PubMed Mentions

The links below are to publications on PubMed referring to NeuroML. This list is gathered weekly from PubMed automatically.

Publication/References
Spikes, synchrony, and attentive learning by laminar thalamocortical circuits. Description: Grossberg, Stephen, et al. Spikes, synchrony, and attentive learning by laminar thalamocortical circuits. ''Brain Res''. 2008 Jul 7; '''1218''': 278-312
Rapid desynchronization of an electrically coupled interneuron network with sparse excitatory synaptic input. Description: Vervaeke, Koen, et al. Rapid desynchronization of an electrically coupled interneuron network with sparse excitatory synaptic input. ''Neuron''. 2010 Aug 12; '''67''' (3):435-51
Burst firing versus synchrony in a gap junction connected olfactory bulb mitral cell network model. Description: O'Connor, Simon, et al. Burst firing versus synchrony in a gap junction connected olfactory bulb mitral cell network model. ''Front Comput Neurosci''. 2012; '''6''': 75
LFPy: a tool for biophysical simulation of extracellular potentials generated by detailed model neurons. Description: Linden, Henrik, et al. LFPy: a tool for biophysical simulation of extracellular potentials generated by detailed model neurons. ''Front Neuroinform''. 2013; '''7''': 41
Neuronal morphology goes digital: a research hub for cellular and system neuroscience. Description: Parekh, Ruchi, et al. Neuronal morphology goes digital: a research hub for cellular and system neuroscience. ''Neuron''. 2013 Mar 20; '''77''' (6):1017-38
Computational modeling of epilepsy for an experimental neurologist. Description: Holt, Abbey B, et al. Computational modeling of epilepsy for an experimental neurologist. ''Exp Neurol''. 2013 Jun; '''244''': 75-86
Improving collaboration by standardization efforts in systems biology. Description: Drager, Andreas, et al. Improving collaboration by standardization efforts in systems biology. ''Front Bioeng Biotechnol''. 2014; '''2''': 61
Bulbar microcircuit model predicts connectivity and roles of interneurons in odor coding. Description: Gilra, Aditya, et al. Bulbar microcircuit model predicts connectivity and roles of interneurons in odor coding. ''PLoS One''. 2015; '''10''' (5):e0098045
The role of markup for enabling interoperability in health informatics. Description: McKeever, Steve, et al. The role of markup for enabling interoperability in health informatics. ''Front Physiol''. 2015; '''6''': 152
Virtual Electrode Recording Tool for EXtracellular potentials (VERTEX): comparing multi-electrode recordings from simulated and biological mammalian cortical tissue. Description: Tomsett, Richard J, et al. Virtual Electrode Recording Tool for EXtracellular potentials (VERTEX): comparing multi-electrode recordings from simulated and biological mammalian cortical tissue. ''Brain Struct Funct''. 2015 Jul; '''220''' (4):2333-53
Modelling and Analysis of Electrical Potentials Recorded in Microelectrode Arrays (MEAs). Description: Ness, Torbjorn V, et al. Modelling and Analysis of Electrical Potentials Recorded in Microelectrode Arrays (MEAs). ''Neuroinformatics''. 2015 Oct; '''13''' (4):403-26
Anatomically Detailed and Large-Scale Simulations Studying Synapse Loss and Synchrony Using NeuroBox. Description: Breit, Markus, et al. Anatomically Detailed and Large-Scale Simulations Studying Synapse Loss and Synchrony Using NeuroBox. ''Front Neuroanat''. 2016; '''10''': 8
PyRhO: A Multiscale Optogenetics Simulation Platform. Description: Evans, Benjamin D, et al. PyRhO: A Multiscale Optogenetics Simulation Platform. ''Front Neuroinform''. 2016; '''10''': 8
NSDF: Neuroscience Simulation Data Format. Description: Ray, Subhasis, et al. NSDF: Neuroscience Simulation Data Format. ''Neuroinformatics''. 2016 Apr; '''14''' (2):147-67
Single Neuron Optimization as a Basis for Accurate Biophysical Modeling: The Case of Cerebellar Granule Cells. Description: Masoli, Stefano, et al. Single Neuron Optimization as a Basis for Accurate Biophysical Modeling: The Case of Cerebellar Granule Cells. ''Front Cell Neurosci''. 2017; '''11''': 71
Wiring variations that enable and constrain neural computation in a sensory microcircuit. Description: Tobin, William F, et al. Wiring variations that enable and constrain neural computation in a sensory microcircuit. ''Elife''. 2017 May 22; '''6''':
Basal Ganglia Neuromodulation Over Multiple Temporal and Structural Scales-Simulations of Direct Pathway MSNs Investigate the Fast Onset of Dopaminergic Effects and Predict the Role of Kv4.2. Description: Lindroos, Robert, et al. Basal Ganglia Neuromodulation Over Multiple Temporal and Structural Scales-Simulations of Direct Pathway MSNs Investigate the Fast Onset of Dopaminergic Effects and Predict the Role of Kv4.2. ''Front Neural Circuits''. 2018; '''12''': 3
