JCR Articles

L.Zaldumbide, A. Erramuzpe, R. Guarch, R.l Pulido, J.M. Cortes and J.I. Lopez. Snail heterogeneity in clear cell renal cell carcinoma. BMC Cancer 16:194, 2016 [pdf] Background: Intratumor heterogeneity may be responsible of the unpredictable aggressive clinical behavior that some clear cell renal cell carcinomas display. This clinical uncertainty may be caused by insufficient sampling, leaving out of histological analysis foci of high grade tumor areas. Although molecular approaches are providing […]

S. Rodrigues, M. Desroches, M. Krupa, J.M. Cortes, T.J. Sejnowski and A.B. Ali. Time-coded neurotransmitter release at excitatory and inhibitory synapses. Proc Natl Acad Sci USA  113:E1108-15, 2016   [pdf] Communication between neurons at chemical synapses is regulated by hundreds of different proteins that control the release of neurotransmitter that is packaged in vesicles, transported to an active zone, and released when an input spike occurs. Neurotransmitter can also be released […]

Julia M. Kroos, Ibai Diez, Jesus M. Cortes, Sebastiano Stramaglia and Luca Gerardo Giorda. Geometry shapes propagation: assessing the presence and absence of cortical symmetries through a computational model of cortical spreading depression. Frontiers in Computational Neuroscience  10:6, 2016  [pdf] Cortical spreading depression (CSD), a depolarization wave which originates in the visual cortex and travels towards the frontal lobe, has been suggested to be one neural correlate of aura migraine. […]

T. A. Amor, R. Russo, I. Diez, P. Mudnal, M. Zirovich, S. Stramaglia, J. M. Cortes, L. de Arcangelis and D. R. Chialvo. Higher order statistics of brain resting activity and its relation with structural connectivity. EPL 111: 68007, 2015. [pdf] The brain exhibits a wide variety of spatiotemporal patterns of neuronal activity recorded using functional magnetic resonance imaging as the so-called blood-oxygenated-level– dependent (BOLD) signal. An active area of […]

A. Erramuzpe, G.J. Ortega, J. Pastor, R. G. de Sola, D. Marinazzo, S. Stramaglia and J.M. Cortes. Identification of redundant and synergetic circuits in triplets of electrophysiological data. Journal of Neural Engineering 12: 066007 , 2015 [pdf] [arxiv] Objective. Neural systems are comprised of interacting units, and relevant information regarding their function or malfunction can be inferred by analyzing the statistical dependencies between the activity of each unit. Whilst correlations […]

Alonso-Montes, I. Diez, L. Remaki, I. Escudero, B. Mateos, Y. Rosseel, D. Marianazzo, S. Stramaglia, Jesus M Cortes. Lagged and instantaneous dynamical influences related to brain structural connectivity. Frontiers in Psychology 6: 1024, 2015 [pdf] Contemporary neuroimaging methods can shed light on the basis of human neural and cognitive specializations, with important implications for neuroscience and medicine. Indeed, different MRI acquisitions provide different brain networks at the macroscale; whilst diffusion-weighted […]

I. Diez*, A. Erramuzpe*, I. Escudero, B. Mateos, D. Marinazzo, E. Sanz-Arigita, S. Stramaglia and J.M. Cortes (* Equal Contribution). Information flow between resting state networks. Brain Connectivity 5:554-564, 2015 [pdf] [arXiv:1505.03560] The resting brain dynamics self-organizes into a finite number of correlated patterns known as resting state networks (RSNs). It is well known that techniques like independent component analysis can separate the brain activity at rest to provide such […]

I. Diez*, P. Bonifazi*, I. Escudero, B. Mateos, M.A. Muñoz, S. Stramaglia and J.M. Cortes (* Equal first-author Contribution). A novel brain partition highlights the modular skeleton shared by structure and function. Scientific Reports 5:10532 , 2015. [pdf] arXiv:1410.7959v2 Elucidating the intricate relationship between brain structure and function, both in healthy and pathological conditions, is a key challenge for modern neuroscience. Recent technical and methodological progress in neuroimaging has helped […]

A. Erramuzpe, J. M. Encinas, A. Sierra, M. Maletic-Savatic, A.L. Brewster, Anne E. Anderson, S. Stramaglia, Jesus M. Cortes. F1000Research 4:144 , 2015 [pdf] Brain Functional Connectivity (FC) quantifies statistical dependencies between areas of the brain. FC has been widely used to address altered function of brain circuits in control conditions compared to different pathological states, including epilepsy, a major neurological disorder. However, FC also has the as yet unexplored […]

J.M. Cortes, D. Marinazzo and Miguel Angel Muñoz. Editorial for the Research Topic: Information based methods for neuroimaging: analyzing structure, function and dynamic. Frontiers in Neuroinformatics 8 (86), 2014 [pdf]

