Lab Publications

Found 267 results
Author Title Type [ Year(Desc)]
2017
Neymotin, S., Suter BA., Dura-Bernal S., Shepherd GM., Migliore M., & Lytton WW. (2017).  Optimizing computer models of corticospinal neurons to replicate in vitro dynamics. J Neurophysiol. 117, 148-162.
Patoary, M. Nazrul Ish, Tropper C., McDougal R. A., Zhongwei L., & Lytton WW. (2017).  Parallel Stochastic discrete event simulation of calcium dynamics in neuron.. IEEE/ACM transactions on computational biology and bioinformatics.
Mcdougal, R. A., Newton A. J. H., Patoary M. N. I., Tropper C., Hines M. L., & Lytton WW. (2017).  Parallel stochastic spines in NEURON reaction-diffusion simulations. Society for Neuroscience 2017 (SFN '17).
Lytton, WW., Knox A., & Rosenthal J. J. C. (2017).  Site-directed mRNA editing of sodium channels has potential to alter neuronal firing and network dynamics: Computer models. Society for Neuroscience 2017 (SFN '17).
Neymotin, S., Talbot ZN., Jung JQ., Fenton AA., & Lytton WW. (2017).  Tracking recurrence of correlation structure in neuronal recordings. J Neurosci Methods. 275, 1-9.
2018
McDougal, R. A., Newton A. J. H., & Lytton W. W. (2018).  Building and visualizing reaction–diffusion simulations in NEURON. Computational Neuroscience Meeting (CNS 18').
Mcdougal, R. A., Newton A., Hines M. L., & Lytton WW. (2018).  Building, simulating, and visualizing reaction-diffusion models with NEURON's enhanced rxd module. Society for Neuroscience 2018 (SFN '18).
Mulugeta, L., Drach A., Erdemir A., Hunt C. A., Horner M., Ku J. P., et al. (2018).  Credibility, Replicability, and Reproducibility in Simulation for Biomedicine and Clinical Applications in Neuroscience. Front. Neuroinform.. 12,
Graham, J. W., Angulo S., Gao P. P., Dura-Bernal S., Sivagnanam S., Hines M.., et al. (2018).  Embedded ensemble encoding: A hypothesis for reconciling cortical coding strategies. Society for Neuroscience 2018 (SFN '18).
Antic, S. D., Hines M., & Lytton WW. (2018).  Embedded ensemble encoding hypothesis: The role of the ``Prepared'' cell. J. Neurosci. Res..
Newton, A. J. H., Seidenstein A. H., McDougal R. A., Hines M., & Lytton W. W. (2018).  Extracellular reaction–diffusion in the NEURON simulator: modeling ischemic stroke. Computational Neuroscience Meeting (CNS 18').
Neymotin, S., Sherif M. A., Jung J. Q., Kabariti J. J., & Lytton WW. (2018).  Genome-wide associations of schizophrenia studied with computer simulation. (Cutsuridis, V., Graham BP., Cobb S., & Vida I., Ed.).Hippocampal Microcircuits: A Computational Modeler's Resource Book. 2,
Cantarelli, M., Marin B., Quintana A., Earnshaw M., Gleeson P., Dura-Bernal S., et al. (2018).  Geppetto: a reusable modular open platform for exploring neuroscience data and models. Phil. Trans. R. Soc. B. 373, 20170380.
Doherty, D. W., Dura-Bernal S., Neymotin S. A., & Lytton WW. (2018).  Identifying avalanches in simulated mouse primary motor cortex (M1). Society for Neuroscience 2018 (SFN '18).
Tepper, Á., Sugi A., Lytton W. W., & Dura-Bernal S. (2018).  Implementation of Cmicrocircuits model in NetPyNE and exploration of the effect of neuronal/synaptic loss on memory recall. Computational Neuroscience Meeting (CNS 18').
Dura-Bernal, S., Neymotin S., Suter BA., Shepherd GMG., & Lytton WW. (2018).  Long-range inputs and H-current regulate different modes of operation in a multiscale model of mouse M1 microcircuits. bioRxiv.
Knox, A. T., Glauser T., Tenney J., Lytton WW., & Holland K. (2018).  Modeling pathogenesis and treatment response in childhood absence epilepsy. Epilepsia. 59, 135–145.
Lytton, WW. (2018).  Multiscale modeling of brain disease. Society for Neuroscience 2018 (SFN '18).
Newton, A., Seidenstein A. H., Hines M. L., Mcdougal R. A., & Lytton WW. (2018).  Multiscale simulation of spreading depolarization in ischemic stroke. Society for Neuroscience 2018 (SFN '18).
Dura-Bernal, S., Suter B. A., Quintana A., Cantarelli M., Gleeson P., Rodriguez F., et al. (2018).  NetPyNE: A GUI-based tool to build, simulate and analyze large-scale, data-driven network models in parallel NEURON. Society for Neuroscience 2018 (SFN '18).
Dura-Bernal, S., Gleeson P., Neymotin S., Suter B. A., Quintana A., Cantarelli M., et al. (2018).  NetPyNE: a high-level interface to NEURON to facilitate the development, parallel simulation and analysis of data-driven multiscale network models. Computational Neuroscience Meeting (CNS 18').
