Pena Lab Computational Neuroscience Lab

Research

Check it out: our fly brain simulation using the VNC connectome: https://www.flybrian.com/

Highlighted

The Drosophila connectome reveals Axo-Axonic Synapses on Descending Neurons.
The Drosophila connectome reveals Axo-Axonic Synapses on Descending Neurons.
Cesar Ceballos, Juan Lopez, Ty Roachford, Diana Sanchez, Sebastián Jara, Kali Robbins, Chelsie L Spencer, Richard Murphey, Rodrigo F O Pena
iScience   ·   15 May 2026   ·   isci:2026-ceballos-drosophila
This study presents a comprehensive analysis of the Drosophila connectome, identifying previously uncharacterized axo-axonic synapses on descending neurons. These findings provide new insights into the circuit organization and computational properties of descending motor pathways, advancing our understanding of how neural circuits control behavior in this model organism.

All

2026

The Drosophila connectome reveals Axo-Axonic Synapses on Descending Neurons.
The Drosophila connectome reveals Axo-Axonic Synapses on Descending Neurons.
Cesar Ceballos, Juan Lopez, Ty Roachford, Diana Sanchez, Sebastián Jara, Kali Robbins, Chelsie L Spencer, Richard Murphey, Rodrigo F O Pena
iScience   ·   15 May 2026   ·   isci:2026-ceballos-drosophila
This study presents a comprehensive analysis of the Drosophila connectome, identifying previously uncharacterized axo-axonic synapses on descending neurons. These findings provide new insights into the circuit organization and computational properties of descending motor pathways, advancing our understanding of how neural circuits control behavior in this model organism.
A benchmark of expert-level academic questions to assess AI capabilities.
A benchmark of expert-level academic questions to assess AI capabilities.
Center for AI Safety, Scale AI, Rodrigo F O Pena, Davide Scaramuzza
Nature   ·   28 Jan 2026   ·   nature:2026-ai-benchmark
This collaborative benchmark study evaluates the capabilities of advanced artificial intelligence systems using expert-level academic questions across multiple domains. The research provides a comprehensive assessment framework for understanding current AI capabilities and limitations, with implications for future AI development and deployment. The work has been featured in major news outlets including The New York Times and Reuters for its significance in evaluating AI advancement.
An in-silico investigation of induced target neural activity through simulation-based inference informed deep brain stimulation.
An in-silico investigation of induced target neural activity through simulation-based inference informed deep brain stimulation.
James Lee, Ty Roachford, Rodrigo F O Pena
FAU Research Journal   ·   01 Jan 2026   ·   faurj:2026-lee-dbs
This computational study investigates how deep brain stimulation can be optimized to induce target neural activity patterns using simulation-based inference. By leveraging detailed neural models and Bayesian inference techniques, the research demonstrates how in-silico approaches can inform DBS parameter selection and improve therapeutic outcomes for neurological conditions.

