2022
Comprehensive Analysis of Ubiquitously Expressed Genes in Humans from a Data-Driven Perspective
Gu J, Dai J, Lu H, Zhao H. Comprehensive Analysis of Ubiquitously Expressed Genes in Humans from a Data-Driven Perspective. Genomics Proteomics & Bioinformatics 2022, 21: 164-176. PMID: 35569803, PMCID: PMC10373092, DOI: 10.1016/j.gpb.2021.08.017.Peer-Reviewed Original ResearchConceptsGlobal expression patternsHuman transcriptomeExpression patternsHuman genesTemporal gene expression patternsVaried expression patternsGene expression patternsInternal reference genesHuman genomeTranscriptomeRegulatory codeGene clusteringMolecular mechanismsReference genesStable expressionIslet beta cellsHuman diseasesGenesExpression measurementsBeta cellsUbiquitouslyPhysiological conditionsValuable resourceComprehensive characterizationExtensive collection
2017
The ancestral levels of transcription and the evolution of sexual phenotypes in filamentous fungi
Trail F, Wang Z, Stefanko K, Cubba C, Townsend JP. The ancestral levels of transcription and the evolution of sexual phenotypes in filamentous fungi. PLOS Genetics 2017, 13: e1006867. PMID: 28704372, PMCID: PMC5509106, DOI: 10.1371/journal.pgen.1006867.Peer-Reviewed Original ResearchConceptsGene expressionFilamentous fungiCommon garden environmentBody developmentWide gene expressionGene expression phenotypesGene deletion studiesGene expression measurementsMulticellular developmentDivergent speciesSexual phenotypeGene familyEvolved increasesDivergent morphologyKnockout phenotypesAncestral levelsWhole genomeGarden environmentExpression phenotypesDeletion studiesRelevant genesPhenotypic analysisDevelopmental stagesExpression measurementsBody morphology
2015
Data-Adaptive Shrinkage via the Hyperpenalized EM Algorithm
Boonstra P, Taylor J, Mukherjee B. Data-Adaptive Shrinkage via the Hyperpenalized EM Algorithm. Statistics In Biosciences 2015, 7: 417-431. PMID: 26834856, PMCID: PMC4728141, DOI: 10.1007/s12561-015-9132-x.Peer-Reviewed Original Research
2006
The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements
Shi L, Shi L, Reid L, Jones W, Shippy R, Warrington J, Baker S, Collins P, de Longueville F, Kawasaki E, Lee K, Luo Y, Sun Y, Willey J, Setterquist R, Fischer G, Tong W, Dragan Y, Dix D, Frueh F, Goodsaid F, Herman D, Jensen R, Johnson C, Lobenhofer E, Puri R, Scherf U, Thierry-Mieg J, Wang C, Wilson M, Wolber P, Zhang L, Amur S, Bao W, Barbacioru C, Lucas A, Bertholet V, Boysen C, Bromley B, Brown D, Brunner A, Canales R, Cao X, Cebula T, Chen J, Cheng J, Chu T, Chudin E, Corson J, Corton J, Croner L, Davies C, Davison T, Delenstarr G, Deng X, Dorris D, Eklund A, Fan X, Fang H, Fulmer-Smentek S, Fuscoe J, Gallagher K, Ge W, Guo L, Guo X, Hager J, Haje P, Han J, Han T, Harbottle H, Harris S, Hatchwell E, Hauser C, Hester S, Hong H, Hurban P, Jackson S, Ji H, Knight C, Kuo W, LeClerc J, Levy S, Li Q, Liu C, Liu Y, Lombardi M, Ma Y, Magnuson S, Maqsodi B, McDaniel T, Mei N, Myklebost O, Ning B, Novoradovskaya N, Orr M, Osborn T, Papallo A, Patterson T, Perkins R, Peters E, Peterson R, Philips K, Pine P, Pusztai L, Qian F, Ren H, Rosen M, Rosenzweig B, Samaha R, Schena M, Schroth G, Shchegrova S, Smith D, Staedtler F, Su Z, Sun H, Szallasi Z, Tezak Z, Thierry-Mieg D, Thompson K, Tikhonova I, Turpaz Y, Vallanat B, Van C, Walker S, Wang S, Wang Y, Wolfinger R, Wong A, Wu J, Xiao C, Xie Q, Xu J, Yang W, Zhang L, Zhong S, Zong Y, Slikker W. The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements. Nature Biotechnology 2006, 24: 1151-1161. PMID: 16964229, PMCID: PMC3272078, DOI: 10.1038/nbt1239.Peer-Reviewed Original ResearchConceptsMicroArray Quality ControlIntroduction of microarray technologyMicroArray Quality Control projectRNA samplesGene expression measurementsGene expression researchMicroarray-basedMicroarray platformExpression dataMicroarray technologyExpression measurementsMicroarrayExpression researchIntraplatformMapping effortsGenesRNAAlternative technology platformsQuality controlData analysis issuesSitesPublication of studiesMultiple test sitesExpression
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