2023
Transcriptomic profiles and 5-year results from the randomized CLL14 study of venetoclax plus obinutuzumab versus chlorambucil plus obinutuzumab in chronic lymphocytic leukemia
Al-Sawaf O, Zhang C, Jin H, Robrecht S, Choi Y, Balasubramanian S, Kotak A, Chang Y, Fink A, Tausch E, Schneider C, Ritgen M, Kreuzer K, Chyla B, Paulson J, Pallasch C, Frenzel L, Peifer M, Eichhorst B, Stilgenbauer S, Jiang Y, Hallek M, Fischer K. Transcriptomic profiles and 5-year results from the randomized CLL14 study of venetoclax plus obinutuzumab versus chlorambucil plus obinutuzumab in chronic lymphocytic leukemia. Nature Communications 2023, 14: 2147. PMID: 37072421, PMCID: PMC10113251, DOI: 10.1038/s41467-023-37648-w.Peer-Reviewed Original ResearchConceptsProgression-free survivalChronic lymphocytic leukemiaUntreated chronic lymphocytic leukemiaLymphocytic leukemiaAssociated with longer progression-free survivalParallel-group phase 3 studyProgression-free survival ratesTreatment of chronic lymphocytic leukemiaLonger progression-free survivalDepth of remissionMedian follow-upPhase 3 studyAssociated with increased expressionLong-term efficacyLong-term outcomesExploratory post hoc analysisPost hoc analysisMRD statusBCL2 inhibitionOverall survivalPrimary endpointSecondary endpointsInflammatory response pathwaysVenetoclax-obinutuzumabFollow-up
2017
Understanding Tissue-Specific Gene Regulation
Sonawane A, Platig J, Fagny M, Chen C, Paulson J, Lopes-Ramos C, DeMeo D, Quackenbush J, Glass K, Kuijjer M. Understanding Tissue-Specific Gene Regulation. Cell Reports 2017, 21: 1077-1088. PMID: 29069589, PMCID: PMC5828531, DOI: 10.1016/j.celrep.2017.10.001.Peer-Reviewed Original ResearchConceptsTissue specificityTissue-specific gene regulationGenotype-Tissue Expression projectControl tissue specificityTissue-specific genesTranscription factor targetsTissue-specific functionsGene expression patternsGene set enrichment analysisTissue-specific mannerTissue-specific processesInvestigate gene expressionGene regulationRegulatory interactionsTranscriptional controlTranscription factor expressionTranscription factorsExpression projectEnrichment analysisGene expressionExpression patternsGenesRegulation nodeFactor targetsTranscriptionExploring regulation in tissues with eQTL networks
Fagny M, Paulson J, Kuijjer M, Sonawane A, Chen C, Lopes-Ramos C, Glass K, Quackenbush J, Platig J. Exploring regulation in tissues with eQTL networks. Proceedings Of The National Academy Of Sciences Of The United States Of America 2017, 114: e7841-e7850. PMID: 28851834, PMCID: PMC5604022, DOI: 10.1073/pnas.1707375114.Peer-Reviewed Original ResearchConceptsExpression quantitative trait lociEQTL networksGenetic variantsCoherent biological processesImpact of genetic variantsActive chromatin regionsQuantitative trait lociTissue-specific processesGene expression levelsChromatin regionsGroup genesTrait lociComplex phenotypesRegulatory potentialGenotype to phenotype mappingPhenotype mappingBiological processesRegulatory functionsExpression levelsGenesRegulatory impactVariantsLociBipartite networksPhenotypeEstimating gene regulatory networks with pandaR
Schlauch D, Paulson J, Young A, Glass K, Quackenbush J. Estimating gene regulatory networks with pandaR. Bioinformatics 2017, 33: 2232-2234. PMID: 28334344, PMCID: PMC5870629, DOI: 10.1093/bioinformatics/btx139.Peer-Reviewed Original Research