Computational Neuroscience of Sensory Systems

Computational Neuroscience of Sensory Systems

Institut de la Vision

  • Research
    • Single neurons
    • Sensory Systems
    • Technology
  • People
    • Romain Brette
    • Sarah Goethals
    • Charlotte Le Mouel
    • Baptiste Lefebvre
    • Marcel Stimberg
    • Francesco Trapani
    • Pierre Yger
  • Publications
  • Material
    • Code
    • Presentations
    • Teaching
  • News
  • Contact

Publications

  • Irene Elices, Anirudh Kulkarni, Nicolas Escoubet, Léa-Laetitia Pontani, Alexis Michel Prevost, Romain Brette, 2022. An electrophysiological and behavioral model of Paramecium, the “swimming neuron”, bioRxiv. [bibtex] [pdf] [doi]
  • Denis Alevi, Marcel Stimberg, Henning Sprekeler, Klaus Obermayer, Moritz Augustin, 2022. Brian2CUDA: Flexible and Efficient Simulation of Spiking Neural Network Models on GPUs, Frontiers in Neuroinformatics, volume 16. [bibtex] [pdf] [doi]
  • Sarah Goethals, Martijn Christiaan Sierksma, Xavier Nicol, Annabelle Réaux-Le Goazigo, Romain Brette, 2021. Electrical match between initial segment and somatodendritic compartment for action potential backpropagation in retinal ganglion cells, Journal of Neurophysiology. [bibtex] [pdf] [doi]
  • Romain D Cazé, Marcel Stimberg, 2021. Neurons with dendrites can perform linearly separable computations with low resolution synaptic weights [version 3; peer review: 3 approved], F1000Research, volume 9. [bibtex] [pdf] [doi]
  • Mickaël Zbili, Sylvain Rama, Pierre Yger, Yanis Inglebert, Norah Boumedine-Guignon, Laure Fronzaroli-Moliniere, Romain Brette, Michaël Russier, Dominique Debanne, 2020. Axonal Na+ channels detect and transmit levels of input synchrony in local brain circuits, Science Advances, volume 6. [bibtex] [pdf] [doi]
  • Sarah Goethals, Romain Brette, 2020. Theoretical relation between axon initial segment geometry and excitability, eLife, volume 9. [bibtex] [pdf] [doi]
  • Marcel Stimberg, Dan F. M. Goodman, Thomas Nowotny, 2020. Brian2GeNN: accelerating spiking neural network simulations with graphics hardware, Sci Rep, volume 10. [bibtex] [pdf] [doi]
  • Anirudh Kulkarni, Irene Elices, Nicolas Escoubet, Léa-Laetitia Pontani, Alexis Michel Prevost, Romain Brette, 2020. A simple device to immobilize protists for electrophysiology and microinjection, Journal of Experimental Biology, volume 223. [bibtex] [pdf] [doi]
  • Charlotte Le Mouel, Romain Brette, 2019. Anticipatory coadaptation of ankle stiffness and sensorimotor gain for standing balance, PLOS Computational Biology, volume 15. [bibtex] [pdf] [doi]
  • Marcel Stimberg, Romain Brette, Dan FM Goodman, 2019. Brian 2, an intuitive and efficient neural simulator, eLife (Frances K Skinner, ed.), volume 8. [bibtex] [pdf] [doi]
  • Charlotte Le Mouel, Romain Tisserand, Thomas Robert, Romain Brette, 2019. Postural adjustments in anticipation of predictable perturbations allow elderly fallers to achieve a balance recovery performance equivalent to elderly non-fallers, Gait & Posture, volume 71. [bibtex] [pdf] [doi]
  • Marcel Stimberg, Dan F. M. Goodman, Romain Brette, Maurizio De Pittà, 2019. Modeling Neuron--Glia Interactions with the Brian 2 Simulator, Chapter in Computational Glioscience (Maurizio De Pittà, Hugues Berry, eds.), Springer. [bibtex] [pdf] [doi]
  • Romain Brette, 2019. Neural coding: The bureaucratic model of the brain, Behavioral and Brain Sciences, volume 42. [bibtex] [pdf] [doi]
  • Romain Brette, 2019. Is coding a relevant metaphor for the brain?, Behavioral and Brain Sciences, volume 42. [bibtex] [pdf] [doi]
