2025
Protocol for finding genetic variation associated with unmeasured traits through GenomicSEM common-factor GWAS
Johnston K, Signer R, Huckins L. Protocol for finding genetic variation associated with unmeasured traits through GenomicSEM common-factor GWAS. STAR Protocols 2025, 6: 103905. PMID: 40531628, PMCID: PMC12213288, DOI: 10.1016/j.xpro.2025.103905.Peer-Reviewed Original ResearchYes Stormtrooper, These Are the Droids You Are Looking for: Identifying and Preliminarily Evaluating Bot and Fraud Detection Strategies in Online Psychological Research
Shaw T, Cascalheira C, Helminen E, Brisbin C, Jackson S, Simone M, Sullivan T, Batchelder A, Scheer J. Yes Stormtrooper, These Are the Droids You Are Looking for: Identifying and Preliminarily Evaluating Bot and Fraud Detection Strategies in Online Psychological Research. Psychological Methods 2025 PMID: 40029298, DOI: 10.1037/met0000724.Peer-Reviewed Original ResearchPrivacy in population protocols with probabilistic scheduling
Amir T, Aspnes J. Privacy in population protocols with probabilistic scheduling. Theoretical Computer Science 2025, 1024: 114926. DOI: 10.1016/j.tcs.2024.114926.Peer-Reviewed Original ResearchPopulation protocol modelProtocol modelProbabilistic schedulingInformation-theoreticInput vectorAnalyze distributed algorithmsDefinition of privacyConcept of anonymityIssues of privacyIoT devicesSensor networksMobile agentsAgents' inputsPopulation protocolsPrivacyAlgorithmIoTSchedulingDeniabilityProtocolInputGuaranteesAnonymityDronesVector
2024
A Research Protocol: Mixed-Mode Designs to Optimize Engagement in Clinical Informatics Research.
Wise K, Schrimpf M, Hobensack M, Zhao Y, Poghosyan L, Alexander G. A Research Protocol: Mixed-Mode Designs to Optimize Engagement in Clinical Informatics Research. Studies In Health Technology And Informatics 2024, 315: 709-710. PMID: 39049392, DOI: 10.3233/shti240291.Peer-Reviewed Original ResearchConceptsNursing homesNurse practitionersU.S. nursing homesCross-sectional surveyResearch protocolClinical informatics researchNH administratorsCare environmentSurvey recruitmentOptimal engagementMixed-mode methodologyInformatics researchMixed-mode designResponse rateSurveyNursesCareHomePractitionersClinicRespondentsProtocolEngagementResearch
2023
3D hepatic organoid production from human pluripotent stem cells
Jin Z, Xu K, Kim J, Guo H, Yao X, Xu Y, Li Y, Ryu D, Kim K, Hong K, Kim Y, Wang L, Cao Q, Kim K, Kim N, Han D. 3D hepatic organoid production from human pluripotent stem cells. Differentiation 2023, 135: 100742. PMID: 38104501, DOI: 10.1016/j.diff.2023.100742.Peer-Reviewed Original ResearchPluripotent stem cellsHuman pluripotent stem cellsHepatic organoidsStem cellsNovel platformOrganoid productionClinical translationHepatic functionalityToxicity screeningDifferentiation procedureOrganoid technologySpontaneous formationProtocolTechnologyOptimal concentrationFunctionalityPlatformIndustrial settingsOrganoidsProductionPSCA narrative commentary about interoperability in medical devices and data used in diabetes therapy from an academic EU/UK/US perspective
