2023
Family and personal history of cancer in the All of Us research program for precision medicine
Bruce L, Paul P, Kim K, Kim J, Keegan T, Hiatt R, Ohno-Machado L, Investigators O. Family and personal history of cancer in the All of Us research program for precision medicine. PLOS ONE 2023, 18: e0288496. PMID: 37459328, PMCID: PMC10351738, DOI: 10.1371/journal.pone.0288496.Peer-Reviewed Original Research
2022
An Overview of Cancer in the First 315,000 All of Us Participants
Aschebrook-Kilfoy B, Zakin P, Craver A, Shah S, Kibriya M, Stepniak E, Ramirez A, Clark C, Cohn E, Ohno-Machado L, Cicek M, Boerwinkle E, Schully S, Mockrin S, Gebo K, Mayo K, Ratsimbazafy F, Sanders A, Shah R, Argos M, Ho J, Kim K, Daviglus M, Greenland P, Ahsan H, . An Overview of Cancer in the First 315,000 All of Us Participants. PLOS ONE 2022, 17: e0272522. PMID: 36048778, PMCID: PMC9436122, DOI: 10.1371/journal.pone.0272522.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 Research
2019
Evaluating and sharing global genetic ancestry in biomedical datasets
Harismendy O, Kim J, Xu X, Ohno-Machado L. Evaluating and sharing global genetic ancestry in biomedical datasets. Journal Of The American Medical Informatics Association 2019, 26: 457-461. PMID: 30869786, PMCID: PMC6433181, DOI: 10.1093/jamia/ocy194.Peer-Reviewed Original ResearchConceptsGenetic diversity measurementsGenetic ancestryAvailable molecular datasetsHuman genetics researchCancer Genome Atlas (TCGA) datasetContinental resolutionGenetic diversityPhenotype-genotype associationsMolecular datasetsGlobal genetic ancestryAncestry informationGenetic researchAtlas datasetDiversity measurementsAncestryTraitsGlobal scaleDiversityBiomedical datasetsAvailable datasetsData repositoryDisease riskAccess datasetDatasetAvailable cohorts
2013
Comparison of four prediction models to discriminate benign from malignant vertebral compression fractures according to MRI feature analysis.
Thawait S, Kim J, Klufas R, Morrison W, Flanders A, Carrino J, Ohno-Machado L. Comparison of four prediction models to discriminate benign from malignant vertebral compression fractures according to MRI feature analysis. American Journal Of Roentgenology 2013, 200: 493-502. PMID: 23436836, DOI: 10.2214/ajr.11.7192.Peer-Reviewed Original ResearchAdultAgedAged, 80 and overAlgorithmsCohort StudiesComputer SimulationDiagnosis, DifferentialFemaleFractures, CompressionHumansImage EnhancementImage Interpretation, Computer-AssistedMagnetic Resonance ImagingMaleMiddle AgedModels, BiologicalNeoplasmsPattern Recognition, AutomatedReproducibility of ResultsSensitivity and SpecificitySpinal FracturesYoung Adult
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
Twist1-Induced Invadopodia Formation Promotes Tumor Metastasis
Eckert M, Lwin T, Chang A, Kim J, Danis E, Ohno-Machado L, Yang J. Twist1-Induced Invadopodia Formation Promotes Tumor Metastasis. Cancer Cell 2011, 19: 372-386. PMID: 21397860, PMCID: PMC3072410, DOI: 10.1016/j.ccr.2011.01.036.Peer-Reviewed Original ResearchMeSH KeywordsAdaptor Proteins, Vesicular TransportAnimalsBase SequenceBreast NeoplasmsCell LineCell Line, TumorCell MovementCell Surface ExtensionsElectrophoresis, Polyacrylamide GelEpithelial-Mesenchymal TransitionFemaleHEK293 CellsHumansMiceMice, NudeNeoplasm MetastasisNeoplasmsNuclear ProteinsReceptor, Platelet-Derived Growth Factor alphaReverse Transcriptase Polymerase Chain ReactionRNA InterferenceSignal TransductionSrc Homology DomainsTwist-Related Protein 1ConceptsInvadopodia formationTumor metastasisFormation of invadopodiaDirect transcriptional targetTwist1 transcription factorEMT-inducing signalsMatrix degradationPromotes Tumor MetastasisMembrane protrusionsExtracellular matrix degradationTranscriptional targetsTranscription factorsInvadopodiaPDGFRα expressionMesenchymal transitionTwist1Central mediatorPDGFRαKey functions
2010
TGF-beta1 interactome: metastasis and beyond.
