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Explore, find and read publications about NetPyNE or that make use of NetPyNE.

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Qian C

Condition Integration Memory Network: An Interpretation of the Meaning of the Neuronal Design
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arXiv preprint arXiv:2106
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5181
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Nguyen M, Vu D, Vo A, Liang L, Giabbanelli PJ

Preserving Simulation Insight While Removing Data: Verification of Compressed Simulation Traces via Machine Learning
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In2023 Annual Modeling and Simulation Conference (ANNSIM) 2023 May 23 (pp
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345-356)
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Delorme A, Truong D, Youn C, Sivagnanam S, Yoshimoto K, Poldrack RA, Majumdar A, Makeig S

NEMAR: An open access data, tools, and compute resource operating on NeuroElectroMagnetic data
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arXiv preprint arXiv:2203
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2568
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Ramanathan S, Ramasundaram M

Multilevel Neuron Model Construction Related to Structural Brain Changes Using Hypergraph
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InProgress in Advanced Computing and Intelligent Engineering 2021 (pp
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204-212)
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Jiang HJ, Qi G, Duarte R, Feldmeyer D, van Albada SJ

A Layered Microcircuit Model of Somatosensory Cortex with Three Interneuron Types and Cell-Type-Specific Short-Term Plasticity
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bioRxiv
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2023:2023-10
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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
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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
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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
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Nakajima R, Shirakami A, Tsumura H, Matsuda K, Nakamura E, Shimono M

Deep neural generation of neuronal spikes.
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bioRxiv
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2023:2023-03
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Johnsen KA, Cruzado NA, Willats AA, Rozell CJ

Cleo: a testbed for bridging model and experiment by simulating closed-loop stimulation, electrode recording, and optogenetics
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bioRxiv
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2023:2023-01
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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
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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
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Hu H, Hostetler RE, Agmon A

Ultrafast (400 Hz) network oscillations induced in mouse barrel cortex by optogenetic activation of thalamocortical axons
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Elife
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2023 May 9;12:e82412
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Birgiolas J, Haynes V, Gleeson P, Gerkin RC, Dietrich SW, Crook S

NeuroML-DB: Sharing and characterizing data-driven neuroscience models described in NeuroML
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PLoS computational biology
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2023 Mar 3;19(3):e1010941
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Angulo Salavarria MM, Dell’Amico C, D’Agostino A, Conti L, Onorati M

Cortico-thalamic development and disease: From cells, to circuits, to schizophrenia
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Frontiers in Neuroanatomy
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2023 Mar 2;17:1130797
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Iavarone E, Simko J, Shi Y, Bertschy M, García-Amado M, Litvak P, Kaufmann AK, O’Reilly C, Amsalem O, Abdellah M, Chevtchenko G

Thalamic control of sensory processing and spindles in a biophysical somatosensory thalamoreticular circuit model of wakefulness and sleep
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Cell Reports
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2023 Mar 28;42(3)
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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
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Wan W, Gao Z, Zhang Q, Gu Z, Chang C, Peng CK, Cui X

Resting state EEG complexity as a predictor of cognitive performance
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Physica A: Statistical Mechanics and its Applications
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2023 Jun 9:128952
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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)
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Cho S, Choi JH

A guide towards optimal detection of transient oscillatory bursts with unknown parameters
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Journal of Neural Engineering
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2023 Jun 20
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Protachevicz PR, da Silva Borges F, Batista AM, da Silva Baptista M, Caldas IL, Macau EE, Lameu EL

Plastic neural network with transmission delays promotes equivalence between function and structure
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Chaos, Solitons & Fractals
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2023 Jun 1;171:113480
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Flynn G, Brewster J, Song D, Gotsis M

Developing Brain-Computer Interfaces with Everyone
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Proceedings of the 16th International Conference on PErvasive Technologies Related to Assistive Environments
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2023 Jul 5
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Geerts H, Bergeler S, Lytton WW, van der Graaf PH

Computational neurosciences and quantitative systems pharmacology: a powerful combination for supporting drug development in neurodegenerative diseases
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Journal of Pharmacokinetics and Pharmacodynamics
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2023 Jul 28:1-1
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Dell’Amico C, D’Agostino A, Conti L, Onorati M

Cortico-thalamic development and disease: From cells, to circuits, to schizophrenia
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Frontiers in Neuroanatomy
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2023 Jan 1;17
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Cobb EA, Petroccione MA, Scimemi A

NRN-EZ: an application to streamline biophysical modeling of synaptic integration using NEURON
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Scientific Reports
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2023 Jan 10;13(1):464
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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
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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
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Haufler D, Ito S, Koch C, Arkhipov A

Simulations of cortical networks using spatially extended conductance‐based neuronal models
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The Journal of Physiology
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2023 Aug;601(15):3123-39
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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
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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
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Knight JC, Ramaswamy S, Girardi-Schappo M, Borges FS, Dura-Bernal S, Borges FS, Moreira JV, Takarabe LM, Lytton WW, Dura-Bernal S

Neuroscience, computing, performance, and benchmarks: Why it matters to neuroscience how fast we can compute
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OPEN ACCESS
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2023 Apr 26:331
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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
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Tolley N, Rodrigues PL, Gramfort A, Jones S

