Featured Publications
G2S3: 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 sparsityCells
2020
Gene coexpression networks reveal novel molecular endotypes in alpha-1 antitrypsin deficiency
Chu JH, Zang W, Vukmirovic M, Yan X, Adams T, DeIuliis G, Hu B, Mihaljinec A, Schupp JC, Becich MJ, Hochheiser H, Gibson KF, Chen ES, Morris A, Leader JK, Wisniewski SR, Zhang Y, Sciurba FC, Collman RG, Sandhaus R, Herzog EL, Patterson KC, Sauler M, Strange C, Kaminski N. Gene coexpression networks reveal novel molecular endotypes in alpha-1 antitrypsin deficiency. Thorax 2020, 76: 134-143. PMID: 33303696, PMCID: PMC10794043, DOI: 10.1136/thoraxjnl-2019-214301.Peer-Reviewed Original ResearchConceptsWeighted gene co-expression network analysisAlpha-1 antitrypsin deficiencyGene modulesGene co-expression network analysisDifferential gene expression analysisCo-expression network analysisPeripheral blood mononuclear cellsGene expression patternsPBMC gene expression patternsGene coexpression networksAATD individualsGene expression profilesGene expression analysisBronchoalveolar lavageAugmentation therapyClinical variablesAntitrypsin deficiencyGene expression assaysRNA-seqCoexpression networkGene validationExpression analysisExpression assaysWGCNA modulesExpression patterns