Featured Publications
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 ResearchiDESC: identifying differential expression in single-cell RNA sequencing data with multiple subjects
Liu Y, Zhao J, Adams T, Wang N, Schupp J, Wu W, McDonough J, Chupp G, Kaminski N, Wang Z, Yan X. iDESC: identifying differential expression in single-cell RNA sequencing data with multiple subjects. BMC Bioinformatics 2023, 24: 318. PMID: 37608264, PMCID: PMC10463720, DOI: 10.1186/s12859-023-05432-8.Peer-Reviewed Original ResearchComputational and Statistical Methods for Single-Cell RNA Sequencing Data
Wang Z, Yan X. Computational and Statistical Methods for Single-Cell RNA Sequencing Data. Springer Handbooks Of Computational Statistics 2022, 3-35. DOI: 10.1007/978-3-662-65902-1_1.ChaptersSingle-cell RNA sequencing technologySingle-cell RNA sequencing dataRNA sequencing technologyPhenotype of interestRNA sequencing dataDifferential expression analysisScRNA-seq dataStatistical methodsSequencing technologiesExpression analysisDropout imputationSequencing dataSeq dataDroplet-based technologiesDropout eventsDisease pathogenesisPopulation composition changesData normalizationHigh noise levelsPhenotypeNoise levelTherapeuticsComposition changesTranscriptomics of bronchoalveolar lavage cells identifies new molecular endotypes of sarcoidosis
Vukmirovic M, Yan X, Gibson KF, Gulati M, Schupp JC, DeIuliis G, Adams TS, Hu B, Mihaljinec A, Woolard TN, Lynn H, Emeagwali N, Herzog EL, Chen ES, Morris A, Leader JK, Zhang Y, Garcia JGN, Maier LA, Collman RG, Drake WP, Becich MJ, Hochheiser H, Wisniewski SR, Benos PV, Moller DR, Prasse A, Koth LL, Kaminski N. Transcriptomics of bronchoalveolar lavage cells identifies new molecular endotypes of sarcoidosis. European Respiratory Journal 2021, 58: 2002950. PMID: 34083402, PMCID: PMC9759791, DOI: 10.1183/13993003.02950-2020.Peer-Reviewed Original ResearchConceptsWeighted gene co-expression network analysisGene co-expression network analysisCo-expression network analysisGene expression programsGene expression patternsDistinct transcriptional programsImmune response pathwaysIon Torrent ProtonMicroarray expression datasetsExpression programsTranscriptional programsPhenotypic traitsGene modulesResponse pathwaysRNA sequencingMolecular endotypesExpression patternsGene expressionHilar lymphadenopathyOrgan involvementGenomic researchMechanistic targetExpression datasetsT helper type 1T cell immune responsesG2S3: A gene graph-based imputation method for single-cell RNA sequencing data
Wu W, Liu Y, Dai Q, Yan X, Wang Z. G2S3: A gene graph-based imputation method for single-cell RNA sequencing data. PLOS Computational Biology 2021, 17: e1009029. PMID: 34003861, PMCID: PMC8189489, DOI: 10.1371/journal.pcbi.1009029.Peer-Reviewed Original ResearchConceptsSingle-cell transcriptomic datasetsTranscriptomic datasetsGene expressionSingle-cell RNA sequencing technologySingle-cell transcriptomic studiesSingle-cell RNA sequencing dataRNA sequencing technologyRNA sequencing dataSingle-cell resolutionGene expression profilesAdjacent genesTranscriptomic studiesSequencing technologiesSequencing dataExpression profilesGene graphDownstream analysisGenesCell trajectoriesDropout eventsCell subtypesExpressionHigh data sparsityCellsA novel pathway-based distance score enhances assessment of disease heterogeneity in gene expression
Yan X, Liang A, Gomez J, Cohn L, Zhao H, Chupp GL. A novel pathway-based distance score enhances assessment of disease heterogeneity in gene expression. BMC Bioinformatics 2017, 18: 309. PMID: 28637421, PMCID: PMC5480187, DOI: 10.1186/s12859-017-1727-4.Peer-Reviewed Original ResearchNoninvasive Analysis of the Sputum Transcriptome Discriminates Clinical Phenotypes of Asthma