  • Inga Blundell, Romain Brette, Thomas A. Cleland, Thomas G. Close, Daniel Coca, Andrew P. Davison, Sandra Diaz Pier, Carlos Fernandez Musoles, Padraig Gleeson, Dan F. M. Goodman, Michael Hines, Michael W. Hopkins, Pramod Kumbhar, David R. Lester, Bóris Marin, Abigail Morrison, Eric Müller, Thomas Nowotny, Alexander Peyser, Dimitri Plotnikov, Paul Richmond, Andrew Rowley, Bernhard Rumpe, Marcel Stimberg, Alan Barry Stokes, Adam Tomkins, Guido Trensch, Marmaduke Woodman, Jochen Martin Eppler, 2018.Code generation in computational neuroscience: a review of tools and techniques, Front. Neuroinform., volume 12. [bibtex] [doi]
  • Maarten HP Kole, Romain Brette, 2018. The electrical significance of axon location diversity, Current Opinion in Neurobiology, volume 51. [bibtex] [pdf] [doi]
  • Maria Teleńczuk, Romain Brette, Alain Destexhe, Bartosz Teleńczuk, 2018. Contribution of the Axon Initial Segment to Action Potentials Recorded Extracellularly, eNeuro, volume 5. [bibtex] [pdf] [doi]
  • Pierre Yger, Giulia LB Spampinato, Elric Esposito, Baptiste Lefebvre, Stéphane Deny, Christophe Gardella, Marcel Stimberg, Florian Jetter, Guenther Zeck, Serge Picaud, Jens Duebel, Olivier Marre, 2018. A spike sorting toolbox for up to thousands of electrodes validated with ground truth recordings in vitro and in vivo, eLife (David Kleinfeld, ed.), eLife Sciences Publications, Ltd, volume 7. [bibtex] [pdf] [doi]
  • Romain Cazé, Marcel Stimberg, Benoît Girard, 2018. [Re] Non-additive coupling enables propagation of synchronous spiking activity in purely random networks, ReScience, volume 4. [bibtex] [pdf] [doi]
  • Romain Brette, 2018. The world is complex, not just noisy, Behavioral and Brain Sciences, volume 41. [bibtex] [pdf] [doi]
  • Yi Zheng, Romain Brette, 2017. On the relation between pitch and level, Hearing Research. [bibtex] [pdf] [doi]
  • Maria Teleńczuk, Bertrand Fontaine, Romain Brette, 2017. The basis of sharp spike onset in standard biophysical models, PLoS ONE, volume 12. [bibtex] [pdf] [doi]
  • Nicolas P Rougier, Konrad Hinsen, Frédéric Alexandre, Thomas Arildsen, Lorena Barba, Fabien CY Benureau, C Titus Brown, Pierre de Buyl, Ozan Caglayan, Andrew P Davison, Marc André Delsuc, Georgios Detorakis, Alexandra K Diem, Damien Drix, Pierre Enel, Benoît Girard, Olivia Guest, Matt G Hall, Rafael Neto Henriques, Xavier Hinaut, Kamil S Jaron, Mehdi Khamassi, Almar Klein, Tiina Manninen, Pietro Marchesi, Dan McGlinn, Christoph Metzner, Owen L Petchey, Hans Ekkehard Plesser, Timothée Poisot, Karthik Ram, Yoav Ram, Etienne Roesch, Cyrille Rossant, Vahid Rostami, Aaron Shifman, Joseph Stachelek, Marcel Stimberg, Frank Stollmeier, Federico Vaggi, Guillaume Viejo, Julien Vitay, Anya Vostinar, Roman Yurchak, Tiziano Zito, 2017. Sustainable computational science: the ReScience initiative, PeerJ Computer Science, volume 3. [bibtex] [pdf] [doi]
  • Charlotte Le Mouel, Romain Brette, 2017. Mobility as the Purpose of Postural Control, Frontiers in Computational Neuroscience, volume 11. [bibtex] [pdf] [doi]
  • Mustafa S. Hamada, Sarah Goethals, Sharon I. de Vries, Romain Brette, Maarten H. P. Kole, 2016. Covariation of axon initial segment location and dendritic tree normalizes the somatic action potential, Proceedings of the National Academy of Sciences of the United States of America, volume 113. [bibtex] [pdf] [doi]
  • Guillaume Bellec, Mathieu Galtier, Romain Brette, Pierre Yger, 2016.Slow feature analysis with spiking neurons and its application to audio stimuli, Journal of computational neuroscience, volume 40. [bibtex] [doi]
  • Michaël Bazelot, Maria T. Teleńczuk, Richard Miles, 2016. Single CA3 pyramidal cells trigger sharp waves in vitro by exciting interneurones, The Journal of physiology, volume 594. [bibtex] [pdf] [doi]
  • Victor Benichoux, Marc Rébillat, Romain Brette, 2016.On the variation of interaural time differences with frequency, The Journal of the Acoustical Society of America, volume 139. [bibtex] [doi]
