Featured Publications
Spatial Modeling of Mycobacterium Tuberculosis Transmission with Dyadic Genetic Relatedness Data
Warren J, Chitwood M, Sobkowiak B, Colijn C, Cohen T. Spatial Modeling of Mycobacterium Tuberculosis Transmission with Dyadic Genetic Relatedness Data. Biometrics 2023, 79: 3650-3663. PMID: 36745619, PMCID: PMC10404301, DOI: 10.1111/biom.13836.Peer-Reviewed Original ResearchA Bayesian framework for incorporating exposure uncertainty into health analyses with application to air pollution and stillbirth
Comess S, Chang HH, Warren JL. A Bayesian framework for incorporating exposure uncertainty into health analyses with application to air pollution and stillbirth. Biostatistics 2022, 25: 20-39. PMID: 35984351, PMCID: PMC10724312, DOI: 10.1093/biostatistics/kxac034.Peer-Reviewed Original ResearchConceptsFull conditional distributionsEfficient model fittingStatistical modeling approachDensity estimation approachBayesian settingKernel density estimation approachPosterior outputBayesian frameworkConditional distributionModel fittingEstimation approachAccurate inferenceKDE approachModeling approachComparison metricsExposure uncertaintyUncertaintySecond stageApproachFittingInferencePredictionSimulationsModel comparison metricsFirst stageCritical window variable selection: estimating the impact of air pollution on very preterm birth
Warren JL, Kong W, Luben TJ, Chang HH. Critical window variable selection: estimating the impact of air pollution on very preterm birth. Biostatistics 2019, 21: 790-806. PMID: 30958877, PMCID: PMC7422642, DOI: 10.1093/biostatistics/kxz006.Peer-Reviewed Original ResearchConceptsHierarchical Bayesian frameworkBayesian frameworkStatistical modelVariable selectionImproved estimationCritical windowPreterm birthRisk parametersVery preterm birthAdverse birth outcomesControl analysisExposure-disease relationshipsDifferent reproductive outcomesBirth outcomesPregnant womenReproductive outcomesCase/control analysisSpatial-Temporal Modeling of the Association Between Air Pollution Exposure and Preterm Birth: Identifying Critical Windows of Exposure
Warren J, Fuentes M, Herring A, Langlois P. Spatial-Temporal Modeling of the Association Between Air Pollution Exposure and Preterm Birth: Identifying Critical Windows of Exposure. Biometrics 2012, 68: 1157-1167. PMID: 22568640, PMCID: PMC3422613, DOI: 10.1111/j.1541-0420.2012.01774.x.Peer-Reviewed Original ResearchAssessment of critical exposure and outcome windows in time-to-event analysis with application to air pollution and preterm birth study
Chang HH, Warren JL, Darrow LA, Reich BJ, Waller LA. Assessment of critical exposure and outcome windows in time-to-event analysis with application to air pollution and preterm birth study. Biostatistics 2015, 16: 509-521. PMID: 25572998, PMCID: PMC5963471, DOI: 10.1093/biostatistics/kxu060.Peer-Reviewed Original ResearchConceptsPreterm birthAir pollution exposureGestational air pollution exposureRisk of PTBPollution exposurePreterm Birth StudyCourse of pregnancyTime-varying exposureOngoing pregnancyBirth StudyGestational exposureReproductive epidemiologyWeek 30PregnancyWeekly exposureBirth recordsVulnerable periodPopulation studiesPositive associationCritical periodExposureInconsistent findingsAssociationExposure lengthFine particulate matterBayesian multinomial probit modeling of daily windows of susceptibility for maternal PM2.5 exposure and congenital heart defects
Warren JL, Stingone JA, Herring AH, Luben TJ, Fuentes M, Aylsworth AS, Langlois PH, Botto LD, Correa A, Olshan AF, Study B. Bayesian multinomial probit modeling of daily windows of susceptibility for maternal PM2.5 exposure and congenital heart defects. Statistics In Medicine 2016, 35: 2786-2801. PMID: 26853919, PMCID: PMC4899303, DOI: 10.1002/sim.6891.Peer-Reviewed Original ResearchConceptsGestational weeks 2Week 2PM2.5 exposureCongenital heartAmbient air pollution exposureMaternal PM2.5 exposureTetralogy of FallotNational Birth Defect Prevention StudyAir pollution exposureCritical periodDaily PM2.5 exposurePrevention StudyExposure modelEpidemiologic studiesFetal developmentHealth outcomesSignificant associationPollution exposureDay 53PregnancyDay 50Adverse effectsElevated exposureExposureHeartSpatial Variability in the Persistence of Pneumococcal Conjugate Vaccine-targeted Pneumococcal Serotypes Among Adults
