2022
SenseLab: Integration of Multidisciplinary Neuroscience Data
Shepherd G, Morse T, Marenco L, Cheung K, Carnevale T, Migliore M, McDougal R, Hines M, Miller P. SenseLab: Integration of Multidisciplinary Neuroscience Data. 2022, 3069-3072. DOI: 10.1007/978-1-0716-1006-0_497.Peer-Reviewed Original Research
2015
Laplacian SVM Based Feature Selection Improves Medical Event Reports Classification
Fodeh S, Miller P, Brandt C, Benin A, Lee K, Koss M. Laplacian SVM Based Feature Selection Improves Medical Event Reports Classification. 2015, 449-454. DOI: 10.1109/icdmw.2015.141.Peer-Reviewed Original ResearchSenseLab: Integration of Multidisciplinary Neuroscience Data
Shepherd G, Morse T, Marenco L, Cheung K, Carnevale T, Migliore M, McDougal R, Hines M, Miller P. SenseLab: Integration of Multidisciplinary Neuroscience Data. 2015, 2655-2657. DOI: 10.1007/978-1-4614-6675-8_497.Peer-Reviewed Original Research
2013
Decision Support and Expert Systems in Public Health
Yasnoff W, Miller P. Decision Support and Expert Systems in Public Health. Health Informatics 2013, 449-467. DOI: 10.1007/978-1-4471-4237-9_23.Peer-Reviewed Original ResearchExpert systemDecision supportDecision support systemSuch systemsWillingness of usersIMM/Computer resourcesSupport systemDevelopment processHealth dataResource managementSound logicExtensive testingSuch supportDevelopersUsersApplicationsSystemVariety of methodsComplexityLogicSupportPublic health practicePublic healthResourcesSenseLab: Integration of Multidisciplinary Neuroscience Data
Shepherd G, Morse T, Marenco L, Cheung K, Carnevale T, Migliore M, McDougal R, Hines M, Miller P. SenseLab: Integration of Multidisciplinary Neuroscience Data. 2013, 1-3. DOI: 10.1007/978-1-4614-7320-6_497-1.Peer-Reviewed Original Research
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 resourcesP1‐141: Modeling the “dendritic hypothesis” of Alzheimer pathogenesis: A neuroinformatics approach for elucidating part of the amyloid beta cascade
Morse T, Mutalik P, Cheung K, Miller P, Shepherd G. P1‐141: Modeling the “dendritic hypothesis” of Alzheimer pathogenesis: A neuroinformatics approach for elucidating part of the amyloid beta cascade. Alzheimer's & Dementia 2008, 4: t248-t248. DOI: 10.1016/j.jalz.2008.05.728.Peer-Reviewed Original Research
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 PipelineThe DART classification of unannotated transcription within the ENCODE regions: Associating transcription with known and novel loci
Rozowsky JS, Newburger D, Sayward F, Wu J, Jordan G, Korbel JO, Nagalakshmi U, Yang J, Zheng D, Guigó R, Gingeras TR, Weissman S, Miller P, Snyder M, Gerstein MB. The DART classification of unannotated transcription within the ENCODE regions: Associating transcription with known and novel loci. Genome Research 2007, 17: 732-745. PMID: 17567993, PMCID: PMC1891334, DOI: 10.1101/gr.5696007.Peer-Reviewed Original ResearchEvidence 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
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 techniquesAn interdepartmental Ph.D. program in computational biology and bioinformatics: The Yale perspective
Gerstein M, Greenbaum D, Cheung K, Miller PL. An interdepartmental Ph.D. program in computational biology and bioinformatics: The Yale perspective. Journal Of Biomedical Informatics 2006, 40: 73-79. PMID: 16650809, DOI: 10.1016/j.jbi.2006.02.008.Peer-Reviewed Original ResearchDesign Issues in Implementing a Portable Sample Tracking and Analysis Research Support (STARS) System for PCR Based Microarray Research