Challenges in Reproducibility, Replicability, and Comparability of Computational Models and Tools for Neuronal and Glial Networks, Cells, and Subcellular Structures. Description: Manninen, Tiina, et al. Challenges in Reproducibility, Replicability, and Comparability of Computational Models and Tools for Neuronal and Glial Networks, Cells, and Subcellular Structures. ''Front Neuroinform''. 2018; '''12''': 20
Web-Based Interfaces for Virtual C. elegans Neuron Model Definition, Network Configuration, Behavioral Experiment Definition and Experiment Results Visualization. Description: Epelde, Gorka, et al. Web-Based Interfaces for Virtual C. elegans Neuron Model Definition, Network Configuration, Behavioral Experiment Definition and Experiment Results Visualization. ''Front Neuroinform''. 2018; '''12''': 80
c302: a multiscale framework for modelling the nervous system of Caenorhabditis elegans. Description: Gleeson, Padraig, et al. c302: a multiscale framework for modelling the nervous system of Caenorhabditis elegans. ''Philos Trans R Soc Lond B Biol Sci''. 2018 Sep 10; '''373''' (1758):
Geppetto: a reusable modular open platform for exploring neuroscience data and models. Description: Cantarelli, Matteo, et al. Geppetto: a reusable modular open platform for exploring neuroscience data and models. ''Philos Trans R Soc Lond B Biol Sci''. 2018 Sep 10; '''373''' (1758):
OpenWorm: overview and recent advances in integrative biological simulation of Caenorhabditis elegans. Description: Sarma, Gopal P, et al. OpenWorm: overview and recent advances in integrative biological simulation of Caenorhabditis elegans. ''Philos Trans R Soc Lond B Biol Sci''. 2018 Sep 10; '''373''' (1758):
NetPyNE, a tool for data-driven multiscale modeling of brain circuits. Description: Dura-Bernal, Salvador, et al. NetPyNE, a tool for data-driven multiscale modeling of brain circuits. ''Elife''. 2019 Apr 26; '''8''':
Open Source Brain: A Collaborative Resource for Visualizing, Analyzing, Simulating, and Developing Standardized Models of Neurons and Circuits. Description: Gleeson, Padraig, et al. Open Source Brain: A Collaborative Resource for Visualizing, Analyzing, Simulating, and Developing Standardized Models of Neurons and Circuits. ''Neuron''. 2019 Aug 7; '''103''' (3):395-411.e5
A Standards Organization for Open and FAIR Neuroscience: the International Neuroinformatics Coordinating Facility. Description: Abrams, Mathew Birdsall, et al. A Standards Organization for Open and FAIR Neuroscience: the International Neuroinformatics Coordinating Facility. ''Neuroinformatics''. 2021 Jan 27;
Multidimensional population activity in an electrically coupled inhibitory circuit in the cerebellar cortex. Description: Gurnani, Harsha, et al. Multidimensional population activity in an electrically coupled inhibitory circuit in the cerebellar cortex. ''Neuron''. 2021 May 19; '''109''' (10):1739-1753.e8
Two opposing hippocampus to prefrontal cortex pathways for the control of approach and avoidance behaviour. Description: Sanchez-Bellot, Candela, et al. Two opposing hippocampus to prefrontal cortex pathways for the control of approach and avoidance behaviour. ''Nat Commun''. 2022 Jan 17; '''13''' (1):339
NeuroML-DB: Sharing and characterizing data-driven neuroscience models described in NeuroML. Description: Birgiolas, Justas, et al. NeuroML-DB: Sharing and characterizing data-driven neuroscience models described in NeuroML. ''PLoS Comput Biol''. 2023 Mar; '''19''' (3):e1010941
Multiscale model of primary motor cortex circuits predicts in vivo cell-type-specific, behavioral state-dependent dynamics. Description: Dura-Bernal, Salvador, et al. Multiscale model of primary motor cortex circuits predicts in vivo cell-type-specific, behavioral state-dependent dynamics. ''Cell Rep''. 2023 Jun 27; '''42''' (6):112574
Online conversion of reconstructed neural morphologies into standardized SWC format. Description: Mehta, Ketan, et al. Online conversion of reconstructed neural morphologies into standardized SWC format. ''Nat Commun''. 2023 Nov 16; '''14''' (1):7429
Data-driven multiscale model of macaque auditory thalamocortical circuits reproduces in vivo dynamics. Description: Dura-Bernal, Salvador, et al. Data-driven multiscale model of macaque auditory thalamocortical circuits reproduces in vivo dynamics. ''Cell Rep''. 2023 Nov 28; '''42''' (11):113378