Sebastiano Stramaglia, Jesus M. Cortes, Daniele Marinazzo. Synergy and redundancy in the Granger causal analysis of dynamical networks. New Journal of Physics 16: 105003, 2014 [pdf] We analyze, by means of Granger causality (GC), the effect of synergy and redundancy in the inference (from time series data) of the information flow between subsystems of a complex network. While we show that fully conditioned GC (CGC) is not affected by synergy, […]

IM De la Fuente, JM Cortes, E Valero, M Desroches, S Rodrigues, I Malaina and L Martinez. On the dynamics of the Adenylate Energy System: Homeorhesis vs Homeostasis. Plos One 9: e108676, 2014 [pdf] Biochemical energy is the fundamental element that maintains both the adequate turnover of the biomolecular structures and the functional metabolic viability of unicellular organisms. The levels of ATP, ADP and AMP reflect roughly the energetic status […]

L. Zaldumbide, A. Erramuzpe, R. Guarch, J.M. Cortes and J.I. Lopez. Large (>3.8 cm) Clear Cell Renal Cell Carcinomas are Morphologically and Immunohistochemically Heterogeneous. Virchows Archives 466:61-66, 2015 [pdf] Heterogeneity is an inherent event to tumor development that is lately receiving much attention in oncologic research. The topic is being addressed primarily at the molecular level and results are promising. However, translation to practical medicine is still pending. Our intention […]

Veronica Maki-Marttunen*, Ibai Diez*, Jesus M. Cortes, Dante R. Chialvo and Mirta Villarreal (*Equal contribution). Disruption of transfer entropy and inter-hemispheric brain functional connectivity in patients with disorder of consciousness. Frontiers in Neuroinformatics 7:24, 2013 [pdf] Severe traumatic brain injury can lead to disorders of consciousness (DOC) characterized by deficit in conscious awareness and cognitive impairment including coma, vegetative state, minimally consciousness, and lock-in syndrome. Of crucial importance is to […]

Jesus M Cortes*, Mathieu Desroches*, Serafim Rodrigues*, Romain Veltz , Miguel A. Muñoz and Terrence J. Sejnowski (* Equal Contribution). Short-term synaptic plasticity in the deterministic Tsodyks-Markram model leads to unpredictable network dynamics. Proc Natl Acad Sci USA 110:16610-16615, 2013 [pdf] Short-term synaptic plasticity strongly affects the neural dynamics of cortical networks. The Tsodyks and Markram (TM) model for short-term synaptic plasticity accurately accounts for a wide range of physiological […]

D. Marinazzo, M. Pellicoro, Guo-Rong Wu, L. Angelini, J.M. Cortes and S. Stramaglia. Information Transfer and Criticality in the Ising Model on the Human Connectome. PLoS One 9: e93616, 2014 [pdf] We implement the Ising model on a structural connectivity matrix describing the brain at two different resolutions. Tuning the model temperature to its critical value, i.e. at the susceptibility peak, we find a maximal amount of total information transfer […]

Ildefonso M. de la Fuente, Jesus M. Cortes, David A. Pelta, Juan Veguillas. Attractor Metabolic Networks. PLoS One 8: e58284, 2013 [pdf] Background The experimental observations and numerical studies with dissipative metabolic networks have shown that cellular enzymatic activity self-organizes spontaneously leading to the emergence of a Systemic Metabolic Structure in the cell, characterized by a set of different enzymatic reactions always locked into active states (metabolic core) while the […]

J.M. Cortes, A. Lopez, R. Molina and A.K. Katsaggelos. Variational Bayesian localization of EEG sources with generalized Gaussian priors. EPJ-Plus 127: 140, 2012 [pdf] Front cover [pdf] Although in the last decades the use of Magnetic Resonance Imaging has grown in popularity as a tool for the structural analysis of the brain, including MRI, fMRI and recently DTI, the ElectroEncephaloGraphy (EEG) is still-today an interesting technique for the understanding of […]

Jorge Hidalgo, Luis F Seoane, Jesus M Cortes and Miguel A Munoz. Stochastic amplification of fluctuations in cortical up-states. PLoS ONE 7: e40710, 2012 [pdf] Cortical neurons are bistable; as a consequence their local field potentials can fluctuate between quiescent and active states, generating slow 0.5-2 Hz oscillations which are widely known as transitions between Up and Down States. Despite a large number of studies on Up-Down transitions, deciphering its […]

Ildefonso M. De la Fuente, Jesus M. Cortes, Martin-Blas Perez-Pinilla, Vicente Ruiz-Rodriguez and Juan Veguillas. The metabolic core and catalytic switches are fundamental elements in the self-regulation of the Systemic Metabolic Structure of Cells. PLoS ONE 6:e27224, 2011 [pdf] Background. Experimental observations and numerical studies with dissipative metabolic networks have shown that cellular enzymatic activity self-organizes spontaneously leading to the emergence of a metabolic core formed by a set of […]

