Yang Yang
Research Associate NeurosurgeryCards
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Research
Publications
2026
An engineered UGA suppressor tRNA gene for disease-agnostic AAV delivery
Xu M, Liu H, Wang J, Vieira A, Zhou X, Liu N, Liang J, Du A, Chen X, Xing R, Yang Y, Gonzalez-Perez M, Kumar V, Wang D. An engineered UGA suppressor tRNA gene for disease-agnostic AAV delivery. Nature Biotechnology 2026, 1-10. PMID: 41555020, DOI: 10.1038/s41587-025-02982-5.Peer-Reviewed Original ResearchRecombinant adeno-associated virusRAAV vector productionAdeno-associated virusPathogenic nonsense variantIn vivo deliveryC-to-T transitionLysosomal storage disorderAAV deliveryMouse modelPotential therapeutic scopeNonsense variantNonsense mutationTherapeutic approachesTherapeutic effectGenes in vivoNormal levelsSuppressor tRNA geneUGA stop codonStorage disorderSuppressor transfer RNATranscriptional regulatory elementsCGA arginine codonTherapeutic scopeTRNA genesTransfer RNA
2025
Align then clip: Refining graph for face clustering
Tu Y, Cao G, Shen J, Huang Y, Wang M, Liu W, Qian C, Yang Y. Align then clip: Refining graph for face clustering. Neural Networks 2025, 197: 108474. PMID: 41435730, DOI: 10.1016/j.neunet.2025.108474.Peer-Reviewed Original ResearchCross-domain generalizationFace clusteringFace recognition datasetsReal-world scenariosReal world applicationsAnnotation costNode representationsRecognition datasetsRefinement graphPruning strategyFacial imagesGraph constructionHyperparameter kGraph structureMethod's scalabilityClean graphsKNN-basedFalse-positive edgesGNNScalabilityGraphInput graphRobustnessNoiseApproach modelStructural and catalytic diversity of coronavirus proofreading exoribonuclease
Li Y, Cao X, Recker L, Yang Y, Liu C. Structural and catalytic diversity of coronavirus proofreading exoribonuclease. Nature Communications 2025 PMID: 41361186, DOI: 10.1038/s41467-025-67140-6.Peer-Reviewed Original ResearchCryo-EM structureProofreading exoribonucleaseRNA substratesCatalytic diversityGenomic mutation rateBiochemical analysisImmune evasionViral life cycleExon structureMERS-CoVAnalysis of exonsRNA proofreadingSarbecovirus subgenusGenome fidelityMutation rateSubgenusResistance to antiviral drugsExonEfficient excisionMolecular basisExoribonucleaseMiddle East respiratory syndrome coronavirusSARS-CoV-2Viral fitnessRespiratory syndrome coronavirusChiralCat: Molecular chirality classification with enhanced spatial representation using learnable queries
Peng Y, Yu G, Shi R, Chen L, Wang X, Du W, Huo X, Yang Y. ChiralCat: Molecular chirality classification with enhanced spatial representation using learnable queries. Artificial Intelligence Chemistry 2025, 3: 100091. DOI: 10.1016/j.aichem.2025.100091.Peer-Reviewed Original ResearchLearnable queriesRepresentation learning modelMulti-modal classifierMachine learning methodsLanguage modelRepresentation modelModel trainingLearning methodsAsymmetric catalysisMolecule datasetLearning modelsMolecular representationsProtein-drug bindingSpatial featuresChiral typeMolecular chiralityChiral studiesQueryExperimental resultsPrediction approachChiralityDatasetSuperior capabilitiesClassificationRepresentationInterplay between age, APOE Ɛ4 and the metabolome in plasma and brain in Alzheimer’s disease
Amin N, Liu J, Sproviero W, Arnold M, Batra R, Bonnechere B, Chiou Y, Fernandes M, Krumsiek J, Newby D, Nho K, Kim J, Saykin A, Shi L, Winchester L, Yang Y, Nevado-Holgado A, Kastenmüller G, Kaddurah-Daouk R, van Duijn C. Interplay between age, APOE Ɛ4 and the metabolome in plasma and brain in Alzheimer’s disease. Translational Psychiatry 2025, 15: 460. PMID: 41173821, PMCID: PMC12578868, DOI: 10.1038/s41398-025-03625-8.Peer-Reviewed Original ResearchConceptsBranched chain amino acidsPlasma concentrationsDevelopment of ADTricarboxylic acidAlzheimer's diseaseDrivers of Alzheimer's diseaseApo E4Brains of AD patientsInsulin-like growth factorConcentrations of branched chain amino acidsProteomic signatureClathrin-mediated endocytosis pathwayPlasma concentrations of branched chain amino acidsApolipoprotein E geneAPOE e4 carriersYears of ageE4 variantE4 carriersE geneEndocytosis pathwayReligious Orders StudyMetabolomicsGrowth factorAmino acidsApoPrecision medicine for sodium channelopathy-related autism and epilepsy