2025

Synaptic summation shapes information transfer in GABA-glutamate co-transmission.
Synaptic summation shapes information transfer in GABA-glutamate co-transmission.
Belle Krubitski, Cesar Ceballos, Ty Roachford, Rodrigo F O Pena
Cognitive Neurodynamics   ·   14 Nov 2025   ·   cogsneuro:2026-krubitski
This research investigates how synaptic summation mechanisms interact with GABA-glutamate co-transmission to shape information transfer in neural circuits. The findings reveal how dual neurotransmitter signaling and nonlinear summation dynamics contribute to the computational properties of neurons and network-level information processing.
Postsynaptic frequency filters shaped by the interplay of synaptic short-term plasticity and cellular time scales.
Postsynaptic frequency filters shaped by the interplay of synaptic short-term plasticity and cellular time scales.
Yugarshi Mondal, Victoria B Benito, Rodrigo F O Pena, Horacio G Rotstein
Journal of Computational Neuroscience   ·   29 Oct 2025   ·   jcn:2025-mondal
This study characterizes how postsynaptic neurons implement frequency filtering through the interaction of short-term synaptic plasticity and intrinsic cellular properties. The research demonstrates that these mechanisms work in concert to shape frequency-dependent responses, providing insights into how neural circuits selectively process information across different frequency bands.
PCT vs. FEP: a comparison between reorganization theory and Bayesian inference.
PCT vs. FEP: a comparison between reorganization theory and Bayesian inference.
Ty Roachford, Warren Mansell, Rodrigo F O Pena
Foundations   ·   27 Oct 2025   ·   foundations:2025-roachford
This theoretical analysis compares Perceptual Control Theory (PCT) with the Free Energy Principle (FEP), two major frameworks for understanding biological organization and adaptive behavior. The comparison reveals complementary insights and differences in how these theories explain neural and behavioral phenomena, with implications for computational neuroscience and theoretical biology.
Frazzled/DCC regulates gap junction formation at a Drosophila giant synapse.
Frazzled/DCC regulates gap junction formation at a Drosophila giant synapse.
Juan Lopez, Jennifer Boerner, Kali Robbins, Rodrigo F O Pena, Richard Murphey
eNeuro   ·   12 Oct 2025   ·   eneuro:2025-lopez
This study identifies the role of Frazzled/DCC in regulating gap junction formation at the giant synapse in Drosophila. The findings reveal molecular mechanisms controlling electrical synaptic connectivity, providing insights into how gap junctions are assembled and organized in neural circuits.
Astrocytic signatures in neuronal activity: a machine learning-based identification approach.
Astrocytic signatures in neuronal activity: a machine learning-based identification approach.
João Paulo Pirola, Paige DeForest, Paulo R Protachevicz, Lauren Fontenas, Rodrigo F Ferreira, Rodrigo F O Pena
Cognitive Neurodynamics   ·   11 Jun 2025   ·   cogsneuro:2025-pirola
This study develops machine learning approaches to identify signatures of astrocytic influence on neuronal activity patterns. The research demonstrates how glial-neuronal interactions shape neural dynamics and provides tools for detecting these interactions in recorded neural data, highlighting the importance of considering glia in computational neuroscience.
Interleaved single and bursting spiking resonance in neurons.
Interleaved single and bursting spiking resonance in neurons.
Cesar C Ceballos, Norberto Chadly, Eric Lowet, Rodrigo F O Pena
PLoS Computational Biology   ·   22 May 2025   ·   ploscompbio:2025-ceballos
This research reveals that neurons can exhibit distinct resonant properties in both single-spike and bursting modes. The findings demonstrate that neurons dynamically switch between different frequency-filtering regimes depending on their spiking pattern, providing new insights into how neural circuits encode and process information.
Consistent model selection for estimating functional interactions among stochastic neurons with variable-length memory.
Consistent model selection for estimating functional interactions among stochastic neurons with variable-length memory.
Rodrigo F Ferreira, Mariana E Pacola, Victor G Schiavone, Rodrigo F O Pena
Neurocomputing   ·   08 May 2025   ·   neurocomputing:2025-ferreira
This work develops methods for selecting appropriate models to estimate functional connectivity between neurons with variable memory properties. The research provides statistical tools for identifying effective interactions in stochastic neural systems, improving the accuracy of functional connectivity estimates from neural recordings.
Dendritic synaptic integration modes under in vivo-like states.
Dendritic synaptic integration modes under in vivo-like states.
Cesar C Ceballos, Rodrigo F O Pena
Biophysical Journal   ·   28 Apr 2025   ·   biophys:2025-ceballos-dendritic
This study investigates how dendrites integrate synaptic inputs under conditions that mimic in vivo neural activity. The research characterizes different modes of dendritic integration and how they depend on the state of neural activity, revealing dynamic changes in neuronal computation during behavior.
Approaching brain levels of organization with computational neuroscience.
Approaching brain levels of organization with computational neuroscience.
Fernando S Borges, Rodrigo F O Pena
PJS   ·   28 Mar 2025   ·   pjs:2025-borges
This perspective article discusses how computational neuroscience bridges different levels of biological organization, from molecular and cellular processes to network and systems-level phenomena. The work addresses the challenges and opportunities for developing multi-scale computational models that capture brain function across organizational levels.

2024

Identifying effective connectivity between stochastic neurons with variable-length memory using a transfer entropy rate estimator.
Identifying effective connectivity between stochastic neurons with variable-length memory using a transfer entropy rate estimator.
João V R Izzi, Rodrigo F Ferreira, Vitor A Girardi, Rodrigo F O Pena
Brain Sciences   ·   29 Apr 2024   ·   brainsci:2024-izzi
This work develops improved transfer entropy estimators for identifying effective connectivity in stochastic neural systems with variable memory properties. The research provides practical tools for analyzing information flow between neurons in complex neural networks, advancing methods for functional connectivity estimation from neural recordings.

