Lab Publications
Parallel reaction-diffusion simulation in NEURON.
Society for Neuroscience 2015 (SFN '15).
(2015). Parallel Network Simulations with NEURON.
J. Computational Neuroscience. 6, 119-129.
(2006). Oscillations in Thalamic Interneurons.
snabs. 21, 12.5.
(1995). Optimizing synaptic conductance calculation for network simulations.
ncomp. 8, 501-510.
(1996). Optimizing computer models of layer 5 motor cortex pyramidal neurons using somatic whole-cell recordings.
Society for Neuroscience.
(2015). Optimizing computer models of corticospinal neurons to replicate in vitro dynamics.
J Neurophysiol. 117, 148-162.
(2017). Optimization by Adaptive Stochastic Descent.
PLOS ONE. 13, 1-16.
(2018). Open Source Brain: a collaborative resource for visualizing, analyzing, simulating and developing standardized models of neurons and circuits.
bioRxiv. 229484.
(2018). One size does not fit all: Calibrating microstimulation to individual subjects using spiking network models.
Society for Neuroscience 2014 (SFN '14).
(2014). Object-oriented reaction-diffusion modeling in the neuron simulator.
Society for Neuroscience 2011 (SFN '11).
(2011). Ntw-mt: A multi-threaded simulator for reaction diffusion simulations in neuron.
Proceedings of the 3rd ACM SIGSIM Conference on Principles of Advanced Discrete Simulation. 157–167.
(2015). Normalized cortical depth (NCD) as a primary coordinate system for cell connectivity in cortex: experiment and model.
Society for Neuroscience 2015 (SFN '15).
(2015).
(2018). Neuronal network bump attractors augmented by calcium up-regulation of Ih in a multiscale computer model of prefrontal cortex.
Society for Neuroscience 2015 (SFN '15).
(2015). Neuronal calcium wave propagation varies with changes in endoplasmic reticulum parameters: a computer model.
Neural Comput. 27, 898–924.
(2015). Neuron time warp.
Simulation Conference (WSC), 2014 Winter. 3447–3458.
(2014). Neural query system: data-mining from within the NEURON simulator.
Neuroinformatics. 4, 163-176.
(2006). Neural discoordination of hippocampus and prefrontal cortex spike trains in a phencyclidine schizophrenia-related animal model.
Society for Neuroscience 2009 (SFN '09).
(2009). Network-level effects of optogenetic stimulation in a computer model of macaque primary motor cortex.
BMC Neuroscience. 15, P107.
(2014). Network-level effects of optogenetic stimulation in a computer model of macaque primary motor cortex.
Computational Neuroscience Meeting (CNS 14').
(2014). Network-level coincidence detection in a computer simulation of primary motor cortex.
Society for Neuroscience 2013 (SFN '13).
(2013). NetPyNE, a tool for data-driven multiscale modeling of brain circuits.
eLife. 8, e44494.
(2019). NetPyNE: a Python package for NEURON to facilitate development and parallel simulation of biological neuronal networks.
Computational Neuroscience.
(2016). NetPyNE: a Python package for NEURON to facilitate development and parallel simulation of biological neuronal networks.
Computational Neuroscience Meeting (CNS 16').
(2016). NetPyNE: a high-level interface to NEURON to facilitate the development, parallel simulation and analysis of data-driven multiscale network models.
Computational Neuroscience Meeting (CNS 18').
(2018). NetPyNE: A GUI-based tool to build, simulate and analyze large-scale, data-driven network models in parallel NEURON.
Society for Neuroscience 2018 (SFN '18).
(2018). Neocortical simulation for epilepsy surgery guidance: localization and intervention.
(Bass, B., & Garbey M., Ed.).Computational Surgery and Dual Training. 339–349.
(2014). Muscarinic receptor mediated responses in thalamic local interneurons.
snabs. 22, 574.8.
(1996). Multithreaded Stochastic PDES for Reactions and Diffusions in Neurons.
ACM Transactions on Modeling and Computer Simulation (TOMACS). 27, 7.
(2017). Multitarget multiscale simulation for pharmacological treatment of dystonia in motor cortex.
Front Pharmacol. 7, 157.
(2016). Multiscale simulation of spreading depolarization in ischemic stroke.
Society for Neuroscience 2018 (SFN '18).
(2018). Multiscale modeling of multitarget pharmacotherapy for dystonia.
Computational Neuroscience Meeting (CNS 16').
(2016). Multiscale modeling of cortical information flow in Parkinson's disease.
Computational Neuroscience Meeting (CNS '13).
(2013). Multiscale modeling of brain disease.
Society for Neuroscience 2018 (SFN '18).
(2018). Multiscale modeling in the clinic: diseases of the brain and nervous system.
Brain Inform. 4, 219-230.
