PubMed Mentions

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

Publication/References
NeuroMorpho.Org: a central resource for neuronal morphologies. Description: Ascoli, Giorgio A, et al. NeuroMorpho.Org: a central resource for neuronal morphologies. ''J Neurosci''. 2007 Aug 29; '''27''' (35):9247-51
L-Measure: a web-accessible tool for the analysis, comparison and search of digital reconstructions of neuronal morphologies. Description: Scorcioni, Ruggero, et al. L-Measure: a web-accessible tool for the analysis, comparison and search of digital reconstructions of neuronal morphologies. ''Nat Protoc''. 2008; '''3''' (5):866-76
NeuroMorpho.Org implementation of digital neuroscience: dense coverage and integration with the NIF. Description: Halavi, Maryam, et al. NeuroMorpho.Org implementation of digital neuroscience: dense coverage and integration with the NIF. ''Neuroinformatics''. 2008 Sep; '''6''' (3):241-52
NETMORPH: a framework for the stochastic generation of large scale neuronal networks with realistic neuron morphologies. Description: Koene, Randal A, et al. NETMORPH: a framework for the stochastic generation of large scale neuronal networks with realistic neuron morphologies. ''Neuroinformatics''. 2009 Sep; '''7''' (3):195-210
On comparing neuronal morphologies with the constrained tree-edit-distance. Description: Gillette, Todd A, et al. On comparing neuronal morphologies with the constrained tree-edit-distance. ''Neuroinformatics''. 2009 Sep; '''7''' (3):191-4
Feed-forward inhibition as a buffer of the neuronal input-output relation. Description: Ferrante, Michele, et al. Feed-forward inhibition as a buffer of the neuronal input-output relation. ''Proc Natl Acad Sci U S A''. 2009 Oct 20; '''106''' (42):18004-9
Local control of postinhibitory rebound spiking in CA1 pyramidal neuron dendrites. Description: Ascoli, Giorgio A, et al. Local control of postinhibitory rebound spiking in CA1 pyramidal neuron dendrites. ''J Neurosci''. 2010 May 5; '''30''' (18):6434-42
On the estimation of population-specific synaptic currents from laminar multielectrode recordings. Description: Gratiy, Sergey L, et al. On the estimation of population-specific synaptic currents from laminar multielectrode recordings. ''Front Neuroinform''. 2011; '''5''': 32
Axonal morphometry of hippocampal pyramidal neurons semi-automatically reconstructed after in vivo labeling in different CA3 locations. Description: Ropireddy, Deepak, et al. Axonal morphometry of hippocampal pyramidal neurons semi-automatically reconstructed after in vivo labeling in different CA3 locations. ''Brain Struct Funct''. 2011 Mar; '''216''' (1):1-15
Automated reconstruction of neuronal morphology: an overview. Description: Donohue, Duncan E, et al. Automated reconstruction of neuronal morphology: an overview. ''Brain Res Rev''. 2011 Jun 24; '''67''' (1-2):94-102
A computer model of unitary responses from associational/commissural and perforant path synapses in hippocampal CA3 pyramidal cells. Description: Baker, John L, et al. A computer model of unitary responses from associational/commissural and perforant path synapses in hippocampal CA3 pyramidal cells. ''J Comput Neurosci''. 2011 Aug; '''31''' (1):137-58
Know your current I(h): interaction with a shunting current explains the puzzling effects of its pharmacological or pathological modulations. Description: Migliore, Michele, et al. Know your current I(h): interaction with a shunting current explains the puzzling effects of its pharmacological or pathological modulations. ''PLoS One''. 2012; '''7''' (5):e36867
Morphology cluster and prediction of growth of human brain pyramidal neurons. Description: Yu, Chao, et al. Morphology cluster and prediction of growth of human brain pyramidal neurons. ''Neural Regen Res''. 2012 Jan 5; '''7''' (1):36-40
Potential connectomics complements the endeavour of 'no synapse left behind' in the cortex. Description: Ascoli, Giorgio A. Potential connectomics complements the endeavour of 'no synapse left behind' in the cortex. ''J Physiol''. 2012 Feb 15; '''590''' (4):651-2
