2025
Multiarea processing in body patches of the primate inferotemporal cortex implements inverse graphics
Yilmaz H, Shah A, Letrou A, Kumar S, Vogels R, Yildirim I. Multiarea processing in body patches of the primate inferotemporal cortex implements inverse graphics. Proceedings Of The National Academy Of Sciences Of The United States Of America 2025, 122: e2420287122. PMID: 40627399, PMCID: PMC12280979, DOI: 10.1073/pnas.2420287122.Peer-Reviewed Original ResearchMeSH KeywordsAlgorithmsAnimalsComputer GraphicsMacaca mulattaModels, NeurologicalTemporal LobeVisual CortexVisual PerceptionConceptsInverse graphicsInference networkIT networksGenerative modelPrimate inferotemporal cortexNeural algorithmMacaque IT cortexUnsupervised variantVision modelsImage statisticsVision capabilitiesTransform sensory inputsComputational neuroscienceObject identityGraphicsNetworkIT cortexNeural representationProcessing networkAlgorithmMap imagesInferotemporal cortexRepresentationInferenceTheory of vision
2021
Avatar Models and Radar Plots: The Future of Intraoperative Anesthesia Monitoring
Rosero-Britton B, Amaya S. Avatar Models and Radar Plots: The Future of Intraoperative Anesthesia Monitoring. Anesthesiology 2021, 135: 770-771. PMID: 34270675, DOI: 10.1097/aln.0000000000003884.Peer-Reviewed Original Research
2019
Oxygen saturation histogram monitoring to reduce death or retinopathy of prematurity: a quality improvement initiative
Gentle S, El-Ferzli G, Winter L, Salas A, Philips III J. Oxygen saturation histogram monitoring to reduce death or retinopathy of prematurity: a quality improvement initiative. Journal Of Perinatology 2019, 40: 163-169. PMID: 31506527, DOI: 10.1038/s41372-019-0486-7.Peer-Reviewed Original ResearchConceptsSevere retinopathy of prematurityRetinopathy of prematuritySevere retinopathyWeeks gestationReduce deathsRate of deathPreterm infantsConclusionIn infantsPrematurityGestationOxygen saturationHospital dischargeInfantsOutcome measuresQuality improvement initiativesDeathChart auditWeeksCare providersPeriodic assessmentRetinopathyIncreasing timeImprovement initiatives
2018
Generalizable and Scalable Visualization of Single-Cell Data Using Neural Networks
Cho H, Berger B, Peng J. Generalizable and Scalable Visualization of Single-Cell Data Using Neural Networks. Cell Systems 2018, 7: 185-191.e4. PMID: 29936184, PMCID: PMC6469860, DOI: 10.1016/j.cels.2018.05.017.Peer-Reviewed Original Research
2017
The Focinator v2-0 Graphical Interface, Four Channels, Colocalization Analysis and Cell Phase Identification
Oeck S, Malewicz NM, Hurst S, Al-Refae K, Krysztofiak A, Jendrossek V. The Focinator v2-0 Graphical Interface, Four Channels, Colocalization Analysis and Cell Phase Identification. Radiation Research 2017, 188: 114-120. PMID: 28492345, DOI: 10.1667/rr14746.1.Peer-Reviewed Original Research
2016
Leveraging syntactic and semantic graph kernels to extract pharmacokinetic drug drug interactions from biomedical literature
Zhang Y, Wu H, Xu J, Wang J, Soysal E, Li L, Xu H. Leveraging syntactic and semantic graph kernels to extract pharmacokinetic drug drug interactions from biomedical literature. BMC Systems Biology 2016, 10: 67. PMID: 27585838, PMCID: PMC5009562, DOI: 10.1186/s12918-016-0311-2.Peer-Reviewed Original ResearchMeSH KeywordsBiomedical ResearchComputational BiologyComputer GraphicsData MiningDrug InteractionsPharmacokineticsPublicationsSemanticsConceptsPaths graph kernelGraph kernelsSemantic classesSemantic informationBiomedical literatureShallow semantic representationsText mining techniquesBest F-scoreAutomatic DDI extractionProblem of sparsenessDependency structureSemantic graphDDI detectionKnowledge basesDDI corpusF-scoreDDI extractionSemantic representationNovel approachExperimental resultsKernelHigh precisionInformationSparsenessGraph
2015
Trending autoregulatory indices during treatment for traumatic brain injury
