl Acad Sci USA. 2003;100:7931{7936
  • Malerba P, Kopell N. Phase resetting reduces theta-gamma rhythmic interaction to a one-dimensional map. J Math Biol. 2013;66:1361{1386.
  • Sauseng P, Klimesch W, Gruber WR, Hanslmayr S, Freunberger R, Doppelmayr M. Are event-related potential components generated by phase resetting of brain oscillations? A critical discussion. Neuroscience. 2007;146(4):1435{1444.
  • V BC, Oprisan SA. Time-scale invariance as an emergent property in a perceptron with realistic, noisy neurons. Behavioral Processes. 2013;95(5):60{70. doi:10.1016/j.beproc.2013.02.015.
  • Oprisan SA, Canavier CC. Stability Analysis of Rings of Pulse-Coupled Oscillators: The Effect of Phase Resetting in the Second Cycle After the Pulse Is Important at Synchrony and For Long Pulses. Journal of Differential Equations and Dynamical Systems. 2002;(3{4):243{258.
  • Oprisan SA, Thirumalai V, Canavier CC. Dynamics from a time series: Can we extract the phase resetting curve from a time series? Biophysical Journal. 2003; p. 2919{2928. doi:10.1016/S0006-3495(03)70019-8.
  • Oprisan SA, Prinz AA, Canavier CC. Phase resetting and phase locking in hybrid circuits of one model and one biological neuron. Biophysical Journal. 2004; p. 2283{2298. doi:10.1529/biophysj.104.046193.

Phase Response Curves

Neuromodulation with ultrasound

Computational Neuroscience

Modeling Neurons

Simple model of spiking neurons, Izhikevich 2003

Modeling Seizures

On the nature of seizure dynamics Unification of Neuronal Spikes, Seizures, and Spreading Depression, Journal of Neuroscience

Network Theory

  • D.J. Watts and S.H. Strogatz, Collective dynamics of 'small-world' networks, Nature 393, 440-442, 1998. Author's PDF, Publisher's web site
  • S. Boccaletti, V. Latora, Y. Moreno, M. Chavez and D.-U. Hwang, Complex networks: Structure and dynamics, Physics Reports 424, 175-308, 2006. Publisher's web site
  • M. E. J. Newman, The structure and function of complex networks, SIAM Rev. 45, 167-256, 2003. Publisher's web site

R. Albert and A.-L. Barabási, Statistical mechanics of complex networks, Reviews of Modern Physics 74, 47-97, 2002. Author's PDF, Publisher's web site

  • A.-L. Barabási and R. Albert, Emergence of scaling in random networks, Science 286, 509–512, 1999. Author's PDF, Publisher's web site
  • P. Erdős and A. Rényi, On Random Graphs. I., Publicationes Mathematicae 6: 290–297. 1959.

T. Nishikawa and A.E. Motter, Maximum performance at minimum cost in network synchronization, Physica D 224, 77-89, 2006. Publisher's web site

Kuramoto papers

  • H. Sompolinsky and A. Crisanti, Chaos in Random Neural Networks, Phys. Rev. Lett. 61, 259-262, 1988. Publisher's web site
  • O. Sporns and R. Kötter, Motifs in Brain Networks, PLoS Biol 2, e369, 2004. Publisher's web site
  • S. Song, P.J. Sjöström, M. Reigl, S. Nelson, and D.B. Chklovskii, Highly nonrandom features of synaptic connectivity in local cortical circuits, PLoS Biol 3, e68, 2005. Publisher's web site
  • T.I. Netoff, R. Clewley, S. Arno, T. Keck, and J.A. White, Epilepsy in small-world networks, J Neurosci. 24,8075-83, 2004. Publisher's web site
  • L.M. Pecora and T.L. Carroll and G.A. Johnson and D.J. Mar J.F. Heagy. Fundamentals of synchronization in chaotic systems, concepts, and applications, Chaos 7, 520-543 ,1997. Publisher's web site
  • J.G. Restrepo, E. Ott, and B.R. Hunt. Emergence of coherence in complex networks of heterogeneous dynamical systems, Phys Rev Lett. 96, 254103, 2006. Publisher's web site

Using CUDA to model networks

Installing CUDA GPU-SNN CUDA tutorial


Control Theory


Neurosurgery talks

Math introductions

SVD decomposition

Matlab Introductions

Neuron Introductions

Personal tools