2021
BrainIAK: The Brain Imaging Analysis Kit
Kumar M, Anderson M, Antony J, Baldassano C, Brooks P, Cai M, Chen P, Ellis C, Henselman-Petrusek G, Huberdeau D, Hutchinson J, Li Y, Lu Q, Manning J, Mennen A, Nastase S, Richard H, Schapiro A, Schuck N, Shvartsman M, Sundaram N, Suo D, Turek J, Turner D, Vo V, Wallace G, Wang Y, Williams J, Zhang H, Zhu X, Capotă M, Cohen J, Hasson U, Li K, Ramadge P, Turk-Browne N, Willke T, Norman K. BrainIAK: The Brain Imaging Analysis Kit. Aperture Neuro 2021, 1: 10.52294/31bb5b68-2184-411b-8c00-a1dacb61e1da. PMID: 35939268, PMCID: PMC9351935, DOI: 10.52294/31bb5b68-2184-411b-8c00-a1dacb61e1da.Peer-Reviewed Original ResearchHigh-performance compute clusterData analysis problemsCompute clustersData simulatorJupyter notebooksComputational innovationsPython packageSame codeReal dataAnalysis problemKey problemReal-time functional magnetic resonance imagingMarkov modelEvent segmentationAforementioned techniquesAnalysis techniquesSimilarity analysisSegmentationLaptopBayesian versionFunctional alignmentSimulatorTechniqueRepresentational similarity analysisVariety of techniques
2020
Development of a Hybrid Training Simulator for Structural Heart Disease Interventions
Jang S, Torabinia M, Dhrif H, Caprio A, Liu J, Wong S, Mosadegh B. Development of a Hybrid Training Simulator for Structural Heart Disease Interventions. Advanced Intelligent Systems 2020, 2 DOI: 10.1002/aisy.202000109.Peer-Reviewed Original ResearchReal-time trackingMR displayPhantom heart modelMixed reality displayVisualization systemTraining scenesHybrid simulatorTraining simulatorReality displayTraining platformTracking sensorsReal timeCustom softwareTraining systemCommercial softwareLearning processSoftwareSimulatorQuantitative feedbackSpatial relationshipsTrackingSame technologyHybrid training systemTarget crossingsSensors
2016
Multithreaded Stochastic PDES for Reactions and Diffusions in Neurons
Lin Z, Tropper C, McDougal RA, Patoary MNI, Lytton WW, Yao Y, Hines ML. Multithreaded Stochastic PDES for Reactions and Diffusions in Neurons. ACM Transactions On Modeling And Computer Simulation 2016, 27: 1-27. PMID: 28943743, PMCID: PMC5604336, DOI: 10.1145/2987373.Peer-Reviewed Original Research
2014
VarSim: a high-fidelity simulation and validation framework for high-throughput genome sequencing with cancer applications
Mu JC, Mohiyuddin M, Li J, Bani Asadi N, Gerstein MB, Abyzov A, Wong WH, Lam HY. VarSim: a high-fidelity simulation and validation framework for high-throughput genome sequencing with cancer applications. Bioinformatics 2014, 31: 1469-1471. PMID: 25524895, PMCID: PMC4410653, DOI: 10.1093/bioinformatics/btu828.Peer-Reviewed Original ResearchConceptsMap data structureCompute frameworkGraphical reportsData structureParallel computationValidation frameworkRead alignmentSupplementary dataValidation toolReal dataHigh-fidelity simulationHigh-throughput genome sequencingDetailed statisticsFrameworkValidation resultsPythonInformationJavaSimulatorSupplementary informationComputationBioinformaticsRealistic modelCodeImplementation
2013
FastMIST: A Fast Molecular Imaging SimulaTor
Ryder W, Angelis G, Bashar R, Kyme A, Fulton R, Liu Y, Meikle S. FastMIST: A Fast Molecular Imaging SimulaTor. 2011 IEEE Nuclear Science Symposium Conference Record 2013, 2723-2726. DOI: 10.1109/nssmic.2012.6551619.Peer-Reviewed Original Research
2012
Simulating Realistic Genomic Data With Rare Variants
Xu Y, Wu Y, Song C, Zhang H. Simulating Realistic Genomic Data With Rare Variants. Genetic Epidemiology 2012, 37: 163-172. PMID: 23161487, PMCID: PMC3543480, DOI: 10.1002/gepi.21696.Peer-Reviewed Original Research
2010
A prospective study of loss of consciousness in epilepsy using virtual reality driving simulation and other video games
Yang L, Morland TB, Schmits K, Rawson E, Narasimhan P, Motelow JE, Purcaro MJ, Peng K, Raouf S, DeSalvo MN, Oh T, Wilkerson J, Bod J, Srinivasan A, Kurashvili P, Anaya J, Manza P, Danielson N, Ransom CB, Huh L, Elrich S, Padin-Rosado J, Naidu Y, Detyniecki K, Hamid H, Farooque P, Astur R, Xiao B, Duckrow RB, Blumenfeld H. A prospective study of loss of consciousness in epilepsy using virtual reality driving simulation and other video games. Epilepsy & Behavior 2010, 18: 238-246. PMID: 20537593, PMCID: PMC2914099, DOI: 10.1016/j.yebeh.2010.04.011.Peer-Reviewed Original ResearchConceptsVideo gamesVirtual realityComputer-based tasksDaily lifePerformance dataProspective studyEssential partGameContinuous video/EEG monitoringVideo/EEG monitoringTraffic accidentsSimulatorNetworkTaskNormal daily lifeSeizure typesDrivingEEG monitoringSeizuresDriving impairmentPatientsImpair consciousnessSpecific typesAnatomical networksReality
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