2024
Biomedical blockchain with practical implementations and quantitative evaluations: a systematic review
Lacson R, Yu Y, Kuo T, Ohno-Machado L. Biomedical blockchain with practical implementations and quantitative evaluations: a systematic review. Journal Of The American Medical Informatics Association 2024, 31: 1423-1435. PMID: 38726710, PMCID: PMC11105130, DOI: 10.1093/jamia/ocae084.Peer-Reviewed Original ResearchConceptsElectronic health recordsSystematic reviewData sharingMedical data sharingSpeed metricsPreferred Reporting ItemsCertificate storageDecentralized InternetNetwork permissionsBlockchain platformBlockchain applicationsEvaluation metricsBiomedical domainBlockchainBiomedical data managementHealth recordsData managementData storageReporting ItemsHealth sectorQuantitative metricsMedical facilitiesMetricsTrial managementClinical trial management
2023
Blockchain-enabled immutable, distributed, and highly available clinical research activity logging system for federated COVID-19 data analysis from multiple institutions
Kuo T, Pham A, Edelson M, Kim J, Chan J, Gupta Y, Ohno-Machado L, Anderson D, Balacha C, Bath T, Baxter S, Becker-Pennrich A, Bell D, Bernstam E, Ngan C, Day M, Doctor J, DuVall S, El-Kareh R, Florian R, Follett R, Geisler B, Ghigi A, Gottlieb A, Hinske L, Hu Z, Ir D, Jiang X, Kim K, Kim J, Knight T, Koola J, Kuo T, Lee N, Mansmann U, Matheny M, Meeker D, Mou Z, Neumann L, Nguyen N, Nick A, Ohno-Machado L, Park E, Paul P, Pletcher M, Post K, Rieder C, Scherer C, Schilling L, Soares A, SooHoo S, Soysal E, Steven C, Tep B, Toy B, Wang B, Wu Z, Xu H, Yong C, Zheng K, Zhou Y, Zucker R. Blockchain-enabled immutable, distributed, and highly available clinical research activity logging system for federated COVID-19 data analysis from multiple institutions. Journal Of The American Medical Informatics Association 2023, 30: 1167-1178. PMID: 36916740, PMCID: PMC10198529, DOI: 10.1093/jamia/ocad049.Peer-Reviewed Original ResearchConceptsFederated data analysisUser activity logsSmart contract deploymentRun-time efficiencyData analysis systemData analysis activitiesActivity logsData discoveryQuerying timeBlockchain systemBlockchain technologyNetwork transactionsCOVID-19 data analysisMultiple institutionsLow deploymentBlockchainGitHub repositoryMultiple nodesLarge networksQueriesAnalysis activitiesHigh availabilityLanguage codeBaseline solutionData analysis
2022
Concordance of SARS-CoV-2 Antibody Results during a Period of Low Prevalence
Miller C, Althoff K, Schlueter D, Anton-Culver H, Chen Q, Garbett S, Ratsimbazafy F, Thomsen I, Karlson E, Cicek M, Pinto L, Malin B, Ohno-Machado L, Williams C, Goldstein D, Kouame A, Ramirez A, Gebo K, Schully S. Concordance of SARS-CoV-2 Antibody Results during a Period of Low Prevalence. MSphere 2022, 7: e00257-22. PMID: 36173112, PMCID: PMC9599436, DOI: 10.1128/msphere.00257-22.Peer-Reviewed Original ResearchConceptsSARS-CoV-2 antibody concentrationsLow prevalenceVaccine availabilitySARS-CoV-2 enzyme-linked immunosorbent assayFalse positivityLow SARS-CoV-2 prevalenceSARS-CoV-2 IgG assaysSARS-CoV-2 IgG testSARS-CoV-2 IgG antibodiesSevere acute respiratory syndrome coronavirus 2Coronavirus disease 2019 prevalenceAcute respiratory syndrome coronavirus 2Antibody concentrationsSARS-CoV-2 testDifferent antigensRespiratory syndrome coronavirus 2SARS-CoV-2 prevalenceSyndrome coronavirus 2SARS-CoV-2 pandemicConcordant positive resultsConcordant negative resultsEnzyme-linked immunosorbent assayPositive resultsFuture pandemic preparednessConcordance of results
2021
Antibodies to Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in All of Us Research Program Participants, 2 January to 18 March 2020
