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1) Publications about NetPyNE
2) Publications that make use of NetPyNE
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Publications about NetPyNE

Dura-Bernal S, Suter B, Gleeson P, Cantarelli M, Quintana A, Rodriguez F, Kedziora DJ, Chadderdon GL, Kerr CC, Neymotin SA, McDougal R, Hines M, Shepherd GMG, Lytton WW

NetPyNE: a tool for data-driven multiscale modeling of brain circuits.
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eLife
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2019

Lytton WW, Seidenstein AH, Dura-Bernal S, McDougal RA, Schurmann F, Hines ML.

Simulation neurotechnologies for advancing brain research: Parallelizing large networks in NEURON.
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Neural Computation
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2016

Publications that make use of NetPyNE

Ahmed M, Campbell SA

Modelling the Effect of Allopregnanolone on the Resolution of Spike-Wave Discharges
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bioRxiv
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2023:2023-07

Zhao Z, Shirinpour S, Tran H, Wischnewski M, Opitz A

Intensity-and frequency-specific effects of transcranial alternating current stimulation are explained by network dynamics
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bioRxiv
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2023:2023-05

Wischnewski M, Tran H, Zhao Z, Shirinpour S, Haigh ZJ, Rotteveel J, Alekseichuk I, Zimmermann J, Opitz A

Induced neural phase precession through exogeneous electric fields
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bioRxiv
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2023:2023-03

Sagalajev B, Zhang T, Abdollahi N, Yousefpour N, Medlock L, Al-Basha D, Ribeiro-da-Silva A, Esteller R, Ratte S, Prescott SA

Paresthesia during spinal cord stimulation depends on synchrony of dorsal column axon activation
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bioRxiv
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2023:2023-01

Borges FS, Protachevicz PR, Souza DL, Bittencourt CF, Gabrick EC, Bentivoglio LE, Szezech Jr JD, Batista AM, Caldas IL, Dura-Bernal S, Pena RF

The Roles of Potassium and Calcium Currents in the Bistable Firing Transition
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Brain Sciences
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2023 Sep 20;13(9):1347

Ponzi A, Dura-Bernal S, Migliore M

Theta-gamma phase amplitude coupling in a hippocampal CA1 microcircuit
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PLOS Computational Biology
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2023 Mar 23;19(3):e1010942

Dura-Bernal S, Neymotin SA, Suter BA, Dacre J, Moreira JV, Urdapilleta E, Schiemann J, Duguid I, Shepherd GM, Lytton WW

Multiscale model of primary motor cortex circuits predicts in vivo cell-type-specific, behavioral state-dependent dynamics
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Cell Reports
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2023 Jun 27;42(6)

Yu Y, Fan Y, Hou S, Wang Q

Optogenetic stimulation of primary motor cortex regulates beta oscillations in the basal ganglia: A Computational study
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Communications in Nonlinear Science and Numerical Simulation
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2023 Feb 1;117:106918

Yu Y, Fan Y, Hou S, Wang Q

Optogenetic stimulation of primary motor cortex regulates beta oscillations in the basal ganglia: A Computational study
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Communications in Nonlinear Science and Numerical Simulation
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2023 Feb 1;117:106918

Ranieri CM, Moioli RC, Vargas PA, Romero RA

A neurorobotics approach to behaviour selection based on human activity recognition
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Cognitive Neurodynamics
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2023 Aug;17(4):1009-28

Yu Y, Han F, Wang Q

A hippocampal-entorhinal cortex neuronal network for dynamical mechanisms of epileptic seizure
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IEEE Transactions on Neural Systems and Rehabilitation Engineering
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2023 Apr 7

Berecki G, Bryson A, Polster T, Petrou S

Biophysical characterization and modelling of SCN1A gain-of-function predicts interneuron hyperexcitability and a predisposition to network instability through …
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Neurobiology of Disease
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2023 Apr 1;179:106059

Haşegan D, Deible M, Earl C, D’Onofrio D, Hazan H, Anwar H, Neymotin SA

Training spiking neuronal networks to perform motor control using reinforcement and evolutionary learning
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Frontiers in Computational Neuroscience
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2022;16

Ranieri CM, Moioli RC, Vargas PA, Romero RA

A neurorobotics approach to behaviour selection based on human activity recognition
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Cognitive Neurodynamics
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2022 Sep 27:1-20

