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  1. Article

    Open Access

    A pipeline for the retrieval and extraction of domain-specific information with application to COVID-19 immune signatures

    The accelerating pace of biomedical publication has made it impractical to manually, systematically identify papers containing specific information and extract this information. This is especially challenging ...

    Adam J. H. Newton, David Chartash, Steven H. Kleinstein… in BMC Bioinformatics (2023)

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  2. Article

    Open Access

    PLD3 affects axonal spheroids and network defects in Alzheimer’s disease

    The precise mechanisms that lead to cognitive decline in Alzheimer’s disease are unknown. Here we identify amyloid-plaque-associated axonal spheroids as prominent contributors to neural network dysfunction. Us...

    Peng Yuan, Mengyang Zhang, Lei Tong, Thomas M. Morse, Robert A. McDougal… in Nature (2022)

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  3. No Access

    Reference Work Entry In depth

    SenseLab: Integration of Multidisciplinary Neuroscience Data

    Gordon M. Shepherd, Thomas M. Morse… in Encyclopedia of Computational Neuroscience (2022)

  4. No Access

    Reference Work Entry In depth

    Deterministic Reaction-Diffusion Simulators

    Haroon Anwar, William W. Lytton… in Encyclopedia of Computational Neuroscience (2022)

  5. No Access

    Reference Work Entry In depth

    ModelDB

    Robert A. McDougal, Rixin Wang… in Encyclopedia of Computational Neuroscience (2022)

  6. No Access

    Reference Work Entry In depth

    NEURON Simulation Environment

    Michael Hines, Ted Carnevale… in Encyclopedia of Computational Neuroscience (2022)

  7. No Access

    Living Reference Work Entry In depth

    NEURON Simulation Environment

    Michael Hines, Ted Carnevale… in Encyclopedia of Computational Neuroscience

  8. No Access

    Living Reference Work Entry In depth

    Deterministic Reaction-Diffusion Simulators

    Haroon Anwar, William W. Lytton… in Encyclopedia of Computational Neuroscience

  9. No Access

    Article

    Automated Metadata Suggestion During Repository Submission

    Knowledge discovery via an informatics resource is constrained by the completeness of the resource, both in terms of the amount of data it contains and in terms of the metadata that exists to describe the data...

    Robert A. McDougal, Isha Dalal, Thomas M. Morse, Gordon M. Shepherd in Neuroinformatics (2019)

  10. Article

    Open Access

    26th Annual Computational Neuroscience Meeting (CNS*2017): Part 3

    Adam J. H. Newton, Alexandra H. Seidenstein, Robert A. McDougal… in BMC Neuroscience (2017)

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  11. No Access

    Article

    Load balancing for multi-threaded PDES of stochastic reaction-diffusion in neurons

    Chemical reactions and molecular diffusion in a neuron play an important role in the transmission of signals within a neuron. Discrete event stochastic simulation of the chemical reactions and diffusion provi...

    Zhongwei Lin, Carl Tropper, Yi** Yao, Robert A. Mcdougal… in Journal of Simulation (2017)

  12. No Access

    Article

    Twenty years of ModelDB and beyond: building essential modeling tools for the future of neuroscience

    Neuron modeling may be said to have originated with the Hodgkin and Huxley action potential model in 1952 and Rall’s models of integrative activity of dendrites in 1964. Over the ensuing decades, these approac...

    Robert A. McDougal, Thomas M. Morse, Ted Carnevale… in Journal of Computational Neuroscience (2017)

  13. Article

    Open Access

    Parallelizing large networks using NEURON-Python

    Alexandra H Seidenstein, Robert A McDougal, Michael L Hines… in BMC Neuroscience (2015)

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  14. No Access

    Article

    ModelView for ModelDB: Online Presentation of Model Structure

    ModelDB (modeldb.yale.edu), a searchable repository of source code of more than 950 published computational neuroscience models, seeks to promote model reuse...

    Robert A. McDougal, Thomas M. Morse, Michael L. Hines… in Neuroinformatics (2015)

  15. No Access

    Reference Work Entry In depth

    SenseLab: Integration of Multidisciplinary Neuroscience Data

    Gordon M. Shepherd, Thomas M. Morse… in Encyclopedia of Computational Neuroscience (2015)

  16. No Access

    Reference Work Entry In depth

    Deterministic Reaction-Diffusion Simulators

    William W. Lytton, Robert A. McDougal in Encyclopedia of Computational Neuroscience (2015)

  17. No Access

    Reference Work Entry In depth

    ModelDB

    Robert A. McDougal, Rixin Wang… in Encyclopedia of Computational Neuroscience (2015)

  18. Article

    Open Access

    A method for multi-simulator reaction-diffusion with NEURON

    Robert A McDougal, Michael L Hines, William W Lytton in BMC Neuroscience (2014)

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  19. Article

    Open Access

    Calcium regulation of HCN supports persistent activity associated with working memory: a multiscale model of prefrontal cortex

    Samuel A Neymotin, Robert A McDougal, Michael Hines, William W Lytton in BMC Neuroscience (2014)

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  20. Article

    Open Access

    Integrating Systems Biology Markup Language(SBML) with NEURON

    Anna S Bulanova, Robert A McDougal, Samuel A Neymotin, Victor K Mutai… in BMC Neuroscience (2014)

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