Dura-Bernal, S., Gleeson P., Kerr C., Graham J., Quintana A., & Lytton WW. (2018).  Neurosim-lab/netpyne: v0.7.7.
Gleeson, P., Cantarelli M., Marin B., Quintana A., Earnshaw M., Piasini E., et al. (2018).  Open Source Brain: a collaborative resource for visualizing, analyzing, simulating and developing standardized models of neurons and circuits. bioRxiv. 229484.
Kerr, C. C., Dura-Bernal S., Smolinski T. G., Chadderdon G. L., & Wilson D. P. (2018).  Optimization by Adaptive Stochastic Descent. PLOS ONE. 13, 1-16.
Gao, P., Graham J., Angulo S., Dura-Bernal S., Hines M., Lytton W. W., et al. (2018).  Recruitment of neurons into neural ensembles based on dendritic plateau potentials. Computational Neuroscience Meeting (CNS 18').
Gao, P. P., Graham J. W., Angulo S. L., Dura-Bernal S., Hines M. L., Lytton WW., et al. (2018).  Recruitment of neurons into neural ensembles based on dendritic plateau potentials. Society for Neuroscience 2018 (SFN '18).
Doherty, D., Sivagnanam S., Dura-Bernal S., & Lytton W. W. (2018).  Simulation of avalanches in mouse primary motor cortex (M1). Computational Neuroscience Meeting (CNS 18').
C Hunt, A., Erdemir A., Gabhann F. Mac, Lytton WW., Sander E. A., Transtrum M. K., et al. (2018).  The Spectrum of Mechanism-oriented Models for Explanations of Biological Phenomena.
Bernard, C. (2018).  Understanding epilepsy across spatial and time scales. Society for Neuroscience 2018 (SFN '18).
Newton, A. J. H., McDougal R. A., Hines M. L., & Lytton W. W. (2018).  Using NEURON for reaction-diffusion modeling of extracellular dynamics. Frontiers in Neuroinformatics.
2019
Angulo, S. L., Henzi T., Neymotin S. A., Suarez M. D., Lytton W. W., Schwaller B., et al. (2019).  Amyloid pathology–produced unexpected modifications of calcium homeostasis in hippocampal subicular dendrites. Alzheimers. Dement..
Doherty, D.. W., Dura-Bernal S.., & Lytton W.. W. (2019).  Computer models of mouse area M1 show avalanches for full model and subcircuits defined by layer or cell type. Society for Neuroscience 2019 (SFN '19).
Dura-Bernal, S., Neymotin S. A., Suter B. A., Kelley C., Tekin R., Shepherd G. M. G., et al. (2019).  Cross-frequency coupling and information flow in a multiscale model of M1 microcircuits. Society for Neuroscience (SFN'19).
Dura-Bernal, S., Griffith E. Y., Marczak A., O'Connell N., McGinnis T., Lytton W. W., et al. (2019).  Data-driven model of auditory thalamocortical system rhythms. Society for Neuroscience (SFN '19).
Kelley, C.., Dura-Bernal S.., Neymotin S.., & Lytton W.. W. (2019).  Dendritic resonance in a detailed model of pyramidal tract neuron of mouse primary motor cortex. Society for Neuroscience 2019 (SFN '19).
Newton, A.. J. H., Conte C.., Eggleston L.., Blasy E.., Hines M.. L., Lytton W.. W., et al. (2019).  Efficient in silico 3D intracellular neuron simulation. Society for Neuroscience 2019 (SFN '19).
Newton, A. J. H., Hines M. L., Lytton W. W., & McDougal R. A. (2019).  Homeostasis and spreading depolarization in multiscale simulation of ischemic stroke.. Society for Neuroscience 2018 (SFN '19).
Graham, J.. W., Gao P.. P., Dura-Bernal S.., Sivagnanam S.., Hines M.. L., Antic S.. D., et al. (2019).  Modeling network effects of dendritic plateau potentials in cortical pyramidal neurons. Society for Neuroscience 2019 (SFN '19).
Dura-Bernal, S., Suter B. A., Gleeson P., Cantarelli M., Quintana A., Rodriguez F., et al. (2019).  NetPyNE, a tool for data-driven multiscale modeling of brain circuits. eLife. 8, e44494.
Patoary, M. Nazrul Ish, Tropper C., McDougal R. A., Lin Z., & Lytton W. W. (2019).  Parallel Stochastic Discrete Event Simulation of Calcium Dynamics in Neuron. IEEE/ACM Trans. Comput. Biol. Bioinform.. 16, 1007–1019.
Dura-Bernal, S.., Neymotin S.. A., Suter B.. A., Kelley C.., Tekin R.., Shepherd G.. M., et al. (2019).  Response to simultaneous long-range inputs and oscillatory inputs in a multiscale model of M1 microcircuits. Society for Neuroscience 2019 (SFN '19).
Neymotin, S.. A., Barczak A.., Oconnell M.. N., Mcginnis T.., Markowitz N.., Espinal E.., et al. (2019).  Tracking rhythmicity of neural oscillations in the auditory thalamocortical system. Society for Neuroscience 2019 (SFN '19).