Sayward F, Yang J, Nelson F, Euskirchen G, Urban A, Bertone P, Rinn J, Weissman S, Gerstein M, Snyder M, Miller P. Design Issues in Implementing a Portable Sample Tracking and Analysis Research Support (STARS) System for PCR Based Microarray Research. 2006, 1578-1598. DOI: 10.1109/ciss.2006.286390.Peer-Reviewed Original Research
2005
ALFRED: An Allele Frequency Database for Microevolutionary Studies
Rajeevan H, Cheung K, Gadagkar R, Stein S, Soundararajan U, Kidd J, Pakstis A, Miller P, Kidd K. ALFRED: An Allele Frequency Database for Microevolutionary Studies. Evolutionary Bioinformatics 2005, 1: 117693430500100006. DOI: 10.1177/117693430500100006.Peer-Reviewed Original Research
2004
Training the Next Generation of Informaticians: The Impact of “BISTI” and Bioinformatics—A Report from the American College of Medical Informatics
Friedman CP, Altman RB, Kohane IS, McCormick KA, Miller PL, Ozbolt JG, Shortliffe EH, Stormo GD, Szczepaniak MC, Tuck D, Williamson J. Training the Next Generation of Informaticians: The Impact of “BISTI” and Bioinformatics—A Report from the American College of Medical Informatics. Journal Of The American Medical Informatics Association 2004, 11: 167-172. PMID: 14764617, PMCID: PMC400513, DOI: 10.1197/jamia.m1520.Peer-Reviewed Original Research
2003
Workshop I – Global Analysis of Protein Activities Using Protein Chips
Zhu H, Bilgin M, Ptacek J, Hall D, Casamayor A, Bertone P, Lopez N, Lan N, Jansen R, Bidlingmaier S, Devgan G, Miller P, Gerstein M, Snyder M. Workshop I – Global Analysis of Protein Activities Using Protein Chips. Biophysical Journal 2003, 84: 3488. DOI: 10.1016/s0006-3495(03)70069-1.Peer-Reviewed Original ResearchDecision Support and Expert Systems in Public Health
Yasnoff W, Miller P. Decision Support and Expert Systems in Public Health. Health Informatics 2003, 494-512. DOI: 10.1007/0-387-22745-8_23.Peer-Reviewed Original ResearchExpert systemDecision supportDecision support systemSuch systemsWillingness of usersIMM/Computer resourcesDevelopment processHealth dataResource managementSound logicExtensive testingSuch supportDevelopersUsersApplicationsSystemVariety of methodsComplexityLogicSupportPublic health practicePublic healthResourcesEnvironment
2002
Senselab: Modeling Heterogenous Data on the Nervous System
Nadkarni P, Mirsky J, Skoufos E, Healy M, Hines M, Miller P, Shepherd G. Senselab: Modeling Heterogenous Data on the Nervous System. 2002, 105-118. DOI: 10.1007/0-306-46903-0_10.Peer-Reviewed Original Research
2001
Global Analysis of Protein Activities Using Proteome Chips
Zhu H, Bilgin M, Bangham R, Hall D, Casamayor A, Bertone P, Lan N, Jansen R, Bidlingmaier S, Houfek T, Mitchell T, Miller P, Dean R, Gerstein M, Snyder M. Global Analysis of Protein Activities Using Proteome Chips. Science 2001, 293: 2101-2105. PMID: 11474067, DOI: 10.1126/science.1062191.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid MotifsAmino Acid SequenceCalmodulinCalmodulin-Binding ProteinsCell MembraneCloning, MolecularFungal ProteinsGlucoseLiposomesMembrane ProteinsMolecular Sequence DataOpen Reading FramesPeptide LibraryPhosphatidylcholinesPhosphatidylinositolsPhospholipidsProtein BindingProteomeRecombinant Fusion ProteinsSaccharomyces cerevisiaeSignal TransductionStreptavidinConceptsYeast proteome microarraysDiverse biochemical activitiesOpen reading framePotential binding motifsProtein-drug interactionsEukaryotic proteomesYeast proteomeProteome chipsPosttranslational modificationsReading frameCorresponding proteinNew calmodulinProtein activityBinding motifBiochemical activityProteome microarrayProteinProteomeMicroarrayCalmodulinGlobal analysisMotifPhospholipidsActivityMaintaining 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 Research