Warren JL, Pingali SC, Weinberger DM. Spatial Variability in the Persistence of Pneumococcal Conjugate Vaccine-targeted Pneumococcal Serotypes Among Adults. Epidemiology 2017, 28: 119-126. PMID: 27541841, PMCID: PMC5131859, DOI: 10.1097/ede.0000000000000551.Peer-Reviewed Original ResearchConceptsVaccine-targeted serotypesInvasive pneumococcal disease casesPneumococcal disease casesDirect vaccinationDisease casesInvasive pneumococcal diseaseConjugate vaccinePneumococcal diseaseVaccine serotypesVaccine uptakePneumococcal serotypesLeading causeBaseline proportionRate of declineNumber of casesAdult populationVaccinationStudy periodVaccineSerotypesAdultsChildrenHigh levelsMorbidityGeographic regionsA Dirichlet process mixture model for clustering longitudinal gene expression data
Sun J, Herazo‐Maya J, Kaminski N, Zhao H, Warren JL. A Dirichlet process mixture model for clustering longitudinal gene expression data. Statistics In Medicine 2017, 36: 3495-3506. PMID: 28620908, PMCID: PMC5583037, DOI: 10.1002/sim.7374.Peer-Reviewed Original ResearchConceptsLongitudinal gene expression profilesDirichlet process prior distributionRegression coefficientsExtensive simulation studyLongitudinal gene expression dataBayesian settingPrior distributionClustering methodFactor analysis modelDimensionality challengeStatistical methodsSimulation studyNovel clustering methodHigh dimensionality challengeSubgroup identificationImportant problemGene expression dataInteresting subgroupsClusteringCoefficientAnalysis modelModelExpression data
2024
Using a Bayesian analytic approach to identify county-level ecological factors associated with survival among individuals with early-onset colorectal cancer
Siddique S, Baum L, Deziel N, Kelly J, Warren J, Ma X. Using a Bayesian analytic approach to identify county-level ecological factors associated with survival among individuals with early-onset colorectal cancer. PLOS ONE 2024, 19: e0311540. PMID: 39471191, PMCID: PMC11521299, DOI: 10.1371/journal.pone.0311540.Peer-Reviewed Original ResearchConceptsAge-of-onset colorectal cancerEarly-onset colorectal cancerEnd Results Program dataCenters for Disease Control and Prevention dataCounty-level factorsColorectal cancerHealth risk behaviorsIdentified principal componentsOdds of survivalPreventive servicesSurvival disparitiesLinear mixed modelsEOCRCChronic diseasesPreventive factorsUS countiesSalt Lake CountyCA residentsRisk behaviorsUnited StatesProgram dataCounty-levelOlder ageBayesian analytical approachYounger ageHigh ambient temperature in pregnancy and risk of childhood acute lymphoblastic leukaemia: an observational study
Rogne T, Wang R, Wang P, Deziel N, Metayer C, Wiemels J, Chen K, Warren J, Ma X. High ambient temperature in pregnancy and risk of childhood acute lymphoblastic leukaemia: an observational study. The Lancet Planetary Health 2024, 8: e506-e514. PMID: 38969477, PMCID: PMC11260908, DOI: 10.1016/s2542-5196(24)00121-9.Peer-Reviewed Original ResearchConceptsRisk of childhood acute lymphoblastic leukemiaChildhood acute lymphoblastic leukemiaAcute lymphoblastic leukemiaLymphoblastic leukemiaLatino childrenNon-Latino white childrenAssociated with risk of adverse pregnancy outcomesCalifornia Cancer RegistryRisk of acute lymphoblastic leukemiaCalifornia birth recordsRisk of adverse pregnancy outcomesPre-pregnancy periodAssociated with riskBayesian meta-regressionNational Institutes of HealthCancer RegistryCases of childhood acute lymphoblastic leukemiaNational Center for Advancing Translational SciencesAdverse pregnancy outcomesAcute lymphoblastic leukemia casesInstitutes of HealthInvestigation of mechanistic pathwaysBirth recordsGestational weeks 8Pre-pregnancyPreterm and Early-Term Delivery After Heat Waves in 50 US Metropolitan Areas
Darrow L, Huang M, Warren J, Strickland M, Holmes H, Newman A, Chang H. Preterm and Early-Term Delivery After Heat Waves in 50 US Metropolitan Areas. JAMA Network Open 2024, 7: e2412055. PMID: 38787560, PMCID: PMC11127119, DOI: 10.1001/jamanetworkopen.2024.12055.Peer-Reviewed Original ResearchConceptsEarly-term birthPreterm birthCohort studyMetropolitan statistical areasAssociated with pregnancy outcomesEarly-term deliveryRate ratiosRates of pretermYears of ageNational Center for Health StatisticsGestational weeksCenter for Health StatisticsInduced deliveryPregnancy outcomesSingleton birthsPretermSocioeconomically disadvantaged subgroupsUS birthsEligible birthsPerinatal healthEthnic minority groupsBirth recordsConsecutive daysBirthHeat wavesIdentifying local foci of tuberculosis transmission in Moldova using a spatial multinomial logistic regression model