Robinson M, Wettschurack K, Halurkar M, Chen X, Zhang Z, Zhang J, Yang Y. Precision medicine for sodium channelopathy-related autism and epilepsy. Trends In Molecular Medicine 2025 PMID: 41162233, PMCID: PMC12801351, DOI: 10.1016/j.molmed.2025.09.007.Peer-Reviewed Original ResearchClustered regularly interspaced short palindromic repeatsVoltage-gated sodium channelsRegularly interspaced short palindromic repeatsPrecision medicineShort palindromic repeatsDisease modelsPalindromic repeatsBrain disordersGenomic revolutionGene replacementBase editingGene therapyPreclinical studiesMonogenic causeClinical trialsSodium channelsSevere epilepsyPrime editingAntisense oligonucleotidesTherapeutic developmentAutism spectrum disorderDiseaseDisordersEpilepsyTRNACharacterizing Infrared Spectra of OH–·(H2O)2 and OH–·(H2O)3 with Constrained Nuclear-Electronic Orbital Molecular Dynamics
Liu Z, Wang Y, Zhang Y, Yang N, Yang Y. Characterizing Infrared Spectra of OH–·(H2O)2 and OH–·(H2O)3 with Constrained Nuclear-Electronic Orbital Molecular Dynamics. The Journal Of Physical Chemistry A 2025, 129: 9883-9894. PMID: 41108635, PMCID: PMC12581138, DOI: 10.1021/acs.jpca.5c04334.Peer-Reviewed Original ResearchVibrational spectraMolecular dynamicsPeak assignmentsEffective potential energy surfacePotential energy surfaceStrong hydrogen bondsNuclear quantum effectsMachine-learning potentialsEnergy surfaceHydrogen bondsExperimental assignmentsQuantum delocalizationQuantum effectsInfrared spectraAnharmonic modesVibrational modesSpectral featuresPhysical interpretationCoupling effectDelocalizationAssignmentBondsModeCNEODynamicsMolecular basis of SARS-CoV-2 proofreading enzyme–mediated resistance to remdesivir
Yang Y, Li Y, Becker S, Khan A, Luo G, Liu B, Liu C. Molecular basis of SARS-CoV-2 proofreading enzyme–mediated resistance to remdesivir. Proceedings Of The National Academy Of Sciences Of The United States Of America 2025, 122: e2519755122. PMID: 41032524, PMCID: PMC12519199, DOI: 10.1073/pnas.2519755122.Peer-Reviewed Original ResearchInhalable Nanovaccine Based on Bioengineered Bacteria‐Derived Membrane Vesicles Against Lung Metastasis
Miao Y, Zhang H, Wang C, Li P, Chen L, Kang Z, Xiao Z, Zhang Q, Wu Z, Yang Y, Chen Q. Inhalable Nanovaccine Based on Bioengineered Bacteria‐Derived Membrane Vesicles Against Lung Metastasis. Advanced Materials 2025, e06174. PMID: 40904209, DOI: 10.1002/adma.202506174.Peer-Reviewed Original ResearchFollicular helper T cellsGerminal center B cellsHelper T cellsT cellsLung metastasesImmune responseLymph nodesB cellsAntigen-specific T cell proliferationSubcutaneous immunizationTumor-infiltrating T cellsAntigen-specific T cellsPrevention of lung metastasisSuperior tumor suppressionMature dendritic cellsAntigen Cross-PresentationT cell proliferationLocal immune responseLung metastasis modelB16-OVAImmunosuppressive microenvironmentMetastatic sitesCancer vaccinesMetastatic malignancyCross-PresentationConstrained Nuclear-Electronic Orbital Theory for Quantum Computation
Culpitt T, Chen Z, Pavošević F, Yang Y. Constrained Nuclear-Electronic Orbital Theory for Quantum Computation. Journal Of Chemical Theory And Computation 2025, 21: 7845-7854. PMID: 40794523, PMCID: PMC12503367, DOI: 10.1021/acs.jctc.5c00815.Peer-Reviewed Original ResearchNuclear quantum effectsQuantum effectsInclusion of nuclear quantum effectsVariational quantum eigensolver algorithmFull configuration interactionVibrational frequenciesFunction of bond lengthWave function methodsPotential energy surfaceHarmonic vibrational frequenciesQuantum entanglementNuclear-electronicQuantum simulationConfiguration interactionCorrelation energyCoupled-clusterQuantum computationMolecular dissociationEnergy surfaceEquilibrium geometryQuantumQuantum algorithmsQuantum computing techniquesBond lengthsOrbital theory
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