Neural Engineering

Transformative Technologies

Publications from NETT

Fellows are highlighted in bold.

Refereed Journal Articles

Angulo-Garcia D. and Torcini A.
Stable chaos in fluctuation driven neural circuits
Chaos, solitons and fractals, 2014, 69, 233-245.

Angulo-Garcia D. and Torcini A.
Stochastic Mean Field Formulation of the Dynamics of Diluted Neural Networks
Phys. Rev. E., 2014, 022928.

Angulo-Garcia D., Berke J.D. and Torcini A.
Cell Assembly Dynamics of Sparsely-Connected Inhibitory Networks: A Simple Model for the Collective Activity of Striatal Projection Neurons
PLoS Computational Biology, 2016, 12(2).

Stefano Luccioli, David Angulo-Garcia, Rosa Cossart, Arnaud Malvache, Laura Modol-Vidal, Vitor H. Sousa,Paolo Bonifazi, and Alessandro Torcini
Numerical and Experimental Evidences of Operational Hubs
In preparation.

Barardi A, Sancristobal B, Garcia-Ojalvo J, 2014.
Phase-Coherence Transitions and Communuication in the Gamma Range between Delay-Coupled Neuronal Populations
PLoS Computational Biology 10(7):e1003723

Barardi A, Malagarriga D, Sancristobal B, Garcia-Ojalvo J, Pons AJ, 2014.
Probing scale interaction in brain dynamics through synchronization
Phil. Trans. Roy. Soc. B 369: 20130533.

Barardi A, Mazzoni A, Garcia-Ojalvo J, 2015.
Transition between functional regimes in an integrate-and-fire network model of the thalamus
PLoS Computational Biology, under review. (preprint)

Barardi A, Lubenov EV, Garcia-Ojalvo J, Siapas AG, 2016.
Long-wavelength propagation in inhibition-dominated neuronal chains, in preparation.

Bozanic N., Mulansky, M. and Kreuz T.
Scholarpedia, 9(12):32344, 2014.,

Bozanic, N. and Kreuz, T.
SPIKY: A graphical user interface for monitoring spike train synchrony
Journal of Neurophysiology, 113 (9), pp 3432-3445, 2015.

Bozanic, N., Mulansky, M. and Kreuz, T.
Latency correction using the time-scale independent SPIKE-distance
In preparation.

Tran-Van-Minh Alexandra, Cazé, Romain D., Abrahamsson Therese, Cathala, Laurence, Gutkin Boris S., DiGregorio, David A.
Contribution of sublinear and supralinear dendritic integration to neuronal computations
Frontiers in Neuroscience 2015, 9, 67.

Cazé Romain D., Clopath Claudia, Schultz Simon
Synaptic clustering or scattering? Insight from model of synaptic plasticity in dendrites
(Submitted, under review) (preprint)

Berditchevskaia Alexandra, Cazé Romain D. and Schultz Simon R.
Performance in a GO/NOGO perceptual task reflects a balance between impulsive and instrumental components of behaviour
Scientific Reports (to appear 2016) (preprint)

Romain D. Cazé, Sarah Jarvis, Amanda Joy Foust, Simon R Schultz
Dendrites enable a robust mechanism for neuronal stimulus selectivity
(Submitted, under review) (preprint)

Romain Daniel Cazé, Amanda Joy Foust, Claudia Clopath, Simon R Schultz
On the distribution and function of synaptic clusters
(Submitted, under review) (preprint)

Gulletta, G. et al
“Nonlinear optimization for the generation of human-like synchronous bimanual movements in anthropomorphic robots”
In preparation

Herzog, N., Johnston, A., Bellamy, T., Russell, N.A.
Considerations for microfluidic flow applications involving activity in cultured neurons.
In Preparation

Maciej Jedynak, Antonio J. Pons and Jordi Garcia-Ojalvo
Cross-frequency transfer in a stochastically driven mesoscopic brain model
Frontiers of Computational Neuroscience journal, 9:14, 2015.

Kasap, B. & Van Opstal, A. J.
A spiking neural network model of the midbrain superior colliculus that generates saccadic motor commands (under review for Biological Cybernetics).

Rivera-Rubio, J.M., Kasap, B., Bozanic, N., Arulkumaran, K. and Bharath, A.A.
Population coding via matrix equilibriation
In preparation.