Jendle J, Adolfsson P, Choudhary P, Dovc K, Fleming A, Klonoff D, Mader J, Oliver N, Sherr J, Šoupal J, Heinemann L. A narrative commentary about interoperability in medical devices and data used in diabetes therapy from an academic EU/UK/US perspective. Diabetologia 2023, 67: 236-245. PMID: 38041737, PMCID: PMC10789828, DOI: 10.1007/s00125-023-06049-5.Peer-Reviewed Original ResearchLimitations of interoperabilityData-sharing protocolsData interoperabilitySecure integrationElectronic health recordsData ownershipInteroperabilitySeamless integrationTransparent handlingData handlingHealth recordsMedical devicesPractical challengesKey issuesTransparent frameworkPrivacyFrameworkDevicesCritical aspectsDifferent sourcesIntegrationProtocolNeeds of peopleLegal issuesIssuesStakeholder-driven development and implementation of CRICIT: an app to support high-quality data capture and protocol monitoring for outpatient clinical trials with vulnerable populations
Clark K, Ruth C, Thomas K, Dunham K, Travis M, Rivera-Santiago K, Brinkely-Rubinstein L, Wang E. Stakeholder-driven development and implementation of CRICIT: an app to support high-quality data capture and protocol monitoring for outpatient clinical trials with vulnerable populations. Journal Of Clinical And Translational Science 2023, 7: e183. PMID: 37706003, PMCID: PMC10495824, DOI: 10.1017/cts.2023.609.Peer-Reviewed Original ResearchElectronic data capture systemRandomized Controlled TrialsUser-centered design principlesEnhanced primary care modelMultisite Randomized Controlled TrialPrimary care modelKnowledge-to-ActionData capture systemCare modelClinical research dataOpioid use disorderCapture systemTracking capabilityControlled TrialsDesign principlesResearch protocolImplementationStudy dataAdministrative burdenUse disorderSite-specific adaptationsRandomized protocolProtocolEfficient collectionResearch activitiesCreating Selenocysteine-Specific Reporters Using Inteins
Chung C, Söll D, Krahn N. Creating Selenocysteine-Specific Reporters Using Inteins. Methods In Molecular Biology 2023, 2676: 69-86. PMID: 37277625, DOI: 10.1007/978-1-0716-3251-2_5.Peer-Reviewed Original ResearchAutomated and manual segmentation of the hippocampus in human infants
Fel J, Ellis C, Turk-Browne N. Automated and manual segmentation of the hippocampus in human infants. Developmental Cognitive Neuroscience 2023, 60: 101203. PMID: 36791555, PMCID: PMC9957787, DOI: 10.1016/j.dcn.2023.101203.Peer-Reviewed Original ResearchConceptsManual segmentationHippocampal segmentationInter-rater reliabilityAutomated SegmentationSegmentation methodSegmentationAnatomical MRI scansEarly hippocampal developmentHead motionFreeSurfer softwareSoftwareHippocampal developmentMRI scansHippocampal structureAwake infantsInfantsHippocampusFMRI protocolAnatomical scansGold standardAdult templateHuman infantsScan qualityScansProtocol
2022
Antiviral Strategies Against SARS-CoV-2: A Systems Biology Approach
Prates ET, Garvin MR, Jones P, Miller JI, Sullivan KA, Cliff A, Gazolla JGFM, Shah MB, Walker AM, Lane M, Rentsch CT, Justice A, Pavicic M, Romero J, Jacobson D. Antiviral Strategies Against SARS-CoV-2: A Systems Biology Approach. Methods In Molecular Biology 2022, 2452: 317-351. PMID: 35554915, DOI: 10.1007/978-1-0716-2111-0_19.ChaptersConceptsSystems biology approachBiology approachHigh-performance computingArtificial intelligence methodologiesDiversity of informationIntelligence methodologiesStructural proteomicsSystem-level infrastructureMultiomics integrationCore frameworkViral pathogenesisAntiviral strategiesWealth of informationUnprecedented accessPathogensComputingComputational protocolPathogen detectionInformationProteomicsAdaptation analysisDevelopment of vaccinesProtocolInfrastructureNetworkA protocol for working with open-source neuroimaging datasets
