2020
Sex Differences in Gene Expression and Regulatory Networks across 29 Human Tissues
Lopes-Ramos C, Chen C, Kuijjer M, Paulson J, Sonawane A, Fagny M, Platig J, Glass K, Quackenbush J, DeMeo D. Sex Differences in Gene Expression and Regulatory Networks across 29 Human Tissues. Cell Reports 2020, 31: 107795. PMID: 32579922, PMCID: PMC7898458, DOI: 10.1016/j.celrep.2020.107795.Peer-Reviewed Original ResearchMeSH KeywordsChromosomes, Human, XDNA-Binding ProteinsFemaleGene Expression RegulationGene Regulatory NetworksHumansMaleOrgan SpecificitySex CharacteristicsTranscription FactorsConceptsGene regulatory networksTranscription factorsGenotype-Tissue ExpressionRegulatory networksArchitecture of gene regulatory networksRepertoire of transcription factorsSets of transcription factorsRegulatory network structureWhole-genome expression profilingTissue-related functionsGenes associated with Parkinson's diseaseHuman healthy tissuesGene regulationGene expressionMolecular basisSystems-based analysisExpression profilesGenesAlzheimer's diseaseRegulatory processesHuman tissuesExpressionTranscriptionTissueSex differences
2017
Age-dependent alterations of glucose clearance and homeostasis are temporally separated and modulated by dietary fat
Damgaard M, Pærregaard S, Søgaard I, Agerholm M, Paulson J, Treebak J, Sina C, Holm J, Kristiansen K, Jensen B. Age-dependent alterations of glucose clearance and homeostasis are temporally separated and modulated by dietary fat. The Journal Of Nutritional Biochemistry 2017, 54: 66-76. PMID: 29268121, DOI: 10.1016/j.jnutbio.2017.09.026.Peer-Reviewed Original ResearchConceptsGlucose homeostasisGut microbial alterationsGene amplicon sequencingInfluence of dietary fat sourceLow-fat dietAmplicon sequencingFatty acidsGut microbiotaResponse to insulinDietary fat sourceMicrobial alterationsAssessed glucose homeostasisMetabolic homeostasisDietary fatGlucose clearanceGlucose regulationLFD-fed miceFat sourcesHomeostasisFish oilGroups of miceInsulin tolerance testWeek 8 to weekSoybean oilSevere nonalcoholic steatohepatitisTissue-aware RNA-Seq processing and normalization for heterogeneous and sparse data
Paulson J, Chen C, Lopes-Ramos C, Kuijjer M, Platig J, Sonawane A, Fagny M, Glass K, Quackenbush J. Tissue-aware RNA-Seq processing and normalization for heterogeneous and sparse data. BMC Bioinformatics 2017, 18: 437. PMID: 28974199, PMCID: PMC5627434, DOI: 10.1186/s12859-017-1847-x.Peer-Reviewed Original ResearchConceptsRNA-seq data setsRNA-seqGenotype-Tissue ExpressionRNA-seq processingGenome-wide transcriptional profilingRNA-seq studiesRNA-seq dataGene filteringDownstream analysisRNA sequencingTranscriptional profilesDiverse tissuesAnalytical pipelineR packageQuality controlSignificant analytical challengeSoftware pipelineGenesRNAMulti-group studyNormalization stepAnalytical challengesResultsWeTissueExpressionExploring 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