  • Pierre Yger, Matthieu Gilson, 2016. Erratum: Addendum: Models of Metaplasticity: A Review of Concepts, Frontiers in computational neuroscience, volume 10. [bibtex] [pdf] [doi]
  • Baptiste Lefebvre, Pierre Yger, Olivier Marre, 2016. Recent progress in multi-electrode spike sorting methods, Journal of Physiology-Paris, volume 110. [bibtex] [pdf] [doi]
  • David Colliaux, Pierre Yger, Kunihiko Kaneko, 2015. Impact of sub and supra-threshold adaptation currents in networks of spiking neurons, Journal of computational neuroscience, volume 39. [bibtex] [pdf] [doi]
  • Romain Brette, 2015. Philosophy of the Spike: Rate-Based vs. Spike-Based Theories of the Brain, Frontiers in systems neuroscience, volume 9. [bibtex] [pdf] [doi]
  • Pierre Yger, Marcel Stimberg, Romain Brette, 2015. Fast Learning with Weak Synaptic Plasticity, The Journal of neuroscience : the official journal of the Society for Neuroscience, volume 35. [bibtex] [pdf] [doi]
  • Victor Benichoux, Bertrand Fontaine, Tom P. Franken, Shotaro Karino, Philip X. Joris, Romain Brette, 2015. Neural tuning matches frequency-dependent time differences between the ears, eLife, volume 4. [bibtex] [pdf] [doi]
  • Charlotte Le Mouel, Kenneth D. Harris, Pierre Yger, 2014. Supervised learning with decision margins in pools of spiking neurons, Journal of computational neuroscience, volume 37. [bibtex] [pdf] [doi]
  • Marc Rébillat, Victor Benichoux, Makoto Otani, Renaud Keriven, Romain Brette, 2014.Estimation of the low-frequency components of the head-related transfer functions of animals from photographs, The Journal of the Acoustical Society of America, volume 135. [bibtex] [doi]
  • Bertrand Fontaine, José Luis Peña, Romain Brette, 2014. Spike-threshold adaptation predicted by membrane potential dynamics in vivo, PLoS computational biology, volume 10. [bibtex] [pdf] [doi]
  • Samuel Garcia, Domenico Guarino, Florent Jaillet, Todd Jennings, Robert Pröpper, Philipp L. Rautenberg, Chris C. Rodgers, Andrey Sobolev, Thomas Wachtler, Pierre Yger, Andrew P. Davison, 2014. Neo: an object model for handling electrophysiology data in multiple formats, Frontiers in neuroinformatics, volume 8. [bibtex] [pdf] [doi]
  • Marcel Stimberg, Dan F. M. Goodman, Victor Benichoux, Romain Brette, 2014. Equation-oriented specification of neural models for simulations, Frontiers in neuroinformatics, volume 8. [bibtex] [pdf] [doi]
  • Caroline Le Duigou, Jean Simonnet, Maria T. Teleńczuk, Desdemona Fricker, Richard Miles, 2014. Recurrent synapses and circuits in the CA3 region of the hippocampus: an associative network, Frontiers in cellular neuroscience, volume 7. [bibtex] [pdf] [doi]
  • Jonathan Laudanski, Yi Zheng, Romain Brette, 2014. A Structural Theory of Pitch(1,2,3), eNeuro, volume 1. [bibtex] [pdf] [doi]
  • Dan F. M. Goodman, Victor Benichoux, Romain Brette, 2013. Decoding neural responses to temporal cues for sound localization, eLife, volume 2. [bibtex] [pdf] [doi]
  • Romain Brette, 2013. Sharpness of spike initiation in neurons explained by compartmentalization, PLoS computational biology, volume 9. [bibtex] [pdf] [doi]
  • Pierre Yger, Kenneth D. Harris, 2013. The Convallis rule for unsupervised learning in cortical networks, PLoS computational biology, volume 9. [bibtex] [pdf] [doi]
  • Bertrand Fontaine, Victor Benichoux, Philip X. Joris, Romain Brette, 2013.Predicting spike timing in highly synchronous auditory neurons at different sound levels, Journal of neurophysiology, volume 110. [bibtex] [doi]
  • Cyrille Rossant, Bertrand Fontaine, Anna K. Magnusson, Romain Brette, 2012.A calibration-free electrode compensation method, Journal of neurophysiology, volume 108. [bibtex] [doi]