Horien C, Lee K, Westwater ML, Noble S, Tejavibulya L, Kayani T, Constable RT, Scheinost D. A protocol for working with open-source neuroimaging datasets. STAR Protocols 2022, 3: 101077. PMID: 35036958, PMCID: PMC8749295, DOI: 10.1016/j.xpro.2021.101077.Peer-Reviewed Original Research
2021
INNV-37. XCELSIOR: A REAL-TIME, REAL-WORLD LEARNING PLATFORM FOR PATIENTS WITH ADVANCED CANCER
Stuhlmiller T, Shapiro M, Wasserman A, Osking Z, Shrager J, Federowicz B, Warner M, Friedland J, Musella A, Blondin N, Fonkem E, Wong E, Kesari S. INNV-37. XCELSIOR: A REAL-TIME, REAL-WORLD LEARNING PLATFORM FOR PATIENTS WITH ADVANCED CANCER. Neuro-Oncology 2021, 23: vi113-vi113. DOI: 10.1093/neuonc/noab196.448.Peer-Reviewed Original ResearchData elementsIndividual data elementsClinical decision support algorithmDecision support algorithmData solutionsBiomedical ontologiesMedical documentsLearning platformSupport algorithmData entryVirtual tumor boardsPlatformAlgorithmOntologyCase studyInfrastructureNon-profit groupsBrain tumor researchDocumentsClinical researchersDatabaseAccessReal-world evidenceResearchProtocolDeep Learning–Based Automated Echocardiographic Quantification of Left Ventricular Ejection Fraction
Asch F, Mor-Avi V, Rubenson D, Goldstein S, Saric M, Mikati I, Surette S, Chaudhry A, Poilvert N, Hong H, Horowitz R, Park D, Diaz-Gomez J, Boesch B, Nikravan S, Liu R, Philips C, Thomas J, Martin R, Lang R. Deep Learning–Based Automated Echocardiographic Quantification of Left Ventricular Ejection Fraction. Circulation Cardiovascular Imaging 2021, 14: e012293. PMID: 34126754, DOI: 10.1161/circimaging.120.012293.Peer-Reviewed Original ResearchConceptsMachine-learning algorithmsAutomated machine-learning algorithmMachine-learning classificationLV functionAutomated classificationPoint-of-careAlgorithmEjection fractionAutomated estimationLV) ejection fractionApical 2-chamber viewParasternal long-axis viewEvaluation of LV functionProtocol 1Point-of-care settingsAccuracyClassificationApical 4-chamberLong-axis viewPoint-of-care physiciansImaging systemMildly-to-moderatelyProtocolEF valuesClinical examination
2020
Low-motion fMRI data can be obtained in pediatric participants undergoing a 60-minute scan protocol
Horien C, Fontenelle S, Joseph K, Powell N, Nutor C, Fortes D, Butler M, Powell K, Macris D, Lee K, Greene AS, McPartland JC, Volkmar FR, Scheinost D, Chawarska K, Constable RT. Low-motion fMRI data can be obtained in pediatric participants undergoing a 60-minute scan protocol. Scientific Reports 2020, 10: 21855. PMID: 33318557, PMCID: PMC7736342, DOI: 10.1038/s41598-020-78885-z.Peer-Reviewed Original ResearchConceptsPediatric participantsMRI protocolMagnetic resonance imaging (MRI) scansFunctional magnetic resonance imaging (fMRI) scansShorter MRI protocolsScan protocolResonance imaging scansImaging scansMRI sessionsFMRI connectivity analysisFMRI dataFMRI findingsSignificant confoundScansReplication groupConnectivity analysisAutism spectrum disorderMock scanSpectrum disorderParticipantsHead motionProtocolISAC Probe Tag Dictionary: Standardized Nomenclature for Detection and Visualization Labels Used in Cytometry and Microscopy Imaging
Blenman K, Spidlen J, Parks DR, Moore W, Treister A, Leif R, Bray C, Goldberg M, Force I, Brinkman R. ISAC Probe Tag Dictionary: Standardized Nomenclature for Detection and Visualization Labels Used in Cytometry and Microscopy Imaging. Cytometry Part A 2020, 99: 103-106. PMID: 32881392, PMCID: PMC8388112, DOI: 10.1002/cyto.a.24224.Peer-Reviewed Original ResearchModified Anesthesia Protocol for Electroconvulsive Therapy Permits Reduction in Aerosol-Generating Bag-Mask Ventilation during the COVID-19 Pandemic
