2008
Issues in the Design of a Pilot Concept-Based Query Interface for the Neuroinformatics Information Framework
Marenco L, Li Y, Martone ME, Sternberg PW, Shepherd GM, Miller PL. Issues in the Design of a Pilot Concept-Based Query Interface for the Neuroinformatics Information Framework. Neuroinformatics 2008, 6: 229-239. PMID: 18953674, PMCID: PMC2664632, DOI: 10.1007/s12021-008-9035-9.Peer-Reviewed Original ResearchConceptsNeuroscience Information FrameworkQuery interfaceBiomedical information retrievalInformation frameworkInformation retrievalResource registryDocument archivesBiomedical vocabulariesSingle interfaceStandardized vocabularyCurrent versionDetailed exampleInterfaceResourcesFrameworkOntologyPilot conceptVocabularyRetrievalIssuesCertain lessonsBackground issuesSearchArchivesPrimary resources
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 ResearchConceptsWeb-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
2006
Dynamic Tables: An Architecture for Managing Evolving, Heterogeneous Biomedical Data in Relational Database Management Systems
Corwin J, Silberschatz A, Miller PL, Marenco L. Dynamic Tables: An Architecture for Managing Evolving, Heterogeneous Biomedical Data in Relational Database Management Systems. Journal Of The American Medical Informatics Association 2006, 14: 86-93. PMID: 17068350, PMCID: PMC2215074, DOI: 10.1197/jamia.m2189.Peer-Reviewed Original ResearchConceptsBiomedical dataRelational database management systemRelational database technologySemantic data modelDatabase management systemRelational database enginePerformance of queriesHeterogeneous biomedical dataBiomedical informatics researchersDatabase engineDatabase technologyDatabase schemaData sparsityBioinformatics communityData modelInformatics researchersEvolution issuesTypes of dataManagement systemPerformance resultsRelational designClinical informaticsArchitecturePast approachesRelational techniques
2001
Domain-constrained Generation of Clinical Condition Sets to Help Test Computer-based Clinical Guidelines
Miller P. Domain-constrained Generation of Clinical Condition Sets to Help Test Computer-based Clinical Guidelines. Journal Of The American Medical Informatics Association 2001, 8: 131-145. PMID: 11230382, PMCID: PMC134553, DOI: 10.1136/jamia.2001.0080131.Peer-Reviewed Original Research
2000
An integrated web interface for large-scale characterization of sequence data
Cheung K, Kumar A, Snyder M, Miller P. An integrated web interface for large-scale characterization of sequence data. Functional & Integrative Genomics 2000, 1: 70-75. PMID: 11793223, DOI: 10.1007/s101420000004.Peer-Reviewed Original ResearchMeSH KeywordsClinical Laboratory Information SystemsComputational BiologyDatabases, GeneticDatabases, ProteinDNA Transposable ElementsDNA, FungalGene Expression ProfilingGenomeGenome, FungalInternetMutagenesis, InsertionalOpen Reading FramesSaccharomyces cerevisiaeSequence Analysis, DNASequence Homology, Nucleic AcidSoftwareUser-Computer InterfaceConceptsWeb interfaceWeb front endGenomic data processingData filesLarge-scale genome projectsIndependent software programsSet of programsMultiple directoriesData directoryData processingRaw dataTransposon insertion eventsSoftware programFilesFront endDirectoryEfficient protocolLarge amountInterfaceLarge numberGeneral approachUsersSetDownloadNavigationIMM/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 ResearchConceptsImmunization registryAcademic medical centerDomain-specific toolsData cleaning processImmunization databaseVaccine seriesCombination vaccinesMedical CenterHistory recordsPreliminary experienceIMM/Dose numberDosesDoseRegistryDeduplicationPilot implementationDifferent preparationsPilot toolAdditional assistanceVaccineForecasting programImplementationNumber of factorsInformatics issues in the national dissemination of a computer-based clinical guideline: a case study in childhood immunization.