2023

The Roles of Potassium and Calcium Currents in the Bistable Firing Transition.
The Roles of Potassium and Calcium Currents in the Bistable Firing Transition.
Fernando S Borges, Paulo R Protachevicz, Diogo L M Souza, Conrado F Bittencourt, Enrique C Gabrick, ..., Jose D Szezech, Antonio M Batista, Ibere L Caldas, Salvador Dura-Bernal, Rodrigo F O Pena
Brain Sciences   ·   20 Sep 2023   ·   pubmed:37645875
This study investigates brain firing patterns, specifically the shift from regular spiking to burst firing in cortical neurons. It focuses on the role of potassium and calcium ion channels under various conditions. Findings suggest that slow potassium currents are vital for high-synchronous activities and spike-to-burst transitions. Bistable dynamics in neuronal networks underlie this transition, offering insights for potential pharmacological interventions to move epileptic brains from pathological bursting to healthier states.
Theta and gamma rhythmic coding through two spike output modes in the hippocampus during spatial navigation.
Theta and gamma rhythmic coding through two spike output modes in the hippocampus during spatial navigation.
Eric Lowet, Daniel J Sheehan, Ulises Chialva, Rodrigo De Oliveira Pena, Rebecca A Mount, ..., Edward S Boyden, Jerome Mertz, Michael E Hasselmo, Horacio G Rotstein, Xue Han
Cell Reports   ·   29 Aug 2023   ·   pubmed:37540599
We examined how hippocampal neurons switch between generating single spikes and bursts of spikes and whether they convey different information. We found that burst spikes are associated with encoding an animal’s position as it enters a place field, linked to theta rhythms, while single spikes are related to exiting a place field and connected to gamma rhythms. These spiking patterns are influenced by the properties of neurons and input frequency, suggesting they perform distinct computations for spatial behavior.

2022

Temporal filters in response to presynaptic spike trains: interplay of cellular, synaptic and short-term plasticity time scales.
Temporal filters in response to presynaptic spike trains: interplay of cellular, synaptic and short-term plasticity time scales.
Yugarshi Mondal, Rodrigo F O Pena, Horacio G Rotstein
Journal of computational neuroscience   ·   23 Jul 2022   ·   pubmed:35869381
We investigate how neurons filter and code sensory inputs using temporal filters. Short-term plasticity (STP) and various processes influence these filters. We develop mathematical tools to understand their generation and extend the findings to complex networks.
Oscillations and variability in neuronal systems: interplay of autonomous transient dynamics and fast deterministic fluctuations.
Oscillations and variability in neuronal systems: interplay of autonomous transient dynamics and fast deterministic fluctuations.
Rodrigo F O Pena, Horacio G Rotstein
Journal of computational neuroscience   ·   02 Jun 2022   ·   pubmed:35653072
We investigate how rapidly fluctuating signals interact with neuronal properties, generating varied and coherent responses. Using linear and non-linear models, we explore the effects of piecewise constant inputs. We find that sustained oscillations and variability arise from the interaction between inputs and intrinsic cell dynamics, independent of input stochasticity.
The voltage and spiking responses of subthreshold resonant neurons to structured and fluctuating inputs: persistence and loss of resonance and variability.
The voltage and spiking responses of subthreshold resonant neurons to structured and fluctuating inputs: persistence and loss of resonance and variability.
Rodrigo F O Pena, Horacio G Rotstein
Biological cybernetics   ·   17 Jan 2022   ·   pubmed:35038010
We analyze neuronal responses to oscillatory currents and synaptic-like inputs. Resonant cells exhibit selective resonance. Conductance-based inputs are attenuated compared to current-based inputs. Variability arises from different input orderings. Poisson-distributed synaptic inputs show attenuated responses. Our findings contribute to understanding oscillatory activity and network resonance.

