2007
YPED: A Web-Accessible Database System for Protein Expression Analysis
Shifman MA, Li Y, Colangelo CM, Stone KL, Wu TL, Cheung KH, Miller PL, Williams KR. YPED: A Web-Accessible Database System for Protein Expression Analysis. Journal Of Proteome Research 2007, 6: 4019-4024. PMID: 17867667, PMCID: PMC3863627, DOI: 10.1021/pr070325f.Peer-Reviewed Original ResearchMeSH KeywordsDatabases, FactualElectrophoresis, Gel, Two-DimensionalInternetPhosphoproteinsProteinsProteomeSoftwareTandem Mass SpectrometryConceptsWeb-accessible software systemWeb-accessible database systemYale Protein Expression DatabaseOpen source systemsSecure web interfaceSoftware systemsDatabase systemsWeb interfaceSource codeExplorer systemExpression databaseProtein Expression DatabaseSource systemEdu/Sample summariesGel imagesTrans-Proteomic Pipeline
2001
Maintaining and Incrementally Revalidating a Computer-Based Clinical Guideline: A Case Study
Miller P, Frawley S, Sayward F. Maintaining and Incrementally Revalidating a Computer-Based Clinical Guideline: A Case Study. Journal Of Biomedical Informatics 2001, 34: 99-111. PMID: 11515416, DOI: 10.1006/jbin.2001.1011.Peer-Reviewed Original ResearchIntegration of Multidisciplinary Sensory Data
Miller P, Nadkarni P, Singer M, Marenco L, Hines M, Shepherd G. Integration of Multidisciplinary Sensory Data. Journal Of The American Medical Informatics Association 2001, 8: 34-48. PMID: 11141511, PMCID: PMC134590, DOI: 10.1136/jamia.2001.0080034.Peer-Reviewed Original ResearchConceptsNeuroinformatics researchFlexible data modelDiverse heterogeneous dataHuman Brain ProjectNew informatics technologiesHeterogeneous dataData modelSensory dataRelated toolsInformatics technologiesBrain ProjectBuilding databaseSingle unifying frameworkUnifying frameworkProject approachIntegrationComputer model
2000
Exploring Performance Issues for a Clinical Database Organized Using an Entity-Attribute-Value Representation
Chen R, Nadkarni P, Marenco L, Levin F, Erdos J, Miller P. Exploring Performance Issues for a Clinical Database Organized Using an Entity-Attribute-Value Representation. Journal Of The American Medical Informatics Association 2000, 7: 475-487. PMID: 10984467, PMCID: PMC79043, DOI: 10.1136/jamia.2000.0070475.Peer-Reviewed Original ResearchMeSH KeywordsDatabase Management SystemsDatabases as TopicDatabases, FactualInformation Storage and RetrievalMicrobiologyPilot ProjectsConceptsEAV/CRDatabase schemaSQL statementsDatabase modelDatabase sizeSystem memoryQuery execution timeHeterogeneous biomedical dataSimple SQL statementsQuery efficiencyQuery performancePowerful hardwareQuery strategyEntity attributesDatabase queriesDatabase representationBiomedical dataExecution timeQueriesMore memoryPerformance issuesSchemaValue representationRepresentationCR modelIMM/Scrub: A Domain-Specific Tool for the Deduplication of Vaccination History Records in Childhood Immunization Registries
Miller P, Frawley S, Sayward F. IMM/Scrub: A Domain-Specific Tool for the Deduplication of Vaccination History Records in Childhood Immunization Registries. Journal Of Biomedical Informatics 2000, 33: 126-143. PMID: 10854120, DOI: 10.1006/cbmr.1999.1534.Peer-Reviewed Original ResearchMeSH KeywordsChildDatabases, FactualHumansMedical Records Systems, ComputerizedPilot ProjectsRegistriesSoftwareVaccinationConceptsImmunization registryAcademic medical centerDomain-specific toolsData cleaning processImmunization databaseVaccine seriesCombination vaccinesMedical CenterHistory recordsPreliminary experienceIMM/Dose numberDosesDoseRegistryDeduplicationPilot implementationDifferent preparationsPilot toolAdditional assistanceVaccineForecasting programImplementationNumber of factorsOlfactory Receptor Database: a sensory chemoreceptor resource
Skoufos E, Marenco L, Nadkarni P, Miller P, Shepherd G. Olfactory Receptor Database: a sensory chemoreceptor resource. Nucleic Acids Research 2000, 28: 341-343. PMID: 10592268, PMCID: PMC102443, DOI: 10.1093/nar/28.1.341.Peer-Reviewed Original ResearchMeSH KeywordsBase SequenceChemoreceptor CellsDatabases, FactualMolecular Sequence DataOlfactory MucosaUser-Computer Interface
1999
Olfactory Receptor Database: a database of the largest eukaryotic gene family
Skoufos E, Healy M, Singer M, Nadkarni P, Miller P, Shepherd G. Olfactory Receptor Database: a database of the largest eukaryotic gene family. Nucleic Acids Research 1999, 27: 343-345. PMID: 9847223, PMCID: PMC148178, DOI: 10.1093/nar/27.1.343.Peer-Reviewed Original ResearchNeuronal database integration: the Senselab EAV data model.
