2017
An Empirical Study for Impacts of Measurement Errors on EHR based Association Studies.
Duan R, Cao M, Wu Y, Huang J, Denny J, Xu H, Chen Y. An Empirical Study for Impacts of Measurement Errors on EHR based Association Studies. AMIA Annual Symposium Proceedings 2017, 2016: 1764-1773. PMID: 28269935, PMCID: PMC5333313.Peer-Reviewed Original Research
2015
Deciphering Signaling Pathway Networks to Understand the Molecular Mechanisms of Metformin Action
Sun J, Zhao M, Jia P, Wang L, Wu Y, Iverson C, Zhou Y, Bowton E, Roden D, Denny J, Aldrich M, Xu H, Zhao Z. Deciphering Signaling Pathway Networks to Understand the Molecular Mechanisms of Metformin Action. PLOS Computational Biology 2015, 11: e1004202. PMID: 26083494, PMCID: PMC4470683, DOI: 10.1371/journal.pcbi.1004202.Peer-Reviewed Original ResearchConceptsGWAS datasetsPathway networkDisease genesGenome-wide association study datasetDrug targetsSignal transduction networksSignal transduction cascadeMultiple signaling pathwaysDrug-induced gene expressionNovel drug targetsTransduction networksTransduction cascadeEnrichment analysisGene expressionCommon genesMolecular mechanismsSignaling pathwaysGenesNovel MycLiterature miningMolecular modePathwayMetformin actionDrug actionDisease pathogenesisA comparative study of disease genes and drug targets in the human protein interactome
Sun J, Zhu K, Zheng W, Xu H. A comparative study of disease genes and drug targets in the human protein interactome. BMC Bioinformatics 2015, 16: s1. PMID: 25861037, PMCID: PMC4402590, DOI: 10.1186/1471-2105-16-s5-s1.Peer-Reviewed Original ResearchMeSH KeywordsCluster AnalysisComputational BiologyDiseaseGene Expression RegulationGenome-Wide Association StudyHumansPharmaceutical PreparationsProtein Interaction MapsProteinsConceptsGenome-wide association studiesDisease genesDrug targetsHuman protein-coding genesHuman protein-protein interaction networkProtein-protein interaction networkProtein-coding genesHuman protein interactomeComplex diseasesNovel drug targetsProtein interactomeAnatomical Therapeutic Chemical (ATC) classificationInteraction networksDisease proteinAssociation studiesGenesDisease categoriesInteractomeProteinMajor disease categoriesDifferent disease categoriesFirst comprehensive comparisonTargetTreatment efficacyHigh betweenness
2014
PhenDisco: phenotype discovery system for the database of genotypes and phenotypes
Doan S, Lin K, Conway M, Ohno-Machado L, Hsieh A, Feupe S, Garland A, Ross M, Jiang X, Farzaneh S, Walker R, Alipanah N, Zhang J, Xu H, Kim H. PhenDisco: phenotype discovery system for the database of genotypes and phenotypes. Journal Of The American Medical Informatics Association 2014, 21: 31-36. PMID: 23989082, PMCID: PMC3912702, DOI: 10.1136/amiajnl-2013-001882.Peer-Reviewed Original ResearchMeSH KeywordsAlgorithmsDatabases, GeneticGenome-Wide Association StudyGenotypeHumansInformation SystemsPhenotypeSubject HeadingsConceptsNew information retrieval systemInformation retrieval systemsInformation retrieval toolsDatabase of GenotypesText processing toolsRetrieval systemSearch scenariosDiscovery systemRetrieval toolsAuthorized usersNon-standardized wayCross-study validationSearch comparisonProcessing toolsPromising performanceUsersPhenotype informationDatabaseInformationBiotechnology InformationQueriesMetadataEntrezResourcesSystem
2013
Systematic comparison of phenome-wide association study of electronic medical record data and genome-wide association study data
Denny J, Bastarache L, Ritchie M, Carroll R, Zink R, Mosley J, Field J, Pulley J, Ramirez A, Bowton E, Basford M, Carrell D, Peissig P, Kho A, Pacheco J, Rasmussen L, Crosslin D, Crane P, Pathak J, Bielinski S, Pendergrass S, Xu H, Hindorff L, Li R, Manolio T, Chute C, Chisholm R, Larson E, Jarvik G, Brilliant M, McCarty C, Kullo I, Haines J, Crawford D, Masys D, Roden D. Systematic comparison of phenome-wide association study of electronic medical record data and genome-wide association study data. Nature Biotechnology 2013, 31: 1102-1111. PMID: 24270849, PMCID: PMC3969265, DOI: 10.1038/nbt.2749.Peer-Reviewed Original Research
2012
Genetic studies of complex human diseases: Characterizing SNP-disease associations using Bayesian networks
Han B, Chen X, Talebizadeh Z, Xu H. Genetic studies of complex human diseases: Characterizing SNP-disease associations using Bayesian networks. BMC Systems Biology 2012, 6: s14. PMID: 23281790, PMCID: PMC3524021, DOI: 10.1186/1752-0509-6-s3-s14.Peer-Reviewed Original ResearchMeSH KeywordsAlgorithmsAlzheimer DiseaseArtificial IntelligenceAutistic DisorderBayes TheoremComputational BiologyComputer SimulationDatabases, GeneticEpistasis, GeneticGenome-Wide Association StudyHumansMacular DegenerationMarkov ChainsModels, GeneticMonte Carlo MethodPolymorphism, Single NucleotideConceptsEpistatic interaction detectionBayesian network structure learning methodTwo-layer Bayesian networkBayesian network-based methodBayesian networkInteraction detectionMarkov chain Monte Carlo methodsStructure learning methodReal disease dataNetwork-based methodReal GWAS datasetMonte Carlo methodHigh-order epistatic interactionsMachine learningSearch spaceLearning methodsDisease datasetCarlo methodTarget nodeModel complexityStatistical methodsReal dataNew scoring functionComplex human diseasesDataset
2011
Facilitating pharmacogenetic studies using electronic health records and natural-language processing: a case study of warfarin
Xu H, Jiang M, Oetjens M, Bowton E, Ramirez A, Jeff J, Basford M, Pulley J, Cowan J, Wang X, Ritchie M, Masys D, Roden D, Crawford D, Denny J. Facilitating pharmacogenetic studies using electronic health records and natural-language processing: a case study of warfarin. Journal Of The American Medical Informatics Association 2011, 18: 387-391. PMID: 21672908, PMCID: PMC3128409, DOI: 10.1136/amiajnl-2011-000208.Peer-Reviewed Original ResearchAlgorithmsAnticoagulantsAryl Hydrocarbon HydroxylasesCytochrome P-450 CYP2C9Data MiningDatabases, Nucleic AcidDrug Dosage CalculationsElectronic Health RecordsGenome-Wide Association StudyHumansLinear ModelsMixed Function OxygenasesNatural Language ProcessingPharmacogeneticsPrecision MedicineUnited StatesVitamin K Epoxide ReductasesWarfarin