2020

Modeling Hippocampal CA1 Gabaergic Synapses of Audiogenic Rats.
Modeling Hippocampal CA1 Gabaergic Synapses of Audiogenic Rats.
Rodrigo F O Pena, Cesar Celis Ceballos, Júnia Lara De Deus, Antonio Carlos Roque, Norberto Garcia-Cairasco, Ricardo Maurício Leão, Alexandra Olimpio Siqueira Cunha
International journal of neural systems   ·   14 Apr 2020   ·   pubmed:32285725
WARs, genetically susceptible to sound-induced seizures, exhibit different GABAergic inhibitory postsynaptic current (IPSC) distributions compared to Wistar rats. Our computational model suggests two populations of GABAergic synapses in WARs, with reduced release frequency in a subset. This finding may contribute to their seizure susceptibility.
Optimal Interplay between Synaptic Strengths and Network Structure Enhances Activity Fluctuations and Information Propagation in Hierarchical Modular Networks.
Optimal Interplay between Synaptic Strengths and Network Structure Enhances Activity Fluctuations and Information Propagation in Hierarchical Modular Networks.
Rodrigo F O Pena, Vinicius Lima, Renan O Shimoura, Joao Paulo Novato, Antonio C Roque
Brain sciences   ·   10 Apr 2020   ·   pubmed:32290351
We study activity propagation in modular spiking networks. Optimal information flow occurs with increased synaptic strength or number of modules. Population-level and pairwise information propagation show different patterns. Increasing synaptic strength and modules enhance information transmission.

2019

Asymmetrical voltage response in resonant neurons shaped by nonlinearities.
Asymmetrical voltage response in resonant neurons shaped by nonlinearities.
R F O Pena, V Lima, R O Shimoura, C C Ceballos, H G Rotstein, A C Roque
Chaos (Woodbury, N.Y.)   ·   01 Oct 2019   ·   pubmed:31675799
High-amplitude oscillatory currents induce asymmetric voltage responses in neurons due to nonlinearities in ionic currents and the voltage equation. Geometrical factors and time-scale separation contribute to these asymmetries. Surprising frequency-dependent patterns emerge in the gating variables of the currents. Our findings shed light on the ionic mechanisms involved in oscillatory information processing by neurons.

