2015
Association Tests of Multiple Phenotypes: ATeMP
Guo X, Li Y, Ding X, He M, Wang X, Zhang H. Association Tests of Multiple Phenotypes: ATeMP. PLOS ONE 2015, 10: e0140348. PMID: 26479245, PMCID: PMC4610695, DOI: 10.1371/journal.pone.0140348.Peer-Reviewed Original ResearchMeSH KeywordsComputational BiologyComputer SimulationGenome-Wide Association StudyGenotypeHumansModels, TheoreticalPhenotypeConceptsExtensive simulation studyStatistical literatureJoint association analysisMultiPhenSimulation studyEquivalence relationshipProportional odds modelReal case studyMeasurement errorMultivariate methodsOdds modelMultiple intermediate phenotypesJoint analysisMultiple phenotypesExplanatory variablesEquivalenceEstimationDistributionPhenotypic distributionATempSolutionError
2009
Willows: a memory efficient tree and forest construction package
Zhang H, Wang M, Chen X. Willows: a memory efficient tree and forest construction package. BMC Bioinformatics 2009, 10: 130. PMID: 19416535, PMCID: PMC2683818, DOI: 10.1186/1471-2105-10-130.Peer-Reviewed Original ResearchMeSH KeywordsComputational BiologyGenome-Wide Association StudyPolymorphism, Single NucleotideSoftwareConceptsMassive genotype dataUser-friendly interfaceExcessive memory demandsHigh-dimensional dataNew software packageGenomic dataFriendly interfaceUse of memoryDimensional dataMassive amountsRandom forestPartitioning techniquesHigh-throughput genomic dataPowerful bioinformatics toolsEfficient treeComputer memorySoftware packageMassive sizeForest methodMemory demandsConstruction packagesSingle nucleotide polymorphismsBioinformatics toolsSNP dataGenotyping platforms
2007
Correlating observed odds ratios from lung cancer case–control studies to SNP functional scores predicted by bioinformatic tools
Zhu Y, Hoffman A, Wu X, Zhang H, Zhang Y, Leaderer D, Zheng T. Correlating observed odds ratios from lung cancer case–control studies to SNP functional scores predicted by bioinformatic tools. Mutation Research/Fundamental And Molecular Mechanisms Of Mutagenesis 2007, 639: 80-88. PMID: 18191955, PMCID: PMC2292456, DOI: 10.1016/j.mrfmmm.2007.11.005.Peer-Reviewed Original Research
2004
A High Productivity/Low Maintenance Approach to High-performance Computation for Biomedicine: Four Case Studies
Carriero N, Osier MV, Cheung KH, Miller PL, Gerstein M, Zhao H, Wu B, Rifkin S, Chang J, Zhang H, White K, Williams K, Schultz M. A High Productivity/Low Maintenance Approach to High-performance Computation for Biomedicine: Four Case Studies. Journal Of The American Medical Informatics Association 2004, 12: 90-98. PMID: 15492032, PMCID: PMC543832, DOI: 10.1197/jamia.m1571.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceComputational BiologyComputing MethodologiesMass SpectrometryMicroarray AnalysisPhenotypeSequence AnalysisConceptsHigh performance computationLow-maintenance approachBioinformatics applicationsRepresentative bioinformatics applicationsIntensive bioinformatics applicationsBioinformatics case studyGenome-wide sequence comparisonHPC expertsHPC platformsComplex genetic analysisBioinformatics researchersSignificant speedupMass spectrometry data setsHigh-throughput biotechnologiesSequence comparisonVast amountProteomic dataOrdinal phenotypesSpectrum of techniquesDNA microarraysGenetic analysisGene expressionCase studyIterative refinementMaintenance approach
2003
Tree‐based disease classification using protein data
Zhu H, Yu C, Zhang H. Tree‐based disease classification using protein data. Proteomics 2003, 3: 1673-1677. PMID: 12973723, DOI: 10.1002/pmic.200300520.Peer-Reviewed Original Research