Yan X, Chu JH, Gomez J, Koenigs M, Holm C, He X, Perez MF, Zhao H, Mane S, Martinez FD, Ober C, Nicolae DL, Barnes KC, London SJ, Gilliland F, Weiss ST, Raby BA, Cohn L, Chupp GL. Noninvasive Analysis of the Sputum Transcriptome Discriminates Clinical Phenotypes of Asthma. American Journal Of Respiratory And Critical Care Medicine 2015, 191: 1116-1125. PMID: 25763605, PMCID: PMC4451618, DOI: 10.1164/rccm.201408-1440oc.Peer-Reviewed Original ResearchConceptsHistory of intubationNitric oxide levelsOxide levelsClinical phenotypeMost subjectsHigher bronchodilator responseNormal lung functionBlood of patientsCohort of childrenLogistic regression analysisSputum gene expressionBlood of childrenAirway transcriptomeMilder asthmaPathophysiologic heterogeneityPrebronchodilator FEV1Steroid requirementsLung functionBronchodilator responseGene expressionPhenotype of diseaseAsthmaBlood samplesGene signatureIntubationDetecting functional rare variants by collapsing and incorporating functional annotation in Genetic Analysis Workshop 17 mini-exome data
Yan X, Li L, Lee JS, Zheng W, Ferguson J, Zhao H. Detecting functional rare variants by collapsing and incorporating functional annotation in Genetic Analysis Workshop 17 mini-exome data. BMC Proceedings 2011, 5: s27. PMID: 22373324, PMCID: PMC3287862, DOI: 10.1186/1753-6561-5-s9-s27.Peer-Reviewed Original ResearchFunctional annotationCommon variantsDisease-associated common variantsGenetic Analysis Workshop 17 mini-exome dataGenetic Analysis Workshop 17 dataRare variantsFunctional rare variantsGenomic blocksSequencing technologiesAssociation studiesSynonymous variantsTag SNPsDifferent rare variantsAnnotationGenetic factorsRecent studiesVariantsVariant assumptionsHeritabilitySNPsCommon diseaseDisease riskRare exceptionsTesting gene set enrichment for subset of genes: Sub-GSE
Yan X, Sun F. Testing gene set enrichment for subset of genes: Sub-GSE. BMC Bioinformatics 2008, 9: 362. PMID: 18764941, PMCID: PMC2543030, DOI: 10.1186/1471-2105-9-362.Peer-Reviewed Original ResearchDetecting differentially expressed genes by relative entropy
Yan X, Deng M, Fung K, Qian M. Detecting differentially expressed genes by relative entropy. Journal Of Theoretical Biology 2005, 234: 395-402. PMID: 15784273, DOI: 10.1016/j.jtbi.2004.11.039.Peer-Reviewed Original Research
2025
A deep generative model for deciphering cellular dynamics and in silico drug discovery in complex diseases
Zheng Y, Schupp J, Adams T, Clair G, Justet A, Ahangari F, Yan X, Hansen P, Carlon M, Cortesi E, Vermant M, Vos R, De Sadeleer L, Rosas I, Pineda R, Sembrat J, Königshoff M, McDonough J, Vanaudenaerde B, Wuyts W, Kaminski N, Ding J. A deep generative model for deciphering cellular dynamics and in silico drug discovery in complex diseases. Nature Biomedical Engineering 2025, 1-26. PMID: 40542107, DOI: 10.1038/s41551-025-01423-7.Peer-Reviewed Original ResearchComplex cellular dynamicsCellular dynamicsSingle-cell transcriptomic dataIn silico drug discoverySingle-cell transcriptomicsTranscriptome dataPotential therapeutic drug candidateComplex diseasesHuman diseasesIdiopathic pulmonary fibrosisTherapeutic drug candidateCell embeddingDrug discoveryPulmonary fibrosisDrug candidatesDisease progressionHuman tissuesHuman precision-cut lung slicesDynamic analysisPrecision-cut lung slicesPathological landscapeComputational toolsAnti-fibrotic effectsUnagiTranscriptomeUnderstanding and Reducing Cardiopulmonary Sequelae Associated With Chronic Hypoxia
Manning E, Ramachandra A, Sharma P, Nikola F, De Man R, Doddaballapur P, Raredon M, Szafron J, Baernthaler T, Justet A, Akingbesote N, Perry R, Adams T, Cavinato C, Yan X, Tellides G, Kaminski N, Humphrey J. Understanding and Reducing Cardiopulmonary Sequelae Associated With Chronic Hypoxia. American Journal Of Respiratory And Critical Care Medicine 2025, 211: a3336-a3336. DOI: 10.1164/ajrccm.2025.211.abstracts.a3336.Peer-Reviewed Original ResearchThe Potential Role of miR205 and miR205HG in Pulmonary Fibrosis
Anderson S, Johad K, Ahangari F, Justet A, Adams T, Yan X, Kaminski N. The Potential Role of miR205 and miR205HG in Pulmonary Fibrosis. American Journal Of Respiratory And Critical Care Medicine 2025, 211: a4662-a4662. DOI: 10.1164/ajrccm.2025.211.abstracts.a4662.Peer-Reviewed Original ResearchEarly IPF Is Characterized by a Dramatic Shift of the Epithelial and Endothelial Populations Within the Alveolar Niche
