2021
Openness weighted association studies: leveraging personal genome information to prioritize non-coding variants
Song S, Shan N, Wang G, Yan X, Liu JS, Hou L. Openness weighted association studies: leveraging personal genome information to prioritize non-coding variants. Bioinformatics 2021, 37: 4737-4743. PMID: 34260700, PMCID: PMC8665759, DOI: 10.1093/bioinformatics/btab514.Peer-Reviewed Original ResearchConceptsGenome-wide association studiesFunctional annotationGWAS signalsAssociation studiesComplex diseasesSpecific functional annotationsTissue-specific patternsNon-coding variationsPotential functional differencesDisease-relevant pathwaysPersonal genome informationGenome informationGenomic regionsComprehensive annotationHuman genomeChromosome accessibilityGenomic segmentsMore heritabilityNoncoding variantsPersonal genomesRelevant pathwaysNovel insightsFunctional differencesGenomeDisease mechanisms
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