2018

Firing properties of ventral medullary respiratory neurons in sino-aortic denervated rats.
Firing properties of ventral medullary respiratory neurons in sino-aortic denervated rats.
Mateus R Amorim, Rodrigo F O Pena, George M P R Souza, Leni G H Bonagamba, Antônio C Roque, Benedito H Machado
Experimental physiology   ·   11 Dec 2018   ·   pubmed:30427561
Sino-aortic denervation (SAD) in rats alters breathing patterns without affecting sympathetic activity or arterial pressure. We observed prolonged inspiration, increased variability in late-inspiratory neurons, and reduced frequency in pre-inspiratory/inspiratory neurons. These findings suggest a timing imbalance in the respiratory network of SAD rats, impacting presympathetic neuron modulation after baroreceptor afferent removal.
Intrinsic and synaptic properties of hippocampal CA1 pyramidal neurons of the Wistar Audiogenic Rat (WAR) strain, a genetic model of epilepsy.
Intrinsic and synaptic properties of hippocampal CA1 pyramidal neurons of the Wistar Audiogenic Rat (WAR) strain, a genetic model of epilepsy.
Alexandra Olimpio Siqueira Cunha, Cesar Celis Ceballos, Júnia Lara de Deus, Rodrigo Felipe de Oliveira Pena, José Antonio Cortes de Oliveira, Antonio Carlos Roque, Norberto Garcia-Cairasco, Ricardo Maurício Leão
Scientific reports   ·   10 Jul 2018   ·   pubmed:29991737
In our study on epilepsy, we examined the electrical properties and synaptic transmission in CA1 pyramidal neurons of the dorsal hippocampus in a genetic model, the Wistar Audiogenic Rat (WARs). We found reduced GABAergic neurotransmission in the dorsal hippocampus of WARs, leading to increased susceptibility to limbic seizures observed during audiogenic kindling.
Dynamics of spontaneous activity in random networks with multiple neuron subtypes and synaptic noise : Spontaneous activity in networks with synaptic noise.
Dynamics of spontaneous activity in random networks with multiple neuron subtypes and synaptic noise : Spontaneous activity in networks with synaptic noise.
Rodrigo F O Pena, Michael A Zaks, Antonio C Roque
Journal of computational neuroscience   ·   19 Jun 2018   ·   pubmed:29923159
We studied spontaneous cortical population activity in networks of spiking neurons. By adjusting inhibitory synaptic strength and synaptic noise, we identified different activity patterns. Noise transformed transient patterns into persistent ones. Networks with strong inhibition and moderate noise showed intermittent switches between oscillatory and quiescent states, resembling cortical states. Our findings reveal mechanisms underlying cortical activity at multiple scales.
Interplay of activation kinetics and the derivative conductance determines resonance properties of neurons.
Interplay of activation kinetics and the derivative conductance determines resonance properties of neurons.
Rodrigo F O Pena, Cesar C Ceballos, Vinicius Lima, Antonio C Roque
Physical review. E   ·   01 Apr 2018   ·   pubmed:29758644
Resonance in neurons with hyperpolarization-activated current (Ih) is determined by the biophysical properties of Ih, specifically the derivative conductance (GDer) and current activation kinetics (τh). The presence and frequency of resonance are controlled by GDer and τh, and their increase leads to enhanced resonance. Voltage dependence of GDer makes resonance voltage-dependent. These findings provide insights into predicting and explaining resonance properties in neurons with Ih.
Self-Consistent Scheme for Spike-Train Power Spectra in Heterogeneous Sparse Networks.
Self-Consistent Scheme for Spike-Train Power Spectra in Heterogeneous Sparse Networks.
Rodrigo F O Pena, Sebastian Vellmer, Davide Bernardi, Antonio C Roque, Benjamin Lindner
Frontiers in computational neuroscience   ·   02 Mar 2018   ·   pubmed:29551968
We determine numerically from an iterative single-neuron simulation spontaneous cortical population activity in networks of spiking neurons with heterogeneous populations of different cellular and connection parameters.
Non-Decaying postsynaptics potentials and delayed spikes in hippocampal pyramidal neurons generated by a zero slope conductance created by the persistent Na
Non-Decaying postsynaptics potentials and delayed spikes in hippocampal pyramidal neurons generated by a zero slope conductance created by the persistent Na
Cesar C Ceballos, Rodrigo F O Pena, Antônio C Roque, Ricardo M Leão
Channels (Austin, Tex.)   ·   01 Jan 2018   ·   pubmed:29380651
The persistent sodium current (INaP) prolongs EPSP decay by increasing the membrane time constant. In the zero slope conductance region, non-decaying EPSPs are observed in CA1 hippocampal pyramidal cells. These EPSPs and delayed spikes are abolished by Na+ channel block and occur in response to small amplitude aEPSCs. This suggests that INaP enhances synaptic integration in distal dendritic regions.

2016

Mechanisms of Self-Sustained Oscillatory States in Hierarchical Modular Networks with Mixtures of Electrophysiological Cell Types.
Mechanisms of Self-Sustained Oscillatory States in Hierarchical Modular Networks with Mixtures of Electrophysiological Cell Types.
Petar Tomov, Rodrigo F O Pena, Antonio C Roque, Michael A Zaks
Frontiers in computational neuroscience   ·   23 Mar 2016   ·   pubmed:27047367
In a diverse neuron network, global activity fluctuates between intense periods and low levels, resembling cortical “up” and “down” states. The distribution of membrane recovery variable plays a key role in initiating and stopping activity. Neuron behavior is more influenced by the presynaptic environment than their formal types.

2014

Sustained oscillations, irregular firing, and chaotic dynamics in hierarchical modular networks with mixtures of electrophysiological cell types.
Sustained oscillations, irregular firing, and chaotic dynamics in hierarchical modular networks with mixtures of electrophysiological cell types.
Petar Tomov, Rodrigo F O Pena, Michael A Zaks, Antonio C Roque
Frontiers in computational neuroscience   ·   02 Sep 2014   ·   pubmed:25228879
The cerebral cortex exhibits spontaneous neural activity without external input. Using computer simulations, we studied the mechanisms behind this activity in hierarchical modular networks. Our models replicated experimental observations of irregular firing and oscillatory patterns. The activity duration depended on initial conditions and network characteristics, highlighting the impact of both structure and neuron types on cortical activity.