2024
Chemical entity normalization for successful translational development of Alzheimer’s disease and dementia therapeutics
Mullin S, McDougal R, Cheung K, Kilicoglu H, Beck A, Zeiss C. Chemical entity normalization for successful translational development of Alzheimer’s disease and dementia therapeutics. Journal Of Biomedical Semantics 2024, 15: 13. PMID: 39080729, PMCID: PMC11290083, DOI: 10.1186/s13326-024-00314-1.Peer-Reviewed Original ResearchConceptsEntity normalizationChemical mentionsNatural language modelDictionary-based methodsDictionary-based approachCRAFT corpusDownstream tasksLanguage modelChemical Entities of Biological InterestPubMedBERT modelDisambiguationChEBIDownstream applicationsArticle abstractsRelationship typesMentionsPubMedBERTOntologyDementia literatureTaskDementia CohortMethodEntitiesAccuracyDementia
2023
A pipeline for the retrieval and extraction of domain-specific information with application to COVID-19 immune signatures
Newton A, Chartash D, Kleinstein S, McDougal R. A pipeline for the retrieval and extraction of domain-specific information with application to COVID-19 immune signatures. BMC Bioinformatics 2023, 24: 292. PMID: 37474900, PMCID: PMC10357743, DOI: 10.1186/s12859-023-05397-8.Peer-Reviewed Original ResearchConceptsDomain-specific informationDocument embeddingsSVM classifierSemi-structured representationsTraining setWeb-based formKnowledge repositoryInformation modelAutomatic analysisClassifier predictionsClassifierSignature informationAutomated systemBiomedical publicationsPaper authorsEmbeddingIncomplete information modelLiterature miningIterative processSpecific informationSuch informationInformationLimited setSetQueries
2022
Multiscale Computer Modeling of Spreading Depolarization in Brain Slices
Kelley C, Newton AJH, Hrabetova S, McDougal RA, Lytton WW. Multiscale Computer Modeling of Spreading Depolarization in Brain Slices. ENeuro 2022, 9: eneuro.0082-22.2022. PMID: 35927026, PMCID: PMC9410770, DOI: 10.1523/eneuro.0082-22.2022.Peer-Reviewed Original ResearchConceptsBrain slicesNeuronal spike rateGreater neuronal densityExtracellular spaceEffects of hypoxiaNeuronal densityNeurologic conditionsNeuronal depolarizationNeuronal silenceNeuronal volumeRelative hypoxiaSD velocityPathologic cycleECS volumeECS shrinkageSD speedMore dendritesSpike rateSDConcentration homeostasisNeuronsDepolarizationHypoxiaSlicesMultiscale computer modeling
2020
Human Neocortical Neurosolver (HNN), a new software tool for interpreting the cellular and network origin of human MEG/EEG data
Neymotin SA, Daniels DS, Caldwell B, McDougal RA, Carnevale NT, Jas M, Moore CI, Hines ML, Hämäläinen M, Jones SR. Human Neocortical Neurosolver (HNN), a new software tool for interpreting the cellular and network origin of human MEG/EEG data. ELife 2020, 9: e51214. PMID: 31967544, PMCID: PMC7018509, DOI: 10.7554/elife.51214.Peer-Reviewed Original ResearchConceptsGraphical user interfaceNew software toolUser interfaceMEG/EEGSoftware toolsMEG/EEG dataTranslational neuroscience researchNew therapiesNeural originReliable markerDisease statesEEG dataBrain rhythmsNetwork originBrain activityHuman brain activityElectro-encephalographyInformation processingEEGUsersNeuroscience research
2019
Open Source Brain: A Collaborative Resource for Visualizing, Analyzing, Simulating, and Developing Standardized Models of Neurons and Circuits
Gleeson P, Cantarelli M, Marin B, Quintana A, Earnshaw M, Sadeh S, Piasini E, Birgiolas J, Cannon RC, Cayco-Gajic NA, Crook S, Davison AP, Dura-Bernal S, Ecker A, Hines ML, Idili G, Lanore F, Larson SD, Lytton WW, Majumdar A, McDougal RA, Sivagnanam S, Solinas S, Stanislovas R, van Albada SJ, van Geit W, Silver RA. Open Source Brain: A Collaborative Resource for Visualizing, Analyzing, Simulating, and Developing Standardized Models of Neurons and Circuits. Neuron 2019, 103: 395-411.e5. PMID: 31201122, PMCID: PMC6693896, DOI: 10.1016/j.neuron.2019.05.019.Peer-Reviewed Original ResearchConceptsData-driven modelsReproducibility of modelsCollaborative interactionsCollaborative resourceExperimental resultsComputational modelAnalyzingReuseStandardized modelModel structureSpecialist knowledgeMultiple scalesComplex biological systemsSharingVisualizingToolInfrastructureNetworkNew modelPlatformPowerful toolSimulatingModelWider communityAdoption
2018
Automated Metadata Suggestion During Repository Submission
McDougal RA, Dalal I, Morse TM, Shepherd GM. Automated Metadata Suggestion During Repository Submission. Neuroinformatics 2018, 17: 361-371. PMID: 30382537, PMCID: PMC6494730, DOI: 10.1007/s12021-018-9403-z.Peer-Reviewed Original ResearchConceptsMetadata annotationMetadata tagsData providersAmount of dataDifferent text sourcesUser data entryData uploaderKnowledge discoveryText sourcesRelevant metadataMetadataHigh recallInformatics resourcesAnnotation schemeResearch communityData entryAnnotationBioinformatics resourcesDiscovery resourcesLow precisionMinimal costResourcesTagsModelDBUpload
