2024
SDePER: a hybrid machine learning and regression method for cell-type deconvolution of spatial barcoding-based transcriptomic data
Liu Y, Li N, Qi J, Xu G, Zhao J, Wang N, Huang X, Jiang W, Wei H, Justet A, Adams T, Homer R, Amei A, Rosas I, Kaminski N, Wang Z, Yan X. SDePER: a hybrid machine learning and regression method for cell-type deconvolution of spatial barcoding-based transcriptomic data. Genome Biology 2024, 25: 271. PMID: 39402626, PMCID: PMC11475911, DOI: 10.1186/s13059-024-03416-2.Peer-Reviewed Original Research
2023
tRFtarget 2.0: expanding the targetome landscape of transfer RNA-derived fragments
Li N, Yao S, Yu G, Lu L, Wang Z. tRFtarget 2.0: expanding the targetome landscape of transfer RNA-derived fragments. Nucleic Acids Research 2023, 52: d345-d350. PMID: 37811890, PMCID: PMC10767876, DOI: 10.1093/nar/gkad815.Peer-Reviewed Original ResearchCis-meQTL for cocaine use-associated DNA methylation in an HIV-positive cohort show pleiotropic effects on multiple traits
Cheng Y, Justice A, Wang Z, Li B, Hancock D, Johnson E, Xu K. Cis-meQTL for cocaine use-associated DNA methylation in an HIV-positive cohort show pleiotropic effects on multiple traits. BMC Genomics 2023, 24: 556. PMID: 37730558, PMCID: PMC10510240, DOI: 10.1186/s12864-023-09661-2.Peer-Reviewed Original ResearchConceptsDNA methylationMultiple traitsPleiotropic effectsGenetic variantsAberrant DNA methylationPhenome-wide association studyCis-meQTLsComplex traitsRelevant traitsDNAm sitesEnrichment analysisMeQTLsAssociation studiesSignificant traitsTraitsImmune pathwaysMethylationNew insightsMendelian randomizationImmunological functionsGenesVariantsCausal rolePathwayCpG
2020
tRFtarget: a database for transfer RNA-derived fragment targets
Li N, Shan N, Lu L, Wang Z. tRFtarget: a database for transfer RNA-derived fragment targets. Nucleic Acids Research 2020, 49: d254-d260. PMID: 33035346, PMCID: PMC7779015, DOI: 10.1093/nar/gkaa831.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBase PairingBase SequenceCaenorhabditis elegansDatabases, Nucleic AcidDrosophila melanogasterGene OntologyHumansMiceMolecular Sequence AnnotationNucleic Acid ConformationNucleic Acid HybridizationRhodobacter sphaeroidesRNA, MessengerRNA, Small UntranslatedRNA, TransferSchizosaccharomycesThermodynamicsXenopusZebrafishConceptsTarget genesTransfer RNASmall non-coding RNAsGene Ontology annotationsNon-coding RNAsFunctional pathway analysisAccessible web-based databaseMolecular functionsOntology annotationsBiological functionsPathway analysisMolecular mechanismsPhysiological processesTarget predictionHuman diseasesGenesMRNA transcriptsRNAWeb-based databaseConvenient linkTRFImportant roleRNAhybridTargetIntaRNA
2015
Isolation and characterization of a poplar d-type cyclin gene associated with the SHORT-ROOT/SCARECROW network
Xu M, Liu S, Xuan L, Huang M, Wang Z. Isolation and characterization of a poplar d-type cyclin gene associated with the SHORT-ROOT/SCARECROW network. Trees 2015, 30: 255-263. DOI: 10.1007/s00468-015-1296-y.Peer-Reviewed Original ResearchAdventitious root developmentRegulatory networksCyclin genesProtoplast transient expression assaysRoot developmentD-type cyclin genesRoot radial patterningGFP fusion proteinBiomolecular fluorescence complementationTransient expression assaysCortex cell layersD-type cyclinsRoot patterningArabidopsis rootsFluorescence complementationRadial patterningCell specificationModel organismsCycle genesDaughter cellsExpression assaysKey regulatorFusion proteinGenesPericlinal divisions
2004
A statistical model for functional mapping of quantitative trait loci regulating drug response
Gong Y, Wang Z, Liu T, Zhao W, Zhu Y, Johnson J, Wu R. A statistical model for functional mapping of quantitative trait loci regulating drug response. The Pharmacogenomics Journal 2004, 4: 315-321. PMID: 15263889, DOI: 10.1038/sj.tpj.6500262.Peer-Reviewed Original ResearchConceptsQuantitative trait lociComplex traitsGenetic mappingTrait lociDifferent QTL genotypesPopulation genetic parametersFunction-valued traitsDrug responseMultiple genesSpecific genesHigh-resolution mappingRecombination eventsQTL genotypesDisequilibrium mappingPolymorphic markersGenetic parametersFunctional mappingTraitsGenesLociPharmacogenomics researchEnvironmental influencesPowerful toolHistoric times