2019
Development of a Natural Language Processing Tool to Extract Radiation Treatment Sites
Walker G, Soysal E, Xu H. Development of a Natural Language Processing Tool to Extract Radiation Treatment Sites. Cureus 2019, 11: e6010. PMID: 31815074, PMCID: PMC6881088, DOI: 10.7759/cureus.6010.Peer-Reviewed Original Research
2018
Association of Hemoglobin A1c Levels With Use of Sulfonylureas, Dipeptidyl Peptidase 4 Inhibitors, and Thiazolidinediones in Patients With Type 2 Diabetes Treated With Metformin
Vashisht R, Jung K, Schuler A, Banda J, Park R, Jin S, Li L, Dudley J, Johnson K, Shervey M, Xu H, Wu Y, Natrajan K, Hripcsak G, Jin P, Van Zandt M, Reckard A, Reich C, Weaver J, Schuemie M, Ryan P, Callahan A, Shah N. Association of Hemoglobin A1c Levels With Use of Sulfonylureas, Dipeptidyl Peptidase 4 Inhibitors, and Thiazolidinediones in Patients With Type 2 Diabetes Treated With Metformin. JAMA Network Open 2018, 1: e181755. PMID: 30646124, PMCID: PMC6324274, DOI: 10.1001/jamanetworkopen.2018.1755.Peer-Reviewed Original ResearchConceptsDPP-4 inhibitorsDipeptidyl peptidase-4 inhibitorsFirst-line therapyPeptidase-4 inhibitorsSecond-line drugsType 2 diabetesMyocardial infarctionEye disordersKidney disordersDrug classesSecond-line treatment choiceTotal hemoglobinObservational Health Data SciencesSecond-line treatment optionNew-user cohort studyEffectiveness of sulfonylureasSecond-line treatmentHemoglobin A1c levelsUse of sulfonylureasHealth Data SciencesLarge international studyElectronic medical recordsRoutine medical practiceInsurance claims dataCohort study
2017
Accurate Identification of Fatty Liver Disease in Data Warehouse Utilizing Natural Language Processing
Redman J, Natarajan Y, Hou J, Wang J, Hanif M, Feng H, Kramer J, Desiderio R, Xu H, El-Serag H, Kanwal F. Accurate Identification of Fatty Liver Disease in Data Warehouse Utilizing Natural Language Processing. Digestive Diseases And Sciences 2017, 62: 2713-2718. PMID: 28861720, DOI: 10.1007/s10620-017-4721-9.Peer-Reviewed Original ResearchConceptsData warehouseFatty liver diseaseLanguage processingNatural language processingLiver diseaseF-measureAlgorithm developmentVeterans Affairs Corporate Data WarehouseMagnetic resonance imaging reportsOutcomes of patientsAlgorithmExpert radiologistsValidation methodElectronic medical recordsCorporate Data WarehouseWarehouseAbdominal ultrasoundManual reviewHepatic steatosisMedical recordsRandom national sampleClinical studiesLarge cohortComputerized tomographyImaging reports
2016
Evaluation of a Prediction Model for the Development of Atrial Fibrillation in a Repository of Electronic Medical Records
Kolek M, Graves A, Xu M, Bian A, Teixeira P, Shoemaker M, Parvez B, Xu H, Heckbert S, Ellinor P, Benjamin E, Alonso A, Denny J, Moons K, Shintani A, Harrell F, Roden D, Darbar D. Evaluation of a Prediction Model for the Development of Atrial Fibrillation in a Repository of Electronic Medical Records. JAMA Cardiology 2016, 1: 1007-1013. PMID: 27732699, PMCID: PMC5293184, DOI: 10.1001/jamacardio.2016.3366.Peer-Reviewed Original ResearchIncident atrial fibrillationElectronic medical recordsCHARGE-AF modelAtrial fibrillationRisk prediction modelMedical recordsEMR cohortHistory of AFInternal medicine outpatient clinicProspective cohort studyDiastolic blood pressureMedicine outpatient clinicIndividuals 40 yearsType 2 diabetesHigh-risk individualsVanderbilt University Medical CenterUniversity Medical CenterLow-risk individualsPoor calibrationAfrican AmericansFuture risk modelsHealth care expendituresAF managementCohort studyEchocardiographic variables
