Lab Publications
Reaction-Diffusion in the NEURON Simulator.
Front Neuroinform. 7:28,
(2013). Reinforcement learning of 2-joint virtual arm reaching in computer model of sensorimotor cortex.
Neural Comput. 25, 3263–3293.
(2013). Synaptic scaling balances learning in a spiking model of neocortex.
Springer LNCS. 7824, 20–29.
(2013). Water-tight membranes from neuronal morphology files.
J Neurosci Methods. 220, 167–178.
(2013). Calcium regulation of HCN supports persistent activity associated with working memory: a multiscale model of prefrontal cortex.
BMC Neuroscience. 15, P108.
(2014). Color opponent receptive fields self-organize in a biophysical model of visual cortex via spike-timing dependent plasticity.
Front Neural Circuits. 8, 16.
(2014). Electrostimulation to reduce synaptic scaling driven progression of Alzheimer's disease.
Front Comput Neurosci. 8, 39.
(2014). Information flow in optogenetically stimulated macaque motor cortex: simulation and experiment.
Neural Control of Movement (NCM) meeting.
(2014). Modeling molecular pathways of neuronal ischemia.
Prog Mol Biol Transl Sci. 123, 249–275.
(2014). Modulation of virtual arm trajectories via microstimulation in a spiking model of sensorimotor cortex.
BMC Neuroscience. 15, P106.
(2014). Motor cortex microcircuit simulation based on brain activity mapping.
Neural Comput. 26, 1239–1262.
(2014). Multiscale modeling for clinical translation in neuropsychiatric disease.
J Comput Surgery. 1, 7.
(2014). Network-level effects of optogenetic stimulation in a computer model of macaque primary motor cortex.
BMC Neuroscience. 15, P107.
(2014). Thalamocortical dynamics of rhythmic selective and tonic suppressive modes in the auditory system.
Society for Neuroscience Abstracts. 44,
(2014). Towards a real-time interface between a biomimetic model of sensorimotor cortex and a robotic arm.
Pattern Recognit Lett. 36, 204–212.
(2014). Towards real-time communication between in vivo neurophysiological data sources and simulator-based brain biomimetic models.
Journal of Computational Surgery. 3, 12.
(2014). Computer modeling of ischemic stroke.
Scholarpedia. 10, 32015; revision \#148671; Accessed Oct 12, 2015.
(2015). Cortical spiking network interfaced with virtual musculoskeletal arm and robotic arm.
Frontiers in Neurorobotics. 9,
(2015). Impaired dendritic inhibition leads to epileptic activity in a computer model of CA3.
Hippocampus. in press.
(2015). Neuronal calcium wave propagation varies with changes in endoplasmic reticulum parameters: a computer model.
Neural Comput. 27, 898–924.
(2015). Calcium regulation of HCN channels supports persistent activity in a multiscale model of neocortex.
Neurosci. 316, 344-366.
(2016). Global dynamics of selective attention and its lapses in primary auditory cortex.
Nat Neurosci. In press.
(2016). Multitarget multiscale simulation for pharmacological treatment of dystonia in motor cortex.
Front Pharmacol. 7, 157.
(2016). Reproducibility in computational neuroscience models and simulations.
{IEEE} Trans Biomed Eng. 63, 2021-2035.
(2016). Restoring behavior via inverse neurocontroller in a lesioned cortical spiking model driving a virtual arm.
Front Neurosci. 10, 28.
(2016). Simulation neurotechnologies for advancing brain research: parallelizing large networks in NEURON.
Neural Comput. 28, 2063-2090.
(2016). Computer modeling for pharmacological treatments for dystonia.
Drug Discov Today: Dis Model. In Press.
(2017). Computer modeling of epilepsy: opportunities for drug discovery.
Drug Discov Today: Dis Model. In press.
(2017). Computer modeling of ischemic stroke.
Drug Discov Today: Dis Model. 30, In press.
(2017). Computers, causality and cure in epilepsy.
Brain. 140, 516-519.
(2017). Evolutionary algorithm optimization of biological learning parameters in a biomimetic neuroprosthesis.
IBM Journal of Research and Development. 61, 6–1.
(2017). Load balancing for multi-threaded PDES of stochastic reaction-diffusion in neurons.
J Simulation. 11, 267.
(2017). Measurement of peripheral vision reaction time identifies white matter disruption in patients with mild traumatic brain injury.
J Neurotrauma.
(2017). Multiscale modeling in the clinic: diseases of the brain and nervous system.
Brain Inform. 4, 219-230.
(2017). Multithreaded Stochastic PDES for Reactions and Diffusions in Neurons.
ACM Transactions on Modeling and Computer Simulation (TOMACS). 27, 7.
(2017). Optimizing computer models of corticospinal neurons to replicate in vitro dynamics.
J Neurophysiol. 117, 148-162.
(2017). Parallel Stochastic discrete event simulation of calcium dynamics in neuron..
IEEE/ACM transactions on computational biology and bioinformatics.
(2017). Tracking recurrence of correlation structure in neuronal recordings.
J Neurosci Methods. 275, 1-9.
(2017). Credibility, Replicability, and Reproducibility in Simulation for Biomedicine and Clinical Applications in Neuroscience.
Front. Neuroinform.. 12,
(2018). Embedded ensemble encoding hypothesis: The role of the ``Prepared'' cell.
J. Neurosci. Res..
(2018). Geppetto: a reusable modular open platform for exploring neuroscience data and models.
Phil. Trans. R. Soc. B. 373, 20170380.
(2018).
(2018). Modeling pathogenesis and treatment response in childhood absence epilepsy.
Epilepsia. 59, 135–145.
(2018). Open Source Brain: a collaborative resource for visualizing, analyzing, simulating and developing standardized models of neurons and circuits.
bioRxiv. 229484.
(2018). Optimization by Adaptive Stochastic Descent.
PLOS ONE. 13, 1-16.
(2018).
(2018). Using NEURON for reaction-diffusion modeling of extracellular dynamics.
Frontiers in Neuroinformatics.
(2018). Amyloid pathology–produced unexpected modifications of calcium homeostasis in hippocampal subicular dendrites.
Alzheimers. Dement..
(2019). NetPyNE, a tool for data-driven multiscale modeling of brain circuits.
eLife. 8, e44494.
(2019). Parallel Stochastic Discrete Event Simulation of Calcium Dynamics in Neuron.
IEEE/ACM Trans. Comput. Biol. Bioinform.. 16, 1007–1019.
(2019).