Non-homogeneous stereological properties of the rat hippocampus from high-resolution 3D serial reconstruction of thin histological sections. Description: Ropireddy, D, et al. Non-homogeneous stereological properties of the rat hippocampus from high-resolution 3D serial reconstruction of thin histological sections. ''Neuroscience''. 2012 Mar 15; '''205''': 91-111
Functional impact of dendritic branch-point morphology. Description: Ferrante, Michele, et al. Functional impact of dendritic branch-point morphology. ''J Neurosci''. 2013 Jan 30; '''33''' (5):2156-65
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
Modulation of hippocampal rhythms by subthreshold electric fields and network topology. Description: Berzhanskaya, Julia, et al. Modulation of hippocampal rhythms by subthreshold electric fields and network topology. ''J Comput Neurosci''. 2013 Jun; '''34''' (3):369-89
Digital reconstruction and morphometric analysis of human brain arterial vasculature from magnetic resonance angiography. Description: Wright, Susan N, et al. Digital reconstruction and morphometric analysis of human brain arterial vasculature from magnetic resonance angiography. ''Neuroimage''. 2013 Nov 15; '''82''': 170-81
A simulation study on the effects of dendritic morphology on layer V prefrontal pyramidal cell firing behavior. Description: Psarrou, Maria, et al. A simulation study on the effects of dendritic morphology on layer V prefrontal pyramidal cell firing behavior. ''Front Cell Neurosci''. 2014; '''8''': 287
Dendritic diameters affect the spatial variability of intracellular calcium dynamics in computer models. Description: Anwar, Haroon, et al. Dendritic diameters affect the spatial variability of intracellular calcium dynamics in computer models. ''Front Cell Neurosci''. 2014; '''8''': 168
NeuroElectro: a window to the world's neuron electrophysiology data. Description: Tripathy, Shreejoy J, et al. NeuroElectro: a window to the world's neuron electrophysiology data. ''Front Neuroinform''. 2014; '''8''': 40
NeuronDepot: keeping your colleagues in sync by combining modern cloud storage services, the local file system, and simple web applications. Description: Rautenberg, Philipp L, et al. NeuronDepot: keeping your colleagues in sync by combining modern cloud storage services, the local file system, and simple web applications. ''Front Neuroinform''. 2014; '''8''': 55
Statistical analysis and data mining of digital reconstructions of dendritic morphologies. Description: Polavaram, Sridevi, et al. Statistical analysis and data mining of digital reconstructions of dendritic morphologies. ''Front Neuroanat''. 2014; '''8''': 138
An efficient and extendable python library to analyze neuronal morphologies. Description: Torben-Nielsen, Benjamin. An efficient and extendable python library to analyze neuronal morphologies. ''Neuroinformatics''. 2014 Oct; '''12''' (4):619-22
Axon-somatic back-propagation in detailed models of spinal alpha motoneurons. Description: Balbi, Pietro, et al. Axon-somatic back-propagation in detailed models of spinal alpha motoneurons. ''Front Comput Neurosci''. 2015; '''9''': 15
Doubling up on the fly: NeuroMorpho.Org Meets Big Data. Description: Nanda, Sumit, et al. Doubling up on the fly: NeuroMorpho.Org Meets Big Data. ''Neuroinformatics''. 2015 Jan; '''13''' (1):127-9
Quantitative arbor analytics: unsupervised harmonic co-clustering of populations of brain cell arbors based on L-measure. Description: Lu, Yanbin, et al. Quantitative arbor analytics: unsupervised harmonic co-clustering of populations of brain cell arbors based on L-measure. ''Neuroinformatics''. 2015 Jan; '''13''' (1):47-63
A neural mechanism for background information-gated learning based on axonal-dendritic overlaps. Description: Mainetti, Matteo, et al. A neural mechanism for background information-gated learning based on axonal-dendritic overlaps. ''PLoS Comput Biol''. 2015 Mar; '''11''' (3):e1004155
Exercises in Anatomy, Connectivity, and Morphology using Neuromorpho.org and the Allen Brain Atlas. Description: Chu, Philip, et al. Exercises in Anatomy, Connectivity, and Morphology using Neuromorpho.org and the Allen Brain Atlas. ''J Undergrad Neurosci Educ''. 2015 Spring; '''13''' (2):A95-A100
