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.ChaptersMeSH KeywordsAntiviral AgentsArtificial IntelligenceCOVID-19 Drug TreatmentHumansPandemicsSARS-CoV-2Systems BiologyConceptsSystems biology approachBiology approachHigh-performance computingArtificial intelligence methodologiesDiversity of informationIntelligence methodologiesStructural proteomicsSystem-level infrastructureMultiomics integrationCore frameworkViral pathogenesisAntiviral strategiesWealth of informationUnprecedented accessPathogensComputingComputational protocolPathogen detectionInformationProteomicsAdaptation analysisDevelopment of vaccinesProtocolInfrastructureNetwork
2021
Dexamethasone in hospitalised COVID-19 patients not on intensive respiratory support
Crothers K, DeFaccio R, Tate J, Alba PR, Goetz MB, Jones B, King JT, Marconi V, Ohl ME, Rentsch CT, Rodriguez-Barradas MC, Shahrir S, Justice AC, Akgün KM, Group F. Dexamethasone in hospitalised COVID-19 patients not on intensive respiratory support. European Respiratory Journal 2021, 60: 2102532. PMID: 34824060, PMCID: PMC8841623, DOI: 10.1183/13993003.02532-2021.Peer-Reviewed Original ResearchConceptsIntensive respiratory supportHospitalised COVID-19 patientsCOVID-19 patientsNasal cannulaEarly dexamethasoneRespiratory supportSevere acute respiratory syndrome coronavirus 2Low-flow nasal cannulaAcute respiratory syndrome coronavirus 2Coronavirus disease 2019 (COVID-19) patientsRespiratory syndrome coronavirus 2Cox proportional hazards modelUS Veterans Affairs hospitalsSyndrome coronavirus 2Veterans Affairs hospitalProportional hazards modelCOVID-19Prior corticosteroidsCause mortalityMortality benefitTotal patientsCoronavirus 2Unexposed groupReal-world findingsEarly initiationPharmacoepidemiology, Machine Learning, and COVID-19: An Intent-to-Treat Analysis of Hydroxychloroquine, With or Without Azithromycin, and COVID-19 Outcomes Among Hospitalized US Veterans
Gerlovin H, Posner DC, Ho YL, Rentsch CT, Tate JP, King JT, Kurgansky KE, Danciu I, Costa L, Linares FA, Goethert ID, Jacobson DA, Freiberg MS, Begoli E, Muralidhar S, Ramoni RB, Tourassi G, Gaziano JM, Justice AC, Gagnon DR, Cho K. Pharmacoepidemiology, Machine Learning, and COVID-19: An Intent-to-Treat Analysis of Hydroxychloroquine, With or Without Azithromycin, and COVID-19 Outcomes Among Hospitalized US Veterans. American Journal Of Epidemiology 2021, 190: 2405-2419. PMID: 34165150, PMCID: PMC8384407, DOI: 10.1093/aje/kwab183.Peer-Reviewed Original ResearchMeSH KeywordsAgedAged, 80 and overAnti-Bacterial AgentsAzithromycinCOVID-19COVID-19 Drug TreatmentDrug Therapy, CombinationFemaleHospitalizationHumansHydroxychloroquineIntention to Treat AnalysisMachine LearningMaleMiddle AgedPharmacoepidemiologyRetrospective StudiesSARS-CoV-2Treatment OutcomeUnited StatesVeteransConceptsUS veteransCOVID-19Veterans Affairs Health Care SystemRecent randomized clinical trialsAdministration of hydroxychloroquineEffectiveness of hydroxychloroquineRisk of intubationEffect of hydroxychloroquineElectronic health record dataRandomized clinical trialsTreatment of patientsUS veteran populationCOVID-19 outcomesCoronavirus disease 2019Health record dataRigorous study designsHealth care systemSurvival benefitTreat analysisEarly therapyHospitalized populationClinical trialsObservational studyDisease 2019HydroxychloroquineCOVID-19 Evidence Accelerator: A parallel analysis to describe the use of Hydroxychloroquine with or without Azithromycin among hospitalized COVID-19 patients
Stewart M, Rodriguez-Watson C, Albayrak A, Asubonteng J, Belli A, Brown T, Cho K, Das R, Eldridge E, Gatto N, Gelman A, Gerlovin H, Goldberg SL, Hansen E, Hirsch J, Ho YL, Ip A, Izano M, Jones J, Justice AC, Klesh R, Kuranz S, Lam C, Mao Q, Mataraso S, Mera R, Posner DC, Rassen JA, Siefkas A, Schrag A, Tourassi G, Weckstein A, Wolf F, Bhat A, Winckler S, Sigal EV, Allen J. COVID-19 Evidence Accelerator: A parallel analysis to describe the use of Hydroxychloroquine with or without Azithromycin among hospitalized COVID-19 patients. PLOS ONE 2021, 16: e0248128. PMID: 33730088, PMCID: PMC7968637, DOI: 10.1371/journal.pone.0248128.Peer-Reviewed Original ResearchMeSH KeywordsAntiviral AgentsAzithromycinCOVID-19 Drug TreatmentData ManagementDrug Therapy, CombinationFemaleHospitalizationHumansHydroxychloroquineMalePandemicsSARS-CoV-2ConceptsHospitalized COVID-19 patientsCOVID-19 patientsUse of hydroxychloroquineElectronic health recordsAdverse eventsTreatment groupsCOVID-19Administration of hydroxychloroquineReagan-Udall FoundationProportional hazards modelHealth systems researchHospitalized patientsElevated riskPropensity score methodsHazards modelHydroxychloroquinePatientsSignificant global threatPharmaceutical interventionsAzithromycinHealth recordsMortalityCOVID-19 pandemicCancer researchTreatment