Methods and considerations for estimating parameters in biophysically detailed neural models with simulation based inference
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bioRxiv
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2023 Apr 17
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Strand, Hakon, Kristin Tondel

Estimating posterior distributions of synaptic strengths in a neural network using Approximate Bayesian Computation and Sequential Neural Posterior Estimation
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Norwegian University of Life Sciences
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2023
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Khan SS, Palmer B, Edelmaierd C, Aktulga HM

OpenRAND: A Performance Portable, Reproducible Random Number Generation Library for Parallel Computations
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arXiv preprint arXiv:2310
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2023
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Menier E, Kaltenbach S, Yagoubi M, Schoenauer M, Koumoutsakos P

Interpretable learning of effective dynamics for multiscale systems
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arXiv preprint arXiv:2309
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2023
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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
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Panagiotou S, Sidiropoulos H, Soudris D, Negrello M, Strydis C

EDEN: A high-performance, general-purpose, NeuroML-based neural simulator
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Frontiers in Neuroinformatics
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2022;16
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Gutierrez CE, Skibbe H, Musset H, Doya K

A Spiking Neural Network Builder for Systematic Data-to-Model Workflow
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Frontiers in Neuroinformatics
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2022;16
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Senk J, Kriener B, Djurfeldt M, Voges N, Jiang HJ, Schüttler L, Gramelsberger G, Diesmann M, Plesser HE, van Albada SJ

Connectivity concepts in neuronal network modeling
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PLOS Computational Biology
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2022 Sep 8;18(9):e1010086
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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
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De Schepper R, Geminiani A, Masoli S, Rizza MF, Antonietti A, Casellato C, D’Angelo E

Model simulations unveil the structure-function-dynamics relationship of the cerebellar cortical microcircuit
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Communications Biology
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2022 Nov 14;5(1):1-9
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Gupta S, Feldman JM, Newton AJ, Kuttippurathu L, Moss A, Schwaber JS, Vadigepalli R, Lytton WW

Biophysical Models of Minipig Right Atrial Ganglionic Plexus Principal Neurons Identified from Transcriptomics Data
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The FASEB Journal
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2022 May;36
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Sinha M, Narayanan R

Active Dendrites and Local Field Potentials: Biophysical Mechanisms and Computational Explorations
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neuroscience
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2022 May 1;489:111-42
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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
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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
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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
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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
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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
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Eriksson O, Bhalla US, Blackwell KT, Crook SM, Keller D, Kramer A, Linne ML, Saudargienė A, Wade RC, Kotaleski JH

Combining hypothesis-and data-driven neuroscience modeling in FAIR workflows
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Elife
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2022 Jul 6;11:e69013
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D’Angelo E, Jirsa V

The quest for multiscale brain modeling
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Trends in Neurosciences
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2022 Jul 27
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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
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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
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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
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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
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Wang C, Chen X, Zhang T, Wu S

BrainPy: a flexible, integrative, efficient, and extensible framework towards general-purpose brain dynamics programming
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bioRxiv
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2022 Jan 1
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Awile O, Kumbhar P, Cornu N, Dura-Bernal S, King JG, Lupton O, Magkanaris I, McDougal RA, Newton AJ, Pereira F, Savulescu A

Modernizing the NEURON simulator for sustainability, portability, and performance
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bioRxiv
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2022 Jan 1
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Hagen E, Magnusson SH, Ness TV, Halnes G, Babu PN, Linssen C, Morrison A, Einevoll GT

Brain signal predictions from multi-scale networks using a linearized framework
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bioRxiv
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2022 Jan 1
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Volk VL, Hines RM, Hines DJ, Fitzpatrick CK

CHAPTER FIVE: NEUROMUSCULOSKELETAL MOUSE HINDLIMB MODEL TO STUDY THE EFFECT OF NEURAL CHANGES IN INDIVIDUALS WITH …
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Boise State University
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2022 Aug:89
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Presigny C, Fallani FD

Colloquium: Multiscale modeling of brain network organization
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Reviews of Modern Physics
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2022 Aug 2;94(3):031002
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Huang C, Zeldenrust F, Celikel T

Cortical representation of touch in silico
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Neuroinformatics
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2022 Apr 29:1-27
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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
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Juvonen J

Pre-stimulus neuronal phase correlates of conscious visual perception in threshold stimuli detection tasks
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Aalto University
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2022
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Garcia-Rodriguez P, Davison AP, Sharma L, Appukuttan S.