Luccarelli J, Fernandez-Robles C, Fernandez-Robles C, Horvath RJ, Berg S, McCoy TH, Seiner SJ, Henry ME. Modified Anesthesia Protocol for Electroconvulsive Therapy Permits Reduction in Aerosol-Generating Bag-Mask Ventilation during the COVID-19 Pandemic. Psychotherapy And Psychosomatics 2020, 89: 314-319. PMID: 32554959, PMCID: PMC7483857, DOI: 10.1159/000509113.Peer-Reviewed Original ResearchConceptsBag-mask ventilationElectroconvulsive therapyAnesthesia protocolSeizure durationAdequate seizure durationChart review studyClinical factorsPatient BMIPsychiatric complicationsApneic periodExpose patientsInfectious aerosolsPsychiatric treatmentPatientsTreatment staffCOVID-19 pandemicVentilationDurationReview studyTreatmentBMIComplicationsPreoxygenationTherapyProtocolRNA-based CRISPR-Mediated Loss-of-Function Mutagenesis in Human Pluripotent Stem Cells
Leung AW, Broton C, Bogacheva MS, Xiao AZ, Garcia-Castro MI, Lou YR. RNA-based CRISPR-Mediated Loss-of-Function Mutagenesis in Human Pluripotent Stem Cells. Journal Of Molecular Biology 2020, 432: 3956-3964. PMID: 32339532, DOI: 10.1016/j.jmb.2020.04.017.Peer-Reviewed Original ResearchConceptsHuman pluripotent stem cellsPluripotent stem cellsTargeting efficiencyShelf cell productsTransfection protocolShort palindromic repeatsStem cellsSelection markerGenome editingPS cell linesFunction mutagenesisImproved protocolBroad applicationsPalindromic repeatsClustered RegularlyAssociated 9Human therapyEfficiencyProtocolCell productsCRISPRCrRNARegularlyApplicationsEditing
2019
The effect of administration mode on CAHPS survey response rates and results: A comparison of mail and web‐based approaches
Fowler FJ, Cosenza C, Cripps LA, Edgman‐Levitan S, Cleary PD. The effect of administration mode on CAHPS survey response rates and results: A comparison of mail and web‐based approaches. Health Services Research 2019, 54: 714-721. PMID: 30656646, PMCID: PMC6505419, DOI: 10.1111/1475-6773.13109.Peer-Reviewed Original ResearchConceptsResponse rateMore primary care visitsPrimary care visitsPrimary care practicesSample of patientsLow response rateSurvey response rateCare visitsPatient populationAdministration protocolCAHPS surveyCare practicesPatientsCharacteristics of respondentsComparison of MailEmail invitationEmail addressesAdministration modeRespondent characteristicsLittle evidenceMailProtocolNonresponse biasVisits
2018
Realizing private and practical pharmacological collaboration
Hie B, Cho H, Berger B. Realizing private and practical pharmacological collaboration. Science 2018, 362: 347-350. PMID: 30337410, PMCID: PMC6519716, DOI: 10.1126/science.aat4807.Peer-Reviewed Original ResearchConceptsArt DTI prediction methodsDrug-target interactionsDTI prediction methodsIntellectual property concernsCryptographic toolsData privacyData sharingMultiple entitiesReal datasetsOpen sharingProperty concernsPrediction methodSharingDatasetPredictive modelPrivacyProtocolConfidentialityBiomedical researchCollaborationToolDataEntitiesSecure genome-wide association analysis using multiparty computation
Cho H, Wu D, Berger B. Secure genome-wide association analysis using multiparty computation. Nature Biotechnology 2018, 36: 547-551. PMID: 29734293, PMCID: PMC5990440, DOI: 10.1038/nbt.4108.Peer-Reviewed Original Research
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