Pablo Varona's research

Pablo Varona

Institute for Nonlinear Science.
University of California, San Diego
9500 Gilman Dr. CMRR Building
La Jolla, CA 92093-0402
email: pvarona(at)ucsd.edu
Tel: (858) 5346753
Fax: (858) 5347664

Mirror site at the
Departamento de Ingeniería Informática
Universidad Autónoma de Madrid

INDEX:

Research interests
Publications

Papers in publications included in the ISI Journal Citation Reports
Book chapters
Papers in Spanish journals
Technical reports
Other publications (conference papers, proceedings, abstracts, etc.)

Electronic suplementary material
XSim
Related links

Research interests:

Computational Neuroscience, Artificial Neural Networks, Spatio-temporal Pattern Analysis, Nonlinear Systems, Biocomputing, and anything related to computation-physics-biology.

Publications: (if your institution has no electronic subscription to the links below, please contact me for reprints)

Papers in publications included in the ISI Journal Citation Reports: (indexed in Current Contents, Pubmed and/or INSPEC)

C. Muñiz, R. Levi, M. Benkrid, F.B. Rodríguez, P. Varona. 2008. Real-time control of stepper motors for mechanosensory stimulation. Journal of Neuroscience Methods 172 (1): 105-111.
M.I. Rabinovich, R. Huerta, P. Varona, V.S. Afraimovich. 2008. Transient Cognitive Dynamics, Metastability and Decision Making. PLoS Computational Biology 4(5): e1000072.
F. Baroni, P. Varona. 2007. Subthreshold oscillations and neuronal input–output relationships. Neurocomputing 70(10-12): 1611-1614.
D. Campos, C. Aguirre, E. Serrano, F.B. Rodriguez, G.G. de Polavieja, P. Varona. 2007. Temporal structure in the bursting activity of the leech heartbeat CPG neurons. Neurocomputing 70(10-12): 1792-1796.
G.R. Stiesberg, M.B. Reyes, P. Varona, R.D. Pinto, R. Huerta. 2007. Connection Topology Selection in Central Pattern Generators by Maximizing the Gain of Information. Neural Computation 19(4): 974-993.
R. Latorre, F.B. Rodriguez, P. Varona. 2007. Reaction to neural signatures through excitatory synapses in central pattern generator models. Neurocomputing 70(10-12): 1797-1801.
S. Ramaswamy, F. Baroni, P. Varona, G.G. de Polavieja. 2007. Time-scales in the interplay between calcium and voltage dynamics. Neurocomputing 70(10-12): 1949-1953.
R. Latorre, F.B. Rodriguez, P. Varona. 2006. Neural Signatures: Multiple Coding in Spiking Bursting Cells. Biological Cybernetics 95(2): 169-183.
M.I. Rabinovich, P. Varona, A.I. Selverston, H.D.I. Abarbanel. 2006. Dynamical Principles in Neuroscience. Reviews of Modern Physics 78(4): 1213-1265.
M.I. Rabinovich, R. Huerta, P. Varona. 2006. Heteroclinic synchronization: Ultra-subharmonic locking. Physical Review Letters 96: 0141001.
M.I. Rabinovich, R. Huerta, P. Varona, V.S. Afraimovich. 2006. Generation and reshaping of sequences in neural systems. Biological Cybernetics 95(6): 519-536.
R. Levi, P. Varona, Y.I. Arshavsky, M.I. Rabinovich, A.I. Selverston. 2005. The role of sensory network dynamics in generating a motor program. Journal of Neuroscience 25 (42): 9807-9815.
A. Venaille, P. Varona, M.I. Rabinovich. 2005. Synchronization and coordination of sequences in two neural ensembles. Physical Review E 71, 061909.
F. Baroni, J.J. Torres, P. Varona. 2005. Interacting Slow and Fast Dynamics in Precise Spiking-Bursting Neurons. Lect. Notes Comput Sc. 3561: 106-115.
C. Muñiz, S. Arganda, F.B. Rodríguez, G.G. de Polavieja, P. Varona. 2005. Realistic Stimulation Through Advanced Dynamic Clamp Protocols. Lect. Notes Comput Sc. 3561: 95-105.
V. Afraimovich, M.I. Rabinovich, P. Varona. 2004. Heteroclinic Contours in Neural Ensembles and the Winnerless Competition Principle. International Journal of Bifurcation and Chaos 14(4): 1195-1208.
R. Latorre, F.B.Rodríguez, P. Varona. 2004. Effect of individual spiking activity on rhythm generation of Central Pattern Generators. Neurocomputing 58-60: 535-540.
A. Tristán, F. de Borja Rodríguez, E. Serrano, P. Varona. 2004. Networks of Neurons that Emit and Recognize Signatures. Neurocomputing 58-60: 41-46.
P. Varona, R. Levi, Y.I. Arshavsky, M.I. Rabinovich, A.I. Selverston. 2004. Competing sensory neurons and motor rhythm coordination. Neurocomputing 58-60: 549-554.
