2007
Evidence for association between multiple complement pathway genes and AMD
Dinu V, Miller PL, Zhao H. Evidence for association between multiple complement pathway genes and AMD. Genetic Epidemiology 2007, 31: 224-237. PMID: 17266113, DOI: 10.1002/gepi.20204.Peer-Reviewed Original ResearchConceptsSingle nucleotide polymorphismsPathway levelGenome-wide association studiesGenome-wide levelWide association studyGenome levelAdditional genesPathway genesAssociation studiesBiological knowledgeSNP signalsComplement factor HGenotype dataGenesNucleotide polymorphismsForms of AMDComplement pathway genesRisk allelesFactor HMBL2 single-nucleotide polymorphismsIntronsHaplotypesComplement pathwayAllelesPathway
1999
Large-scale analysis of the yeast genome by transposon tagging and gene disruption
Ross-Macdonald P, Coelho P, Roemer T, Agarwal S, Kumar A, Jansen R, Cheung K, Sheehan A, Symoniatis D, Umansky L, Heidtman M, Nelson F, Iwasaki H, Hager K, Gerstein M, Miller P, Roeder G, Snyder M. Large-scale analysis of the yeast genome by transposon tagging and gene disruption. Nature 1999, 402: 413-418. PMID: 10586881, DOI: 10.1038/46558.Peer-Reviewed Original ResearchMeSH KeywordsAlgorithmsDNA Transposable ElementsEscherichia coliFungal ProteinsGene Expression ProfilingGenetic TechniquesGenome, FungalMolecular Sequence DataMutagenesisOligonucleotide Array Sequence AnalysisOpen Reading FramesPhenotypePolymerase Chain ReactionSaccharomyces cerevisiaeTransformation, GeneticConceptsGene functionDisruption phenotypesLarge-scale analysisNon-annotated open reading framesGenome-wide analysisOpen reading frameSingle genetic backgroundTransposon taggingYeast genomeYeast mutantsGenomic scaleYeast SaccharomycesDifferent growth conditionsProtein localizationGene disruptionReading frameGene expressionFunctional analysisVegetative growthGenetic backgroundGenesGenomeTransposonGrowth conditionsYeast
1996
CONTIG EXPLORER: Interactive Marker-Content Map Assembly
Nadkarni P, Banks A, Montgomery K, LeBlanc-Stracewski J, Miller P, Krauter K. CONTIG EXPLORER: Interactive Marker-Content Map Assembly. Genomics 1996, 31: 301-310. PMID: 8838311, DOI: 10.1006/geno.1996.0052.Peer-Reviewed Original Research
1994
Computer-assisted restriction mapping: an integrated approach to handling experimental uncertainty
Wright L, Lichter J, Reinitz J, Shifman M, Kidd K, Miller P. Computer-assisted restriction mapping: an integrated approach to handling experimental uncertainty. Bioinformatics 1994, 10: 435-442. PMID: 7804876, DOI: 10.1093/bioinformatics/10.4.435.Peer-Reviewed Original Research
1992
Molecular dynamics simulation on a network of workstations using a machine-independent parallel programming language
Shifman M, Windemuth A, Schulten K, Miller P. Molecular dynamics simulation on a network of workstations using a machine-independent parallel programming language. Journal Of Biomedical Informatics 1992, 25: 168-180. PMID: 1582193, DOI: 10.1016/0010-4809(92)90019-7.Peer-Reviewed Original ResearchConceptsMachine-independent parallel programming languageParallel programming languageProgramming languageShared memory parallel computerHigh performance Unix workstationsNetwork of workstationsParallel computing approachMemory parallel computersComputing approachNetworked workstationsUNIX workstationsParallel computersExpensive phaseEffective algorithmResearch communityPerformance benchmarksWorkstationsAlgorithmNetworkGlobal motionLanguageComputerLindaSimulationsBenchmarksHarnessing networked workstations as a powerful parallel computer: a general paradigm illustrated using three programs for genetic linkage analysis
Miller P, Nadkarni P, Bercovitz P. Harnessing networked workstations as a powerful parallel computer: a general paradigm illustrated using three programs for genetic linkage analysis. Bioinformatics 1992, 8: 141-147. PMID: 1591609, DOI: 10.1093/bioinformatics/8.2.141.Peer-Reviewed Original ResearchConceptsParallel computersMachine-independent parallel programming languageParallel programming languagePowerful parallel computersParallel programsProgramming languageNetworked workstationsComputational resourcesParallel machinesGeneral paradigmBiological computationWorkstationsComputerLindaNetworkInstitutions networkMathematical techniquesParadigmHardwareMachineComputationLanguageCapabilityResourcesComparing machine-independent versus machine-specific parallelization of a software platform for biological sequence comparison
Miller P, Nadkarni P, Pearson W. Comparing machine-independent versus machine-specific parallelization of a software platform for biological sequence comparison. Bioinformatics 1992, 8: 167-175. PMID: 1591612, DOI: 10.1093/bioinformatics/8.2.167.Peer-Reviewed Original ResearchConceptsDatabase of sequencesBiological sequence comparisonParallel computationMachine-independent parallel programming languageParallel programming languageHypercube parallel computerProgramming languageSoftware platformParallel computersParallel machinesExpressive powerBiological sequencesParallelizationPlatform programComputationModest sacrificeBenchmark testsLogicDatabaseCase studyComputerPortabilityMachineLindaRelative advantagesFast Computation of Genetic Likelihoods on Human Pedigree Data
