2022
A research agenda to support the development and implementation of genomics-based clinical informatics tools and resources
Wiley K, Findley L, Goldrich M, Rakhra-Burris T, Stevens A, Williams P, Bult C, Chisholm R, Deverka P, Ginsburg G, Green E, Jarvik G, Mensah G, Ramos E, Relling M, Roden D, Rowley R, Alterovitz G, Aronson S, Bastarache L, Cimino J, Crowgey E, Del Fiol G, Freimuth R, Hoffman M, Jeff J, Johnson K, Kawamoto K, Madhavan S, Mendonca E, Ohno-Machado L, Pratap S, Taylor C, Ritchie M, Walton N, Weng C, Zayas-Cabán T, Manolio T, Williams M. A research agenda to support the development and implementation of genomics-based clinical informatics tools and resources. Journal Of The American Medical Informatics Association 2022, 29: 1342-1349. PMID: 35485600, PMCID: PMC9277642, DOI: 10.1093/jamia/ocac057.Peer-Reviewed Original Research
2020
Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples
Bailey MH, Meyerson WU, Dursi LJ, Wang LB, Dong G, Liang WW, Weerasinghe A, Li S, Li Y, Kelso S, Saksena G, Ellrott K, Wendl M, Wheeler D, Getz G, Simpson J, Gerstein M, Ding L. Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples. Nature Communications 2020, 11: 4748. PMID: 32958763, PMCID: PMC7505971, DOI: 10.1038/s41467-020-18151-y.Peer-Reviewed Original ResearchiDASH secure genome analysis competition 2018: blockchain genomic data access logging, homomorphic encryption on GWAS, and DNA segment searching
Kuo T, Jiang X, Tang H, Wang X, Bath T, Bu D, Wang L, Harmanci A, Zhang S, Zhi D, Sofia H, Ohno-Machado L. iDASH secure genome analysis competition 2018: blockchain genomic data access logging, homomorphic encryption on GWAS, and DNA segment searching. BMC Medical Genomics 2020, 13: 98. PMID: 32693816, PMCID: PMC7372776, DOI: 10.1186/s12920-020-0715-0.Peer-Reviewed Original Research
2018
Genomics and electronic health record systems
Ohno-Machado L, Kim J, Gabriel R, Kuo G, Hogarth M. Genomics and electronic health record systems. Human Molecular Genetics 2018, 27: r48-r55. PMID: 29741693, PMCID: PMC5946823, DOI: 10.1093/hmg/ddy104.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsConceptsElectronic health recordsHigh-level viewElectronic health record systemsHealth record systemsNext generation systemsEHR systemsSeamless fashionOpen issuesMyriad of approachesHealth recordsRecord systemSpecific solutionsEnd goalSources of informationAnalysis of genomesInformationCustomizationSystemGeneration systemVisionDegrees of successFunctionality
2017
Whole genome sequencing of an African American family highlights toll like receptor 6 variants in Kawasaki disease susceptibility
Kim J, Shimizu C, Kingsmore S, Veeraraghavan N, Levy E, dos Santos A, Yang H, Flatley J, Hoang L, Hibberd M, Tremoulet A, Harismendy O, Ohno-Machado L, Burns J. Whole genome sequencing of an African American family highlights toll like receptor 6 variants in Kawasaki disease susceptibility. PLOS ONE 2017, 12: e0170977. PMID: 28151979, PMCID: PMC5289527, DOI: 10.1371/journal.pone.0170977.Peer-Reviewed Original ResearchConceptsWhole genome sequencesGenome-wide association studiesToll-like receptor 6Single nucleotide variantsCommon disease-rare variant hypothesisExpression quantitative trait loci (eQTL) analysisDifferential expressionQuantitative trait locus (QTL) analysisCommon disease–common variantPathogen-associated molecular pattern recognitionIntegrative genomics approachIntronic single nucleotide variantsComplex genetic diseasesSequence quality scoresMolecular pattern recognitionWhole-genome sequencingGenomic approachesTranscriptome dataGenome sequenceSequence variationLocus analysisGenome sequencingAssociation studiesFunction of genotypeNucleotide variants
2014
Choosing blindly but wisely: differentially private solicitation of DNA datasets for disease marker discovery
Zhao Y, Wang X, Jiang X, Ohno-Machado L, Tang H. Choosing blindly but wisely: differentially private solicitation of DNA datasets for disease marker discovery. Journal Of The American Medical Informatics Association 2014, 22: 100-108. PMID: 25352565, PMCID: PMC4433380, DOI: 10.1136/amiajnl-2014-003043.Peer-Reviewed Original ResearchConceptsData ownersData usersHuman genomic datasetsHuman genomic dataPatient privacyPrivacyGeneration approachUsersData selectionReal dataDatasetGenomic datasetsPrivate solicitationDNA datasetsScientific discoveryNew approachGenomic dataHigh confidencePilot versionEvaluation methodRight choiceOwnersAlgorithmNew techniqueDisease marker discovery
2012
SurfaceomeDB: a cancer-orientated database for genes encoding cell surface proteins.