R. Levi, P. Varona, Y.I. Arshavsky, M.I. Rabinovich, A.I. Selverston. 2004. Dual sensory-motor function for a molluskan statocyst network. Journal of Neurophysiology 91: 336-345.
Nazareth P. Castellanos, Francisco B. Rodríguez, P. Varona. 2003. Stochastic Networks with Subthreshold Oscillations and Spiking Activity. Lect. Notes Comput. Sc. 2686: 32-39.
L. López-Aguado L., J.M. Ibarz, P. Varona and O. Herreras. 2002. Structural inhomogeneities differentially modulate action currents and population spikes initiated in the axon or dendrites. Journal of Neurophysiology 88(5): 2809-2820 (for additional model details click here).
P. Varona, M.I. Rabinovich, A.I. Selverston, Y.I. Arshavsky. 2002. Winnerless competition between sensory neurons generates chaos: a possible mechanism for molluscan huting behavior. Chaos 12(3):672-677.
P. Varona, C. Aguirre, J.J. Torres, M.I. Rabinovich, H.D.I. Abarbanel. 2002. Spatio-temporal patterns of network activity in the inferior olive. Neurocomputing 44-46: 685-690.
R. Latorre, F.B. Rodríguez, P. Varona. 2002. Characterization of Triphasic Rhythms in Central Pattern Generators (I): Interspike Interval Analysis. Lect. Notes Comput. Sc. 2415: 160-166.
F.B. Rodríguez, R. Latorre, P. Varona. 2002. Characterization of Triphasic Rhythms in Central Pattern Generators (II): Burst Information Analysis. Lect. Notes Comput. Sc. 2415: 167-173.
P. Varona, J.J. Torres, R. Huerta, H.D.I. Abarbanel, M.I. Rabinovich. 2001. Regularization mechanisms of spiking-bursting neurons. Neural Networks, 14: 865-875.
F.B. Rodríguez, P. Varona, R. Huerta, M.I. Rabinovich, H.D.I. Abarbanel. 2001. Richer network dynamics of intrinsically non-regular neurons measured through mutual information. Lect. Notes Comput. Sc., 2084: 490-497.
O. Herreras, J.M. Ibarz, L. López-Aguado, P. Varona. 2001. Dendrites: the last-generation computers. Lect. Notes Comput. Sc., 2084: 1-13.
P. Varona, J.J. Torres, H.D.I. Abarbanel, M.I. Rabinovich, R. C. Elson. 2001. Dynamics of two electrically coupled chaotic neurons: Experimental observations and model analysis. Biological Cybernetics. 84 (2): 91-101.
R. Huerta, P. Varona, M.I. Rabinovich, H.D.I. Abarbanel. 2001. Topology selection by chaotic neurons of a pyloric central pattern generator. Biological Cybernetics 84 (1): L1-L8.
R.D. Pinto, P. Varona, A.R. Volkovskii, A. Szücs, H.D.I. Abarbanel and M.I. Rabinovich. 2000. Synchronous behavior of two coupled electronic neurons. Physical Review E, 62(2): 2644-56.
A.I. Selverston, M.I. Rabinovich, H.D.I. Abarbanel, R. Elson, A. Szücs, R.D. Pinto, R. Huerta and P. Varona. 2000. Reliable circuits from irregular neurons: a dynamical approach to unterstanding central pattern generators. J. Physiol. (Paris), 94: 357-374.
P. Varona, J. M. Ibarz, L. López, O. Herreras. 2000. Macroscopic and Subcellular Factors Shaping Population Spikes. Journal of Neurophysiology, 83 (4): 2192-2208 (for additional model details click here).
A. Szücs, P. Varona, A.R. Volkovskii, H. D. I. Abarbanel, M.I. Rabinovich, A.I. Selverston. 2000. Interacting Biological and Electronic Neurons Generate Realistic Oscillatory Rhythms. NeuroReport, 11 (3): 563-569.
M.I. Rabinovich, P. Varona, H.D.I. Abarbanel. Nonlinear Cooperative Dynamics of Living Neurons. 2000. International Journal of Bifurcation and Chaos, 10 (5): 913-933.
M.I. Rabinovich, P. Varona, J.J. Torres, R. Huerta, H.D.I. Abarbanel. 1999. Slow dynamics and regularization phenomena in ensembles of chaotic neurons. Physica A, 263: 405-414.
M.I. Rabinovich, J.J. Torres, P. Varona, R. Huerta, P. Weidman. 1999. Origin of Coherent Structures in a Discrete Chaotic Medium. Physical Review E, 60 (2): R1130-R1133.
P. Varona, J.M. Ibarz, J. A. Sigüenza, O. Herreras. 1997. Current Source Density Analysis as a Tool to Constrain the Parameter Space in Hippocampal CA1 Neuron Models. Lect. Notes Comput. Sc., 1240: 82-90.
B. Kappen, P. Varona. 1996. Dynamic Feature Linking in Stochastic Networks with Short Range Interactions. Lect. Notes Comput. Sc., 1112: 101-106.
P. Varona, J.A. Sigüenza. 1995. Introducing XSim: A Neural Network Simulator That Incorporates Biological Parameters. Lect. Notes Comput. Sc., 930: 650-657.