Rivera-Rubio, J.M., Kasap, B., Bozanic, N. and Bharath, A.A.
Reconstructing place fields with visual stimuli.
In preparation.

Melinscak, F., Montesano, L., Minguez, J.
Asynchronous detection of kinesthetic attention during mobilization of lower limbs using EEG measurements
Journal of Neural Engineering, 13(1):016018, 2016.

Melinscak, F., Montesano, L.
Beyond p-values in the evaluation of brain-computer interfaces.
PeerJ Preprints, No. e1828v1, 2016.

Melinscak, F., Montesano, L.
Beyond p-values in the evaluation of brain–computer interfaces: A Bayesian estimation approach. Journal of Neuroscience Methods 270: p. 30-45, 2016.

Melinscak, F., Montesano, L.
Simulation-based experimental design for brain decoding studies
In preparation.

Mario Mulanksy and Karsten Ahnert
Odeint Library
Scholarpedia, 9(12):32342 (2014).,

M. Mulansky and T. Kreuz
PySpike - A Python library for analyzing spike train synchrony
SoftwareX, in press (2016);

Thomas Kreuz, Mario Mulansky and Nebojsa Bozanic
SPIKY: A graphical user interface for monitoring spike train synchrony
Journal of Neurophysiology, 113, 9, pp 3432-3445 (2015).

C. Quintero-Quiroz, M.G. Cosenza,
Collective behaviour of chaotic oscillators with environmental coupling, Chaos, Solitons and Fractals, 2014.

T. Sorrentino, C. Quintero-Quiroz, A, Aragoneses, M.C. Torrent, C. Masoller
Effects of periodic forcing on the temporally correlated spikes of a semiconductor laser with feedback
Optics Express, 2014.

Taciano Sorrentino, C. Quintero-Quiroz, M.C. Torrent, C. Masoller
Analysis of the spike rate and spike correlations in modulated semiconductor lasers with optical feedback
IEEE JSTQE 21(6), 2015

C. Quintero-Quiroz, S. Pigolotti, M. C. Torrent, and C. Masoller
Numerical and experimental study of the effects of noise on the permutation entropy
New Journal of Physics 17, 093002 2015

Kappen, Hilbert Johan, and Hans Christian Ruiz
Adaptive importance sampling for control and inference
Journal of Statistical Physics 162, no. 5 (2016): 1244-1266.

Ruiz, H-Ch, and H. J. Kappen.
Particle Smoothing for Hidden Diffusion Processes: Adaptive Path Integral Smoother
Submitted to IEEE Transactions on Signal Processing, 2016.
arXiv preprint

Sburlea A.I., Montesano, L., Minguez, J.
Continuous detection of the self-initiated walking pre-movement state from EEG correlates without session-to-session recalibration.
Journal of Neural Engineering, 12, 3, 036007, 2014.

Sburlea, A. I., Montesano, L., Cano de la Cuerda, R., Alguacil Diego, I., Miangolarra-Page, J. C., Minguez, J.
Detecting intention to walk in stroke patients from pre-movement EEG correlates.
Journal of NeuroEngineering and Rehabilitation, 12:113, 2015.

Sburlea, A. I., Montesano, L. Minguez, J.
Advantages of EEG phase patterns for the detection of gait intention in healthy and stroke patients.
Submitted to Frontiers in Neuroscience, section Neuroprosthetics.

Thalmeier, Dominik, Marvin Uhlmann, Hilbert J. Kappen, and Raoul-Martin Memmesheimer.
Learning universal computations with spikes
Plos Computational Biology, 2016.

Thalmeier, Dominik, Vicenç Gómez, and Hilbert J. Kappen.
Action selection in growing state spaces: Control of Network Structure Growth
Submitted to J Phys A, 2016.
arXiv preprint

S. Visser and S.A. van Gils
Lumping Izhikevich neurons
EPJ Nonlinear Biomedical Physics 2:6 (2014)

Bas-Jan Zandt , Sid Visser, Michel J. A. M. van Putten, Bennie ten Haken
A neural mass model based on single cell dynamics to model pathophysiology
Journal of Computational Neuroscience, December 2014, Volume 37, Issue 3, pp 549-568.

K. Dijkstraa, S.A. van Gils, S.G. Janssens, Yu.A. Kuznetsov, S. Visser
Pitchfork–Hopf bifurcations in 1D neural field models with transmission delays
Physica D, March 2015, 297, pp88-101.