Kim N, Krasner A, Kosinski C, Wininger M, Qadri M, Kappus Z, Danish S, Craelius W. Trending autoregulatory indices during treatment for traumatic brain injury. Journal Of Clinical Monitoring And Computing 2015, 30: 821-831. PMID: 26446002, DOI: 10.1007/s10877-015-9779-3.Peer-Reviewed Original ResearchMeSH KeywordsArtifactsAutomationBrain Injuries, TraumaticCerebrovascular CirculationComputer GraphicsElectronic Data ProcessingHemodynamicsHumansIntensive Care UnitsIntracranial HypertensionIntracranial PressureLeast-Squares AnalysisLinear ModelsMedical InformaticsMonitoring, PhysiologicRetrospective StudiesSignal Processing, Computer-AssistedConceptsPressure reactivity indexSurgical intensive care unitGraphical user interfaceTraumatic brain injuryIntracranial pressureRetrospective patient dataUser interfaceIntracranial hypertensionBrain injuryData distributionPatient dataData scanningEvent detectorData monitoringIntensive care unitElevated intracranial pressureReal-time predictorStore signalsAutoregulatory indexHypertensive eventsAdverse eventsArterial BPCare unitSingle patientPatientsGPU-Accelerated Framework for Intracoronary Optical Coherence Tomography Imaging at the Push of a Button
Han M, Kim K, Jang S, Cho H, Bouma B, Oh W, Ryu S. GPU-Accelerated Framework for Intracoronary Optical Coherence Tomography Imaging at the Push of a Button. PLOS ONE 2015, 10: e0124192. PMID: 25880375, PMCID: PMC4400174, DOI: 10.1371/journal.pone.0124192.Peer-Reviewed Original ResearchMeSH KeywordsAutomationComputer GraphicsCoronary VesselsHumansStentsTomography, Optical CoherenceUltrasonographyConceptsOptical coherence tomographyStent strutsCoherence tomographyIntracoronary OCT imagingLong coronary arteryCoronary artery diseaseCause of deathIntracoronary optical coherence tomographyImportant clinical toolRaw OCT dataOCT dataArtery diseaseCoronary arteryGPU-Accelerated FrameworkIntracoronary imagingFD-OCT imagesGraphics processing unitsAccurate diagnosisClinical tool
2014
Visual presentation of statistical concepts in diagnostic testing: the 2 × 2 diagram.
Johnson K, Johnson B. Visual presentation of statistical concepts in diagnostic testing: the 2 × 2 diagram. American Journal Of Roentgenology 2014, 203: w14-20. PMID: 24951225, DOI: 10.2214/ajr.13.11954.Peer-Reviewed Original ResearchMAGI: a Node.js web service for fast microRNA-Seq analysis in a GPU infrastructure
Kim J, Levy E, Ferbrache A, Stepanowsky P, Farcas C, Wang S, Brunner S, Bath T, Wu Y, Ohno-Machado L. MAGI: a Node.js web service for fast microRNA-Seq analysis in a GPU infrastructure. Bioinformatics 2014, 30: 2826-2827. PMID: 24907367, PMCID: PMC4173015, DOI: 10.1093/bioinformatics/btu377.Peer-Reviewed Original ResearchMeSH KeywordsComputational BiologyComputer GraphicsInternetMicroRNAsProgramming LanguagesSequence Analysis, RNASoftwareConceptsWeb servicesWeb reportsLarge input filesNovel feature extractionEnd performance improvementsExploration of resultsGPU infrastructureInteractive visualizationJavaScript frameworkParallel computingGPU devicesHypertext PreprocessorCUDA CFeature extractionDrop operationInput filesPlot generationSalient featuresPerformance improvementInfrastructureNodesServicesData analysisComputingBrowserGAMUT: GPU accelerated microRNA analysis to uncover target genes through CUDA-miRanda
Wang S, Kim J, Jiang X, Brunner S, Ohno-Machado L. GAMUT: GPU accelerated microRNA analysis to uncover target genes through CUDA-miRanda. BMC Medical Genomics 2014, 7: s9. PMID: 25077821, PMCID: PMC4101446, DOI: 10.1186/1755-8794-7-s1-s9.Peer-Reviewed Original ResearchConceptsCompute Unified Device ArchitectureGraphics processing unitsHigh performance computeParallel computingNVIDIA Compute Unified Device ArchitectureUnified Device ArchitectureMultiple test datasetsGiga cell updatesTimes performance gainsSmith-Waterman algorithmGPU developersSW implementationSource codeExecution timeGHz CPUIntel XeonLong reference sequencesProcessing unitTarget identification algorithmCell updatesTest datasetProjects/Such large scalePerformance gainsBiomedical research community