Book chapters:

M.I. Rabinovich, J.J. Torres, P. Varona. 1999. Pattern Formation in Networks of Chaotic Spiking-Bursting Neurons. In Dynamical Systems: from Cristal to Chaos. World Scientific Books, 2000. ISBN 981-02-4217-4.

Papers in spanish journals:

P. Varona. J.A. Sigüenza. 1996. Niveles de Modelado Neuronal en el Simulador de Neurocomputación XSim. Boletín de la AEPIA, 5: 22-29.

Technical reports:

P. Varona, J.A. Sigüenza. 1997. Model Templates for XSim Neural Network Simulator. IIC Technical Report B01/97.
P. Varona, A. Cobas, J.A. Sigüenza. 1994. XSim Neural Network Simulator. 1994. Version 2.0 (Book). IIC Technical Report B03/94.

Other publications (conference papers, proceedings, abstracts, etc.): (some of them indexed in INSPEC and BIOSIS)

C. Muñiz, R. Levi, F.B. Rodriguez, P. Varona. 2007. Pushing the envelope of real-time technology in neuroscience. XII Congreso de la Sociedad Española de Neurociencia, pp 46.
R. Latorre, F.B. Rodriguez, P. Varona. 2007. Origin and role of neural signatures in bursting neurons. In Cooperative Behavior in Neural Systems. AIP Conference Proceedings, vol. 887: 51-60.
P. Varona. 2006. Neural Bursting Codes. Proceedings of Modeling the Brain's Labyrinth, Crete Anniversary Meeting of the EU Course in Computational Neuroscience. T-08: 25-26.
C. Muniz, S. Arganda, F.B. Rodriguez, G.G. de Polavieja, P. Varona. 2005. Advanced Dynamic-Clamp Software for the Stimulation of Excitable Cells. Society for Neuroscience Abs. 2005, 569.21.
R. Levi, P. Varona, Y.I. Arshavsky, M.I. Rabinovich, A.I. Selverston. 2004. Wing and tail motor coordination in the search behavior of Clione limacina and its relation to the statocyst activity. Society for Neuroscience Abs. 2004, 601.4.
R. Levi, P. Varona, Y.I. Arshavsky, M.I. Rabinovich, A.I. Selverston. 2004. Interaction of sensory and motor systems during searching motor program in the marine mollusk Clione limacina. 7th International Congress of Neuroethology. Nuyborg, Denmark. P0221.
M.I. Rabinovich, P. Varona, V.I. Afraimovich. 2003. Neurocomputation with separatrices. AIP Conference Proceedings, 7th Experimental Chaos Conference, San Diego (USA), Vol 676, issue 1: 239-250.
P. Varona, R. Levi, Y.I. Arshavsky, M.I. Rabinovich, A.I. Selverston. 2003. Dual role for a statocyst: as a sensory organ and as a part of the motor pattern generator. Society for Neuroscience Abs., Vol 29, 403.16 New Orleans (USA).
A. I. Selverston, M. Rabinovich, H. Abarbanel, A. Szucs, R. Huerta, P. Varona, R. Elson, R. Pinto, A. Volkovskii. Synchronization of CPG neurons studied with hybrid circuits. 10th Symposium on Invertebrate Neurobiology, Tihany (Hungary), 5 - 9 July, 2003.
M.I. Rabinovich, R. Levi, P. Varona, Y.I. Arshavsky, A.I. Selverston. 2003. Animal behaviour controlled through the dynamics of a sensory network. Sixth IBRO World Congress of Neuroscience, July 10-15, 2003 Prague, Czech Republic.
R. Levi, P. Varona, Y.I. Arshavsky, A.I. Selverston, M.I. Rabinovich. 2003. Generation of an irregular motor program by a sensory organ. Topical Problems of Nonlinear Wave Physics (NWP-2003), Nizhny Novgorod, Russia, 6-12 September 2003.
M.I. Rabinovich, P. Varona, VS. Afraimovich. Information dynamics in neural systems: computing with separatrices. Prikladnaya Nelineinaya Dinamika, vol.11, no.1, 2003, pp.86-97. Publisher: Izdatelstvo GozYNTS `Kolledzh', Russia.
R. Levi, P. Varona, M.I. Rabinovich, A.I. Selverston, Y.I. Arshavsky. 2002. Control of hunting behavior in the mollusk clione: winnerless competition between the statocyst receptor neurons. Society for Neuroscience Abs., Vol 28, Part 1, 60.1. Orlando (USA).
