2017
Smooth quantile normalization
Hicks S, Okrah K, Paulson J, Quackenbush J, Irizarry R, Bravo H. Smooth quantile normalization. Biostatistics 2017, 19: 185-198. PMID: 29036413, PMCID: PMC5862355, DOI: 10.1093/biostatistics/kxx028.Peer-Reviewed Original ResearchMeSH KeywordsBiostatisticsData Interpretation, StatisticalGenomicsHigh-Throughput Nucleotide SequencingHumansModels, StatisticalConceptsMonte Carlo simulation studyGlobal normalization methodsQuantile normalizationBias-variance tradeoffSimulation studyHigh-throughput datasetsSequencing read countsHigh-throughput dataGenomic data analysisSmooth quantile normalizationTechnical variationBetween-sample normalizationBiological conditionsGlobal propertiesStatistical distributionBiological groupsNormalizationReducing other formsGlobal differences
2016
Individual-specific changes in the human gut microbiota after challenge with enterotoxigenic Escherichia coli and subsequent ciprofloxacin treatment
Pop M, Paulson J, Chakraborty S, Astrovskaya I, Lindsay B, Li S, Bravo H, Harro C, Parkhill J, Walker A, Walker R, Sack D, Stine O. Individual-specific changes in the human gut microbiota after challenge with enterotoxigenic Escherichia coli and subsequent ciprofloxacin treatment. BMC Genomics 2016, 17: 440. PMID: 27277524, PMCID: PMC4898365, DOI: 10.1186/s12864-016-2777-0.Peer-Reviewed Original ResearchConceptsGene sequencesBackgroundEnterotoxigenic Escherichia coliHuman gut microbiotaRRNA gene sequencesEnterotoxigenic Escherichia coliHuman intestinal microbiotaFecal E. coliCiprofloxacin treatmentETEC infectionETEC diarrheaRibosomal RNAGut microbiotaFecal microbiotaIntestinal microbiotaE. coliMicrobiotaMonthly follow-up visitsCompared to variationsETECFollow-up visitQuantitative PCRHuman challenge studiesCiprofloxacinQuantitative culturesSequence