Bok I, Haber I, Qu X, Hai A

In silico assessment of electrophysiological neuronal recordings mediated by magnetoelectric nanoparticles
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Scientific Reports
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2022 May 19;12(1):1-4

Caspi Y, Mazar M, Kushnir Y, Mazor Y, Katz B, Lev S, Binshtok AM

Structural plasticity of axon initial segment in spinal cord neurons underlies inflammatory pain
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PAIN
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2022 May 13:10-97

Anwar H, Caby S, Dura-Bernal S, D’Onofrio D, Hasegan D, Deible M, Grunblatt S, Chadderdon GL, Kerr CC, Lakatos P, Lytton WW

Training a spiking neuronal network model of visual-motor cortex to play a virtual racket-ball game using reinforcement learning
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Plos one
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2022 May 11;17(5):e0265808

Yu Y, Han F, Wang Q

Exploring phase–amplitude coupling from primary motor cortex-basal ganglia-thalamus network model
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Neural Networks
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2022 Jun 6

Zarei Eskikand P, Koussoulas K, Gwynne RM, Bornstein JC

Computational simulations and Ca2+ imaging reveal that slow synaptic depolarizations (slow EPSPs) inhibit fast EPSP evoked action potentials for most of …
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PLOS Computational Biology
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2022 Jun 13;18(6):e1009717

Haşegan D, Deible M, Earl C, D’Onofrio D, Hazan H, Anwar H, Neymotin SA

Evolutionary and spike-timing-dependent reinforcement learning train spiking neuronal network motor control
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bioRxiv
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2022 Jan 1:2021-11

Dura-Bernal S, Griffith EY, Barczak A, O’Connell MN, McGinnis T, Schroeder CE, Lytton WW, Lakatos P, Neymotin SA

Data-driven multiscale model of macaque auditory thalamocortical circuits reproduces in vivo dynamics
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bioRxiv
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2022 Jan 1

Borges FS, Moreira JV, Takarabe LM, Lytton WW, Dura-Bernal S

Large-scale biophysically detailed model of somatosensory thalamocortical circuits in NetPyNE
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bioRxiv
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2022 Jan 1

Dura-Bernal S, Neymotin SA, Suter BA, Dacre J, Schiemann J, Duguid I, Shepherd GM, Lytton WW

Multiscale model of primary motor cortex circuits reproduces in vivo cell type-specific dynamics associated with behavior
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bioRxiv
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2022 Jan 1

Medlock L, Sekiguchi K, Hong S, Dura-Bernal S, Lytton WW, Prescott SA

Multiscale computer model of the spinal dorsal horn reveals changes in network processing associated with chronic pain
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Journal of Neuroscience
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2022 Apr 13;42(15):3133-49

Bryson A, Berkovic SF, Petrou S, Grayden DB

State transitions through inhibitory interneurons in a cortical network model
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PLoS Computational Biology
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2021 Oct 15;17(10):e1009521

Volk VL, Hamilton LD, Hume DR, Shelburne KB, Fitzpatrick CK

Integration of neural architecture within a finite element framework for improved neuromusculoskeletal modeling
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Scientific Reports
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2021 Nov 26;11(1):1-0

Romaro C, Najman FA, Lytton WW, Roque AC, Dura-Bernal S

NetPyNE implementation and scaling of the Potjans-Diesmann cortical microcircuit model
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Neural computation
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2021 Jun 11;33(7):1993-2032

Pimentel JM, Moioli RC, De Araujo MF, Ranieri CM, Romero RA, Broz F, Vargas PA

Neuro4PD: An Initial Neurorobotics Model of Parkinson's Disease
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Frontiers in neurorobotics
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2021 Jul 1;15:640449

Hasegan D, Deible M, Earl C, D'Onofrio D, Hazan H, Anwar H, Neymotin SA

Multi-timescale biological learning algorithms train spiking neuronal network motor control
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bioRxiv
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2021 Jan 1

Ranieri CM, Pimentel JM, Romano MR, Elias LA, Romero RAF, Lones MA, Araujo MFP, Vargas PA, Moioli RC

A Data-Driven Biophysical Computational Model of Parkinson’s Disease Based on Marmoset Monkeys
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IEEE Access
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2021

Gao P, Graham J, Zhou W, Jang J, Angulo S, Dura-Bernal S, Hines ML, Lytton WW

Local Glutamate-Mediated Dendritic Plateau Potentials Change the State of the Cortical Pyramidal Neuron
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Journal of Neurophysiology
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2020

Neymotin, S.A., Daniels, D.S., Caldwell, B., McDougal, R.A., Carnevale, N.T., Jas, M., Moore, C.I., Hines, M.L., Hamalainen, M. and Jones, S.R.