Marenco L, Nadkarni P, Skoufos E, Shepherd G, Miller P. Neuronal database integration: the Senselab EAV data model. AMIA Annual Symposium Proceedings 1999, 102-6. PMID: 10566329, PMCID: PMC2232788.Peer-Reviewed Original ResearchMeSH KeywordsDatabases, FactualHumansHypermediaInformation Storage and RetrievalInternetNervous SystemSystems Integration
1998
Database tools for integrating and searching membrane property data correlated with neuronal morphology
Mirsky J, Nadkarni P, Healy M, Miller P, Shepherd G. Database tools for integrating and searching membrane property data correlated with neuronal morphology. Journal Of Neuroscience Methods 1998, 82: 105-121. PMID: 10223520, DOI: 10.1016/s0165-0270(98)00049-1.Peer-Reviewed Original ResearchConceptsDatabase toolsWeb resourcesSearch toolsCritical problemUsersSequence databasesSimple canonical modelFunctional operationDatabaseToolSearchDifferent neuronsInternetAnnotationEquivalent compartmentsModelersDataProperty dataCanonical modelDifferent typesInformationState of acceptanceResourcesVehiclesProperty space
1997
Olfactory Receptor Database (ORDB): A Resource for Sharing and Analyzing Published and Unpublished Data
Healy M, Smith J, Singer M, Nadkarni P, Skoufos E, Miller P, Shepherd G. Olfactory Receptor Database (ORDB): A Resource for Sharing and Analyzing Published and Unpublished Data. Chemical Senses 1997, 22: 321-326. PMID: 9218144, DOI: 10.1093/chemse/22.3.321.Peer-Reviewed Original ResearchUsing explicitly represented biological relationships for database navigation and searching via the World-Wide Web
Panzer S, Cooley L, Miller P. Using explicitly represented biological relationships for database navigation and searching via the World-Wide Web. Bioinformatics 1997, 13: 281-290. PMID: 9183533, DOI: 10.1093/bioinformatics/13.3.281.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBiologyComputer Communication NetworksCytoskeletal ProteinsCytoskeletonDatabases, FactualGenesUser-Computer InterfaceConceptsWorld Wide WebCGI scriptsDatabase navigationDatabase schemaBiological databasesRetrieval capabilitiesHypertext linksPrototype databaseRelated entitiesDatabase entriesDifferent entitiesPublic useWebWealth of informationDatabaseHyperlinksInformationNavigationBiological relationshipsEntitiesSchemaRequestsScriptsCapabilityNew typeEvaluating IAIMS at Yale
Grajek S, Calarco P, Frawley S, McKay J, Miller P, Paton J, Roderer N, Sullivan J. Evaluating IAIMS at Yale. Journal Of The American Medical Informatics Association 1997, 4: 138-149. PMID: 9067879, PMCID: PMC61503, DOI: 10.1136/jamia.1997.0040138.Peer-Reviewed Original ResearchConceptsNetworked information resourcesInformation resourcesUsage dataMedical Center communityTraditional library resourcesMultiple sourcesInformation accessInformation systemsWorkstation usersUser commentsMultiple resourcesEvaluation resultsLibrary resourcesCenter communityTrue integrationMedical librariesRemote locationsSame informationUse of resourcesResourcesIndividual resourcesInformationIAIMSUsersLibrary
1996
ModelDB: An Environment for Running and Storing Computational Models and Their Results Applied to Neuroscience
Peterson B, Healy M, Nadkarni P, Miller P, Shepherd G. ModelDB: An Environment for Running and Storing Computational Models and Their Results Applied to Neuroscience. Journal Of The American Medical Informatics Association 1996, 3: 389-398. PMID: 8930855, PMCID: PMC116323, DOI: 10.1136/jamia.1996.97084512.Peer-Reviewed Original ResearchConceptsWorld Wide Web interfaceCluster of databasesHuman Brain ProjectWeb interfaceComputational modelIndividual databasesSmall databaseDatabase developmentBrain ProjectComplex informationRelated databasesFormal mannerVast quantitiesSystem functionDiverse sourcesDatabaseInformationWebProjectResearch groupsInitial approachPilot projectIssuesGeneral issuesTechnologyCONTIG 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