Lan Y, Crudu V, Ciobanu N, Codreanu A, Chitwood M, Sobkowiak B, Warren J, Cohen T. Identifying local foci of tuberculosis transmission in Moldova using a spatial multinomial logistic regression model. EBioMedicine 2024, 102: 105085. PMID: 38531172, PMCID: PMC10987885, DOI: 10.1016/j.ebiom.2024.105085.Peer-Reviewed Original ResearchConceptsPatterns of spatial aggregationMtb strainsMDR-TBLogistic regression modelsGenome Epidemiology StudySpecific strainsMultidrug-resistant tuberculosisTreated TB casesNational Institute of AllergyMDR phenotypeRegression modelsM. tuberculosisInstitute of AllergyMultinomial logistic regression modelUS National Institutes of HealthNational Institutes of HealthMDR diseasePublic health concernAssociated with local transmissionIncident TBInstitutes of HealthMtbResistant tuberculosisStrainDiagnosing TBA scalar-on-quantile-function approach for estimating short-term health effects of environmental exposures
Zhang Y, Chang H, Warren J, Ebelt S. A scalar-on-quantile-function approach for estimating short-term health effects of environmental exposures. Biometrics 2024, 80: ujae008. PMID: 38477485, PMCID: PMC10934338, DOI: 10.1093/biomtc/ujae008.Peer-Reviewed Original ResearchConceptsEmergency departmentAir pollutionHealth effects of environmental exposuresShort-term health effectsAnalysis of air pollutionStochastic Human ExposureAmbient air pollutionEnvironmental epidemiology studiesEffects of environmental exposuresAggregate health outcomesPopulation-level exposureHealth outcomesED visitsPopulation exposureHuman exposureExposure heterogeneitySpatial variationEpidemiological studiesEnvironmental exposuresPollutionHealth analysisEstimated effectsEffects of short-termVisitsQuantile function
2023
Association of Neighborhood-Level Socioeconomic Factors With Delay to Hospital Arrival in Patients With Acute Stroke
Forman R, Okumu R, Mageid R, Baker A, Neu D, Parker R, Peyravi R, Schindler J, Sansing L, Sheth K, de Havenon A, Jasne A, Narula R, Wira C, Warren J, Sharma R. Association of Neighborhood-Level Socioeconomic Factors With Delay to Hospital Arrival in Patients With Acute Stroke. Neurology 2023, 102: e207764. PMID: 38165368, PMCID: PMC10834135, DOI: 10.1212/wnl.0000000000207764.Peer-Reviewed Original ResearchConceptsEmergency department arrival timesEmergency medical servicesLate presentationAcute ischemic stroke therapyYale-New Haven HospitalGuidelines-Stroke registryNeighborhood-level socioeconomic factorsPatient-level factorsRetrospective observational studyIschemic stroke therapyMixed-effects logistic regression modelNon-white patientsNon-white raceUnivariate logistic regressionNew Haven HospitalLogistic regression modelsHospital presentationTreatment ineligibilityStroke RegistryAcute strokeHospital arrivalStroke therapyUnivariate analysisObservational studyPatientsEffects of air pollution on adverse birth outcomes and pregnancy complications in the U.S. state of Kansas (2000–2015)
Hao H, Yoo S, Strickland M, Darrow L, D’Souza R, Warren J, Moss S, Wang H, Zhang H, Chang H. Effects of air pollution on adverse birth outcomes and pregnancy complications in the U.S. state of Kansas (2000–2015). Scientific Reports 2023, 13: 21476. PMID: 38052850, PMCID: PMC10697947, DOI: 10.1038/s41598-023-48329-5.Peer-Reviewed Original ResearchConceptsGestational diabetes mellitusAdverse birth outcomesLow birth weightGestational hypertensionBirth outcomesBirth weightPregnancy complicationsPreterm birthFirst trimesterRisk of GDMMaternal medical complicationsSingleton live birthsWeeks of pregnancyO3 exposureAdverse pregnancyPregnancy exposurePregnancy outcomesDiabetes mellitusMedical complicationsAdverse birthThird trimesterNeonatal mortalityResidential census tractsSocio-economic status factorsDiscrete-time survivalIncorporating Data from Multiple Endpoints in the Analysis of Clinical Trials: Example from RSV Vaccines