Miller P, Frawley S, Sayward F. Informatics issues in the national dissemination of a computer-based clinical guideline: a case study in childhood immunization. AMIA Annual Symposium Proceedings 2000, 580-4. PMID: 11079950, PMCID: PMC2243834.Peer-Reviewed Original Research
1999
Using semantic constraints to help verify the completeness of a computer-based clinical guideline for childhood immunization
Miller D, Frawley S, Miller P. Using semantic constraints to help verify the completeness of a computer-based clinical guideline for childhood immunization. Computer Methods And Programs In Biomedicine 1999, 58: 267-280. PMID: 10094231, DOI: 10.1016/s0169-2607(98)00090-x.Peer-Reviewed Original Research
1998
Tools for Immunization Guideline Knowledge Maintenance II. Automated Web-Based Generation of User-Customized Test Cases
Miller P, Frawley S, Brandt C, Sayward F. Tools for Immunization Guideline Knowledge Maintenance II. Automated Web-Based Generation of User-Customized Test Cases. Journal Of Biomedical Informatics 1998, 31: 190-208. PMID: 9628750, DOI: 10.1006/cbmr.1998.1471.Peer-Reviewed Original ResearchTools for Immunization Guideline Knowledge Maintenance I. Automated Generation of the Logic “Kernel” for Immunization Forecasting
Miller P. Tools for Immunization Guideline Knowledge Maintenance I. Automated Generation of the Logic “Kernel” for Immunization Forecasting. Journal Of Biomedical Informatics 1998, 31: 172-189. PMID: 9628749, DOI: 10.1006/cbmr.1998.1472.Peer-Reviewed Original ResearchIssues in accommodating national changes and local variation in a computer-based guideline for childhood immunization and in related knowledge maintenance tools.
Miller P, Frawley S, Sayward F. Issues in accommodating national changes and local variation in a computer-based guideline for childhood immunization and in related knowledge maintenance tools. AMIA Annual Symposium Proceedings 1998, 563-7. PMID: 9929282, PMCID: PMC2232304.Peer-Reviewed Original ResearchConceptsChildhood immunizationNational recommendationsNew national recommendationsClinical practice guidelinesIndian Health ServiceVaccine seriesComputer-based guidelinePractice guidelinesPractice variationImmunization registryHealth servicesImmunizationUS Indian Health ServiceIMM/ServeGuidelinesNational changesRegistry
1996
IMM/Serve: a rule-based program for childhood immunization.
Miller P, Frawley S, Sayward F, Yasnoff W, Duncan L, Fleming D. IMM/Serve: a rule-based program for childhood immunization. AMIA Annual Symposium Proceedings 1996, 184-8. PMID: 8947653, PMCID: PMC2233221.Peer-Reviewed Original ResearchDNA Workbench: A Database Package to Manage Regional Physical Mapping
Nadkarni P, Cheung K, Castiglione C, Miller P, Kidd K. DNA Workbench: A Database Package to Manage Regional Physical Mapping. Journal Of Computational Biology 1996, 3: 319-329. PMID: 8811490, DOI: 10.1089/cmb.1996.3.319.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
1993
Using a network menu and the UMLS Information Sources Map to facilitate access to online reference materials.
Clyman J, Powsner S, Paton J, Miller P. Using a network menu and the UMLS Information Sources Map to facilitate access to online reference materials. Journal Of The Medical Library Association 1993, 81: 207-16. PMID: 8472006, PMCID: PMC225763.Peer-Reviewed Original ResearchConceptsInformation Sources MapUnified Medical Language System (UMLS) projectMedicine's Unified Medical Language System (UMLS) projectInformation systemsHigh-speed computer networksBibliographic retrieval systemOnline information systemOnline information sourcesOnline reference materialRetrieval systemNetwork workstationsComputer networksLocal prototypeComputer technologyInformation servicesSystem projectSource mapsUsersInformation sourcesComputer workstationWorkstationsBiomedical researchersOrder entryNetworkNational LibraryAn information sources map for Occupational and Environmental Medicine: guidance to network-based information through domain-specific indexing.
Silverstein S, Miller P, Cullen M. An information sources map for Occupational and Environmental Medicine: guidance to network-based information through domain-specific indexing. AMIA Annual Symposium Proceedings 1993, 616-20. PMID: 8130548, PMCID: PMC2850650.Peer-Reviewed Original ResearchNetMenu: experience in the implementation of an institutional menu of information sources.
Shifman M, Clyman J, Paton J, Powsner S, Roderer N, Miller P. NetMenu: experience in the implementation of an institutional menu of information sources. AMIA Annual Symposium Proceedings 1993, 554-8. PMID: 8130535, PMCID: PMC2850638.Peer-Reviewed Original ResearchAugmenting GRATEFUL MED with the UMLS Metathesaurus: an initial evaluation.
Jachna J, Powsner S, Miller P. Augmenting GRATEFUL MED with the UMLS Metathesaurus: an initial evaluation. Journal Of The Medical Library Association 1993, 81: 20-8. PMID: 8428185, PMCID: PMC225723.Peer-Reviewed Original ResearchConceptsGrateful MedIntelligent solutionsNovice usersInexperienced usersEffective searchLexical mismatchesUMLS MetathesaurusBibliographic retrievalOnline bibliographic databasesUsersComputer literacyTest setTyping errorsCitation retrievalIndexing termsThesaurusRetrievalSearch strategyOngoing projectSearchBibliographic databasesMetathesaurusToolDatabaseSet
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 techniquesParadigmHardwareMachineComputationLanguageCapabilityResources