  • Michael Okun, Pierre Yger, Stephan L. Marguet, Florian Gerard-Mercier, Andrea Benucci, Steffen Katzner, Laura Busse, Matteo Carandini, Kenneth D. Harris, 2012. Population rate dynamics and multineuron firing patterns in sensory cortex, The Journal of neuroscience : the official journal of the Society for Neuroscience, volume 32. [bibtex] [pdf] [doi]
  • Romain Brette, Dan F. M. Goodman, 2012.Simulating spiking neural networks on GPU, Network (Bristol, England), volume 23. [bibtex] [doi]
  • Boris Gourévitch, Romain Brette, 2012.The impact of early reflections on binaural cues, The Journal of the Acoustical Society of America, volume 132. [bibtex] [doi]
  • Sami El Boustani, Pierre Yger, Yves Frégnac, Alain Destexhe, 2012.Stable learning in stochastic network states, The Journal of neuroscience : the official journal of the Society for Neuroscience, volume 32. [bibtex] [doi]
  • Cyrille Rossant, Sara Leijon, Anna K. Magnusson, Romain Brette, 2011.Sensitivity of noisy neurons to coincident inputs, The Journal of neuroscience : the official journal of the Society for Neuroscience, volume 31. [bibtex] [doi]
  • Lyle Muller, Romain Brette, Boris Gutkin, 2011. Spike-timing dependent plasticity and feed-forward input oscillations produce precise and invariant spike phase-locking, Frontiers in computational neuroscience, volume 5. [bibtex] [pdf] [doi]
  • Brian J. Fischer, Louisa J. Steinberg, Bertrand Fontaine, Romain Brette, Jose L. Peña, 2011. Effect of instantaneous frequency glides on interaural time difference processing by auditory coincidence detectors, Proceedings of the National Academy of Sciences of the United States of America, volume 108. [bibtex] [pdf] [doi]
  • Pierre Yger, Sami El Boustani, Alain Destexhe, Yves Frégnac, 2011.Topologically invariant macroscopic statistics in balanced networks of conductance-based integrate-and-fire neurons, Journal of computational neuroscience, volume 31. [bibtex] [doi]
  • Yves Kremer, Jean-François Léger, Dan Goodman, Romain Brette, Laurent Bourdieu, 2011.Late emergence of the vibrissa direction selectivity map in the rat barrel cortex, The Journal of neuroscience : the official journal of the Society for Neuroscience, volume 31. [bibtex] [doi]
  • Bertrand Fontaine, Dan F. M. Goodman, Victor Benichoux, Romain Brette, 2011. Brian hears: online auditory processing using vectorization over channels, Frontiers in neuroinformatics, volume 5. [bibtex] [pdf] [doi]
  • Romain Brette, Dan F. M. Goodman, 2011.Vectorized algorithms for spiking neural network simulation, Neural computation, volume 23. [bibtex] [doi]
  • Jonathan Platkiewicz, Romain Brette, 2011. Impact of fast sodium channel inactivation on spike threshold dynamics and synaptic integration, PLoS computational biology, volume 7. [bibtex] [pdf] [doi]
  • Bastian Venthur, Simon Scholler, John Williamson, Sven Dähne, Matthias S. Treder, Maria T. Kramarek, Klaus-Robert Müller, Benjamin Blankertz, 2010.Pyff - a pythonic framework for feedback applications and stimulus presentation in neuroscience, Frontiers in neuroscience, volume 4. [bibtex] [doi]
  • Dan F. M. Goodman, Romain Brette, 2010. Spike-timing-based computation in sound localization, PLoS computational biology, volume 6. [bibtex] [pdf] [doi]
  • Romain Brette, 2010.On the interpretation of sensitivity analyses of neural responses, The Journal of the Acoustical Society of America, volume 128. [bibtex] [doi]
  • Jonathan Platkiewicz, Romain Brette, 2010. A threshold equation for action potential initiation, PLoS computational biology, volume 6. [bibtex] [pdf] [doi]
  • Cyrille Rossant, Dan F. M. Goodman, Jonathan Platkiewicz, Romain Brette, 2010. Automatic fitting of spiking neuron models to electrophysiological recordings, Frontiers in neuroinformatics, volume 4. [bibtex] [pdf] [doi]