de Souza J, Galante P, de Almeida R, da Cunha J, Ohara D, Ohno-Machado L, Old L, de Souza S. SurfaceomeDB: a cancer-orientated database for genes encoding cell surface proteins. Cancer Immunology Research 2012, 12: 15. PMID: 23390370, PMCID: PMC3554024.Peer-Reviewed Original ResearchConceptsCell surface proteinsSurface proteinsProtein-protein interactionsUCSC Genome BrowserImportant data repositoryUser-friendly web interfaceGene annotationProtein domainsGenome browserHuman genesGene expressionGene namesGenesSomatic mutationsProteinExcellent targetAnnotationTherapeutic reagentsWeb interfaceNCBIMutationsExpressionDomainTarget
2011
Distinct patterns of somatic alterations in a lymphoblastoid and a tumor genome derived from the same individual
Galante P, Parmigiani R, Zhao Q, Caballero O, de Souza J, Navarro F, Gerber A, Nicolás M, Salim A, Silva A, Edsall L, Devalle S, Almeida L, Ye Z, Kuan S, Pinheiro D, Tojal I, Pedigoni R, de Sousa R, Oliveira T, de Paula M, Ohno-Machado L, Kirkness E, Levy S, da Silva W, Vasconcelos A, Ren B, Zago M, Strausberg R, Simpson A, de Souza S, Camargo A. Distinct patterns of somatic alterations in a lymphoblastoid and a tumor genome derived from the same individual. Nucleic Acids Research 2011, 39: 6056-6068. PMID: 21493686, PMCID: PMC3152357, DOI: 10.1093/nar/gkr221.Peer-Reviewed Original ResearchConceptsTumor genomesSomatic alterationsProtein-protein interaction analysisSynonymous substitutionsKEGG analysisEndogenous mutagensGenomeTumorigenic transformationNucleotide substitutionsBreast tumor cell linesReplication errorsTumor cell linesGenetic alterationsFrequency of mutationsCell linesTumorigenesisMutationsSynergistic functionDistinct patternsInteraction analysisLymphoblastoidAlterationsGenesSame individualPathway
2010
A potential role for intragenic miRNAs on their hosts' interactome
Hinske L, Galante P, Kuo W, Ohno-Machado L. A potential role for intragenic miRNAs on their hosts' interactome. BMC Genomics 2010, 11: 533. PMID: 20920310, PMCID: PMC3091682, DOI: 10.1186/1471-2164-11-533.Peer-Reviewed Original ResearchConceptsIntragenic miRNAsHost genesAdenylate/uridylate-rich elementsMiRNA targetsMRNA targetsHost interactomeGene cohortsMiRNA biogenesis pathwayNon-coding RNA moleculesHigh-confidence setMiRNA target genesProtein-coding regionsKEGG pathway analysisTight regulatory controlNegative feedback regulatorIntronic miRNAsMore intronsBiogenesis pathwayMiRNA genesNegative feedback loopUridylate-rich elementsCellular homeostasisTarget genesRNA moleculesInteractome
2006
Approximation properties of haplotype tagging
Vinterbo S, Dreiseitl S, Ohno-Machado L. Approximation properties of haplotype tagging. BMC Bioinformatics 2006, 7: 8. PMID: 16401341, PMCID: PMC1395335, DOI: 10.1186/1471-2105-7-8.Peer-Reviewed Original ResearchConceptsApproximation propertiesCombinatorial optimization problemsOptimization problemImplementable algorithmComputational effortSolution qualityTerms of complexitySimple algorithmSize m.Population membersSingle processor machineAlgorithmProblemAsymptoticsApproximationProcessor machineHaplotype taggingNPsUnique identification