Goradia T, Lange K, Miller P, Nadkarni P. Fast Computation of Genetic Likelihoods on Human Pedigree Data. Human Heredity 1992, 42: 42-62. PMID: 1555846, DOI: 10.1159/000154045.Peer-Reviewed Original ResearchConceptsHuman pedigree dataNetwork of workstationsLarge-scale computationsHardware techniquesParallel machinesComputational speedDifferent architecturesLinkage problemFast computationVectorized versionComputationFast calculationLarge numberParallelizationSupercomputersVectorizationComplete phenotypingWorkstationsArchitectureGenetic likelihoodMachineNetworkVersionNew methodSubstantial improvement
1991
A parallel computing approach to genetic sequence comparison: The master-worker paradigm with interworker communication
Sittig D, Foulser D, Carriero N, McCorkle G, Miller P. A parallel computing approach to genetic sequence comparison: The master-worker paradigm with interworker communication. Journal Of Biomedical Informatics 1991, 24: 152-169. PMID: 2036781, DOI: 10.1016/0010-4809(91)90027-t.Peer-Reviewed Original ResearchConceptsTuple spaceGenetic sequence comparisonC-LindaMachine-independent parallel programming languageComparison algorithmsSimilarity scoresParallel programming languageMaster-worker paradigmTest sequencesParallel computing approachTotal search timeSequence comparison algorithmComputing approachParallel programsProgramming languageParallel computersWorker processesParallel implementationSequent SymmetryMaster processSequential versionIntel HypercubeParallel versionString comparisonSearch timeMolecular dynamics simulation on a network of workstations using a machine-independent parallel programming language.
Shifman M, Windemuth A, Schulten K, Miller P. Molecular dynamics simulation on a network of workstations using a machine-independent parallel programming language. AMIA Annual Symposium Proceedings 1991, 414-8. PMID: 1807634, PMCID: PMC2247565.Peer-Reviewed Original ResearchConceptsMachine-independent parallel programming languageParallel programming languageProgramming languageShared memory parallel computerHigh performance Unix workstationsNetwork of workstationsParallel computing approachMemory parallel computersComputing approachNetworked workstationsUNIX workstationsParallel computersExpensive phaseEffective algorithmResearch communityPerformance benchmarksWorkstationsAlgorithmNetworkGlobal motionLanguageComputerLindaSimulationsBenchmarksParallel computation for biological sequence comparison: comparing a portable model to the native model for the Intel Hypercube.
Nadkarni P, Miller P. Parallel computation for biological sequence comparison: comparing a portable model to the native model for the Intel Hypercube. AMIA Annual Symposium Proceedings 1991, 404-8. PMID: 1807632, PMCID: PMC2247563.Peer-Reviewed Original ResearchConceptsMachine-independent parallel programming languageIntel HypercubeVirtual parallel machineParallel programming languageBiological sequence comparisonNumber of processorsParallel programmingParallel programsProgramming languageParallel computationDesktop workstationsParallel machinesProgramming commandsApplication areasPortable modelProcessorsLindaBenchmark testsNative modelsHypercubeParallelizationCase studyWorkstationsVersionMachineParallel computation and FASTA: confronting the problem of parallel database search for a fast sequence comparison algorithm
Miller P, Nadkarni P, Carriero N. Parallel computation and FASTA: confronting the problem of parallel database search for a fast sequence comparison algorithm. Bioinformatics 1991, 7: 71-78. PMID: 2004277, DOI: 10.1093/bioinformatics/7.1.71.Peer-Reviewed Original ResearchConceptsSequence comparison algorithmAmount of computationMachine-independent parallel programming languageComparison algorithmsDisk I/OParallel programming languageParallel program runsO bottleneck problemDifferent parallel machinesBiological sequence comparisonNumber of processorsTime-consuming computationProgramming languageParallelization strategyParallel computationParallel machinesProgram design strategiesProgram runBottleneck problemFASTA algorithmFASTAAlgorithmComputationBottleneckGeneral problem
1990
PATHMASTER: Modelling differential diagnosis as “dynamic competition” between systematic analysis and disease-directed deduction
Frohlich M, Miller P, Morrow J. PATHMASTER: Modelling differential diagnosis as “dynamic competition” between systematic analysis and disease-directed deduction. Journal Of Biomedical Informatics 1990, 23: 499-513. PMID: 2276261, DOI: 10.1016/0010-4809(90)90037-d.Peer-Reviewed Original Research
1987
Hydra
Miller P, Blumenfrucht S, Rose J, Rothschild M, Swett H, Weltin G, Mars N. Hydra. Medical Decision Making 1987, 7: 12-21. PMID: 3807686, DOI: 10.1177/0272989x8700700106.Peer-Reviewed Original ResearchChoice and Explanation in Medical Management
Rennels G, Shortliffe E, Miller P. Choice and Explanation in Medical Management. Medical Decision Making 1987, 7: 22-31. PMID: 3807687, DOI: 10.1177/0272989x8700700107.Peer-Reviewed Original Research