[HTML][HTML] Continuing progress of spike sorting in the era of big data

D Carlson, L Carin - Current opinion in neurobiology, 2019 - Elsevier
Highlights•Novel devices are posing challenges to existing spike sorting pipelines.•Spike
sorting methodology is expanding to handle thousands to millions of neurons.•Multi-stage …

[HTML][HTML] Credibility, replicability, and reproducibility in simulation for biomedicine and clinical applications in neuroscience

L Mulugeta, A Drach, A Erdemir, CA Hunt… - Frontiers in …, 2018 - frontiersin.org
Modeling and simulation in computational neuroscience is currently a research enterprise to
better understand neural systems. It is not yet directly applicable to the problems of patients …

[HTML][HTML] NetPyNE, a tool for data-driven multiscale modeling of brain circuits

S Dura-Bernal, BA Suter, P Gleeson, M Cantarelli… - Elife, 2019 - elifesciences.org
Biophysical modeling of neuronal networks helps to integrate and interpret rapidly growing
and disparate experimental datasets at multiple scales. The NetPyNE tool (www. netpyne …

[HTML][HTML] Extremely scalable spiking neuronal network simulation code: from laptops to exascale computers

J Jordan, T Ippen, M Helias, I Kitayama… - Frontiers in …, 2018 - frontiersin.org
State-of-the-art software tools for neuronal network simulations scale to the largest
computing systems available today and enable investigations of large-scale networks of up …

[HTML][HTML] Modernizing the NEURON simulator for sustainability, portability, and performance

O Awile, P Kumbhar, N Cornu… - Frontiers in …, 2022 - frontiersin.org
The need for reproducible, credible, multiscale biological modeling has led to the
development of standardized simulation platforms, such as the widely-used NEURON …

Exploring phase–amplitude coupling from primary motor cortex-basal ganglia–thalamus network model

Y Yu, F Han, Q Wang - Neural Networks, 2022 - Elsevier
The purpose of this study is to develop a primary motor cortex (M1)-basal ganglia–thalamus
model capable of reproducing the physiological phenomenon of exaggerated phase …

[HTML][HTML] Data-driven multiscale model of macaque auditory thalamocortical circuits reproduces in vivo dynamics

S Dura-Bernal, EY Griffith, A Barczak, MN O'Connell… - Cell reports, 2023 - cell.com
We developed a detailed model of macaque auditory thalamocortical circuits, including
primary auditory cortex (A1), medial geniculate body (MGB), and thalamic reticular nucleus …

[HTML][HTML] Large-scale biophysically detailed model of somatosensory thalamocortical circuits in NetPyNE

FS Borges, JVS Moreira, LM Takarabe… - Frontiers in …, 2022 - frontiersin.org
The primary somatosensory cortex (S1) of mammals is critically important in the perception
of touch and related sensorimotor behaviors. In 2015, the Blue Brain Project (BBP) …

Optogenetic stimulation of primary motor cortex regulates beta oscillations in the basal ganglia: A Computational study

Y Yu, Y Fan, S Hou, Q Wang - Communications in Nonlinear Science and …, 2023 - Elsevier
The primary motor cortex (M1) contains interconnected and diverse layers that play an
important role in motor execution. In recent years, M1 has emerged as one of the hot targets …

[HTML][HTML] Multiscale model of primary motor cortex circuits predicts in vivo cell-type-specific, behavioral state-dependent dynamics

S Dura-Bernal, SA Neymotin, BA Suter, J Dacre… - Cell reports, 2023 - cell.com
Understanding cortical function requires studying multiple scales: molecular, cellular, circuit,
and behavioral. We develop a multiscale, biophysically detailed model of mouse primary …