2013
Characterization of Statin Dose Response in Electronic Medical Records
Wei W, Feng Q, Jiang L, Waitara M, Iwuchukwu O, Roden D, Jiang M, Xu H, Krauss R, Rotter J, Nickerson D, Davis R, Berg R, Peissig P, McCarty C, Wilke R, Denny J. Characterization of Statin Dose Response in Electronic Medical Records. Clinical Pharmacology & Therapeutics 2013, 95: 331-338. PMID: 24096969, PMCID: PMC3944214, DOI: 10.1038/clpt.2013.202.Peer-Reviewed Original ResearchMeSH KeywordsAlgorithmsAllelesAtorvastatinCholesterol, LDLCohort StudiesDatabases, FactualDose-Response Relationship, DrugElectronic Health RecordsGenotypeHeptanoic AcidsHumansHydroxymethylglutaryl-CoA Reductase InhibitorsHyperlipidemiasLipid MetabolismLipidsPhenotypePolymorphism, Single NucleotidePyrrolesRandomized Controlled Trials as TopicSimvastatinDevelopment and evaluation of an ensemble resource linking medications to their indications
Wei W, Cronin R, Xu H, Lasko T, Bastarache L, Denny J. Development and evaluation of an ensemble resource linking medications to their indications. Journal Of The American Medical Informatics Association 2013, 20: 954-961. PMID: 23576672, PMCID: PMC3756263, DOI: 10.1136/amiajnl-2012-001431.Peer-Reviewed Original ResearchDevelopment of an ensemble resource linking MEDications to their Indications (MEDI).
Wei W, Cronin R, Xu H, Lasko T, Bastarache L, Denny J. Development of an ensemble resource linking MEDications to their Indications (MEDI). AMIA Joint Summits On Translational Science Proceedings 2013, 2013: 172. PMID: 24303333.Peer-Reviewed Original Research
2012
Data mining methodologies for pharmacovigilance
Liu M, Matheny M, Hu Y, Xu H. Data mining methodologies for pharmacovigilance. ACM SIGKDD Explorations Newsletter 2012, 14: 35-42. DOI: 10.1145/2408736.2408742.Peer-Reviewed Original ResearchAdverse drug reactionsElectronic medical recordsLong-term adverse drug reactionsTerm adverse drug reactionPrevention of ADRsAdverse drug eventsPatient-reported dataPotential adverse drug reactionsNational surveillance systemEmergency departmentDrug eventsDrug reactionsPreclinical dataMedical recordsADR monitoringClinical trialsMedication safetyPreclinical characteristicsSpontaneous reportsPostmarketing phaseOnline health forumsPostmarketing stageDrug developmentHealth forumsPre-marketing stagesComparative analysis of pharmacovigilance methods in the detection of adverse drug reactions using electronic medical records
Liu M, Hinz E, Matheny M, Denny J, Schildcrout J, Miller R, Xu H. Comparative analysis of pharmacovigilance methods in the detection of adverse drug reactions using electronic medical records. Journal Of The American Medical Informatics Association 2012, 20: 420-426. PMID: 23161894, PMCID: PMC3628053, DOI: 10.1136/amiajnl-2012-001119.Peer-Reviewed Original ResearchConceptsAdverse drug reactionsElectronic medical recordsProportional reporting ratioVanderbilt University Medical CenterSpontaneous reporting systemDrug-event pairsDrug reactionsMedical recordsMedication ordersAbnormal laboratory resultsDrug-exposed groupNew adverse drug reactionsUniversity Medical CenterSpecific drug administrationReference standardLaboratory resultsUnexposed groupGamma Poisson ShrinkerMedical CenterPatient harmDrug AdministrationPharmacovigilance measuresBayesian confidence propagation neural networkEarly detectionReporting ratioA study of transportability of an existing smoking status detection module across institutions.
