Junchen Yang
PhD Student, Computational Biology and BioinformaticsAbout
Research
Publications
2023
Multi-modal Differentiable Unsupervised Feature Selection.
Yang J, Lindenbaum O, Kluger Y, Jaffe A. Multi-modal Differentiable Unsupervised Feature Selection. Proceedings Of Machine Learning Research 2023, 216: 2400-2410. PMID: 41623695, PMCID: PMC12859758.Peer-Reviewed Original ResearchUnsupervised feature selection frameworkLatent low-dimensional structureNuisance featuresHigh-dimensional measurementsThroughput biological dataReal datasetsGraph LaplacianSelection frameworkScoring operatorComputational challengesSharing structureMulti-modal measurementsLow-dimensional structuresHigh-throughput biological dataDatasetFeaturesSensorDifferential structureInformative variablesGraphBiological data
2022
Longitudinal single-cell analysis of a patient receiving adoptive cell therapy reveals potential mechanisms of treatment failure
Qu R, Kluger Y, Yang J, Zhao J, Hafler D, Krause D, Bersenev A, Bosenberg M, Hurwitz M, Lucca L, Kluger H. Longitudinal single-cell analysis of a patient receiving adoptive cell therapy reveals potential mechanisms of treatment failure. Molecular Cancer 2022, 21: 219. PMID: 36514045, PMCID: PMC9749221, DOI: 10.1186/s12943-022-01688-5.Peer-Reviewed Original ResearchConceptsAdoptive cell therapySingle-cell analysisDepth single-cell analysisSingle-cell RNAACT productsDisease progressionT-cell receptor sequencingCell therapyFamily genesFeatures of exhaustionMultiple tumor typesCell expansionGenesNew clonotypesTIL preparationsClonal cell expansionCytokine therapyTreatment failureSerial bloodClonesEffector functionsSerial samplesTumor typesCellular therapyTherapyComprehensive visualization of cell–cell interactions in single-cell and spatial transcriptomics with NICHES
Raredon M, Yang J, Kothapalli N, Lewis W, Kaminski N, Niklason L, Kluger Y. Comprehensive visualization of cell–cell interactions in single-cell and spatial transcriptomics with NICHES. Bioinformatics 2022, 39: btac775. PMID: 36458905, PMCID: PMC9825783, DOI: 10.1093/bioinformatics/btac775.Peer-Reviewed Original ResearchConceptsCell-cell interactionsCell-cell signalingSingle-cell resolutionSingle-cell dataLocal cellular microenvironmentSingle-cell levelSpatial transcriptomics dataCell clustersExtracellular signalingTranscriptomic dataGene expression valuesSpatial transcriptomicsSignaling mechanismCellular microenvironmentNicheExpression valuesSupplementary dataSignalingTranscriptomicsComprehensive visualizationBioinformaticsInteraction