S. Coombes, R. Nicks and S. Visser
Standing and travelling waves in a spherical brain model: the Nunez model revisited
Physica D (submitted).

S. Visser
Efficient evaluation of discretized neural fields with many delays
In preparation.

Ferreira, F., Erlhagen, W., Wotjak, W., Sousa, E., Bicho, E.
Rapid learning of complex sequences with time constraints: A neural field model
Submitted to IEEE Transactions on Cognitive and Developmental Systems

Wojtak, W., Ferreira, F., Louro, L., Bicho E., Erlhagen, W.
Adaptive timing for fluent human-robot interactions.
In preparation

Conference Proceedings

Annecchino L., Morris A., Agabi O., Chadderton P. and Schultz S.R. Two-photon targeted robotic patch-clamp electrophysiological recording in vivo Program No. 585.13. 2013
Abstract Viewer/Itinerary Planner. Washington, DC: Society for Neuroscience. Online.

Barardi A, Mazzoni A, Garcia-Ojalvo J Modelling thalamic dynamics with a network of integrate and fire neurons CNS Conference, Prague, Czech Republic, BMC Neuroscience 16(76), 2015.

Loncar-Turukalo, T., Mijatovic, G., Bozanic, N., Stoll, F., Bajic, D., Procyk E. Time-Frequency Characterization of Local Field Potential in a Decision Making Task Proceedings of the 37th Annual International Conference of the IEEE Engineering In Medicine and Biology Society, Milan, August 2015.

Gulletta, G., Araújo, S. M., Costa e Silva, E., Costa, M.F., Erlhagen, W., Bicho, E. Nonlinear optimization for human-like synchronous movements of a dual arm-hand robotics system AIP Conference Proceedings of the 12th International Conference of Numerical Analysis and Applied Mathematics (ICNAAM 2014), Rhodes, Greece, September, 22-28, 2014

Herzog N., Johnstone A., Idinyang S., Bellamy T.C., and Russell N.A. Rapid Drug Delivery to In Vitro Neuronal Cultures The 18th International Conference on Miniaturized Systems for Chemistry and Life Sciences (Conference), Vol. 2014.

Herzog, N., Johnston, A., Bellamy, T.C., Russell, N.A.
Stability of neuronal culture spiking activity under rapid microfluidic flow
10th International Meeting on Substrate-Integrated Microelectrode Arrays (Conference)

Kasap, B., & Van Opstal, A. J. A one-dimensional spiking neural network model of the midbrain superior colliculus. 7th International IEEE/EMBS Conference on Neural Engineering, pp 324-327. 2015.

Kasap, B., & Van Opstal, A. J. Lateral connections synchronize population activity in a spiking neural network model of midbrain superior colliculus. BMC Neuroscience, 16, Suppl 1, p. 273. 2015.

Melinscak, F., Montesano, L. and Minguez, J.
Discriminating Between Attention and Mind Wandering During Movement Using EEG Proceedings of the 6th International Brain-Computer Interface Conference 2014, Graz, Austria, September 2014.

Melinscak, F., Montesano, L., Minguez, J.
Improved estimates of BCI accuracy with hierarchical Bayesian models
Proceedings of the 6th International Brain-Computer Interface Meeting 2016, Asilomar, CA, USA, June 2016.

Melinscak, F., Montesano, L.
Sample size determination for BCI studies: how many subjects and trials?
Proceedings of the 38th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC’16), Orlando, FL, USA, 2016.

Mulansky, M., Sburlea, A., Bozanic, N. and Kreuz, T.
A guide to time-resolved and parameter-free measures of spike-train synchrony
IEEE Proc. First Intl. Conf on Event-Based Control, Communication and Signal Processing, pp 1-8, 2015. Also poster abstract in BMC Neuroscience. (BMC version) (IEEE version)

C. Quintero-Quiroz ; Taciano Sorrentino ; M. C. Torrent ; Cristina Masoller Analysis of the effects of periodic forcing in the spike rate and spike correlation's in semiconductor lasers with optical feedback Proc. SPIE 9892, Semiconductor Lasers and Laser Dynamics VII, 98921T (April 28, 2016).