From Curves to Trees: A Tree-like Shapes Distance Using the Elastic Shape Analysis Framework. Description: Mottini, A, et al. From Curves to Trees: A Tree-like Shapes Distance Using the Elastic Shape Analysis Framework. ''Neuroinformatics''. 2015 Apr; '''13''' (2):175-91
The importance of metadata to assess information content in digital reconstructions of neuronal morphology. Description: Parekh, Ruchi, et al. The importance of metadata to assess information content in digital reconstructions of neuronal morphology. ''Cell Tissue Res''. 2015 Apr; '''360''' (1):121-7
Neuron encyclopaedia fires up to reveal brain secrets. Description: Shen, Helen. Neuron encyclopaedia fires up to reveal brain secrets. ''Nature''. 2015 Apr 2; '''520''' (7545):13-4
Towards the automatic classification of neurons. Description: Armananzas, Ruben, et al. Towards the automatic classification of neurons. ''Trends Neurosci''. 2015 May; '''38''' (5):307-18
Quantitative investigations of axonal and dendritic arbors: development, structure, function, and pathology. Description: Parekh, Ruchi, et al. Quantitative investigations of axonal and dendritic arbors: development, structure, function, and pathology. ''Neuroscientist''. 2015 Jun; '''21''' (3):241-54
Topological characterization of neuronal arbor morphology via sequence representation: II--global alignment. Description: Gillette, Todd A, et al. Topological characterization of neuronal arbor morphology via sequence representation: II--global alignment. ''BMC Bioinformatics''. 2015 Jul 4; '''16''': 209
Topological characterization of neuronal arbor morphology via sequence representation: I--motif analysis. Description: Gillette, Todd A, et al. Topological characterization of neuronal arbor morphology via sequence representation: I--motif analysis. ''BMC Bioinformatics''. 2015 Jul 10; '''16''': 216
Sharing Neuron Data: Carrots, Sticks, and Digital Records. Description: Ascoli, Giorgio A. Sharing Neuron Data: Carrots, Sticks, and Digital Records. ''PLoS Biol''. 2015 Oct; '''13''' (10):e1002275
Dendritic and Axonal Wiring Optimization of Cortical GABAergic Interneurons. Description: Anton-Sanchez, Laura, et al. Dendritic and Axonal Wiring Optimization of Cortical GABAergic Interneurons. ''Neuroinformatics''. 2016 Oct; '''14''' (4):453-64
Focal Local Field Potential Signature of the Single-Axon Monosynaptic Thalamocortical Connection. Description: Hagen, Espen, et al. Focal Local Field Potential Signature of the Single-Axon Monosynaptic Thalamocortical Connection. ''J Neurosci''. 2017 May 17; '''37''' (20):5123-5143
Revealing the distribution of transmembrane currents along the dendritic tree of a neuron from extracellular recordings. Description: Cserpan, Dorottya, et al. Revealing the distribution of transmembrane currents along the dendritic tree of a neuron from extracellular recordings. ''Elife''. 2017 Nov 17; '''6''':
Cross-Regional Gradient of Dendritic Morphology in Isochronically-Sourced Mouse Supragranular Pyramidal Neurons. Description: Holley, Zachary Logan, et al. Cross-Regional Gradient of Dendritic Morphology in Isochronically-Sourced Mouse Supragranular Pyramidal Neurons. ''Front Neuroanat''. 2018; '''12''': 103
The effects of model composition design choices on high-fidelity simulations of motoneuron recruitment and firing behaviors. Description: Allen, John M, et al. The effects of model composition design choices on high-fidelity simulations of motoneuron recruitment and firing behaviors. ''J Neural Eng''. 2018 Jun; '''15''' (3):036024
Large-scale Exploration of Neuronal Morphologies Using Deep Learning and Augmented Reality. Description: Li, Zhongyu, et al. Large-scale Exploration of Neuronal Morphologies Using Deep Learning and Augmented Reality. ''Neuroinformatics''. 2018 Oct; '''16''' (3-4):339-349
Morphological Neuron Classification Based on Dendritic Tree Hierarchy. Description: Cervantes, Evelyn Perez, et al. Morphological Neuron Classification Based on Dendritic Tree Hierarchy. ''Neuroinformatics''. 2019 Jan; '''17''' (1):147-161