  • Olivier Marre, Pierre Yger, Andrew P. Davison, Yves Frégnac, 2009.Reliable recall of spontaneous activity patterns in cortical networks, The Journal of neuroscience : the official journal of the Society for Neuroscience, volume 29. [bibtex] [doi]
  • Marcel Stimberg, Klaus Wimmer, Robert Martin, Lars Schwabe, Jorge Mariño, James Schummers, David C. Lyon, Mriganka Sur, Klaus Obermayer, 2009. The operating regime of local computations in primary visual cortex, Cerebral cortex (New York, N.Y. : 1991), volume 19. [bibtex] [pdf] [doi]
  • Sami El Boustani, Olivier Marre, Sébastien Béhuret, Pierre Baudot, Pierre Yger, Thierry Bal, Alain Destexhe, Yves Frégnac, 2009. Network-state modulation of power-law frequency-scaling in visual cortical neurons, PLoS computational biology, volume 5. [bibtex] [pdf] [doi]
  • Dan F. M. Goodman, Romain Brette, 2009. The brian simulator, Frontiers in neuroscience, volume 3. [bibtex] [pdf] [doi]
  • Romain Brette, 2009.Generation of correlated spike trains, Neural computation, volume 21. [bibtex] [doi]
  • Dan Goodman, Romain Brette, 2008. Brian: a simulator for spiking neural networks in python, Frontiers in neuroinformatics, volume 2. [bibtex] [pdf] [doi]
  • Jonathan Touboul, Romain Brette, 2008.Dynamics and bifurcations of the adaptive exponential integrate-and-fire model, Biological cybernetics, volume 99. [bibtex] [doi]
  • Zuzanna Piwkowska, Martin Pospischil, Romain Brette, Julia Sliwa, Michelle Rudolph-Lilith, Thierry Bal, Alain Destexhe, 2008.Characterizing synaptic conductance fluctuations in cortical neurons and their influence on spike generation, Journal of neuroscience methods, volume 169. [bibtex] [doi]
  • Romain Brette, 2008. The Cauchy problem for one-dimensional spiking neuron models, Cognitive neurodynamics, volume 2. [bibtex] [pdf] [doi]
  • Laurent Badel, Sandrine Lefort, Romain Brette, Carl C. H. Petersen, Wulfram Gerstner, Magnus J. E. Richardson, 2008.Dynamic I-V curves are reliable predictors of naturalistic pyramidal-neuron voltage traces, Journal of neurophysiology, volume 99. [bibtex] [doi]
  • Andrew P. Davison, Daniel Brüderle, Jochen Eppler, Jens Kremkow, Eilif Muller, Dejan Pecevski, Laurent Perrinet, Pierre Yger, 2008. PyNN: A Common Interface for Neuronal Network Simulators, Frontiers in neuroinformatics, volume 2. [bibtex] [pdf] [doi]
  • James Schummers, Beau Cronin, Klaus Wimmer, Marcel Stimberg, Robert Martin, Klaus Obermayer, Konrad Koerding, Mriganka Sur, 2007. Dynamics of orientation tuning in cat v1 neurons depend on location within layers and orientation maps, Frontiers in neuroscience, volume 1. [bibtex] [pdf] [doi]
  • Romain Brette, 2007.Exact simulation of integrate-and-fire models with exponential currents, Neural computation, volume 19. [bibtex] [doi]
  • Romain Brette, 2006.Exact simulation of integrate-and-fire models with synaptic conductances, Neural computation, volume 18. [bibtex] [doi]
  • Pierrick Coupé, Pierre Yger, Christian Barillot, 2006. Fast non local means denoising for 3D MR images, Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention, volume 9. [bibtex] [pdf]
  • Romain Brette, Wulfram Gerstner, 2005.Adaptive exponential integrate-and-fire model as an effective description of neuronal activity, Journal of neurophysiology, volume 94. [bibtex] [doi]
  • Romain Brette, 2004.Dynamics of one-dimensional spiking neuron models, Journal of mathematical biology, volume 48. [bibtex] [doi]
  • Romain Brette, Emmanuel Guigon, 2003.Reliability of spike timing is a general property of spiking model neurons, Neural computation, volume 15. [bibtex] [doi]

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