P. Varona, C. Aguirre, M.I. Rabinovich, H.D.I.Abarbanel. 2001. Coexistence of rhythms in inferior olive networks under the action of stimuli. Society for Neuroscience Abs., Vol. 27, Part 1, 70.2. San Diego (USA).
M.I. Rabinovich, P. Varona, Y.I. Arshavsky, A.I. Selverston. 2001. Dynamical origin of the random-like hunting behavior of the marine mollusk Clione. Society for Neuroscience Abs., Vol. 27, Part 2, 943.13. San Diego (USA).
P. Varona, M.I. Rabinovich. Spatio-temporal patterns in inferior olive networks. 2001. Fifth SIAM Conference on Control and its applications. San Diego, USA. MS 31. Page 244.
P. Varona, H.D.I. Abarbanel. Electronic and Biological Neurons. Proceedings of the 19th Symposium for Energy Engineering Sciences, Argonne (Chicago) 2001.
M.I. Rabinovich, P. Varona, A. Volkovskii. Information dynamics: winner-less competition principle. Proceedings of the 19th Symposium for Energy Engineering Sciences, Argonne (Chicago) 2001.
Selverston, Allen I., Mikhail I. Rabinovich, Atilla Szucs, Pablo Varona, Alexander Volkovskii, Robert Elson, H.D.I. Abarbanel. 2000. Artificial electronic neurons as probes for understanding small neural circuits in crustacea. Proceedeings of the Crustacean Society 2000 Summer-Meeting. In Modern Approaches to the Study of Crustacea. Eds. Escobar-Briones and Alvarez. Kluwer Academic/Plenum Publishers.
O. Herreras, P. Varona, L. López-Aguado, J.M. Ibarz. 2000. Computer reproduction of in vivo CA1 population spikes along the somatodendritic axis: dendritic initiation versus backpropagation. Workshop on Dendrites. Columbia University, New York. Proceedings del Centro de Reuniones Internacionales sobre Biologia del Instituto Juan March. Vol. 111, pág. 66.
A. Szücs, R. D. Pinto, A.I. Selverston, P. Varona, M.I. Rabinovich, H. D .I. Abarbanel. 2000. Generation of oscillatory activity in small networks of interacting electronic and biological neurons. Society for Neuroscience Abs., Vol 26, Part 2, 748.6. New Orleans (USA).
J.M. Ibarz, P. Varona, L. López, O. Herreras. 2000. Un Modelo Multineuronal de la Región CA1 Como Banco de Pruebas de Modelos Unitarios y de Medidas Experimentales. VIII Congreso de la Sociedad Española de Neurociencia. Murcia. Rev. Neurol. 2000, 30 (3):262.
M.I. Rabinovich, P. Varona, H.D.I. Abarbanel. Nonlinear Dynamics of Living Neurons. Proceedings of ``Global Dynamics, Complexity and Catastrophes''. In Science for survival and sustainable development. Pontifical Academy of Science, Vatican, 2000: 185-215. ISBN 88-7761-071-9
P. Varona, J.J. Torres, H.D.I. Abarbanel, V.I. Makarenko, R. Llinas, M.I. Rabinovich. 1999. Modeling Collective Oscillations in the Inferior Olive. Society for Neuroscience Abs., Vol. 25, Part 1, 668.8. Miami (USA).
P. Varona, J.J. Torres, R. Huerta, H.D.I. Abarbanel, M.I. Rabinovich. 1999. Subcellular Mechanisms for the Regularization of Neural Bursting Activity. Proceedings 5th SIAM Conference on Applications of Dynamical Systems. Snowbird, Utah (USA).
M.I. Rabinovich, J.J. Torres, Pablo Varona, R. Huerta, P. Weidman. 1999. Genesis of Coherent Structures in a Discrete Chaotic Neural Medium. Proceedings 5th SIAM Conference on Applications of Dynamical Systems. Snowbird, Utah (USA).
J.J. Torres, P. Varona, R. Huerta, H.D.I. Abarbanel, M.I. Rabinovich. 1999. Spatial Clusters of Synchronization in Neural Networks of Chaotic Spiking-bursting Neurons. 1998 Conference on Computational Physics. Granada (Spain). Comp. Phys. Comm. Vol 121-122, p. 745 (1999).
