Featured Publications
Differential abundance analysis for microbial marker-gene surveys
Paulson J, Stine O, Bravo H, Pop M. Differential abundance analysis for microbial marker-gene surveys. Nature Methods 2013, 10: 1200-1202. PMID: 24076764, PMCID: PMC4010126, DOI: 10.1038/nmeth.2658.Peer-Reviewed Original ResearchMeSH KeywordsAlgorithmsAnimalsArea Under CurveCluster AnalysisComputer SimulationDatabases, GeneticGene Expression ProfilingGenetic MarkersGenetic VariationHumansIntestinesMetagenomicsMiceMicrobiotaModels, GeneticModels, StatisticalNormal DistributionPhenotypeRNA, Ribosomal, 16SSequence Analysis, DNASoftware
2017
Tissue-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 challengesResultsWeTissueExpressionRegulatory network changes between cell lines and their tissues of origin
Lopes-Ramos C, Paulson J, Chen C, Kuijjer M, Fagny M, Platig J, Sonawane A, DeMeo D, Quackenbush J, Glass K. Regulatory network changes between cell lines and their tissues of origin. BMC Genomics 2017, 18: 723. PMID: 28899340, PMCID: PMC5596945, DOI: 10.1186/s12864-017-4111-x.Peer-Reviewed Original ResearchMeSH KeywordsCell CycleCell LineGene Expression ProfilingGene Regulatory NetworksHumansOrgan SpecificityConceptsLymphoblastoid cell linesCell linesTranscription factor (TFChIP-seq dataRegulatory network changesRNA-seq dataTissue of originRegulatory network analysisCell cycle genesPrimary tissuesGene expression analysisEpstein-Barr virus-transformed lymphoblastoid cell linesChIP-seqVirus-transformed lymphoblastoid cell linesTF-targetRNA-seqGTEx projectTF regulationCycle genesTranscriptomic differencesBackgroundCell linesTranscript levelsExpression analysisFibroblast cell lineNetwork analysis