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
2023
The Network Zoo: a multilingual package for the inference and analysis of gene regulatory networks
Ben Guebila M, Wang T, Lopes-Ramos C, Fanfani V, Weighill D, Burkholz R, Schlauch D, Paulson J, Altenbuchinger M, Shutta K, Sonawane A, Lim J, Calderer G, van IJzendoorn D, Morgan D, Marin A, Chen C, Song Q, Saha E, DeMeo D, Padi M, Platig J, Kuijjer M, Glass K, Quackenbush J. The Network Zoo: a multilingual package for the inference and analysis of gene regulatory networks. Genome Biology 2023, 24: 45. PMID: 36894939, PMCID: PMC9999668, DOI: 10.1186/s13059-023-02877-1.Peer-Reviewed Original ResearchMeSH KeywordsAlgorithmsComputational BiologyGene Regulatory NetworksHumansMultiomicsNeoplasmsSoftware
2022
GameRank: R package for feature selection and construction
Henneges C, Paulson J. GameRank: R package for feature selection and construction. Bioinformatics 2022, 38: 4840-4842. PMID: 35951761, PMCID: PMC9563696, DOI: 10.1093/bioinformatics/btac552.Peer-Reviewed Original Research
2020
MicrobiomeExplorer: an R package for the analysis and visualization of microbial communities
Reeder J, Huang M, Kaminker J, Paulson J. MicrobiomeExplorer: an R package for the analysis and visualization of microbial communities. Bioinformatics 2020, 37: 1317-1318. PMID: 32960962, PMCID: PMC8193707, DOI: 10.1093/bioinformatics/btaa838.Peer-Reviewed Original ResearchmicrobiomeDASim: Simulating longitudinal differential abundance for microbiome data
Williams J, Bravo H, Tom J, Paulson J. microbiomeDASim: Simulating longitudinal differential abundance for microbiome data. F1000Research 2020, 8: 1769. PMID: 32148761, PMCID: PMC7047923, DOI: 10.12688/f1000research.20660.2.Peer-Reviewed Original Research
2019
metagenomeFeatures: an R package for working with 16S rRNA reference databases and marker-gene survey feature data
Olson N, Shah N, Kancherla J, Wagner J, Paulson J, Bravo H. metagenomeFeatures: an R package for working with 16S rRNA reference databases and marker-gene survey feature data. Bioinformatics 2019, 35: 3870-3872. PMID: 30821316, PMCID: PMC6761971, DOI: 10.1093/bioinformatics/btz136.Peer-Reviewed Original Research
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 challengesResultsWeTissueExpressionEstimating 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
2016
Privacy-preserving microbiome analysis using secure computation
Wagner J, Paulson J, Wang X, Bhattacharjee B, Corrada Bravo H. Privacy-preserving microbiome analysis using secure computation. Bioinformatics 2016, 32: 1873-1879. PMID: 26873931, PMCID: PMC4908319, DOI: 10.1093/bioinformatics/btw073.Peer-Reviewed Original ResearchConceptsDNA of micro-organismsMicrobiome research communityPrivacy concernsSensitive attributesResearch participant dataFeature countsSharing dataSupplementary dataMetagenomic analysisResearch datasetsMicrobiome sequencingSequencing studiesMicrobial DNAHuman DNAResearch communityMicrobiome analysisMicrobiomeDNAAnalysis toolsDatasetComputerMicro-organismsBioinformaticsImplementationIndividual collections