2016
STarMir Tools for Prediction of microRNA Binding Sites
Kanoria S, Rennie W, Liu C, Carmack CS, Lu J, Ding Y. STarMir Tools for Prediction of microRNA Binding Sites. Methods In Molecular Biology 2016, 1490: 73-82. PMID: 27665594, PMCID: PMC5353976, DOI: 10.1007/978-1-4939-6433-8_6.Peer-Reviewed Original ResearchConceptsMessenger RNAEndogenous short noncoding RNAsGene expressionMammalian biological processesHigh-throughput miRNATarget messenger RNAsShort noncoding RNAsMicroRNA Binding SitesCertain human diseasesCross-species validationTranslational repressionMiRNA functionGene regulationSeedless sitesMRNA degradationNoncoding RNAsRegulatory moleculesBiological processesSequence featuresHuman diseasesImmunoprecipitation studiesMiRNAComputational predictionsBinding sitesMiRNAs
2015
microRNA Expression Profiling: Technologies, Insights, and Prospects
Roden C, Mastriano S, Wang N, Lu J. microRNA Expression Profiling: Technologies, Insights, and Prospects. Advances In Experimental Medicine And Biology 2015, 888: 409-421. PMID: 26663195, DOI: 10.1007/978-3-319-22671-2_21.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBase SequenceCell Line, TumorDisease Models, AnimalGene Expression ProfilingGene Expression Regulation, NeoplasticHigh-Throughput Nucleotide SequencingHumansMicroRNAsMolecular Sequence DataNeoplasmsReverse Transcriptase Polymerase Chain ReactionSequence Homology, Nucleic AcidSignal TransductionConceptsLong small noncoding RNAsExpression profilingMiRNA isoformsMiRNA expressionProfiling technologiesDiverse biological processesSingle-cell variabilitySmall noncoding RNAsMiRNA profiling technologiesGlobal miRNA expressionNext-generation sequencingNoncoding RNAsCell variabilitySingle-molecule measurementsBiological functionsBiological processesTumor suppressorMicroRNA researchQuantitative RT-PCRCareful experimental designMiRNAsIsoformsRT-PCRProfilingExpression
2014
A High-Throughput MicroRNA Expression Profiling System
Guo Y, Mastriano S, Lu J. A High-Throughput MicroRNA Expression Profiling System. Methods In Molecular Biology 2014, 1176: 33-44. PMID: 25030917, DOI: 10.1007/978-1-4939-0992-6_4.Peer-Reviewed Original ResearchConceptsHundreds of miRNAsSmall noncoding RNAsDiverse biological functionsMiRNA-related researchGlobal miRNA expressionTotal RNA samplesNoncoding RNAsBiological functionsHundreds of samplesMiRNA expressionRNA samplesMiRNA levelsBiochemical reactionsPathological processesRobust protocolBead-based detectionExpressionLarge numberMiRNAsMicroRNAsHigh detection specificityRNADetection specificityDeregulationHundreds
2008
Dicer-dependent pathways regulate chondrocyte proliferation and differentiation
Kobayashi T, Lu J, Cobb BS, Rodda SJ, McMahon AP, Schipani E, Merkenschlager M, Kronenberg HM. Dicer-dependent pathways regulate chondrocyte proliferation and differentiation. Proceedings Of The National Academy Of Sciences Of The United States Of America 2008, 105: 1949-1954. PMID: 18238902, PMCID: PMC2538863, DOI: 10.1073/pnas.0707900105.Peer-Reviewed Original ResearchConceptsDicer-dependent pathwaysSkeletal developmentBiogenesis of miRNAsMiRNA target genesMammalian skeletal developmentSmall noncoding RNAsSkeletal growth defectsChondrocyte proliferationSuppress gene expressionNormal skeletal developmentDiverse organismsCritical roleGrowth defectNoncoding RNAsRNA abundanceGene expressionExpression changesMicroarray analysisBiological processesSignaling systemMiRNAsBase pairingDistinct mechanismsIhh-PTHrPHypertrophic chondrocytes
2007
Impaired microRNA processing enhances cellular transformation and tumorigenesis
Kumar MS, Lu J, Mercer KL, Golub TR, Jacks T. Impaired microRNA processing enhances cellular transformation and tumorigenesis. Nature Genetics 2007, 39: 673-677. PMID: 17401365, DOI: 10.1038/ng2003.Peer-Reviewed Original ResearchConceptsTarget mRNA transcriptsShort hairpin RNAGlobal repressionCellular transformationMRNA transcriptsMiRNA processing machinerySmall noncoding RNAsMature miRNA expressionMiRNA lossMiRNA maturationMiRNA processingMicroRNA processingNoncoding RNAsUndifferentiated stateProcessing machineryMiRNA expressionHairpin RNAConditional deletionTumorigenesisMiRNA levelsCancer cellsTumor developmentRepressionTranscriptsRNA