Andrés Aragoneses ; Taciano Sorrentino ; C. Quintero-Quiroz ; Sandro Perrone ; M. C. Torrent ; Cristina Masoller Effects of modulation in the complex dynamics of a semiconductor laser with feedback Proc. SPIE 9892, Semiconductor Lasers and Laser Dynamics VII, 98920E (April 28, 2016)

Sburlea, A.I., Montesano, L., Minguez, J. Intersession adaptation of the EEG-based detector of self-paced walking intention in stroke patients. 36th International IEEE conf. of Engineering in Medicine and Biology Society, Milan, Italy, 2015.

Sburlea, A., Montesano, L. and Minguez, J.
Detecting walking intention using EEG phase patterns
Proceedings of the 6th International Brain-Computer Interface Meeting 2016, Asilomar, CA, USA, June 2016.

Schuck, R., Annecchino L.A. and Schultz S.R. Scaling Up Multiphoton Neural Scanning: the SSA algorithm Proceedings of the 36th Annual International IEEE EMBS Conference of the IEEE Engineering in Medicine and Biology Society, Chicago, Illinois, USA, 26-30 August 2014, pp 2837-2840.

Schuck, R, Quicke, P, Copeland, C, Garasto, S, Annecchino, LA, Hwang, JK, Schultz, SR Rapid Three Dimensional Two Photon Neural Population Scanning Proceedings of the IEEE EMBS conference in Milano Italy, August 2015, pp 5867-5870.

SR Schultz, C Copeland, A Foust, P Quicke and R Schuck Advances in two photon scanning and scanless microscopic technologies for imaging neural circuits Proceedings of the IEEE, 2016, in press.

Wojtak, W., Ferreira, F., Erlhagen, W., and Bicho, E. Learning Joint Representations for Order and Timing of Perceptual-Motor Sequences: a Dynamic Neural Field Approach Proceedings of 2015 International Joint Conference on Neural Network (IJCNN 2015), Killarney, Ireland, July 12 - 17, 2015

Wojtak W., Coombes S., Bicho E., Erlhagen W. Combining spatial and parametric working memory in a dynamic neural field model Proceedings of the 25th International Conference on Artificial Neural Networks
ICANN 2016, Lecture Notes in Computer Science Vol. 9886, pp 411-418

Publications not directly involving fellows but related to NETT activity


Andrzejak RG, Mormann F, Kreuz T. Detecting determinism from point processes. Physical Review E 90, 062906 (2014)
Ashwin P, Coombes S and Nicks R
Mathematical frameworks for oscillatory network dynamics in neuroscience
Journal of Mathematical Neuroscience, 6:2, 2016

Byrne Á, Brookes M J and Coombes S
A mean field model for movement induced changes in the beta rhythm
Submitted 2016

Coombes S and Byrne Á
Next generation neural mass models
Lecture Notes in Nonlinear Dynamics in Computational Neuroscience: from Physics and Biology to ICT, Ed. A Torcini and F Corinto, Springer, 2016

Delgado Ruz I. and Schultz S.R.
Localising and classifying neurons from high density MEA recordings
Journal of Neuroscience Methods, 2014, under review

Faria, C., Erlhagen, W., Rito, M., de Momi, E., Ferrigno G. and Bicho, E.
Review of Robotic Technology for Stereotactic Neurosurger
IEEE Reviews in Biomedical Engineering, Vol. 8, pp. 125-137, 30 April 2015.
Faria, C., Vale, C., Machado, T., Erlhagen, W., Rito, M., Monteiro, S. and Bicho, E.
Experiential Learning of Robotics Fundamentals Based on a Case Study of Robot-Assisted Stereotactic Neurosurgery
IEEE Transactions on Education, in Press.

Gago, M.F., Fernandes, V., Ferreira, J., Yelshyna, D., Silva, H.D., Rodrigues, M.L., Rocha, L., Bicho E. and Sousa, N.
Role of the visual and auditory systems in postural stability in Alzheimer’s disease
J Alzheimers Dis. 2015 May 30;46(2):441-9. doi: 10.3233/JAD-150131.