New Features for Neuron Classification. Description: Hernandez-Perez, Leonardo A, et al. New Features for Neuron Classification. ''Neuroinformatics''. 2019 Jan; '''17''' (1):5-25
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
Database of literature derived cellular measurements from the murine basal ganglia. Description: Bjerke, Ingvild E, et al. Database of literature derived cellular measurements from the murine basal ganglia. ''Sci Data''. 2020 Jul 6; '''7''' (1):211
Organization of the inputs and outputs of the mouse superior colliculus. Description: Benavidez, Nora L, et al. Organization of the inputs and outputs of the mouse superior colliculus. ''Nat Commun''. 2021 Jun 28; '''12''' (1):4004
Benchmarking of tools for axon length measurement in individually-labeled projection neurons. Description: Rubio-Teves, Mario, et al. Benchmarking of tools for axon length measurement in individually-labeled projection neurons. ''PLoS Comput Biol''. 2021 Dec; '''17''' (12):e1009051
Quantitative neuronal morphometry by supervised and unsupervised learning. Description: Bijari, Kayvan, et al. Quantitative neuronal morphometry by supervised and unsupervised learning. ''STAR Protoc''. 2021 Dec 17; '''2''' (4):100867
Classical-Contextual Interactions in V1 May Rely on Dendritic Computations. Description: Jin, Lei, et al. Classical-Contextual Interactions in V1 May Rely on Dendritic Computations. ''Neuroscience''. 2022 May 1; '''489''': 234-250
The Neuron Phenotype Ontology: A FAIR Approach to Proposing and Classifying Neuronal Types. Description: Gillespie, Thomas H, et al. The Neuron Phenotype Ontology: A FAIR Approach to Proposing and Classifying Neuronal Types. ''Neuroinformatics''. 2022 Jul; '''20''' (3):793-809
An in vitro whole-cell electrophysiology dataset of human cortical neurons. Description: Howard, Derek, et al. An in vitro whole-cell electrophysiology dataset of human cortical neurons. ''Gigascience''. 2022 Nov 15; '''11''':
Altered synaptic plasticity at hippocampal CA1-CA3 synapses in Alzheimer's disease: integration of amyloid precursor protein intracellular domain and amyloid beta effects into computational models. Description: Dainauskas, Justinas J, et al. Altered synaptic plasticity at hippocampal CA1-CA3 synapses in Alzheimer's disease: integration of amyloid precursor protein intracellular domain and amyloid beta effects into computational models. ''Front Comput Neurosci''. 2023; '''17''': 1305169
Full-scale scaffold model of the human hippocampus CA1 area. Description: Gandolfi, Daniela, et al. Full-scale scaffold model of the human hippocampus CA1 area. ''Nat Comput Sci''. 2023 Mar; '''3''' (3):264-276
A guide to the BRAIN Initiative Cell Census Network data ecosystem. Description: Hawrylycz, Michael, et al. A guide to the BRAIN Initiative Cell Census Network data ecosystem. ''PLoS Biol''. 2023 Jun; '''21''' (6):e3002133
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
Integrin beta3 regulates apical dendritic morphology of pyramidal neurons throughout hippocampal CA3. Description: Handwerk, Christopher J, et al. Integrin beta3 regulates apical dendritic morphology of pyramidal neurons throughout hippocampal CA3. ''Hippocampus''. 2023 Aug; '''33''' (8):936-947
Neuronal branching is increasingly asymmetric near synapses, potentially enabling plasticity while minimizing energy dissipation and conduction time. Description: Desai-Chowdhry, Paheli, et al. Neuronal branching is increasingly asymmetric near synapses, potentially enabling plasticity while minimizing energy dissipation and conduction time. ''J R Soc Interface''. 2023 Sep; '''20''' (206):20230265
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
Topology recapitulates morphogenesis of neuronal dendrites. Description: Liao, Maijia, et al. Topology recapitulates morphogenesis of neuronal dendrites. ''Cell Rep''. 2023 Nov 28; '''42''' (11):113268
Evolution of Consciousness. Description: Georgiev, Danko D. Evolution of Consciousness. ''Life (Basel)''. 2023 Dec 27; '''14''' (1):
Biophysical modeling of the whole-cell dynamics of C. elegans motor and interneurons families. Description: Nicoletti, Martina, et al. Biophysical modeling of the whole-cell dynamics of C. elegans motor and interneurons families. ''PLoS One''. 2024; '''19''' (3):e0298105