Prunas O, Willemsen J, Bont L, Pitzer V, Warren J, Weinberger D. Incorporating Data from Multiple Endpoints in the Analysis of Clinical Trials: Example from RSV Vaccines. Epidemiology 2023, 35: 103-112. PMID: 37793120, DOI: 10.1097/ede.0000000000001680.Peer-Reviewed Original ResearchSpatially-targeted tuberculosis screening has limited impact beyond household contact tracing in Lima, Peru: A model-based analysis
Havumaki J, Warren J, Zelner J, Menzies N, Calderon R, Contreras C, Lecca L, Becerra M, Murray M, Cohen T. Spatially-targeted tuberculosis screening has limited impact beyond household contact tracing in Lima, Peru: A model-based analysis. PLOS ONE 2023, 18: e0293519. PMID: 37903091, PMCID: PMC10615320, DOI: 10.1371/journal.pone.0293519.Peer-Reviewed Original ResearchGlobal, regional, and national estimates of tuberculosis incidence and case detection among incarcerated individuals from 2000 to 2019: a systematic analysis
Martinez L, Warren J, Harries A, Croda J, Espinal M, Olarte R, Avedillo P, Lienhardt C, Bhatia V, Liu Q, Chakaya J, Denholm J, Lin Y, Kawatsu L, Zhu L, Horsburgh C, Cohen T, Andrews J. Global, regional, and national estimates of tuberculosis incidence and case detection among incarcerated individuals from 2000 to 2019: a systematic analysis. The Lancet Public Health 2023, 8: e511-e519. PMID: 37393090, PMCID: PMC10323309, DOI: 10.1016/s2468-2667(23)00097-x.Peer-Reviewed Original ResearchConceptsTuberculosis incidenceCase detection ratioIncidence rateCase detectionHigh tuberculosis incidence ratesGlobal tuberculosis control effortsIncident tuberculosis casesTuberculosis incidence rateIncarcerated individualsTuberculosis control effortsTuberculosis case detectionTuberculosis casesNotification ratesNational incidenceTuberculosis notificationsGlobal incidenceHigh riskPrevalence estimatesNational estimatesWHO regionsIncidenceStudy periodMeta-regression frameworkTuberculosisNational InstituteDevelopment of treatment-decision algorithms for children evaluated for pulmonary tuberculosis: an individual participant data meta-analysis
Gunasekera K, Marcy O, Muñoz J, Lopez-Varela E, Sekadde M, Franke M, Bonnet M, Ahmed S, Amanullah F, Anwar A, Augusto O, Aurilio R, Banu S, Batool I, Brands A, Cain K, Carratalá-Castro L, Caws M, Click E, Cranmer L, García-Basteiro A, Hesseling A, Huynh J, Kabir S, Lecca L, Mandalakas A, Mavhunga F, Myint A, Myo K, Nampijja D, Nicol M, Orikiriza P, Palmer M, Sant'Anna C, Siddiqui S, Smith J, Song R, Thuong Thuong N, Ung V, van der Zalm M, Verkuijl S, Viney K, Walters E, Warren J, Zar H, Marais B, Graham S, Debray T, Cohen T, Seddon J. Development of treatment-decision algorithms for children evaluated for pulmonary tuberculosis: an individual participant data meta-analysis. The Lancet Child & Adolescent Health 2023, 7: 336-346. PMID: 36924781, PMCID: PMC10127218, DOI: 10.1016/s2352-4642(23)00004-4.Peer-Reviewed Original ResearchConceptsTreatment decision algorithmsPrimary health care settingsIndividual participant dataHigh tuberculosis incidencePulmonary tuberculosisManagement of tuberculosisHealth care centersComposite reference standardHealth care settingsClinical featuresTuberculosis incidenceClinical evaluationParticipant dataTreatment decisionsChest X-ray featuresPrimary health care centersFuture prospective evaluationTuberculosis-related mortalityEvidence-based algorithmChest X-rayVariable diagnostic performanceMultivariable prediction modelReference standardEvidence-based approachTuberculosis expertsPatterns of Infectious Disease Associated With Injection Drug Use in Massachusetts
Gonsalves G, Paltiel A, Thornhill T, DeMaria A, Cranston K, Klevens R, Warren J. Patterns of Infectious Disease Associated With Injection Drug Use in Massachusetts. Clinical Infectious Diseases 2023, 76: 2134-2139. PMID: 36757712, PMCID: PMC10273381, DOI: 10.1093/cid/ciad073.Peer-Reviewed Original ResearchConceptsSoft tissue infectionsHuman immunodeficiency virusHepatitis C virusInjection drug useHCV casesInfective endocarditisHIV casesDrug useSubstance use disordersLogistic regression modelsClinical sequalaeSSTI casesPublic health crisisTissue infectionsImmunodeficiency virusDisease AssociatedHIV outbreakAbscess incisionC virusUse disordersInfectious diseasesInfectionMultiple outbreaksMedical proceduresSuch associations