An improved empirical bayes approach to estimating differential gene expression in microarray time-course data: BETR (Bayesian Estimation of Temporal Regulation). - Martin J. Aryee; José A. Gutiérrez-Pabello; Igor Kramnik; Tapabrata Maiti; John Quackenbush (BMC Bioinform., 2009)

Subset Quantile Normalization Using Negative Control Features. - Zhijin Wu; Martin J. Aryee (J. Comput. Biol., 2010)

nEASE: a method for gene ontology subclassification of high-throughput gene expression data. - Thomas W. Chittenden; Eleanor Howe; Jennifer M. Taylor; Jessica Cara Mar; Martin J. Aryee; Harold Gómez; Razvan Sultana; John C. Braisted; Sarita J. Nair; John Quackenbush; Chris Holmes (Bioinform., 2012)

Identification of direction in gene networks from expression and methylation. - David M. Simcha; Laurent Younes; Martin J. Aryee; Donald Geman (BMC Syst. Biol., 2013)

Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays. - Martin J. Aryee; Andrew E. Jaffe; Héctor Corrada Bravo; Christine Ladd-Acosta; Andrew P. Feinberg; Kasper D. Hansen; Rafael A. Irizarry (Bioinform., 2014)

diffloop: a computational framework for identifying and analyzing differential DNA loops from sequencing data. - Caleb A. Lareau; Martin J. Aryee (Bioinform., 2018)

A (fire)cloud-based DNA methylation data preprocessing and quality control platform. - Divy Kangeyan; Andrew J. Dunford; Sowmya Iyer; Chip Stewart; Megan Hanna; Gad Getz; Martin J. Aryee (BMC Bioinform., 2019)