Perera M, Tsang C, Distel R, Lacy J, Ohno-Machado L, Ricchiuti V, Samaranayake L, Smejkal G, Smith M, Trachtenberg A, Kuo W. TGF-beta1 interactome: metastasis and beyond. Cancer Genomics & Proteomics 2010, 7: 217-29. PMID: 20656987.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsConceptsDifferential expression profilesCancer therapeuticsPersonalized cancer therapeuticsRegulation of tumorEffective cancer therapeuticsNovel cancer biomarkersGenomic dataExpression profilesMetastatic attributesInteractomeUbiquitous cytokineTumor progressionCancer biomarkersPolarity changeTherapeuticsValuable insightsImmense valueRegulationInsightsInducerImportant stepMappingGrowth
2007
Current status of the Japanese cancer registry system: results of a nationwide survey.
Sawa T, Yuji K, Kami M, Ohno-Machado L, Nakata Y. Current status of the Japanese cancer registry system: results of a nationwide survey. AMIA Annual Symposium Proceedings 2007, 1104. PMID: 18694201.Peer-Reviewed Original ResearchMODELING CANCER: INTEGRATION OF "OMICS" INFORMATION IN DYNAMIC SYSTEMS
STRANSKY B, BARRERA J, OHNO-MACHADO L, DE SOUZA S. MODELING CANCER: INTEGRATION OF "OMICS" INFORMATION IN DYNAMIC SYSTEMS. Journal Of Bioinformatics And Computational Biology 2007, 5: 977-986. PMID: 17787066, DOI: 10.1142/s0219720007002990.Peer-Reviewed Original Research
2005
Small, fuzzy and interpretable gene expression based classifiers
Vinterbo S, Kim E, Ohno-Machado L. Small, fuzzy and interpretable gene expression based classifiers. Bioinformatics 2005, 21: 1964-1970. PMID: 15661797, DOI: 10.1093/bioinformatics/bti287.Peer-Reviewed Original Research
2004
The Goodman-Kruskal coefficient and its applications in genetic diagnosis of cancer
Jaroszewicz S, Simovici D, Kuo W, Ohno-Machado L. The Goodman-Kruskal coefficient and its applications in genetic diagnosis of cancer. IEEE Transactions On Biomedical Engineering 2004, 51: 1095-1102. PMID: 15248526, DOI: 10.1109/tbme.2004.827267.Peer-Reviewed Original Research
2002
Building an asynchronous web-based tool for machine learning classification.
Weber G, Vinterbo S, Ohno-Machado L. Building an asynchronous web-based tool for machine learning classification. AMIA Annual Symposium Proceedings 2002, 869-73. PMID: 12463949, PMCID: PMC2244467.Peer-Reviewed Original ResearchConceptsClassification methodDownloadable software toolsWeb-based applicationSupervised learning methodsSupport vector machineNearest neighbor classifierWeb-based toolWeb-based analysis toolWeb applicationBioinformatics LaboratorySoftware toolsFree softwareLearning methodsSophisticated algorithmsVector machineNeighbor classifierLinear discriminant analysisAnalysis toolsDisease classificationClassification treesLimited budgetShort amountRemote locationsHigh-throughput gene expression dataGene expression data
1993
Prognostic classification for aids patients in Brazil
Ohno-Machado L. Prognostic classification for aids patients in Brazil. Journal Of Medical Systems 1993, 17: 163-172. PMID: 8254260, DOI: 10.1007/bf00996941.Peer-Reviewed Original ResearchMeSH KeywordsAcquired Immunodeficiency SyndromeAdolescentAdultAgedAIDS-Related Opportunistic InfectionsBrazilCause of DeathChildChild, PreschoolCross-Sectional StudiesDeveloping CountriesDiscriminant AnalysisFemaleHospitalizationHumansIncidenceInfantInfant, NewbornMaleMiddle AgedNeoplasmsSurvival RateConceptsHospitalized AIDS patientsPrognosis of deathHistory of transfusionGroup IV patientsNumber of infectionsEsophageal candidiasisIV patientsAIDS patientsFirst manifestationAID patientsRisk groupsPrognostic classificationPrognostic variablesSurvival ratePatientsFinal discriminant functionInfectionDiseaseDeathAnalysis groupHospitalizationTransfusionPrognosisGroupCandidiasis