Kreuz T., Chicharro D., Houghton C., Andrzejak R.G. and Mormann F.
Monitoring spike train synchrony
J Neurophysiol 109, 1457. 2013

Kreuz T.
Scholarpedia 7(12), 30652. 2012

Luccioli S., Ben-Jacob E., Barzilai A., Bonifazi P., and Torcini A.
Clique of functional hubs orchestrates population bursts in developmentally regulated neural networks
PLOS Computational Biology, 10(9): e1003823 (2014)

Mikkelsen K., Imparato A. and Torcini A.
Emergence of slow collective oscillations in neural networks with spike timing dependent plasticity
Phys. Rev. Lett. 110, 208101. 2013

Mikkelsen K., Imparato A., and Torcini A.
Sisyphus Effect in Pulse Coupled Excitatory Neural Networks with Spike-Timing Dependent Plasticity
Phys. Rev. E 89, 062701 (2014)

Olmi S., Politi A. and Torcini A.
Linear Stability in networks of pulse-coupled neurons
Frontiers in Computational neuroscience 8:8. 2014.

Olmi S. and Torcini A.
Coherent activity in excitatory pulse-coupled networks
Scholarpedia, 8(10):30928. 2013

Olmi S, Martens EA, Thutupalli S, and Torcini A
Intermittent chaotic chimeras for coupled rotators
Phys. Rev. E 92, 030901(R) (2015)

Oñativia J., Schultz S.R. and Dragotti P.L.
A Finite Rate of Innovation algorithm for fast and accurate spike detection from two-photon calcium imaging
Journal of Neural Engineering. 2013

Sousa, E., Erlhagen, W., Ferreira, F., and Bicho, E.
Off-line simulation inspires insight: A neurodynamics approach to efficient robot task learning
Neural Networks, in Press

Thul R, Coombes S and Laing C R
Neural field models with threshold noise
Journal of Mathematical Neuroscience, 6:3, 2016

Torres J.J., Kappen H.J.
Emerging phenomena in neural networks with dynamic synapses and their computational implications
Front Comput Neurosci. 2013

di Volo M., Livi R., Luccioli S., Politi A. and Torcini A.
Synchronous dynamics in the presence of short-term plasticity
Phys. Rev. E 87, 032801. 2013

Yelshyna, D. Gago, M.F.,  Bicho, E., Fernandes, V., Silva, H.D.,  Rodrigues, M.L., Rocha L., and Sousa, N.
Compensatory postural adjustments in Parkinson's disease assessed via a Virtual Reality environment
Behav Brain Res. 2015 Aug 21. pii: S0166-4328(15)30150-9. doi: 10.1016/j.bbr.2015.08.017.

Conference Proceedings

Agabi O., Marchand P., Mutlu M., Klotz L. and Schultz S.R.
Calcium imaging in temporal focus
Proceedings of the 6th International IEEE/EMBS Conference on Neural Engineering, San Diego, November 2013.

Jarvis S., Nikolic K., Grossman N. and Schultz S.R.
Controlling the neuronal balancing act: Optical coactivation of excitation and inhibition in neuronal subdomains
BMC Neuroscience 14 Suppl 1, P348. 2013 (Abstracts from CNS 2013 – Computational Neuroscience Meeting, July 2013)

Jarvis S., Nikolic K. and Schultz. S.R.
Optical coactivation in cortical cells: reprogramming the excitation-inhibition balancing act to control neuronal gain in abstract and detailed models.
Proceedings of the 23rd Annual Computational Neuroscience Conference. Quebec City 2014. BMC Neuroscience pp.-, in press.

Kappen H.J., Bierkens J.
A stochastic control mechanism for planning of goal directed behaviour
Proceedings of RLDM 2013, Princeton (Reinforcement Learning and Decision Making Meeting), October 2013.

Nikolic K., Jarvis S., Grossman N. and Schultz S.R.
Computational models of optogenetic tools for controlling neural circuits with light
Proceedings of the 35th Annual International Conference of the IEEE Engineering in Medicine & Biology Society (EMBC ’13), Osaka, Japan, July 2013, pp. 5934-7. 2013


Jarvis S., Grossman N., Schultz S.R. and Nikolic K.
Computational optogenetic models for controlling neural circuits with light
Ion Channels in Health and Disease: a symposium to celebrate the 50th anniversary of the Nobel Prize awarded to Alan Hodgkin and Andrew Huxley. 2013

Luccioli S., Olmi S., Politi A. and Torcini A.
Critical connectivity for emergence of collective oscillations in strongly diluted neural networks
BMC Neuroscience 14.Suppl 1 P394. 2013