Kinetics and functional consequences of BK channels activation by N-type Ca(2+) channels in the dendrite of mouse neocortical layer-5 pyramidal neurons. Description: Blomer, Laila Ananda, et al. Kinetics and functional consequences of BK channels activation by N-type Ca(2+) channels in the dendrite of mouse neocortical layer-5 pyramidal neurons. ''Front Cell Neurosci''. 2024; '''18''': 1353895
Hippocampome.org v2.0: a knowledge base enabling data-driven spiking neural network simulations of rodent hippocampal circuits. Description: Wheeler, Diek W, et al. Hippocampome.org v2.0: a knowledge base enabling data-driven spiking neural network simulations of rodent hippocampal circuits. ''bioRxiv''. 2024 Jan 8;
Hippocampome.org 2.0 is a knowledge base enabling data-driven spiking neural network simulations of rodent hippocampal circuits. Description: Wheeler, Diek W, et al. Hippocampome.org 2.0 is a knowledge base enabling data-driven spiking neural network simulations of rodent hippocampal circuits. ''Elife''. 2024 Feb 12; '''12''':
A Novel Method for Clustering Cellular Data to Improve Classification. Description: Wheeler, Diek W, et al. A Novel Method for Clustering Cellular Data to Improve Classification. ''ArXiv''. 2024 Mar 5;
Accelerating the continuous community sharing of digital neuromorphology data. Description: Tecuatl, Carolina, et al. Accelerating the continuous community sharing of digital neuromorphology data. ''bioRxiv''. 2024 Mar 18;
Gossamer: Scaling Image Processing and Reconstruction to Whole Brains. Description: Marrett, Karl, et al. Gossamer: Scaling Image Processing and Reconstruction to Whole Brains. ''bioRxiv''. 2024 Apr 9;
Functional specialization of hippocampal somatostatin-expressing interneurons. Description: Chamberland, Simon, et al. Functional specialization of hippocampal somatostatin-expressing interneurons. ''Proc Natl Acad Sci U S A''. 2024 Apr 23; '''121''' (17):e2306382121
Automated neuronal reconstruction with super-multicolour Tetbow labelling and threshold-based clustering of colour hues. Description: Leiwe, Marcus N, et al. Automated neuronal reconstruction with super-multicolour Tetbow labelling and threshold-based clustering of colour hues. ''Nat Commun''. 2024 Jun 25; '''15''' (1):5279
A strong direct link from the layer 3/4 border to layer 6 of cat primary visual cortex. Description: Martin, Kevan A C, et al. A strong direct link from the layer 3/4 border to layer 6 of cat primary visual cortex. ''Brain Struct Funct''. 2024 Jul; '''229''' (6):1397-1415
Synthesis of geometrically realistic and watertight neuronal ultrastructure manifolds for in silico modeling. Description: Abdellah, Marwan, et al. Synthesis of geometrically realistic and watertight neuronal ultrastructure manifolds for in silico modeling. ''Brief Bioinform''. 2024 Jul 25; '''25''' (5):
Ten simple rules for recognizing data and software contributions in hiring, promotion, and tenure. Description: Puebla, Iratxe, et al. Ten simple rules for recognizing data and software contributions in hiring, promotion, and tenure. ''PLoS Comput Biol''. 2024 Aug; '''20''' (8):e1012296
Learning meaningful representation of single-neuron morphology via large-scale pre-training. Description: Fan, Yimin, et al. Learning meaningful representation of single-neuron morphology via large-scale pre-training. ''Bioinformatics''. 2024 Sep 1; '''40''' (Suppl 2):ii128-ii136
DendroTweaks: An interactive approach for unraveling dendritic dynamics. Description: Makarov, Roman, et al. DendroTweaks: An interactive approach for unraveling dendritic dynamics. ''bioRxiv''. 2024 Sep 10;
Synaptic interactions between stellate cells and parvalbumin interneurons in layer 2 of the medial entorhinal cortex are organized at the scale of grid cell clusters. Description: Huang, Li-Wen, et al. Synaptic interactions between stellate cells and parvalbumin interneurons in layer 2 of the medial entorhinal cortex are organized at the scale of grid cell clusters. ''Elife''. 2024 Nov 1; '''12''':