Human Neocortical Neurosolver (HNN), a new software tool for interpreting the cellular and network origin of human MEG/EEG data
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eLife
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2020

Metzner C, Mäki-Marttunen T, Karni G, McMahon-Cole H, Steuber V

The Effect of Alterations of Schizophrenia-Associated Genes on Gamma Band Oscillations
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bioRxiv
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2020

Sivagnanam S, Gorman W, Doherty D, Neymotin S, Hovhannisyan H, Fang S, Lytton W, Dura-Bernal S

Simulating large-scale models of brain neuronal circuits using Google Cloud Platform
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Practice and Experience in Advanced Research Computing
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2020

Lytton WW, Sherif MA, Dura-Bernal S, Neymotin S

Multiscale modeling of a “mental” disease
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Virtual Physiological Human Conference
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2020

Dai K, Hernando J, Billeh YN, Gratiy SL, Planas J, Davison AP, et al.

The SONATA Data Format for Efficient Description of Large-Scale Network Models
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PLoS Comput Biol
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2020

Gleeson P, Cantarelli M, Quintana A, Earnsah M, Piasini E, Birgiolas J, Cannon RC, Cayco- Gajic A, Crook S, Davison AP, Dura-Bernal S, et al.

Open Source Brain: a collaborative resource for visualizing, analyzing, simulating and developing standardized models of neurons and circuits
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Neuron
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2019

Dura-Bernal S, Neymotin SA, Suter BA, Shepherd GMG, Lytton WW

Multiscale dynamics and information flow in a data-driven model of the primary motor cortex microcircuit
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bioRxiv
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2019

Gerkin, R.C., Birgiolas, J., Jarvis, R.J., Omar, C. and Crook, S.M.

NeuronUnit: A package for data-driven validation of neuron models using SciUnit
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bioRxiv
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2019

Dura-Bernal S, Neymotin SA, Suter BA, Shepherd GMG, Lytton WW

Long-range inputs and H-current regulate different modes of operation in a multiscale model of mouse M1 microcircuits
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bioRxiv
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2018

Terra HD, Borges FD, Moraes MF, Cota VR

Implementation of Intra and Extracellular Nonperiodic Scale-Free Stimulation for the NEURON Simulator
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InLatin American Workshop on Computational Neuroscience 2022 (pp
event
119-131)

Publications that cite NetPyNE

Gast, R., Rose, D., Salomon, C., Möller, H.E., Weiskopf, N. and Knösche, T.R..

PyRates—A Python framework for rate-based neural simulations.
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PLoS ONE
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2019

Alber M, Buganza A, Cannon W, De S, Dura-Bernal S, Garikipati K, Karmiadakis G, Lytton W, Perdikaris P, Petzold L, Kuhl E.

Integrating Machine Learning and Multiscale Modeling: Perspectives, Challenges, and Opportunities in the Biological, Biomedical, and Behavioral Sciences.
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Nature Partner Journals (npj) Digital Medicine
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2019

Tejada J, Roque AC,

Conductance-based models and the fragmentation problem: A case study based on hippocampal CA1 pyramidal cell models and epilepsy
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Epilepsy & Behavior
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2019

Spreizer S, Senk J, Rotter S, Diesmann M, Weyers,

NEST Desktop, an Educational Application for Neuroscience
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eNeuro
event
2021

Tran, H., Ranta, R., Le Cam, S. and Louis-Dorr, V.,

Fast simulation of extracellular action potential signatures based on a morphological filtering approximation.
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Journal of Computational Neuroscience
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2020

Billeh, Y.N., Cai, B., Gratiy, S.L., Dai, K., Iyer, R., Gouwens, N.W., Abbasi-Asl, R., Jia, X., Siegle, J.H., Olsen, S.R. and Koch, C.,.

Systematic integration of structural and functional data into multi-scale models of mouse primary visual cortex.
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Neuron
event
2020

Amsalem, O., Eyal, G., Rogozinski, N., Gevaert, M., Kumbhar, P., Schürmann, F. and Segev, I.,

An efficient analytical reduction of detailed nonlinear neuron models.
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Nature Communications
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2020