Liu M, Shah A, Jiang M, Peterson N, Dai Q, Aldrich M, Chen Q, Bowton E, Liu H, Denny J, Xu H. A study of transportability of an existing smoking status detection module across institutions. AMIA Annual Symposium Proceedings 2012, 2012: 577-86. PMID: 23304330, PMCID: PMC3540509.Peer-Reviewed Original ResearchConceptsDetection moduleNatural language processing systemsKnowledge Extraction SystemEMR dataRule-based classifierClinical Text AnalysisHighest F-measureLanguage processing systemElectronic medical recordsF-measureLevels of classificationProcessing systemSpecific tasksText analysisClassifierDesirable performanceModuleModest effortExtraction systemCTAKESSmoking moduleMachineSystemTaskClassificationDetecting Adverse Drug Reactions using Inpatient Medication Orders and Laboratory Tests Data
Liu M, Matheny M, Wu Y, Hinz E, Denny J, Schildcrout J, Miller R, Xu H. Detecting Adverse Drug Reactions using Inpatient Medication Orders and Laboratory Tests Data. 2012, 1: 131-131. DOI: 10.1109/hisb.2012.56.Peer-Reviewed Original ResearchAdverse drug reactionsElectronic medical recordsSpontaneous reporting systemProportional reporting ratioDrug reactionsMedication ordersDrug ordersInpatient medication ordersAbnormal laboratory resultsTime of admissionDrug-exposed groupChi-square testLaboratory resultsGamma Poisson ShrinkerUnexposed groupMedical recordsOdds ratioMedication safetyPatient harmBayesian confidence propagation neural networkEarly detectionReporting ratioEMR dataDay zeroReporting systemElectronic Medical Records as a Tool in Clinical Pharmacology: Opportunities and Challenges
Roden D, Xu H, Denny J, Wilke R. Electronic Medical Records as a Tool in Clinical Pharmacology: Opportunities and Challenges. Clinical Pharmacology & Therapeutics 2012, 91: 1083-1086. PMID: 22534870, PMCID: PMC3819803, DOI: 10.1038/clpt.2012.42.Peer-Reviewed Original ResearchThe use of a DNA biobank linked to electronic medical records to characterize pharmacogenomic predictors of tacrolimus dose requirement in kidney transplant recipients
Birdwell K, Grady B, Choi L, Xu H, Bian A, Denny J, Jiang M, Vranic G, Basford M, Cowan J, Richardson D, Robinson M, Ikizler T, Ritchie M, Stein C, Haas D. The use of a DNA biobank linked to electronic medical records to characterize pharmacogenomic predictors of tacrolimus dose requirement in kidney transplant recipients. Pharmacogenetics And Genomics 2012, 22: 32-42. PMID: 22108237, PMCID: PMC3237759, DOI: 10.1097/fpc.0b013e32834e1641.Peer-Reviewed Original ResearchMeSH KeywordsAdultAge FactorsATP Binding Cassette Transporter, Subfamily BATP Binding Cassette Transporter, Subfamily B, Member 1Body WeightCytochrome P-450 CYP3ADatabases, Nucleic AcidDose-Response Relationship, DrugDrug MonitoringElectronic Health RecordsFemaleGenetic Association StudiesGenotypeHemoglobinsHumansImmunosuppressive AgentsKidney TransplantationLinkage DisequilibriumMaleMiddle AgedPolymorphism, Single NucleotidePregnane X ReceptorReceptors, SteroidTacrolimusConceptsTacrolimus dose requirementsKidney transplant recipientsDose requirementsElectronic medical recordsBlood concentrationsTransplant recipientsMedical recordsCYP3A5 rs776746Electronic medical record dataInterindividual pharmacokinetic variabilityTacrolimus blood concentrationsNarrow therapeutic indexDNA biobanksMedical record dataTherapeutic drug monitoringDrug-metabolizing enzymesKidney transplantationClinical factorsPrimary outcomeImmunosuppressive drugsPharmacokinetic variabilityTacrolimus clearanceClinical covariatesPharmacogenomic predictorsTherapeutic index
2011
Modeling drug exposure data in electronic medical records: an application to warfarin.