(2017). Multiscale modeling for clinical translation in neuropsychiatric disease.
J Comput Surgery. 1, 7.
(2014). Multiscale computer modeling of penumbral zones in brain ischemia.
Society for Neuroscience 2017 (SFN '17).
(2017).
(2015). Multimodal integration of micro-Doppler sonar and auditory signals for behavior classification with convolutional networks.
International Journal of Neural Systems. 23, 1350021.
(2013). Motor cortex neurons: from experiment to model via evolutionary algorithms.
Computational Neuroscience.
(2015). Motor cortex microcircuit simulation based on brain activity mapping.
Neural Comput. 26, 1239–1262.
(2014). Mosaic multiscale computer modeling of ischemic stroke.
Society for Neuroscience 2016 (SFN '16).
(2016). Modulation of virtual arm trajectories via microstimulation in a spiking model of sensorimotor cortex.
Computational Neuroscience Meeting (CNS '14). 15, P106.
(2014). Modulation of virtual arm trajectories via microstimulation in a spiking model of sensorimotor cortex.
BMC Neuroscience. 15, P106.
(2014). Modulation of stimulus fields in a computer model of the thalamocortical system.
Society for Neuroscience.
(2011). Modeling thalamocortical oscillations.
(Ulinski, P., Jones EG., & Peters A., Ed.).Cerebral Cortex. 13, 479-509.
(1999). Modeling pathogenesis and treatment response in childhood absence epilepsy.
Epilepsia. 59, 135–145.
(2018). Modeling network effects of dendritic plateau potentials in cortical pyramidal neurons.
Society for Neuroscience 2019 (SFN '19).
(2019). Modeling molecular pathways of neuronal ischemia.
Prog Mol Biol Transl Sci. 123, 249–275.
(2014). Modeling electrodiffusion with the NEURON reaction-diffusion module.
Society for Neuroscience 2017 (SFN '17).
(2017). Microconnectomics of primary motor cortex: a multiscale computer model.
Multiscale Modeling. National Institutes of Health.
(2015). A method for multi-simulator reaction-diffusion with NEURON.
Computational Neuroscience.
(2014). Measuring the quality of neuronal identification in ensemble recordings.
jnsci. 31, 16398–16409.
(2011).
(2017).
(2018).
Long-range inputs and H-current regulate different modes of operation in a multiscale model of mouse M1 microcircuits.
Society for Neuroscience 2017 (SFN '17).
(2017).
(1989). Local axon collaterals of area ca1 support spread of epileptiform discharges within CA1, but propagation is unidirectional.
Hippocampus. 18, 1021-1033.
(2008). Load balancing for multi-threaded PDES of stochastic reaction-diffusion in neurons.
J Simulation. 11, 267.
(2017). Large-scale M1 microcircuit model with plastic input connections from biological PMd neurons used for prosthetic arm control.
24th Annual Computational Neuroscience Meeting (CNS15).
(2015). Ketamine disrupts theta modulation of gamma in a computer model of hippocampus.
J Neurosci. 31, 11733-11743.
(2011). Just-in-time connectivity for very large neuronal networks.
Computational Neuroscience Meeting (CNS 07').
(2007). Just-in-time connectivity for large spiking networks.
ncomp. 20, 2745-2756.
(2008). An intrinsic oscillation in interneurons of the rat lateral geniculate nucleus.
jnphys. 81, 702-711.
(1999). Interlaminar Granger causality and alpha oscillations in a model of macaque cortex.
Computational Neuroscience.
(2011). Interlaminar feedback connections dominate in macaque inferotemporal cortex: in vivo and in silico studies.
Society for Neuroscience.
(2011). Interictal EEG Discoordination in a Rat Seizure Model.
J Clin Neurophysiol. 27, 438–444.
(2010). Interictal EEG discoordination in a rat seizure model.
Statistical Analysis of Neuronal Data.
(2010). Interfacing a biomimetic model of sensorimotor cortex with a musculoskeletal model and a robotic arm.
Society for Neuroscience 2013 (SFN '13).
(2013). Interfaces in multiscale reaction-diffusion models in the NEURON simulator.
Society for Neuroscience 2013 (SFN '13).
(2013). Integrating Systems Biology Markup Language (SBML) with NEURON.
Society for Neuroscience 2014 (SFN '14).
(2014). Integrating Systems Biology Markup Language (SBML) with NEURON.
Computational Neuroscience.
(2014). Input-to-output transformation in a model of the rat hippocampal CA1 network.
Front Comput Neurosci. 6, 57.
(2012). Inhibition Can Disrupt Hypersynchrony In Model Neuronal Networks.
Progress in neuro-psychopharmacology & biological psychiatry.
(1997). Information transmission vs processing in computer models of neocortical columns.
Society for Neuroscience 2009 (SFN '09).
(2009).