2023
mbQTL: an R/Bioconductor package for microbial quantitative trait loci (QTL) estimation
Movassagh M, Schiff S, Paulson J. mbQTL: an R/Bioconductor package for microbial quantitative trait loci (QTL) estimation. Bioinformatics 2023, 39: btad565. PMID: 37707523, PMCID: PMC10516520, DOI: 10.1093/bioinformatics/btad565.Peer-Reviewed Original ResearchConceptsSingle nucleotide variationsRNA sequencingMicrobial abundance dataQuantitative trait lociSingle nucleotide polymorphism dataRibosomal RNA sequencingField of genomicsWhole-genome sequencingEvidence of interplayMutational profileTrait lociMicrobial communitiesMicrobial abundancePolymorphism dataMicrobial populationsGenome sequencingAbundance dataFirst R packageHuman geneticsBioconductor packageGenetic variantsMicrobiome dataSequencingR packageAbundance
2017
Exploring 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 networksPhenotype