1995
Internet-based Support for Bioscience Research: A Collaborative Genome center for Human Chromosome 12
Miller P, Nadkarni P, Kidd K, Cheung K, Ward D, Banks A, Bray-Ward P, Cupelli L, Herdman V, Marondel I, Montcomery K, Renault B, Yoon S, Krauter K, Kucherlapati R. Internet-based Support for Bioscience Research: A Collaborative Genome center for Human Chromosome 12. Journal Of The American Medical Informatics Association 1995, 2: 351-364. PMID: 8581551, PMCID: PMC116278, DOI: 10.1136/jamia.1995.96157828.Peer-Reviewed Original ResearchMeSH KeywordsChromosome MappingChromosomes, Artificial, YeastChromosomes, Human, Pair 12Computer Communication NetworksConnecticutData DisplayDatabases, FactualGenetic MarkersGenome, HumanHumansInterinstitutional RelationsLocal Area NetworksModels, GeneticNew York CityOrganizational ObjectivesSoftware DesignSystems IntegrationUser-Computer InterfaceConceptsUser-friendly front endInternet-based supportExternal databasesMedical informaticsGenome CenterGenome informaticsDatabase programMapping communityCandidate mapsInformaticsAssembly toolsAreas of bioscienceFront endDatabaseServerSybaseSuch supportCase studySetToolBioscience researchCertain issuesClientsTechnologySupport
1992
Prototyping an institutional IAIMS/UMLS information environment for an academic medical center.
Miller P, Paton J, Clyman J, Powsner S. Prototyping an institutional IAIMS/UMLS information environment for an academic medical center. Journal Of The Medical Library Association 1992, 80: 281-7. PMID: 1326371, PMCID: PMC225668.Peer-Reviewed Original ResearchConceptsIntegrated Academic Information Management SystemUnified Medical Language SystemInformation resourcesAcademic Information Management SystemInformation management systemInformation environmentNetwork-based implementationComputer networksInformation architectureMacintosh computerManagement systemInformation capabilitiesInformation sourcesLanguage systemIntegrated fashionPrototypeDiverse setNational LibraryResourcesCapabilityUsersComputerArchitectureEnvironmentNetworkComparing 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 ResearchMeSH KeywordsAlgorithmsComputer SystemsDatabases, FactualEvaluation Studies as TopicProgramming LanguagesSequence AlignmentSoftwareSoftware DesignConceptsDatabase of sequencesBiological sequence comparisonParallel computationMachine-independent parallel programming languageParallel programming languageHypercube parallel computerProgramming languageSoftware platformParallel computersParallel machinesExpressive powerBiological sequencesParallelizationPlatform programComputationModest sacrificeBenchmark testsLogicDatabaseCase studyComputerPortabilityMachineLindaRelative advantagesPFGE MAPPER and PFGE READER: two tools to aid in the analysis and data input of pulse field gel electrophoresis maps.
Shifman M, Nadkarni P, Miller P. PFGE MAPPER and PFGE READER: two tools to aid in the analysis and data input of pulse field gel electrophoresis maps. AMIA Annual Symposium Proceedings 1992, 361-5. PMID: 1482898, PMCID: PMC2248078.Peer-Reviewed Original ResearchCHROMINFO: a database for viewing and editing top-level chromosome data.
Nadkarni P, Reeders S, Shifman M, Miller P. CHROMINFO: a database for viewing and editing top-level chromosome data. AMIA Annual Symposium Proceedings 1992, 366-70. PMID: 1482899, PMCID: PMC2248058.Peer-Reviewed Original Research
1991
Modeling uncertainty in a database for physical gene mapping data.
Miller P, Shifman M, Kidd K. Modeling uncertainty in a database for physical gene mapping data. AMIA Annual Symposium Proceedings 1991, 409-13. PMID: 1807633, PMCID: PMC2247564.Peer-Reviewed Original Research