Ildefonso M. De la Fuente and Jesus M. Cortes. Quantitative analysis of the effective inter-enzyme connectivity in glycolysis. PLoS ONE 7:e30162, 2012 [pdf] Yeast glycolysis is considered the prototype of dissipative biochemical oscillator. In cellular conditions, under sinusoidal source of glucose, the activity of enzymes can display either periodic, quasi-periodic or chaotic behavior. By means of a system of non-linear differential equations with delay we have obtained different time series […]

J. M. Cortes, D. Marinazzo, P. Series, M.W. Oram, T.J. Sejnowski and M.C.W. van Rossum. The effect of neural adaptation on population coding accuracy. Journal of Computational Neuroscience 32:387-402, 2012 [pdf] Most neurons in the primary visual cortex initially respond vigorously when a preferred stimulus is presented, but adapt as stimulation continues. The functional consequences of adaptation are unclear. Typically a reduction of firing rate would reduce single neuron accuracy […]

J.M. Cortes, A. Greve, A. Barrett and M.C.W. van Rossum. Dynamics and Robustness of Familiarity Memory. Neural Computation 22: 448-466, 2010 [pdf] When presented with an item or a face, one might have a sense of recognition without the ability to recall when or where the stimulus has been encountered before. This sense of recognition is called familiarity memory. Following previous computational studies of familiarity memory, we investigate the dynamical […]

J.J. Torres, J. Marro, J.M. Cortes and B. Wemmenhove. Instabilities in attractor networks with fast synaptic fluctuations and partial updating of the neurons activity. Neural Networks 21: 1272-1277, 2008 [pdf] We present and study a probabilistic neural automaton in which the fraction of simultaneously-updated neurons is a parameter, rhoin(0,1). For small rho, there is relaxation towards one of the attractors and a great sensibility to external stimuli and, for rho […]

J. Marro, J.J. Torres and J.M. Cortes. Complex behavior in a network with time-dependent connections and silent nodes. Journal of Statistical Mechanics P02017, 2008 [pdf] We studied, both analytically and numerically, excitable networks in which connections are time-dependent and some of the nodes remain silent at each time step, and we show that these two features may induce intriguing functional complexity. More specifically, we consider (a) a heterogeneous distribution of […]

J.M.A.M. Kusters, J.M. Cortes, W.P.M. van Meerwijk, D.L. Ypey, A.P.R. Theuvenet and C.C.A.M. Gielen. Hysteresis and bi-stability by an interplay of calcium oscillations and action potential firing. Physical Review Letters 98: 098107, 2007. Nomination of PRL HighLights in the Magazine The Biological Physicist 7, April 2007 [pdf] Many cells reveal oscillatory behavior. Some cells reveal action-potential firing resulting from Hodgkin-Huxley (HH) type dynamics of ion channels in the cell membrane. […]

J. Marro, J.J. Torres and J.M. Cortes. Networks with Heterogeneously Weighted Connections and Partial Synchronization of Nodes. Computer Physics Communications 177: 180-183, 2007 [pdf] A network of stochastic nodes in which connections are heterogeneously weighted and dynamics may by varied from single-node updating to full synchronization as in familiar cellular automata is studied concerning computational strategies and states of attention in the brain.

J.J. Torres, J. M. Cortes, J. Marro and H.J. Kappen. Attractor Neural Networks with Activity-Dependent Synapses: The Role of Synaptic Facilitation. Neurocomputing 70: 2022-2025, 2007 [pdf] We studied an autoassociative neural network with dynamic synapses which include a facilitating mechanism. We have developed a general mean-field framework to study the relevance of the different parameters defining the dynamics of the synapses and their influence on the collective properties of the […]

J. Marro, J.J. Torres and J.M. Cortes. Chaotic hopping between attractors in neural automata. Neural Networks 20: 230-235, 2007 [pdf] We present a neurobiologically-inspired stochastic cellular automaton whose state jumps with time between the attractors corresponding to a series of stored patterns. The jumping varies from regular to chaotic as the model parameters are modified. The resulting irregular behavior, which mimics the state of attention in which a system shows […]

J.J. Torres, J.M. Cortes, J. Marro and H.J. Kappen. Competition between synaptic depression and facilitation in attractor neural networks. Neural Computation 19: 2739-2755, 2007 [pdf] We study the effect of competition between short-term synaptic depression and facilitation on the dynamic properties of attractor neural networks, using Monte Carlo simulation and a mean-field analysis. Depending on the balance of depression, facilitation, and the underlying noise, the network displays different behaviors, including […]