Liu M, Jiang M, Kawai V, Stein C, Roden D, Denny J, Xu H. Modeling drug exposure data in electronic medical records: an application to warfarin. AMIA Annual Symposium Proceedings 2011, 2011: 815-23. PMID: 22195139, PMCID: PMC3243123.Peer-Reviewed Original ResearchConceptsNatural language processingMachine learning technologiesElectronic medical recordsDrug exposure informationLearning technologyLanguage processingTemporal informationInformatics frameworkClinical narrativesDrug mentionsMedical recordsDrug exposure dataFrameworkReceiver operator characteristic curveDrug exposure historyInformationDrug-related researchWarfarin exposureDrug regimensHospital admissionDrug exposureAccurate modelingDrug informationExposure informationExposure dataThe Emerging Role of Electronic Medical Records in Pharmacogenomics
Wilke R, Xu H, Denny J, Roden D, Krauss R, McCarty C, Davis R, Skaar T, Lamba J, Savova G. The Emerging Role of Electronic Medical Records in Pharmacogenomics. Clinical Pharmacology & Therapeutics 2011, 89: 379-386. PMID: 21248726, PMCID: PMC3204342, DOI: 10.1038/clpt.2010.260.Peer-Reviewed Original Research
2010
Extracting timing and status descriptors for colonoscopy testing from electronic medical records
Denny J, Peterson J, Choma N, Xu H, Miller R, Bastarache L, Peterson N. Extracting timing and status descriptors for colonoscopy testing from electronic medical records. Journal Of The American Medical Informatics Association 2010, 17: 383-388. PMID: 20595304, PMCID: PMC2995656, DOI: 10.1136/jamia.2010.004804.Peer-Reviewed Original ResearchConceptsElectronic medical recordsMedical recordsColorectal cancer screening ratesCRC screening statusCancer screening ratesManual reviewStatus indicatorsHealth services researchersColonoscopy testingEMR notesTypes of CRCScreening statusScreening ratesColonoscopy screeningBilling codesUseful adjunctGold standardElectronic recordsColonoscopyPatientsServices researchersFurther investigationRandom sampleTemporal expressionMedEx: a medication information extraction system for clinical narratives
Xu H, Stenner S, Doan S, Johnson K, Waitman L, Denny J. MedEx: a medication information extraction system for clinical narratives. Journal Of The American Medical Informatics Association 2010, 17: 19-24. PMID: 20064797, PMCID: PMC2995636, DOI: 10.1197/jamia.m3378.Peer-Reviewed Original ResearchConceptsClinic visit notesVisit notesMedication informationClinical notesDischarge summariesElectronic medical record dataMedical record dataElectronic medical recordsMedication dataMedical recordsClinical dataClinical researchRecord dataHealthcare safetyDrug namesMedexF-measureClinical narrativesNatural language processing systemsInformation extraction system
2009
Development of a natural language processing system to identify timing and status of colonoscopy testing in electronic medical records.
Denny J, Peterson J, Choma N, Xu H, Miller R, Bastarache L, Peterson N. Development of a natural language processing system to identify timing and status of colonoscopy testing in electronic medical records. AMIA Annual Symposium Proceedings 2009, 2009: 141. PMID: 20351837, PMCID: PMC2815478.Peer-Reviewed Original ResearchConceptsNatural language processingNatural language processing systemsElectronic medical recordsLanguage processing systemNLP systemsIdentifier systemLanguage processingMedical recordsProcessing systemElectronic textsColorectal cancer screening ratesCancer screening ratesPrimary care populationColonoscopy testingScreening ratesCare populationBilling codesQueriesColonoscopySystemStatus indicatorsAlgorithmCodeProcessingStatus