Justet A, Adams T, Khoury J, Balayev A, Abu Hussein N, Schupp J, Zhao A, Manning E, Ahangari F, Yan X, Ravaglia C, Tomassetti S, Poletti V, Kaminski N. Early IPF Is Characterized by a Dramatic Shift of the Epithelial and Endothelial Populations Within the Alveolar Niche. American Journal Of Respiratory And Critical Care Medicine 2025, 211: a7109-a7109. DOI: 10.1164/ajrccm.2025.211.abstracts.a7109.Peer-Reviewed Original ResearchSingle-cell Analysis Reveals Somatic Mutation Accumulation, Loss of Differentiation, and Increased Transcriptional Entropy in Aged Human Lungs
De Man R, Cala Garcia J, Adams T, Nekola F, Moss B, Waich A, Rangel R, Anderson S, Mcdonough J, Raredon M, Yan X, Rosas I, Kaminski N. Single-cell Analysis Reveals Somatic Mutation Accumulation, Loss of Differentiation, and Increased Transcriptional Entropy in Aged Human Lungs. American Journal Of Respiratory And Critical Care Medicine 2025, 211: a5278-a5278. DOI: 10.1164/ajrccm.2025.211.abstracts.a5278.Peer-Reviewed Original ResearchThe Human Proximal Pulmonary Artery Plays a Critical Role in Regulating Cardiopulmonary Function in Health and Disease
Manning E, Lee S, Ashadujjaman M, De Man R, Cai Z, Adams T, Raredon M, Ramachandra A, Cavinato C, Heerdt P, Singh I, Choudhary G, Yan X, Bellini C, Tellides G, Humphrey J, Kaminski N. The Human Proximal Pulmonary Artery Plays a Critical Role in Regulating Cardiopulmonary Function in Health and Disease. American Journal Of Respiratory And Critical Care Medicine 2025, 211: a2891-a2891. DOI: 10.1164/ajrccm.2025.211.abstracts.a2891.Peer-Reviewed Original ResearchApplying Single-Cell Spatial Profiling to Assess Niches in Human Fibrotic Silica Lung
Abu Hussein N, Adams T, Anderson S, Kramer M, Nekola F, Homer R, Najjar A, Sharma P, Rangel R, Yang L, Zhang Y, Yan X, Pertzov B, Kaminski N. Applying Single-Cell Spatial Profiling to Assess Niches in Human Fibrotic Silica Lung. American Journal Of Respiratory And Critical Care Medicine 2025, 211: a5093-a5093. DOI: 10.1164/ajrccm.2025.211.abstracts.a5093.Peer-Reviewed Original ResearchA 3' RNA-Modification Enzyme Regulates the Angiogenic Switch in Non-small Cell Lung Cancer
Korde A, Jin L, Boffa D, Yan X, Takyar S. A 3' RNA-Modification Enzyme Regulates the Angiogenic Switch in Non-small Cell Lung Cancer. American Journal Of Respiratory And Critical Care Medicine 2025, 211: a2887-a2887. DOI: 10.1164/ajrccm.2025.211.abstracts.a2887.Peer-Reviewed Original ResearchAsthma Exacerbations: Integrative Analysis of Mirna Activity in Using Single-cell Transcriptomics
Hadikhani P, Yan X, Chupp G, Liu Q, Ban G, Piparia S, Mcgeachie M, Sharma R, Weiss S, Kho A, Tantisira K. Asthma Exacerbations: Integrative Analysis of Mirna Activity in Using Single-cell Transcriptomics. American Journal Of Respiratory And Critical Care Medicine 2025, 211: a7773-a7773. DOI: 10.1164/ajrccm.2025.211.abstracts.a7773.Peer-Reviewed Original ResearchApplying single cell profiling to assess drug anti fibrotic properties in the human precision cut lung slice model of fibrosis
Justet A, Mitash N, Pineda R, Adams T, Balayev A, Abu Hussein N, Ishizuka M, Kim H, Khoury J, Cala-GarcĂa J, Ahangari F, Yan X, Kaminski N, Königshoff M. Applying single cell profiling to assess drug anti fibrotic properties in the human precision cut lung slice model of fibrosis. Revue Des Maladies Respiratoires 2025, 42: 223. DOI: 10.1016/j.rmr.2025.02.083.Peer-Reviewed Original ResearchAbnormal cell populationsAlveolar epithelial cellsTreated with drugsAnti-fibrotic propertiesSingle cell platformsSingle nuclear RNA sequencingLigand-receptor analysisPreclinical evidencePulmonary fibrosisBasaloid cellsFibrotic propertiesReceptor analysisFibrotic pathwaysCell signaturesClinical trialsProfibrotic genesAnti-fibroticFDA-approved drugsGene signatureAnimal modelsEpithelial cellsGene expression changesDay 5Drug efficacyCell profiles
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