Model descriptions in neuroscience: computational performance and collaboration
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HAL Open Science
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2022
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Masoli S, Rizza MF, Tognolina M, Prestori F, D�Angelo E

Computational models of neurotransmission at cerebellar synapses unveil the impact on network computation
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Frontiers in Computational Neuroscience
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2022
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Abrego AM, Khan W, Wright CE, Prajapati N, Islam MR, Ghajar MH, Bai X, Tandon N, Seymour JP

Sensing Local Field Potentials with a Directional and Scalable Depth Array: The DISC electrode
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bioRxiv
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2022
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Lazar AA, Liu T, Turkcan MK, Zhou Y

Accelerating with FlyBrainLab the discovery of the functional logic of the Drosophila brain in the connectomic and synaptomic era
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Elife
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2021;10
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Bonzanni M, Kaplan DL

On the prediction of neuronal microscale topology descriptors based on mesoscale recordings
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European Journal of Neuroscience
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2021 Sep;54(6):6147-67
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Shimoura RO, Pena RF, Lima V, Kamiji NL, Girardi-Schappo M, Roque AC

Building a model of the brain: from detailed connectivity maps to network organization
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The European Physical Journal Special Topics
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2021 Oct;230(14):2887-909
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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
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Cakan C, Jajcay N, Obermayer K

neurolib: a simulation framework for whole-brain neural mass modeling
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Cognitive Computation
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2021 Oct 12:1-21
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Spreizer S, Senk J, Rotter S, Diesmann M, Weyers B

NEST Desktop, an Educational Application for Neuroscience
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Eneuro
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2021 Nov;8(6)
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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
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Vieth M, Stöber TM, Triesch J

PymoNNto: A Flexible Modular Toolbox for Designing Brain-Inspired Neural Networks
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Frontiers in Neuroinformatics
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2021 Nov 1;15:715131
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Radev ST, D'Alessandro M, Mertens UK, Voss A, Köthe U, Bürkner PC

Amortized Bayesian model comparison with evidential deep learning
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IEEE Transactions on Neural Networks and Learning Systems
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2021 Nov 15
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Peng GC, Alber M, Buganza Tepole A, Cannon WR, De S, Dura-Bernal S, Garikipati K, Karniadakis G, Lytton WW, Perdikaris P, Petzold L

Multiscale modeling meets machine learning: What can we learn?
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Archives of Computational Methods in Engineering
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2021 May;28(3):1017-37
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Bloomingdale P, Karelina T, Cirit M, Muldoon SF, Baker J, McCarty WJ, Geerts H, Macha S

Quantitative systems pharmacology in neuroscience: Novel methodologies and technologies
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CPT: Pharmacometrics & Systems Pharmacology
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2021 May;10(5):412-9
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Amgalan A, Taylor P, Mujica-Parodi LR, Siegelmann HT

Unique scales preserve self-similar integrate-and-fire functionality of neuronal clusters
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Scientific Reports
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2021 Mar 5;11(1):1-0
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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
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Vuillaume R, Lorenzo J, Binczak S, Jacquir S

A Computational Study on Synaptic Plasticity Regulation and Information Processing in Neuron-Astrocyte Networks
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Neural Computation
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2021 Jun 11;33(7):1970-92
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Kwessi EA, Edwards LJ

Analysis of EEG data using complex geometric structurization
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Neural Computation
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2021 Jun 11;33(7):1942-69
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Alotaibi N, Maharatna K

Classification of autism spectrum disorder from EEG-based functional brain connectivity analysis
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Neural Computation
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2021 Jun 11;33(7):1914-41
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Zhang W, Li P

Skip-connected self-recurrent spiking neural networks with joint intrinsic parameter and synaptic weight training
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Neural Computation
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2021 Jun 11;33(7):1886-913
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Watanabe C, Kameoka H

X-DC: Explainable Deep Clustering Based on Learnable Spectrogram Templates
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Neural Computation
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2021 Jun 11;33(7):1853-85
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Bi W, Yang C, XueLian L, JunFu C

Lifelong classification in open world with limited storage requirements
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Neural Computation
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2021 Jun 11;33(7):1818-52
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Kim YJ, Brackbill N, Batty E, Lee J, Mitelut C, Tong W, Chichilnisky EJ, Paninski L

Nonlinear decoding of natural images from large-scale primate retinal ganglion recordings
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Neural Computation
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2021 Jun 11;33(7):1719-50
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Plenz D, Ribeiro TL, Miller SR, Kells PA, Vakili A, Capek EL

Self-organized criticality in the brain
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Frontiers in Physics
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2021 Jul 7;9:639389
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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
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Ribeiro TL, Chialvo DR, Plenz D

Scale-free dynamics in animal groups and brain networks
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Frontiers in Systems Neuroscience
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2021 Jan 20;14:591210
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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
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De Schepper R, Geminiani A, Masoli S, Rizza MF, Antonietti A, Casellato C, D’Angelo E

Scaffold modelling captures the structure-function-dynamics relationship in brain microcircuits
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bioRxiv
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2021 Jan 1
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Birgiolas J, Haynes V, Gleeson P, Gerkin RC, Dietrich SW, Crook SM

NeuroML-DB: Sharing and characterizing data-driven neuroscience models described in NeuroML
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bioRxiv
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2021 Jan 1
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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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2021 Aug 1;121:106841
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Silva AA

Modelagem de microcircuito neocortical explorando o modelo de rede de Potjans-Diesmann e neurônios multicompartimentais
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Universidade de Sao Paulo
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2021
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Podeus H

Neural response of a Neuron population: A mathematical modelling approach
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DiVA
event
2021
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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
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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
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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
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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
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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
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