2017
Parallel Stochastic Discrete Event Simulation of Calcium Dynamics in Neuron
Patoary M, Tropper C, McDougal RA, Lin Z, Lytton WW. Parallel Stochastic Discrete Event Simulation of Calcium Dynamics in Neuron. IEEE/ACM Transactions On Computational Biology And Bioinformatics 2017, 16: 1007-1019. PMID: 28961124, PMCID: PMC5869087, DOI: 10.1109/tcbb.2017.2756930.Peer-Reviewed Original ResearchConceptsStochastic reaction-diffusion systemsDeterministic modelWave modelReaction-diffusion systemStochastic discrete event simulationStochastic modelDeterministic simulationDiscrete event simulationParallel simulationCalcium wave modelBuffer modelEvent simulationDiscrete event simulation environmentSimulationsContinuous simulationNontrivial differencesDynamicsModelSimulation environmentRare eventSystem
2016
ORDB, HORDE, ODORactor and other on-line knowledge resources of olfactory receptor-odorant interactions
Marenco L, Wang R, McDougal R, Olender T, Twik M, Bruford E, Liu X, Zhang J, Lancet D, Shepherd G, Crasto C. ORDB, HORDE, ODORactor and other on-line knowledge resources of olfactory receptor-odorant interactions. Database 2016, 2016: baw132. PMID: 27694208, PMCID: PMC5045865, DOI: 10.1093/database/baw132.Peer-Reviewed Original ResearchTwenty years of ModelDB and beyond: building essential modeling tools for the future of neuroscience
McDougal RA, Morse TM, Carnevale T, Marenco L, Wang R, Migliore M, Miller PL, Shepherd GM, Hines ML. Twenty years of ModelDB and beyond: building essential modeling tools for the future of neuroscience. Journal Of Computational Neuroscience 2016, 42: 1-10. PMID: 27629590, PMCID: PMC5279891, DOI: 10.1007/s10827-016-0623-7.Peer-Reviewed Original ResearchConceptsComputational neuroscience modelsHigh performance computationEssential modeling toolUser experienceData-based modelsPerformance computationModelDBGraphical toolUser-friendly databaseModeling toolsResearch topicNeuroscience modelsCollect dataNew challengesNeuron modelingConvenient venueMassive developmentComplex modelsNew technologiesLarge research groupsRunning modelFuture of neuroscienceUsersMultiple scalesModel of interestSimulation Neurotechnologies for Advancing Brain Research: Parallelizing Large Networks in NEURON
Lytton WW, Seidenstein AH, Dura-Bernal S, McDougal RA, Schürmann F, Hines ML. Simulation Neurotechnologies for Advancing Brain Research: Parallelizing Large Networks in NEURON. Neural Computation 2016, 28: 2063-2090. PMID: 27557104, PMCID: PMC5295685, DOI: 10.1162/neco_a_00876.Peer-Reviewed Original ResearchConceptsHigh-performance computersLarge networksData management approachNew simulation technologyNeuronal network simulationsTypes of networksSimulation run timeMore big dataNumber of nodesNeuroscience GatewayBig dataData storageNetwork simulationComputational neuroscienceSimulation technologyHybrid networkNEURON simulatorNetwork sizeRun timeNetworkSimulation setupSuch simulationsFire neuronsMajor research initiativeNodes
2015
Calcium regulation of HCN channels supports persistent activity in a multiscale model of neocortex
Neymotin SA, McDougal RA, Bulanova AS, Zeki M, Lakatos P, Terman D, Hines ML, Lytton WW. Calcium regulation of HCN channels supports persistent activity in a multiscale model of neocortex. Neuroscience 2015, 316: 344-366. PMID: 26746357, PMCID: PMC4724569, DOI: 10.1016/j.neuroscience.2015.12.043.Peer-Reviewed Original ResearchConceptsHCN channelsExcitation/inhibition balancePersistent activityMetabotropic glutamate receptorsCalcium regulationNeuronal persistent activityEndoplasmic reticulum storesIonotropic inputsGABAB receptorsGlutamate receptorsInhibition balanceMultiple pathwaysCell excitabilityCortical layersMembrane depolarizationCompartmental neuronsInositol triphosphateIP3 receptorReceptorsNeuronsActivationMolecular eventsNeocortical modelsDepolarizationPathwayModelView for ModelDB: Online Presentation of Model Structure
McDougal RA, Morse TM, Hines ML, Shepherd GM. ModelView for ModelDB: Online Presentation of Model Structure. Neuroinformatics 2015, 13: 459-470. PMID: 25896640, PMCID: PMC4618280, DOI: 10.1007/s12021-015-9269-2.Peer-Reviewed Original ResearchConceptsSource codeModel source codeComputational neuroscience modelsWeb applicationModel reuseUser interfaceVisualization algorithmsWeb presentationCode sharingGraphical viewModelDBContextual informationSearchable repositoryManual curationModel structureNeuroscience modelsOnline presentationCodeNecessary dataData analysisKey featuresUsersRepositoryStructures of hundredsSharing