2013
A Graphics Processing Unit Accelerated Motion Correction Algorithm and Modular System for Real-time fMRI
Scheinost D, Hampson M, Qiu M, Bhawnani J, Constable RT, Papademetris X. A Graphics Processing Unit Accelerated Motion Correction Algorithm and Modular System for Real-time fMRI. Neuroinformatics 2013, 11: 291-300. PMID: 23319241, PMCID: PMC3644525, DOI: 10.1007/s12021-013-9176-3.Peer-Reviewed Case Reports and Technical NotesMeSH KeywordsAlgorithmsBrainBrain MappingComputer GraphicsHumansImage Processing, Computer-AssistedMagnetic Resonance ImagingMotionOxygenConceptsGraphics processing unitsNovel graphics processing unitMotion correction algorithmProcessing unitReal-time methodProcessing delayCorrection algorithmSystem designMotion correction strategiesOffline methodsAlgorithmAvailable softwareReal-time functional magnetic resonance imagingModular approachValuable featuresModular systemPresent algorithmReal-time fMRIMotion correctionMotion parametersSoftwareNew technologiesNew systemCorrection strategyEstimates of motion
2012
SHARE: system design and case studies for statistical health information release
Gardner J, Xiong L, Xiao Y, Gao J, Post A, Jiang X, Ohno-Machado L. SHARE: system design and case studies for statistical health information release. Journal Of The American Medical Informatics Association 2012, 20: 109-116. PMID: 23059729, PMCID: PMC3555328, DOI: 10.1136/amiajnl-2012-001032.Peer-Reviewed Original ResearchConceptsDifferential privacy frameworkPrivacy frameworkDifferential privacyMultidimensional histogramsReal medical datasetsMedical data warehouseOriginal data distributionInformation releaseHigh-dimensional dataBreast cancer datasetPattern queriesMedical datasetsElectronic medical record datasetHeterogeneous dataData warehouseUse casesElectronic health recordsMedical domainBiomedical dataThree-dimensional data cubeArt methodsData distributionMedical dataDimensional dataData cubeSpecification, annotation, visualization and simulation of a large rule-based model for ERBB receptor signaling
Creamer M, Stites E, Aziz M, Cahill J, Tan C, Berens M, Han H, Bussey K, Von Hoff D, Hlavacek W, Posner R. Specification, annotation, visualization and simulation of a large rule-based model for ERBB receptor signaling. BMC Systems Biology 2012, 6: 107. PMID: 22913808, PMCID: PMC3485121, DOI: 10.1186/1752-0509-6-107.Peer-Reviewed Original ResearchMeSH KeywordsComputational BiologyComputer GraphicsModels, BiologicalReceptor Protein-Tyrosine KinasesSignal TransductionConceptsCell signaling networksSignaling networksErbB receptor signalingRule-based modeling approachSignaling proteinsPost-translational modification stateSites of post-translational modificationsNetwork-free simulationCellular signaling networksProtein-protein interactionsPost-translational modificationsReceptor signalingSite of modificationActivation of ERKModification statesProtein complexesProtein interactionsContact mapsCellular signalingTyrosine residuesIndividual serinesDevelopment of softwareProteinRule-based modelKinetics of molecular interactions
2010
Dissociable brain mechanisms for processing social exclusion and rule violation
Bolling DZ, Pitskel NB, Deen B, Crowley MJ, McPartland JC, Mayes LC, Pelphrey KA. Dissociable brain mechanisms for processing social exclusion and rule violation. NeuroImage 2010, 54: 2462-2471. PMID: 20974272, PMCID: PMC3006641, DOI: 10.1016/j.neuroimage.2010.10.049.Peer-Reviewed Original ResearchMeSH KeywordsBrainCerebral CortexComputer GraphicsData Interpretation, StatisticalFemaleGames, ExperimentalHumansImage Processing, Computer-AssistedInterpersonal RelationsMagnetic Resonance ImagingMaleNerve NetNeural PathwaysPsychophysicsRejection, PsychologySocial EnvironmentSocial PerceptionYoung AdultConceptsVentral anterior cingulate cortexBrain regionsMagnetic resonance imaging studyDifferential functional connectivityResonance imaging studyFunctional magnetic resonance imaging studyAnterior cingulate cortexCingulate cortex activityMiddle temporal gyrusLateral parietal cortexVentrolateral prefrontal cortexCingulate cortexParietal cortexImaging studiesCortex activityFunctional connectivityTemporal gyrusPrefrontal cortexPosterior cingulate cortex activityActivation patternsCortexBrain mechanismsFunctional dissociationVirtual ball-tossing gameNeural systems