Althoff K, Schlueter D, Anton-Culver H, Cherry J, Denny J, Thomsen I, Karlson E, Havers F, Cicek M, Thibodeau S, Pinto L, Lowy D, Malin B, Ohno-Machado L, Williams C, Goldstein D, Kouame A, Ramirez A, Roman A, Sharpless N, Gebo K, Schully S. Antibodies to Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in All of Us Research Program Participants, 2 January to 18 March 2020. Clinical Infectious Diseases 2021, 74: 584-590. PMID: 34128970, PMCID: PMC8384413, DOI: 10.1093/cid/ciab519.Peer-Reviewed Original ResearchConceptsEnzyme-linked immunosorbent assayBlood specimensSARS-CoV-2 enzyme-linked immunosorbent assaySARS-CoV-2 immunoglobulin G (IgG) antibodiesSARS-CoV-2 antibodiesIgG enzyme-linked immunosorbent assayConfidence intervalsImmunoglobulin G antibodiesSARS-CoV-2Sequential testing algorithmEUROIMMUN assaysSymptomatic patientsTesting algorithmStudy visitG antibodiesCommunity transmissionTravel historyStudy participantsUS epidemicEarly weeksImmunosorbent assayTesting capacityAntibodiesWeeksUS statesPrivacy-protecting, reliable response data discovery using COVID-19 patient observations
Kim J, Neumann L, Paul P, Day M, Aratow M, Bell D, Doctor J, Hinske L, Jiang X, Kim K, Matheny M, Meeker D, Pletcher M, Schilling L, SooHoo S, Xu H, Zheng K, Ohno-Machado L, Anderson D, Anderson N, Balacha C, Bath T, Baxter S, Becker-Pennrich A, Bernstam E, Carter W, Chau N, Choi Y, Covington S, DuVall S, El-Kareh R, Florian R, Follett R, Geisler B, Ghigi A, Gottlieb A, Hu Z, Ir D, Knight T, Koola J, Kuo T, Lee N, Mansmann U, Mou Z, Murphy R, Neumann L, Nguyen N, Niedermayer S, Park E, Perkins A, Post K, Rieder C, Scherer C, Soares A, Soysal E, Tep B, Toy B, Wang B, Wu Z, Zhou Y, Zucker R. Privacy-protecting, reliable response data discovery using COVID-19 patient observations. Journal Of The American Medical Informatics Association 2021, 28: 1765-1776. PMID: 34051088, PMCID: PMC8194878, DOI: 10.1093/jamia/ocab054.Peer-Reviewed Original Research
2020
How do we share data in COVID-19 research? A systematic review of COVID-19 datasets in PubMed Central Articles
Zuo X, Chen Y, Ohno-Machado L, Xu H. How do we share data in COVID-19 research? A systematic review of COVID-19 datasets in PubMed Central Articles. Briefings In Bioinformatics 2020, 22: 800-811. PMID: 33757278, PMCID: PMC7799277, DOI: 10.1093/bib/bbaa331.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsUse of electronic health records to support a public health response to the COVID-19 pandemic in the United States: a perspective from 15 academic medical centers
Madhavan S, Bastarache L, Brown J, Butte A, Dorr D, Embi P, Friedman C, Johnson K, Moore J, Kohane I, Payne P, Tenenbaum J, Weiner M, Wilcox A, Ohno-Machado L. Use of electronic health records to support a public health response to the COVID-19 pandemic in the United States: a perspective from 15 academic medical centers. Journal Of The American Medical Informatics Association 2020, 28: 393-401. PMID: 33260207, PMCID: PMC7665546, DOI: 10.1093/jamia/ocaa287.Commentaries, Editorials and LettersCOVID-19 TestNorm: A tool to normalize COVID-19 testing names to LOINC codes
Dong X, Li J, Soysal E, Bian J, DuVall S, Hanchrow E, Liu H, Lynch K, Matheny M, Natarajan K, Ohno-Machado L, Pakhomov S, Reeves R, Sitapati A, Abhyankar S, Cullen T, Deckard J, Jiang X, Murphy R, Xu H. COVID-19 TestNorm: A tool to normalize COVID-19 testing names to LOINC codes. Journal Of The American Medical Informatics Association 2020, 27: 1437-1442. PMID: 32569358, PMCID: PMC7337837, DOI: 10.1093/jamia/ocaa145.Peer-Reviewed Original ResearchConceptsElectronic health recordsLOINC codesSecondary useRule-based toolOnline web applicationOpen-source packageCritical data elementsWeb applicationData networksEnd usersData elementsIndependent test setHealth recordsTest setKey challengesData normalizationCritical resourcesTest namesRoutine clinical practice dataCodeClinical practice dataCoronavirus disease 2019COVID-19 diagnostic testsToolDevelopersCoronavirus: indexed data speed up solutions
Ohno-Machado L, Xu H. Coronavirus: indexed data speed up solutions. Nature 2020, 584: 192-192. PMID: 32782375, DOI: 10.1038/d41586-020-02331-3.Commentaries, Editorials and Letters