2021
NEBULA is a fast negative binomial mixed model for differential or co-expression analysis of large-scale multi-subject single-cell data
He L, Davila-Velderrain J, Sumida TS, Hafler DA, Kellis M, Kulminski AM. NEBULA is a fast negative binomial mixed model for differential or co-expression analysis of large-scale multi-subject single-cell data. Communications Biology 2021, 4: 629. PMID: 34040149, PMCID: PMC8155058, DOI: 10.1038/s42003-021-02146-6.Peer-Reviewed Original ResearchConceptsNegative binomial mixed modelsBinomial mixed modelsSingle-cell dataHigh-dimensional integralsLarge sample approximationLaplace approximationCell-level expressionMixed modelsApproximationNebulaSpeed gainData setsOrders of magnitudeMarker gene identificationIntegralsModelOverdispersionFalse positive errors
2016
Power estimation for non-standardized multisite studies
Keshavan A, Paul F, Beyer MK, Zhu AH, Papinutto N, Shinohara RT, Stern W, Amann M, Bakshi R, Bischof A, Carriero A, Comabella M, Crane JC, D'Alfonso S, Demaerel P, Dubois B, Filippi M, Fleischer V, Fontaine B, Gaetano L, Goris A, Graetz C, Gröger A, Groppa S, Hafler DA, Harbo HF, Hemmer B, Jordan K, Kappos L, Kirkish G, Llufriu S, Magon S, Martinelli-Boneschi F, McCauley JL, Montalban X, Mühlau M, Pelletier D, Pattany PM, Pericak-Vance M, Cournu-Rebeix I, Rocca MA, Rovira A, Schlaeger R, Saiz A, Sprenger T, Stecco A, Uitdehaag BMJ, Villoslada P, Wattjes MP, Weiner H, Wuerfel J, Zimmer C, Zipp F, Consortium I, Hauser SL, Oksenberg JR, Henry RG. Power estimation for non-standardized multisite studies. NeuroImage 2016, 134: 281-294. PMID: 27039700, PMCID: PMC5656257, DOI: 10.1016/j.neuroimage.2016.03.051.Peer-Reviewed Original Research
2005
Evaluating the role of the 620W allele of protein tyrosine phosphatase PTPN22 in Crohn's disease and multiple sclerosis
De Jager PL, Sawcer S, Waliszewska A, Farwell L, Wild G, Cohen A, Langelier D, Bitton A, Compston A, Hafler DA, Rioux JD. Evaluating the role of the 620W allele of protein tyrosine phosphatase PTPN22 in Crohn's disease and multiple sclerosis. European Journal Of Human Genetics 2005, 14: 317-321. PMID: 16391555, DOI: 10.1038/sj.ejhg.5201548.Peer-Reviewed Original ResearchMeSH KeywordsAllelesCanadaCase-Control StudiesCrohn DiseaseGene FrequencyGenetic Predisposition to DiseaseGenotypeHumansInflammationModels, StatisticalMultiple SclerosisOdds RatioPolymorphism, GeneticProtein Tyrosine Phosphatase, Non-Receptor Type 1Protein Tyrosine Phosphatase, Non-Receptor Type 22Protein Tyrosine PhosphatasesRiskUnited KingdomConceptsSystemic lupus erythematosusCases of CDCrohn's diseaseMultiple sclerosisPTPN22 620W alleleAutoimmune thyroiditisRheumatoid arthritisInflammatory diseasesEvidence of associationCases of MSProtein tyrosine phosphatase PTPN22Chronic inflammatory diseaseType 1 diabetesTyrosine phosphatase PTPN22PTPN22 alleleLupus erythematosusPooled analysisControl subjectsModest odds ratiosOdds ratioDiseaseRisk allelesPhosphatase PTPN22SclerosisPossible role