2009
The filamentous fungal gene expression database (FFGED)
Zhang Z, Townsend JP. The filamentous fungal gene expression database (FFGED). Fungal Genetics And Biology 2009, 47: 199-204. PMID: 20025988, PMCID: PMC2822089, DOI: 10.1016/j.fgb.2009.12.001.Peer-Reviewed Original ResearchMeSH KeywordsAlgorithmsChromosome MappingComputational BiologyComputer GraphicsDatabase Management SystemsDatabases, GeneticGene ExpressionGene Expression ProfilingGene Expression Regulation, FungalGenes, FungalGenome, FungalInternetModels, GeneticModels, StatisticalOligonucleotide Array Sequence AnalysisSaccharomyces cerevisiaeSequence AlignmentSoftwareSystems IntegrationUser-Computer InterfaceConceptsEfficient web interfaceExpression databaseUser-friendly managementCollection of toolsGene expression databaseDifferent usersData sharingWeb interfaceCollaborative platformExperimental metadataFree databaseRaw dataData submissionUsersMultiple experimentsGene expression dataSharingDatabaseEssential informationAjaxMetadataExpression dataDifferent experimentsRetrievalRelated experiments
2008
Novel Interaction Techniques for Neurosurgical Planning and Stereotactic Navigation
Joshi A, Scheinost D, Vives KP, Spencer DD, Staib LH, Papademetris X. Novel Interaction Techniques for Neurosurgical Planning and Stereotactic Navigation. IEEE Transactions On Visualization And Computer Graphics 2008, 14: 1587-1594. PMID: 18989014, PMCID: PMC2633029, DOI: 10.1109/tvcg.2008.150.Peer-Reviewed Original Research
2007
Tilescope: online analysis pipeline for high-density tiling microarray data
Zhang ZD, Rozowsky J, Lam H, Du J, Snyder M, Gerstein M. Tilescope: online analysis pipeline for high-density tiling microarray data. Genome Biology 2007, 8: r81. PMID: 17501994, PMCID: PMC1929149, DOI: 10.1186/gb-2007-8-5-r81.Peer-Reviewed Original Research
2006
The tYNA platform for comparative interactomics: a web tool for managing, comparing and mining multiple networks
Yip KY, Yu H, Kim PM, Schultz M, Gerstein M. The tYNA platform for comparative interactomics: a web tool for managing, comparing and mining multiple networks. Bioinformatics 2006, 22: 2968-2970. PMID: 17021160, DOI: 10.1093/bioinformatics/btl488.Peer-Reviewed Original ResearchConceptsMultiple networksInteractive graphical interfaceWeb systemPublic networkGraphical interfaceSource codeDefective cliquesCuration effortsWeb toolCellular networksBiological datasetsSmall network motifsLarge-scale experimentsNetworkComplex networksPreliminary versionNetwork motifsVariety of criteriaGlobal statisticsWSDLNetwork analysisDifferent categoriesComparative interactomicsPluginAPIPhenotype-genotype association grid: a convenient method for summarizing multiple association analyses
Levy D, DePalma S, Benjamin E, O'Donnell C, Parise H, Hirschhorn J, Vasan R, Izumo S, Larson M. Phenotype-genotype association grid: a convenient method for summarizing multiple association analyses. BMC Genomic Data 2006, 7: 30. PMID: 16716207, PMCID: PMC1526453, DOI: 10.1186/1471-2156-7-30.Peer-Reviewed Original ResearchConceptsMultiple association analysisLarge-scale genetic studiesIndividual SNP associationsHTML pagesWeb ToolkitInteractive explorationOracle databaseLarge-scale association studiesWeb serverTcl scriptsMouse clicksGene-environment associationVast amountGenetic lociGenotypic dataNumerous phenotypesAssociation studiesGenetic studiesAssociation analysisSNP associationsMultiple phenotypesSingle SNPIdentification of patternsIndividual cellsGrid display
This site is protected by hCaptcha and its Privacy Policy and Terms of Service apply