P. Varona, J.M. Ibarz, O. Herreras. 1998. CA1 Population Spikes Depend Critically on Factors Other Than the Number of Firing Cells. Society for Neuroscience Abs., Vol. 24, Part 2, 719.12. Los Angeles (USA).
R. C. Elson, M.P. Maher, P. Varona, J.J. Torres, M.I. Rabinovich, H.D.I. Abarbanel, A.I. Selverston. 1998. Regular Rhythms From the Mutual Synaptic Interation of Irregular Bursters. Society for Neuroscience Abs., Vol. 24, Part 2, 655.8. LosAngeles (USA).
M.P. Maher, P. Varona, J.J. Torres, R. C. Elson, H.D.I. Abarbanel, M.I. Rabinovich. 1998. Calcium Dynamics and Regularization of Chaotic Behavior in Stomatogastric Neurons. Society for Neuroscience Abs., Vol. 24, Part 1, 63.1. Los Angeles (USA).
P. Varona, J. Torres, M. Falcke, R. Huerta, H.D.I. Abarbanel, M.I. Rabinovich. 1998. Synchronous Behavior of Two Electrically Coupled Chaotic Model Neurons. Proceedings of the 5th Joint Symp. on Neural Computation. UCSD. La Jolla (USA): 178-185.
M.I. Rabinovich, P. Varona, J.J. Torres, R. Huerta, H.D.I. Abarbanel. 1998. The Role of Ca2+ dynamics on the cooperative behavior of chaotic neurons. Book of Abstracts Statphys 20, XXth IUPAP International Conference on Statistical Physics. Paris (France).
A. de la Fuente, P. Varona, J.A. Sigüenza. 1997. Motol Control by the Spinal Cord: A Teaching Model. J. Physiol. Biochem, 53 (1): 114.
O. Herreras, J.M. Ibarz, C. Largo, P. Varona. 1997. Computer Shaping of Field Potentials and CSD profiles during Antidromic Activation of CA1 Neurons. Society for Neuroscience Abs. Vol. 23, Part 2, 892.14. New Orleans (USA).
P. Varona, J.M. Ibarz, C. Largo, O. Herreras. 1997. Reconstrucción Computerizada de Potenciales de Campo y Fuentes de Corriente Durante la Activación Sincrónica de la Region CA1. Congreso de la Sociedad Española de Neurociencia, Santander. Revista Española de Neurología, Vol. 25. 147. 1765. 1997.
J.M. Ibarz, P. Varona, O. Herreras. 1997. Corrientes de Sodio y Potenciales de Acción Dendríticos: un Modelo Neuronal. Congreso de la Sociedad Española de Neurociencia, Santander. Revista Española de Neurología, Vol. 25. 147. 1785.
P. Varona, J.A. Sigüenza. 1995. Niveles de Modelado Neuronal en el simulador de Neurocomputación XSim. Actas de la VI Conferencia CAEPIA'95, Alicante. ISBN: 84-920982-0-1.

Electronic supplementary material:

Detailed equation description and parameter values for the model used in the paper "Structural inhomogeneities differentially modulate action currents and population spikes initiated in the axon or dendrites" by L. López-Aguado L., J.M. Ibarz, P. Varona and O. Herreras, J. Neurophysiol. 88(5): 2809-2820 (2002).
Detailed equation description and parameter values for the model used in Macroscopic and Subcellular Factors Shaping Population Spikes, J. Neurophysiol., 83 (4): 2192-2208 by P. Varona, J. M. Ibarz, L. López, O. Herreras. 2000.

XSim:

XSim is a neural network simulator that allows to construct a wide variety of neural network architectures. It was specially designed to implement neural networks that incorporate any kind of biological parameters. XSim supports different levels of biological modeling, from basic single-cell models to networks with thousands of units. Unfortunately I cannot maintain the support or the free distribution of XSim any more. However if you are a former user of this simulator and you still want to get the latest version please contact me.

Related links: