2019
Sfold Tools for MicroRNA Target Prediction
Rennie W, Kanoria S, Liu C, Carmack CS, Lu J, Ding Y. Sfold Tools for MicroRNA Target Prediction. Methods In Molecular Biology 2019, 1970: 31-42. PMID: 30963486, DOI: 10.1007/978-1-4939-9207-2_3.Peer-Reviewed Original Research
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
2014
Effects of genetic variations on microRNA: target interactions
Liu C, Rennie WA, Carmack CS, Kanoria S, Cheng J, Lu J, Ding Y. Effects of genetic variations on microRNA: target interactions. Nucleic Acids Research 2014, 42: 9543-9552. PMID: 25081214, PMCID: PMC4150780, DOI: 10.1093/nar/gku675.Peer-Reviewed Original ResearchMeSH KeywordsBinding SitesDiseaseGenetic VariationHumansMicroRNAsPhenotypePolymorphism, Single NucleotideRNA, MessengerConceptsMiRNA binding sitesGenetic variationGene regulationGenetic variantsMiRNA-mediated gene regulationBinding sitesModulation of miRNAPotential of miRNARare variantsLow mutation frequencyFlanking regionsHuman diseasesVariant densityStructural accessibilityMiRNACommon variantsMutation frequencyMicroRNAsTarget interactionsRegulationStructure alterationsVariantsNew associationsTranscriptomeSitesSTarMir: a web server for prediction of microRNA binding sites
Rennie W, Liu C, Carmack CS, Wolenc A, Kanoria S, Lu J, Long D, Ding Y. STarMir: a web server for prediction of microRNA binding sites. Nucleic Acids Research 2014, 42: w114-w118. PMID: 24803672, PMCID: PMC4086099, DOI: 10.1093/nar/gku376.Peer-Reviewed Original Research
2006
Hematopoietic gene promoters subjected to a group-combinatorial study of DNA samples: identification of a megakaryocytic selective DNA signature
Hazony Y, Lu J, St. Hilaire C, Ravid K. Hematopoietic gene promoters subjected to a group-combinatorial study of DNA samples: identification of a megakaryocytic selective DNA signature. Nucleic Acids Research 2006, 34: 4416-4428. PMID: 16936310, PMCID: PMC1636359, DOI: 10.1093/nar/gkl578.Peer-Reviewed Original ResearchConceptsCell-specific gene expressionNon-coding regionsRelated DNA sequencesDNA sequencesGene expressionMegakaryocytic lineageUnique transcription factorsCommon DNA sequenceNon-coding sequencesGroup of genesGene promoter sequencesMammalian genomesRegulatory sequencesTranscription factorsPromoter sequencesCross-species differencesGene promoterDNA signaturesLineagesSpecific sequencesCommon sequenceDNA samplesSequencePromoter groupExpression
1999
Mpl ligand enhances the transcription of the cyclin D3 gene: a potential role for Sp1 transcription factor.
Wang Z, Zhang Y, Lu J, Sun S, Ravid K. Mpl ligand enhances the transcription of the cyclin D3 gene: a potential role for Sp1 transcription factor. Blood 1999, 93: 4208-21. PMID: 10361118, DOI: 10.1182/blood.v93.12.4208.412k17_4208_4221.Peer-Reviewed Original ResearchConceptsProtein phosphatase 1Cyclin D3 promoterMpl ligandCyclin D3 geneTranscription factorsSp1-dependent genesD3 geneSp1 transcription factorForm of Sp1Basal promoter activityMegakaryocytic cell linesCyclin D3 proteinSp familySp1 proteinD3 gene expressionSp1 sitesPhosphatase 1Okadaic acidCyclin D3 gene expressionNuclear runSp1DNase IGene expressionPromoter activityPromoter region